Adding metadata

author: root <root@alpha.trunkmasters.com> 2026-06-04 16:24:49 -0500
committer: root <root@alpha.trunkmasters.com> 2026-06-04 16:24:49 -0500
commit: a3ceca1b4c0d9bdb550dc23f06ffbb5a8e033bc7 (patch)
tree: 0c52bbae1c242fbc296bd650fcd1167685f81492 /sci-biology
parent: bfd9c39e4712ebdb442d4ca0673061faed1e70e1 (diff)
download: baldeagleos-repo-a3ceca1b4c0d9bdb550dc23f06ffbb5a8e033bc7.tar.gz
baldeagleos-repo-a3ceca1b4c0d9bdb550dc23f06ffbb5a8e033bc7.tar.xz
baldeagleos-repo-a3ceca1b4c0d9bdb550dc23f06ffbb5a8e033bc7.zip
525 files changed, 0 insertions, 20753 deletions
diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest
deleted file mode 100644
index d97c61cb21c0..000000000000
--- a/sci-biology/STAR/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST STAR-2.7.10a.tar.gz 12270915 BLAKE2B 51a9cf2c838cfeb313df9e5024b53cd5a89088f08ac88c8dc57a9e08cd3ba394e46ffe86a8ff3b9484b25b681ecd960098c06d879e772d21afe8cc2d0d35175d SHA512 19a5f3c25d147bcd96cf68249d275dad7fd11425031a40c97c7ae15846f55839ced897d541ed60b426a6bf089d968ac86625af774db3950dc459035ac2b659c9
diff --git a/sci-biology/STAR/STAR-2.7.10a.ebuild b/sci-biology/STAR/STAR-2.7.10a.ebuild
deleted file mode 100644
index c3deb5a94b0a..000000000000
--- a/sci-biology/STAR/STAR-2.7.10a.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays"
-HOMEPAGE="https://github.com/alexdobin/STAR"
-SRC_URI="https://github.com/alexdobin/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="sci-libs/htslib:="
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-2.7.10a-fix-build-system.patch
-	"${FILESDIR}"/${PN}-2.7.10a-missing-include.patch
-)
-DOCS=( README.md CHANGES.md RELEASEnotes.md doc/STARmanual.pdf )
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
-}
-
-src_prepare() {
-	default
-
-	# remove bundled htslib
-	rm -r source/htslib || die
-}
-
-src_configure() {
-	tc-export CC CXX PKG_CONFIG
-}
-
-src_compile() {
-	emake -C source STAR
-}
-
-src_install() {
-	dobin source/STAR
-	einstalldocs
-}
diff --git a/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch b/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch
deleted file mode 100644
index 0f06c94fb109..000000000000
--- a/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch
+++ /dev/null
@@ -1,195 +0,0 @@
---- a/source/bam_cat.c
-+++ b/source/bam_cat.c
-@@ -52,8 +52,8 @@
- #include <stdlib.h>
- #include <unistd.h>
- 
--#include "htslib/htslib/bgzf.h"
--#include "htslib/htslib/sam.h"
-+#include <htslib/bgzf.h>
-+#include <htslib/sam.h>
- #include <cstring>
- 
- #define BUF_SIZE 0x10000
---- a/source/bam_cat.h
-+++ b/source/bam_cat.h
-@@ -1,7 +1,7 @@
- #ifndef CODE_bam_cat
- #define CODE_bam_cat
- 
--#include "htslib/htslib/sam.h"
-+#include <htslib/sam.h>
- 
- int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam);
- 
---- a/source/BAMfunctions.cpp
-+++ b/source/BAMfunctions.cpp
-@@ -1,5 +1,5 @@
- #include "BAMfunctions.h"
--#include "htslib/htslib/kstring.h"
-+#include <htslib/kstring.h>
- 
- 
- string bam_cigarString (bam1_t *b) {//output CIGAR string
---- a/source/bamRemoveDuplicates.cpp
-+++ b/source/bamRemoveDuplicates.cpp
-@@ -1,7 +1,7 @@
- #include <unordered_map>
- #include "bamRemoveDuplicates.h"
- #include <iostream>
--#include "htslib/htslib/sam.h"
-+#include <htslib/sam.h>
- #include "IncludeDefine.h"
- #include SAMTOOLS_BGZF_H
- #include "ErrorWarning.h"
---- a/source/IncludeDefine.h
-+++ b/source/IncludeDefine.h
-@@ -30,8 +30,8 @@
- #define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ )
- 
- //external libs
--#define SAMTOOLS_BGZF_H "htslib/htslib/bgzf.h"
--#define SAMTOOLS_SAM_H  "htslib/htslib/sam.h"
-+#define SAMTOOLS_BGZF_H <htslib/bgzf.h>
-+#define SAMTOOLS_SAM_H  <htslib/sam.h>
- 
- using namespace std;
- 
---- a/source/Makefile
-+++ b/source/Makefile
-@@ -12,11 +12,7 @@
- CXX ?= g++
- 
- # pre-defined flags
--LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
--LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
--LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
--LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
--LDFLAGS_gdb := $(LDFLAGS_shared)
-+LIBS := -pthread -lhts -lz
- 
- DATE_FMT = --iso-8601=seconds
- ifdef SOURCE_DATE_EPOCH
-@@ -27,7 +23,7 @@
- 
- BUILD_PLACE ?= $(HOSTNAME):$(shell pwd)
- 
--COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(BUILD_DATE) $(BUILD_PLACE)"'
-+COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE=""'
- 
- 
- GIT_CHECK := $(shell git status 1> /dev/null 2> /dev/null && echo 0)
-@@ -41,13 +37,13 @@
- 
- # Defaults, can be overridden by make arguments or environment
- CXXFLAGS ?= -pipe -Wall -Wextra
--CFLAGS ?= -pipe -Wall -Wextra -O3
-+CFLAGS ?= -pipe -Wall -Wextra
- CXXFLAGS_SIMD ?= -mavx2
- 
- # Unconditionally set essential flags and optimization options
- CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) $(GIT_BRANCH_COMMIT_DIFF)
--CXXFLAGS_main := -O3 $(CXXFLAGS_common)
--CXXFLAGS_gdb := -O0 -g3 $(CXXFLAGS_common)
-+CXXFLAGS_main := $(CXXFLAGS_common)
-+CXXFLAGS_gdb := $(CXXFLAGS_common)
- 
- ##########################################################################################################
- OBJECTS = SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o \
-@@ -130,7 +126,7 @@
- ifneq ($(MAKECMDGOALS),clean_solo)
- ifneq ($(MAKECMDGOALS),STARforMac)
- ifneq ($(MAKECMDGOALS),STARforMacGDB)
--Depend.list: $(SOURCES) parametersDefault.xxd htslib
-+Depend.list: $(SOURCES) parametersDefault.xxd
- 	echo $(SOURCES)
- 	'rm' -f ./Depend.list
- 	$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
-@@ -142,57 +138,43 @@
- endif
- endif
- 
--htslib : htslib/libhts.a
--
--htslib/libhts.a :
--	$(MAKE) -C htslib lib-static
--
- parametersDefault.xxd: parametersDefault
- 	xxd -i parametersDefault > parametersDefault.xxd
- 
- STAR$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
--STAR$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
- STAR$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
- 
- STARstatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
--STARstatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
- STARstatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
- 
- STARlong$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
--STARlong$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
- STARlong$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
- 
- STARlongStatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
--STARlongStatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
- STARlongStatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
- 
- 
- 
- POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS)
--POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
- POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
- 
- gdb : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) $(CXXFLAGS)
--gdb : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
- gdb : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS)
- 
- gdb-long : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
--gdb-long : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
- gdb-long : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS)
- 
- STARforMacStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
--STARforMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
- STARforMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS)
- 
- STARlongForMacStatic : CXXFLAGS := -D'COMPILE_FOR_LONG_READS' $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
--STARlongForMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
- STARlongForMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS)
---- a/source/signalFromBAM.h
-+++ b/source/signalFromBAM.h
-@@ -1,6 +1,6 @@
- #ifndef CODE_signalFromBAM
- #define CODE_signalFromBAM
--#include "htslib/htslib/sam.h"
-+#include <htslib/sam.h>
- #include  <fstream>
- #include <string>
- #include "Stats.h"
---- a/source/STAR.cpp
-+++ b/source/STAR.cpp
-@@ -29,7 +29,7 @@
- 
- #include "twoPassRunPass1.h"
- 
--#include "htslib/htslib/sam.h"
-+#include <htslib/sam.h>
- #include "parametersDefault.xxd"
- 
- void usage(int usageType) {
diff --git a/sci-biology/STAR/files/STAR-2.7.10a-missing-include.patch b/sci-biology/STAR/files/STAR-2.7.10a-missing-include.patch
deleted file mode 100644
index c056a8aad887..000000000000
--- a/sci-biology/STAR/files/STAR-2.7.10a-missing-include.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From f5ad94329db4fd81fc6ae30684c298772002e30b Mon Sep 17 00:00:00 2001
-From: David Seifert <soap@gentoo.org>
-Date: Sat, 7 May 2022 15:06:11 +0200
-Subject: [PATCH] Add missing `#include <array>` (GCC 12)
-
-Bug: https://bugs.gentoo.org/840586
----
- source/SoloCommon.h | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/source/SoloCommon.h b/source/SoloCommon.h
-index 2a1d5fcf..5adc5040 100644
---- a/source/SoloCommon.h
-+++ b/source/SoloCommon.h
-@@ -1,6 +1,7 @@
- #ifndef H_SoloCommon
- #define H_SoloCommon
- 
-+#include <array>
- #include <unordered_map>
- 
- typedef struct{
diff --git a/sci-biology/STAR/metadata.xml b/sci-biology/STAR/metadata.xml
deleted file mode 100644
index dd2e23471998..000000000000
--- a/sci-biology/STAR/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">alexdobin/STAR</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/aaindex/Manifest b/sci-biology/aaindex/Manifest
deleted file mode 100644
index e939baf4ddd4..000000000000
--- a/sci-biology/aaindex/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST aaindex-9.1.tar.bz2 133780 BLAKE2B 2e0a3c9f6f9e9a6d18f7812196595776a03e688b83799a24b63f659fe4c08b50de396d6aa07e80e3beea776d29210c1c71194deecea19faa8bf36204d8544f42 SHA512 d35760712a3f9d8c0d64e32ff450802eab20294851e569cbb9614610704f687c9ec56c440e6009b5c75c45ae12bd7968e28afcc414309318e94b092507df16d8
diff --git a/sci-biology/aaindex/aaindex-9.1-r2.ebuild b/sci-biology/aaindex/aaindex-9.1-r2.ebuild
deleted file mode 100644
index dea4b6531d4b..000000000000
--- a/sci-biology/aaindex/aaindex-9.1-r2.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="Amino acid indices and similarity matrices"
-HOMEPAGE="https://www.genome.jp/aaindex/"
-SRC_URI="mirror://gentoo/${P}.tar.bz2"
-
-LICENSE="public-domain"
-SLOT="0"
-# Minimal build keeps only the indexed files (if applicable) and the
-# documentation. The non-indexed database is not installed.
-KEYWORDS="~amd64 ~x86"
-IUSE="emboss minimal"
-
-BDEPEND="emboss? ( sci-biology/emboss )"
-RDEPEND="${BDEPEND}"
-
-src_compile() {
-	if use emboss; then
-		mkdir AAINDEX || die
-		einfo
-		einfo "Indexing AAindex for usage with EMBOSS"
-		EMBOSS_DATA="." aaindexextract -auto -infile ${PN}1 || die "Indexing AAindex failed"
-		einfo
-	fi
-}
-
-src_install() {
-	dodoc ${PN}.doc
-
-	if ! use minimal; then
-		insinto /usr/share/${PN}
-		doins ${PN}{1,2,3}
-	fi
-
-	if use emboss; then
-		insinto /usr/share/EMBOSS/data/AAINDEX
-		doins -r AAINDEX/.
-	fi
-}
diff --git a/sci-biology/aaindex/metadata.xml b/sci-biology/aaindex/metadata.xml
deleted file mode 100644
index 44422e7c1cfd..000000000000
--- a/sci-biology/aaindex/metadata.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		Amino acid indices and similarity matrices maintained at Kyoto
-		University. An amino acid index is a set of 20 numerical values
-		representing any of the different physicochemical and biological
-		properties of amino acids.  The AAindex1 section of the Amino Acid
-		Index Database is a collection of published indices together with the
-		result of cluster analysis using the correlation coefficient as the
-		distance between two indices.  This section currently contains 494
-		indices. Another important feature of amino acids that can be
-		represented numerically is the similarity between amino acids.  Thus, a
-		similarity matrix, also called a mutation matrix, is a set of 210
-		numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used
-		for sequence alignments and similarity searches.  The AAindex2 section
-		of the Amino Acid Index Database is a collection of published amino
-		acid mutation matrices together with the result of cluster analysis.
-		This section currently contains 83 matrices.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
deleted file mode 100644
index 9c9041e2c936..000000000000
--- a/sci-biology/abyss/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST abyss-2.3.4.tar.gz 3511137 BLAKE2B 2b7449233055d22330f44951f9f6d5ff1a116fa3e19c09c17cd4fa517d2fc055c4f00ccb82c7e09b1b939ac6f7a1caf73cf73c33bd3c8aa9ff11879c227a2aaa SHA512 9d4e418399dd62883b53e831f51a0bd2ba228da73eda6c6459cd729c002eb0487f9613fca1c9bd0f4fbb076eed8a9b952505ee97143ab7dde537c23e4a246cd4
diff --git a/sci-biology/abyss/abyss-2.3.4.ebuild b/sci-biology/abyss/abyss-2.3.4.ebuild
deleted file mode 100644
index 2c2c14d35bd5..000000000000
--- a/sci-biology/abyss/abyss-2.3.4.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools flag-o-matic toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="https://www.bcgsc.ca/resources/software/abyss/"
-SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	dev-cpp/sparsehash
-	dev-libs/boost:=
-	misc-haskell? (
-		dev-libs/gmp:0=
-		dev-libs/libffi:0=
-	)
-	sys-cluster/openmpi
-	dev-db/sqlite:3
-"
-DEPEND="${RDEPEND}
-	misc-haskell? (
-		dev-lang/ghc
-	)
-"
-
-# todo: --enable-maxk=N configure option
-# todo: also allow build with mpich (--enable-mpich)
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-src_prepare() {
-	default
-	sed -i -e "s/-Werror//" configure.ac || die #365195
-	eautoreconf
-}
-
-src_configure() {
-	# -Werror=lto-type-mismatch
-	# https://bugs.gentoo.org/862252
-	# https://github.com/bcgsc/abyss/issues/474
-	filter-lto
-
-	# disable building haskell tool Misc/samtobreak
-	# unless request by user: bug #534412
-	use misc-haskell || export ac_cv_prog_ac_ct_GHC=
-
-	econf $(use_enable openmp) --enable-maxk=256
-}
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
deleted file mode 100644
index 04e203d593eb..000000000000
--- a/sci-biology/abyss/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<use>
-		<flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">bcgsc/abyss</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest
deleted file mode 100644
index 178d054cf6f7..000000000000
--- a/sci-biology/augustus/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST augustus-3.4.0.tar.gz 221652100 BLAKE2B dfc8c98107f5a955f688f3d2976ca936faf2ef7004095f6b9d7c1902a36ca5d3c9aef59cab1b82b56cd5c2abc7b67195c5030111ed68557d53128814b1bf6bab SHA512 ca1df1016589f55527a883429edd5024cbc32c1b32036c81f9df5e0967a7d194f5b7a82109e924f380627427d9731caa478e63cad8cd804c01521aed76d8c4a6
-DIST augustus-3.5.0.tar.gz 225918930 BLAKE2B 26e934f3d3f50d183fb0ee7874352c5ac9af9877eaa40a9a6195ae79cfd9a78a321bd9261e8bd3435b1d4984589d0bdd4e0821ba6600c717d6afd95f511702de SHA512 0869e54b3126b3ab2f6fb2c28ff07b779265a139968e5277352f5230d3c317415324ca61dce4a0cd6c3f1fb5399447ae815bec7732a285ce652cf44e6cd23e5d
diff --git a/sci-biology/augustus/augustus-3.4.0-r3.ebuild b/sci-biology/augustus/augustus-3.4.0-r3.ebuild
deleted file mode 100644
index 1799ee8621a8..000000000000
--- a/sci-biology/augustus/augustus-3.4.0-r3.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DOCS_BUILDER="doxygen"
-DOCS_CONFIG_NAME="doxygen.conf"
-inherit docs toolchain-funcs
-
-DESCRIPTION="Eukaryotic gene predictor"
-HOMEPAGE="https://bioinf.uni-greifswald.de/augustus/"
-SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${P^}"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-RDEPEND="
-	dev-db/sqlite:3
-	dev-db/mysql++:=
-	dev-db/mysql-connector-c:=
-	dev-libs/boost:=[zlib]
-	sci-biology/bamtools:=
-	sci-biology/samtools:0
-	sci-libs/gsl:=
-	sci-libs/htslib:=
-	sci-libs/suitesparse
-	sci-mathematics/lpsolve:=
-	virtual/zlib:=
-"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/augustus-3.4.0-missing-cstdint.patch
-)
-
-src_compile() {
-	tc-export CC CXX
-
-	emake LINK.cc="$(tc-getCXX)"
-
-	docs_compile
-}
-
-src_install() {
-	einstalldocs
-	# from upstream Makefile install:
-	dodir "opt/${P}"
-	cp -a config bin scripts "${ED}/opt/${P}" || die
-	local file
-	for file in bin/*; do
-		dosym "../${P}/${file}" "/opt/${file}"
-	done
-}
diff --git a/sci-biology/augustus/augustus-3.5.0.ebuild b/sci-biology/augustus/augustus-3.5.0.ebuild
deleted file mode 100644
index 81df833c68a6..000000000000
--- a/sci-biology/augustus/augustus-3.5.0.ebuild
+++ /dev/null
@@ -1,94 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DOCS_BUILDER="doxygen"
-DOCS_CONFIG_NAME="doxygen.conf"
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-inherit docs python-any-r1 toolchain-funcs
-
-DESCRIPTION="Eukaryotic gene predictor"
-HOMEPAGE="https://bioinf.uni-greifswald.de/augustus/"
-SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${P^}"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
-	dev-db/sqlite:3
-	dev-db/mysql++:=
-	dev-db/mysql-connector-c:=
-	dev-libs/boost:=[zlib]
-	sci-biology/bamtools:=
-	sci-biology/samtools:0
-	sci-libs/gsl:=
-	sci-libs/htslib:=
-	sci-libs/suitesparse
-	sci-mathematics/lpsolve:=
-	virtual/zlib:=
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	test? (
-		${PYTHON_DEPS}
-	)
-"
-
-PATCHES=(
-	"${FILESDIR}"/augustus-3.4.0-missing-cstdint.patch
-	"${FILESDIR}"/augustus-3.5.0-fix-gcc15.patch
-)
-
-pkg_setup() {
-	use test && python-any-r1_pkg_setup
-}
-
-src_compile() {
-	tc-export CC CXX AR
-
-	emake
-
-	# Vendored gtest
-	use test && emake -C src unittest
-
-	docs_compile
-}
-
-src_test() {
-	if use elibc_musl; then
-		# Upstream already does this for non-amd64 and non-linux environments
-		# Probably related https://github.com/Gaius-Augustus/Augustus/issues/247
-		# bug #873025
-		emake test TEST_COMPARE= TEST_HTML=
-	else
-		emake test
-	fi
-
-	pushd src/unittests >/dev/null || die
-	if use elibc_musl; then
-		# Float issues
-		./unittests --gtest_filter='-CodonEvoTest.CodonEvoRateReadWrite' || die
-	else
-		./unittests || die
-	fi
-	popd >/dev/null || die
-}
-
-src_install() {
-	einstalldocs
-	# from upstream Makefile install:
-	dodir "opt/${P}"
-	cp -a config bin scripts "${ED}/opt/${P}" || die
-	local file
-	for file in bin/*; do
-		dosym "../${P}/${file}" "/opt/${file}"
-	done
-}
diff --git a/sci-biology/augustus/files/augustus-3.4.0-missing-cstdint.patch b/sci-biology/augustus/files/augustus-3.4.0-missing-cstdint.patch
deleted file mode 100644
index 3c0095241636..000000000000
--- a/sci-biology/augustus/files/augustus-3.4.0-missing-cstdint.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-https://bugs.gentoo.org/895204
-
-https://github.com/Gaius-Augustus/Augustus/commit/1ed97dc4ce2909c5f89737005b8ea4a664fbe728
-https://github.com/Gaius-Augustus/Augustus/pull/395
-
-From 1ed97dc4ce2909c5f89737005b8ea4a664fbe728 Mon Sep 17 00:00:00 2001
-From: Kuoi <kuoi@bioarchlinux.org>
-Date: Sun, 11 Jun 2023 23:47:49 +0800
-Subject: [PATCH] fix: gcc13 failed with this
-
---- a/include/sqliteDB.hh
-+++ b/include/sqliteDB.hh
-@@ -11,6 +11,7 @@
- #include <string>
- #include <vector>
- #include <sqlite3.h>
-+#include <cstdint>
- 
- using namespace std;
- 
-
-https://github.com/Gaius-Augustus/Augustus/commit/3dbe752e4cf3f6778168166a2c662d02d8623f15
-https://github.com/Gaius-Augustus/Augustus/pull/395
-
-From 3dbe752e4cf3f6778168166a2c662d02d8623f15 Mon Sep 17 00:00:00 2001
-From: Kuoi <kuoi@bioarchlinux.org>
-Date: Mon, 12 Jun 2023 01:32:02 +0800
-Subject: [PATCH] fix: without it compile fail
-
---- a/auxprogs/homGeneMapping/include/sqliteDB.hh
-+++ b/auxprogs/homGeneMapping/include/sqliteDB.hh
-@@ -13,6 +13,7 @@
- #include <string>
- #include <vector>
- #include <sqlite3.h>
-+#include <cstdint>
- 
- using namespace std;
- 
diff --git a/sci-biology/augustus/files/augustus-3.5.0-fix-gcc15.patch b/sci-biology/augustus/files/augustus-3.5.0-fix-gcc15.patch
deleted file mode 100644
index 4c5916ad402f..000000000000
--- a/sci-biology/augustus/files/augustus-3.5.0-fix-gcc15.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-https://bugs.gentoo.org/949617
-https://github.com/Gaius-Augustus/Augustus/pull/431
-
-From b7cbe782e840c82da1eeb2aae7a1a757ecef9fb0 Mon Sep 17 00:00:00 2001
-From: Alfred Wingate <parona@protonmail.com>
-Date: Tue, 11 Feb 2025 14:57:23 +0200
-Subject: [PATCH] filterBam: include missing header for gcc15
-
-Bug: https://bugs.gentoo.org/949617
-Signed-off-by: Alfred Wingate <parona@protonmail.com>
---- a/auxprogs/filterBam/src/headers/bamaccess.hh
-+++ b/auxprogs/filterBam/src/headers/bamaccess.hh
-@@ -7,6 +7,7 @@
- #include <iostream>
- #include <vector>
- #include <memory>
-+#include <cstdint>
- 
- class BamAlignmentRecord;
- typedef std::shared_ptr<BamAlignmentRecord> BamAlignmentRecord_;
diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml
deleted file mode 100644
index a4352248acda..000000000000
--- a/sci-biology/augustus/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="github">Gaius-Augustus/Augustus</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest
deleted file mode 100644
index 48e3770f13d9..000000000000
--- a/sci-biology/bamtools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bamtools-2.5.3.tar.gz 245648 BLAKE2B f387dd1dbae87ba22e811f81afd144d1c0fab02cd3c61f0442a3383a4f91d019a3ec8f0765e8d2ab8727bb9f1b3b22f4a2aff424a7c0aaa93396eb7afe0e9ba7 SHA512 bde9d98048d9f30d7f3c4e75db97e610ab58148dedadd09a36ad2421a6357b24510abda2451452d1fb9b40e22e1b8fe6f4e4c6ee1c529c426055a050a24b52d8
diff --git a/sci-biology/bamtools/bamtools-2.5.3.ebuild b/sci-biology/bamtools/bamtools-2.5.3.ebuild
deleted file mode 100644
index 6dfe1b0b9cef..000000000000
--- a/sci-biology/bamtools/bamtools-2.5.3.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake
-
-DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
-HOMEPAGE="https://github.com/pezmaster31/bamtools"
-
-if [[ ${PV} == *9999 ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git"
-else
-	SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="amd64 ~x86"
-fi
-
-LICENSE="MIT"
-SLOT="0/${PV}" # no stable ABI yet
-
-RDEPEND="
-	>=dev-libs/jsoncpp-1.8.0:=
-	virtual/zlib:="
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-	# delete bundled libs, just to be safe
-	rm -rf src/third_party/{gtest-1.6.0,jsoncpp} || die
-
-	cmake_src_prepare
-}
diff --git a/sci-biology/bamtools/bamtools-9999.ebuild b/sci-biology/bamtools/bamtools-9999.ebuild
deleted file mode 100644
index e6793562c6a4..000000000000
--- a/sci-biology/bamtools/bamtools-9999.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake
-
-DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
-HOMEPAGE="https://github.com/pezmaster31/bamtools"
-
-if [[ ${PV} == *9999 ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git"
-else
-	SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="MIT"
-SLOT="0/${PV}" # no stable ABI yet
-
-RDEPEND="
-	>=dev-libs/jsoncpp-1.8.0:=
-	virtual/zlib:="
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-	# delete bundled libs, just to be safe
-	rm -rf src/third_party/{gtest-1.6.0,jsoncpp} || die
-
-	cmake_src_prepare
-}
diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml
deleted file mode 100644
index aaba26efdc12..000000000000
--- a/sci-biology/bamtools/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription>
-  <upstream>
-    <remote-id type="github">pezmaster31/bamtools</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
deleted file mode 100644
index ac638db4665d..000000000000
--- a/sci-biology/bcftools/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST bcftools-1.20.tar.bz2 7883049 BLAKE2B 36bfd82c9500f384b75ef93242a5879123f7fd63c893c95a1ce5efbfa9396f2c1fd75025ea2dd48d37e7dc93426ffaffbb2f3c6bdf64128fbdd3af2a2f760b17 SHA512 c77294923a6bb5cb97a2c4947e79aa215612a62f71ba0e4dde627cd3d97ee9a28a3682e8ab2f3bedd0e75e2bb9800915d9430f9504f09ead4492d3583553db2a
-DIST bcftools-1.21.tar.bz2 7982173 BLAKE2B 7da808d1b06d2cdc0ed9ae2768a71f9e3e1de07f6e9c74504eb6f19b06481e509630e14f209ec0250c0689bf9d5807936288ba48f17830a2b004b7cfa3c23c59 SHA512 f8fb2e50a1a9e7a7e8a4f71d71d052f6019d54c60ae060d0abfbd01ab61a2c44e04e069c479ea9f6156513b54a611a9a46930a0ff4454019bb715fdb9558d07d
-DIST bcftools-1.22.tar.bz2 8176878 BLAKE2B 62df4b50e8ee6d4e9614f9317a58a72cc75adf89329cf2759f0e2b65027c51cbb4728e60128b22b4786e2ec541433664f3d7af5d70611dd32d362d2be7f56d0e SHA512 20daee4ecb6b7d0034e0d9590fcc42712ac78c4e511d519ac0dd98d2b2b920d85d234cf1a08abd1be62d1be994788de53d6010af642099f2b75753ecc19efd15
-DIST bcftools-1.23.tar.bz2 8133124 BLAKE2B 3d56c6aacf286414d51e8cd6c3a3d6c5b7357e04119f233fa9272bf9c7f4efb6e126cb3b7572cbe85afc3f2c3ef09ae7cb52880817a12f94f61f534a3e9d60bf SHA512 6daf9bbc0b5ad430c555d70d9bf2a9eeb5b477f564282a86702a2ab4b62240b3aa4867cf1dd7357d3ce7b95b2917ecadc3999c0c67b4150d9c9140f46c945909
diff --git a/sci-biology/bcftools/bcftools-1.20.ebuild b/sci-biology/bcftools/bcftools-1.20.ebuild
deleted file mode 100644
index 7e040f93dcaf..000000000000
--- a/sci-biology/bcftools/bcftools-1.20.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-inherit python-single-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	dev-lang/perl
-	$(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]')
-	=sci-libs/htslib-$(ver_cut 1-2)*:=
-	virtual/zlib:=
-	${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-BDEPEND="${PYTHON_DEPS}"
-
-src_prepare() {
-	default
-
-	python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-}
-
-src_configure() {
-	econf \
-		--disable-bcftools-plugins \
-		--disable-libgsl \
-		--with-htslib=system
-}
diff --git a/sci-biology/bcftools/bcftools-1.21.ebuild b/sci-biology/bcftools/bcftools-1.21.ebuild
deleted file mode 100644
index 7e040f93dcaf..000000000000
--- a/sci-biology/bcftools/bcftools-1.21.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-inherit python-single-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	dev-lang/perl
-	$(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]')
-	=sci-libs/htslib-$(ver_cut 1-2)*:=
-	virtual/zlib:=
-	${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-BDEPEND="${PYTHON_DEPS}"
-
-src_prepare() {
-	default
-
-	python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-}
-
-src_configure() {
-	econf \
-		--disable-bcftools-plugins \
-		--disable-libgsl \
-		--with-htslib=system
-}
diff --git a/sci-biology/bcftools/bcftools-1.22.ebuild b/sci-biology/bcftools/bcftools-1.22.ebuild
deleted file mode 100644
index 7e040f93dcaf..000000000000
--- a/sci-biology/bcftools/bcftools-1.22.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-inherit python-single-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	dev-lang/perl
-	$(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]')
-	=sci-libs/htslib-$(ver_cut 1-2)*:=
-	virtual/zlib:=
-	${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-BDEPEND="${PYTHON_DEPS}"
-
-src_prepare() {
-	default
-
-	python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-}
-
-src_configure() {
-	econf \
-		--disable-bcftools-plugins \
-		--disable-libgsl \
-		--with-htslib=system
-}
diff --git a/sci-biology/bcftools/bcftools-1.23.ebuild b/sci-biology/bcftools/bcftools-1.23.ebuild
deleted file mode 100644
index 7166b3a176bd..000000000000
--- a/sci-biology/bcftools/bcftools-1.23.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-inherit python-single-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	dev-lang/perl
-	$(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]')
-	=sci-libs/htslib-$(ver_cut 1-2)*:=
-	virtual/zlib:=
-	${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-BDEPEND="${PYTHON_DEPS}"
-
-src_prepare() {
-	default
-
-	python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-}
-
-src_configure() {
-	econf \
-		--disable-bcftools-plugins \
-		--disable-libgsl \
-		--with-htslib=system
-}
diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml
deleted file mode 100644
index 0ba86185e50d..000000000000
--- a/sci-biology/bcftools/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">samtools/bcftools</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
deleted file mode 100644
index 4b33688aa042..000000000000
--- a/sci-biology/bedtools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bedtools-2.31.1.tar.gz 19629373 BLAKE2B f09742ee74494c783cef4909c56abd7b8542344539fe006140716b0a6a1d972db4e3df4a03fb3996a71cb57709b0494be8686879cba15c0985236f3a1282c92d SHA512 fbdc23011566697b2fc44bf3e7b466949487d3f648e81957fa80e8ad4b192d0ef7e2e3944b9b18612774a7984ec99e3fc339c3fddb8889caa632b8ce8defa20d
diff --git a/sci-biology/bedtools/bedtools-2.31.1.ebuild b/sci-biology/bedtools/bedtools-2.31.1.ebuild
deleted file mode 100644
index 9c05c3d56eb9..000000000000
--- a/sci-biology/bedtools/bedtools-2.31.1.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-inherit python-any-r1 toolchain-funcs
-
-DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
-HOMEPAGE="https://bedtools.readthedocs.io/"
-SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
-S="${WORKDIR}/${PN}2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
-	app-arch/bzip2
-	app-arch/xz-utils
-	virtual/zlib:="
-DEPEND="${RDEPEND}"
-BDEPEND="
-	${PYTHON_DEPS}
-	test? ( >=sci-biology/samtools-1.10:0 )"
-
-# bedtools2 has a *terrible* build system and development practices.
-# Upstream has forked htslib 1.9 and extended it by adding clever callbacks
-# that make unbundling it nigh impossible. There are no signs of upstream porting
-# their fork to 1.10, which means we're stuck with the bundled version.
-PATCHES=(
-	"${FILESDIR}"/${PN}-2.31.1-buildsystem.patch
-	"${FILESDIR}"/${PN}-2.31.1-python.patch
-	"${FILESDIR}"/${PN}-2.31.1-includes.patch
-)
-
-src_configure() {
-	tc-export AR CC CXX RANLIB
-}
-
-src_install() {
-	default
-
-	insinto /usr/share/bedtools
-	doins -r genomes
-}
diff --git a/sci-biology/bedtools/files/bedtools-2.31.1-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.31.1-buildsystem.patch
deleted file mode 100644
index 8bb2a096e917..000000000000
--- a/sci-biology/bedtools/files/bedtools-2.31.1-buildsystem.patch
+++ /dev/null
@@ -1,84 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -4,46 +4,29 @@
- # (c) 2009 Aaron Quinlan
- # ==========================
- 
--SHELL := /bin/bash -e
-+SHELL := bash -e
- 
- VERSION_FILE=./src/utils/version/version_git.h
- RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
- 
- 
- # define our object and binary directories
--ifeq ($(VERBOSE),1)
- CCPREFIX =
--else
--CCPREFIX = @
--endif
- 
- OBJ_DIR	= obj
- BIN_DIR	= bin
- SRC_DIR	= src
- 
--CXX     = g++
--
--PYTHON ?= $(shell python --version >/dev/null 2>&1 && echo "python" || echo python3)
--
--ifeq ($(DEBUG),1)
--BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
--BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0
--else
- BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
--BT_CXXFLAGS = -g -Wall -O2
--endif
-+BT_CXXFLAGS = -Wall
- 
- # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
--ifeq ($(USE_RAND),1)
--BT_CXXFLAGS += -DUSE_RAND
--else
- BT_CXXFLAGS += -std=c++11
--endif
- 
- BT_LDFLAGS =
- BT_LIBS    = -lz -lm -lbz2 -llzma -lpthread
- 
--prefix ?= /usr/local
-+prefix = $(EPREFIX)/usr
- 
- SUBDIRS = $(SRC_DIR)/annotateBed \
- 		  $(SRC_DIR)/bamToBed \
-@@ -213,7 +196,7 @@
- 
- # make the "obj/" and "bin/" directories, if they don't exist
- $(OBJ_DIR) $(BIN_DIR):
--	@mkdir -p $@
-+	mkdir -p $@
- 
- 
- # Usually HTSlib's configure script has not been used (detected via config.mk
---- a/src/utils/htslib/Makefile
-+++ b/src/utils/htslib/Makefile
-@@ -22,20 +22,13 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- 
--CC     = gcc
--AR     = ar
--RANLIB = ranlib
--
- # Default libraries to link if configure is not used
- htslib_default_libs = -lz -lm -lbz2 -llzma
- 
--CPPFLAGS =
- # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
- # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
- #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
--CFLAGS   = -g -Wall -O2
- EXTRA_CFLAGS_PIC = -fpic
--LDFLAGS  =
- LIBS     = $(htslib_default_libs)
- 
- prefix      = /usr/local
diff --git a/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch b/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch
deleted file mode 100644
index 927b1b944d6e..000000000000
--- a/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch
+++ /dev/null
@@ -1,180 +0,0 @@
-https://github.com/arq5x/bedtools2/pull/1087
-
-From 3fbf2ddc8ebf0fc1bd492d14a6046aadd59ecadb Mon Sep 17 00:00:00 2001
-From: David Seifert <soap@gentoo.org>
-Date: Thu, 25 Apr 2024 11:18:48 +0200
-Subject: [PATCH] Add missing `stdint.h` includes
-
-* Musl is a lot stricter with transitive includes:
-  Bug: https://bugs.gentoo.org/907971
---- a/src/bamToBed/bamToBed.cpp
-+++ b/src/bamToBed/bamToBed.cpp
-@@ -22,6 +22,7 @@ using namespace BamTools;
- #include <sstream>
- #include <fstream>
- #include <stdlib.h>
-+#include <stdint.h>
- 
- using namespace std;
- 
---- a/src/clusterBed/clusterBed.cpp
-+++ b/src/clusterBed/clusterBed.cpp
-@@ -12,6 +12,8 @@
- #include "lineFileUtilities.h"
- #include "clusterBed.h"
- 
-+#include <stdint.h>
-+
- // = Constructor =
- BedCluster::BedCluster(string &bedFile, 
-                    int  maxDistance, 
---- a/src/pairToBed/pairToBed.h
-+++ b/src/pairToBed/pairToBed.h
-@@ -22,6 +22,7 @@ using namespace BamTools;
- #include <vector>
- #include <iostream>
- #include <fstream>
-+#include <stdint.h>
- 
- using namespace std;
- 
---- a/src/randomBed/randomBed.h
-+++ b/src/randomBed/randomBed.h
-@@ -22,6 +22,7 @@
- #include <unistd.h>
- #include <sys/types.h>
- #include <algorithm>  // for binary search
-+#include <stdint.h>
- using namespace std;
- 
- const int MAX_TRIES = 1000000;
---- a/src/summaryFile/summaryFile.h
-+++ b/src/summaryFile/summaryFile.h
-@@ -12,6 +12,8 @@
- #include "ToolBase.h"
- #include "ContextSummary.h"
- 
-+#include <stdint.h>
-+
- struct Interval {
-   CHRPOS start;
-   CHRPOS end;
---- a/src/utils/BamTools/include/BamAlignment.mapping.hpp
-+++ b/src/utils/BamTools/include/BamAlignment.mapping.hpp
-@@ -1,3 +1,4 @@
-+#include <stdint.h>
- 
- struct _RefID_t {
-     operator int32_t() const {return (int32_t)(_ptr()->core.tid);}
---- a/src/utils/BamTools/include/api/BamAux.h
-+++ b/src/utils/BamTools/include/api/BamAux.h
-@@ -1,4 +1,5 @@
- #include <string>
-+#include <stdint.h>
- 
- #ifndef BAMAUX_H
- #define BAMAUX_H
---- a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
-+++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
-@@ -9,6 +9,7 @@
- #define SINGLELINETEXTFILEREADER_H_
- 
- #include <algorithm>
-+#include <stdint.h>
- #include "FileReader.h"
- #include "string.h"
- #include "lineFileUtilities.h"
---- a/src/utils/FileRecordTools/Records/BamRecord.cpp
-+++ b/src/utils/FileRecordTools/Records/BamRecord.cpp
-@@ -10,6 +10,8 @@
- #include "BamFileReader.h"
- #include "RecordKeyVector.h"
- 
-+#include <stdint.h>
-+
- BamRecord::BamRecord()
- : _bamChromId(-1)
- {
---- a/src/utils/GenomeFile/GenomeFile.h
-+++ b/src/utils/GenomeFile/GenomeFile.h
-@@ -19,6 +19,7 @@
- #include <fstream>
- #include <cstring>
- #include <cstdio>
-+#include <stdint.h>
- #include <algorithm> // for bsearch lower_bound()
- #include "api/BamReader.h"
- #include "api/BamAux.h"
---- a/src/utils/GenomeFile/NewGenomeFile.h
-+++ b/src/utils/GenomeFile/NewGenomeFile.h
-@@ -14,6 +14,7 @@
- #define NEW_GENOMEFILE_H
- 
- #include <algorithm> // for bsearch lower_bound()
-+#include <stdint.h>
- 
- #include "BedtoolsTypes.h"
- 
---- a/src/utils/bedFilePE/bedFilePE.h
-+++ b/src/utils/bedFilePE/bedFilePE.h
-@@ -8,6 +8,7 @@
- #include <fstream>
- #include <sstream>
- #include <cstring>
-+#include <stdint.h>
- #include <algorithm>
- #include "bedFile.h"
- #include "lineFileUtilities.h"
---- a/src/utils/general/ParseTools.cpp
-+++ b/src/utils/general/ParseTools.cpp
-@@ -2,7 +2,7 @@
- #include <climits>
- #include <cctype>
- #include <cstring>
--#include <cstdint>
-+#include <stdint.h>
- #include <cstdio>
- #include <cstdlib>
- #include <sstream>
---- a/src/utils/lineFileUtilities/lineFileUtilities.h
-+++ b/src/utils/lineFileUtilities/lineFileUtilities.h
-@@ -4,6 +4,7 @@
- #include <vector>
- #include <string>
- #include <cstring>
-+#include <stdint.h>
- #include <cstdlib>
- #include <sstream>
- #include <iostream>
---- a/src/utils/sequenceUtilities/sequenceUtils.h
-+++ b/src/utils/sequenceUtilities/sequenceUtils.h
-@@ -4,6 +4,7 @@
- #include <string>
- #include <algorithm>
- #include <cctype>
-+#include <stdint.h>
- 
- using namespace std;
- 
---- a/src/windowMaker/windowMaker.h
-+++ b/src/windowMaker/windowMaker.h
-@@ -12,6 +12,8 @@ Licenced under the GNU General Public License 2.0 license.
- #include "NewGenomeFile.h"
- #include "bedFile.h"
- 
-+#include <stdint.h>
-+
- using namespace std;
- 
- 
---- a/src/windowMaker/windowMakerMain.cpp
-+++ b/src/windowMaker/windowMakerMain.cpp
-@@ -12,6 +12,8 @@ Licenced under the GNU General Public License 2.0 license.
- #include "windowMaker.h"
- #include "version.h"
- 
-+#include <stdint.h>
-+
- using namespace std;
- 
- // define our program name
diff --git a/sci-biology/bedtools/files/bedtools-2.31.1-python.patch b/sci-biology/bedtools/files/bedtools-2.31.1-python.patch
deleted file mode 100644
index 99fc1b1d480b..000000000000
--- a/sci-biology/bedtools/files/bedtools-2.31.1-python.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-https://github.com/arq5x/bedtools2/pull/1087
-
-From eabcd3dcb9caa1fcc17acd43df2ded4170ed1449 Mon Sep 17 00:00:00 2001
-From: David Seifert <soap@gentoo.org>
-Date: Thu, 25 Apr 2024 11:18:47 +0200
-Subject: [PATCH] Allow PYTHON from environment
-
-* Distros need to be able to specify exactly which python
-  interpreter to run tests under.
---- a/test/bigchroms/test-bigchroms.sh
-+++ b/test/bigchroms/test-bigchroms.sh
-@@ -28,7 +28,7 @@ check obs abig.bed
- rm obs
- 
- if [[ "$BT_NO_BIG_FILES" != "" ]]; then
--python make-big-chrom.py
-+${PYTHON:-python} make-big-chrom.py
- 
- echo -e "    bigchroms.t03...big get fasta \c"
- $BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs
---- a/test/fisher/cmp.sh
-+++ b/test/fisher/cmp.sh
-@@ -3,7 +3,7 @@ set -eo pipefail
- echo "fisher,shuffled"
- 
- for i in $(seq 1000); do
--    fisher=$(python ./sim.py | tail -1 | cut -f 2)
-+    fisher=$(${PYTHON:-python} ./sim.py | tail -1 | cut -f 2)
-     shuffle=$(bash shuf.sh)
-     echo "$fisher,$shuffle"
- done
---- a/test/genomecov/test-genomecov.sh
-+++ b/test/genomecov/test-genomecov.sh
-@@ -288,7 +288,7 @@ CRAM_REFERENCE=test_ref.fa $BT genomecov -ibam empty.cram > obs
- check obs exp
- rm obs exp
- 
--python mk-deep.py > deep.sam
-+${PYTHON:-python} mk-deep.py > deep.sam
- echo -e "    genomecov.t18...\c"
- echo "c1	1	1000000" > exp
- $BT genomecov -d -ibam deep.sam | head -1 > obs
diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml
deleted file mode 100644
index 063085dad8ee..000000000000
--- a/sci-biology/bedtools/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="google-code">bedtools</remote-id>
-    <remote-id type="github">arq5x/bedtools2</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/bfast/Manifest b/sci-biology/bfast/Manifest
deleted file mode 100644
index 43bf85bb09b8..000000000000
--- a/sci-biology/bfast/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bfast-0.7.0a.tar.gz 2456617 BLAKE2B a841e7651e731dbb3faf22eb03dce5d2008c84f9a6198204d3c41aea26626058e3a23375bc0e7e8fc142d4898e09ddbb168016c71a7b79527e602e06ec329151 SHA512 16e7ec5101c478f0dfc171016cbacb2b9240773e43b2d40eeb42d0e47afcee50a6dd5838e043a0326fc1ca9a87d3e55b42326a7f17b7c5654ef9825913860836
diff --git a/sci-biology/bfast/bfast-0.7.0a-r1.ebuild b/sci-biology/bfast/bfast-0.7.0a-r1.ebuild
deleted file mode 100644
index 56c2f6035994..000000000000
--- a/sci-biology/bfast/bfast-0.7.0a-r1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools
-
-DESCRIPTION="Blat-like Fast Accurate Search Tool"
-HOMEPAGE="https://sourceforge.net/projects/bfast/"
-SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="test" # tests broken, upstream unresponsive
-
-RDEPEND="dev-perl/XML-Simple"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-autotools.patch
-	"${FILESDIR}"/${P}-test-sourcing.patch
-	"${FILESDIR}"/${P}-C99-inline.patch
-	"${FILESDIR}"/${P}-gzeof.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/bfast/files/bfast-0.7.0a-C99-inline.patch b/sci-biology/bfast/files/bfast-0.7.0a-C99-inline.patch
deleted file mode 100644
index 86450c96048a..000000000000
--- a/sci-biology/bfast/files/bfast-0.7.0a-C99-inline.patch
+++ /dev/null
@@ -1,74 +0,0 @@
---- a/bfast/AlignNTSpace.c
-+++ b/bfast/AlignNTSpace.c
-@@ -478,7 +478,7 @@
- 	}
- }
- 
--inline void AlignNTSpaceFillInCell(char *read,
-+void AlignNTSpaceFillInCell(char *read,
- 		int32_t readLength,
- 		char *reference,
- 		int32_t referenceLength,
---- a/bfast/AlignNTSpace.h
-+++ b/bfast/AlignNTSpace.h
-@@ -10,5 +10,5 @@
- void AlignNTSpaceRecoverAlignmentFromMatrix(AlignedEntry*, AlignMatrix*, char*, int, char*, int, int32_t, int32_t, int, int32_t, char, int);
- void AlignNTSpaceInitializeAtStart(AlignMatrix*, ScoringMatrix*, int32_t, int32_t);
- void AlignNTSpaceInitializeToExtend(AlignMatrix*, ScoringMatrix*, int32_t, int32_t, int32_t, int32_t);
--inline void AlignNTSpaceFillInCell(char*, int32_t, char*, int32_t, ScoringMatrix*, AlignMatrix*, int32_t, int32_t, int32_t, int32_t);
-+void AlignNTSpaceFillInCell(char*, int32_t, char*, int32_t, ScoringMatrix*, AlignMatrix*, int32_t, int32_t, int32_t, int32_t);
- #endif
---- a/bfast/BLib.c
-+++ b/bfast/BLib.c
-@@ -90,7 +90,7 @@
- }
- 
- /* TODO */
--inline char ToUpper(char a)
-+char ToUpper(char a)
- {
-   if(97 <= a && a < 122) return (char)(a - 32);
-   return a;
---- a/bfast/BLib.h
-+++ b/bfast/BLib.h
-@@ -16,7 +16,7 @@
- int ParseFastaHeaderLine(char*);
- char ToLower(char);
- void ToLowerRead(char*, int);
--inline char ToUpper(char);
-+char ToUpper(char);
- void ToUpperRead(char*, int);
- void ReverseRead(char*, char*, int);
- void ReverseReadFourBit(int8_t*, int8_t*, int);
---- a/bfast/ScoringMatrix.c
-+++ b/bfast/ScoringMatrix.c
-@@ -98,14 +98,14 @@
- 	return 1;
- }
- 
--inline int32_t ScoringMatrixGetNTScore(char a,
-+int32_t ScoringMatrixGetNTScore(char a,
- 		char b,
- 		ScoringMatrix *sm)
- {
- 	return (ToUpper(a) == ToUpper(b)) ? sm->ntMatch : sm->ntMismatch;
- }
- 
--inline int32_t ScoringMatrixGetColorScore(char a, 
-+int32_t ScoringMatrixGetColorScore(char a, 
- 		char b, 
- 		ScoringMatrix *sm) 
- {
---- a/bfast/ScoringMatrix.h
-+++ b/bfast/ScoringMatrix.h
-@@ -3,8 +3,8 @@
- 
- #include "BLibDefinitions.h"
- 
--inline int32_t ScoringMatrixGetNTScore(char, char, ScoringMatrix*);
--inline int32_t ScoringMatrixGetColorScore(char, char, ScoringMatrix*);
-+int32_t ScoringMatrixGetNTScore(char, char, ScoringMatrix*);
-+int32_t ScoringMatrixGetColorScore(char, char, ScoringMatrix*);
- 
- int ScoringMatrixRead(char*, ScoringMatrix*, int);
- void ScoringMatrixInitialize(ScoringMatrix*);
diff --git a/sci-biology/bfast/files/bfast-0.7.0a-autotools.patch b/sci-biology/bfast/files/bfast-0.7.0a-autotools.patch
deleted file mode 100644
index 993f6a554662..000000000000
--- a/sci-biology/bfast/files/bfast-0.7.0a-autotools.patch
+++ /dev/null
@@ -1,41 +0,0 @@
---- a/configure.ac
-+++ b/configure.ac
-@@ -8,7 +8,7 @@
- AC_INIT([bfast],[0.7.0a],[bfast-help@lists.sourceforge.net],[bfast])
- AC_COPYRIGHT([See LICENSE for copyright information.])
- AC_CONFIG_AUX_DIR(config)
--AM_INIT_AUTOMAKE([dist-bzip2 subdir-objects])
-+AM_INIT_AUTOMAKE([dist-bzip2 subdir-objects serial-tests])
- AC_CONFIG_SRCDIR([config.h.in])
- AC_CONFIG_HEADERS([config.h])
- 
-@@ -21,10 +21,10 @@
- 
- AC_PROG_INSTALL
- AC_GNU_SOURCE
-+AC_SYS_LARGEFILE
- 
- # set CFLAGS and CXXFLAGS
--default_CFLAGS="-Wall -g -O2 -pthread";
--extended_CFLAGS="";# "-m64 -D_FILE_OFFSET_BITS=64";
-+default_CFLAGS="-Wall -pthread"
- 
- # Define some variables
- GITREV="Revision: undefined$";
-@@ -42,7 +42,7 @@
- 					AC_DEFINE(HAVE_LIBBZ2, 1, [Define to 1 if you have the <bzlib.h> header file.])], 
- 					AC_MSG_ERROR("could not find the bzlib library.  Please use --disable-bzlib if you wish to disable bzlib support."))])
- 
--CFLAGS="${default_CFLAGS} ${extended_CFLAGS}";
-+CFLAGS="${CFLAGS} ${default_CFLAGS} ${extended_CFLAGS}";
- 
- # Enable large file support; disable with --disable-largefile
- AC_SYS_LARGEFILE
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -16,5 +16,4 @@
- 
- SUBDIRS = bfast butil scripts tests
- 
--docdir = ${datadir}/doc/${PACKAGE}
- dist_doc_DATA = LICENSE manual/bfast-book.pdf
diff --git a/sci-biology/bfast/files/bfast-0.7.0a-gzeof.patch b/sci-biology/bfast/files/bfast-0.7.0a-gzeof.patch
deleted file mode 100644
index b0b992abf1bc..000000000000
--- a/sci-biology/bfast/files/bfast-0.7.0a-gzeof.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Use correct gzip function to check for the end of file
-https://bugs.gentoo.org/919254
---- a/bfast/RGMatch.c
-+++ b/bfast/RGMatch.c
-@@ -20,7 +20,7 @@
- 	/* Read in the read length */
- 	if(gzread64(fp, &m->readLength, sizeof(int32_t))!=sizeof(int32_t)||
- 			gzread64(fp, &m->qualLength, sizeof(int32_t))!=sizeof(int32_t)) {
--		if(feof(fp) != 0) {
-+		if(gzeof(fp) != 0) {
- 			return EOF;
- 		}
- 		else {
diff --git a/sci-biology/bfast/files/bfast-0.7.0a-test-sourcing.patch b/sci-biology/bfast/files/bfast-0.7.0a-test-sourcing.patch
deleted file mode 100644
index f4dd64e75cac..000000000000
--- a/sci-biology/bfast/files/bfast-0.7.0a-test-sourcing.patch
+++ /dev/null
@@ -1,79 +0,0 @@
---- a/tests/test.cleanup.sh
-+++ b/tests/test.cleanup.sh
-@@ -1,6 +1,6 @@
- #!/bin/sh
- 
--. test.definitions.sh
-+. ./test.definitions.sh
- 
- echo "      Cleaning up files.";
- 
---- a/tests/test.diff.sh
-+++ b/tests/test.diff.sh
-@@ -1,6 +1,6 @@
- #!/bin/sh
- 
--. test.definitions.sh
-+. ./test.definitions.sh
- 
- #error()
- #{
---- a/tests/test.fasta2brg.sh
-+++ b/tests/test.fasta2brg.sh
-@@ -1,6 +1,6 @@
- #!/bin/sh
- 
--. test.definitions.sh
-+. ./test.definitions.sh
- TMP_DIR="tmp/";
- 
- echo "      Building a reference genome.";
---- a/tests/test.index.sh
-+++ b/tests/test.index.sh
-@@ -1,5 +1,5 @@
- #!/bin/sh 
--. test.definitions.sh
-+. ./test.definitions.sh
- 
- echo "      Building an index.";
- 
---- a/tests/test.initialize.sh
-+++ b/tests/test.initialize.sh
-@@ -1,6 +1,6 @@
- #!/bin/sh
- 
--. test.definitions.sh
-+. ./test.definitions.sh
- 
- echo "      Initializing data for tests.";
- 
---- a/tests/test.localalign.sh
-+++ b/tests/test.localalign.sh
-@@ -1,6 +1,6 @@
- #!/bin/sh
- 
--. test.definitions.sh
-+. ./test.definitions.sh
- 
- echo "      Running local alignment.";
- 
---- a/tests/test.match.sh
-+++ b/tests/test.match.sh
-@@ -1,6 +1,6 @@
- #!/bin/sh
- 
--. test.definitions.sh
-+. ./test.definitions.sh
- 
- echo "      Finding matches.";
- 
---- a/tests/test.postprocess.sh
-+++ b/tests/test.postprocess.sh
-@@ -1,6 +1,6 @@
- #!/bin/sh
- 
--. test.definitions.sh
-+. ./test.definitions.sh
- 
- echo "      Running postprocessing.";
- 
diff --git a/sci-biology/bfast/metadata.xml b/sci-biology/bfast/metadata.xml
deleted file mode 100644
index 5ec4a95ff146..000000000000
--- a/sci-biology/bfast/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">bfast</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/biogrep/Manifest b/sci-biology/biogrep/Manifest
deleted file mode 100644
index 1666ad7c813c..000000000000
--- a/sci-biology/biogrep/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST biogrep-1.0.pdf 22179 BLAKE2B 9a401b50480ae8fe903b96082b8011cc02d8f65d97cdcc2659e835d8fc01969f756d33e14428aeee802f5dd994e3b5277b6e705ec73f92c0fb2be255e5a1588f SHA512 b0430bded7529a14e3e551e4c7deeffdbdbbe674b5a4bd68afa359b2a4e9f0b8fb4a6474673d298508fa728cf83a328327860e60b3777e92afb15fa87f076411
-DIST biogrep-1.0.tar.gz 71867 BLAKE2B 48baf2b13f65e3b2d79fabccf978c8a3b275e6b915fed56a2fa9a0cd98ab36ff3810dbe9be1447a32b5f95b5ed006cc19dbd0673ec9e617e4a9115dcddf240a4 SHA512 da07ea6f5f6fd601a94dc1b9495b204affcdc4d5e7fedfebbb65d6382ef0573e43b4ebd081c24909b2790ec2ae532505604112d4943c3e4e6575e13bdcdf1ae3
diff --git a/sci-biology/biogrep/biogrep-1.0-r3.ebuild b/sci-biology/biogrep/biogrep-1.0-r3.ebuild
deleted file mode 100644
index cfdeeb440f72..000000000000
--- a/sci-biology/biogrep/biogrep-1.0-r3.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools
-
-DESCRIPTION="Multithreaded tool for matching large sets of patterns against biosequence DBs"
-HOMEPAGE="http://stephanopoulos.openwetware.org/BIOGREP.html"
-SRC_URI="
-	http://www.openwetware.org/images/3/3d/${P^}.tar.gz -> ${P}.tar.gz
-	doc? ( http://www.openwetware.org/images/4/49/${PN^}.pdf -> ${P}.pdf )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc examples"
-
-PATCHES=( "${FILESDIR}"/${P}-c23.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_install() {
-	default
-
-	use doc && dodoc "${DISTDIR}"/${P}.pdf
-	if use examples; then
-		# remove cruft before installing examples
-		find examples/ \( -name 'CVS' -o -name '*~' \) -exec rm -rf '{}' + || die
-
-		dodoc -r examples
-		docompress -x /usr/share/doc/${PF}/examples
-	fi
-}
diff --git a/sci-biology/biogrep/files/biogrep-1.0-c23.patch b/sci-biology/biogrep/files/biogrep-1.0-c23.patch
deleted file mode 100644
index a287dd905b48..000000000000
--- a/sci-biology/biogrep/files/biogrep-1.0-c23.patch
+++ /dev/null
@@ -1,35 +0,0 @@
---- a/src/main.c
-+++ b/src/main.c
-@@ -198,8 +198,8 @@
- 	int i;
- 	int regExsPerThread;
- 	int completedRegExs;
--	int (*parseFunct) () = &ParseTxtLine;
--	fSeq_t *(*seqReadFunct) () = &ReadTxtSeqs;
-+	int (*parseFunct) (char*, int,  tPat_t*) = &ParseTxtLine;
-+	fSeq_t *(*seqReadFunct) (FILE*, int*) = &ReadTxtSeqs;
- 	printFormat_t myFormat;
- 	int ignoreCase = 0;
- 
---- a/src/patternFunctions.c
-+++ b/src/patternFunctions.c
-@@ -39,7 +39,7 @@
- // output file from Teiresias, which may or may not have logOdds values
- // 
- tPat_t *
--ReadTPats(FILE * INPUT, int getOffsets, int *numberOfPatterns, int (*parseFunct) ())
-+ReadTPats(FILE * INPUT, int getOffsets, int *numberOfPatterns, int (*parseFunct) (char*, int,  tPat_t*))
- {
- 	int i;
- 	int countedPatterns;
---- a/src/patternFunctions.h
-+++ b/src/patternFunctions.h
-@@ -33,7 +33,7 @@
- int MeasurePattern(char *pattern);
- int ParseTPatLine(char *buffer, int getOffsets, tPat_t * myTeiresiasPattern);
- int ParseTxtLine(char *buffer, int getOffsets, tPat_t * myTeiresiasPattern);
--tPat_t *ReadTPats(FILE * INPUT, int getOffsets, int *numberOfPatterns, int (*parseFunct)() );
-+tPat_t *ReadTPats(FILE * INPUT, int getOffsets, int *numberOfPatterns, int (*parseFunct)(char*, int,  tPat_t*) );
- int printTPat(FILE * OUTPUT, tPat_t * myTeiresiasPattern, int hasOffsets);
- int FreeTPatA(tPat_t * arrayOfTeiresiasPatterns, int numberOfPatterns);
- 
diff --git a/sci-biology/biogrep/metadata.xml b/sci-biology/biogrep/metadata.xml
deleted file mode 100644
index bdabd1d83788..000000000000
--- a/sci-biology/biogrep/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/bioperl-db/Manifest b/sci-biology/bioperl-db/Manifest
deleted file mode 100644
index 9a21d61ff2e9..000000000000
--- a/sci-biology/bioperl-db/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST BioPerl-DB-1.006900.tar.gz 492799 BLAKE2B fb923533ecdb74e868a3aef0c0c6ba8da419ae3c0e9d2e8c55297aad15563b135b6b00fd158481b31dcacd1125f7e10a557052bd4b04eed3a400c972653ff757 SHA512 e06b8b9aa4188a83128f910d7b4a031f69d36f75e4f2d7210357366379024ef39b58eca97112b5b419f141c82b7518086273cc97c9637382ee5e0ddb9ce28746
diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9-r2.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9-r2.ebuild
deleted file mode 100644
index 435dc4a67173..000000000000
--- a/sci-biology/bioperl-db/bioperl-db-1.6.9-r2.ebuild
+++ /dev/null
@@ -1,103 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-BIOPERL_RELEASE=1.6.9
-
-DIST_NAME=BioPerl-DB
-DIST_AUTHOR=CJFIELDS
-DIST_VERSION=1.006900
-DIST_TEST="do" # Parallelism probably bad
-inherit perl-module
-
-DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema"
-HOMEPAGE="http://www.bioperl.org/"
-
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-IUSE="test"
-RESTRICT="test"
-
-RDEPEND="
-	>=sci-biology/bioperl-${PV}
-	dev-perl/DBD-mysql
-	dev-perl/DBI
-	sci-biology/biosql"
-DEPEND="
-	${RDEPEND}
-	test? (
-		dev-perl/Data-Stag
-		dev-perl/Sub-Uplevel
-		dev-perl/Test-Warn
-		dev-perl/Test-Exception
-		virtual/perl-Test-Simple
-	)"
-BDEPEND="dev-perl/Module-Build"
-
-PATCHES=( "${FILESDIR}"/${PN}-1.6.9-db.patch )
-
-src_prepare() {
-	export GENTOO_DB_HOSTNAME=localhost
-	perl-module_src_prepare
-}
-
-src_test() {
-	einfo "Removing bundled test libraries t/lib"
-	rm -r "${S}/t/lib" || die "Cannot remove t/lib"
-
-	ebegin "Setting up test database"
-
-	local mysql_install_db="${EPREFIX}/usr/share/mariadb/scripts/mysql_install_db"
-	[[ ! -x "${mysql_install_db}" ]] && mysql_install_db="${EPREFIX}/usr/bin/mysql_install_db"
-	[[ ! -x "${mysql_install_db}" ]] && die "mysql_install_db command not found!"
-
-	local mysqld="${EPREFIX}/usr/sbin/mysqld"
-	local socket="${T}/mysql.sock"
-	local pidfile="${T}/mysql.pid"
-	local datadir="${T}/mysql-data-dir"
-	local mysql="${EPREFIX}/usr/bin/mysql"
-
-	mkdir -p "${datadir}" || die "Can't make mysql database dir";
-	chmod 755 "${datadir}" || die "Can't fix mysql database dir perms";
-
-	"${mysql_install_db}" \
-		--basedir="${EPREFIX}/usr" \
-		--datadir="${datadir}" \
-		--user=$(whoami) \
-		|| die "Failed to initalize test database"
-
-	"${mysqld}" \
-		--no-defaults \
-		--user=$(whoami) \
-		--skip-networking \
-		--skip-grant \
-		--socket="${socket}" \
-		--pid-file="${pidfile}" \
-		--datadir="${datadir}" &
-
-	local maxtry=20
-	while ! [[ -S "${socket}" || "${maxtry}" -lt 1 ]] ; do
-		maxtry=$((${maxtry}-1))
-		echo -n "."
-		sleep 1
-	done
-
-	local rc=1
-	[[ -S "${socket}" ]] && rc=0
-
-	eend ${rc}
-
-	[[ ${rc} -ne 0 ]] && die "Failed to start mysqld test instance"
-
-	export MYSQL_UNIX_PORT="${socket}"
-	perl-module_src_test
-	ebegin "Shutting down mysql test database"
-	pkill -F "${pidfile}"
-	eend $?
-}
-
-src_install() {
-	mydoc="AUTHORS BUGS FAQ"
-	perl-module_src_install
-}
diff --git a/sci-biology/bioperl-db/files/bioperl-db-1.6.9-db.patch b/sci-biology/bioperl-db/files/bioperl-db-1.6.9-db.patch
deleted file mode 100644
index 36698651c7d1..000000000000
--- a/sci-biology/bioperl-db/files/bioperl-db-1.6.9-db.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-From d689a1473977b0aa368590ba1f913521e4f466c7 Mon Sep 17 00:00:00 2001
-From: Kent Fredric <kentfredric@gmail.com>
-Date: Tue, 18 Jul 2017 16:02:26 +1200
-Subject: [PATCH] Allow custom host/port configurations
-
----
- Build.PL           | 4 ++--
- t/DBTestHarness.pm | 4 ++--
- 2 files changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/Build.PL b/Build.PL
-index ecc402e..a61190f 100755
---- a/Build.PL
-+++ b/Build.PL
-@@ -97,9 +97,9 @@ sub biosql_conf {
-         or die "Error: could not write to config file '$config_file'\n";
-     
-     my %config = (driver     => $drivers[0],
--                  host       => '127.0.0.1',
-+                  host       => $ENV{GENTOO_DB_HOSTNAME} || '127.0.0.1',
-                   user       => 'root',
--                  port       => 3306,
-+                  port       => $ENV{GENTOO_DB_PORT} || undef,
-                   password   => '',
-                   dbname     => 'bioseqdb',
-                   database   => 'biosql',
-diff --git a/t/DBTestHarness.pm b/t/DBTestHarness.pm
-index b660429..91e0c54 100755
---- a/t/DBTestHarness.pm
-+++ b/t/DBTestHarness.pm
-@@ -47,9 +47,9 @@ my $counter=0;
- # Default settings as a hash
- my $dflt = {
-     'driver'        => 'mysql',
--    'host'          => 'localhost',
-+    'host'          => $ENV{GENTOO_DB_HOST} || 'localhost',
-     'user'          => 'root',
--    'port'          => undef,
-+    'port'          => $ENV{GENTOO_DB_PORT} || undef,
-     'password'      => '',
-     'schema_sql'    => ['../biosql-schema/sql/biosqldb-mysql.sql'],
-     'database'      => 'biosql',
--- 
-2.13.1
-
diff --git a/sci-biology/bioperl-db/metadata.xml b/sci-biology/bioperl-db/metadata.xml
deleted file mode 100644
index 171d7d240b71..000000000000
--- a/sci-biology/bioperl-db/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="cpan">BioPerl-DB</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/bioperl-network/Manifest b/sci-biology/bioperl-network/Manifest
deleted file mode 100644
index 6411c750971a..000000000000
--- a/sci-biology/bioperl-network/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST BioPerl-Network-1.006900.tar.gz 2198089 BLAKE2B 67197ed356f642d9e85f779019f6854f4baa3963e059895b89c75ae56f8b5a075ca04b04ce5c7622d46a3a2f55e1c7d80af695085c607ed7fda5517c71c579f3 SHA512 d0a95af17cb024cbc615c784f1dbcddd7bfc5b54524163ab127f1077ded18df222fe067c085f3dd17dd416d6417b8f726526be164e1e33144991393f6b6d5842
diff --git a/sci-biology/bioperl-network/bioperl-network-1.6.9-r1.ebuild b/sci-biology/bioperl-network/bioperl-network-1.6.9-r1.ebuild
deleted file mode 100644
index fc51a12da036..000000000000
--- a/sci-biology/bioperl-network/bioperl-network-1.6.9-r1.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-BIOPERL_RELEASE=1.6.9
-
-DIST_AUTHOR=CJFIELDS
-DIST_NAME=BioPerl-Network
-DIST_VERSION=1.006900
-inherit perl-module
-
-DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks"
-HOMEPAGE="http://www.bioperl.org/"
-
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-RESTRICT="test" # bug 298326
-
-RDEPEND="
-	>=sci-biology/bioperl-${PV}
-	>=dev-perl/Graph-0.86"
-DEPEND="${RDEPEND}"
-BDEPEND="dev-perl/Module-Build"
-
-mydoc="AUTHORS BUGS"
diff --git a/sci-biology/bioperl-network/metadata.xml b/sci-biology/bioperl-network/metadata.xml
deleted file mode 100644
index 868dd703d25b..000000000000
--- a/sci-biology/bioperl-network/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="cpan">BioPerl-Network</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/bioperl-run/Manifest b/sci-biology/bioperl-run/Manifest
deleted file mode 100644
index f1a12f80dfc3..000000000000
--- a/sci-biology/bioperl-run/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST BioPerl-Run-1.006900.tar.gz 14546677 BLAKE2B 9faf58796b9874b19b66e74abc51ed1d1b6e2928bcf9904506b2af6b2b7c1772a90eab24bf0e7c050fd4a2b120ba506ad5edb8a693496b7468fe7c8d05d11f0a SHA512 47f2b853885c604291ac0aba3269b897de59cf7da6f7d54a50ff950cca836338091309df550f32695159c620be23391306d0421d2bbc22eebbb61a9e280ad83c
diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild
deleted file mode 100644
index 9c32c7eaa5f7..000000000000
--- a/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-BIOPERL_RELEASE=1.6.9
-
-DIST_AUTHOR=CJFIELDS
-DIST_NAME=BioPerl-Run
-DIST_VERSION=1.006900
-inherit perl-module
-
-DESCRIPTION="Perl wrapper modules for key bioinformatics applications"
-HOMEPAGE="http://www.bioperl.org/"
-
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-IUSE="minimal test"
-RESTRICT="test"
-
-RDEPEND="
-	>=sci-biology/bioperl-${BIOPERL_RELEASE}
-	!minimal? (
-		dev-perl/Algorithm-Diff
-		dev-perl/XML-Twig
-		dev-perl/IO-String
-		dev-perl/IPC-Run
-		dev-perl/File-Sort
-	)"
-DEPEND="${RDEPEND}"
-BDEPEND="dev-perl/Module-Build"
-
-mydoc="AUTHORS BUGS FAQ"
diff --git a/sci-biology/bioperl-run/metadata.xml b/sci-biology/bioperl-run/metadata.xml
deleted file mode 100644
index f3bb1f1db1d9..000000000000
--- a/sci-biology/bioperl-run/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="cpan">BioPerl-Run</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/bioperl/Manifest b/sci-biology/bioperl/Manifest
deleted file mode 100644
index 4858ef718510..000000000000
--- a/sci-biology/bioperl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST BioPerl-1.6.901.tar.gz 12284856 BLAKE2B 004947fde9d02355ac96f71b67a33a27d6d0163892c978ac9059e70e089fb83b473e21252c5217dfba8faaa65bc3d2eebb8826d03f29a13409e2b6d337316b42 SHA512 227387437c940da1435ed83fad6ec2168ca12a729c90dc557e84750c6474213874c23a8f23e50db4027909469627baee581faa11be6208c8e0a5453a01c7eca4
diff --git a/sci-biology/bioperl/bioperl-1.6.9-r1.ebuild b/sci-biology/bioperl/bioperl-1.6.9-r1.ebuild
deleted file mode 100644
index a692fe812401..000000000000
--- a/sci-biology/bioperl/bioperl-1.6.9-r1.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DIST_AUTHOR=CJFIELDS
-DIST_NAME=BioPerl
-DIST_VERSION=1.6.901
-inherit perl-module
-
-SUBPROJECTS="+db +network +run"
-MIN_PV="${PV}"
-
-DESCRIPTION="Perl tools for bioinformatics - Core modules"
-HOMEPAGE="http://www.bioperl.org/"
-
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-IUSE="minimal graphviz sqlite ${SUBPROJECTS}"
-REQUIRED_USE="minimal? ( !graphviz )"
-
-RDEPEND="
-	dev-perl/libwww-perl
-	!minimal? (
-		dev-perl/Algorithm-Munkres
-		dev-perl/Array-Compare
-		dev-perl/YAML
-		dev-perl/Bio-ASN1-EntrezGene
-		dev-perl/Clone
-		dev-perl/Convert-Binary-C
-		dev-perl/Data-Stag
-		dev-perl/GD
-		dev-perl/Graph
-		>=dev-perl/HTML-Parser-3.60
-		dev-perl/List-MoreUtils
-		dev-perl/Math-Random
-		dev-perl/PostScript
-		dev-perl/Set-Scalar
-		dev-perl/SOAP-Lite
-		dev-perl/Sort-Naturally
-		dev-perl/Spreadsheet-ParseExcel
-		>=virtual/perl-Storable-2.05
-		>=dev-perl/SVG-2.26
-		>=dev-perl/SVG-Graph-0.01
-		dev-perl/URI
-		>=dev-perl/XML-DOM-XPath-0.13
-		dev-perl/XML-Parser
-		>=dev-perl/XML-SAX-0.15
-		dev-perl/XML-Simple
-		dev-perl/XML-Twig
-		>=dev-perl/XML-Writer-0.4
-		dev-perl/XML-DOM
-		dev-perl/XML-XPath
-	)
-	graphviz? ( dev-perl/GraphViz )
-	sqlite? ( dev-perl/DBD-SQLite )"
-DEPEND="${RDEPEND}"
-PDEPEND="
-	db? ( >=sci-biology/bioperl-db-${MIN_PV} )
-	network? ( >=sci-biology/bioperl-network-${MIN_PV} )
-	run? ( >=sci-biology/bioperl-run-${MIN_PV} )"
-BDEPEND="dev-perl/Module-Build"
-
-mydoc="AUTHORS BUGS FAQ"
diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml
deleted file mode 100644
index 20c00d4288ef..000000000000
--- a/sci-biology/bioperl/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <use>
-    <flag name="run">Install <pkg>sci-biology/bioperl-run</pkg></flag>
-    <flag name="network">Install <pkg>sci-biology/bioperl-run</pkg></flag>
-    <flag name="db">Install <pkg>sci-biology/bioperl-run</pkg></flag>
-  </use>
-  <upstream>
-    <remote-id type="cpan">BioPerl</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
deleted file mode 100644
index 958821fd58aa..000000000000
--- a/sci-biology/biopython/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST biopython-1.87.tar.gz 19855264 BLAKE2B 04e98210f5addcd2e18ef085fb054b322cdf4377c0fee51300a2581555967f03e46285dd2d3ecec63864e42fecf91d9c9b9b7763c9497e3413a817eb007845d3 SHA512 aed9131f85b28d1b6fb7b1878d6afe2b701eddae092514ec43c69b623c871e16dbf5aaed464709423031169c0c13709bfbc0055e4cdc89c766e4445b959ba7a5
diff --git a/sci-biology/biopython/biopython-1.87.ebuild b/sci-biology/biopython/biopython-1.87.ebuild
deleted file mode 100644
index d7b0506361a6..000000000000
--- a/sci-biology/biopython/biopython-1.87.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-DISTUTILS_USE_PEP517="setuptools"
-DISTUTILS_EXT=1
-
-inherit distutils-r1 optfeature pypi
-
-DESCRIPTION="Python modules for computational molecular biology"
-HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/"
-
-LICENSE="HPND"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/rdflib[${PYTHON_USEDEP}]
-	dev-python/pygraphviz[${PYTHON_USEDEP}]
-	>=dev-python/reportlab-3.5.13-r1[${PYTHON_USEDEP}]
-	dev-python/pydot[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
-BDEPEND="app-alternatives/lex"
-
-DOCS=( {CONTRIB,DEPRECATED,NEWS,README}.rst Doc/. )
-
-python_test() {
-	cd Tests || die
-	"${EPYTHON}" run_tests.py --offline --verbose || die
-}
-
-python_install_all() {
-	# remove files causing ecompressdir to fail
-	rm Doc/examples/ls_orchid.gbk.{gz,bz2} || die
-
-	distutils-r1_python_install_all
-
-	dodir /usr/share/${PN}
-	cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
-}
-
-pkg_postinst() {
-	optfeature_header "For database support you need to install:"
-	optfeature "MySQL database support" dev-python/mysqlclient
-	optfeature "PostgreSQL database support" dev-python/psycopg:2
-
-	optfeature_header "Some applications need extra packages:"
-	optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss
-}
diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml
deleted file mode 100644
index cd20d153fc2e..000000000000
--- a/sci-biology/biopython/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="pypi">biopython</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/biosql/Manifest b/sci-biology/biosql/Manifest
deleted file mode 100644
index 44fca7f843af..000000000000
--- a/sci-biology/biosql/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST biosql-1.0.1.tar.bz2 253516 BLAKE2B d2b0d6c3f03389fbcf9dfca823b02c611b63d4c1ee1356150f92bb8c14c534d988644253fd1a6ed6522b8d2d06cacf7b21d7a9e9fe7b9464704497e7f976b283 SHA512 2e1fef6ab9b4386f146910937700f9108f8ef266161b7adfbbc52c0011eebc84716637c897a01a399ff39b066ff0a5905ba3fa27e7b41f53a87baf58d5b32695
diff --git a/sci-biology/biosql/biosql-1.0.1-r2.ebuild b/sci-biology/biosql/biosql-1.0.1-r2.ebuild
deleted file mode 100644
index 838f3b443ed8..000000000000
--- a/sci-biology/biosql/biosql-1.0.1-r2.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="A generic bioinformatics relational database model"
-HOMEPAGE="https://biosql.org/"
-SRC_URI="https://biosql.org/DIST/${P}.tar.bz2"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-IUSE="mysql postgres"
-
-# WARNING: bioperl-db is claimed to be incompatible with >=postgresql-8.3 (see INSTALL)
-
-DEPEND="
-	mysql? ( dev-perl/DBD-mysql )
-	postgres? ( dev-perl/DBD-Pg )"
-RDEPEND="
-	${DEPEND}
-	dev-lang/perl"
-
-src_install() {
-	insinto /usr/share/biosql
-	doins -r sql scripts/.
-
-	dodoc Changes README Release.txt doc/*.pdf
-
-	docinto biopython
-	dodoc doc/{README,schema-overview.txt,biopython/{cor6_6.gb,*.pdf}}
-	docompress -x /usr/share/doc/${PF}/biopython
-
-	docinto html
-	dodoc doc/{biopython/,}*.htm*
-}
-
-pkg_postinst() {
-	elog
-	elog "Please read the BioSQL schema installation instructions in"
-	elog "${EROOT}/usr/share/doc/${PF} to begin using the schema."
-	elog
-}
diff --git a/sci-biology/biosql/metadata.xml b/sci-biology/biosql/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/biosql/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/blat/Manifest b/sci-biology/blat/Manifest
deleted file mode 100644
index bfb1512a0aec..000000000000
--- a/sci-biology/blat/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST blatSrc34.zip 2142975 BLAKE2B 88a2da3b1551d5d50aaa507978c17cbe34de5a27efee9405829aea51b0950b748775f21e8d806470ba5ee7831fe71d6d87cd126c38727f25306a0f793543912e SHA512 67a1dc9a93d8ddee0fca7ce94096ecfffc71d4e0697afb285f4b64205e9eb62150a145375c29dd1ccb3cea8e8a7a71a817c8e73d7aba3e97616f1606b751afe8
diff --git a/sci-biology/blat/blat-34-r3.ebuild b/sci-biology/blat/blat-34-r3.ebuild
deleted file mode 100644
index 18c4128ec578..000000000000
--- a/sci-biology/blat/blat-34-r3.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-MY_PN="${PN}Src"
-
-DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner"
-HOMEPAGE="http://www.cse.ucsc.edu/~kent/"
-SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip"
-S="${WORKDIR}/${MY_PN}"
-
-LICENSE="blat"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-BDEPEND="app-arch/unzip"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-34-fix-build-system.patch
-	"${FILESDIR}"/${PN}-34-fno-common.patch
-)
-
-src_compile() {
-	tc-export AR CC
-
-	export HOME="${S}"
-	export MACHTYPE="$(tc-arch)"
-	[[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386"
-
-	mkdir -p bin/${MACHTYPE} || die
-	default
-}
-
-src_install() {
-	export MACHTYPE="$(tc-arch)"
-	[[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386"
-
-	dobin bin/${MACHTYPE}/*
-}
diff --git a/sci-biology/blat/files/blat-34-fix-build-system.patch b/sci-biology/blat/files/blat-34-fix-build-system.patch
deleted file mode 100644
index 9aca3f841315..000000000000
--- a/sci-biology/blat/files/blat-34-fix-build-system.patch
+++ /dev/null
@@ -1,348 +0,0 @@
---- a/blat/makefile
-+++ b/blat/makefile
-@@ -7,8 +7,7 @@
- O = blat.o
- 
- blat: $O $(MYLIBS)
--	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L
--	${STRIP} ${BINDIR}/blat${EXE}
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L
- 
- all:
- 	cd ../lib && ${MAKE}
---- a/gfClient/makefile
-+++ b/gfClient/makefile
-@@ -8,5 +8,4 @@
- X = gfClient
- 
- gfClient: $O $(MYLIBS)
--	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
--	${STRIP} ${BINDIR}/$X${EXE}
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
---- a/gfServer/makefile
-+++ b/gfServer/makefile
-@@ -8,8 +8,7 @@
- X = gfServer
- 
- gfServer: $O $(MYLIBS)
--	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
--	${STRIP} ${BINDIR}/$X${EXE}
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
- 
- test:
- 	${MKDIR} tests/output
---- a/hg/pslPretty/makefile
-+++ b/hg/pslPretty/makefile
-@@ -8,7 +8,7 @@
- O = pslPretty.o
- 
- pslPretty: $O $(MYLIBS)
--	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L
- 
- test:: testRna testDnax
- 
---- a/hg/pslReps/makefile
-+++ b/hg/pslReps/makefile
-@@ -9,7 +9,7 @@
- O = pslReps.o 
- 
- pslReps: $O $(MYLIBS)
--	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L
- 
- lib:
- 	cd ../../lib && ${MAKE}
---- a/hg/pslSort/makefile
-+++ b/hg/pslSort/makefile
-@@ -8,7 +8,7 @@
- O = pslSort.o
- 
- pslSort: $O $(MYLIBS)
--	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L
-+	${CC} ${LDFLAGS} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L
- 
- 
- lib:
---- a/inc/cgi_build_rules.mk
-+++ b/inc/cgi_build_rules.mk
-@@ -12,7 +12,6 @@
- 	mv $A${EXE} ${CGI_BIN}-beta/$A
- 
- strip::  compile
--	${STRIP} $A${EXE}
- 	chmod g+w $A${EXE}
- 	chmod a+rx $A${EXE}
- 
---- a/inc/common.mk
-+++ b/inc/common.mk
-@@ -1,20 +1,15 @@
--CC=gcc
--ifeq (${COPT},)
--    COPT=-O
--endif
--CFLAGS=
- HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
- HG_WARN=-Wformat -Wimplicit -Wuninitialized -Wreturn-type
- HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc
- 
- # Stronger warning checks, and warnings-->errors, for libraries and CGIs:
- ifeq (darwin,$(findstring darwin,${OSTYPE}))
--    HG_WARN_ERR = -DJK_WARN -Wall -Werror -Wno-unused-variable
-+    HG_WARN_ERR = -DJK_WARN -Wall -Wno-unused-variable
- else
-   ifeq (solaris,$(findstring solaris,${OSTYPE}))
-     HG_WARN_ERR = -DJK_WARN -Wall
-   else
--    HG_WARN_ERR = -DJK_WARN -Wall -Werror
-+    HG_WARN_ERR = -DJK_WARN -Wall
-   endif
- endif
- # Apply the stronger checks to all code on our development machine:
-@@ -36,9 +31,6 @@
-     BINDIR = ${HOME}/bin/${MACHTYPE}
- endif
- MKDIR=mkdir -p
--ifeq (${STRIP},)
--   STRIP=strip
--endif
- CVS=cvs
- 
- # portable naming of compiled executables: add ".exe" if compiled on 
-@@ -55,6 +47,6 @@
- STRINGIFY = ${BINDIR}/stringify
- 
- %.o: %.c
--	${CC} ${COPT} ${CFLAGS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<
-+	${CC} ${CPPFLAGS} ${CFLAGS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<
- 
- 
---- a/jkOwnLib/makefile
-+++ b/jkOwnLib/makefile
-@@ -9,7 +9,7 @@
- T = ../lib/$(MACHTYPE)/jkOwnLib.a
- 
- $(T): $(O) ../lib/$(MACHTYPE)
--	ar rcus $(T) $(O)
-+	$(AR) rcus $(T) $(O)
- 
- ../lib/$(MACHTYPE):
- 	mkdir ../lib/$(MACHTYPE)
---- a/jkOwnLib/tests/freen/makefile
-+++ b/jkOwnLib/tests/freen/makefile
-@@ -7,5 +7,5 @@
- O = freen.o
- 
- hello: freen.o
--	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/freen $O $(MYLIBS) $L
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/freen $O $(MYLIBS) $L
- 
---- a/lib/makefile
-+++ b/lib/makefile
-@@ -32,7 +32,7 @@
- 
- 
- $(MACHTYPE)/jkweb.a: $(O) $(MACHTYPE)
--	ar rcus $(MACHTYPE)/jkweb.a $(O)
-+	$(AR) rcus $(MACHTYPE)/jkweb.a $(O)
- 
- $(MACHTYPE):
- 	mkdir $(MACHTYPE)
---- a/lib/tests/makefile
-+++ b/lib/tests/makefile
-@@ -14,22 +14,19 @@
- 	${MKDIR} output ${BIN_DIR}
- 
- errCatchTest: errCatchTest.o ${MYLIBS} mkdirs
--	${CC} ${COPT} -o ${BIN_DIR}/errCatchTest errCatchTest.o ${MYLIBS} $L
--	${STRIP} ${BIN_DIR}/errCatchTest${EXE}
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/errCatchTest errCatchTest.o ${MYLIBS} $L
- 	${BIN_DIR}/errCatchTest secret > output/errCatch.good
- 	diff expected/errCatch.good output/errCatch.good
- 	${BIN_DIR}/errCatchTest bad > output/errCatch.bad
- 	diff expected/errCatch.bad output/errCatch.bad
- 
- htmlExpandUrlTest: htmlExpandUrlTest.o ${MYLIBS} mkdirs
--	${CC} ${COPT} -o ${BIN_DIR}/htmlExpandUrlTest htmlExpandUrlTest.o ${MYLIBS} $L
--	${STRIP} ${BIN_DIR}/htmlExpandUrlTest${EXE}
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlExpandUrlTest htmlExpandUrlTest.o ${MYLIBS} $L
- 	${BIN_DIR}/htmlExpandUrlTest > output/htmlExpandUrlTest 2>&1
- 	diff expected/htmlExpandUrlTest output/htmlExpandUrlTest
- 
- htmlPageTest: htmlPageTest.o ${MYLIBS} mkdirs
--	${CC} ${COPT} -o ${BIN_DIR}/htmlPageTest htmlPageTest.o ${MYLIBS} $L
--	${STRIP} ${BIN_DIR}/htmlPageTest${EXE}
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlPageTest htmlPageTest.o ${MYLIBS} $L
- 	${BIN_DIR}/htmlPageTest input/google.html > output/google.out
- 	diff expected/google.out output/google.out
- 
-@@ -86,20 +83,20 @@
- 	diff -b expected/$@.err output/$@.err
- 
- ${BIN_DIR}/pipelineTester:  mkdirs pipelineTester.o ${MYLIBS}
--	${CC} ${COPT} -o ${BIN_DIR}/pipelineTester pipelineTester.o ${MYLIBS} $L
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/pipelineTester pipelineTester.o ${MYLIBS} $L
- 
- 
- dyStringTest: ${BIN_DIR}/dyStringTester mkdirs
- 	${BIN_DIR}/dyStringTester
- 
- ${BIN_DIR}/dyStringTester:  mkdirs dyStringTester.o ${MYLIBS}
--	${CC} ${COPT} -o ${BIN_DIR}/dyStringTester dyStringTester.o ${MYLIBS} $L
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/dyStringTester dyStringTester.o ${MYLIBS} $L
- 
- 
- mimeTests: mime1 mime2 mime3 mime4 mimeBin mime5 mimeAltHead mimeAutoBoundary mimeBlat
- 
- ${BIN_DIR}/mimeTester:  mkdirs mimeTester.o ${MYLIBS}
--	${CC} ${COPT} -o ${BIN_DIR}/mimeTester mimeTester.o ${MYLIBS} $L
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/mimeTester mimeTester.o ${MYLIBS} $L
- 
- 
- mime1: ${BIN_DIR}/mimeTester mkdirs
-@@ -142,7 +139,7 @@
- 	${BIN_DIR}/mimeTester -sizeSeries=3000
- 
- ${BIN_DIR}/htmlMimeTest:  mkdirs htmlMimeTest.o ${MYLIBS}
--	${CC} ${COPT} -o ${BIN_DIR}/htmlMimeTest htmlMimeTest.o ${MYLIBS} $L
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlMimeTest htmlMimeTest.o ${MYLIBS} $L
- 
- htmlMime1: ${BIN_DIR}/htmlMimeTest mkdirs
- 	${BIN_DIR}/htmlMimeTest http://hgwdev.cse.ucsc.edu/cgi-bin/hgBlat input/htmlMime.txt 3490 3502 > output/$@.out
-@@ -152,7 +149,7 @@
- base64Tests: base64Encode base64Decode
- 
- ${BIN_DIR}/testBase64:  mkdirs testBase64.o ${MYLIBS}
--	${CC} ${COPT} -o ${BIN_DIR}/testBase64 testBase64.o ${MYLIBS} $L
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/testBase64 testBase64.o ${MYLIBS} $L
- 
- base64Encode: ${BIN_DIR}/testBase64 mkdirs
- 	${BIN_DIR}/testBase64 'My Test String' > output/$@.out
-@@ -167,7 +164,7 @@
- quotedPTests: quotedPEncode quotedPDecode
- 
- ${BIN_DIR}/testQuotedP:  mkdirs testQuotedP.o ${MYLIBS}
--	${CC} ${COPT} -o ${BIN_DIR}/testQuotedP testQuotedP.o ${MYLIBS} $L
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/testQuotedP testQuotedP.o ${MYLIBS} $L
- 
- quotedPEncode: ${BIN_DIR}/testQuotedP mkdirs
- 	${BIN_DIR}/testQuotedP 'taxes are quite high ' > output/$@.out
-@@ -178,14 +175,14 @@
- 	diff expected/$@.out output/$@.out
- 
- ${BIN_DIR}/mimeDecodeTest:  mkdirs mimeDecodeTest.o ${MYLIBS}
--	${CC} ${COPT} -o ${BIN_DIR}/mimeDecodeTest mimeDecodeTest.o ${MYLIBS} $L
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/mimeDecodeTest mimeDecodeTest.o ${MYLIBS} $L
- 
- mimeDecodeTest: ${BIN_DIR}/mimeDecodeTest mkdirs
- 	${BIN_DIR}/mimeDecodeTest -cid -autoBoundary output < input/$@.txt
- 	diff expected/noName1.html output/noName1.html
- 
- ${BIN_DIR}/safeTester:  mkdirs safeTester.o ${MYLIBS}
--	${CC} ${COPT} -o ${BIN_DIR}/safeTester safeTester.o ${MYLIBS} $L
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/safeTester safeTester.o ${MYLIBS} $L
- 
- safeTest: ${BIN_DIR}/safeTester mkdirs
- 	${BIN_DIR}/safeTester
---- a/makefile
-+++ b/makefile
-@@ -1,18 +1,18 @@
- all:
--	cd lib && ${MAKE}
--	cd jkOwnLib && ${MAKE}
--	cd blat && $(MAKE)
--	cd gfClient && $(MAKE)
--	cd gfServer && $(MAKE)
--	cd hg/pslPretty && $(MAKE)
--	cd hg/pslReps && $(MAKE)
--	cd hg/pslSort && $(MAKE)
--	cd utils/nibFrag && $(MAKE)
--	cd utils/faToNib && $(MAKE)
--	cd utils/faToTwoBit && $(MAKE)
--	cd utils/twoBitToFa && $(MAKE)
--	cd utils/twoBitInfo && $(MAKE)
--	cd webBlat && $(MAKE)
-+	$(MAKE) -C lib
-+	$(MAKE) -C jkOwnLib
-+	$(MAKE) -C blat
-+	$(MAKE) -C gfClient
-+	$(MAKE) -C gfServer
-+	$(MAKE) -C hg/pslPretty
-+	$(MAKE) -C hg/pslReps
-+	$(MAKE) -C hg/pslSort
-+	$(MAKE) -C utils/nibFrag
-+	$(MAKE) -C utils/faToNib
-+	$(MAKE) -C utils/faToTwoBit
-+	$(MAKE) -C utils/twoBitToFa
-+	$(MAKE) -C utils/twoBitInfo
-+	$(MAKE) -C webBlat
- 
- clean:
- 	rm -f */*.o */*/*.o
---- a/utils/faToNib/makefile
-+++ b/utils/faToNib/makefile
-@@ -8,4 +8,4 @@
- O = faToNib.o
- 
- faToNib: $O $(MYLIBS)
--	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L
---- a/utils/faToTwoBit/makefile
-+++ b/utils/faToTwoBit/makefile
-@@ -7,8 +7,7 @@
- O = faToTwoBit.o
- 
- faToTwoBit: $O ${MYLIBS}
--	${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L
--	${STRIP} ${BINDIR}/faToTwoBit${EXE}
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L
- 
- clean:
- 	rm -f $O
---- a/utils/nibFrag/makefile
-+++ b/utils/nibFrag/makefile
-@@ -4,7 +4,7 @@
- O = nibFrag.o 
- 
- nibFrag: $(O)
--	${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a
- 
- 
- 
---- a/utils/twoBitInfo/makefile
-+++ b/utils/twoBitInfo/makefile
-@@ -7,8 +7,7 @@
- O = twoBitInfo.o
- 
- twoBitInfo: $O ${MYLIBS}
--	${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L
--	${STRIP} ${BINDIR}/twoBitInfo${EXE}
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L
- 
- clean:
- 	rm -f $O
---- a/utils/twoBitToFa/makefile
-+++ b/utils/twoBitToFa/makefile
-@@ -8,8 +8,7 @@
- O = twoBitToFa.o
- 
- twoBitToFa: $O ${MYLIBS}
--	${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L
--	#${STRIP} ${BINDIR}/twoBitToFa${EXE}
-+	${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L
- 
- clean:
- 	rm -f $O
---- a/webBlat/makefile
-+++ b/webBlat/makefile
-@@ -7,8 +7,7 @@
- O = webBlat.o
- 
- webBlat: $O ${MYLIBS}
--	${CC} ${COPT} -o webBlat $O ${MYLIBS} $L
--	${STRIP} webBlat${EXE}
-+	${CC} ${LDFLAGS} ${CFLAGS} -o webBlat $O ${MYLIBS} $L
- 
- installOsX: webBlat
- 	cp webBlat /Library/WebServer/CGI-Executables
diff --git a/sci-biology/blat/files/blat-34-fno-common.patch b/sci-biology/blat/files/blat-34-fno-common.patch
deleted file mode 100644
index 63a49cf81299..000000000000
--- a/sci-biology/blat/files/blat-34-fno-common.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/inc/htmshell.h
-+++ b/inc/htmshell.h
-@@ -85,7 +85,7 @@ void htmlBadVar(char *varName);
- void htmlImage(char *fileName, int width, int height); 
- /* Display centered image file. */
- 
--jmp_buf htmlRecover;  /* Error recovery jump. Exposed for cart's use. */
-+extern jmp_buf htmlRecover;  /* Error recovery jump. Exposed for cart's use. */
- 
- void htmlVaWarn(char *format, va_list args);
- /* Write an error message.  (Generally you just call warn() or errAbort().
diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/blat/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
deleted file mode 100644
index fb01787b9ecb..000000000000
--- a/sci-biology/bowtie/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bowtie2-2.5.1-source.zip 10528859 BLAKE2B 9dc22bfef4b3a1cfaa606cb235acd1d7688015678d82e8ca80d3d7cf269e1f45d6cb60bc29eb334fb6f0c25d5afd8202e83a83e53668c8965857b8885d2692c8 SHA512 31cc642e318ab50e7ef6035a9c2095024d46d92a317011ed0c3ac3ccb3d427a13bf724d0158d29a4f1e07115ddcb85229b95bcb2d4351164fcadd6568293565f
diff --git a/sci-biology/bowtie/bowtie-2.5.1.ebuild b/sci-biology/bowtie/bowtie-2.5.1.ebuild
deleted file mode 100644
index 4e0b6a41032d..000000000000
--- a/sci-biology/bowtie/bowtie-2.5.1.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 2021-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-inherit python-single-r1 toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="https://bowtie-bio.sourceforge.net/bowtie2/"
-SRC_URI="https://downloads.sourceforge.net/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip"
-S="${WORKDIR}/${PN}2-${PV}"
-
-LICENSE="GPL-3"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="test cpu_flags_x86_sse2 examples"
-# Test script missing from tarball
-# ./scripts/sim/run.sh: No such file or directory
-RESTRICT="test"
-REQUIRED_USE="cpu_flags_x86_sse2 ${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	dev-lang/perl
-	virtual/zlib:=
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	app-arch/unzip
-	test? (
-		dev-perl/App-cpanminus
-		dev-perl/B-COW
-		dev-perl/Clone
-		dev-perl/Config-General
-		dev-perl/File-Which
-		dev-perl/local-lib
-		dev-perl/Math-Random
-		dev-perl/Test-Deep
-		dev-perl/Text-Template
-	)
-"
-
-src_compile() {
-	emake \
-		CXX="$(tc-getCXX)" \
-		CXXFLAGS="" \
-		CPPFLAGS="${CPPFLAGS}" \
-		EXTRA_FLAGS="${LDFLAGS}" \
-		RELEASE_FLAGS="${CXXFLAGS} -msse2"
-}
-
-src_install() {
-	dobin bowtie2 bowtie2-*
-
-	exeinto /usr/libexec/bowtie2
-	doexe scripts/*
-
-	HTML_DOCS=( doc/{manual.html,style.css} )
-	einstalldocs
-	dodoc TUTORIAL
-	newman MANUAL bowtie2.1
-
-	python_fix_shebang "${ED}"/usr/bin/bowtie2-{build,inspect}
-
-	if use examples; then
-		docinto examples
-		dodoc -r example/.
-		docompress -x /usr/share/doc/${PF}/examples
-	fi
-}
diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml
deleted file mode 100644
index c48ae535cfaf..000000000000
--- a/sci-biology/bowtie/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">bowtie-bio</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
deleted file mode 100644
index 5f912dc43cf0..000000000000
--- a/sci-biology/bwa/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bwa-0.7.17.tar.gz 232593 BLAKE2B fa48aad72a47547d66c767e2e2a5aadfcfc7c77c517410812230f51a2222ee66bb04383b068036b696af0a57b04b35e97bed11e3c44793aa899a8c0807f3df5e SHA512 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48
diff --git a/sci-biology/bwa/bwa-0.7.17.ebuild b/sci-biology/bwa/bwa-0.7.17.ebuild
deleted file mode 100644
index e7c3a944b33e..000000000000
--- a/sci-biology/bwa/bwa-0.7.17.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic toolchain-funcs
-
-DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
-HOMEPAGE="https://github.com/lh3/bwa/"
-SRC_URI="https://github.com/lh3/bwa/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-DEPEND="virtual/zlib:="
-RDEPEND="
-	${DEPEND}
-	dev-lang/perl"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-0.7.17-Makefile.patch
-	"${FILESDIR}"/${PN}-0.7.17-gcc-10.patch
-)
-DOCS=( NEWS.md README-alt.md README.md )
-
-src_configure() {
-	# -Werror=lto-type-mismatch
-	# https://bugs.gentoo.org/862255
-	# https://github.com/lh3/bwa/issues/411
-	#
-	# Fix merged upstream. Remove on next revbump.
-	filter-lto
-
-	tc-export CC AR
-}
-
-src_install() {
-	dobin bwa
-
-	exeinto /usr/libexec/${PN}
-	doexe qualfa2fq.pl xa2multi.pl
-
-	einstalldocs
-	doman bwa.1
-}
diff --git a/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch
deleted file mode 100644
index cbdd136e87aa..000000000000
--- a/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch
+++ /dev/null
@@ -1,46 +0,0 @@
-https://github.com/lh3/bwa/pull/267
-
-Rejected, but small parts of it included in https://github.com/lh3/bwa/pull/263
-
---- a/Makefile
-+++ b/Makefile
-@@ -1,9 +1,7 @@
--CC=			gcc
- #CC=			clang --analyze
--CFLAGS=		-g -Wall -Wno-unused-function -O2
-+CFLAGS+=		-Wall -Wno-unused-function
- WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
--AR=			ar
--DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
-+CPPFLAGS+=		-DHAVE_PTHREAD $(WRAP_MALLOC)
- LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o \
- 			QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
- AOBJS=		bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
-@@ -21,16 +19,13 @@
- 
- .SUFFIXES:.c .o .cc
- 
--.c.o:
--		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
--
- all:$(PROG)
- 
- bwa:libbwa.a $(AOBJS) main.o
--		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
-+		$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
- 
- bwamem-lite:libbwa.a example.o
--		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
-+		$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
- 
- libbwa.a:$(LOBJS)
- 		$(AR) -csru $@ $(LOBJS)
-@@ -39,7 +34,7 @@
- 		rm -f gmon.out *.o a.out $(PROG) *~ *.a
- 
- depend:
--	( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c )
-+	( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c )
- 
- # DO NOT DELETE THIS LINE -- make depend depends on it.
- 
diff --git a/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch
deleted file mode 100644
index 4d2762cef84c..000000000000
--- a/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-https://github.com/lh3/bwa/pull/267
-
---- a/rle.h
-+++ b/rle.h
-@@ -30,7 +30,7 @@
-  *** 43+3 codec ***
-  ******************/
- 
--const uint8_t rle_auxtab[8];
-+extern const uint8_t rle_auxtab[8];
- 
- #define RLE_MIN_SPACE 18
- #define rle_nptr(block) ((uint16_t*)(block))
diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml
deleted file mode 100644
index 21fbf032d0bf..000000000000
--- a/sci-biology/bwa/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">lh3/bwa</remote-id>
-		<remote-id type="sourceforge">bio-bwa</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest
deleted file mode 100644
index a20e0ea6d439..000000000000
--- a/sci-biology/cd-hit/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cd-hit-4.6.6.tar.gz 1152570 BLAKE2B 6a7cf99be947376af19172739626b571e06936b7b0bc8c5cb52069c63e98f0949a44edf7560fa50810d2d96e310df87dcf2e3ebf5a3856ada46dcdcd3595b6c0 SHA512 8241d6674fb041559792dbbb58c12b41302d2275d3bacb1362946094b48a0b8e1236e71b5dc77d13405220b60f8253e6f996753a8b051995a72c8353d4333c51
diff --git a/sci-biology/cd-hit/cd-hit-4.6.6-r1.ebuild b/sci-biology/cd-hit/cd-hit-4.6.6-r1.ebuild
deleted file mode 100644
index 18d126aa8653..000000000000
--- a/sci-biology/cd-hit/cd-hit-4.6.6-r1.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-RELDATE="2016-0711"
-RELEASE="${PN}-v${PV}-${RELDATE}"
-
-DESCRIPTION="Clustering Database at High Identity with Tolerance"
-HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
-SRC_URI="https://github.com/weizhongli/cdhit/releases/download/V${PV}/${RELEASE}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}"/${RELEASE}
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="openmp"
-
-RDEPEND="dev-lang/perl"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-4.6.6-fix-perl-shebangs.patch
-	"${FILESDIR}"/${PN}-4.6.6-fix-build-system.patch
-)
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-src_compile() {
-	tc-export CXX
-	emake openmp=$(usex openmp)
-}
-
-src_install() {
-	dodir /usr/bin
-	PREFIX="${EPREFIX}"/usr/bin default
-
-	dodoc doc/*.pdf
-}
diff --git a/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-build-system.patch b/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-build-system.patch
deleted file mode 100644
index c668d5c6154e..000000000000
--- a/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-build-system.patch
+++ /dev/null
@@ -1,122 +0,0 @@
-Fix build system, in order to honour user variables
-
---- a/makefile
-+++ b/makefile
-@@ -1,7 +1,4 @@
--
--CC = g++ -Wall -ggdb
--CC = g++ -pg
--CC = g++
-+CXX ?= g++
- 
- # without OpenMP
- 
-@@ -9,35 +6,19 @@
- # in command line: 
- # make openmp=yes
- ifeq ($(openmp),no)
--  CCFLAGS = -DNO_OPENMP
--else
--  CCFLAGS = -fopenmp
--endif
--
--# support debugging
--# in command line:
--# make debug=yes
--# make openmp=yes debug=yes
--ifeq ($(debug),yes)
--CCFLAGS += -ggdb
-+  my_CPPFLAGS = -DNO_OPENMP
- else
--CCFLAGS += -O2
-+  my_CXXFLAGS = -fopenmp
- endif
- 
- ifdef MAX_SEQ
--CCFLAGS += -DMAX_SEQ=$(MAX_SEQ)
-+my_CPPFLAGS += -DMAX_SEQ=$(MAX_SEQ)
- endif
- 
--#LDFLAGS = -static -o
--LDFLAGS += -o
--
- PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
- 
--# Propagate hardening flags
--CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS)
--
- .c++.o:
--	$(CC) $(CCFLAGS) -c $<
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $<
- 
- all: $(PROGS)
- 
-@@ -47,52 +28,52 @@
- # programs
- 
- cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
--	$(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit
- 
- cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
--	$(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d
- 
- cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
--	$(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est
- 
- cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
--	$(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d
- 
- cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
--	$(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div
- 
- cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o
--	$(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454
- 
- # objects
- cdhit-common.o: cdhit-common.c++ cdhit-common.h
--	$(CC) $(CCFLAGS) cdhit-common.c++ -c
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-common.c++ -c
- 
- cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-utility.c++ -c
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-utility.c++ -c
- 
- cdhit.o: cdhit.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit.c++ -c
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit.c++ -c
- 
- cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-2d.c++ -c
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-2d.c++ -c
- 
- cdhit-est.o: cdhit-est.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-est.c++ -c
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-est.c++ -c
- 
- cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
--	$(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-est-2d.c++ -c
- 
- cdhit-div.o: cdhit-div.c++ cdhit-common.h
--	$(CC) $(CCFLAGS) cdhit-div.c++ -c
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-div.c++ -c
- 
- cdhit-454.o: cdhit-454.c++ cdhit-common.h
--	$(CC) $(CCFLAGS) cdhit-454.c++ -c
-+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-454.c++ -c
- 
- PREFIX ?= /usr/local/bin
- 
- install:
- 	for prog in $(PROGS); do \
--		install -m 0755 $$prog $(PREFIX); \
-+		install -m 0755 $$prog $(DESTDIR)$(PREFIX); \
- 	done
--	install -m 0755 *.pl $(PREFIX);
-+	install -m 0755 *.pl $(DESTDIR)$(PREFIX);
diff --git a/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-perl-shebangs.patch b/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-perl-shebangs.patch
deleted file mode 100644
index 3784296f2e94..000000000000
--- a/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-perl-shebangs.patch
+++ /dev/null
@@ -1,219 +0,0 @@
-Make perl shebangs more Prefix friendly
-See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/
-
---- a/cd-hit-2d-para.pl
-+++ b/cd-hit-2d-para.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl -w
-+#!/usr/bin/env perl
- # =============================================================================
- # CD-HIT
- # http://cd-hit.org/
---- a/cd-hit-div.pl
-+++ b/cd-hit-div.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- #not like cd-hit-div, this script do not sort input
- #or throw away seq
---- a/cd-hit-para.pl
-+++ b/cd-hit-para.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl -w
-+#!/usr/bin/env perl
- # =============================================================================
- # CD-HIT
- # http://cd-hit.org/
---- a/clstr2tree.pl
-+++ b/clstr2tree.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- $clstr = shift;
- $fr = shift; # for nr80.clstr $fr = 0.8
---- a/clstr2txt.pl
-+++ b/clstr2txt.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- my $no = 0;
- my $clstr_no = "";
---- a/clstr2xml.pl
-+++ b/clstr2xml.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- #usage: clstr_xml.pl [-len|-size] level1.clstr [level2.clstr level3.clstr ...]
- #purpose: to create xml file from cd-hit or hierarchical cd-hit(h-cd-hit) results
---- a/clstr_cut.pl
-+++ b/clstr_cut.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- #keep only top $no proteins in cluster
- 
---- a/clstr_merge_noorder.pl
-+++ b/clstr_merge_noorder.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- # order of clusters don't need to be the same
- # but then I have to read everything into memory
---- a/clstr_merge.pl
-+++ b/clstr_merge.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- # the order of clusters need to be identical
- my ($master_clstr, @clstr) = @ARGV;
---- a/clstr_quality_eval_by_link.pl
-+++ b/clstr_quality_eval_by_link.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- ## calculate the sensitivity and specificity of clusters
- ## if the input fasta file has pre-defined classification term
---- a/clstr_quality_eval.pl
-+++ b/clstr_quality_eval.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- ## calculate the sensitivity and specificity of clusters
- ## if the input fasta file has pre-defined classification term
---- a/clstr_reduce.pl
-+++ b/clstr_reduce.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- 
- $file90 = shift;
---- a/clstr_renumber.pl
-+++ b/clstr_renumber.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- $no = 0;
- while($ll=<>){
-   if ($ll =~ /^>Cluster (\d+)/) {
---- a/clstr_rep.pl
-+++ b/clstr_rep.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- $rep = "";
- $no = 0;
---- a/clstr_reps_faa_rev.pl
-+++ b/clstr_reps_faa_rev.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- # output single fasta file
- # for each cluster output at least $cutoff seqs
- 
---- a/clstr_rev.pl
-+++ b/clstr_rev.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- # if nr90 from nr100 and
- #    nr80 from nr90, so I have nr90.clstr and nr80.clstr
- # but, in nr80.clstr, some gi numbers whose from nr100 are there
---- a/clstr_select.pl
-+++ b/clstr_select.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- #my $by = shift;
- my $min;
---- a/clstr_select_rep.pl
-+++ b/clstr_select_rep.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- #my $by = shift;
- my $min;
---- a/clstr_size_histogram.pl
-+++ b/clstr_size_histogram.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- if(@ARGV==0){
-    print "Usage:\n\tclstr_size_histogram.pl [-bin N] clstr_file\n";
---- a/clstr_size_stat.pl
-+++ b/clstr_size_stat.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- if(@ARGV==0){
-    print "Usage:\n\tclstr_size_stat.pl clstr_file\n";
---- a/clstr_sort_by.pl
-+++ b/clstr_sort_by.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- my $sort_by_what = shift;
-    $sort_by_what = "no" unless $sort_by_what;
---- a/clstr_sort_prot_by.pl
-+++ b/clstr_sort_prot_by.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- my $sort_by = shift;
-    $sort_by = "len" unless ($sort_by);
---- a/clstr_sql_tbl.pl
-+++ b/clstr_sql_tbl.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- if(@ARGV==0){
-   print "Usage:\n\tclstr_sql_tbl.pl clstr_file tbl_file\n";
---- a/clstr_sql_tbl_sort.pl
-+++ b/clstr_sql_tbl_sort.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- if(@ARGV==0){
-    print "Usage:\n\tclstr_sql_tbl_sort.pl table_file level\n";
---- a/make_multi_seq.pl
-+++ b/make_multi_seq.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- #note you have to use "-d 0" in the cd-hit run
- #note you better to use "-g 1" in the cd-hit run
---- a/plot_2d.pl
-+++ b/plot_2d.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- use Image::Magick;
- 
---- a/plot_len1.pl
-+++ b/plot_len1.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl
-+#!/usr/bin/env perl
- 
- $file90 = shift;
- $segs = shift;
diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml
deleted file mode 100644
index 3bb799e0ba9e..000000000000
--- a/sci-biology/cd-hit/metadata.xml
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-CD-HIT is a very widely used program for clustering and comparing large sets 
-of protein or nucleotide sequences. CD-HIT is very fast and can handle 
-extremely large databases. CD-HIT helps to significantly reduce the 
-computational and manual efforts in many sequence analysis tasks and aids in 
-understanding the data structure and correct the bias within a dataset.
-The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, 
-CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT 
-(CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a 
-user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2 
-datasets and identifies the sequences in db2 that are similar to db1 above 
-a threshold. CD-HIT-454 is a program to identify natural and artificial 
-duplicates from pyrosequencing reads. The usage of other programs and 
-scripts can be found in CD-HIT user's guide.
-	</longdescription>
-	<upstream>
-		<remote-id type="google-code">cdhit</remote-id>
-		<remote-id type="github">weizhongli/cdhit</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/clustal-omega/Manifest b/sci-biology/clustal-omega/Manifest
deleted file mode 100644
index 55a68a04db22..000000000000
--- a/sci-biology/clustal-omega/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST clustal-omega-1.2.4.tar.gz 1170516 BLAKE2B 0751a30a8d7bab2bac01980b84a28720e127dfeeec5b72f1826c8d9da4e84d5d9434b0f138b600155cc76f4385320913edb9bbdeb463ed757364feb3538f325b SHA512 b31514c30b412d731ee22c9020156b65a6a6cbc6fd51edc195d17b560935184bc070feeb58964c54df9eecdefb00e5a21ce859cb0ea69d92917f6bd8e93b819e
diff --git a/sci-biology/clustal-omega/clustal-omega-1.2.4-r1.ebuild b/sci-biology/clustal-omega/clustal-omega-1.2.4-r1.ebuild
deleted file mode 100644
index 50d8ce873de9..000000000000
--- a/sci-biology/clustal-omega/clustal-omega-1.2.4-r1.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools dot-a
-
-DESCRIPTION="Scalable multiple alignment of protein sequences"
-HOMEPAGE="http://www.clustal.org/omega/"
-SRC_URI="http://www.clustal.org/omega/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-DEPEND="dev-libs/argtable"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
-	sed \
-		-e "s:-O3::g" \
-		-i configure.ac || die
-	default
-	eautoreconf
-}
-
-src_configure() {
-	lto-guarantee-fat
-	default
-}
-
-src_install() {
-	default
-	find "${ED}" -name '*.la' -delete || die
-	strip-lto-bytecode
-}
diff --git a/sci-biology/clustal-omega/metadata.xml b/sci-biology/clustal-omega/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/clustal-omega/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/clustalw-mpi/Manifest b/sci-biology/clustalw-mpi/Manifest
deleted file mode 100644
index d819c8f2a13c..000000000000
--- a/sci-biology/clustalw-mpi/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST clustalw-mpi-0.13.tar.gz 154911 BLAKE2B 705f62263340b0ac13895657c97e185f395910f25653bdcc20cf867732c270c65eebebe5b914367a534a5d058909d0baf307c0a3727a2095d4f21c313e83b94d SHA512 e0008accb6c07584dc5ad1b953e0c668fad43ca3a86d88dbcf50fbfa858870131e4db005cc87b46f5268cd0795e9a2ce01326d8318d66b694a92b85e6f9635df
diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild
deleted file mode 100644
index 334c34e78ce6..000000000000
--- a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="An MPI implemention of the ClustalW general purpose multiple alignment algorithm"
-HOMEPAGE="http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php"
-SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="mpi-njtree static-pairalign"
-
-DEPEND="virtual/mpi"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-makefile.patch
-	"${FILESDIR}"/${P}-fno-common.patch
-)
-
-src_prepare() {
-	default
-
-	if use mpi-njtree; then
-		sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \
-			die "Failed to configure MPI code for NJ trees"
-	fi
-
-	if use static-pairalign; then
-		sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \
-			die "Failed to configure static scheduling for pair alignments"
-	fi
-}
-
-src_install() {
-	dobin clustalw-mpi
-	newdoc README.clustalw-mpi README
-}
diff --git a/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch
deleted file mode 100644
index da74f0ba172d..000000000000
--- a/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- a/parallel_compare.c
-+++ b/parallel_compare.c
-@@ -74,8 +74,8 @@
- static sint 	**accum;
- static sint 	*diag_index;
- static char 	*slopes;
--sint ktup,window,wind_gap,signif; 
--sint *zza, *zzb, *zzc, *zzd;
-+extern sint ktup,window,wind_gap,signif;
-+extern sint *zza, *zzb, *zzc, *zzd;
- extern Boolean percent;
- static void make_p_ptrs(sint *tptr, sint *pl, sint naseq, sint l);
- static void make_n_ptrs(sint *tptr, sint *pl, sint naseq, sint len);
diff --git a/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch
deleted file mode 100644
index 6e36061cbb39..000000000000
--- a/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch
+++ /dev/null
@@ -1,23 +0,0 @@
- Makefile |    6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index f2107ce..835232b 100644
---- a/Makefile
-+++ b/Makefile
-@@ -25,12 +25,12 @@ TREES_FLAG = -DSERIAL_NJTREE
- PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN 
- #PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN
- 
--CFLAGS  = -c -O3
-+CFLAGS  += -c
- #CFLAGS  = -c -O3 -funroll-all-loops
--LFLAGS	= -lm 
-+LIBS	= -lm 
- 
- clustalw-mpi: $(OBJECTS) 
--	$(CC) -o $@ $(OBJECTS) $(LFLAGS)
-+	$(CC) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS)
- 
- interface.o : interface.c $(HEADERS) param.h
- 	$(CC) $(CFLAGS) $*.c
diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml
deleted file mode 100644
index bda43acf10c1..000000000000
--- a/sci-biology/clustalw-mpi/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<use>
-		<flag name="mpi-njtree">Use MPI (as opposed to serial) code for computing neighbor-joining trees</flag>
-		<flag name="static-pairalign">Use static (as opposed to dynamic) scheduling for pair alignments</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-biology/clustalw/Manifest b/sci-biology/clustalw/Manifest
deleted file mode 100644
index 65ff8b3584d9..000000000000
--- a/sci-biology/clustalw/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST clustalw-2.1.tar.gz 350761 BLAKE2B 479acb42ec0b0adee8e04e99132a782c947a1261f48e674c6a11e4f38e44e5709d03f0c864f0cd3cf7eb4faf76a36b6121c3e3d3573c86ee3895971df07f1a58 SHA512 659cfe0121015dd2b84578b1a0a7f016fc944de155686b9bdef31122200a21e792203f3a6ab93a31676a50ffb70858b506ceb7ac27d921189a8381dbe0887921
-DIST clustalw1.83.UNIX.tar.gz 166863 BLAKE2B a3b1eabad8bc736cde4655f13fa8544759b7b5c50ea97fd45ee0be45ac6c361db5ced8ad21622ac2530b57c37c77dfd67657afd2c411acbfb7ff2a3ba014637e SHA512 c0cc9ebf4c8869be819065546b499b547990342c87425fae8f921a141704343f2a518ecfc2b8bfd527061902825fc5befcb2cd080c83ba887390e48338c9dc1a
diff --git a/sci-biology/clustalw/clustalw-1.83-r4.ebuild b/sci-biology/clustalw/clustalw-1.83-r4.ebuild
deleted file mode 100644
index b11c6e2bf48c..000000000000
--- a/sci-biology/clustalw/clustalw-1.83-r4.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="General purpose multiple alignment program for DNA and proteins"
-HOMEPAGE="http://www.embl-heidelberg.de/~seqanal/"
-SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz"
-S="${WORKDIR}/${PN}${PV}"
-
-LICENSE="clustalw"
-SLOT="1"
-KEYWORDS="amd64 ~ppc ppc64 ~sparc ~x86"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-as-needed.patch
-	"${FILESDIR}"/${PV}-clang.patch
-)
-
-src_prepare() {
-	default
-	sed \
-		-e "s|clustalw_help|${EPREFIX}/usr/share/doc/${PF}/clustalw_help|" \
-		-i clustalw.c || die
-}
-
-src_configure() {
-	tc-export CC
-}
-
-src_install() {
-	dobin clustalw
-	dodoc README clustalv.doc clustalw{.doc,.ms,_help}
-}
diff --git a/sci-biology/clustalw/clustalw-2.1-r2.ebuild b/sci-biology/clustalw/clustalw-2.1-r2.ebuild
deleted file mode 100644
index 7b45d9b4cb84..000000000000
--- a/sci-biology/clustalw/clustalw-2.1-r2.ebuild
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="General purpose multiple alignment program for DNA and proteins"
-HOMEPAGE="http://www.clustal.org/"
-SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz"
-
-LICENSE="GPL-3 LGPL-3"
-SLOT="2"
-KEYWORDS="amd64 ~ppc ~ppc64 ~sparc ~x86"
-
-src_install() {
-	default
-	rmdir "${ED}"/usr/share/aclocal || die
-}
diff --git a/sci-biology/clustalw/files/1.83-as-needed.patch b/sci-biology/clustalw/files/1.83-as-needed.patch
deleted file mode 100644
index 54b78b0811e0..000000000000
--- a/sci-biology/clustalw/files/1.83-as-needed.patch
+++ /dev/null
@@ -1,36 +0,0 @@
---- a/makefile
-+++ b/makefile
-@@ -10,25 +10,22 @@
- 
- HEADERS = general.h clustalw.h
- 
--CC	= cc
--CFLAGS  = -c -O
--LFLAGS	= -O -lm 
-+# C99 for gets()
-+CFLAGS	+= -std=gnu99
-+LIBS	+= -lm
- 
- clustalw : $(OBJECTS) amenu.o clustalw.o
--	$(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS)
- 
- interface.o : interface.c $(HEADERS) param.h
--	$(CC) $(CFLAGS) $*.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) -c $<
- 
- amenu.o : amenu.c $(HEADERS) param.h
--	$(CC) $(CFLAGS) $*.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) -c $<
- 
- readmat.o : readmat.c $(HEADERS) matrices.h
--	$(CC) $(CFLAGS) $*.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) -c $<
- 
- trees.o : trees.c $(HEADERS) dayhoff.h
--	$(CC) $(CFLAGS) $*.c
--
--.c.o :
--	$(CC) $(CFLAGS) $?
-+	$(CC) $(CFLAGS) $(CPPFLAGS) -c $<
- 
diff --git a/sci-biology/clustalw/files/1.83-clang.patch b/sci-biology/clustalw/files/1.83-clang.patch
deleted file mode 100644
index ea1202079d9e..000000000000
--- a/sci-biology/clustalw/files/1.83-clang.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/interface.c
-+++ b/interface.c
-@@ -210,7 +210,7 @@
- 		Boolean 	name1 = FALSE;
- 		sint ajb;
- 
--	if(args[0]==NULL) return;
-+	if(args[0]==NULL) return 0;
- 
- 
- 
diff --git a/sci-biology/clustalw/metadata.xml b/sci-biology/clustalw/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/clustalw/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/cutg/Manifest b/sci-biology/cutg/Manifest
deleted file mode 100644
index ff4a4b903266..000000000000
--- a/sci-biology/cutg/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cutg-160.tar.xz 178015420 BLAKE2B acfc65f4f152b7293cb8ec8e2bfa3c2c33c5da7bcdcae5349d13122e36c4061931195034548963cb78f6350bce88f72e4fc764f119e181f1f6278ee837b65b6e SHA512 9b72283f311fb805b7b22f59f3ca8fed2ab0af72b82247900922999792c1b112dcaca9b29b265a1e0e7b9eaf9ff846a1dc4c196fb95ddbfb3ee5175755ffb8e7
diff --git a/sci-biology/cutg/cutg-160-r1.ebuild b/sci-biology/cutg/cutg-160-r1.ebuild
deleted file mode 100644
index 07bf5566a84b..000000000000
--- a/sci-biology/cutg/cutg-160-r1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Codon usage tables calculated from GenBank"
-HOMEPAGE="http://www.kazusa.or.jp/codon/"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-# Minimal build keeps only the indexed files (if applicable) and the
-# documentation. The non-indexed database is not installed.
-IUSE="emboss minimal"
-RESTRICT="binchecks strip"
-
-RDEPEND="emboss? ( sci-biology/emboss )"
-BDEPEND="${RDEPEND}"
-
-src_compile() {
-	if use emboss; then
-		mkdir CODONS || die
-		ebegin "Indexing CUTG for usage with EMBOSS."
-		EMBOSS_DATA="." cutgextract -auto -directory "${S}"
-		eend $? "Indexing CUTG failed" || die
-	fi
-}
-
-src_install() {
-	dodoc README CODON_LABEL SPSUM_LABEL
-
-	if ! use minimal; then
-		insinto /usr/share/cutg
-		doins *.codon *.spsum
-	fi
-
-	if use emboss; then
-		insinto /usr/share/EMBOSS/data
-		doins -r CODONS
-	fi
-}
diff --git a/sci-biology/cutg/metadata.xml b/sci-biology/cutg/metadata.xml
deleted file mode 100644
index aa55dcc37fe9..000000000000
--- a/sci-biology/cutg/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		Codon usage tables maintained at the Kazusa DNA Research Institute.
-		Codon usage in individual genes has been calculated using the
-		nucleotide sequence data obtained from the GenBank Genetic Sequence
-		Database. The compilation of codon usage is synchronized with each
-		major release of GenBank.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/cytoscape-bin/Manifest b/sci-biology/cytoscape-bin/Manifest
deleted file mode 100644
index 37d8d06695f0..000000000000
--- a/sci-biology/cytoscape-bin/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cytoscape-unix-3.10.4.tar.gz 357480347 BLAKE2B 85f25e2a3950bd9c60721b354c0fe6b00aefc9239ec6073c1ae797677f584e9f36501a2b822a2c48e788e649955fa79384984d1cf9c79eb7189cd5124c23cd65 SHA512 36948acca38a465dedc0b2fc6063f1c1a9bdadc6d378970c21fd910ddcfc436ecc246ba685cb958b5d9f7b4505a96533da82783d91500d6fe788cbd01c958a4e
diff --git a/sci-biology/cytoscape-bin/cytoscape-bin-3.10.4.ebuild b/sci-biology/cytoscape-bin/cytoscape-bin-3.10.4.ebuild
deleted file mode 100644
index e259d4684eca..000000000000
--- a/sci-biology/cytoscape-bin/cytoscape-bin-3.10.4.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="8"
-
-inherit desktop java-pkg-2
-
-DESCRIPTION="A visualization platform for molecular interaction networks"
-HOMEPAGE="https://www.cytoscape.org/"
-SRC_URI="https://github.com/cytoscape/cytoscape/releases/download/${PV}/cytoscape-unix-${PV}.tar.gz"
-
-S="${WORKDIR}"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-RDEPEND="virtual/jdk:17"
-
-src_install() {
-	MY_PN="cytoscape"
-	MYW="${WORKDIR}/${MY_PN}-unix-${PV}"
-
-	insinto "/opt/${MY_PN}"
-	doins -r ${MYW}/apps
-	doins -r ${MYW}/framework
-	doins -r ${MYW}/sampleData
-
-	cd ${MYW}
-	sh gen_vmoptions.sh
-	doins Cytoscape.vmoptions
-	exeinto "/opt/${MY_PN}"
-	doexe "${MYW}/${MY_PN}.sh"
-	dosym "${EPREFIX}/opt/${MY_PN}/${MY_PN}.sh" "${EPREFIX}/opt/bin/${MY_PN}"
-
-	exeinto "/opt/${MY_PN}/framework/bin"
-	doexe framework/bin/karaf
-
-	newicon framework/cytoscape_logo_512.png cytoscape_logo.png
-	make_desktop_entry ${MY_PN} CytoScape cytoscape_logo Science
-}
diff --git a/sci-biology/cytoscape-bin/metadata.xml b/sci-biology/cytoscape-bin/metadata.xml
deleted file mode 100644
index fd4219e20956..000000000000
--- a/sci-biology/cytoscape-bin/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>andres.becerra@gmail.com</email>
-		<name>Andrés Becerra Sandoval</name>
-	</maintainer>
-	<upstream>
-		<bugs-to>
-			https://cytoscape.org/bug-report.html
-		</bugs-to>
-		<changelog>
-			https://cytoscape.org/releasenotes.html
-		</changelog>
-		<remote-id type="github">cytoscape/cytoscape</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/dialign-tx/Manifest b/sci-biology/dialign-tx/Manifest
deleted file mode 100644
index 6cf412f93444..000000000000
--- a/sci-biology/dialign-tx/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST DIALIGN-TX_1.0.2.tar.gz 1765296 BLAKE2B 3cce811a58fcf210f42c4a783e8ebb56c66436912ff04bce270058193f0d7b21114d75e2d67829c7abfbb35814e5a16f7f952611729ab211d066403a411db94a SHA512 ff43f1f2900bdd12b7a8ba382a4d6ad68e6c2e6d7ceb1a65f0e571bb891cc2dc2661fb6ce698aaabf0e20c14565b5927ae0076a7170c8611679f936851a00c43
diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild
deleted file mode 100644
index 78681265a0b7..000000000000
--- a/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-MY_P=${PN^^}_${PV}
-
-DESCRIPTION="Greedy and progressive approaches for segment-based multiple sequence alignment"
-HOMEPAGE="http://dialign-tx.gobics.de/"
-SRC_URI="http://dialign-tx.gobics.de/${MY_P}.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/${MY_P}"
-PATCHES=(
-	"${FILESDIR}"/${P}-fix-build-system.patch
-	"${FILESDIR}"/${P}-implicits.patch
-	"${FILESDIR}"/${P}-modernize.patch
-	"${FILESDIR}"/${P}-gnu89-inline.patch
-	"${FILESDIR}"/${P}-fno-common.patch
-)
-
-src_configure() {
-	tc-export CC
-}
-
-src_compile() {
-	emake -C source clean
-	emake -C source
-}
-
-src_install() {
-	dobin source/dialign-tx
-	insinto /usr/$(get_libdir)/dialign-tx/conf
-	doins -r conf/.
-}
-
-pkg_postinst() {
-	einfo "The configuration directory is"
-	einfo "${EROOT}/usr/$(get_libdir)/dialign-tx/conf"
-	einfo "You will need to pass this to dialign-tx on every run."
-}
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch
deleted file mode 100644
index cbfd458043c5..000000000000
--- a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- a/source/Makefile
-+++ b/source/Makefile
-@@ -1,4 +1,3 @@
--CC=gcc
- # debug
- #CPPFLAGS=-g -O0 -Q -v -da
- #CPPFLAGS=-g -O0 -fstack-check -Q -v -da
-@@ -8,7 +7,6 @@
- # THIS IS FOR THE OPTIMIZED ONE
- #CPPFLAGS=-g 
- #CPPFLAGS=-O3 -march=i686 -funroll-loops
--CPPFLAGS=-O3 -funroll-loops -march=i686 -mfpmath=sse -msse  -mmmx
- #CPPFLAGS=-march=athlon-mp -g -O0 -Wall -D_USE_XOPEN -D__unix__
- 
- OBJ_DIR=.
-@@ -33,7 +31,7 @@
- 
- museq:	$(OBJ)
- 	rm -f $(TARGET)/$@
--	$(CC) -o $(TARGET)/$@ \
-+	$(CC) $(LDFLAGS) -o $(TARGET)/$@ \
- 	$(OBJ) \
- 	-pipe -Wall -lm 
- 	mv museq dialign-tx
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch
deleted file mode 100644
index de3104fa0ebb..000000000000
--- a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- a/source/parameters.c
-+++ b/source/parameters.c
-@@ -26,6 +26,8 @@
- 
- extern char *optarg;
- extern int optind, opterr, optopt;
-+
-+struct parameters* para;
- /****************************
- * PROTEIN DEFAULT VALUES!   *
- ****************************/
---- a/source/parameters.h
-+++ b/source/parameters.h
-@@ -138,7 +138,7 @@
-     /*              global variable                 */
-     /*                                              */
-     /************************************************/
--struct parameters* para;
-+extern struct parameters* para;
- 
- 
- 
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch
deleted file mode 100644
index fc8d0284e6ab..000000000000
--- a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch
+++ /dev/null
@@ -1,31 +0,0 @@
---- a/source/assemble.c
-+++ b/source/assemble.c
-@@ -574,7 +574,7 @@
-  * returns a value <0 if there is an non-conflicting overlap
-  * returns 0 in all other non-conflicting cases
-  */
--inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) {
-+static inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) {
-   //  if(dg1->multi_dg || dg2->multi_dg) error(" confl_diag(): cannot accept multi dgs!");
-   int s1_1 = dg1->seq_p1.num;
-   int s1_2 = dg1->seq_p2.num;
---- a/source/diag.c
-+++ b/source/diag.c
-@@ -312,7 +312,7 @@
- /** 
-  * calculates the overlap weight for the given diag 
-  */ 
--inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,  
-+void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,  
- 		    struct prob_dist *pdist) { 
-   int sn1 = dg->seq_p1.num; 
-   int sn2 = dg->seq_p2.num; 
-@@ -958,7 +958,7 @@
-  * The pointer returned (and the ones included in the struct)  
-  * has to be deallocted explicitely from memory. 
-  */ 
--inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix,  
-+static inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix,  
- 				struct prob_dist *pdist, struct seq* seq1,  
- 				struct seq* seq2, struct alignment *algn, 
- 				 long double **tmp_dist, int round) { 
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch
deleted file mode 100644
index d82a5bf4be33..000000000000
--- a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- a/source/museq.c
-+++ b/source/museq.c
-@@ -38,6 +38,7 @@
- //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
- //		 struct prob_dist *pdist);
- //extern struct diag_col *create_diag_col(int seq_amount);
-+extern void free_diag(struct diag* dg);
- extern void free_diag_col(struct diag_col* dcol);
- extern struct diag_col *find_all_diags(struct scr_matrix *smatrix, 
- 				struct prob_dist *pdist, 
-@@ -52,6 +53,7 @@
- 
- // alig.c
- extern struct alignment* create_empty_alignment(struct seq_col *scol);
-+extern void free_alignment(struct alignment *algn);
- //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
- extern int  simple_aligner(struct seq_col *scol, struct diag_col *dcol, 
- 			    struct scr_matrix* smatrix, 
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-modernize.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-modernize.patch
deleted file mode 100644
index b732e34da81c..000000000000
--- a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-modernize.patch
+++ /dev/null
@@ -1,130 +0,0 @@
-Fix changed gnu89->gnu11 inline semantics with GCC-5, Gentoo Bug #570252
-https://bugs.gentoo.org/show_bug.cgi?id=570252
-
-In addition, fixed multiple -Wformat= warnings, such as
-
-io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 3 has type ‘int *’ [-Wformat=]
-   while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
-                    ^
-io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 4 has type ‘int *’ [-Wformat=]
-io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 5 has type ‘int *’ [-Wformat=]
-io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 6 has type ‘int *’ [-Wformat=]
-io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 7 has type ‘int *’ [-Wformat=]
-
---- DIALIGN-TX_1.0.2/source/alig.c
-+++ DIALIGN-TX_1.0.2/source/alig.c
-@@ -10,9 +10,9 @@
- 
- extern void error(char *message);
- extern void merror(char *msg1, char *msg2);
--extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
-+extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
- 			struct prob_dist *pdist);
--extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, 
-+extern void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, 
- 		    struct prob_dist *pdist);
- //extern struct seq_part* create_seq_part(int num, struct seq* aSeq, unsigned int startpos);
- extern struct diag* create_diag(struct seq_part* part1, struct seq_part* part2, 
-@@ -520,7 +520,7 @@
-  * datastructure (i.e. frontiers). The given diag must be consistent
-  * to the given alignment !
-  */
--inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) {
-+char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) {
- 
-   char alignedSomething = 0;
-   int i,j,k;
---- DIALIGN-TX_1.0.2/source/assemble.c
-+++ DIALIGN-TX_1.0.2/source/assemble.c
-@@ -10,9 +10,9 @@
- 
- extern void error(char *message);
- extern void merror(char *msg1, char *msg2);
--extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
-+extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
- 			struct prob_dist *pdist);
--extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, 
-+extern void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, 
- 		    struct prob_dist *pdist);
- //extern struct seq_part* create_seq_part(int num, struct seq* aSeq, unsigned int startpos);
- extern long double** create_tmp_pdist(struct prob_dist *pdist);
-@@ -22,7 +22,7 @@
-                          int n2, struct seq* sq2, unsigned int sp2,
-                          int dlength);
- extern void free_diag(struct diag* dg);
--extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,  
-+extern struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,  
- 							struct prob_dist *pdist, 
- 							struct gt_node* n1,  
- 							struct gt_node* n2, 
-@@ -34,10 +34,10 @@
- 
- extern struct alignment* create_empty_alignment(struct seq_col *scol);
- extern void free_alignment(struct alignment *algn);
--extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
-+extern struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
- extern struct alignment* copy_alignment( struct alignment *o_algn, struct alignment *algn, char doDgc);
- //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
--extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
-+extern char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
- //extern inline struct diag_cont* enter_sorted(struct diag_cont* backlog_diags, struct diag_cont *cand);
- //extern inline char fit_fpos_diag(struct alignment *algn, struct diag* dg);
- 
---- DIALIGN-TX_1.0.2/source/diag.c
-+++ DIALIGN-TX_1.0.2/source/diag.c
-@@ -183,7 +183,7 @@
-  * omitScore = 0:  normal 
-  * omitScore = 1:  no score calculation 
-  */ 
--inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
-+void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
- 		 struct prob_dist *pdist, char omitScore, long double **tmp_dist, struct alignment *algn ) { 
-    
-   if(dg->multi_dg) {
-@@ -302,7 +302,7 @@
-   } 
- } 
-  
--inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
-+void calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
- 		 struct prob_dist *pdist) { 
-   real_calc_weight(dg, smatrix, pdist, 0,NULL,NULL); 
- } 
---- DIALIGN-TX_1.0.2/source/io.c
-+++ DIALIGN-TX_1.0.2/source/io.c
-@@ -267,7 +267,7 @@
-     for( c=r; c<length; c++) {
-       // check whether it is a regular acid or a special character like '$',...
-       if( (r<length-additional) && (c<length-additional)) {
--		fscanf( fp, "%i", &is);
-+		if( fscanf( fp, "%i", &is) ){};
-       } else {
- 		is = 0;
-       }
-@@ -279,7 +279,7 @@
-       // ensure symmetry of the weight matrix
-       data[length*c+r] = is;
-     }
--    fscanf(fp, "%s\n", rline);
-+    if( fscanf(fp, "%s\n", rline) ){};
-   }
-   fclose(fp);
- 
-@@ -368,7 +368,7 @@
-     }
-     for(scr=0;scr<=mxscr;scr++) {
-       dist[i][scr]=1.0;
--      fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight );
-+      if( fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ) ){};
-       //if(i!=ti || tscr!=scr) merror("read_scr_matrix(): (4) Invalid format of file ",filename);
-       scr = tscr;
-       if(weight==0.0) weight = 1.0;
-@@ -532,7 +532,7 @@
-   sdcol->data = malloc(sizeof (struct diag*)*alloc_size);
-   sdcol->length=0;
- 
--  while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
-+  while( fscanf(fp,"%i %i %i %i %i %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
-     if(sdcol->length >= alloc_size) {
-       alloc_size+=16;
-       sdcol->data = realloc(sdcol->data,sizeof (struct diag*)*alloc_size);
diff --git a/sci-biology/dialign-tx/metadata.xml b/sci-biology/dialign-tx/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/dialign-tx/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/dialign2/Manifest b/sci-biology/dialign2/Manifest
deleted file mode 100644
index 90219054dfcd..000000000000
--- a/sci-biology/dialign2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST dialign-2.2.1-src.tar.gz 209015 BLAKE2B daf903b735e164879a8ceb998ca5ea0c5243927d9b88b4041633af06da7d1f608d58933ee098393e99093b7d11587a59277d9d0927214df0341a8a623b0d5608 SHA512 eb51fbc8d81e384ac19e9cc957be233287a1d81a7f020d77ab16ee6943382bd4e81099c0c9028fcff130def62cdf19de59e9a9c08ea4cb67b9d8f1939eb3bc45
diff --git a/sci-biology/dialign2/dialign2-2.2.1-r1.ebuild b/sci-biology/dialign2/dialign2-2.2.1-r1.ebuild
deleted file mode 100644
index 264c43a03c17..000000000000
--- a/sci-biology/dialign2/dialign2-2.2.1-r1.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Multiple sequence alignment"
-HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/dialign"
-SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-${PV}-src.tar.gz"
-S="${WORKDIR}/dialign_package"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-2.2.1-fix-build-system.patch
-	"${FILESDIR}"/${PN}-2.2.1-Wimplicit.patch
-)
-
-src_configure() {
-	tc-export CC
-}
-
-src_compile() {
-	emake -C src
-}
-
-src_install() {
-	dobin src/dialign2-2
-
-	insinto /usr/share/dialign2
-	doins -r dialign2_dir/.
-
-	newenvd - 80dialign2 <<- EOF
-		DIALIGN2_DIR="${EPREFIX}/usr/share/dialign2"
-	EOF
-}
diff --git a/sci-biology/dialign2/files/dialign2-2.2.1-Wimplicit.patch b/sci-biology/dialign2/files/dialign2-2.2.1-Wimplicit.patch
deleted file mode 100644
index 3f886171b070..000000000000
--- a/sci-biology/dialign2/files/dialign2-2.2.1-Wimplicit.patch
+++ /dev/null
@@ -1,205 +0,0 @@
---- a/src/alig_graph_closure.c
-+++ b/src/alig_graph_closure.c
-@@ -27,7 +27,7 @@
- void init_seq(CLOSURE *clos, int nbreseq, int *longseq);
- void desinit_seq(CLOSURE *clos);
- 
--int print_aligSets(CLOSURE *clos, int nseq, int i);
-+void print_aligSets(CLOSURE *clos, int nseq, int i);
- 
- char DEBUG=0;
- 
-@@ -309,7 +309,7 @@
- }
- 
- 
--int print_aligSets(CLOSURE *clos, int nseq, int i)
-+void print_aligSets(CLOSURE *clos, int nseq, int i)
- {
- char nouveau_, terminer;
- int n, ng, nd, nn, k;
-@@ -395,7 +395,7 @@
- liberer(clos);
- }
- 
--int addAlignedPositions(CLOSURE *clos, int seq1, int i, int seq2, int j)
-+void addAlignedPositions(CLOSURE *clos, int seq1, int i, int seq2, int j)
- {
- char nouveau_, terminer;
- int n, n1, n2, ng1, ng2, nd1, nd2, nn, k;
-@@ -623,7 +623,7 @@
- 	return(!path(clos, y, j, x, i));
- }
- 
--int addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l)
-+void addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l)
- {
- int k;
- 
---- a/src/alig_graph_closure.h
-+++ b/src/alig_graph_closure.h
-@@ -43,13 +43,13 @@
- 
- void freeAligGraphClosure(CLOSURE *clos);
- 
--int addAlignedPositions(CLOSURE *clos, int x, int i, int y, int j);
-+void addAlignedPositions(CLOSURE *clos, int x, int i, int y, int j);
- 
- int alignablePositions(CLOSURE *clos, int x, int i, int y, int j);
- 
- int alignedPositions(CLOSURE *clos, int x, int i, int y, int j);
- 
--int addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l);
-+void addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l);
- 
- int alignableSegments(CLOSURE *clos, int x, int i, int y, int j, int l);
- 
---- a/src/anchor.c
-+++ b/src/anchor.c
-@@ -17,6 +17,7 @@
- #include "define.h"
- #include "dialign.h"
- #include "alig_graph_closure.h"
-+#include "pratique.h"
- 
- 
- extern int  anc_num, *seqlen ;
-@@ -24,6 +25,8 @@
- extern char *seq[MAX_SEQNUM];
- extern struct multi_frag *anchor_frg ;
- 
-+extern int word_count( char *seq );
-+
- void anchor_check( int s1, int s2, int b1, int b2, int l ,  float scr ) {  
- 
-       if(  
-@@ -101,7 +104,7 @@
- }
- 
- 
--int multi_anc_read( char *file_name ) {
-+void multi_anc_read( char *file_name ) {
- 
-   char anc_file_name[ NAME_LEN ] ;
-   FILE *fp;
---- a/src/dialign.c
-+++ b/src/dialign.c
-@@ -218,7 +218,7 @@
-  extern void subst_mat(char *file_name, int fragno , struct  multi_frag *smp );
-  extern int seq_read( char *in_file , char *sq[MAX_SEQNUM] , char **sqn , char **fsqn) ;
-  extern int anc_read( char *file_name ) ;
-- extern int multi_anc_read( char *file_name ) ;
-+ extern void multi_anc_read( char *file_name ) ;
-  extern void randomize( int r_numb , FILE *fp1 );
-  extern int mini2(int a, int b);
-  extern int maxi2(int a, int b);
-@@ -250,6 +250,9 @@
-  extern void av_tree_print();
-  extern void matrix_read( FILE *fp_mat ) ;
-  extern void mem_alloc( ) ;
-+ extern void regex_parse( char *mot_regex ) ;
-+ extern void seq_parse( char *mot_regex ) ;
-+ extern void exclude_frg_read( char *file_name , int ***exclude_list) ;
-  
- 
-                     /******************************/
-@@ -258,7 +261,7 @@
- 
- 
- 
--main(int argc, char **argv)
-+int main(int argc, char **argv)
- {
-  int k,  anc1, dia_counter, tmpi1, tmpi2 ;
- 
---- a/src/functions.c
-+++ b/src/functions.c
-@@ -853,7 +853,7 @@
-       }
-   }
- 
--wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
-+void wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
-            int *nuc_cnt , int *frg_inv, struct multi_frag *dia )      {
- 
- int i, dc, pc, s1, pos;
-@@ -882,7 +882,7 @@
- 
- 
- 
--plot_calc( int num , int e_len, float *w_count, float *pl, 
-+void plot_calc( int num , int e_len, float *w_count, float *pl, 
-            struct multi_frag *dia , FILE *fp_csc )
-   {
-     int i, dc, pc, s1, pos;
---- a/src/input.c
-+++ b/src/input.c
-@@ -17,6 +17,7 @@
- #include "define.h"
- #include "dialign.h"
- #include "alig_graph_closure.h"
-+#include "pratique.h"
- 
- extern int max_dia , self_comparison ; 
- extern int sim_score[21][21]; 
-@@ -370,8 +371,11 @@
-  }
- 
- 
--  if ( fgets( line , MLINE , fp ) == NULL ) 
--    erreur("\n\n problem with file %s  \n\n", file_name );
-+  if ( fgets( line , MLINE , fp ) == NULL )  {
-+    char buffer [500];
-+    snprintf ( buffer, 500, "\n\n problem with file %s  \n\n", file_name );
-+    erreur( buffer );
-+  }
-   else
-     if( w_type % 2 )  
-       av_sim_score_nuc = atof( line );
---- a/src/output.c
-+++ b/src/output.c
-@@ -61,9 +61,9 @@
-  extern void mini(int *a, int b);
-  extern void maxi(int *a, int b);
-  extern int int_test(float f);
-- extern plot_calc( int num , int e_len, float *w_count, float *pl,
-+ extern void plot_calc( int num , int e_len, float *w_count, float *pl,
-            struct multi_frag *dia , FILE *fp_csc ) ;
-- extern wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
-+ extern void wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
-            int *nuc_cnt , int *frg_inv, struct multi_frag *dia ) ;  
- 
- 
---- a/src/pratique.c
-+++ b/src/pratique.c
-@@ -4,7 +4,7 @@
- 
- /* ------------------------------------------------------------*/
- 
--void erreur(char *message)
-+_Noreturn void erreur(char *message)
- {
- printf("%s\n", message);
- exit(1);
---- a/src/pratique.h
-+++ b/src/pratique.h
-@@ -12,7 +12,7 @@
- 
- #define	TAILLE_MAX_LIGNE_FICHIER	10000
- 
--void erreur(char *message);
-+_Noreturn void erreur(char *message);
- 
- void *allouer(size_t taille);
- void *reallouer(void *pointeur, size_t taille);
---- a/src/regex.c
-+++ b/src/regex.c
-@@ -151,7 +151,7 @@
- 
- }
-  
--seq_parse( char *mot_regex ) { 
-+void seq_parse( char *mot_regex ) { 
-   int sn, ok , i ; 
-   int sp, ap, rp, hv, match;
-   max_mot_offset = sqrt ( - log ( 0.1 ) *  10 / mot_factor ) * mot_offset_factor; 
diff --git a/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch b/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch
deleted file mode 100644
index a4940ee867ee..000000000000
--- a/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch
+++ /dev/null
@@ -1,48 +0,0 @@
---- a/src/makefile
-+++ b/src/makefile
-@@ -10,9 +10,7 @@
-     ###############################
- 
- 
--CC = gcc
--CFLAGS =  -c -O -I$ -DCONS
--#CFLAGS =  -g -c -I$ -DCONS
-+CPPFLAGS += -I. -DCONS
- LIBS = -lm
- #
- 
-@@ -23,33 +21,4 @@
- 
- #
- dialign2-2: $(OBJS)  
--	$(CC) $(OBJS) $(LIBS) -o dialign2-2
--#	$(CC) -g $(OBJS) $(LIBS) -o dialign2-2_db
--#
--#
--# Subroutines
--#
--
--dialign.o: dialign.c
--	$(CC) $(CFLAGS) dialign.c
--functions.o: functions.c 
--	$(CC) $(CFLAGS) functions.c
--input.o: input.c
--	$(CC) $(CFLAGS) input.c
--frag_chain.o: frag_chain.c
--	$(CC) $(CFLAGS) frag_chain.c
--para.o: para.c
--	$(CC) $(CFLAGS) para.c
--output.o: output.c
--	$(CC) $(CFLAGS) output.c
--wgt.o: wgt.c
--	$(CC) $(CFLAGS) wgt.c
--regex.o: regex.c
--	$(CC) $(CFLAGS) regex.c
--anchor.o: anchor.c
--	$(CC) $(CFLAGS) anchor.c
--
--#
--
--
--
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS)
diff --git a/sci-biology/dialign2/metadata.xml b/sci-biology/dialign2/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/dialign2/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/elph/Manifest b/sci-biology/elph/Manifest
deleted file mode 100644
index f2ca47f1b782..000000000000
--- a/sci-biology/elph/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ELPH-1.0.1.tar.gz 113476 BLAKE2B 7c34e9f847560bf46d1bc6bbb720a0cd0afd91b29c23dac98056d2b9eea39146dda72468cad96892eb551cdfb03b224ea22b8e4cee40f19774e24fa843f55192 SHA512 a76cdcdaa1dc406fb0f1204b6a40ffc9f4c0840611b960a3d4299d447446e5bbf941abe7f70cee38f69a64862e186133fd60c1aac18b4b58d86f2ed5c4dd7d72
diff --git a/sci-biology/elph/elph-1.0.1-r3.ebuild b/sci-biology/elph/elph-1.0.1-r3.ebuild
deleted file mode 100644
index e0ac9eece3b5..000000000000
--- a/sci-biology/elph/elph-1.0.1-r3.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program"
-HOMEPAGE="http://cbcb.umd.edu/software/ELPH/"
-SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz"
-S="${WORKDIR}/${PN^^}/sources"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.0.1-fix-build-system.patch
-	"${FILESDIR}"/${PN}-1.0.1-drop-register-keyword.patch
-)
-
-src_configure() {
-	tc-export CC CXX
-}
-
-src_install() {
-	dobin elph
-
-	cd "${WORKDIR}"/ELPH || die
-	dodoc VERSION
-	newdoc Readme.ELPH README
-}
diff --git a/sci-biology/elph/files/elph-1.0.1-drop-register-keyword.patch b/sci-biology/elph/files/elph-1.0.1-drop-register-keyword.patch
deleted file mode 100644
index c05a280d4679..000000000000
--- a/sci-biology/elph/files/elph-1.0.1-drop-register-keyword.patch
+++ /dev/null
@@ -1,102 +0,0 @@
-Bug: https://bugs.gentoo.org/898116
-
---- a/GBase.cpp
-+++ b/GBase.cpp
-@@ -208,8 +208,8 @@ char* rstrstr(char* rstart, char *lend, char* substr) {  /*like strstr, but star
- 
- //hash function used for strings in GHash
- int strhash(const char* str){
--  register int h=0;
--  register int g;
-+  int h=0;
-+  int g;
-   while (*str) {
-     h=(h<<4)+*str++;
-     g=h&0xF0000000;
---- a/GString.cpp
-+++ b/GString.cpp
-@@ -364,8 +364,8 @@ GString& GString::appendfmt(const char *fmt,...) {
-   }
- 
- GString& GString::trim(char c) {
-- register int istart;
-- register int iend;
-+ int istart;
-+ int iend;
-  for (istart=0; istart<length() && chars()[istart]==c;istart++);
-  if (istart==length()) {
-        make_unique(); //edit operation ahead
-@@ -384,8 +384,8 @@ GString& GString::trim(char c) {
-  }
- 
- GString& GString::trim(char* c) {
-- register int istart;
-- register int iend;
-+ int istart;
-+ int iend;
-  for (istart=0; istart<length() && strchr(c, chars()[istart])!=NULL ;istart++);
-  if (istart==length()) {
-         replace_data(0); //string was entirely trimmed
-@@ -405,7 +405,7 @@ GString& GString::trim(char* c) {
- GString& GString::trimR(char c) {
-  //only trim the right end
-  //register int istart;
-- register int iend;
-+ int iend;
-  for (iend=length()-1; iend>=0 && chars()[iend]==c;iend--);
-  if (iend==-1) {
-        replace_data(0); //string was entirely trimmed
-@@ -423,7 +423,7 @@ GString& GString::trimR(char c) {
-  }
- 
- GString& GString::trimR(char* c) {
-- register int iend;
-+ int iend;
-  for (iend=length()-1; iend>=0 && strchr(c,chars()[iend])!=NULL;iend--);
-  if (iend==-1) {
-        replace_data(0); //string was entirely trimmed
-@@ -440,7 +440,7 @@ GString& GString::trimR(char* c) {
-  }
- 
- GString& GString::trimL(char c) {
-- register int istart;
-+ int istart;
-  for (istart=0; istart<length() && chars()[istart]==c;istart++);
-  if (istart==length()) {
-        replace_data(0); //string was entirely trimmed
-@@ -457,7 +457,7 @@ GString& GString::trimL(char c) {
-  }
- 
- GString& GString::trimL(char* c) {
-- register int istart;
-+ int istart;
-  for (istart=0; istart<length() && strchr(c,chars()[istart])!=NULL;istart++);
-  if (istart==length()) {
-        replace_data(0); //string was entirely trimmed
-@@ -598,7 +598,7 @@ bool GString::is_space() const {
-     if (my_data == &null_data)
-         return false;
- 
--    for (register const char *p = chars(); *p; p++)
-+    for (const char *p = chars(); *p; p++)
-         if (!isspace(*p))
-             return false;
- 
-@@ -889,7 +889,7 @@ GString& GString::append(const GString& s) {
- 
- GString& GString::upper() {
-   make_unique(); //edit operation ahead
--  for (register char *p = chrs(); *p; p++)
-+  for (char *p = chrs(); *p; p++)
-             *p = (char) toupper(*p);
- 
-     return *this;
-@@ -900,7 +900,7 @@ GString& GString::upper() {
- GString& GString::lower() {
-     make_unique();
- 
--    for (register char *p = chrs(); *p; p++)
-+    for (char *p = chrs(); *p; p++)
-           *p = (char) tolower(*p);
- 
-     return *this;
diff --git a/sci-biology/elph/files/elph-1.0.1-fix-build-system.patch b/sci-biology/elph/files/elph-1.0.1-fix-build-system.patch
deleted file mode 100644
index 9afbb68666d6..000000000000
--- a/sci-biology/elph/files/elph-1.0.1-fix-build-system.patch
+++ /dev/null
@@ -1,55 +0,0 @@
-Make build system respect user variables
-
---- a/Makefile
-+++ b/Makefile
-@@ -1,42 +1,26 @@
--CLASSDIR := .
--
--# Directories to search for header files
--SEARCHDIRS := -I- -I${CLASSDIR}
--
--
--SYSTYPE :=     $(shell uname)
--
--# C compiler
--
--CC      := g++
--CFLAGS  = -Wall ${SEARCHDIRS} -fno-exceptions -fno-rtti -D_REENTRANT -g
-+my_CPPFLAGS = -D_REENTRANT -I.
- 
- %.o : %.c
--	${CC} ${CFLAGS} -c $< -o $@
-+	$(CC) -Wall $(CFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@
- 
- %.o : %.cc
--	${CC} ${CFLAGS} -c $< -o $@
-+	$(CXX) -Wall $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@
- 
- %.o : %.C
--	${CC} ${CFLAGS} -c $< -o $@
-+	$(CXX) -Wall $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@
- 
- %.o : %.cpp
--	${CC} ${CFLAGS} -c $< -o $@
-+	$(CXX) -Wall $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@
- 
- %.o : %.cxx
--	${CC} ${CFLAGS} -c $< -o $@
-+	$(CXX) -Wall $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $< -o $@
- 
- # C/C++ linker
--
--LINKER    := g++
--LDFLAGS    =
--LOADLIBES := 
--
- .PHONY : all
- all:    elph
- 
--elph:  ./elph.o ${CLASSDIR}/motif.o ${CLASSDIR}/GBase.o ${CLASSDIR}/GString.o ${CLASSDIR}/GArgs.o
--	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
-+elph: elph.o motif.o GBase.o GString.o GArgs.o
-+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $@ $^
- 
- # target for removing all object files
- 
diff --git a/sci-biology/elph/metadata.xml b/sci-biology/elph/metadata.xml
deleted file mode 100644
index 3be54ddaef3c..000000000000
--- a/sci-biology/elph/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		ELPH is a general-purpose Gibbs sampler for finding motifs in a set of
-		DNA or protein sequences. The program takes as input a set containing
-		anywhere from a few dozen to thousands of sequences, and searches
-		through them for the most common motif, assuming that each sequence
-		contains one copy of the motif.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/embassy-cbstools/Manifest b/sci-biology/embassy-cbstools/Manifest
deleted file mode 100644
index 3b25def8831a..000000000000
--- a/sci-biology/embassy-cbstools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-cbstools-1.0.0.660.tar.gz 452594 BLAKE2B 68d13e14b4805af7ba1742537e6ebd621553ba6c895cd4bb13a5c1e93e72e03916ba62833f31ec35e69fa9a4ab15d9348dbfe19eb55a82f3ecd86141726e6c01 SHA512 8f16f726220a36f998d8a0f1d8aec9ec6b2db8160b15bed7bafc5a65d57a937bd91ee831ecabe2e9aaa8cecaa18d050f16439a276a882730fde3fa4937bec384
diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660-r1.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660-r1.ebuild
deleted file mode 100644
index d2a1341fe194..000000000000
--- a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660-r1.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="Applications from the CBS group"
-
-inherit autotools emboss-r3
-
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/CBSTOOLS-1.0.0.650"
-PATCHES=( "${FILESDIR}"/${PN}-1.0.0.650_fix-build-system.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch
deleted file mode 100644
index 7ed96e5ff23b..000000000000
--- a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch
+++ /dev/null
@@ -1,110 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- a/emboss_acd/Makefile.am
-+++ b/emboss_acd/Makefile.am
-@@ -1,3 +1,3 @@
- 
--pkgdata_DATA = *.acd
-+pkgdata_DATA = $(srcdir)/*.acd
- pkgdatadir=$(prefix)/share/EMBOSS/acd
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -19,9 +19,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -36,7 +34,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -64,6 +62,6 @@
- 	../../../plplot/libeplplot.la \
- 	$(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+        -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-cbstools/metadata.xml b/sci-biology/embassy-cbstools/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-cbstools/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy-clustalomega/Manifest b/sci-biology/embassy-clustalomega/Manifest
deleted file mode 100644
index 49d1ed88474a..000000000000
--- a/sci-biology/embassy-clustalomega/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-clustalomega-1.1.0.660.tar.gz 618177 BLAKE2B 5d3f300a0dd825c92c3f953219b2ae8be271a7d89a1237980571b3f9a9027d6a0191ad9e61be87d1ad3334ddd56f9ff11c05d3e277683dc8cdfe511ef3739877 SHA512 fc16f9505e0300ae184e292fb1d96ce6b90eaf80298f847769466a84726d10ea58e3f4c14ed21a9e2c36d7fa533c7ad248b4995bf41c8abbd0fed1faf1fd4801
diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660-r1.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660-r1.ebuild
deleted file mode 100644
index ad0926d1d2f4..000000000000
--- a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660-r1.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="Clustal Omega - Multiple Sequence Alignment"
-
-inherit autotools emboss-r3
-
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="sci-biology/clustal-omega"
-
-S="${WORKDIR}/CLUSTALOMEGA-1.1.0"
-PATCHES=( "${FILESDIR}"/${PN}-1.1.0_fix-build-system.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch
deleted file mode 100644
index 024f8bfc3a09..000000000000
--- a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch
+++ /dev/null
@@ -1,103 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,9 +17,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -34,7 +32,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -61,6 +59,6 @@
- 	../../../plplot/libeplplot.la \
- 	$(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+        -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-clustalomega/metadata.xml b/sci-biology/embassy-clustalomega/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-clustalomega/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy-domainatrix/Manifest b/sci-biology/embassy-domainatrix/Manifest
deleted file mode 100644
index fe1d993d145d..000000000000
--- a/sci-biology/embassy-domainatrix/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-domainatrix-0.1.660.tar.gz 474066 BLAKE2B ac5e081ac1a18d8abfbcdf687a43d4a09436c83fd54bed8c75487f8ed74852979adc96fa592df9f86c161fc8b398f1225ec44e565b470c59a5c2268898943270 SHA512 151e026445abb171a9141ae5576442307121646c66dc811320a6f73be1103203bf04d37b813e5c95ef0873be261cd474835f4dffd042f33f99d7dd4fda19be7b
diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660-r1.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660-r1.ebuild
deleted file mode 100644
index 98e38b44b0b0..000000000000
--- a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660-r1.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="Protein domain analysis add-on package"
-
-inherit autotools emboss-r3
-
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/DOMAINATRIX-0.1.650"
-PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch
deleted file mode 100644
index 849da318d245..000000000000
--- a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch
+++ /dev/null
@@ -1,103 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,9 +17,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -34,7 +32,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -63,6 +61,6 @@
- 	../../../plplot/libeplplot.la \
- 	$(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+        -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-domainatrix/metadata.xml b/sci-biology/embassy-domainatrix/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-domainatrix/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy-domalign/Manifest b/sci-biology/embassy-domalign/Manifest
deleted file mode 100644
index 669a45a1b5cf..000000000000
--- a/sci-biology/embassy-domalign/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-domalign-0.1.660.tar.gz 498669 BLAKE2B d21352b28ca046c1bfe8600a7eba641d670e232571f95f9c75b47486a63f2a2b02516191706c0688e81bc33cda90ebf88a9ce800535dce9a955ccc15e25dd20a SHA512 14e86664e9038acc60fbec92fa218e218921fb1e51cc2e482fb1760ccd9ea16041dc8a2a9f5f320fca3340b7efdc48ea9d753b048a43966fc3431acdaddc7846
diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.660-r1.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.660-r1.ebuild
deleted file mode 100644
index 00f7c7c4468a..000000000000
--- a/sci-biology/embassy-domalign/embassy-domalign-0.1.660-r1.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="Protein domain alignment add-on package"
-
-inherit autotools emboss-r3
-
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/DOMALIGN-0.1.650"
-PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch
deleted file mode 100644
index 873deaa645ab..000000000000
--- a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch
+++ /dev/null
@@ -1,104 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,10 +17,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I../include -I${embprefix}/include \
--	-I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -35,7 +32,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
- $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -62,6 +59,6 @@
- 	../../../ajax/zlib/libezlib.la \
- 	../../../plplot/libeplplot.la $(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--	-lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+	-lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-domalign/metadata.xml b/sci-biology/embassy-domalign/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-domalign/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy-domsearch/Manifest b/sci-biology/embassy-domsearch/Manifest
deleted file mode 100644
index 4b39f057cd68..000000000000
--- a/sci-biology/embassy-domsearch/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-domsearch-0.1.660.tar.gz 504183 BLAKE2B 598ba359558519967d0e8d895bca453aaeffef3d8a62c3d77b6b2f321118e890ec70c3baa3dd3acc03fc9a19cc380909cf3f14e5569c4ae90d3d5e88817d6e6d SHA512 a242100dc7b4b1f4a838dbf65dffb0475b6b890c7d68efae6a74beb3d4784d031f92365a50a41c0d7ea7d1b4be5e65a298626a798970c74df0d5f85427a51589
diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660-r1.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660-r1.ebuild
deleted file mode 100644
index d00a21f42efc..000000000000
--- a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660-r1.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="Protein domain search add-on package"
-
-inherit autotools emboss-r3
-
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/DOMSEARCH-0.1.650"
-PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch
deleted file mode 100644
index 2fe1803f8452..000000000000
--- a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch
+++ /dev/null
@@ -1,103 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,9 +17,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -34,7 +32,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -61,6 +59,6 @@
- 	../../../ajax/pcre/libepcre.la \
- 	../../../plplot/libeplplot.la $(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+        -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-domsearch/metadata.xml b/sci-biology/embassy-domsearch/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-domsearch/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest
deleted file mode 100644
index 00b8072ad8cb..000000000000
--- a/sci-biology/embassy-emnu/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-emnu-1.05.660.tar.gz 425595 BLAKE2B ed6ab4a0572ac4b57cf0f0b75a3894b1f950f7f373a7c6797ea0c34ba1b0d0e044f2c6951aec7c084340c6b207aa4c8b386055e92ceb9fc83c920fc70e83e665 SHA512 0cb0dafd53c4fd410409430dc12353989d2c226191acace26e81b457602b6b6c60f8eb1d0d9b36ea90b2420010c1a3e887a2458e8487008a36775961e378d0dd
diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.660-r1.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.660-r1.ebuild
deleted file mode 100644
index 33c8039eb166..000000000000
--- a/sci-biology/embassy-emnu/embassy-emnu-1.05.660-r1.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="Simple menu of EMBOSS applications"
-
-inherit autotools emboss-r3
-
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="sys-libs/ncurses:0="
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/EMNU-1.05.650"
-PATCHES=( "${FILESDIR}"/${PN}-1.05.650_fix-build-system.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	# --disable-curses is not a thing,
-	# EMNU hard depends on ncurses really, #752216
-	emboss-r3_src_configure --enable-curses
-}
diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch
deleted file mode 100644
index 3039ac9c83f0..000000000000
--- a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch
+++ /dev/null
@@ -1,140 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
-@@ -899,20 +864,16 @@
- 
- 
- dnl emnu and mse only: uses curses
--dnl Test if --with-curses is given
--AC_ARG_WITH([curses],
--[AS_HELP_STRING([--with-curses], [curses (or ncurses)])])
--
--AC_MSG_CHECKING([for curses])
--
--AS_IF([test "${with_curses}"],
--[
--  CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses"
--  LDFLAGS="$LDFLAGS -L${with_curses}/lib"
-+dnl Test if --enable-curses is given
-+AC_ARG_ENABLE([curses],
-+[AS_HELP_STRING([--enable-curses], [curses])])
-+
-+AS_IF([test "x$enable_curses" = "xyes"], [
-+  PKG_CHECK_MODULES([NCURSES], [ncurses])
-+  PKG_CHECK_MODULES([FORM], [form])
-+  PKG_CHECK_MODULES([MENU], [menu])
- ])
- 
--AC_CHECK_LIB([ncurses], [main], [LIBS="$LIBS -lncurses"], [LIBS="$LIBS -lcurses"])
--
- 
- 
- 
---- a/emboss_acd/Makefile.am
-+++ b/emboss_acd/Makefile.am
-@@ -1,3 +1,3 @@
- 
--pkgdata_DATA = *.acd
-+pkgdata_DATA = $(srcdir)/*.acd
- pkgdatadir=$(prefix)/share/EMBOSS/acd
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,9 +17,8 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) \
-+	$(NCURSES_CFLAGS) $(FORM_CFLAGS) $(MENU_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -34,7 +33,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -56,6 +55,6 @@
- 	../../../ajax/pcre/libepcre.la \
- 	../../../plplot/libeplplot.la -lmenu -lform $(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot -lmenu -lform $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+        -lajax $(NLADD) $(NCURSES_LIBS) $(FORM_LIBS) $(MENU_LIBS) $(XLIB)
- endif
diff --git a/sci-biology/embassy-emnu/metadata.xml b/sci-biology/embassy-emnu/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-emnu/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest
deleted file mode 100644
index 97873ce451cf..000000000000
--- a/sci-biology/embassy-esim4/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-esim4-1.0.0.660.tar.gz 473261 BLAKE2B d15029b0723dd739fa9208f9b0ffd7814cbddc630ca2ff15955412f493f7983753acf82bcc8a3fc6ddfd49abe630982ead377e6941dcbff44ddc5d8ab4e7d6e5 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152
diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild
deleted file mode 100644
index 940abbd9e388..000000000000
--- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA"
-
-inherit autotools emboss-r3 flag-o-matic
-
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/ESIM4-1.0.0.650"
-PATCHES=( "${FILESDIR}"/${PN}-1.0.0.650_fix-build-system.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	# -Werror=lto-type-mismatch
-	# https://bugs.gentoo.org/862258
-	#
-	# Upstream is dead since 2013.
-	filter-lto
-
-	emboss-r3_src_configure
-}
diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
deleted file mode 100644
index 7ffa00c52f75..000000000000
--- a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
+++ /dev/null
@@ -1,110 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- a/emboss_acd/Makefile.am
-+++ b/emboss_acd/Makefile.am
-@@ -1,3 +1,3 @@
- 
--pkgdata_DATA = *.acd
-+pkgdata_DATA = $(srcdir)/*.acd
- pkgdatadir=$(prefix)/share/EMBOSS/acd
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,9 +17,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -34,7 +32,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -62,6 +60,6 @@
- 	../../../plplot/libeplplot.la \
- 	$(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+        -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-esim4/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest
deleted file mode 100644
index 2caca16c49c3..000000000000
--- a/sci-biology/embassy-hmmer/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-hmmer-2.3.2.660.tar.gz 587775 BLAKE2B ae7f7c8722bb06d4e28333837b082045e48179a596026a76c2a42f7905c7ebc42f98dd4f36915e4603322bb6d976ac4fa4e8ce6246cdee025b39ecfcb250bd10 SHA512 eb2c037fec70f4113b9ab59cc4eca9a608e8d0971a7bcc4612d60b1e28556444dd3ecdea4ff7b8f8b34711ad9f655334857e7510e89060459c81994a3abcc02a
diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660-r1.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660-r1.ebuild
deleted file mode 100644
index 7f38492396b1..000000000000
--- a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660-r1.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="HMMER wrapper - sequence analysis with profile HMMs"
-
-inherit autotools emboss-r3
-
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="sci-biology/hmmer:2"
-
-S="${WORKDIR}/HMMER-2.3.2.650"
-PATCHES=(
-	"${FILESDIR}"/${PN}-2.3.2.650_fix-build-system.patch
-	# sci-biology/hmmer:2 has renamed commandline program names
-	"${FILESDIR}"/${PN}-2.3.2.660-slotted-hmmer2.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch
deleted file mode 100644
index dd1660dfbd5b..000000000000
--- a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch
+++ /dev/null
@@ -1,103 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,9 +17,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -34,7 +32,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -66,6 +64,6 @@
- 	../../../plplot/libeplplot.la \
- 	$(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+        -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch
deleted file mode 100644
index f202ddf3d0b5..000000000000
--- a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch
+++ /dev/null
@@ -1,101 +0,0 @@
-Amend command-line names for Gentoo SLOTed hmmer:2
-
---- a/src/ehmmalign.c
-+++ b/src/ehmmalign.c
-@@ -99,7 +99,7 @@
-        iii.HMMER 'options' (that don't appear in ACD file)
-        iv. HMMER & new parameters.
-        */
--    ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmalign"));
-+    ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmalign2"));
-     if(mapali)
- 	ajFmtPrintAppS(&cmd, " --mapali %s ", ajFileGetNameC(mapali));
-     if(withali)
---- a/src/ehmmbuild.c
-+++ b/src/ehmmbuild.c
-@@ -146,7 +146,7 @@
-        iii.HMMER 'options' (that don't appear in ACD file)
-        iv. HMMER & new parameters.
-        */
--    ajStrAssignS(&cmd, ajAcdGetpathC("hmmbuild"));
-+    ajStrAssignS(&cmd, ajAcdGetpathC("hmmbuild2"));
-     if(prior)
- 	ajFmtPrintAppS(&cmd, " --prior %s ", ajFileGetNameC(prior));
-     if(null)
---- a/src/ehmmcalibrate.c
-+++ b/src/ehmmcalibrate.c
-@@ -98,7 +98,7 @@
-        iii.HMMER 'options' (that don't appear in ACD file)
-        iv. HMMER & new parameters.
-        */
--    ajStrAssignS(&cmd, ajAcdGetpathC("hmmcalibrate"));
-+    ajStrAssignS(&cmd, ajAcdGetpathC("hmmcalibrate2"));
-     if(cpu)
- 	ajFmtPrintAppS(&cmd, " --cpu %d ", cpu);
-     if(fixed)
---- a/src/ehmmconvert.c
-+++ b/src/ehmmconvert.c
-@@ -72,7 +72,7 @@
-        iii.HMMER 'options' (that don't appear in ACD file)
-        iv. HMMER & new parameters.
-        */
--    ajStrAssignS(&cmd, ajAcdGetpathC("hmmconvert"));
-+    ajStrAssignS(&cmd, ajAcdGetpathC("hmmconvert2"));
- 
-     /* ACD option only allows one selection */
-     option = ajStrGetCharFirst(format);
---- a/src/ehmmemit.c
-+++ b/src/ehmmemit.c
-@@ -79,7 +79,7 @@
-        iii.HMMER 'options' (that don't appear in ACD file)
-        iv. HMMER & new parameters.
-        */
--    ajStrAssignS(&cmd, ajAcdGetpathC("hmmemit"));
-+    ajStrAssignS(&cmd, ajAcdGetpathC("hmmemit2"));
-     ajFmtPrintAppS(&cmd, " --seed %d ", seed);
-     if(a)
- 	ajStrAppendC(&cmd, " -a ");
---- a/src/ehmmfetch.c
-+++ b/src/ehmmfetch.c
-@@ -74,7 +74,7 @@
-        iii.HMMER 'options' (that don't appear in ACD file)
-        iv. HMMER & new parameters.
-        */
--    ajStrAssignS(&cmd, ajAcdGetpathC("hmmfetch"));
-+    ajStrAssignS(&cmd, ajAcdGetpathC("hmmfetch2"));
-     if(nhmm)
- 	ajStrAppendC(&cmd, " -n ");
-     /* Note the output redirected to outfname  */
---- a/src/ehmmindex.c
-+++ b/src/ehmmindex.c
-@@ -68,7 +68,7 @@
-        iii.HMMER 'options' (that don't appear in ACD file)
-        iv. HMMER & new parameters.
-        */
--    ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmindex"));
-+    ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmindex2"));
-     ajStrAppendC(&cmd, ajFileGetNameC(database));
- 
-     
---- a/src/ehmmpfam.c
-+++ b/src/ehmmpfam.c
-@@ -122,7 +122,7 @@
-        iii.HMMER 'options' (that don't appear in ACD file)
-        iv. HMMER & new parameters.
-        */
--    ajStrAssignS(&cmd, ajAcdGetpathC("hmmpfam"));
-+    ajStrAssignS(&cmd, ajAcdGetpathC("hmmpfam2"));
-     if(nuc)
- 	ajStrAppendC(&cmd, " -n ");
-     ajFmtPrintAppS(&cmd, " -A %d -E %f -T %f -Z %d", A, E, T, Z);
---- a/src/ehmmsearch.c
-+++ b/src/ehmmsearch.c
-@@ -102,7 +102,7 @@
-        iii.HMMER 'options' (that don't appear in ACD file)
-        iv. HMMER & new parameters.
-        */
--    ajStrAssignS(&cmd, ajAcdGetpathC("hmmsearch"));
-+    ajStrAssignS(&cmd, ajAcdGetpathC("hmmsearch2"));
-     ajFmtPrintAppS(&cmd, " -A %d -E %f -T %f -Z %d", A, E, T, Z);
-     if(compat)
- 	ajStrAppendC(&cmd, " --compat ");
diff --git a/sci-biology/embassy-hmmer/metadata.xml b/sci-biology/embassy-hmmer/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-hmmer/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest
deleted file mode 100644
index 93cdda1f4e5e..000000000000
--- a/sci-biology/embassy-iprscan/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-iprscan-4.3.1.660.tar.gz 406720 BLAKE2B a7e5a20b8fd1eb1ba562b5db6643542d5062b270d69a2c53aa66f5cb58f48f1d3a480ae062e53341a884eb497fff22d546df42256cdc131afb183067166fa8b6 SHA512 eed75693557f141331dfb6bec6961a8f6eab93780cad3b629d547b8635be2df6ec85e5ae0e9646d174a562a0f6d31c3c487a4dacac9efdd393a7144cd5716878
diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660-r1.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660-r1.ebuild
deleted file mode 100644
index 0ba710626f5b..000000000000
--- a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660-r1.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="InterProScan motif detection add-on package"
-
-inherit autotools emboss-r3
-
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/IPRSCAN-4.3.1.650"
-PATCHES=( "${FILESDIR}"/${PN}-4.3.1.650_fix-build-system.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
deleted file mode 100644
index 7af8ae2f9ca5..000000000000
--- a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
+++ /dev/null
@@ -1,110 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- a/emboss_acd/Makefile.am
-+++ b/emboss_acd/Makefile.am
-@@ -1,3 +1,3 @@
- 
--pkgdata_DATA = *.acd
-+pkgdata_DATA = $(srcdir)/*.acd
- pkgdatadir=$(prefix)/share/EMBOSS/acd
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,9 +17,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -34,7 +32,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -57,6 +55,6 @@
- 	../../../plplot/libeplplot.la \
- 	$(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+        -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-iprscan/metadata.xml b/sci-biology/embassy-iprscan/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-iprscan/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest
deleted file mode 100644
index 82978ad5411f..000000000000
--- a/sci-biology/embassy-mse/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-mse-3.0.0.660.tar.gz 491747 BLAKE2B 7d072458577a90fc367c5b6ed72d1d36592e42b83b3a4e31126b925ddc76f1946fba14e22b7410f66eb837f686f848bdb1033f3b62084f1423543d7605c4f6b9 SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3
diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.660-r1.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.660-r1.ebuild
deleted file mode 100644
index 32a91d8b75ba..000000000000
--- a/sci-biology/embassy-mse/embassy-mse-3.0.0.660-r1.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor"
-
-inherit autotools emboss-r3 flag-o-matic
-
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="sys-libs/ncurses:="
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/MSE-3.0.0.650"
-PATCHES=( "${FILESDIR}"/${PN}-3.0.0.650_fix-build-system.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	# -Werror=lto-type-mismatch
-	# https://bugs.gentoo.org/927386
-	#
-	# Upstream is dead since 2013.
-	filter-lto
-
-	emboss-r3_src_configure --enable-curses
-}
-
-src_install() {
-	emboss-r3_src_install
-
-	insinto /usr/include/emboss/mse
-	doins h/*.h
-}
diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch
deleted file mode 100644
index 72d7932a188d..000000000000
--- a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch
+++ /dev/null
@@ -1,146 +0,0 @@
---- a/ckit/Makefile.am
-+++ b/ckit/Makefile.am
-@@ -2,7 +2,7 @@
- 
- lib_LTLIBRARIES = libckit.la
- 
--AM_CPPFLAGS = -I../h
-+AM_CPPFLAGS = -I$(top_srcdir)/h
- 
- CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \
- seqspec.c ttyinterface.c nextseqentry.c \
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
-@@ -1000,17 +965,13 @@
- 
- 
- 
--dnl emnu and mse only: uses curses
--dnl Test if --with-curses is given
--AC_ARG_WITH([curses],
--   [AS_HELP_STRING([--with-curses],
--                  [curses (or ncurses)])])
--if test "${with_curses}" ; then
--AC_MSG_CHECKING([for curses])
--CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses"
--LDFLAGS="$LDFLAGS -L${with_curses}/lib"
--fi
--AC_CHECK_LIB(ncurses, main, LIBS="$LIBS -lncurses", LIBS="$LIBS -lcurses")
-+dnl Test if --enable-curses is given
-+AC_ARG_ENABLE([curses],
-+[AS_HELP_STRING([--enable-curses], [curses])])
-+
-+AS_IF([test "x$enable_curses" = "xyes"], [
-+  PKG_CHECK_MODULES([NCURSES], [ncurses])
-+])
- 
- 
- 
---- a/emboss_acd/Makefile.am
-+++ b/emboss_acd/Makefile.am
-@@ -1,3 +1,3 @@
- 
--pkgdata_DATA = *.acd
-+pkgdata_DATA = $(srcdir)/*.acd
- pkgdatadir=$(prefix)/share/EMBOSS/acd
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -18,9 +18,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I../h -I${embprefix}/include \
--	-I${embprefix}/include/eplplot -I${embprefix}/include/epcre \
--	$(NLINCLUDES)
-+AM_CPPFLAGS = -I$(top_srcdir)/h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -35,7 +33,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -59,6 +57,6 @@
- 	../../../plplot/libeplplot.la \
- 	$(XLIB)
- else
--LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \
--	-lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = ../ckit/libckit.la -lnucleus -lacd -lajaxdb \
-+	-lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB)
- endif
diff --git a/sci-biology/embassy-mse/metadata.xml b/sci-biology/embassy-mse/metadata.xml
deleted file mode 100644
index a956caede067..000000000000
--- a/sci-biology/embassy-mse/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">emboss</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest
deleted file mode 100644
index 136dafabbc28..000000000000
--- a/sci-biology/embassy-phylipnew/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-phylipnew-3.69.660.tar.gz 1741298 BLAKE2B 58a2c66ffb9c447fa17462bf54d7b8e65702701d74c1f16ec6906a3acaf076ebcab30982befe6334101bc483901132069a71ffa0e2334aaee0da02a30276b7f2 SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5
diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660-r1.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660-r1.ebuild
deleted file mode 100644
index 2adbcda3d6dc..000000000000
--- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660-r1.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="The Phylogeny Inference Package"
-
-inherit autotools emboss-r3 flag-o-matic
-
-LICENSE+=" free-noncomm"
-
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/PHYLIPNEW-3.69.650"
-PATCHES=(
-	"${FILESDIR}"/${PN}-3.69.650_fix-build-system.patch
-	"${FILESDIR}"/${PN}-3.69.650-fno-common.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	# -Werror=lto-type-mismatch
-	# https://bugs.gentoo.org/862261
-	#
-	# Upstream is dead since 2013.
-	filter-lto
-
-	emboss-r3_src_configure
-}
diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-fno-common.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-fno-common.patch
deleted file mode 100644
index 448000547471..000000000000
--- a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-fno-common.patch
+++ /dev/null
@@ -1,627 +0,0 @@
---- a/include/draw.h
-+++ b/include/draw.h
-@@ -116,19 +116,19 @@
- 
- 
- #ifndef X_DISPLAY_MISSING
--Display *display;               /* the X display */
-+extern Display *display;               /* the X display */
- extern Window  mainwin;         /* the main display window */
--int x, y;                       /* the corner of the window */
--unsigned int width, height;     /* the width and height of the window */
-+extern int x, y;                       /* the corner of the window */
-+extern unsigned int width, height;     /* the width and height of the window */
- #define FONT "-*-new century schoolbook-medium-r-*-*-14-*"
--char *fontrsc;                  /* the font resource */
--XFontStruct *fontst;            /* the font strcture for the font */
--XGCValues gcv;                  /* graphics context values */
--GC gc1;                         /* a graphics context */
--XtAppContext appcontext;
--Widget toplevel;
--int nargc;
--char** nargv;
-+extern char *fontrsc;                  /* the font resource */
-+extern XFontStruct *fontst;            /* the font strcture for the font */
-+extern XGCValues gcv;                  /* graphics context values */
-+extern GC gc1;                         /* a graphics context */
-+extern XtAppContext appcontext;
-+extern Widget toplevel;
-+extern int nargc;
-+extern char** nargv;
- extern String res[16];
- 
- #define DEFGEOMETRY "600x400+20+50"
---- a/include/phylip.h
-+++ b/include/phylip.h
-@@ -349,7 +349,8 @@
- extern AjPFile embossancfile;
- extern AjPFile embossmixfile;
- extern AjPFile embossfactfile;
--extern long spp, words, bits;
-+extern AjPPhyloState* phylostates;
-+extern long spp, words, bits, outgrno;
- extern boolean ibmpc, ansi, tranvsp;
- extern naym *nayme;                     /* names of species */
- 
---- a/src/clique.c
-+++ b/src/clique.c
-@@ -9,7 +9,6 @@
- 
- #define FormWide        80   /* width of outfile page */
- 
--AjPPhyloState* phylostates;
- AjPPhyloProp phyloanc = NULL;
- AjPPhyloProp phylofact = NULL;
- AjPPhyloProp phyloweights = NULL;
-@@ -72,10 +71,8 @@
- Char infilename[FNMLNGTH], ancfilename[FNMLNGTH], factfilename[FNMLNGTH], weightfilename[FNMLNGTH];
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
--long ActualChars, Cliqmin, outgrno,
-+long ActualChars, Cliqmin,
-        col, ith, msets, setsz;
- boolean ancvar, Clmin, Factors, outgropt, trout, weights, noroot, justwts,
-                printcomp, progress, treeprint, mulsets, firstset;
---- a/src/cons.c
-+++ b/src/cons.c
-@@ -6,7 +6,7 @@
- Char intreename[FNMLNGTH], intree2name[FNMLNGTH];
- node *root;
- 
--long numopts, outgrno, col, setsz;
-+long numopts, col, setsz;
- long maxgrp;               /* max. no. of groups in all trees found  */
- 
- boolean trout, firsttree, noroot, outgropt, didreroot, prntsets,
---- a/src/consense.c
-+++ b/src/consense.c
-@@ -19,8 +19,6 @@
- 
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
- long trees_in;
- 
---- a/src/contml.c
-+++ b/src/contml.c
-@@ -69,10 +69,8 @@
- 
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
--long nonodes2, loci, totalleles, df, outgrno, col,
-+long nonodes2, loci, totalleles, df, col,
-       datasets, ith, njumble, jumb=0;
- long inseed, inseed0;
- long *alleles, *locus, *weight;
---- a/src/contrast.c
-+++ b/src/contrast.c
-@@ -40,7 +40,6 @@
- 
- 
- const char* outfilename;
--AjPFile embossoutfile;
- 
- 
- 
---- a/src/discboot.c
-+++ b/src/discboot.c
-@@ -56,7 +56,6 @@
- 
- 
- const char* outfilename;
--AjPFile embossoutfile;
- 
- const char* outweightfilename;
- AjPFile embossoutweightfile;
---- a/src/disc.c
-+++ b/src/disc.c
-@@ -1,7 +1,6 @@
- #include "phylip.h"
- #include "disc.h"
- 
--AjPPhyloState* phylostates;
- 
- /* version 3.6. (c) Copyright 1993-2002 by the University of Washington.
-    Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe.
---- a/src/discrete.c
-+++ b/src/discrete.c
-@@ -6,7 +6,7 @@
-    Permission is granted to copy and use this program provided no fee is
-    charged for it and provided that this copyright notice is not removed. */
- 
--long nonodes, endsite, outgrno, nextree, which;
-+long nonodes, endsite, nextree, which;
- boolean interleaved, printdata, outgropt, treeprint, dotdiff;
- steptr weight, category, alias, location, ally;
- sequence y, convtab;
---- a/src/dnacomp.c
-+++ b/src/dnacomp.c
-@@ -53,8 +53,6 @@
- 
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
- node *root, *p;
- long chars, col, ith, njumble, jumb, msets, numtrees;
---- a/src/dnadist.c
-+++ b/src/dnadist.c
-@@ -27,7 +27,6 @@
- 
- Char infilename[FNMLNGTH], catfilename[FNMLNGTH], weightfilename[FNMLNGTH];
- const char* outfilename;
--AjPFile embossoutfile;
- 
- long sites, categs, weightsum, datasets, ith, rcategs;
- boolean freqsfrom, jukes, kimura, logdet, gama, invar, similarity, lower, f84,
---- a/src/dnainvar.c
-+++ b/src/dnainvar.c
-@@ -51,7 +51,6 @@
- Char infilename[FNMLNGTH], weightfilename[FNMLNGTH];
- 
- const char* outfilename;
--AjPFile embossoutfile;
- 
- long sites, msets, ith;
- boolean weights, progress, prntpat, printinv, mulsets, firstset, justwts;
---- a/src/dnaml.c
-+++ b/src/dnaml.c
-@@ -93,12 +93,10 @@
- 
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
- double *rate, *rrate, *probcat;
- long nonodes2, sites, weightsum, categs, datasets, ith, njumble, jumb;
--long parens, outgrno;
-+long parens;
- boolean  freqsfrom, global, jumble, weights, trout, usertree,
-   ctgry, rctgry, auto_, hypstate, ttr, progress, mulsets, justwts,
-   firstset, improve, smoothit, polishing, lngths, gama, invar,inserting=false;
---- a/src/dnamlk.c
-+++ b/src/dnamlk.c
-@@ -119,8 +119,6 @@
- 
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- double *rrate;
- long sites, weightsum, categs, datasets, ith, njumble, jumb, numtrees, shimotrees;
- /*  sites = number of sites in actual sequences
---- a/src/dnamove.c
-+++ b/src/dnamove.c
-@@ -127,7 +127,6 @@
- node *root;
- 
- const char* outtreename;
--AjPFile embossouttree;
- 
- long chars, screenlines, col, treelines, leftedge, topedge, vmargin,
-    hscroll, vscroll, scrollinc, screenwidth, farthest, whichtree, othertree;
---- a/src/dnapenny.c
-+++ b/src/dnapenny.c
-@@ -47,8 +47,6 @@
- 
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- node *root, *p;
- long *zeros=NULL;
- long chars, howmany, howoften, col, msets, ith;
---- a/src/dollop.c
-+++ b/src/dollop.c
-@@ -10,7 +10,6 @@
- 
- #define maxtrees        100  /* maximum number of tied trees stored     */
- 
--AjPPhyloState* phylostates = NULL;
- AjPPhyloProp phyloanc = NULL;
- AjPPhyloProp phyloweights = NULL;
- AjPPhyloTree* phylotrees = NULL;
-@@ -47,8 +46,6 @@
- 
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
- 
- node *root;
---- a/src/dolmove.c
-+++ b/src/dolmove.c
-@@ -11,7 +11,6 @@
- #define overr           4
- #define which           1
- 
--AjPPhyloState* phylostates = NULL;
- AjPPhyloProp phyloanc = NULL;
- AjPPhyloProp phylofact = NULL;
- AjPPhyloProp phyloweights = NULL;
-@@ -73,10 +72,9 @@
- Char infilename[FNMLNGTH],intreename[FNMLNGTH], ancfilename[FNMLNGTH], factfilename[FNMLNGTH], weightfilename[FNMLNGTH];
- 
- const char* outtreename;
--AjPFile embossouttree;
- 
- node *root;
--long outgrno, col, screenlines, screenwidth, scrollinc,treelines,
-+long col, screenlines, screenwidth, scrollinc,treelines,
-         leftedge,topedge,vmargin,hscroll,vscroll,farthest;
- /* outgrno indicates outgroup */
- boolean weights, thresh, ancvar, questions, dollo, factors,
---- a/src/dolpenny.c
-+++ b/src/dolpenny.c
-@@ -15,7 +15,6 @@
- typedef double *valptr;
- typedef long *placeptr;
- 
--AjPPhyloState* phylostates = NULL;
- AjPPhyloProp phyloanc = NULL;
- AjPPhyloProp phyloweights = NULL;
- 
-@@ -40,8 +39,6 @@
- Char infilename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH];
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
- node *root;
- long howmany, howoften, col, msets, ith;
---- a/src/draw.c
-+++ b/src/draw.c
-@@ -10,6 +10,20 @@
- #include "phylip.h"
- #include "draw.h"
- 
-+#ifndef X_DISPLAY_MISSING
-+Display *display;
-+int x, y;
-+unsigned int width, height;
-+char *fontrsc;
-+XFontStruct *fontst;
-+XGCValues gcv;
-+GC gc1;
-+XtAppContext appcontext;
-+Widget toplevel;
-+int nargc;
-+char** nargv;
-+#endif
-+
- #ifdef QUICKC
- struct videoconfig myscreen;
- void   setupgraphics();
---- a/src/factor.c
-+++ b/src/factor.c
-@@ -54,7 +54,6 @@
- const char* outfactname;
- const char* outancname;
- AjPFile inputfile;
--AjPFile embossoutfile;
- AjPFile embossoutfact;
- AjPFile embossoutanc;
- 
---- a/src/fitch.c
-+++ b/src/fitch.c
-@@ -60,11 +60,9 @@
- 
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
- Char infilename[FNMLNGTH], intreename[FNMLNGTH];
--long nonodes2, outgrno, nums, col, datasets, ith, njumble, jumb=0, numtrees;
-+long nonodes2, nums, col, datasets, ith, njumble, jumb=0, numtrees;
- long inseed;
- vector *x;
- intvector *reps;
---- a/src/freqboot.c
-+++ b/src/freqboot.c
-@@ -52,7 +52,6 @@
- 
- 
- const char* outfilename;
--AjPFile embossoutfile;
- 
- const char* outweightfilename;
- AjPFile embossoutweightfile;
---- a/src/gendist.c
-+++ b/src/gendist.c
-@@ -24,7 +24,6 @@
- #endif
- 
- const char* outfilename;
--AjPFile embossoutfile;
- 
- long loci, totalleles, df, datasets, ith;
- long nonodes;
---- a/src/kitsch.c
-+++ b/src/kitsch.c
-@@ -51,8 +51,6 @@
- 
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
- 
- Char infilename[FNMLNGTH], intreename[FNMLNGTH];
---- a/src/mix.c
-+++ b/src/mix.c
-@@ -13,7 +13,6 @@
- 
- typedef long *placeptr;
- 
--AjPPhyloState* phylostates = NULL;
- AjPPhyloProp phyloweights = NULL;
- AjPPhyloProp phyloanc = NULL;
- AjPPhyloProp phylomix = NULL;
-@@ -52,11 +51,9 @@
- Char infilename[FNMLNGTH], intreename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH];
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
- node2 *root;
--long outgrno, msets, ith, njumble, jumb, numtrees;
-+long msets, ith, njumble, jumb, numtrees;
- /*  outgrno indicates outgroup */
- long inseed, inseed0;
- boolean jumble, usertree, weights, ancvar, questions, allsokal,
---- a/src/move.c
-+++ b/src/move.c
-@@ -13,7 +13,6 @@
- #define which           1
- 
- 
--AjPPhyloState* phylostates = NULL;
- AjPPhyloProp phyloweights = NULL;
- AjPPhyloProp phyloanc = NULL;
- AjPPhyloProp phylomix = NULL;
-@@ -77,10 +76,9 @@
-  
- char infilename[FNMLNGTH],intreename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH], factfilename[FNMLNGTH];
- const char* outtreename;
--AjPFile embossouttree;
- 
- node *root;
--long outgrno, screenlines, col, treelines, leftedge, topedge,
-+long screenlines, col, treelines, leftedge, topedge,
-   vmargin, hscroll, vscroll, scrollinc, screenwidth, farthest;
- /* outgrno indicates outgroup */
- boolean weights, outgropt, ancvar, questions, allsokal,
---- a/src/neighbor.c
-+++ b/src/neighbor.c
-@@ -32,11 +32,9 @@
- 
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
- Char infilename[FNMLNGTH];
--long nonodes2, outgrno, col, datasets, ith;
-+long nonodes2, col, datasets, ith;
- long inseed;
- vector *x;
- intvector *reps;
---- a/src/pars.c
-+++ b/src/pars.c
-@@ -9,7 +9,6 @@
- 
- #define MAXNUMTREES     1000000  /* bigger than number of user trees can be */
- 
--AjPPhyloState* phylostates = NULL;
- AjPPhyloProp phyloweights = NULL;
- AjPPhyloTree* phylotrees = NULL;
- 
---- a/src/penny.c
-+++ b/src/penny.c
-@@ -12,7 +12,6 @@
- #define often           100  /* how often to notify how many trees examined */
- #define many            1000 /* how many multiples of howoften before stop  */
- 
--AjPPhyloState* phylostates = NULL;
- AjPPhyloProp phyloweights = NULL;
- AjPPhyloProp phyloanc = NULL;
- AjPPhyloProp  phylomix = NULL;
-@@ -44,11 +43,9 @@
- Char infilename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH];
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
- node2 *root;
--long outgrno, rno, howmany, howoften, col, msets, ith;
-+long rno, howmany, howoften, col, msets, ith;
- /*  outgrno indicates outgroup                                        */
- 
- boolean weights, ancvar, questions, allsokal, allwagner,
---- a/src/phylip.c
-+++ b/src/phylip.c
-@@ -46,7 +46,8 @@
- AjPFile embossancfile;
- AjPFile embossmixfile;
- AjPFile embossfactfile;
--long spp, words, bits;
-+AjPPhyloState* phylostates = NULL;
-+long spp, words, bits, outgrno;
- boolean ibmpc, ansi, tranvsp;
- naym *nayme;                     /* names of species */
- 
---- a/src/proml.c
-+++ b/src/proml.c
-@@ -89,8 +89,6 @@
- Char infilename[100], intreename[100], catfilename[100], weightfilename[100];
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
- double *rate, *rrate, *probcat;
- long nonodes2, sites, weightsum, categs,
---- a/src/promlk.c
-+++ b/src/promlk.c
-@@ -88,8 +88,6 @@
- 
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
- Char infilename[FNMLNGTH], intreename[FNMLNGTH],
-      catfilename[FNMLNGTH], weightfilename[FNMLNGTH];
---- a/src/protdist.c
-+++ b/src/protdist.c
-@@ -79,7 +79,6 @@
- char infilename[100], catfilename[100], weightfilename[100];
- 
- const char* outfilename;
--AjPFile embossoutfile;
- 
- 
- /* Local variables for makedists, propagated globally for c version: */
---- a/src/protpars.c
-+++ b/src/protpars.c
-@@ -76,8 +76,6 @@
- 
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
- node *root;
- long chars, col, msets, ith, njumble, jumb, numtrees;
---- a/src/restboot.c
-+++ b/src/restboot.c
-@@ -54,7 +54,6 @@
- 
- 
- const char* outfilename;
--AjPFile embossoutfile;
- 
- const char* outweightfilename;
- AjPFile embossoutweightfile;
---- a/src/restdist.c
-+++ b/src/restdist.c
-@@ -13,7 +13,6 @@
- 
- extern sequence y;
- 
--AjPPhyloState* phylostates = NULL;
- 
- 
- #ifndef OLDC
-@@ -40,7 +39,6 @@
- Char infilename[FNMLNGTH];
- 
- const char* outfilename;
--AjPFile embossoutfile;
- 
- long sites, weightsum, datasets, ith;
- boolean  restsites, neili, gama, weights, lower,
---- a/src/restml.c
-+++ b/src/restml.c
-@@ -17,7 +17,6 @@
- 
- AjPPhyloProp phyloweights = NULL;
- AjPPhyloTree* phylotrees;
--AjPPhyloState* phylostates = NULL;
- 
- #ifndef OLDC
- /* function prototypes */
-@@ -101,8 +100,6 @@
- 
- const char* outfilename;
- const char* outtreename;
--AjPFile embossoutfile;
--AjPFile embossouttree;
- 
- 
- ajint numwts;
---- a/src/retree.c
-+++ b/src/retree.c
-@@ -123,7 +123,7 @@
- 
- node *root, *garbage;
- 
--long nonodes, outgrno, screenwidth, vscreenwidth,
-+long nonodes, screenwidth, vscreenwidth,
-      screenlines, col, treenumber, leftedge, topedge, treelines,
-      hscroll, vscroll, scrollinc, whichtree, othertree,
-      numtrees, treesread;
-@@ -145,7 +145,6 @@
- char       intreename[FNMLNGTH];
- 
- const char* outtreename;
--AjPFile embossouttree;
- 
- boolean    subtree, written, readnext;
- node      *nuroot;
---- a/src/seqbootall.c
-+++ b/src/seqbootall.c
-@@ -109,7 +109,6 @@
- 
- 
- const char* outfilename;
--AjPFile embossoutfile;
- 
- const char* outweightfilename;
- AjPFile embossoutweightfile;
---- a/src/seqboot.c
-+++ b/src/seqboot.c
-@@ -92,7 +92,6 @@
- 
- 
- const char* outfilename;
--AjPFile embossoutfile;
- 
- const char* outweightfilename;
- AjPFile embossoutweightfile;
---- a/src/seq.c
-+++ b/src/seq.c
-@@ -7,7 +7,7 @@
-    Permission is granted to copy and use this program provided no fee is
-    charged for it and provided that this copyright notice is not removed. */
- 
--long nonodes, endsite, outgrno, nextree, which;
-+long nonodes, endsite, nextree, which;
- boolean interleaved, printdata, outgropt, treeprint, dotdiff, transvp;
- steptr weight, category, alias, location, ally;
- sequence y;
---- a/src/treedist.c
-+++ b/src/treedist.c
-@@ -16,7 +16,6 @@
- extern node *root;
- 
- const char* outfilename;
--AjPFile embossoutfile;
- 
- long trees_in_1, trees_in_2;
- 
---- a/src/treedistpair.c
-+++ b/src/treedistpair.c
-@@ -16,7 +16,6 @@
- extern node *root;
- 
- const char* outfilename;
--AjPFile embossoutfile;
- 
- long trees_in_1, trees_in_2;
- 
diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch
deleted file mode 100644
index 589408ed4a9e..000000000000
--- a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch
+++ /dev/null
@@ -1,111 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -781,21 +754,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -918,6 +876,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- a/emboss_acd/Makefile.am
-+++ b/emboss_acd/Makefile.am
-@@ -1,3 +1,3 @@
- 
--pkgdata_DATA = *.acd
-+pkgdata_DATA = $(srcdir)/*.acd
- pkgdatadir=$(prefix)/share/EMBOSS/acd
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -16,10 +16,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I../include -I${embprefix}/include \
--	-I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I$(top_srcdir)/include -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -34,7 +31,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -119,6 +116,6 @@
- 	../../../ajax/pcre/libepcre.la \
- 	../../../plplot/libeplplot.la $(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+        -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-phylipnew/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy-signature/Manifest b/sci-biology/embassy-signature/Manifest
deleted file mode 100644
index e92389900dd7..000000000000
--- a/sci-biology/embassy-signature/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-signature-0.1.660.tar.gz 622294 BLAKE2B 8d495b164d7aa18b4bc2db14d12e3f3ef46f2d9c6d9f98e46bebd888781ee71e7ddf88dbdb37c7be52fdd1182337ea7c70cca1247489a14f652b86918e58c46a SHA512 4989693b17c29ece16f94934e1b2f5e62f31c345bc8cbac938450db0d8f5d56ae37be6090c46e96725e63621c5951f8a65461cd36d4aafb1b509f3f554b4e952
diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.660-r1.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.660-r1.ebuild
deleted file mode 100644
index 61c7792dcd21..000000000000
--- a/sci-biology/embassy-signature/embassy-signature-0.1.660-r1.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="Protein signature add-on package"
-
-inherit autotools emboss-r3
-
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/SIGNATURE-0.1.650"
-PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch
deleted file mode 100644
index a453b25bde66..000000000000
--- a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch
+++ /dev/null
@@ -1,103 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,9 +17,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -34,7 +32,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -67,6 +65,6 @@
- 	../../../plplot/libeplplot.la \
- 	$(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+        -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-signature/metadata.xml b/sci-biology/embassy-signature/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-signature/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy-structure/Manifest b/sci-biology/embassy-structure/Manifest
deleted file mode 100644
index 57aff8927070..000000000000
--- a/sci-biology/embassy-structure/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-structure-0.1.660.tar.gz 588118 BLAKE2B 2723eebc309c81cc94fea687819de2c76d30ce87bb7c6dac12e9964c73fd18b497a31db07d12803d87799e42063b73d406520434482bcdb29f23a14756d11750 SHA512 56fb0ed975bfd95b1fbbccaf694e0617ec23971d53bdc230eeb6ca177907e784805697193e7630e4a513f1b4ee7a1a7974136520963557c452185be4ed22b641
diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.660-r1.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.660-r1.ebuild
deleted file mode 100644
index 022213a391cd..000000000000
--- a/sci-biology/embassy-structure/embassy-structure-0.1.660-r1.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="Protein structure add-on package"
-
-inherit autotools emboss-r3
-
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/STRUCTURE-0.1.650"
-PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch
deleted file mode 100644
index 32826f8ebbbe..000000000000
--- a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch
+++ /dev/null
@@ -1,103 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,9 +17,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -34,7 +32,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -65,6 +63,6 @@
- 	../../../plplot/libeplplot.la \
- 	$(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+        -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-structure/metadata.xml b/sci-biology/embassy-structure/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-structure/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy-topo/Manifest b/sci-biology/embassy-topo/Manifest
deleted file mode 100644
index 13d541332ce9..000000000000
--- a/sci-biology/embassy-topo/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-topo-2.0.660.tar.gz 443510 BLAKE2B ba49debdfb9f13051bd32d0d14de3b446a8fde83923e6927df52fd989460c60b5d3023aeaa84d3ab920533c40607f7ba274f64827cefa611a1513f203e08316c SHA512 8ef157a61ac47680734bed3d07cfe2bcd86730998453daa704b74aad667944ad6b0cc6f7fce36be4566cb19a626f1648d5f6793ce227cf57939fcfd0d10690a8
diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.660-r1.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.660-r1.ebuild
deleted file mode 100644
index d6cbcd3b920b..000000000000
--- a/sci-biology/embassy-topo/embassy-topo-2.0.660-r1.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="Transmembrane protein display"
-
-inherit autotools emboss-r3
-
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/TOPO-2.0.650"
-PATCHES=( "${FILESDIR}"/${PN}-2.0.650_fix-build-system.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch
deleted file mode 100644
index e1a2439b713b..000000000000
--- a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch
+++ /dev/null
@@ -1,110 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- a/emboss_acd/Makefile.am
-+++ b/emboss_acd/Makefile.am
-@@ -1,3 +1,3 @@
- 
--pkgdata_DATA = *.acd
-+pkgdata_DATA = $(srcdir)/*.acd
- pkgdatadir=$(prefix)/share/EMBOSS/acd
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,9 +17,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -34,7 +32,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -59,6 +57,6 @@
- 	../../../plplot/libeplplot.la \
- 	$(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+        -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-topo/metadata.xml b/sci-biology/embassy-topo/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-topo/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest
deleted file mode 100644
index 9806f921a280..000000000000
--- a/sci-biology/embassy-vienna/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-vienna-1.7.2.660.tar.gz 873165 BLAKE2B 46e976e52ad65490237563af09e483c212a6170c8c79fac8a2f2609040ee6a4cf60c04b00159c4c33d8c2a10f6e457e412287409fc0ea5724c5687dbd65ff06c SHA512 1484ca419ebcb7776d8f92dd633d4fda1a752a73ccb5189b58f7417a5611e015e9b42cbb37b51f4d5c7a27df0d5cab2cdf1e95ebd70a8359ffc8fa1633d28103
diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660-r1.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660-r1.ebuild
deleted file mode 100644
index d7cee6658cf9..000000000000
--- a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660-r1.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="Vienna RNA package - RNA folding"
-
-inherit autotools emboss-r3
-
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/VIENNA-1.7.2.650"
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.7.2.650_fix-build-system.patch
-	"${FILESDIR}"/${PN}-1.7.2.650-C99-inline.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650-C99-inline.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650-C99-inline.patch
deleted file mode 100644
index 1eda10172dc5..000000000000
--- a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650-C99-inline.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- a/src/fold.c
-+++ b/src/fold.c
-@@ -65,9 +65,9 @@
- PRIVATE int fill_arrays(const char *sequence);
- /*@unused@*/
- INLINE PRIVATE  int oldLoopEnergy(int i, int j, int p, int q, int type, int type_2);
--INLINE int  LoopEnergy(int n1, int n2, int type, int type_2,
-+int  LoopEnergy(int n1, int n2, int type, int type_2,
- 			 int si1, int sj1, int sp1, int sq1);
--INLINE int  HairpinE(int size, int type, int si1, int sj1, const char *string);
-+int  HairpinE(int size, int type, int si1, int sj1, const char *string);
- int loop_energy(short * ptable, short *s, short *s1, int i);
- char *backtrack_fold_from_pair(char *sequence, int i, int j);
- void export_circfold_arrays(int *Fc_p, int *FcH_p, int *FcI_p, int *FcM_p, int **fM2_p,
-@@ -831,7 +831,7 @@
- }
- /*---------------------------------------------------------------------------*/
- 
--INLINE int HairpinE(int size, int type, int si1, int sj1, const char *string) {
-+int HairpinE(int size, int type, int si1, int sj1, const char *string) {
-   int energy;
-   energy = (size <= 30) ? P->hairpin[size] :
-     P->hairpin[30]+(int)(P->lxc*log((size)/30.));
-@@ -901,7 +901,7 @@
- 
- /*--------------------------------------------------------------------------*/
- 
--INLINE int LoopEnergy(int n1, int n2, int type, int type_2,
-+int LoopEnergy(int n1, int n2, int type, int type_2,
- 		      int si1, int sj1, int sp1, int sq1) {
-   /* compute energy of degree 2 loop (stack bulge or interior) */
-   int nl, ns, energy;
diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
deleted file mode 100644
index ea96e9d47fa9..000000000000
--- a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
+++ /dev/null
@@ -1,120 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -649,33 +649,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -751,21 +724,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -888,6 +846,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -10,7 +10,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -leplplot -leexpat \
- -lezlib -lepcre
- else
--CYGWIN_LDVIENNA = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl \
-+CYGWIN_LDVIENNA = -lnucleus -lacd -lajaxdb -lensembl \
-                 -lajaxg -lajax -leplplot -leexpat -lezlib -lepcre
- endif
- endif
-@@ -32,9 +32,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I../H -I${embprefix}/include -I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I$(top_srcdir)/H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -49,7 +47,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -87,6 +85,7 @@
- endif
- 
- liboviennarna_la_LDFLAGS = $(LINKFLAGS)
-+liboviennarna_la_LIBADD = -lajax
- 
- ovrnaalifold_SOURCES = vrnaalifold.c
- ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c
-@@ -118,6 +117,6 @@
- 	../../../plplot/libeplplot.la \
- 	$(XLIB)
- else
--LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \
--	-lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = liboviennarna.la -lnucleus -lacd -lajaxdb \
-+	-lensembl -lajaxg -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-vienna/metadata.xml b/sci-biology/embassy-vienna/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-vienna/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/embassy/embassy-6.6.0-r3.ebuild b/sci-biology/embassy/embassy-6.6.0-r3.ebuild
deleted file mode 100644
index ec357be2f02f..000000000000
--- a/sci-biology/embassy/embassy-6.6.0-r3.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)"
-HOMEPAGE="http://emboss.sourceforge.net/embassy/"
-
-LICENSE="metapackage"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	>=sci-biology/embassy-cbstools-1.0.0.660
-	>=sci-biology/embassy-clustalomega-1.1.0.660
-	>=sci-biology/embassy-domainatrix-0.1.660
-	>=sci-biology/embassy-domalign-0.1.660
-	>=sci-biology/embassy-domsearch-0.1.660
-	>=sci-biology/embassy-emnu-1.05.660
-	>=sci-biology/embassy-esim4-1.0.0.660
-	>=sci-biology/embassy-hmmer-2.3.2.660
-	>=sci-biology/embassy-iprscan-4.3.1.660
-	>=sci-biology/embassy-mse-3.0.0.660
-	>=sci-biology/embassy-phylipnew-3.69.660
-	>=sci-biology/embassy-signature-0.1.660
-	>=sci-biology/embassy-structure-0.1.660
-	>=sci-biology/embassy-topo-2.0.660
-	>=sci-biology/embassy-vienna-1.7.2.660
-"
diff --git a/sci-biology/embassy/metadata.xml b/sci-biology/embassy/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
deleted file mode 100644
index ccdb0846835b..000000000000
--- a/sci-biology/emboss/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST EMBOSS-6.6.0.tar.gz 117962028 BLAKE2B 91bf3c680290bd975d2ddb5251089d7f75f8a44a26e1247e93d2c9cf2f23e6b89c4218022ba1af0c940136ff56782f40d2c4604dc756b400ae23f223da7f3cca SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a
-DIST emboss-6.6.0-patches-r2.tar.xz 10616 BLAKE2B 123251c54cccdbec84232a9b14f1907f27ed8885c25166265d679aed4f530717692ed3217a53b67582d7f9ac296b922e19be6096ab23d8bd0ff9470f56fe06eb SHA512 6db0c33f1f114dda2cea97200b7cd05d2173c68b5f939d681220d7ca7e253dc08b83070393b8844d1fb0292fe9cb8b23463459badcacd6421220e775d533b589
diff --git a/sci-biology/emboss/emboss-6.6.0-r4.ebuild b/sci-biology/emboss/emboss-6.6.0-r4.ebuild
deleted file mode 100644
index f06a93896d10..000000000000
--- a/sci-biology/emboss/emboss-6.6.0-r4.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools emboss-r3 readme.gentoo-r1
-
-DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
-SRC_URI="
-	ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${P}-patches-r2.tar.xz"
-S="${WORKDIR}/${P^^}"
-
-LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
-KEYWORDS="~amd64 ~x86"
-IUSE="minimal"
-
-RDEPEND="
-	!dev-build/cons
-	!games-action/xbomber
-"
-PDEPEND="
-	!minimal? (
-		sci-biology/aaindex
-		sci-biology/cutg
-		sci-biology/primer3
-		sci-biology/prints
-		sci-biology/prosite
-		sci-biology/rebase
-	)"
-
-PATCHES=( "${WORKDIR}"/patches/ )
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_install() {
-	emboss-r3_src_install
-
-	readme.gentoo_create_doc
-
-	# Install env file for setting libplplot and acd files path.
-	newenvd - 22emboss <<- EOF
-		# ACD files location
-		EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
-		EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"
-	EOF
-
-	# Remove useless dummy files
-	find "${ED}"/usr/share/EMBOSS -name dummyfile -delete \
-		|| die "Failed to remove dummy files"
-
-	# Move the provided codon files to a different directory. This will avoid
-	# user confusion and file collisions on case-insensitive file systems (see
-	# bug #115446). This change is documented in "README.gentoo".
-	mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} \
-		|| die "Failed to move CODON directory"
-
-	# collision with dev-texlive/texlive-latexextra, bug #927976
-	mv "${ED}"/usr/bin/{,emboss-}wordcount || die
-}
-
-pkg_postinst() {
-	readme.gentoo_print_elog
-}
diff --git a/sci-biology/emboss/files/README.gentoo b/sci-biology/emboss/files/README.gentoo
deleted file mode 100644
index d1879bd0811c..000000000000
--- a/sci-biology/emboss/files/README.gentoo
+++ /dev/null
@@ -1,34 +0,0 @@
-Administrating EMBOSS on Gentoo systems
-=======================================
-
-
-Codon data files location
--------------------------
-
-The codon data files that are distributed with EMBOSS are installed in the
-``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual
-``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between
-these codon files and those installed with the CUTG database. The names of
-these files sometimes vary only by their case. Having both sets of files in
-the same directory is also impossible on systems such as MacOSX, where the
-root filesystem is case insensitive. If you do not have the CUTG database
-installed and want to use the codon files distributed with EMBOSS, you can
-symlink the ``CODONS.orig`` directory to ``CODONS``::
-
-	# cd ${EPREFIX}/usr/share/EMBOSS/data
-	# ln -s CODONS.orig CODONS
-
-
-Restriction enzymes equivalence file location
----------------------------------------------
-
-The restriction enzymes equivalence file distributed with EMBOSS is installed
-as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual
-``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file
-collision with the equivalence file provided by the Rebase database. If you do
-not have the Rebase database installed and want to use the equivalence file
-distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to
-``embossre.equ``::
-
-	# cd ${EPREFIX}/usr/share/EMBOSS/data
-	# ln -s embossre.equ.orig embossre.equ
diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml
deleted file mode 100644
index e08634d4ff12..000000000000
--- a/sci-biology/emboss/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		EMBOSS is "The European Molecular Biology Open Software Suite".
-		EMBOSS is a free Open Source software analysis package specially
-		developed for the needs of the molecular biology (e.g. EMBnet) user
-		community. The software automatically copes with data in a variety
-		of formats and even allows transparent retrieval of sequence data
-		from the web. Also, as extensive libraries are provided with the
-		package, it is a platform to allow other scientists to develop and
-		release software in true open source spirit. EMBOSS also integrates
-		a range of currently available packages and tools for sequence
-		analysis into a seamless whole. EMBOSS breaks the historical trend
-		towards commercial software packages.
-	</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">emboss</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest
deleted file mode 100644
index da51818cd95e..000000000000
--- a/sci-biology/eugene/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST eugene-4.1d.tar.gz 7473965 BLAKE2B 537ba871b701a5c199791809f76ea883ff77fe768e27a69b95186ef82ab32cab9b5761405a9fadfeea9f58fe88cadce83bba4b1fa6cba5f4ede2347a516d1df0 SHA512 dab37930e211b3783954f6e4a762450760201b77e0b4214f16724516d9be583d0a7ec44a2f510e73f4370e9c2dc67a425456a057fdba8f51cb72386e16a26ef5
diff --git a/sci-biology/eugene/eugene-4.1d-r1.ebuild b/sci-biology/eugene/eugene-4.1d-r1.ebuild
deleted file mode 100644
index 3800d7a2bdc3..000000000000
--- a/sci-biology/eugene/eugene-4.1d-r1.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools
-
-DESCRIPTION="Prokaryotic and Eukaryotic gene predictor"
-HOMEPAGE="http://eugene.toulouse.inra.fr/"
-SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1359/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-RESTRICT="test"
-
-DEPEND="
-	media-libs/gd[png]
-	media-libs/libpng:="
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	# https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170
-	"${FILESDIR}"/${PN}-3.6-overflow.patch
-	"${FILESDIR}"/${PN}-3.6-plugins.patch
-	"${FILESDIR}"/${PN}-4.1-format-security.patch
-	"${FILESDIR}"/${PN}-4.1d-fix-c++14.patch
-	"${FILESDIR}"/${PN}-4.1d-Wformat.patch
-	"${FILESDIR}"/${PN}-4.1d-portable-getopt.patch
-	"${FILESDIR}"/${PN}-4.1d-clang16.patch
-)
-
-src_prepare() {
-	default
-	sed \
-		-e '/SUBDIRS/ s/doc//' \
-		-e '/INSTALL.*doc/ s/\(.*\)//' \
-		-i Makefile.am || die
-	rm src/getopt.h || die
-	eautoreconf
-}
diff --git a/sci-biology/eugene/files/eugene-3.6-overflow.patch b/sci-biology/eugene/files/eugene-3.6-overflow.patch
deleted file mode 100644
index 7222530ad771..000000000000
--- a/sci-biology/eugene/files/eugene-3.6-overflow.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-http://bugs.gentoo.org/show_bug.cgi?id=336607
-
---- eugene-3.6/src/Sensor.cc
-+++ eugene-3.6/src/Sensor.cc
-@@ -224,7 +224,7 @@
- //--------------------------
- void Signals :: PrintS ()
- {
--  char t[7];
-+  char t[10];
-   char s = '+';
- 
-   switch (type) {
diff --git a/sci-biology/eugene/files/eugene-3.6-plugins.patch b/sci-biology/eugene/files/eugene-3.6-plugins.patch
deleted file mode 100644
index e7424f73fc63..000000000000
--- a/sci-biology/eugene/files/eugene-3.6-plugins.patch
+++ /dev/null
@@ -1,53 +0,0 @@
-https://bugs.gentoo.org/297536
-
---- a/configure.ac
-+++ b/configure.ac
-@@ -28,6 +28,7 @@
- AC_PROG_CC
- AC_PROG_AWK
- AC_PROG_LN_S 
-+AM_PROG_AR
- AC_PROG_RANLIB
- 
- 
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -137,7 +137,7 @@
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Style
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Javascripts
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Images
--	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/plugins
-+	$(INSTALL) -d $(DESTDIR)/$(libdir)/eugene/plugins
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/cfg
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models/WAM
-@@ -160,6 +160,6 @@
- 	$(INSTALL) -m 644 $(srcdir)/web/Images/*jpg $(DESTDIR)/$(pkgdatadir)/web/Images
- 	$(INSTALL) -m 644 $(srcdir)/cfg/*.obo $(DESTDIR)/$(pkgdatadir)/cfg
- 	$(INSTALL) -m 644 $(srcdir)/cfg/*.par $(DESTDIR)/$(pkgdatadir)/cfg
--	$(INSTALL) src/SensorPlugins/*/*.so  $(DESTDIR)/$(pkgdatadir)/plugins
-+	$(INSTALL) src/SensorPlugins/*/*.so  $(DESTDIR)/$(libdir)/eugene/plugins
- 	$(INSTALL) $(srcdir)/Procedures/Eval/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Eval
- 	$(INSTALL) $(srcdir)/Procedures/Get/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Get
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -20,7 +20,7 @@
- 
- SUBDIRS = Parametrization GDIF . SensorPlugins
- 
--AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\"
-+AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\" -DLIB_DIR=\"${libdir}\"
- AM_CFLAGS = 
- 
- bin_PROGRAMS = eugene
---- a/src/MSensor.cc
-+++ b/src/MSensor.cc
-@@ -97,7 +97,7 @@
-   std::string use_name;
- 
-   if (!IsInitialized) {
--    PluginsDir = (std::string)PAR.getC("eugene_dir")+"/"+PLUGINS_DIR+"/";
-+    PluginsDir = (std::string)LIB_DIR+"/eugene/"+PLUGINS_DIR+"/";
- 
-     // On r�cup�re les couples nom de sensor/priorit� du .par
-     PAR.ResetIter();
diff --git a/sci-biology/eugene/files/eugene-4.1-format-security.patch b/sci-biology/eugene/files/eugene-4.1-format-security.patch
deleted file mode 100644
index e6e4a6cc8bd7..000000000000
--- a/sci-biology/eugene/files/eugene-4.1-format-security.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/Hits.cc | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/Hits.cc b/src/Hits.cc
-index edfe178..b228be6 100755
---- a/src/Hits.cc
-+++ b/src/Hits.cc
-@@ -166,7 +166,7 @@ Hits* Hits::ReadFromFile(FILE* HitFile, int *NumHits, int level, int margin, int
-     while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %as\n", &deb, &fin,
-                         &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,HSP)) >= 8)
-     {
--        if (HSP) fprintf(stderr,HSP);
-+        if (HSP) fprintf(stderr, "%s", HSP);
-         if (phase < 0  &&  deb > fin)
-         {
-             int tmp = deb;
diff --git a/sci-biology/eugene/files/eugene-4.1d-Wformat.patch b/sci-biology/eugene/files/eugene-4.1d-Wformat.patch
deleted file mode 100644
index ab6d2bd1d2ee..000000000000
--- a/sci-biology/eugene/files/eugene-4.1d-Wformat.patch
+++ /dev/null
@@ -1,84 +0,0 @@
-Fix -Wformat warnings caused by wrong printf specifiers:
-* Sensor.Riken.cc:95:61: warning: format ‘%d’ expects argument of type ‘int’, but
-* argument 3 has type ‘std::vector<RAFLgene>::size_type {aka long unsigned int}’ [-Wformat=]
-*    fprintf(stderr, "%d RAFL EST pairs read, ", RAFLtmp.size());
-
---- a/src/Hits.cc
-+++ b/src/Hits.cc
-@@ -163,7 +163,7 @@
-     if (ThisHit != NULL)
-         for (int i=0; i<*NumHits-1; i++) ThisHit = ThisHit->Next;
- 
--    while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %as\n", &deb, &fin,
-+    while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %ss\n", &deb, &fin,
-                         &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,HSP)) >= 8)
-     {
-         if (HSP) fprintf(stderr, "%s", HSP);
---- a/src/SensorPlugins/Est/Sensor.Est.cc
-+++ b/src/SensorPlugins/Est/Sensor.Est.cc
-@@ -1353,13 +1353,13 @@
-     exit(2);
-   }
- 
--  fprintf(fp, "vPos %d\n",  vPos.size());
-+  fprintf(fp, "vPos %zu\n",  vPos.size());
-   for (int i=0; i< vPos.size();i++ )
-   {
-     fprintf(fp, "vPos %d\t%d\n",i,  vPos[i]);
-   }
-   
--  fprintf(fp, "vESTMatch %d\n",  vESTMatch.size());
-+  fprintf(fp, "vESTMatch %zu\n",  vESTMatch.size());
-   for (int i=0; i< vESTMatch.size();i++ )
-   {
-     fprintf(fp, "vESTMatch %d\t\n", vESTMatch[i]);
---- a/src/SensorPlugins/Riken/Sensor.Riken.cc
-+++ b/src/SensorPlugins/Riken/Sensor.Riken.cc
-@@ -92,7 +92,7 @@
-   
-   
-   
--  fprintf(stderr, "%d RAFL EST pairs read, ", RAFLtmp.size());
-+  fprintf(stderr, "%zu RAFL EST pairs read, ", RAFLtmp.size());
-   
-   sort(RAFLtmp.begin(), RAFLtmp.end(), Before);
-   
-@@ -148,7 +148,7 @@
-     }
-   }
-   
--  fprintf(stderr,"resulting %d\n",RAFL.size());
-+  fprintf(stderr,"resulting %zu\n",RAFL.size());
-   fflush(stderr);
- 
-   //    for (RAFLtmpindice=0; RAFLtmpindice< (int)RAFL.size(); RAFLtmpindice++) {
---- a/src/SensorPlugins/SMachine/Sensor.SMachine.cc
-+++ b/src/SensorPlugins/SMachine/Sensor.SMachine.cc
-@@ -197,7 +197,7 @@
-   fclose(fp);
- 
-   if (end ==2) {
--    fprintf(stderr, "Error in SpliceMachine splice site file %s, line %d\n", name, len);
-+    fprintf(stderr, "Error in SpliceMachine splice site file %s, line %zu\n", name, len);
-     exit(2);
-   }
- }
---- a/src/SoTerms.cc
-+++ b/src/SoTerms.cc
-@@ -67,14 +67,14 @@
-     j++;
-     if (line[0] == 'i' && line[1] == 'd') 
-     {
--      i = sscanf(line, "id: %s", &value);
-+      i = sscanf(line, "id: %s", value);
-       if (i > 0) 
-       {
- 	char soId[60];
- 	char soName[60];
- 	strcpy (soId, value );
- 	fgets (line, MAX_LINE, fp);
--	i = sscanf(line, "name: %s", &value);
-+	i = sscanf(line, "name: %s", value);
- 	strcpy (soName, value );
- 	idToName_[to_string(soId)]=to_string(soName);
- 	nameToId_[to_string(soName)]=to_string(soId);
diff --git a/sci-biology/eugene/files/eugene-4.1d-clang16.patch b/sci-biology/eugene/files/eugene-4.1d-clang16.patch
deleted file mode 100644
index 21a3ec0a8b62..000000000000
--- a/sci-biology/eugene/files/eugene-4.1d-clang16.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- a/src/GDIF/gdIF.c
-+++ b/src/GDIF/gdIF.c
-@@ -228,7 +228,7 @@
- 		    ToY(phase, pos), (unsigned char *)st, Col[col]);
- }
- 
--void ClosePNG()
-+void ClosePNG(void)
- {
-   int i;
- 
---- a/src/SensorPlugins/0_SensorTk/markov.cc
-+++ b/src/SensorPlugins/0_SensorTk/markov.cc
-@@ -790,7 +790,7 @@
- // cumule les valeurs des cases des codons synonymes et renvoie le total.
- template<class CHAINE, typename T> T TabChaine<CHAINE,T> :: cumuleVAL (int indice) const
- {
--  char* codegenetique=CODEGENETIQUE;
-+  const char* codegenetique=CODEGENETIQUE;
-   T cumul=0;
-   for (int i=0 ; i<64 ; i++) {
-     if ( codegenetique[i] == codegenetique[indice] )
diff --git a/sci-biology/eugene/files/eugene-4.1d-fix-c++14.patch b/sci-biology/eugene/files/eugene-4.1d-fix-c++14.patch
deleted file mode 100644
index a27261c68c06..000000000000
--- a/sci-biology/eugene/files/eugene-4.1d-fix-c++14.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Fix building with C++14, which errors out due to collisions with isinf
-from cmath. We don't need to fix ancient broken OSX toolchains.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=594700
-
---- a/src/SensorPlugins/Tester/Sensor.Tester.cc
-+++ b/src/SensorPlugins/Tester/Sensor.Tester.cc
-@@ -18,9 +18,7 @@
- // ------------------------------------------------------------------
- 
- // MacOS-X kludge. cmath undefines these macros. Turn them into inlines 
--#include <math.h>
--inline int (isinf)(double r) { return isinf(r); }
--inline int (isnan)(double r) { return isnan(r); }
-+#include <cmath>
- 
- #include <iomanip>
- #include <fstream>
diff --git a/sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch b/sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch
deleted file mode 100644
index 156cb4bbdfac..000000000000
--- a/sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch
+++ /dev/null
@@ -1,74 +0,0 @@
---- a/src/Param.h
-+++ b/src/Param.h
-@@ -28,26 +28,14 @@
- #include <vector>
- #include <string>
- #include <string.h>
-+#include <unistd.h>
- #ifdef HAVE_STRINGS_H
- #include <strings.h>
- #endif
--// MacOS-X has getopt() defined is stdlib and the library in the libSystem
--#ifndef __APPLE__
--#ifdef HAVE_GETOPT_H
--#include <getopt.h>
--#else
--#ifndef HAVE_GETOPT
--#include "getopt.h"
--#endif
--#endif
--#endif
- 
- #include "Const.h"
- #include "System.h"
- 
--extern char   *optarg;   
--extern int     optind;
--
- 
- class ltstr
- {
---- a/src/SensorPlugins/MarkovIMM/GetData/CEM.cc
-+++ b/src/SensorPlugins/MarkovIMM/GetData/CEM.cc
-@@ -22,18 +22,11 @@
- #include "../../../../config.h"
- #endif
- 
--#ifdef HAVE_GETOPT_H
--#include <getopt.h>
--#else
--#ifndef HAVE_GETOPT
--#include "../../../getopt.h"
--#endif
--#endif
--
- #include "../../../System.cc"
- #include "../../../Const.h"
- #include "../../0_SensorTk/EndianConv.h"
- #include "strarray.h"
-+#include "unistd.h"
- #include <vector>
- 
- // Constantes
---- a/src/SensorPlugins/MarkovIMM/GetData/TrainIMM.cc
-+++ b/src/SensorPlugins/MarkovIMM/GetData/TrainIMM.cc
-@@ -22,18 +22,11 @@
- #include "../../../../config.h"
- #endif
- 
--#ifdef HAVE_GETOPT_H
--#include <getopt.h>
--#else
--#ifndef HAVE_GETOPT
--#include "../../../getopt.h"
--#endif
--#endif
--
- #include "../../../System.cc"
- #include "../../../Const.h"
- #include "../../0_SensorTk/EndianConv.h"
- #include "strarray.h"
-+#include "unistd.h"
- 
- 
- // Constantes
diff --git a/sci-biology/eugene/metadata.xml b/sci-biology/eugene/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/eugene/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/exonerate/Manifest b/sci-biology/exonerate/Manifest
deleted file mode 100644
index 81a4cb240d5a..000000000000
--- a/sci-biology/exonerate/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST exonerate-2.2.0.tar.gz 509870 BLAKE2B 58b12338ef7d819a8e33ab87d72afe807ca219581a8f35ae38951860915a676bb9ba34a481f685e970948d9272be3e5f28d6b63c14f4d5facf35c4be52530d3b SHA512 c0aec4df83fbf6bcd1b27242397349769211ab88d71e2d081e20cb5453a03acd805807535a69841e991cf543d99fcd458cbd22d60b21f0fc6ce813eac45b838c
diff --git a/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild
deleted file mode 100644
index 05a7156ef5c8..000000000000
--- a/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools flag-o-matic toolchain-funcs
-
-DESCRIPTION="Generic tool for pairwise sequence comparison"
-HOMEPAGE="https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate"
-SRC_URI="https://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-IUSE="test utils"
-REQUIRED_USE="test? ( utils )"
-RESTRICT="!test? ( test )"
-
-DEPEND="dev-libs/glib:2"
-RDEPEND="${DEPEND}"
-
-PATCHES=( "${FILESDIR}"/${P}-autotools.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	# -Werror=lto-type-mismatch
-	# https://bugs.gentoo.org/862264
-	# Upstream doesn't use a bug tracker, so I fired them an email about it. -- Eli
-	filter-lto
-
-	# the bootstrapping code loads AR and CC from the environment
-	tc-export CC RANLIB
-	export C4_AR="$(tc-getAR)"
-
-	econf \
-		--enable-glib2 \
-		--enable-largefile \
-		--enable-pthreads \
-		$(use_enable utils utilities)
-}
-
-src_install() {
-	default
-
-	doman doc/man/man1/*.1
-}
diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch b/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch
deleted file mode 100644
index af95b5c8f77a..000000000000
--- a/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-Fix build with --as-needed
-
-https://bugs.gentoo.org/268094
-
---- a/configure.in
-+++ b/configure.in
-@@ -144,11 +145,6 @@
- elif test "$enable_assert" = no; then
-     CFLAGS="$CFLAGS -DG_DISABLE_ASSERT"
-     echo "Turning assertions off"
--    if test "$GCC" = "yes"; then
--        # Not currently using -fomit-frame-pointer as clashes with -pg
--        # CFLAGS="$CFLAGS -O3 -fomit-frame-pointer -finline-functions"
--        CFLAGS="$CFLAGS -O3 -finline-functions"
--    fi
- else
-     echo "error: must be yes or no: --enable-assert:[$enable_assert]"
-     exit 1
-@@ -289,7 +285,7 @@
- if test "$enable_pthreads" = yes; then
-     echo "Using PTHREADS"
-     CFLAGS="$CFLAGS -DUSE_PTHREADS"
--    LDFLAGS="$LDFLAGS -lpthread"
-+    LIBS="$LIBS -lpthread"
- elif test "$enable_pthreads" = no; then
-     echo "Not using pthreads"
- else
---- a/src/model/bootstrapper.c
-+++ b/src/model/bootstrapper.c
-@@ -146,8 +146,12 @@
- 
- static void Bootstrapper_index_archive(Bootstrapper *bs){
-     register gchar *command;
-+    register gchar *ranlib = "ranlib";
-+    register gchar *tmp = (gchar*)g_getenv("RANLIB");
-+    if(tmp)
-+        ranlib = tmp;
-     register gint ret_val;
--    command = g_strdup_printf("ranlib %s", bs->archive_path);
-+    command = g_strdup_printf("%s %s", ranlib, bs->archive_path);
-     g_message("Indexing archive [%s]", bs->archive_path);
-     g_print("%s\n", command);
-     ret_val = system(command);
diff --git a/sci-biology/exonerate/metadata.xml b/sci-biology/exonerate/metadata.xml
deleted file mode 100644
index 421b8ef55beb..000000000000
--- a/sci-biology/exonerate/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<use>
-		<flag name="utils">Install the follow binaries: esd2esi, fasta2esd, fastaannotatecdna, fastachecksum, fastaclean, fastaclip, fastacomposition, fastadiff, fastaexplode, fastafetch, fastahardmask, fastaindex, fastalength, fastanrdb, fastaoverlap, fastareformat, fastaremove, fastarevcomp, fastasoftmask, fastasort, fastasplit, fastasubseq, fastatranslate, fastavalidcds</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
deleted file mode 100644
index 8144c91b5e78..000000000000
--- a/sci-biology/fasta/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST fasta-36.3.8h.tar.gz 1257682 BLAKE2B e6bd9087563150355fed6edf52a24a0b31ef0658b1e95c3df6d5b5711fc4d137ddd773fb8b3b2fa82fe3f5c310689b2f89668f5b51654eed41ed71f9ef140f99 SHA512 30d160ad083a605397c6c35d2b28f6064cd96f51f99b3664b424ec1dbbbd09772c72e89731a7257306ab58c4ad4b877e229873abd0e09407c64fae643bc04391
-DIST fasta-36.3.8i.tar.gz 1402674 BLAKE2B 5653ae18d38a8f99ac1a76235ebad7189faeaacf9a043ab81ec56036e851d45fcc47435413f81f989efc6dfbccd6e3235c9cd14a6f129719d978ffc69e5def0f SHA512 6f34bd1a5f74362fd569d9c8e7ca7c9fcb0648ea7e861c3d0b54bbdc32ba0caad4beb2aad204122178ee6bcefd579d824412a863163050c305da0a661d55c234
diff --git a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
deleted file mode 100644
index 3c3f5ebd009a..000000000000
--- a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit flag-o-matic toolchain-funcs
-
-MY_PV="${PV}_04-May-2020"
-
-DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
-HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
-SRC_URI="https://github.com/wrpearson/fasta36/archive/refs/tags/v${MY_PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${PN}36-${MY_PV}"
-
-LICENSE="fasta"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~x64-macos"
-IUSE="debug cpu_flags_x86_sse2"
-
-src_prepare() {
-	CC_ALT=
-	CFLAGS_ALT=
-	ALT=
-
-	use debug && append-flags -DDEBUG
-
-	if [[ "$(tc-getCC)" == *icc* ]]; then
-		CC_ALT=icc
-		ALT="${ALT}_icc"
-	else
-		CC_ALT="$(tc-getCC)"
-		use x86 && ALT="32"
-		use amd64 && ALT="64"
-	fi
-
-	if use cpu_flags_x86_sse2 ; then
-		ALT="${ALT}_sse2"
-		append-flags -msse2
-		[[ "$(tc-getCC)" == *icc* ]] || append-flags -ffast-math
-	fi
-
-	export CC_ALT="${CC_ALT}"
-	export ALT="${ALT}"
-
-	# -Werror=lto-type-mismatch
-	# https://bugs.gentoo.org/862267
-	# https://github.com/wrpearson/fasta36/issues/63
-	filter-lto
-
-	eapply "${FILESDIR}"/${P}-ldflags.patch
-
-	sed \
-		-e 's:-ffast-math::g' \
-		-i make/Makefile* || die
-
-	eapply_user
-}
-
-src_compile() {
-	emake -C src -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all
-}
-
-src_test() {
-	cd test || die
-	FASTLIBS="../conf" bash test.sh || die
-}
-
-src_install() {
-	dobin bin/*
-
-	pushd bin >/dev/null || die
-		local i
-		for i in *36; do
-			dosym ${i} /usr/bin/${i%36}
-		done
-	popd >/dev/null || die
-
-	insinto /usr/share/${PN}
-	doins -r conf/. data seq
-
-	doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1}
-	dodoc FASTA_LIST README* doc/{README*,readme*,fasta*,changes*}
-}
diff --git a/sci-biology/fasta/fasta-36.3.8i-r1.ebuild b/sci-biology/fasta/fasta-36.3.8i-r1.ebuild
deleted file mode 100644
index 3c5343e1f042..000000000000
--- a/sci-biology/fasta/fasta-36.3.8i-r1.ebuild
+++ /dev/null
@@ -1,85 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit flag-o-matic toolchain-funcs
-
-MY_PV="${PV}_14-Nov-2020"
-
-DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
-HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
-SRC_URI="https://github.com/wrpearson/fasta36/archive/refs/tags/v${MY_PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${PN}36-${MY_PV}"
-
-LICENSE="fasta"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~x64-macos"
-IUSE="debug cpu_flags_x86_sse2"
-
-PATCHES=(
-	"${FILESDIR}/${PN}-36.3.8i-musl-build-fix.patch"
-)
-
-src_prepare() {
-	CC_ALT=
-	CFLAGS_ALT=
-	ALT=
-
-	use debug && append-flags -DDEBUG
-
-	if [[ "$(tc-getCC)" == *icc* ]]; then
-		CC_ALT=icc
-		ALT="${ALT}_icc"
-	else
-		CC_ALT="$(tc-getCC)"
-		use x86 && ALT="32"
-		use amd64 && ALT="64"
-	fi
-
-	if use cpu_flags_x86_sse2 ; then
-		ALT="${ALT}_sse2"
-		append-flags -msse2
-		[[ "$(tc-getCC)" == *icc* ]] || append-flags -ffast-math
-	fi
-
-	export CC_ALT="${CC_ALT}"
-	export ALT="${ALT}"
-
-	# -Werror=lto-type-mismatch
-	# https://bugs.gentoo.org/862267
-	# https://github.com/wrpearson/fasta36/issues/63
-	filter-lto
-
-	sed \
-		-e 's:-ffast-math::g' \
-		-i make/Makefile* || die
-
-	default
-}
-
-src_compile() {
-	emake -C src -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS}" all
-}
-
-src_test() {
-	cd test || die
-	FASTLIBS="../conf" bash test.sh || die
-}
-
-src_install() {
-	dobin bin/*
-
-	pushd bin >/dev/null || die
-		local i
-		for i in *36; do
-			dosym ${i} /usr/bin/${i%36}
-		done
-	popd >/dev/null || die
-
-	insinto /usr/share/${PN}
-	doins -r conf/. data seq
-
-	doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1}
-	dodoc FASTA_LIST README* doc/{README*,readme*,fasta*,changes*}
-}
diff --git a/sci-biology/fasta/fasta-36.3.8i.ebuild b/sci-biology/fasta/fasta-36.3.8i.ebuild
deleted file mode 100644
index 9e377150e889..000000000000
--- a/sci-biology/fasta/fasta-36.3.8i.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit flag-o-matic toolchain-funcs
-
-MY_PV="${PV}_14-Nov-2020"
-
-DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
-HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
-SRC_URI="https://github.com/wrpearson/fasta36/archive/refs/tags/v${MY_PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${PN}36-${MY_PV}"
-
-LICENSE="fasta"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~x64-macos"
-IUSE="debug cpu_flags_x86_sse2"
-
-src_prepare() {
-	CC_ALT=
-	CFLAGS_ALT=
-	ALT=
-
-	use debug && append-flags -DDEBUG
-
-	if [[ "$(tc-getCC)" == *icc* ]]; then
-		CC_ALT=icc
-		ALT="${ALT}_icc"
-	else
-		CC_ALT="$(tc-getCC)"
-		use x86 && ALT="32"
-		use amd64 && ALT="64"
-	fi
-
-	if use cpu_flags_x86_sse2 ; then
-		ALT="${ALT}_sse2"
-		append-flags -msse2
-		[[ "$(tc-getCC)" == *icc* ]] || append-flags -ffast-math
-	fi
-
-	export CC_ALT="${CC_ALT}"
-	export ALT="${ALT}"
-
-	# -Werror=lto-type-mismatch
-	# https://bugs.gentoo.org/862267
-	# https://github.com/wrpearson/fasta36/issues/63
-	filter-lto
-
-	sed \
-		-e 's:-ffast-math::g' \
-		-i make/Makefile* || die
-
-	eapply_user
-}
-
-src_compile() {
-	emake -C src -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS}" all
-}
-
-src_test() {
-	cd test || die
-	FASTLIBS="../conf" bash test.sh || die
-}
-
-src_install() {
-	dobin bin/*
-
-	pushd bin >/dev/null || die
-		local i
-		for i in *36; do
-			dosym ${i} /usr/bin/${i%36}
-		done
-	popd >/dev/null || die
-
-	insinto /usr/share/${PN}
-	doins -r conf/. data seq
-
-	doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1}
-	dodoc FASTA_LIST README* doc/{README*,readme*,fasta*,changes*}
-}
diff --git a/sci-biology/fasta/files/fasta-36.3.8h-ldflags.patch b/sci-biology/fasta/files/fasta-36.3.8h-ldflags.patch
deleted file mode 100644
index 40070d50fe76..000000000000
--- a/sci-biology/fasta/files/fasta-36.3.8h-ldflags.patch
+++ /dev/null
@@ -1,63 +0,0 @@
---- a/make/Makefile.pcom
-+++ b/make/Makefile.pcom
-@@ -216,14 +216,14 @@
- 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB)
- 
- map_db : map_db.c uascii.h ncbl2_head.h
--	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
-+	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
- 
- list_db : list_db.c
--	$(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
-+	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
- 
- 
- lav2ps : lav2plt.o lavplt_ps.o
--	$(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
-+	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
- 
- lav2svg : lav2plt.o lavplt_svg.o
--	$(CC) -DUNIX -o $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
-+	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
---- a/make/Makefile.pcom_s
-+++ b/make/Makefile.pcom_s
-@@ -149,14 +149,14 @@
- 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB)
- 
- map_db : map_db.c uascii.h ncbl2_head.h
--	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
-+	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
- 
- list_db : list_db.c
--	$(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
-+	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
- 
- 
- lav2ps : lav2plt.o lavplt_ps.o
--	$(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
-+	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
- 
- lav2svg : lav2plt.o lavplt_svg.o
--	$(CC) -DUNIX -o $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
-+	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
---- a/make/Makefile.pcom_t
-+++ b/make/Makefile.pcom_t
-@@ -171,14 +171,14 @@
- 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB)
- 
- map_db : map_db.c uascii.h ncbl2_head.h
--	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
-+	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
- 
- list_db : list_db.c
--	$(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
-+	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
- 
- 
- lav2ps : lav2plt.o lavplt_ps.o
--	$(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
-+	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
- 
- lav2svg : lav2plt.o lavplt_svg.o
--	$(CC) -DUNIX -o $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
-+	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
diff --git a/sci-biology/fasta/files/fasta-36.3.8i-musl-build-fix.patch b/sci-biology/fasta/files/fasta-36.3.8i-musl-build-fix.patch
deleted file mode 100644
index 1ce5e0089611..000000000000
--- a/sci-biology/fasta/files/fasta-36.3.8i-musl-build-fix.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-https://patch-diff.githubusercontent.com/raw/wrpearson/fasta36/pull/64.patch
---- a/make/Makefile.linux64_sse2
-+++ b/make/Makefile.linux64_sse2
-@@ -28,7 +28,7 @@ LIB_DB=
- 
- # standard options
- 
--CFLAGS += -DPOSIX_C_SOURCE=2 -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit  -DM10_CONS  -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP  -D_LARGEFILE64_SOURCE  -DBIG_LIB64
-+CFLAGS += -DPOSIX_C_SOURCE=2 -D_GNU_SOURCE -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit  -DM10_CONS  -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP  -D_LARGEFILE64_SOURCE  -DBIG_LIB64
- 
- # -I/usr/include/mysql -DMYSQL_DB
- # -DSUPERFAMNUM -DSFCHAR="'|'" 
--- 
-2.46.0
-
diff --git a/sci-biology/fasta/metadata.xml b/sci-biology/fasta/metadata.xml
deleted file mode 100644
index be62121d4e2d..000000000000
--- a/sci-biology/fasta/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">wrpearson/fasta36</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest
deleted file mode 100644
index cf6d3bc20337..000000000000
--- a/sci-biology/fasttree/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST FastTree-2.1.11.c 395543 BLAKE2B 5bea3fba66ddf077ce42c3e1791505a9fa909bb619e30e0c0370631996d932c63ca172fffc1721ac9f081a16bed3b1c99a9c7f6e4a3bb269b82545e2978904d3 SHA512 2bbb1cc078b04125a55b8c02f65c9fbfb6db894c2fbfdaac8f86cc0084f2579723cdc4f6aa63bf4338b767d0fdaffa8dd503e4126c3f5f700d4f3da9fc085ee5
-DIST FastTreeUPGMA-2.1.11.c 95271 BLAKE2B 1de328881f6452b9c7423c9ed381ab2eb31c4f3ee6426481a6b1089c1359627d4cbbfbea868ebeab9538f82e17f45f1bff8ec07c7370e6432bef6bae449798a8 SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c
-DIST MOTreeComparison-2.1.11.tar.gz 13523 BLAKE2B 97638edd945412ff00e3dfcfc89ec6ea52ae8c43531d5cb680d97e9c62fcad80e861f58ec987abcd2282166dd7886101edba4875531bd9d6ac23df242e0dbd5b SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b
diff --git a/sci-biology/fasttree/fasttree-2.1.11.ebuild b/sci-biology/fasttree/fasttree-2.1.11.ebuild
deleted file mode 100644
index 979e8427e476..000000000000
--- a/sci-biology/fasttree/fasttree-2.1.11.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake
-
-DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees"
-HOMEPAGE="https://morgannprice.github.io/fasttree/"
-SRC_URI="
-	http://www.microbesonline.org/fasttree/FastTree-${PV}.c
-	http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-${PV}.c
-	http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-${PV}.tar.gz
-"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="double-precision openmp cpu_flags_x86_sse3"
-
-REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )"
-
-DOCS=( README )
-
-PATCHES=( "${FILESDIR}"/${P}-format-security.patch )
-
-src_unpack() {
-	mkdir "${S}" || die
-	pushd "${S}" > /dev/null || die
-		unpack ${A}
-		cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die
-		cp "${FILESDIR}"/CMakeLists.txt . || die
-	popd > /dev/null || die
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DVERSION="${PV}"
-		-DHAS_SSE3=$(usex cpu_flags_x86_sse3)
-		-DUSE_OPENMP=$(usex openmp)
-		-DUSE_DOUBLE=$(usex double-precision)
-	)
-	cmake_src_configure
-}
diff --git a/sci-biology/fasttree/files/CMakeLists.txt b/sci-biology/fasttree/files/CMakeLists.txt
deleted file mode 100644
index db60e2594cd7..000000000000
--- a/sci-biology/fasttree/files/CMakeLists.txt
+++ /dev/null
@@ -1,31 +0,0 @@
-cmake_minimum_required (VERSION 3.31)
-project(fasttree C)
-
-include(GNUInstallDirs)
-
-option(USE_OPENMP "Use OpenMP to parallelize many of the steps in computing a tree" ON)
-option(USE_DOUBLE "Use double precision" OFF)
-option(HAS_SSE3 "Use SSE2/SSE3 instructions to speed up some inner loops" ON)
-
-if(USE_OPENMP)
-	set( CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} -DOPENMP -fopenmp" )
-	set( CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -DOPENMP -fopenmp" )
-endif()
-
-if(USE_DOUBLE)
-	set( CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} -DUSE_DOUBLE" )
-endif()
-
-if(NOT HAS_SSE3)
-	set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DNO_SSE" )
-endif()
-
-add_executable(FastTree FastTree-${VERSION}.c)
-add_executable(FastTreeUPGMA FastTreeUPGMA-${VERSION}.c)
-
-target_link_libraries(FastTree m)
-target_link_libraries(FastTreeUPGMA m)
-
-install (TARGETS FastTree FastTreeUPGMA DESTINATION ${CMAKE_INSTALL_BINDIR})
-
-install(FILES MOTree.pm CompareTree.pl CompareToBootstrap.pl DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/fasttree)
diff --git a/sci-biology/fasttree/files/fasttree-2.1.11-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.11-format-security.patch
deleted file mode 100644
index 45023e4215f6..000000000000
--- a/sci-biology/fasttree/files/fasttree-2.1.11-format-security.patch
+++ /dev/null
@@ -1,25 +0,0 @@
- FastTreeUPGMA-2.1.11.c | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/FastTreeUPGMA-2.1.11.c b/FastTreeUPGMA-2.1.11.c
-index af76cb1..4065f42 100644
---- a/FastTreeUPGMA-2.1.11.c
-+++ b/FastTreeUPGMA-2.1.11.c
-@@ -535,7 +535,7 @@ int main(int argc, char **argv) {
-       break;
-   }
-   if(iArg < argc-1) {
--    fprintf(stderr, usage);
-+    fprintf(stderr, "%s", usage);
-     exit(1);
-   }
- 
-@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names,
-       assert(first >= 0);
-       /* Print the name, or the subtree of duplicate names */
-       if (nameNext[first] == -1) {
--	fprintf(fp, names[uniqueFirst[node]]);
-+	fprintf(fp, "%s", names[uniqueFirst[node]]);
-       } else {
- 	fprintf(fp,"(%s:0.0",names[first]);
- 	int iName = nameNext[first];
diff --git a/sci-biology/fasttree/metadata.xml b/sci-biology/fasttree/metadata.xml
deleted file mode 100644
index d0bfe0bf14a2..000000000000
--- a/sci-biology/fasttree/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<use>
-		<flag name="double-precision">
-			use double precision instead of single-precision floating point
-			(2x memroy required)
-		</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">morgannprice/fasttree</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/fastx_toolkit/Manifest b/sci-biology/fastx_toolkit/Manifest
deleted file mode 100644
index abb3cfa08aed..000000000000
--- a/sci-biology/fastx_toolkit/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST fastx_toolkit-0.0.14.tar.bz2 543018 BLAKE2B d61456252ada507efd4cc45ff2f0d54f7a6c55b185d41eb5f5accd7e73184b8b80b2c415b38f8e4ccd687ae715191785a89e64f790fe598ba477901c12d514a1 SHA512 e1df1486e853b3ecee71e677cd6e86246a3993174016111eb84910625dc7ec11d37aff75de7ccefad1e019e75fe72050d6529add2116b759d5056b8096286c05
diff --git a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14-r1.ebuild b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14-r1.ebuild
deleted file mode 100644
index 24c67f24c536..000000000000
--- a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14-r1.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools
-
-DESCRIPTION="Tools for Short Read FASTA/FASTQ file processing"
-HOMEPAGE="http://hannonlab.cshl.edu/fastx_toolkit"
-SRC_URI="https://github.com/agordon/fastx_toolkit/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="sci-biology/libgtextutils:="
-RDEPEND="
-	${DEPEND}
-	dev-perl/PerlIO-gzip
-	dev-perl/GDGraph
-	sci-visualization/gnuplot"
-BDEPEND="virtual/pkgconfig"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-fix-build-system.patch
-	"${FILESDIR}"/${P}-gcc7.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/fastx_toolkit/files/fastx_toolkit-0.0.14-fix-build-system.patch b/sci-biology/fastx_toolkit/files/fastx_toolkit-0.0.14-fix-build-system.patch
deleted file mode 100644
index a8b22579f737..000000000000
--- a/sci-biology/fastx_toolkit/files/fastx_toolkit-0.0.14-fix-build-system.patch
+++ /dev/null
@@ -1,63 +0,0 @@
---- a/configure.ac
-+++ b/configure.ac
-@@ -14,12 +14,12 @@
-         [fastx_toolkit])
- AC_CONFIG_AUX_DIR(config)
- AC_CONFIG_MACRO_DIR([m4])
--AM_CONFIG_HEADER(config.h)
-+AC_CONFIG_HEADERS([config.h])
- AM_INIT_AUTOMAKE([dist-bzip2])
- 
- AC_PROG_CC
- AC_PROG_CXX
--AC_PROG_LIBTOOL
-+LT_INIT
- AX_C_LONG_LONG
- AX_CXX_HEADER_STDCXX_TR1
- AX_CXX_COMPILE_STDCXX_11([noext],[optional])
-@@ -31,9 +31,9 @@
- PKG_CHECK_MODULES([GTEXTUTILS],[gtextutils])
- 
- dnl --enable-wall
--EXTRA_CHECKS="-Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror"
-+EXTRA_CHECKS="-Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal"
- AC_ARG_ENABLE(wall,
--[  --enable-wall          Enable many common GCC warnings (-Wall,-Wextra, -Werror etc., default enabled)],
-+[  --enable-wall          Enable many common GCC warnings (-Wall,-Wextra etc., default enabled)],
- [case "${enableval}" in
-   yes) wall=true ;;
-   no)  wall=false ;;
-@@ -45,22 +45,6 @@
-   CXXFLAGS="${CXXFLAGS} ${EXTRA_CHECKS}"
- fi
- 
--dnl --enable-debug
--AC_ARG_ENABLE(debug,
--[  --enable-debug          Enable debug mode (default enabled)],
--[case "${enableval}" in
--  yes) debug=true ;;
--  no)  debug=false ;;
--  *) AC_MSG_ERROR(bad value ${enableval} for --enable-debug) ;;
--esac],[debug=true])
--if test "$debug" = "true"
--then
--  CFLAGS="${CFLAGS} -DDEBUG -g -O1"
--  CXXFLAGS="${CXXFLAGS} -DDEBUG -g -O1"
--else
--  CFLAGS="${CFLAGS} -O3"
--  CXXFLAGS="${CXXFLAGS} -O3"
--fi
- 
- dnl 'all-static' marco copied from subversion's configure.ac
- dnl Check for --enable-all-static option
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -10,7 +10,7 @@
- 
- EXTRA_DIST = reconf configure README install_galaxy_files.sh
- 
--SUBDIRS = m4 src doc galaxy scripts build_scripts
-+SUBDIRS = src doc galaxy scripts build_scripts
- 
- ACLOCAL_AMFLAGS = -I m4
- 
diff --git a/sci-biology/fastx_toolkit/files/fastx_toolkit-0.0.14-gcc7.patch b/sci-biology/fastx_toolkit/files/fastx_toolkit-0.0.14-gcc7.patch
deleted file mode 100644
index e47717785517..000000000000
--- a/sci-biology/fastx_toolkit/files/fastx_toolkit-0.0.14-gcc7.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/src/fasta_formatter/fasta_formatter.cpp
-+++ b/src/fasta_formatter/fasta_formatter.cpp
-@@ -103,6 +103,7 @@
- 		switch(opt) {
- 		case 'h':
- 			usage();
-+			exit(EXIT_SUCCESS);
- 		
- 		case 'i':
- 			input_filename = optarg;
diff --git a/sci-biology/fastx_toolkit/metadata.xml b/sci-biology/fastx_toolkit/metadata.xml
deleted file mode 100644
index 85393fae8f0d..000000000000
--- a/sci-biology/fastx_toolkit/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">agordon/fastx_toolkit</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/foldingathome/Manifest b/sci-biology/foldingathome/Manifest
deleted file mode 100644
index cfd020a01a88..000000000000
--- a/sci-biology/foldingathome/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST fahclient_7.6.13-64bit-release.tar.bz2 3951134 BLAKE2B 2748b7c1987d166bdda08caf5ff2f331523ff519e24768cd7e111c6d3a93f54c10c88d8adbf733230b6c51547360135dbcb272e5d43fd06d01918481601382a1 SHA512 f39f2990d78d075e1061ceaff9453b703a000770a3422965b7b8a91d1814f8804837628d8a34be5afd914228ef787f699f2488523baad295a8d9c1e3bb4f35cf
-DIST fahclient_7.6.21-64bit-release.tar.bz2 4081015 BLAKE2B b47f99bb2c568ee78dfb8998f6faa6c19aa78492a7882d128917596fa51ca7fb9f02dc0a822b6859ee4b333812f961cbcba504b9b188a3a16e7c5c9489cbfbdb SHA512 b52d97c0169eea8686ac3e52a713bb8513ae2b33a853fbf88a0311569aee22681e9ac87bcc01acdaf31d5af5c3641bd5611d34fcbdbb6c1f0ebbb3fc1efeabdb
diff --git a/sci-biology/foldingathome/files/7.3/folding-conf.d b/sci-biology/foldingathome/files/7.3/folding-conf.d
deleted file mode 100644
index b4e0448226a6..000000000000
--- a/sci-biology/foldingathome/files/7.3/folding-conf.d
+++ /dev/null
@@ -1,10 +0,0 @@
-# Config file for /etc/init.d/foldingathome
-#
-# The f@h client configuration can be found in /opt/foldingathome/config.xml
-# Run /opt/foldingathome/initfolding to reconfigure that.
-#
-# The options that may be passed to the Folding client can be obtained
-# by running /opt/foldingathome/FAHClient --help
-#
-FOLD_OPTS=""
-PIDFILE=/run/folding
diff --git a/sci-biology/foldingathome/foldingathome-7.6.13-r1.ebuild b/sci-biology/foldingathome/foldingathome-7.6.13-r1.ebuild
deleted file mode 100644
index da7afcc45f70..000000000000
--- a/sci-biology/foldingathome/foldingathome-7.6.13-r1.ebuild
+++ /dev/null
@@ -1,138 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit systemd
-
-DESCRIPTION="Folding@Home is a distributed computing project for protein folding"
-HOMEPAGE="https://foldingathome.org/"
-SRC_URI="https://download.foldingathome.org/releases/public/release/fahclient/centos-6.7-64bit/v$(ver_cut 1-2)/fahclient_${PV}-64bit-release.tar.bz2"
-S="${WORKDIR}/fahclient_${PV}-64bit-release"
-
-LICENSE="FAH-EULA-2014 FAH-special-permission"
-SLOT="0"
-KEYWORDS="~amd64"
-RESTRICT="mirror bindist strip"
-
-# Expressly listing all deps, as this is a binpkg and it is doubtful whether
-# i.e. uclibc or clang can provide what is necessary at runtime
-DEPEND="dev-util/patchelf"
-RDEPEND="
-	acct-group/foldingathome
-	acct-group/video
-	acct-user/foldingathome
-	app-arch/bzip2
-	|| (
-		dev-libs/openssl-compat:1.0.0
-		=dev-libs/openssl-1.0*:*
-	)
-	sys-devel/gcc
-	sys-libs/glibc
-	virtual/zlib:=
-"
-
-QA_PREBUILT="opt/foldingathome/*"
-
-pkg_setup() {
-	elog ""
-	elog "Special permission is hereby granted to the Gentoo project to provide an"
-	elog "automated installer package which downloads and installs the Folding@home client"
-	elog "software. Permission is also granted for future Gentoo installer packages on the"
-	elog "condition that they continue to adhere to all of the terms of the accompanying"
-	elog "Folding@home license agreements and display this notice."
-	elog "-- Vijay S. Pande, Stanford University, 07 May 2013"
-	elog ""
-	elog "(ref: http://foldingforum.org/viewtopic.php?f=16&t=22524&p=241992#p241992 )"
-	elog ""
-}
-
-src_install() {
-	patchelf --set-rpath "${EPREFIX}/opt/foldingathome" FAHClient || die
-	patchelf --set-rpath "${EPREFIX}/opt/foldingathome" FAHCoreWrapper || die
-
-	dosym "../../usr/$(get_libdir)/libssl.so.1.0.0" /opt/foldingathome/libssl.so.10
-	dosym "../../usr/$(get_libdir)/libcrypto.so.1.0.0" /opt/foldingathome/libcrypto.so.10
-
-	exeinto /opt/foldingathome
-	doexe {FAHClient,FAHCoreWrapper}
-
-	insinto /opt/foldingathome
-	doins sample-config.xml
-
-	newconfd "${FILESDIR}"/7.3/folding-conf.d foldingathome
-	cat <<EOF >"${T}"/fah-init
-#!/sbin/openrc-run
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-start_stop_daemon_args="--chdir \"${EPREFIX}/opt/foldingathome\""
-command="${EPREFIX}/opt/foldingathome/FAHClient"
-command_args="\${FOLD_OPTS}"
-command_user=foldingathome
-command_background=1
-pidfile="\${PIDFILE}"
-EOF
-	newinitd "${T}"/fah-init foldingathome
-
-	cat <<EOF >"${T}"/fah-init.service
-[Unit]
-Description=Folding@Home V7 Client
-Documentation=https://foldingathome.org
-
-[Service]
-Type=simple
-User=foldingathome
-Group=foldingathome
-Nice=19
-WorkingDirectory=${EPREFIX}/opt/foldingathome
-ExecStart=${EPREFIX}/opt/foldingathome/FAHClient --fork=false --pid=false --respawn=false --service=false
-NoNewPrivileges=yes
-PrivateTmp=yes
-ProtectControlGroups=yes
-ProtectSystem=full
-RestrictRealtime=true
-ProtectControlGroups=yes
-
-[Install]
-WantedBy=multi-user.target
-EOF
-	systemd_newunit "${T}"/fah-init.service foldingathome.service
-
-	fowners -R foldingathome:foldingathome /opt/foldingathome
-}
-
-pkg_postinst() {
-	elog "To run Folding@home in the background at boot:"
-	elog "(openrc)\trc-update add foldingathome default"
-	elog "(systemd)\tsystemctl enable foldingathome"
-	elog ""
-	if [ ! -e "${EPREFIX}"/opt/foldingathome/config.xml ]; then
-		elog "No config.xml file found -- please run"
-		elog "emerge --config ${P} to configure your client, or specify"
-		elog "all necessary runtime options in FOLD_OPTS within"
-		elog "${EPREFIX}/etc/conf.d/foldingathome"
-		elog ""
-	fi
-	if [[ -n ${REPLACING_VERSIONS} ]]; then
-		elog "NOTE, the 'initfolding' helper script has been dropped, please"
-		elog "use emerge --config ${P} or run FAHClient --configure directly"
-		elog "and adjust file permissions and ownership yourself"
-		elog ""
-	fi
-	elog "Please see ${EPREFIX}/opt/foldingathome/FAHClient --help for more details."
-	einfo ""
-	einfo "The original package maintainer encourages you to acquire a username and join team 36480."
-	einfo "http://folding.stanford.edu/English/Download#ntoc2"
-	einfo ""
-}
-
-pkg_postrm() {
-	elog "Folding@home data files were not removed."
-	elog "Remove them manually from ${EPREFIX}/opt/foldingathome"
-}
-
-pkg_config() {
-	cd "${EPREFIX}"/opt/foldingathome || die
-	su foldingathome -s /bin/sh -c "./FAHClient --configure"
-}
diff --git a/sci-biology/foldingathome/foldingathome-7.6.21.ebuild b/sci-biology/foldingathome/foldingathome-7.6.21.ebuild
deleted file mode 100644
index 8d312ae14720..000000000000
--- a/sci-biology/foldingathome/foldingathome-7.6.21.ebuild
+++ /dev/null
@@ -1,138 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit systemd
-
-DESCRIPTION="Folding@Home is a distributed computing project for protein folding"
-HOMEPAGE="https://foldingathome.org/"
-SRC_URI="https://download.foldingathome.org/releases/public/release/fahclient/centos-6.7-64bit/v$(ver_cut 1-2)/fahclient_${PV}-64bit-release.tar.bz2"
-S="${WORKDIR}/fahclient_${PV}-64bit-release"
-
-LICENSE="FAH-EULA-2014 FAH-special-permission"
-SLOT="0"
-KEYWORDS="~amd64"
-RESTRICT="mirror bindist strip"
-
-# Expressly listing all deps, as this is a binpkg and it is doubtful whether
-# i.e. uclibc or clang can provide what is necessary at runtime
-DEPEND="dev-util/patchelf"
-RDEPEND="
-	acct-group/foldingathome
-	acct-group/video
-	acct-user/foldingathome
-	app-arch/bzip2
-	|| (
-		dev-libs/openssl-compat:1.0.0
-		=dev-libs/openssl-1.0*:*
-	)
-	sys-devel/gcc
-	sys-libs/glibc
-	virtual/zlib:=
-"
-
-QA_PREBUILT="opt/foldingathome/*"
-
-pkg_setup() {
-	elog ""
-	elog "Special permission is hereby granted to the Gentoo project to provide an"
-	elog "automated installer package which downloads and installs the Folding@home client"
-	elog "software. Permission is also granted for future Gentoo installer packages on the"
-	elog "condition that they continue to adhere to all of the terms of the accompanying"
-	elog "Folding@home license agreements and display this notice."
-	elog "-- Vijay S. Pande, Stanford University, 07 May 2013"
-	elog ""
-	elog "(ref: http://foldingforum.org/viewtopic.php?f=16&t=22524&p=241992#p241992 )"
-	elog ""
-}
-
-src_install() {
-	patchelf --set-rpath "${EPREFIX}/opt/foldingathome" FAHClient || die
-	patchelf --set-rpath "${EPREFIX}/opt/foldingathome" FAHCoreWrapper || die
-
-	dosym "../../usr/$(get_libdir)/libssl.so.1.0.0" /opt/foldingathome/libssl.so.10
-	dosym "../../usr/$(get_libdir)/libcrypto.so.1.0.0" /opt/foldingathome/libcrypto.so.10
-
-	exeinto /opt/foldingathome
-	doexe {FAHClient,FAHCoreWrapper}
-
-	insinto /opt/foldingathome
-	doins sample-config.xml
-
-	newconfd "${FILESDIR}"/7.3/folding-conf.d foldingathome
-	cat <<EOF >"${T}"/fah-init || die
-#!/sbin/openrc-run
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-start_stop_daemon_args="--chdir \"${EPREFIX}/opt/foldingathome\""
-command="${EPREFIX}/opt/foldingathome/FAHClient"
-command_args="\${FOLD_OPTS}"
-command_user=foldingathome
-command_background=1
-pidfile="\${PIDFILE}"
-EOF
-	newinitd "${T}"/fah-init foldingathome
-
-	cat <<EOF >"${T}"/fah-init.service || die
-[Unit]
-Description=Folding@Home V7 Client
-Documentation=https://foldingathome.org
-
-[Service]
-Type=simple
-User=foldingathome
-Group=foldingathome
-Nice=19
-WorkingDirectory=${EPREFIX}/opt/foldingathome
-ExecStart=${EPREFIX}/opt/foldingathome/FAHClient --fork=false --pid=false --respawn=false --service=false
-NoNewPrivileges=yes
-PrivateTmp=yes
-ProtectControlGroups=yes
-ProtectSystem=full
-RestrictRealtime=true
-ProtectControlGroups=yes
-
-[Install]
-WantedBy=multi-user.target
-EOF
-	systemd_newunit "${T}"/fah-init.service foldingathome.service
-
-	fowners -R foldingathome:foldingathome /opt/foldingathome
-}
-
-pkg_postinst() {
-	elog "To run Folding@home in the background at boot:"
-	elog "(openrc)\trc-update add foldingathome default"
-	elog "(systemd)\tsystemctl enable foldingathome"
-	elog ""
-	if [ ! -e "${EPREFIX}"/opt/foldingathome/config.xml ]; then
-		elog "No config.xml file found -- please run"
-		elog "emerge --config ${P} to configure your client, or specify"
-		elog "all necessary runtime options in FOLD_OPTS within"
-		elog "${EPREFIX}/etc/conf.d/foldingathome"
-		elog ""
-	fi
-	if [[ -n ${REPLACING_VERSIONS} ]]; then
-		elog "NOTE, the 'initfolding' helper script has been dropped, please"
-		elog "use emerge --config ${P} or run FAHClient --configure directly"
-		elog "and adjust file permissions and ownership yourself"
-		elog ""
-	fi
-	elog "Please see ${EPREFIX}/opt/foldingathome/FAHClient --help for more details."
-	einfo ""
-	einfo "The original package maintainer encourages you to acquire a username and join team 36480."
-	einfo "http://folding.stanford.edu/English/Download#ntoc2"
-	einfo ""
-}
-
-pkg_postrm() {
-	elog "Folding@home data files were not removed."
-	elog "Remove them manually from ${EPREFIX}/opt/foldingathome"
-}
-
-pkg_config() {
-	cd "${EPREFIX}"/opt/foldingathome || die
-	su foldingathome -s /bin/sh -c "./FAHClient --configure" || die
-}
diff --git a/sci-biology/foldingathome/metadata.xml b/sci-biology/foldingathome/metadata.xml
deleted file mode 100644
index b5b66eeee084..000000000000
--- a/sci-biology/foldingathome/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<maintainer type="project">
-	<email>sci-biology@gentoo.org</email>
-	<name>Gentoo Biology Project</name>
-</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/geneathome/Manifest b/sci-biology/geneathome/Manifest
deleted file mode 100644
index 806447644dd0..000000000000
--- a/sci-biology/geneathome/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST geneathome-1.10.tar.gz 73686241 BLAKE2B 4a4e9930e3faeaf0b6d687d26adb3267af1a70096397e9e4001066a7029a854b95cd35b6779a0e6bcf6c9cb3ad662b5f9e6adf4ab9d608ed2d73c65d3dadc10b SHA512 c8c1bb65f0021d9c9d9f14375212c458694dbb21abbfa90f6b8fb958bc6d86a522bbe13846b5930f6df0a4e755256f2016c5edd4447ae147cb1381eccce06b9e
diff --git a/sci-biology/geneathome/files/app_info.xml b/sci-biology/geneathome/files/app_info.xml
deleted file mode 100644
index 82ce7a9cd93a..000000000000
--- a/sci-biology/geneathome/files/app_info.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<app_info>
-<app>
-	<name>gene_pcim</name>
-	<user_friendly_name>gene@home PC-IM</user_friendly_name>
-</app>
-
-<file_info>
-	<name>gene_pcim_v@PV@</name>
-	<sticky/>
-	<executable/>
-</file_info>
-
-<app_version>
-	<app_name>gene_pcim</app_name>
-	<version_num>110</version_num>
-	<plan_class>avx</plan_class>
-	<file_ref>
-		<file_name>gene_pcim_v@PV@</file_name>
-		<main_program/>
-	</file_ref>
-</app_version>
-</app_info>
diff --git a/sci-biology/geneathome/files/geneathome-1.10-include.patch b/sci-biology/geneathome/files/geneathome-1.10-include.patch
deleted file mode 100644
index 9130b88e30e5..000000000000
--- a/sci-biology/geneathome/files/geneathome-1.10-include.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-Fixes build with GCC 13.
-
---- a/src/simd/Vector.hpp
-+++ b/src/simd/Vector.hpp
-@@ -23,6 +23,7 @@
- 
- #include <type_traits>
- #include <cassert>
-+#include <cstdint>
- 
- // std::negation requires C++17, so defined own one
- template<typename B>
diff --git a/sci-biology/geneathome/files/geneathome-1.10-iostream.patch b/sci-biology/geneathome/files/geneathome-1.10-iostream.patch
deleted file mode 100644
index 24d47cee4038..000000000000
--- a/sci-biology/geneathome/files/geneathome-1.10-iostream.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-Fixes "inlining failed in call to ..."
-
---- a/src/main.cpp
-+++ b/src/main.cpp
-@@ -22,8 +22,8 @@ int appMain(int argc, char* argv[]);
- 
- #if defined(__i386__) || defined (__x86_64__)
- 
-+#include <iostream>
- #include <cpuid.h>
--#include <stdio.h>
- 
- __attribute__((target("no-avx,no-sse")))
- bool checkRequiredInstructionSets() {
-@@ -34,14 +34,14 @@ bool checkRequiredInstructionSets() {
- 	unsigned int a, b, c, d;
- 
- 	if (!__get_cpuid(1, &a, &b, &c, &d)) {
--		fprintf(stderr, "CPUID instruction is not supported by your CPU!\n");
-+		std::cerr << "CPUID instruction is not supported by your CPU!\n";
- 		return false;
- 	}
- 
- #ifdef __SSE2__
- 	//printf("Checking for SSE2 support\n");
- 	if (0 == (d & bit_SSE2)) {
--		fprintf(stderr, "SSE2 instructions are not supported by your CPU!\n");
-+		std::cerr << "SSE2 instructions are not supported by your CPU!\n";
- 		return false;
- 	}
- #endif
-@@ -49,13 +49,13 @@ bool checkRequiredInstructionSets() {
- #ifdef __AVX__
- 	//printf("Checking for AVX support\n");
- 	if (0 == (c & bit_AVX)) {
--		fprintf(stderr, "AVX instructions are not supported by your CPU!\n");
-+		std::cerr << "AVX instructions are not supported by your CPU!\n";
- 		return false;
- 	}
- 
- 	// AVX also needs OS support, check for it
- 	if (0 == (c & bit_OSXSAVE)) {
--		fprintf(stderr, "OSXSAVE instructions are not supported by your CPU!\n");
-+		std::cerr << "OSXSAVE instructions are not supported by your CPU!\n";
- 		return false;
- 	}
- 
-@@ -63,7 +63,7 @@ bool checkRequiredInstructionSets() {
- 	unsigned int ecx = 0; // _XCR_XFEATURE_ENABLED_MASK
- 	__asm__ ("xgetbv" : "=a" (eax), "=d" (edx) : "c" (ecx));
- 	if (0x6 != (eax & 0x6)) { // XSTATE_SSE | XSTATE_YMM
--		fprintf(stderr, "AVX instructions are not supported by your OS!\n");
-+		std::cerr << "AVX instructions are not supported by your OS!\n";
- 		return false;
- 	}
- #endif
-@@ -71,7 +71,7 @@ bool checkRequiredInstructionSets() {
- #ifdef __FMA__
- 	//printf("Checking for FMA support\n");
- 	if (0 == (c & bit_FMA)) {
--		fprintf(stderr, "FMA instructions are not supported by your CPU!\n");
-+		std::cerr << "FMA instructions are not supported by your CPU!\n";
- 		return false;
- 	}
- #endif
-@@ -79,14 +79,14 @@ bool checkRequiredInstructionSets() {
- #ifdef __AVX2__
- 	//printf("Checking for AVX2 support\n");
- 	if (__get_cpuid_max(0, 0) < 7) {
--		fprintf(stderr, "Extended CPUID 0x7 instruction is not supported by your CPU!\n");
-+		std::cerr << "Extended CPUID 0x7 instruction is not supported by your CPU!\n";
- 		return false;
- 	}
- 
- 	__cpuid_count(7, 0, a, b, c, d);
- 
- 	if (0 == (b & bit_AVX2)) {
--		fprintf(stderr, "AVX2 instructions are not supported by your CPU!\n");
-+		std::cerr << "AVX2 instructions are not supported by your CPU!\n";
- 		return false;
- 	}
- #endif
diff --git a/sci-biology/geneathome/files/geneathome-1.10-makefile.patch b/sci-biology/geneathome/files/geneathome-1.10-makefile.patch
deleted file mode 100644
index 7025b694df36..000000000000
--- a/sci-biology/geneathome/files/geneathome-1.10-makefile.patch
+++ /dev/null
@@ -1,44 +0,0 @@
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -22,20 +22,16 @@
- BOINC_DIR ?= ../../..
- BOINC_API_DIR ?= $(BOINC_DIR)/api
- BOINC_LIB_DIR ?= $(BOINC_DIR)/lib
--BOINC_ZIP_DIR ?= $(BOINC_DIR)/zip
--BOINC_LIBS ?= $(BOINC_API_DIR)/libboinc_api.a $(BOINC_LIB_DIR)/libboinc.a
-+BOINC_LIBS ?= -lboinc_api -lboinc
- 
- ifdef BOINC_STUB
- BOINC_DIR = ../boinc_stub
- BOINC_LIBS =
- endif
- 
--FREETYPE_DIR = /usr/include/freetype2
--CPPFLAGS += -I$(BOINC_DIR) -I$(BOINC_LIB_DIR) -I$(BOINC_API_DIR) -I$(BOINC_ZIP_DIR) -I$(FREETYPE_DIR) -Isimd
--CFLAGS += -c -O3 $(ARCH) -Wall -Wextra -pedantic -Werror $(VARIANTFLAGS)  -MMD -MP
--CXXFLAGS += $(CFLAGS) -std=gnu++11
--LDFLAGS += $(ARCH) -L/usr/X11R6/lib -L. -static
--LIBS ?= -static-libgcc -static-libstdc++ -pthread -Wl,-Bstatic -lbz2
-+CPPFLAGS += -I$(BOINC_DIR) -Isimd
-+CXXFLAGS += -std=gnu++11
-+LIBS ?= -pthread -lbz2
- CXXSOURCES = BoincFile.cpp Graph.cpp boinc_functions.cpp utility.cpp pc.cpp main.cpp
- CSOURCES = erf.c
- OBJECTS = $(CXXSOURCES:.cpp=.o) $(CSOURCES:.c=.o)
-@@ -44,13 +40,13 @@
- all: $(EXECUTABLE)
- 
- $(EXECUTABLE): $(OBJECTS)
--	$(CXX) $(LDFLAGS) $(OBJECTS) -o $@ $(LIBS) $(BOINC_LIBS)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS) $(BOINC_LIBS)
- 
- .cpp.o:
--	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $< -o $@
-+	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@
- 
- .c.o:
--	$(CC) $(CPPFLAGS) $(CFLAGS) $< -o $@
-+	$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@
- 
- clean:
- 	rm -rf ../bin/$(EXECUTABLE) *.o *~ *.d
diff --git a/sci-biology/geneathome/geneathome-1.10-r5.ebuild b/sci-biology/geneathome/geneathome-1.10-r5.ebuild
deleted file mode 100644
index 64c1db7d3acd..000000000000
--- a/sci-biology/geneathome/geneathome-1.10-r5.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-BOINC_MASTER_URL="https://gene.disi.unitn.it/test/"
-BOINC_INVITATION_CODE="science@tn"
-BOINC_HELPTEXT=\
-"gene@home is a part of TN-Grid BOINC project."
-
-inherit boinc-app edo toolchain-funcs
-
-MY_PN="pc-boinc"
-COMMIT="3186afba409a"
-
-DESCRIPTION="BOINC application for expanding Gene Regulatory Networks (GRN)"
-HOMEPAGE+=" https://bitbucket.org/francesco-asnicar/pc-boinc"
-SRC_URI="https://bitbucket.org/francesco-asnicar/${MY_PN}/get/${COMMIT}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/francesco-asnicar-${MY_PN}-${COMMIT}"
-
-LICENSE="sunpro public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~arm64 ~x86"
-
-DEPEND="app-arch/bzip2"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.10-include.patch
-	"${FILESDIR}"/${PN}-1.10-iostream.patch
-	"${FILESDIR}"/${PN}-1.10-makefile.patch
-)
-
-DOCS=( Readme.md )
-
-boinc-app_add_deps
-
-src_compile() {
-	tc-export CC CXX
-
-	emake -C src BOINC_DIR="${ESYSROOT}"/usr/include/boinc
-}
-
-src_test() {
-	edo bash ./test_run.sh
-	edo bash ./test_run2.sh
-}
-
-src_install() {
-	doappinfo "${FILESDIR}"/app_info.xml
-
-	exeinto $(get_project_root)
-	exeopts -m 0755 --owner root --group boinc
-	newexe bin/pc "gene_pcim_v${PV}"
-}
diff --git a/sci-biology/geneathome/metadata.xml b/sci-biology/geneathome/metadata.xml
deleted file mode 100644
index 7ad3b4b682c6..000000000000
--- a/sci-biology/geneathome/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<upstream>
-		<remote-id type="bitbucket">francesco-asnicar/pc-boinc</remote-id>
-	</upstream>
-	<!-- maintainer-needed -->
-</pkgmetadata>
diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest
deleted file mode 100644
index aa2a22056a4f..000000000000
--- a/sci-biology/glimmer/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST glimmer302b.tar.gz 5637975 BLAKE2B 76c0b19fe08e9ece3e930fe3e53444a2b620e565ac3c83db484294627403e34c3ab77165e4b82176282df340fe47672bf28e5694edbcea9e17a57b61a502ae11 SHA512 00d44a02a8099ceac4b4d2a1cd5d69cc2b787942bb87f612cd63edacf7e502bc9a65cdf9b9270ad789981a84c940cc01e187882d21d2c9de4dcc12b492b041a6
diff --git a/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch
deleted file mode 100644
index 91498b116d12..000000000000
--- a/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff -ru glimmer3.02-orig/src/Makefile glimmer3.02/src/Makefile
---- glimmer3.02-orig/src/Makefile	2006-06-12 21:40:14.000000000 +0200
-+++ glimmer3.02/src/Makefile	2010-03-18 14:30:15.000000000 +0100
-@@ -2,12 +2,12 @@
- 
- 
- all:
--	@ TGT=objs
--	@ $(dosubdirs)
--	@ TGT=libs
--	@ $(dosubdirs)
--	@ TGT=progs
--	@ $(dosubdirs)
-+	@+ TGT=objs
-+	@+ $(dosubdirs)
-+	@+ TGT=libs
-+	@+ $(dosubdirs)
-+	@+ TGT=progs
-+	@+ $(dosubdirs)
- 
- 
- install: all
diff --git a/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch
deleted file mode 100644
index dc41ef00de7e..000000000000
--- a/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch
+++ /dev/null
@@ -1,92 +0,0 @@
---- a/src/c_make.gen
-+++ b/src/c_make.gen
-@@ -200,45 +200,11 @@
- #### Do not redefine if (a) passed in on command line, or (b)
- #### defined in an environment variable.
- 
--ifneq "$(origin CC)" "environment"
--CC      = cc
--endif
--
--ifneq "$(origin CPPFLAGS)" "environment"
--CPPFLAGS=
--endif
--
--ifneq "$(origin CFLAGS)" "environment"
--CFLAGS  =
--endif
--
--ifneq "$(origin CDEFS)" "environment"
--CDEFS  =
--endif
--
--ifneq "$(origin CXX)" "environment"
--CXX	= g++
--endif
--
--ifneq "$(origin CXXFLAGS)" "environment"
--CXXFLAGS=
--endif
--
--ifneq "$(origin CXXDEFS)" "environment"
--CXXDEFS= -D__cplusplus
--endif
--
--ifneq "$(origin AR)" "environment"
--AR      = ar
--endif
--
--ifneq "$(origin ARFLAGS)" "environment"
--ARFLAGS = rvs
--endif
--
--ifneq "$(origin LDFLAGS)" "environment"
--LDFLAGS =
--endif
-+CC      ?= cc
-+CXX	?= g++
-+CXXFLAGS ?=
-+AR      ?= ar
-+ARFLAGS ?= rvs
- 
- #### Delete default suffix rules
- .SUFFIXES:
-@@ -359,13 +325,13 @@
- 	  cd $(LOCAL_OBJ); \
- 	    if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \
-                $(LD_DIRS) $(filter-out lib%.a, $+) \
--	       $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \
-+	       $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \
- 			true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \
- 	else \
- 	  cd $(LOCAL_OBJ); \
- 	    if $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \
-                $(LD_DIRS) $(filter-out lib%.a, $+) \
--	       $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \
-+	       $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \
- 			true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \
- 	fi ;
- 
---- a/src/c_make.glm
-+++ b/src/c_make.glm
-@@ -8,18 +8,14 @@
- 
- SUBDIRS = Common ICM Glimmer Util
- 
--CFLAGS = -g -Wall
--CXXFLAGS = -g -Wall
--
--LDFLAGS = -g -lm
-+LIBS = -lm
- 
- 
- #AS_BUILD_DIR =$(LOCAL_WORK)
- INC_IMPORT_DIRS += \
- 		$(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) \
-                 $(LOCAL_WORK)/inc
--LIB_IMPORT_DIRS += $(LOCAL_WORK)/lib /usr/lib /usr/shlib /usr/X11R6/lib \
--     $(SYBASE)/lib
-+LIB_IMPORT_DIRS += $(LOCAL_WORK)/lib
- 
- OBJ_SEARCH_PATH = $(LOCAL_WORK)/obj
- 
diff --git a/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch b/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch
deleted file mode 100644
index 6eebc5610414..000000000000
--- a/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch
+++ /dev/null
@@ -1,196 +0,0 @@
-diff -r -u glimmer3.02.old/docs/notes.tex glimmer3.02/docs/notes.tex
---- glimmer3.02.old/docs/notes.tex	2006-06-12 21:40:14.000000000 +0200
-+++ glimmer3.02/docs/notes.tex	2015-05-25 22:41:39.450340098 +0200
-@@ -306,7 +306,7 @@
-   The script would then run the commands:
- \BSV\begin{verbatim}
-   long-orfs -n -t 1.15 genom.seq run1.longorfs
--  extract -t genom.seq run1.longorfs > run1.train
-+  glimmer_extract -t genom.seq run1.longorfs > run1.train
-   build-icm -r run1.icm < run1.train
-   glimmer3 -o50 -g110 -t30 genom.seq run1.icm run1
- \end{verbatim}\ESV
-@@ -330,9 +330,9 @@
- \end{verbatim}\ESV
-   The script would then run the commands:
- \BSV\begin{verbatim}
--  extract -t genom.seq train.coords > run2.train
-+  glimmer_extract -t genom.seq train.coords > run2.train
-   build-icm -r run2.icm < run2.train
--  upstream-coords.awk 25 0 train.coords | extract genom.seq - > run2.upstream
-+  upstream-coords.awk 25 0 train.coords | glimmer_extract genom.seq - > run2.upstream
-   elph run2.upstream LEN=6 | get-motif-counts.awk > run2.motif
-   set startuse = `start-codon-distrib -3 genom.seq train.coords`
-   glimmer3 -o50 -g110 -t30 -b run2.motif -P $startuse genom.seq run2.icm run2
-@@ -358,11 +358,11 @@
-   The script would then run the commands:
- \BSV\begin{verbatim}
-   long-orfs -n -t 1.15 genom.seq run3.longorfs
--  extract -t genom.seq run3.longorfs > run3.train
-+  glimmer_extract -t genom.seq run3.longorfs > run3.train
-   build-icm -r run3.icm < run3.train
-   glimmer3 -o50 -g110 -t30 genom.seq run3.icm run3.run1
-   tail +2 run3.run1.predict > run3.coords
--  upstream-coords.awk 25 0 run3.coords | extract genom.seq - > run3.upstream
-+  upstream-coords.awk 25 0 run3.coords | glimmer_extract genom.seq - > run3.upstream
-   elph run3.upstream LEN=6 | get-motif-counts.awk > run3.motif
-   set startuse = `start-codon-distrib -3 genom.seq run3.coords`
-   glimmer3 -o50 -g110 -t30 -b run3.motif -P $startuse genom.seq run3.icm run3
-@@ -1081,12 +1081,12 @@
-   \Pg{entropy-score}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
- \eq
- 
--\subsubsection{\Pg{extract} Program}
-+\subsubsection{\Pg{glimmer_extract} Program}
- This program reads a genome sequence and a list of coordinates
- for it and outputs a multi-fasta file of the regions specified
- by the coordinates.  Output goes to standard output.
- \bq
--  \Pg{extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
-+  \Pg{glimmer_extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
- \eq
- 
- \subsubsection{\Pg{multi-extract} Program}
-diff -r -u glimmer3.02.old/sample-run/g3-from-scratch.csh glimmer3.02/sample-run/g3-from-scratch.csh
---- glimmer3.02.old/sample-run/g3-from-scratch.csh	2006-06-12 21:46:35.000000000 +0200
-+++ glimmer3.02/sample-run/g3-from-scratch.csh	2015-05-25 22:40:18.450338748 +0200
-@@ -50,7 +50,7 @@
- step2:
- # Extract the training sequences from the genome file
- echo "Step 2 of ${numsteps}:  Extracting training sequences"
--$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
-+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
- if  ($status != 0)  then
-   echo "Failed to extract training sequences"
-   exit
-diff -r -u glimmer3.02.old/sample-run/g3-from-training.csh glimmer3.02/sample-run/g3-from-training.csh
---- glimmer3.02.old/sample-run/g3-from-training.csh	2006-06-12 21:46:35.000000000 +0200
-+++ glimmer3.02/sample-run/g3-from-training.csh	2015-05-25 22:40:18.450338748 +0200
-@@ -42,7 +42,7 @@
- step1:
- # Extract the training sequences from the genome file
- echo "Step 1 of ${numsteps}:  Extracting training sequences"
--$glimmerpath/extract -t $genome $coords > $tag.train
-+$glimmerpath/glimmer_extract -t $genome $coords > $tag.train
- if  ($status != 0)  then
-   echo "Failed to extract training sequences"
-   exit
-@@ -66,7 +66,7 @@
- # upstream of the start locations in $coords
- echo "Step 3 of ${numsteps}:  Making PWM from upstream regions"
- $awkpath/upstream-coords.awk 25 0 $coords \
--   | $glimmerpath/extract $genome - > $tag.upstream
-+   | $glimmerpath/glimmer_extract $genome - > $tag.upstream
- $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
- if  ($status != 0)  then
-   echo "Failed to create PWM"
-diff -r -u glimmer3.02.old/sample-run/g3-iterated.csh glimmer3.02/sample-run/g3-iterated.csh
---- glimmer3.02.old/sample-run/g3-iterated.csh	2006-06-13 14:15:28.000000000 +0200
-+++ glimmer3.02/sample-run/g3-iterated.csh	2015-05-25 22:40:18.450338748 +0200
-@@ -57,7 +57,7 @@
- step2:
- # Extract the training sequences from the genome file
- echo "Step 2 of ${numsteps}:  Extracting training sequences"
--$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
-+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
- if  ($status != 0)  then
-   echo "Failed to extract training sequences"
-   exit
-@@ -103,7 +103,7 @@
- # upstream of the start locations in $tag.coords
- echo "Step 6 of ${numsteps}:  Making PWM from upstream regions"
- $awkpath/upstream-coords.awk 25 0 $tag.coords \
--   | $glimmerpath/extract $genome - > $tag.upstream
-+   | $glimmerpath/glimmer_extract $genome - > $tag.upstream
- $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
- if  ($status != 0)  then
-   echo "Failed to create PWM"
-diff -r -u glimmer3.02.old/scripts/g3-from-scratch.csh glimmer3.02/scripts/g3-from-scratch.csh
---- glimmer3.02.old/scripts/g3-from-scratch.csh	2006-06-12 21:40:14.000000000 +0200
-+++ glimmer3.02/scripts/g3-from-scratch.csh	2015-05-25 22:44:44.190343177 +0200
-@@ -50,7 +50,7 @@
- step2:
- # Extract the training sequences from the genome file
- echo "Step 2 of ${numsteps}:  Extracting training sequences"
--$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
-+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
- if  ($status != 0)  then
-   echo "Failed to extract training sequences"
-   exit
-diff -r -u glimmer3.02.old/scripts/g3-from-training.csh glimmer3.02/scripts/g3-from-training.csh
---- glimmer3.02.old/scripts/g3-from-training.csh	2006-06-12 21:40:14.000000000 +0200
-+++ glimmer3.02/scripts/g3-from-training.csh	2015-05-25 22:44:44.190343177 +0200
-@@ -42,7 +42,7 @@
- step1:
- # Extract the training sequences from the genome file
- echo "Step 1 of ${numsteps}:  Extracting training sequences"
--$glimmerpath/extract -t $genome $coords > $tag.train
-+$glimmerpath/glimmer_extract -t $genome $coords > $tag.train
- if  ($status != 0)  then
-   echo "Failed to extract training sequences"
-   exit
-@@ -66,7 +66,7 @@
- # upstream of the start locations in $coords
- echo "Step 3 of ${numsteps}:  Making PWM from upstream regions"
- $awkpath/upstream-coords.awk 25 0 $coords \
--   | $glimmerpath/extract $genome - > $tag.upstream
-+   | $glimmerpath/glimmer_extract $genome - > $tag.upstream
- $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
- if  ($status != 0)  then
-   echo "Failed to create PWM"
-diff -r -u glimmer3.02.old/scripts/g3-iterated.csh glimmer3.02/scripts/g3-iterated.csh
---- glimmer3.02.old/scripts/g3-iterated.csh	2006-06-13 14:15:46.000000000 +0200
-+++ glimmer3.02/scripts/g3-iterated.csh	2015-05-25 22:44:44.190343177 +0200
-@@ -57,7 +57,7 @@
- step2:
- # Extract the training sequences from the genome file
- echo "Step 2 of ${numsteps}:  Extracting training sequences"
--$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
-+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
- if  ($status != 0)  then
-   echo "Failed to extract training sequences"
-   exit
-@@ -103,7 +103,7 @@
- # upstream of the start locations in $tag.coords
- echo "Step 6 of ${numsteps}:  Making PWM from upstream regions"
- $awkpath/upstream-coords.awk 25 0 $tag.coords \
--   | $glimmerpath/extract $genome - > $tag.upstream
-+   | $glimmerpath/glimmer_extract $genome - > $tag.upstream
- $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
- if  ($status != 0)  then
-   echo "Failed to create PWM"
-diff -r -u glimmer3.02.old/src/Util/Makefile glimmer3.02/src/Util/Makefile
---- glimmer3.02.old/src/Util/Makefile	2006-06-12 21:40:14.000000000 +0200
-+++ glimmer3.02/src/Util/Makefile	2015-05-25 22:43:12.760341653 +0200
-@@ -8,7 +8,7 @@
- SOURCES = $(UTIL_SRCS)
- OBJECTS = $(UTIL_OBJS)
- 
--PROGS = entropy-profile entropy-score extract multi-extract start-codon-distrib \
-+PROGS = entropy-profile entropy-score glimmer_extract multi-extract start-codon-distrib \
-   uncovered window-acgt
- 
- LIBRARIES = 
-diff -r -u glimmer3.02.old/src/Util/extract.cc glimmer3.02/src/Util/extract.cc
---- glimmer3.02.old/src/Util/extract.cc	2006-06-12 21:40:14.000000000 +0200
-+++ glimmer3.02/src/Util/extract.cc	2015-05-25 22:44:01.760342470 +0200
-@@ -297,7 +297,7 @@
- 
-   {
-    fprintf (stderr,
--       "USAGE:  extract [options] <sequence-file> <coords>\n"
-+       "USAGE:  glimmer_extract [options] <sequence-file> <coords>\n"
-        "\n"
-        "Read fasta-format <sequence-file> and extract from it the\n"
-        "subsequences specified by <coords>.  By default, <coords>\n"
---- glimmer3.02.old/src/Util/Makefile	2015-05-25 22:43:12.760341653 +0200
-+++ glimmer-3.02-r3/work/glimmer3.02/src/Util/Makefile	2015-05-25 23:13:34.230372010 +0200
-@@ -21,7 +21,7 @@
- 
- entropy-score:  entropy-score.o libGLMcommon.a
- 
--extract:  extract.o libGLMcommon.a
-+glimmer_extract:  extract.o libGLMcommon.a
- 
- multi-extract:  multi-extract.o libGLMcommon.a
- 
diff --git a/sci-biology/glimmer/glimmer-3.02b.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild
deleted file mode 100644
index 35bea17dd8ab..000000000000
--- a/sci-biology/glimmer/glimmer-3.02b.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-MY_PV=${PV//./}
-
-DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
-HOMEPAGE="https://ccb.jhu.edu/software/glimmer/index.shtml"
-SRC_URI="https://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
-S="${WORKDIR}/${PN}3.02"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	app-shells/tcsh
-	sci-biology/elph"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-jobserver-fix.patch
-	"${FILESDIR}"/${P}-ldflags.patch
-	"${FILESDIR}"/${P}-rename_extract.patch
-)
-
-src_prepare() {
-	sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \
-		-e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths"
-	# Fix Makefile to die on failure
-	sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die
-	# GCC 4.3 include fix
-	sed -i 's/include  <string>/include  <string.h>/' src/Common/delcher.hh || die
-	#
-	sed -i "s:/fs/szgenefinding/Glimmer3/bin:%${EPREFIX}/usr/bin/glimmer3:" scripts/g3-* || die
-	sed -i "s:/fs/szgenefinding/Glimmer3/scripts:%${EPREFIX}/usr/share/glimmer/scripts:" scripts/g3-* || die
-	sed -i "s:/nfshomes/adelcher/bin/elph:%${EPREFIX}/usr/bin/elph:" scripts/g3-* || die
-	sed -i "s/@ if/if/" src/c_make.gen || die
-
-	# avoid file collision on /usr/bin/extract #247394
-	default
-}
-
-src_compile() {
-	emake \
-		-C src \
-		CC="$(tc-getCC)" \
-		CXX="$(tc-getCXX)" \
-		AR="$(tc-getAR)" \
-		CXXFLAGS="${CXXFLAGS}" \
-		CFLAGS="${CFLAGS}" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	rm bin/test || die
-	dobin bin/*
-
-	insinto /usr/share/glimmer
-	doins -r scripts
-
-	dodoc glim302notes.pdf
-}
diff --git a/sci-biology/glimmer/metadata.xml b/sci-biology/glimmer/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/glimmer/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest
deleted file mode 100644
index 20a57a2ca4b6..000000000000
--- a/sci-biology/glimmerhmm/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST GlimmerHMM-3.0.1.tar.gz 45475952 BLAKE2B 355f4e9f26c31167e0935de8012fa99a243838d0dd47e0e46ae4cb1df4eaf188a13fb365025bc4be82805c89f36f534a9907030515f96b9422340e9e966f4ea6 SHA512 15307d1982527bd83433882552cd3e12c76a65a2a119b6911a748dc801f80b1fc5732cb769a52e5c6281bdd48cf619a02edbd1b96ee40319fc620a3a7cdd82b7
-DIST GlimmerHMM-3.0.4.tar.gz 45692137 BLAKE2B e271ea506e77d0038e343030be1875de0c92265ac2808cf35b7ba872a2d2f9416d645cd373f2ba6816f8352b4367a3a7c878c4dea772fcadf8954aabd91fca64 SHA512 e10d89550c938faf4b1e2a259213ad88a7443b7597cf753c7041698ac78d468f4ed93e0f7736640cd2fe97abe227d54eb7feca1fe7450d72f83896a94ef7a70b
diff --git a/sci-biology/glimmerhmm/files/0001-fix-ridiculous-ODR-violation.patch b/sci-biology/glimmerhmm/files/0001-fix-ridiculous-ODR-violation.patch
deleted file mode 100644
index 58fa92819b59..000000000000
--- a/sci-biology/glimmerhmm/files/0001-fix-ridiculous-ODR-violation.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-From 282b1a113e002d8b90dedb6a5b6a6dc35e7310d1 Mon Sep 17 00:00:00 2001
-From: Eli Schwartz <eschwartz93@gmail.com>
-Date: Tue, 12 Mar 2024 01:45:16 -0400
-Subject: [PATCH] fix ridiculous ODR violation
-
-The return value of a function defined in another file is whatever that
-file defines, not "void because we didn't assign it to anything".
----
- sources/oc1.h | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/sources/oc1.h b/sources/oc1.h
-index 7b068c8..e28017d 100644
---- a/sources/oc1.h
-+++ b/sources/oc1.h
-@@ -49,7 +49,7 @@ struct tree_node
-   EDGE edge; /* used only in the display module. */
-  };
- 
--void error(char *);
-+int error(char *);
- void free_ivector(int *,int,int);
- void free_vector(float *,int,int);
- void free_dvector(double*,int,float);
--- 
-2.43.2
-
diff --git a/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch b/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch
deleted file mode 100644
index 949a4fe3e92d..000000000000
--- a/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch
+++ /dev/null
@@ -1,153 +0,0 @@
- sources/makefile |   15 +++++--------
- train/makefile   |   59 +++++++++++++++++++++++++++++++----------------------
- 2 files changed, 40 insertions(+), 34 deletions(-)
-
-diff --git a/sources/makefile b/sources/makefile
-index f287d71..c560f48 100644
---- a/sources/makefile
-+++ b/sources/makefile
-@@ -2,25 +2,22 @@
- 
- 
- 
--CC=g++
--CFLAGS=-g
--
- all: glimmerhmm
- 
- glimmerhmm: glimmerhmm.o graph.o sites.o tree_util_prob.o util.o
--	$(CC) $(CFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o  -lm 
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o  -lm 
- 
- glimmerhmm.o: glimmerhmm.c
--	$(CC) $(CFLAGS) -c glimmerhmm.c
-+	$(CXX) $(CXXFLAGS) -c glimmerhmm.c
- 
- graph.o: graph.c 
--	$(CC) $(CFLAGS) -c graph.c
-+	$(CXX) $(CXXFLAGS) -c graph.c
- 
- sites.o: sites.c
--	$(CC) $(CFLAGS) -c sites.c
-+	$(CXX) $(CXXFLAGS) -c sites.c
- 
- tree_util_prob.o: tree_util_prob.c
--	$(CC) $(CFLAGS) -c tree_util_prob.c
-+	$(CXX) $(CXXFLAGS) -c tree_util_prob.c
- 
- util.o: util.c
--	$(CC) $(CFLAGS) -c util.c
-+	$(CXX) $(CXXFLAGS) -c util.c
-diff --git a/train/makefile b/train/makefile
-index 2383f18..d5a7107 100644
---- a/train/makefile
-+++ b/train/makefile
-@@ -2,9 +2,6 @@
- 
- # C compiler
- 
--C       = gcc 
--CC      = g++ 
--CFLAGS  = -O1 ${SEARCHDIRS}
- #CFLAGS  = -O3 -g -Wall
- LIBS    = -lm
- 
-@@ -15,64 +12,76 @@ all:    build-icm build-icm-noframe build1 build2 falsecomp findsites karlin sco
- 
- 
- misc.o: misc.c
--	${C} ${CFLAGS} -c misc.c
-+	$(CC) $(CFLAGS) -c misc.c
- 
- build-icm.o: build-icm.c
--	${C} ${CFLAGS} -c build-icm.c
-+	$(CC) $(CFLAGS) -c build-icm.c
- 
- build-icm: build-icm.o misc.o
--	$(C) -o $@ build-icm.o misc.o $(LIBS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm.o misc.o $(LIBS)
- 
- build-icm-noframe.o: build-icm-noframe.c
--	${C} ${CFLAGS} -c build-icm-noframe.c
-+	$(CC) $(CFLAGS) -c build-icm-noframe.c
- 
- build-icm-noframe: build-icm-noframe.o misc.o
--	$(C) -o $@ build-icm-noframe.o misc.o $(LIBS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm-noframe.o misc.o $(LIBS)
- 
- build1: build1.o
--	${CC} build1.c -o build1 $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) build1.c -o build1 $(LIBS)
- 
- build2: build2.o
--	${CC} build2.c -o build2 $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) build2.c -o build2 $(LIBS)
- 
- falsecomp: falsecomp.o
--	${CC} falsecomp.c -o falsecomp $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) falsecomp.c -o falsecomp $(LIBS)
- 
- findsites: findsites.o
--	${CC} findsites.c -o findsites $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) findsites.c -o findsites $(LIBS)
- 
- karlin: karlin.o
--	${CC} karlin.c -o karlin $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) karlin.c -o karlin $(LIBS)
- 
- score: score.o
--	${CC} score.c -o score $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) score.c -o score $(LIBS)
- 
- score2: score2.o
--	${CC} score2.c -o score2 $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) score2.c -o score2 $(LIBS)
- 
- scoreATG: scoreATG.o
--	${CC} scoreATG.c -o scoreATG $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG.c -o scoreATG $(LIBS)
- 
- scoreATG2: scoreATG2.o
--	${CC} scoreATG2.c -o scoreATG2 $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG2.c -o scoreATG2 $(LIBS)
- 
- scoreSTOP: scoreSTOP.o
--	${CC} scoreSTOP.c -o scoreSTOP $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP.c -o scoreSTOP $(LIBS)
- 
- escoreSTOP2: scoreSTOP2.o
--	${CC} scoreSTOP2.c -o scoreSTOP2 $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP2.c -o scoreSTOP2 $(LIBS)
- 
--rfapp: erfapp.o
--	${CC} erfapp.c -o erfapp $(LIBS)
-+erfapp: erfapp.o
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) erfapp.c -o erfapp $(LIBS)
- 
- sites.o: sites.c
--	${CC} ${CFLAGS} -c sites.c
-+	$(CXX) $(CXXFLAGS) -c sites.c
-+
-+scoreATG.o: scoreATG.c
-+	$(CXX) $(CXXFLAGS) -c scoreATG.c
-+	
-+scoreSTOP.o: scoreSTOP.c
-+	$(CXX) $(CXXFLAGS) -c scoreSTOP.c
-+
-+scoreSTOP2.o: scoreSTOP2.c
-+	$(CXX) $(CXXFLAGS) -c scoreSTOP2.c
-+
-+scoreATG2.o: scoreATG2.c
-+	$(CXX) $(CXXFLAGS) -c scoreATG2.c
- 
- utils.o: utils.c 
--	${CC} ${CFLAGS} -c utils.c
-+	$(CXX) $(CXXFLAGS) -c utils.c
- 
- splicescore.o: splicescore.c
--	${CC} ${CFLAGS} -c splicescore.c
-+	$(CXX) $(CXXFLAGS) -c splicescore.c
- 
- splicescore: splicescore.o sites.o utils.o
--	${CC} splicescore.o sites.o utils.o -o splicescore $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) splicescore.o sites.o utils.o -o splicescore $(LIBS)
diff --git a/sci-biology/glimmerhmm/files/3.0.4-gentoo.patch b/sci-biology/glimmerhmm/files/3.0.4-gentoo.patch
deleted file mode 100644
index d3838b1dc9bc..000000000000
--- a/sci-biology/glimmerhmm/files/3.0.4-gentoo.patch
+++ /dev/null
@@ -1,153 +0,0 @@
-diff --git a/sources/makefile b/sources/makefile
-index f287d71..c560f48 100644
---- a/sources/makefile
-+++ b/sources/makefile
-@@ -2,25 +2,22 @@
- 
- 
- 
--CC=g++
--CFLAGS=-g
--
- all: glimmerhmm
- 
- glimmerhmm: glimmerhmm.o graph.o sites.o tree_util_prob.o util.o
--	$(CC) $(CFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o  -lm 
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o  -lm 
- 
- glimmerhmm.o: glimmerhmm.c
--	$(CC) $(CFLAGS) -c glimmerhmm.c
-+	$(CXX) $(CXXFLAGS) -c glimmerhmm.c
- 
- graph.o: graph.c 
--	$(CC) $(CFLAGS) -c graph.c
-+	$(CXX) $(CXXFLAGS) -c graph.c
- 
- sites.o: sites.c
--	$(CC) $(CFLAGS) -c sites.c
-+	$(CXX) $(CXXFLAGS) -c sites.c
- 
- tree_util_prob.o: tree_util_prob.c
--	$(CC) $(CFLAGS) -c tree_util_prob.c
-+	$(CXX) $(CXXFLAGS) -c tree_util_prob.c
- 
- util.o: util.c
--	$(CC) $(CFLAGS) -c util.c
-+	$(CXX) $(CXXFLAGS) -c util.c
-diff --git a/train/makefile b/train/makefile
-index 56eaa13..d660cf1 100644
---- a/train/makefile
-+++ b/train/makefile
-@@ -2,11 +2,8 @@
- 
- # C compiler
- 
--C       = gcc 
--CC      = g++ 
- #CFLAGS  = -O1 ${SEARCHDIRS}
- #CFLAGS  = -O3 -g -Wall
--CFLAGS = -Wall -g
- LIBS    = -lm
- 
- MAKEFILE= makefile
-@@ -16,67 +13,79 @@ all:    build-icm build-icm-noframe build1 build2 falsecomp findsites karlin sco
- 
- 
- misc.o: misc.c
--	${C} ${CFLAGS} -c misc.c
-+	$(CC) $(CFLAGS) -c misc.c
- 
- build-icm.o: build-icm.c
--	${C} ${CFLAGS} -c build-icm.c
-+	$(CC) $(CFLAGS) -c build-icm.c
- 
- build-icm: build-icm.o misc.o
--	$(C) ${CFLAGS} -o $@ build-icm.o misc.o $(LIBS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm.o misc.o $(LIBS)
- 
- build-icm-noframe.o: build-icm-noframe.c
--	${C} ${CFLAGS} -c build-icm-noframe.c
-+	$(CC) $(CFLAGS) -c build-icm-noframe.c
- 
- build-icm-noframe: build-icm-noframe.o misc.o
--	$(C) ${CFLAGS} -o $@ build-icm-noframe.o misc.o $(LIBS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm-noframe.o misc.o $(LIBS)
- 
- build1: build1.o
--	${CC} ${CFLAGS} build1.c -o build1 $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) build1.o -o build1 $(LIBS)
- 
- build2: build2.o
--	${CC} ${CFLAGS} build2.c -o build2 $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) build2.o -o build2 $(LIBS)
- 
- falsecomp: falsecomp.o
--	${CC} ${CFLAGS} falsecomp.c -o falsecomp $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) falsecomp.o -o falsecomp $(LIBS)
- 
- findsites: findsites.o
--	${CC} ${CFLAGS} findsites.c -o findsites $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) findsites.o -o findsites $(LIBS)
- 
- karlin: karlin.o
--	${CC} ${CFLAGS} karlin.c -o karlin $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) karlin.o -o karlin $(LIBS)
- 
- score: score.o
--	${CC} ${CFLAGS} score.c -o score $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) score.o -o score $(LIBS)
- 
- score2: score2.o
--	${CC} ${CFLAGS} score2.c -o score2 $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) score2.o -o score2 $(LIBS)
- 
- scoreATG: scoreATG.o
--	${CC} ${CFLAGS} scoreATG.c -o scoreATG $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG.o -o scoreATG $(LIBS)
- 
- scoreATG2: scoreATG2.o
--	${CC} ${CFLAGS} scoreATG2.c -o scoreATG2 $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG2.o -o scoreATG2 $(LIBS)
- 
- scoreSTOP: scoreSTOP.o
--	${CC} ${CFLAGS} scoreSTOP.c -o scoreSTOP $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP.o -o scoreSTOP $(LIBS)
- 
- escoreSTOP2: scoreSTOP2.o
--	${CC} ${CFLAGS} scoreSTOP2.c -o scoreSTOP2 $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP2.o -o scoreSTOP2 $(LIBS)
- 
- rfapp: erfapp.o
--	${CC} ${CFLAGS} erfapp.c -o erfapp $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) erfapp.c -o erfapp $(LIBS)
- 
- sites.o: sites.c
--	${CC} ${CFLAGS} -c sites.c
-+	$(CXX) $(CXXFLAGS) -c sites.c
-+
-+scoreATG.o: scoreATG.c
-+	$(CXX) $(CXXFLAGS) -c scoreATG.c
-+       
-+scoreSTOP.o: scoreSTOP.c
-+	$(CXX) $(CXXFLAGS) -c scoreSTOP.c
-+
-+scoreSTOP2.o: scoreSTOP2.c
-+	$(CXX) $(CXXFLAGS) -c scoreSTOP2.c
-+
-+scoreATG2.o: scoreATG2.c
-+	$(CXX) $(CXXFLAGS) -c scoreATG2.c
- 
- utils.o: utils.c 
--	${CC} ${CFLAGS} -c utils.c
-+	$(CXX) $(CXXFLAGS) -c utils.c
- 
- splicescore.o: splicescore.c
--	${CC} ${CFLAGS} -c splicescore.c
-+	$(CXX) $(CXXFLAGS) -c splicescore.c
- 
- splicescore: splicescore.o sites.o utils.o
--	${CC} splicescore.o sites.o utils.o -o splicescore $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) splicescore.o sites.o utils.o -o splicescore $(LIBS)
- .PHONY : clean
- clean::
- 	/bin/rm -f core* splicescore *.o score build? build-icm \
diff --git a/sci-biology/glimmerhmm/files/glimmerhmm-3.0.1-fix-data-path.patch b/sci-biology/glimmerhmm/files/glimmerhmm-3.0.1-fix-data-path.patch
deleted file mode 100644
index 3ad5090086eb..000000000000
--- a/sci-biology/glimmerhmm/files/glimmerhmm-3.0.1-fix-data-path.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- a/train/trainGlimmerHMM
-+++ b/train/trainGlimmerHMM
-@@ -12,7 +12,7 @@
- use Cwd;
- 
- use FindBin;
--use lib $FindBin::Bin;
-+use lib "/usr/share/glimmerhmm/lib";
- use orf;
- use formtrain;
- use dectree_allinfo;
-@@ -20,7 +20,7 @@
- use splitiso;
- 
- my $workdir=cwd();
--my $scriptdir=$FindBin::Bin; # directory where all training programs should be
-+my $scriptdir="/usr/libexec/glimmerhmm/training_utils"; # directory where all training programs should be
- 
- #print "workdir=$workdir scriptdir=$scriptdir\n";exit;
- 
diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
deleted file mode 100644
index d118ce0996da..000000000000
--- a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-MY_P=GlimmerHMM
-
-DESCRIPTION="A eukaryotic gene finding system from TIGR"
-HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/"
-SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-gentoo.patch
-	"${FILESDIR}"/${PN}-3.0.1-fix-data-path.patch
-	"${FILESDIR}"/0001-fix-ridiculous-ODR-violation.patch
-)
-
-src_configure() {
-	tc-export CC CXX
-}
-
-src_compile() {
-	emake -C sources
-	emake -C train
-}
-
-src_install() {
-	dobin sources/glimmerhmm train/trainGlimmerHMM
-
-	insinto /usr/share/${PN}/lib
-	doins train/*.pm
-
-	insinto /usr/share/${PN}/models
-	doins -r trained_dir/.
-
-	exeinto /usr/libexec/${PN}/training_utils
-	doexe train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore}
-
-	dodoc README.first train/readme.train
-}
diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild
deleted file mode 100644
index 4d72bf617794..000000000000
--- a/sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-MY_P=GlimmerHMM
-
-DESCRIPTION="A eukaryotic gene finding system from TIGR"
-HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/"
-SRC_URI="https://ccb.jhu.edu/software/glimmerhmm/dl/${MY_P}-${PV}.tar.gz"
-S="${WORKDIR}/${MY_P}"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-gentoo.patch
-	"${FILESDIR}"/${PN}-3.0.1-fix-data-path.patch
-	"${FILESDIR}"/0001-fix-ridiculous-ODR-violation.patch
-)
-
-src_configure() {
-	tc-export CC CXX
-}
-
-src_compile() {
-	emake -C sources
-	emake -C train
-}
-
-src_install() {
-	dobin sources/glimmerhmm train/trainGlimmerHMM
-
-	insinto /usr/share/${PN}/lib
-	doins train/*.pm
-
-	insinto /usr/share/${PN}/models
-	doins -r trained_dir/.
-
-	exeinto /usr/libexec/${PN}/training_utils
-	doexe train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore}
-
-	dodoc README.first train/readme.train
-}
diff --git a/sci-biology/glimmerhmm/metadata.xml b/sci-biology/glimmerhmm/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/glimmerhmm/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/gmap/Manifest b/sci-biology/gmap/Manifest
deleted file mode 100644
index 6f045f9bf37f..000000000000
--- a/sci-biology/gmap/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST gmap-gsnap-2020-10-27.tar.gz 4480720 BLAKE2B 9f8e8bfab19c079111d42ec466dd145385d35e3fde0a809e46776ed1b62b599664f12618803ea4475b6961a053423a8794d0b77eb0b308bdfa927b5bcaa7d49c SHA512 22e59adf404f5ef524b3cd472fb3124d03c8c55aa7946b9dc3901f5070339dc765f8f1ecc7e394b69a14bf80923f7a9db8d545e45328a346996b3288115a535b
diff --git a/sci-biology/gmap/files/gmap-2020.10.27-fno-common.patch b/sci-biology/gmap/files/gmap-2020.10.27-fno-common.patch
deleted file mode 100644
index cc225a78c26e..000000000000
--- a/sci-biology/gmap/files/gmap-2020.10.27-fno-common.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- a/src/dynprog_end.c
-+++ b/src/dynprog_end.c
-@@ -109,7 +109,7 @@
- static Trieoffset_T *trieoffsets_max;
- static Triecontent_T *triecontents_max;
- 
--bool homopolymerp;
-+static bool homopolymerp;
- 
- void
- Dynprog_end_setup (Univcoord_T *splicesites_in, Splicetype_T *splicetypes_in,
---- a/src/dynprog_single.c
-+++ b/src/dynprog_single.c
-@@ -91,7 +91,7 @@
- 
- #define T Dynprog_T
- 
--bool homopolymerp;
-+static bool homopolymerp;
- 
- void
- Dynprog_single_setup (bool homopolymerp_in) {
diff --git a/sci-biology/gmap/gmap-2020.10.27.ebuild b/sci-biology/gmap/gmap-2020.10.27.ebuild
deleted file mode 100644
index a90f0f631068..000000000000
--- a/sci-biology/gmap/gmap-2020.10.27.ebuild
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MY_PV="$(ver_rs 1- '-')"
-
-DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences"
-HOMEPAGE="http://research-pub.gene.com/gmap/"
-SRC_URI="http://research-pub.gene.com/gmap/src/gmap-gsnap-${MY_PV}.tar.gz"
-
-LICENSE="gmap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/gmap-${MY_PV}"
-PATCHES=( "${FILESDIR}"/${PN}-2020.10.27-fno-common.patch )
diff --git a/sci-biology/gmap/metadata.xml b/sci-biology/gmap/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/gmap/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest
deleted file mode 100644
index bc29341da8af..000000000000
--- a/sci-biology/hmmer/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST hmmer-2.3.2.tar.gz 1024933 BLAKE2B 34fdc7b24b28d653022c80a63b2fd8376c15c961e1550a04cb310943d165575a2721cc5e4cb516335f57414f8621b7e62c4e30ee1f107bb714e40c59ed37d418 SHA512 5abf9c304de38b183a5beab7a5cfc75c3774ff6e161b7b8e55a0eae9fd156dbb7ed95d216c16d3c585c494bb69e3a9fdfabfb5dc729b7050a4d1be95c74df7d7
-DIST hmmer-3.1b2.tar.gz 5965253 BLAKE2B 38d1d6fb43aa814c0e3ddc551469ebd6b967f181c45df3802598f31abef10998595218167555a8862c0d2caa9118d9a7f1c22b673b6d596665f797ba903093f5 SHA512 64c8a840cb62160a1c13a20e64f42d297edb7969425d5047eefd8ee9f992d66612d62843523e8f33a2c38568ce1b0a9df23dd1d3ecf6773007f6db12d4cc4771
diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch
deleted file mode 100644
index 110c61f11821..000000000000
--- a/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-Make the build system respect DESTDIR, in order to allow staged builds.
-
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -109,13 +109,13 @@
- #          installs man pages in MANDIR/man1/  (e.g. if MANSUFFIX is 1)
- #          Creates these directories if they don't exist.
- install: 
--	mkdir -p ${BINDIR}
--	-mkdir -p ${MANDIR}/man${MANSUFFIX}
-+	mkdir -p ${DESTDIR}${BINDIR}
-+	-mkdir -p ${DESTDIR}${MANDIR}/man${MANSUFFIX}
- 	for file in $(PROGS) $(PVMPROGS); do\
--	   cp src/$$file $(BINDIR)/;\
-+	   cp src/$$file ${DESTDIR}$(BINDIR)/;\
- 	done
- 	-for file in hmmer $(PROGS); do\
--	   $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
-+	   $(INSTMAN) documentation/man/$$file.man ${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
- 	done
- 
- # uninstall: Reverses the steps of "make install".
diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch
deleted file mode 100644
index 37683d425edb..000000000000
--- a/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- a/squid/configure	2024-05-08 09:21:15.751063495 -0000
-+++ b/squid/configure	2024-05-08 09:22:50.491502934 -0000
-@@ -2493,6 +2493,7 @@
- cat confdefs.h >>conftest.$ac_ext
- cat >>conftest.$ac_ext <<_ACEOF
- /* end confdefs.h.  */
-+#include <stdlib.h>
- int
- main ()
- {
-@@ -3500,6 +3501,7 @@
- cat >>conftest.$ac_ext <<_ACEOF
- /* end confdefs.h.  */
- #include <ctype.h>
-+#include <stdlib.h>
- #if ((' ' & 0x0FF) == 0x020)
- # define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
- # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch
deleted file mode 100644
index 783d0530aa7a..000000000000
--- a/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch
+++ /dev/null
@@ -1,108 +0,0 @@
-* Fix ancient perl 4 modules that are long gone.
-* Fix perl shebangs to be portable and usable on Prefix.
-See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/
-
---- a/squid/Testsuite/bug-1-sfetch-paths
-+++ b/squid/Testsuite/bug-1-sfetch-paths
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Test for bug #1: sfetch/SSI path bug.
- # sfetch can't follow paths out of current directory if it's using
---- a/squid/Testsuite/x-base-afetch
-+++ b/squid/Testsuite/x-base-afetch
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- use testsuite;
- 
---- a/squid/Testsuite/x-base-alistat
-+++ b/squid/Testsuite/x-base-alistat
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- use testsuite;
- 
---- a/squid/Testsuite/x-base-seqstat
-+++ b/squid/Testsuite/x-base-seqstat
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- use testsuite;
- 
---- a/squid/Testsuite/x-base-sfetch
-+++ b/squid/Testsuite/x-base-sfetch
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- use testsuite;
- 
---- a/squid/Testsuite/x-base-shuffle
-+++ b/squid/Testsuite/x-base-shuffle
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- use testsuite;
- 
---- a/squid/Testsuite/x-base-sindex
-+++ b/squid/Testsuite/x-base-sindex
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- use testsuite;
- 
---- a/squid/Testsuite/x-base-sreformat
-+++ b/squid/Testsuite/x-base-sreformat
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- use testsuite;
- 
---- a/testsuite/sqc
-+++ b/testsuite/sqc
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # sqc 
- # quality control script for exercising code, regression testing, 
-@@ -176,12 +176,11 @@
- # SRE, Tue Aug  6 11:16:39 2002
- # CVS $Id: sqc,v 1.3 2003/01/05 23:40:57 eddy Exp $
- 
--require "getopts.pl";
--require "importenv.pl";
-+use Getopt::Std;
- 
- # Parse our command line
- #
--&Getopts('mp:r:v');
-+getopts('mp:r:v');
- if ($opt_m) { $do_memtest = 1;    }
- if ($opt_p) { push @prepdirs, $opt_p; }
- if ($opt_r) { push @olddirs,  $opt_r; }
-@@ -506,7 +505,7 @@
- #
- sub tempname {
-     my ($dir, $name, $suffix);
--    if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";}
-+    if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";}
- 
-     foreach $suffix ("aa".."zz") {
-         $name = "$dir"."sre".$suffix.$$;
---- a/testsuite/test1-conversion.pl
-+++ b/testsuite/test1-conversion.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Test hmmconvert.
- #
diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch
deleted file mode 100644
index 39fdbd50e457..000000000000
--- a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch
+++ /dev/null
@@ -1,331 +0,0 @@
-Fix perl shebangs to be portable and usable on Prefix.
-See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/
-
---- a/easel/demotic/infernal_tab2gff.pl
-+++ b/easel/demotic/infernal_tab2gff.pl
-@@ -1,4 +1,4 @@
--#!/usr/bin/perl -w -I/groups/eddy/home/jonest/Demotic
-+#!/usr/bin/env perl
- 
- # TAJ 6/23/08 last mod 7/10/08
- # Purpose: flexibly convert "cmsearch --tabfile TAB.out" output to GFF format
---- a/easel/demotic/test.pl
-+++ b/easel/demotic/test.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- use demotic_blast;
- 
---- a/easel/devkit/rmanprocess.pl
-+++ b/easel/devkit/rmanprocess.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # rmanprocess.pl <rman LaTeX2e output>
- # 
---- a/easel/miniapps/esl-afetch.itest.pl
-+++ b/easel/miniapps/esl-afetch.itest.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Testing the esl-afetch miniapp
- #
---- a/easel/miniapps/esl-alimanip.itest.pl
-+++ b/easel/miniapps/esl-alimanip.itest.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Integrated test of the esl-alimanip miniapp.
- #
---- a/easel/miniapps/esl-alimap.itest.pl
-+++ b/easel/miniapps/esl-alimap.itest.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Integrated test of the esl-alimap miniapp.
- #
---- a/easel/miniapps/esl-alimask.itest.pl
-+++ b/easel/miniapps/esl-alimask.itest.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Integrated test of esl-alimask miniapp.
- #
---- a/easel/miniapps/esl-alimerge.itest.pl
-+++ b/easel/miniapps/esl-alimerge.itest.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Integrated test of esl-alimerge miniapp.
- #
---- a/easel/miniapps/esl-alistat.itest.pl
-+++ b/easel/miniapps/esl-alistat.itest.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Integrated test of the esl-alistat miniapp.
- #
---- a/easel/miniapps/esl-compalign.itest.pl
-+++ b/easel/miniapps/esl-compalign.itest.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Integrated test of the esl-compalign miniapp.
- #
---- a/easel/miniapps/esl-construct.itest.pl
-+++ b/easel/miniapps/esl-construct.itest.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Integrated test of the esl-construct miniapp.
- #
---- a/easel/miniapps/esl-mask.itest.pl
-+++ b/easel/miniapps/esl-mask.itest.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Integrated test of esl-mask miniapp.
- #
---- a/easel/miniapps/esl-seqrange.itest.pl
-+++ b/easel/miniapps/esl-seqrange.itest.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Integrated test of the esl-seqrange miniapp.
- #
---- a/easel/miniapps/esl-shuffle.itest.pl
-+++ b/easel/miniapps/esl-shuffle.itest.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Integrated test of esl-shuffle miniapp
- #
---- a/easel/miniapps/esl-ssdraw.itest.pl
-+++ b/easel/miniapps/esl-ssdraw.itest.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Integrated test of the esl-ssdraw miniapp.
- #
---- a/easel/testsuite/coverage_report.pl
-+++ b/easel/testsuite/coverage_report.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Measures testsuite coverage (as percentage of source lines),
- # using gcov.
---- a/easel/testsuite/driver_report.pl
-+++ b/easel/testsuite/driver_report.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Make sure that all drivers compile.
- # (Eventually, we should also make sure they run! But that 
---- a/easel/testsuite/i1-degen-residues.pl
-+++ b/easel/testsuite/i1-degen-residues.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Integration tests of reading all valid protein sequence residue characters.
- #
---- a/easel/testsuite/i2-ncbi-indices.pl
-+++ b/easel/testsuite/i2-ncbi-indices.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Testing that we can read FASTA files, even if they have NCBI
- # formatted BLAST databases in the same directory.
---- a/easel/testsuite/i3-blank-gf.pl
-+++ b/easel/testsuite/i3-blank-gf.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Bug #e5: blank text line following #=GF <tag> handled improperly.
- #
---- a/easel/testsuite/valgrind_report.pl
-+++ b/easel/testsuite/valgrind_report.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Run the testsuite under Valgrind, to check for memory leakage.
- #
---- a/profmark/pmark-master.pl
-+++ b/profmark/pmark-master.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl -w
-+#!/usr/bin/env perl
- 
- # The top level script that runs a pmark benchmark.
- #
---- a/profmark/rocplot.pl
-+++ b/profmark/rocplot.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- $nsearches = 2809;
- 
---- a/src/hmmpress.itest.pl
-+++ b/src/hmmpress.itest.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Integrated test of hmmpress 
- #
---- a/testsuite/i10-duplicate-names.pl
-+++ b/testsuite/i10-duplicate-names.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Check that we can deal with profiles and sequences that contain
- # duplicate names, both as queries and targets. 
---- a/testsuite/i11-hmmalign-mapali.pl
-+++ b/testsuite/i11-hmmalign-mapali.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Another test of the hmmalign --mapali option, after Elena reports
- # bug #h73 in bad interaction of checksum calculation and marking
---- a/testsuite/i12-delete-corruption.pl
-+++ b/testsuite/i12-delete-corruption.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Bug #h77: hmmalign corrupts column preceding an all-delete column
- #
---- a/testsuite/i13-msa-integrity.pl
-+++ b/testsuite/i13-msa-integrity.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Look for any problems in hmmalign that corrupt the input sequences.
- #
---- a/testsuite/i14-hmmemit-consensus.pl
-+++ b/testsuite/i14-hmmemit-consensus.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Tests hmmemit -c and hmmemit -C consensus-generating options.
- #
---- a/testsuite/i15-hmmconvert.pl
-+++ b/testsuite/i15-hmmconvert.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Bug #h80: hmmconvert can't read H2 Nucleic files
- #
---- a/testsuite/i16-build-allins.pl
-+++ b/testsuite/i16-build-allins.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Bug #h82: hmmbuild corrupts resave alignment on all-insert seq
- #
---- a/testsuite/i17-stdin.pl
-+++ b/testsuite/i17-stdin.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Test that programs accept and reject argument of '-' (for reading
- # data from stdin, rather than from files) as they're supposed to.
---- a/testsuite/i18-nhmmer-generic.pl
-+++ b/testsuite/i18-nhmmer-generic.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Test of hmmbuild/nhmmer as used to build a DNA model, then query a  
- # a database of long (1MB).
---- a/testsuite/i19-hmmpgmd-ga.pl
-+++ b/testsuite/i19-hmmpgmd-ga.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Test that hmmpgmd is correctly applying bit score thresholds;
- # in this case, the --cut_ga threshold, using an example that
---- a/testsuite/i20-fmindex-core.pl
-+++ b/testsuite/i20-fmindex-core.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Test of makenhmmerdb and the core fm-index search functionality, using extactmatch  
- # 
---- a/testsuite/i5-hmmbuild-naming.pl
-+++ b/testsuite/i5-hmmbuild-naming.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Test that HMM naming in hmmbuild works as advertised.
- # Written to test for #h50.
---- a/testsuite/i6-hmmalign-mapali.pl
-+++ b/testsuite/i6-hmmalign-mapali.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Test the hmmalign --mapali option.
- # 
---- a/testsuite/i7-hmmbuild-fragments.pl
-+++ b/testsuite/i7-hmmbuild-fragments.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Test the ability of hmmbuild to deal with crappy alignments
- # of lots of sequence fragments.
---- a/testsuite/i8-nonresidues.pl
-+++ b/testsuite/i8-nonresidues.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Regression test of handling a nonresidue '*' character. By design,
- # '*' residues score 0 in insert states and N,C,J; and -inf in match
---- a/testsuite/i9-optional-annotation.pl
-+++ b/testsuite/i9-optional-annotation.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Check that we can deal with HMMs with no optional annotation, in either
- # hmmscan or hmmsearch mode.
---- a/testsuite/test-make.pl
-+++ b/testsuite/test-make.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl -w
-+#!/usr/bin/env perl
- 
- # Usage:   test-make.pl <builddir> <srcdir> <tmppfx>
- # 
diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch
deleted file mode 100644
index 1c08d67e7bdd..000000000000
--- a/sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch
+++ /dev/null
@@ -1,110 +0,0 @@
-* Install headers into 'hmmer3' subdir and not into global includedir
-* Respect AR
-
---- a/easel/Makefile.in
-+++ b/easel/Makefile.in
-@@ -465,11 +465,12 @@
- 	${INSTALL} -d ${DESTDIR}${bindir}
- 	${INSTALL} -d ${DESTDIR}${libdir}
- 	${INSTALL} -d ${DESTDIR}${includedir}
-+	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
- 	${INSTALL} -m 0644 libeasel.a ${DESTDIR}${libdir}/
- 	for file in ${HDRS}; do\
--	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
-+	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
- 	done
--	${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/
-+	${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/hmmer3/
- 	${QUIET_SUBDIR0}miniapps      ${QUIET_SUBDIR1} install
- 
- # "make uninstall" reverses the steps of "make install"
---- a/libdivsufsort/Makefile.in
-+++ b/libdivsufsort/Makefile.in
-@@ -16,7 +16,7 @@
- CFLAGS    = @CFLAGS@ @PTHREAD_CFLAGS@ @PIC_FLAGS@
- CPPFLAGS  = @CPPFLAGS@
- MPILIBS   = @MPILIBS@
--AR        = @AR@ rc
-+AR        = @AR@
- RANLIB    = @RANLIB@
- INSTALL   = @INSTALL@
- 
-@@ -43,7 +43,7 @@
- 
- 
- libdivsufsort.a: $(OBJS)
--	${QUIET_AR}${AR} libdivsufsort.a $(OBJS)
-+	${QUIET_AR}${AR} rc libdivsufsort.a $(OBJS)
- 	@${RANLIB} libdivsufsort.a
- 	@chmod 644 libdivsufsort.a
- 
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -143,6 +143,7 @@
- 	${INSTALL} -d ${DESTDIR}${bindir}
- 	${INSTALL} -d ${DESTDIR}${libdir}
- 	${INSTALL} -d ${DESTDIR}${includedir}
-+	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
- 	${INSTALL} -d ${DESTDIR}${man1dir}
- 	${INSTALL} -d ${DESTDIR}${pdfdir}
- 	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} install
---- a/src/impl_dummy/Makefile.in
-+++ b/src/impl_dummy/Makefile.in
-@@ -152,8 +152,9 @@
- 	${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
- 
- install:
-+	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
- 	for file in ${HDRS}; do \
--	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
-+	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
- 	done
- 
- uninstall:
---- a/src/impl_sse/Makefile.in
-+++ b/src/impl_sse/Makefile.in
-@@ -155,8 +155,9 @@
- 
- 
- install:
-+	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
- 	for file in ${HDRS}; do \
--	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
-+	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
- 	done
- 
- uninstall:
---- a/src/impl_vmx/Makefile.in
-+++ b/src/impl_vmx/Makefile.in
-@@ -152,8 +152,9 @@
- 	${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
- 
- install:
-+	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
- 	for file in ${HDRS}; do \
--	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
-+	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
- 	done
- 
- uninstall:
---- a/src/Makefile.in
-+++ b/src/Makefile.in
-@@ -322,15 +322,16 @@
- 	${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
- 
- install:
-+	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
- 	${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} install
- 	for file in ${PROGS}; do \
- 	   ${INSTALL} -m 0755 $$file ${DESTDIR}${bindir}/ ;\
- 	done
- 	${INSTALL} -m 0755 libhmmer.a ${DESTDIR}${libdir}/
- 	for file in ${HDRS}; do \
--	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
-+	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
- 	done
--	${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/ ;\
-+	${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/hmmer3/ ;\
- 
- uninstall:
- 	${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} uninstall
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild
deleted file mode 100644
index 7766710967f5..000000000000
--- a/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild
+++ /dev/null
@@ -1,88 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit dot-a flag-o-matic toolchain-funcs
-
-DESCRIPTION="Sequence analysis using profile hidden Markov models"
-HOMEPAGE="http://hmmer.org/"
-SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_ppc_altivec test"
-RESTRICT="!test? ( test )"
-
-BDEPEND="test? ( dev-lang/perl )"
-
-PATCHES=(
-	"${FILESDIR}/${P}-fix-perl-shebangs.patch"
-	"${FILESDIR}/${P}-fix-build-system-destdir.patch"
-	"${FILESDIR}/${P}-fix-missing-include-in-configure.patch"
-)
-
-src_configure() {
-	# required to expose pthread_setconcurrency(), #882279
-	append-cppflags -D_XOPEN_SOURCE=500
-
-	lto-guarantee-fat
-
-	# prevent stray environmental variable
-	# from causing issues in the test phase
-	unset TMPDIR
-
-	econf \
-		--enable-lfs \
-		--enable-threads \
-		$(use_enable cpu_flags_ppc_altivec altivec)
-}
-
-src_compile() {
-	emake AR="$(tc-getAR) rcs"
-}
-
-src_install() {
-	default
-
-	newlib.a src/libhmmer.a libhmmer2.a
-	insinto /usr/include/hmmer2
-	doins src/*.h
-
-	dobin squid/{afetch,alistat,compalign,compstruct,revcomp,seqstat,seqsplit,sfetch,shuffle,sreformat,sindex,weight,translate}
-	dolib.a squid/libsquid.a
-	insinto /usr/include/hmmer2
-	doins squid/*.h
-
-	strip-lto-bytecode
-
-	dodoc NOTES Userguide.pdf
-	newdoc 00README README
-
-	# rename files due to collisions with hmmer-3
-	# in order to make SLOTing possible
-	local i
-
-	# first rename man pages...
-	pushd "${ED}"/usr/share/man/man1/ >/dev/null || die
-	for i in hmm*.1; do
-		mv ${i%.1}{,2}.1 || die
-	done
-	popd >/dev/null || die
-
-	# ... then rename binaries
-	pushd "${ED}"/usr/bin/ >/dev/null || die
-	for i in hmm*; do
-		mv ${i}{,2} || die
-	done
-	popd >/dev/null || die
-}
-
-pkg_postinst() {
-	elog "All ${P} binaries have been renamed, in order"
-	elog "to avoid collisions with hmmer-3. For instance"
-	elog
-	elog "    hmmalign -> hmmalign2"
-	elog
-}
diff --git a/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild b/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild
deleted file mode 100644
index cbb524dc3454..000000000000
--- a/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit dot-a toolchain-funcs
-
-MY_PV="${PV/_beta/b}"
-
-DESCRIPTION="Sequence analysis using profile hidden Markov models"
-HOMEPAGE="http://hmmer.org/"
-SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz"
-S="${WORKDIR}/${PN}-${MY_PV}"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_ppc_altivec cpu_flags_x86_sse gsl mpi test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
-	mpi? ( virtual/mpi )
-	gsl? ( sci-libs/gsl:= )"
-DEPEND="${RDEPEND}"
-BDEPEND="test? ( dev-lang/perl )"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-3.1_beta2-fix-perl-shebangs.patch
-	"${FILESDIR}"/${PN}-3.1_beta2-makefile.patch
-)
-
-src_configure() {
-	# make build verbose, bug #429308
-	export V=1
-
-	lto-guarantee-fat
-
-	econf \
-		--disable-pic \
-		--enable-threads \
-		$(use_enable cpu_flags_ppc_altivec vmx) \
-		$(use_enable cpu_flags_x86_sse sse) \
-		$(use_enable mpi) \
-		$(use_with gsl)
-}
-
-src_compile() {
-	emake AR="$(tc-getAR)"
-}
-
-src_install() {
-	default
-	strip-lto-bytecode
-	dodoc Userguide.pdf
-
-	insinto /usr/share/hmmer
-	doins -r tutorial
-}
diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml
deleted file mode 100644
index bdabd1d83788..000000000000
--- a/sci-biology/hmmer/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/iedera/Manifest b/sci-biology/iedera/Manifest
deleted file mode 100644
index 407d55a22853..000000000000
--- a/sci-biology/iedera/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST iedera-1.05.tar.gz 129163 BLAKE2B fe499276da7571be83b847ab98bbe4878470b07fb13ee80ffb55bff1b5674b54fd4bf5e21fa34e10b8296d9c6aad298dbde79910cfa45670ea8afe047de1a979 SHA512 60d35227d5479fea693e8a3c0e629aae9e21f3c7e2be7b2f10aaddcade70cc6525fa18dea1851f73d6c1aadbb5e8776dd4a146b1a81ecfe8c910729a2300066f
diff --git a/sci-biology/iedera/files/iedera-1.05-fix-buildsystem.patch b/sci-biology/iedera/files/iedera-1.05-fix-buildsystem.patch
deleted file mode 100644
index 8803ab64b4e1..000000000000
--- a/sci-biology/iedera/files/iedera-1.05-fix-buildsystem.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-iedera sets default flags that override user {C,CXX,LD}FLAGS
-
---- iedera-1.05/configure.in
-+++ iedera-1.05/configure.in
-@@ -4,11 +4,5 @@
- AC_PROG_INSTALL
- AC_PROG_CXX
- AC_HEADER_STDC
--CFLAGS="$CFLAGS $UNAME_DEFS -O3 -pipe -funroll-loops -Wall"
--CXXFLAGS="$CFLAGS"
--LDFLAGS="$LDFLAGS -lm"
--AC_SUBST(CFLAGS)
--AC_SUBST(CXXFLAGS)
--AC_SUBST(LDFLAGS)
- AC_CONFIG_FILES([Makefile])
- AC_OUTPUT
diff --git a/sci-biology/iedera/iedera-1.05-r2.ebuild b/sci-biology/iedera/iedera-1.05-r2.ebuild
deleted file mode 100644
index 22a4bd9225f2..000000000000
--- a/sci-biology/iedera/iedera-1.05-r2.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools
-
-DESCRIPTION="Subset seed design tool for DNA sequence alignment"
-HOMEPAGE="https://bioinfo.lifl.fr/yass/iedera.php"
-SRC_URI="https://bioinfo.lifl.fr/yass/files/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-PATCHES=( "${FILESDIR}"/${P}-fix-buildsystem.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/iedera/metadata.xml b/sci-biology/iedera/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/iedera/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/infernal/Manifest b/sci-biology/infernal/Manifest
deleted file mode 100644
index 5fb5d5b04546..000000000000
--- a/sci-biology/infernal/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST infernal-1.0.2.tar.gz 15205421 BLAKE2B 3570ae42feb96ead383c2f1c09d34b4719ae0a5ae8fa973fd02f9ea6e8935c81ab49c7db21dad2e20c1ae6ab6fb9514f12704bbf5917f15f6582effae480312f SHA512 0399be14c17f053574e95d8c5b9eaf990545795a9268e20f0940e11a8e78fc49beb4b23994e9ea427764fbb29e9b39f6da9cb1d85eb4b56d354057b48515c4af
diff --git a/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch b/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch
deleted file mode 100644
index 41ab3103594b..000000000000
--- a/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch
+++ /dev/null
@@ -1,135 +0,0 @@
-* Fix parallel build
-* Respect AR
-* Respect DESTDIR
-* Respect LDFLAGS
-
---- a/easel/Makefile.in
-+++ b/easel/Makefile.in
-@@ -17,7 +17,6 @@
- #
- CC       = @CC@
- CFLAGS   = @CFLAGS@
--AR       = @AR@ rcv
- LN       = ln
- RANLIB   = @RANLIB@
- LDFLAGS  = -static @LDFLAGS@
-@@ -132,13 +131,13 @@
- 	esl_wuss.o
- 
- all: libeasel.a
--	(cd miniapps; make)
-+	$(MAKE) -C miniapps
- 
- .c.o: 
- 	${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $<		
- 
- libeasel.a: $(OBJS)
--	$(AR) libeasel.a $(OBJS)
-+	$(AR) rcv libeasel.a $(OBJS)
- 	$(RANLIB) libeasel.a
- 	chmod 644 libeasel.a
- 
---- a/easel/testsuite/Makefile.in
-+++ b/easel/testsuite/Makefile.in
-@@ -15,7 +15,6 @@
- LIBS     = @LIBGSL@ @LIBS@ -lm
- MPILIBS  = @MPILIBS@
- 
--AR      = @AR@ rcv
- RANLIB  = @RANLIB@
- 
- ESLDIR = ..
---- a/iinfernal-1/Makefile.in
-+++ b/iinfernal-1/Makefile.in
-@@ -20,7 +20,6 @@
- #  only used for building the testsuite anyway... e.g. we
- #  make a "libhmmer.a" library for building the testsuite.
- #
--AR     = @AR@ rcv 
- RANLIB = @RANLIB@
- 
- MPILIBS   = @MPILIBS@
-@@ -63,7 +62,7 @@
- module: libinfernal.a
- 
- libinfernal.a: $(OBJS) 
--	$(AR) libinfernal.a $(OBJS) 
-+	$(AR) rcv libinfernal.a $(OBJS) 
- 	$(RANLIB) libinfernal.a
- 	chmod 644 libinfernal.a
- 
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -82,9 +82,10 @@
- all: core 
- 
- core:
--	(cd easel;     make CC="$(CC)" CFLAGS="$(CFLAGS)"; make)
--	(cd src;       make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module)
--	(cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)")
-+	$(MAKE) -C easel
-+	$(MAKE) -C src 
-+	$(MAKE) -C src module
-+	$(MAKE) -C testsuite
- 
- #.PHONY: $(RIGFILTERS)
- #$(RIGFILTERS): core
-@@ -202,9 +203,9 @@
- # "make install" installs the programs in BINDIR
- #
- install:
--	mkdir -p ${BINDIR}
-+	mkdir -p $(DESTDIR)${BINDIR}
- 	for file in $(PROGS); do\
--		cp src/$$file $(BINDIR)/;\
-+		cp src/$$file $(DESTDIR)$(BINDIR)/;\
- 	done
- #	if test -d $(RIGFILTERS); then\
- #	   for file in $(RFPROGS); do\
---- a/rigfilters/cfsqp/Makefile.in
-+++ b/rigfilters/cfsqp/Makefile.in
-@@ -24,7 +24,6 @@
- ## archiving command, and ranlib command.
- # these are used to create the libcfsqp.a library, necessary for cm2hmm
- #
--AR     = @AR@ rcv 
- RANLIB = @RANLIB@
- 
- OBJS  = cfsqp.o\
-@@ -41,7 +40,7 @@
- all: libcfsqp.a
- 
- libcfsqp.a: $(OBJS) ${HDRS}
--	$(AR) libcfsqp.a $(OBJS) 
-+	$(AR) rcv libcfsqp.a $(OBJS)
- 	$(RANLIB) libcfsqp.a
- 	chmod 644 libcfsqp.a
- 
---- a/src/Makefile.in
-+++ b/src/Makefile.in
-@@ -27,7 +27,6 @@
- #  only used for building the testsuite anyway... e.g. we
- #  make a "libinfernal.a" library for building the testsuite.
- #
--AR     = @AR@ rcv 
- RANLIB = @RANLIB@
- 
- # configuration for optional MPI functionality
-@@ -86,7 +85,7 @@
- all: 	$(PROGS) 
- 
- $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS}
--	$(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS)
- 
- 
- #################################################################
-@@ -95,7 +94,7 @@
- module: libinfernal.a
- 
- libinfernal.a: $(OBJS) ${HDRS}
--	$(AR) libinfernal.a $(OBJS) 
-+	$(AR) rcv libinfernal.a $(OBJS)
- 	$(RANLIB) libinfernal.a
- 	chmod 644 libinfernal.a
- 
diff --git a/sci-biology/infernal/files/infernal-1.0.2-overflows.patch b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch
deleted file mode 100644
index 67190c4c1d42..000000000000
--- a/sci-biology/infernal/files/infernal-1.0.2-overflows.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Fix buffer overflow
-
-http://bugs.gentoo.org/show_bug.cgi?id=338179
-
---- a/easel/esl_getopts.c
-+++ b/easel/esl_getopts.c
-@@ -1270,7 +1270,7 @@
- 		   "Arg looks like option? Use %.24s%.24s if you really mean it.",
- 		   g->opt[opti].name, *ret_optarg);
-       } else 
--	ESL_FAIL(eslESYNTAX, "Option %.24s requires an argument", g->opt[opti].name);
-+	ESL_FAIL(eslESYNTAX, g->errbuf, "Option %.24s requires an argument", g->opt[opti].name);
- 
-       g->optstring = NULL;   /* An optchar that takes an arg must terminate an optstring. */
-     }
diff --git a/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch b/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch
deleted file mode 100644
index c96dcae7b296..000000000000
--- a/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch
+++ /dev/null
@@ -1,147 +0,0 @@
- benchmarks/cmsearch-rmark/sre.pl   | 4 +---
- easel/devkit/autodoc               | 4 ++--
- easel/devkit/esl-dependencies      | 4 ++--
- easel/devkit/sqc                   | 7 +++----
- easel/testsuite/coverage_report.pl | 4 ++--
- easel/testsuite/driver_report.pl   | 4 ++--
- easel/testsuite/valgrind_report.pl | 4 ++--
- 7 files changed, 14 insertions(+), 17 deletions(-)
-
-diff --git a/benchmarks/cmsearch-rmark/sre.pl b/benchmarks/cmsearch-rmark/sre.pl
-index 9136717..e4df233 100644
---- a/benchmarks/cmsearch-rmark/sre.pl
-+++ b/benchmarks/cmsearch-rmark/sre.pl
-@@ -6,8 +6,6 @@
- 
- package SRE_perlstuff;
- 
--require "importenv.pl";
--
- # Function: tempname
- #
- # Returns a unique temporary filename. 
-@@ -26,7 +24,7 @@ require "importenv.pl";
- #
- sub main'tempname {
-     local ($dir, $name);
--    if ($TMPDIR) { $dir = $TMPDIR; } else {$dir = "/tmp";}
-+    if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}; } else {$dir = "/tmp";}
- 
-     foreach $suffix ("aa".."zz") {
- 	$name = "$dir/sre$suffix$$";
-diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc
-old mode 100755
-new mode 100644
-index 045ce36..22268f6
---- a/easel/devkit/autodoc
-+++ b/easel/devkit/autodoc
-@@ -49,8 +49,8 @@
- #
- # SRE, Tue Nov 30 19:43:47 2004
- 
--require  "getopts.pl";
--&Getopts('n:t');
-+use Getopt::Std;
-+getopts('n:t');
- $cfile = shift;
- 
- if ($opt_t) { $show_api_table = 1; }
-diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies
-old mode 100755
-new mode 100644
-index a4dc126..b61fa7a
---- a/easel/devkit/esl-dependencies
-+++ b/easel/devkit/esl-dependencies
-@@ -13,8 +13,8 @@
- # SRE, Mon Jun 11 11:15:31 2007
- # SVN $Id$
- 
--require "getopts.pl"
--&Getopts('1afr');
-+use Getopt::Std;
-+getopts('1afr');
- 
- if ($opt_1) { $show_summary_table = 1; }
- if ($opt_a) { $list_augfiles      = 1; }
-diff --git a/easel/devkit/sqc b/easel/devkit/sqc
-old mode 100755
-new mode 100644
-index 81d03de..6201d3d
---- a/easel/devkit/sqc
-+++ b/easel/devkit/sqc
-@@ -176,12 +176,11 @@
- # SRE, Tue Aug  6 11:16:39 2002
- # SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $
- 
--require "getopts.pl";
--require "importenv.pl";
-+use Getopt::Std;
- 
- # Parse our command line
- #
--&Getopts('mp:r:v');
-+getopts('mp:r:v');
- if ($opt_m) { $do_memtest = 1;    }
- if ($opt_p) { push @prepdirs, $opt_p; }
- if ($opt_r) { push @olddirs,  $opt_r; }
-@@ -510,7 +509,7 @@ check_ccmalloc_status
- #
- sub tempname {
-     my ($dir, $name, $suffix);
--    if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";}
-+    if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";}
- 
-     foreach $suffix ("aa".."zz") {
-         $name = "$dir"."esltmp".$suffix.$$;
-diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl
-old mode 100755
-new mode 100644
-index 9c77791..024ed34
---- a/easel/testsuite/coverage_report.pl
-+++ b/easel/testsuite/coverage_report.pl
-@@ -16,9 +16,9 @@
- #
- # SRE, Thu Mar  1 19:22:57 2007 (Janelia)
- # SVN $Id: coverage_report.pl 231 2008-03-25 14:43:57Z eddys $
--require  "getopts.pl";
-+use Getopt::Std;
- $have_sloccount = 1;
--&Getopts('cs');
-+getopts('cs');
- if ($opt_c) { $do_recompile     = 1; }
- if ($opt_s) { $have_sloccount   = 0; }
- 
-diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl
-old mode 100755
-new mode 100644
-index d1b4a9a..db4378f
---- a/easel/testsuite/driver_report.pl
-+++ b/easel/testsuite/driver_report.pl
-@@ -19,8 +19,8 @@
- # SRE, Fri Mar  2 10:01:44 2007 (Janelia)
- # SVN $Id: driver_report.pl 231 2008-03-25 14:43:57Z eddys $
- 
--require  "getopts.pl";
--&Getopts('c');
-+use Getopt::Std;
-+getopts('c');
- if ($opt_c) { $do_recompile = 1; }
- 
- if ($ENV{'CC'}     ne "") { $CC     = $ENV{'CC'};     } else { $CC       = "gcc"; } 
-diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl
-old mode 100755
-new mode 100644
-index 186a392..07026a0
---- a/easel/testsuite/valgrind_report.pl
-+++ b/easel/testsuite/valgrind_report.pl
-@@ -10,8 +10,8 @@
- #
- # SRE, Fri Mar  2 08:37:48 2007 [Janelia]
- # SVN $Id: valgrind_report.pl 231 2008-03-25 14:43:57Z eddys $
--require  "getopts.pl";
--&Getopts('c');
-+use Getopt::Std;
-+getopts('c');
- if ($opt_c) { $do_recompile = 1; }
- 
- if ($ENV{'CC'}     ne "") { $CC     = $ENV{'CC'};     } else { $CC       = "gcc"; } 
diff --git a/sci-biology/infernal/infernal-1.0.2-r1.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild
deleted file mode 100644
index 9aa5fd13f4db..000000000000
--- a/sci-biology/infernal/infernal-1.0.2-r1.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Inference of RNA alignments"
-HOMEPAGE="http://infernal.janelia.org/"
-SRC_URI="ftp://selab.janelia.org/pub/software/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-IUSE="mpi"
-
-RDEPEND="mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-fix-build-system.patch
-	"${FILESDIR}"/${P}-overflows.patch
-	"${FILESDIR}"/${P}-perl-5.16-2.patch
-)
-
-src_configure() {
-	tc-export AR
-	econf $(use_enable mpi)
-}
-
-src_install() {
-	DOCS=( 00README* Userguide.pdf documentation/release-notes )
-	default
-
-	pushd documentation/manpages >/dev/null || die
-	local i
-	for i in *.man; do
-		newman "${i}" "${i/.man/.1}"
-	done
-	popd >/dev/null || die
-
-	insinto /usr/share/${PN}
-	doins -r benchmarks tutorial intro matrices
-}
diff --git a/sci-biology/infernal/metadata.xml b/sci-biology/infernal/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/infernal/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/iqpnni/Manifest b/sci-biology/iqpnni/Manifest
deleted file mode 100644
index 30d111d23542..000000000000
--- a/sci-biology/iqpnni/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST iqpnni-3.3.2.tar.gz 646603 BLAKE2B 9e4b281b148518b367d9aa7f1cfcc76f032657ac8ae480b84276c16d05afe64845ebfcea33d0325cfb1048d06713a5eb7ed4d9993abed4b739a700e57b849d33 SHA512 6e603117b746956ad0c3b140968abf2b3b3065a18dc78cee4975f1d2e7971334fdde15e2e8d2fd7435b9490aaaffaf17a38f72a3897c951f493d866e21d94156
diff --git a/sci-biology/iqpnni/files/iqpnni-3.3.2-cpp14.patch b/sci-biology/iqpnni/files/iqpnni-3.3.2-cpp14.patch
deleted file mode 100644
index 69a4aacb61b1..000000000000
--- a/sci-biology/iqpnni/files/iqpnni-3.3.2-cpp14.patch
+++ /dev/null
@@ -1,48 +0,0 @@
-Fix problems with compilation in C++14 (GCC 6.x). Changes in iostream library
-caused that comparison of istream to 0 or NULL is unavailable.
-Gentoo bug: https://bugs.gentoo.org/show_bug.cgi?id=594332
-
---- a/src/interface.cpp
-+++ b/src/interface.cpp
-@@ -1340,7 +1340,7 @@
- 
- 
- 	int isExistedFile_ = 1;
--	if (existedFile_ == 0)
-+	if (!existedFile_)
- 		isExistedFile_ = 0;
- 
- 	existedFile_.close ();
---- a/src/iqp.cpp
-+++ b/src/iqp.cpp
-@@ -508,7 +508,7 @@
- 		if (in_pam.tree_file != NULL) {
- 			std::ifstream userTreeFile_;
- 			userTreeFile_.open (in_pam.tree_file);
--			if (userTreeFile_ != 0) {
-+			if (userTreeFile_) {
- 				initialTree_.readFile (in_pam.tree_file);
- 				initialTree_.createUrTree ();
- 				hasInitTree = true;
---- a/src/main.cpp
-+++ b/src/main.cpp
-@@ -118,7 +118,7 @@
- 
- 	ifstream in;
- 	in.open (boottree_file_name.c_str());
--	if (in == 0)
-+	if (!in)
- 		Utl::announceError ("Cannot open the user tree file ...");
- 
- 	int num_tree = 0;
---- a/src/usertree.cpp
-+++ b/src/usertree.cpp
-@@ -94,7 +94,7 @@
- void UserTree::readFile (const char *userTreeFile) {
- 	ifstream in;
- 	in.open (userTreeFile);
--	if (in == 0)
-+	if (!in)
- 		Utl::announceError ("Cannot open the user tree file ...");
- 
- 	readFile(in);
diff --git a/sci-biology/iqpnni/iqpnni-3.3.2-r2.ebuild b/sci-biology/iqpnni/iqpnni-3.3.2-r2.ebuild
deleted file mode 100644
index 4175330026a1..000000000000
--- a/sci-biology/iqpnni/iqpnni-3.3.2-r2.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="Important Quartet Puzzling and NNI Operation"
-HOMEPAGE="http://www.cibiv.at/software/iqpnni/"
-SRC_URI="http://www.cibiv.at/software/iqpnni/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-cpp14.patch # bug #594332
-)
-
-src_install() {
-	dobin src/iqpnni
-
-	if use doc ; then
-		HTML_DOCS=( manual/iqpnni-manual.html )
-		dodoc manual/iqpnni-manual.pdf
-	fi
-	einstalldocs
-}
diff --git a/sci-biology/iqpnni/metadata.xml b/sci-biology/iqpnni/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/iqpnni/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/jalview-bin/Manifest b/sci-biology/jalview-bin/Manifest
deleted file mode 100644
index ceafa46b360c..000000000000
--- a/sci-biology/jalview-bin/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jalview-all-2.11.5.1-j1.8.jar 51193467 BLAKE2B 7fdabea94eaa932b8775b0bfaad5fac2169cf070608ca531e0a64a34a04da95ed14d1f08c1cb0f0ba75ef126671bc4e4007212af05e8aaf33f6a1725b9f8c694 SHA512 bfb1228984484bc32c00eb212cac7af0d33bb02773cbc81bcdda0757643625c0d6a72bd19d1153b196062fce52d435d3d15509b75d9af8cb264888f4d695de89
diff --git a/sci-biology/jalview-bin/jalview-bin-2.11.5.1.ebuild b/sci-biology/jalview-bin/jalview-bin-2.11.5.1.ebuild
deleted file mode 100644
index 1fde572cf704..000000000000
--- a/sci-biology/jalview-bin/jalview-bin-2.11.5.1.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-JAVA_PKG_WANT_TARGET=1.8
-
-inherit desktop java-pkg-2
-
-DESCRIPTION="Editor of multiple sequence alignments."
-HOMEPAGE="https://www.jalview.org/"
-SRC_URI="https://www.jalview.org/getdown/release/jalview-all-${PV}-j1.8.jar"
-
-S="${WORKDIR}"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="app-arch/unzip"
-
-RDEPEND="virtual/jre:1.8"
-
-src_unpack() {
-	cp -v "${DISTDIR}/${A}" . || die
-	unzip -u ${A} images/jalview_logo-48.png || die
-}
-
-src_install() {
-	java-pkg_newjar "jalview-all-${PV}-j1.8.jar"
-	java-pkg_dolauncher "${PN}" --jar "${PN}.jar"
-	newicon images/jalview_logo-48.png jalview_logo_48.png
-	make_desktop_entry "${PN}" JalView jalview_logo_48 Science
-}
diff --git a/sci-biology/jalview-bin/metadata.xml b/sci-biology/jalview-bin/metadata.xml
deleted file mode 100644
index 0ee7367c6a24..000000000000
--- a/sci-biology/jalview-bin/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>andres.becerra@gmail.com</email>
-		<name>Andrés Becerra Sandoval</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/kalign/Manifest b/sci-biology/kalign/Manifest
deleted file mode 100644
index 179a5acb2e37..000000000000
--- a/sci-biology/kalign/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST kalign_2.03.orig.tar.gz 114022 BLAKE2B 3637bde4e9b900def668043e75b2a52ed17a8aed6f894e323b1b76f216ad50784fb2ee352389f8888b5365efd5681361af3818ba0ca593721b19c497ffb83930 SHA512 d60152bd7124f77ea972ea7dac19f47eb731646a12ecafbee8a99335c20a36fb3ce2bdc633b346e4da1016d8e56a0f297f9b33c9b6285197946f404dbc390b0a
diff --git a/sci-biology/kalign/files/kalign-2.03-makefile.patch b/sci-biology/kalign/files/kalign-2.03-makefile.patch
deleted file mode 100644
index 61e65c0b73ce..000000000000
--- a/sci-biology/kalign/files/kalign-2.03-makefile.patch
+++ /dev/null
@@ -1,39 +0,0 @@
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -1,7 +1,11 @@
--PREFIX			= /usr/local/bin
-+prefix			= @prefix@
-+exec_prefix		= @exec_prefix@
-+bindir			= @bindir@
- TEST				= test/
--CC					= gcc  
--CFLAGS			= -O9  -Wall 
-+CC				= @CC@  
-+CFLAGS			= @CFLAGS@
-+CPPFLAGS		= @CPPFLAGS@
-+LDFLAGS			= @LDFLAGS@
- DEBUGFLAGS		= -ggdb -Wall 
- 
- SOURCES			= kalign2_distance_calculation.c kalign2_dp.c kalign2_input.c kalign2_main.c kalign2_mem.c kalign2_inferface.c kalign2_misc.c kalign2_tree.c  kalign2_profile.c kalign2_alignment_types.c kalign2_feature.c kalign2_hirschberg.c  kalign2_advanced_gaps.c kalign2_hirschberg_dna.c  kalign2_output.c kalign2_string_matching.c kalign2_profile_alignment.c 
-@@ -16,10 +20,7 @@
- .PHONY: clean
- 
- all: $(OBJECTS)
--	$(CC) $(CFLAGS) $(OBJECTS) -o $(PROGS)
--	
--%.o:	%.c
--	$(CC) $(CFLAGS) -c $<
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(OBJECTS) -o $(PROGS)
- 	
- debug: $(DEBUGOBJECTS)
- 	$(CC) $(DEBUGFLAGS) $(DEBUGOBJECTS) -o $(DEBUGPROGS)	
-@@ -29,7 +30,8 @@
- 
- 
- install:
--	cp $(PROGS) /usr/local/bin/
-+	mkdir -p $(DESTDIR)$(bindir)
-+	cp $(PROGS) $(DESTDIR)$(bindir)
- 	
- clean: 
- 	rm -f $(PROGS) $(OBJECTS)
diff --git a/sci-biology/kalign/kalign-2.03-r3.ebuild b/sci-biology/kalign/kalign-2.03-r3.ebuild
deleted file mode 100644
index 22d92963a0ea..000000000000
--- a/sci-biology/kalign/kalign-2.03-r3.ebuild
+++ /dev/null
@@ -1,15 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="Global and progressive multiple sequence alignment"
-HOMEPAGE="http://msa.cgb.ki.se/"
-SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz"
-S="${WORKDIR}/${PN}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-PATCHES=( "${FILESDIR}"/${P}-makefile.patch )
diff --git a/sci-biology/kalign/metadata.xml b/sci-biology/kalign/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/kalign/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/kallisto/Manifest b/sci-biology/kallisto/Manifest
deleted file mode 100644
index a880b853ffd7..000000000000
--- a/sci-biology/kallisto/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST kallisto-0.46.2.tar.gz 2693869 BLAKE2B 73d725e74133d64b9f7910f69a5fff85eac05b93ad6891807a6fd4e16a1fa16a55306058db3fcb4e0fbfeb0719d3a9d3c8da7d2b76b64dde5a2fea51b0254b99 SHA512 6aca29afa0abe1c6896d27745fd2436c9b9aaf298d70276baf877dbf0aaaba94df54b9a42829c8f8f7c02e7262ecd1837b8a021625c3066a10c0cc0551179093
diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch b/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch
deleted file mode 100644
index 3ff6a0c33be0..000000000000
--- a/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch
+++ /dev/null
@@ -1,38 +0,0 @@
---- a/unit_tests/main.cpp
-+++ b/unit_tests/main.cpp
-@@ -1,2 +1,2 @@
- #define CATCH_CONFIG_MAIN
--#include "catch.hpp"
-+#include <catch2/catch_all.hpp>
---- a/unit_tests/test_index.cpp
-+++ b/unit_tests/test_index.cpp
-@@ -1,4 +1,4 @@
--#include "catch.hpp"
-+#include <catch2/catch_all.hpp>
- 
- #include "common.h"
- #include "KmerIndex.h"
---- a/unit_tests/test_kmerhashtable.cpp
-+++ b/unit_tests/test_kmerhashtable.cpp
-@@ -1,4 +1,4 @@
--#include "catch.hpp"
-+#include <catch2/catch_all.hpp>
- 
- #include <random>
- #include <string>
---- a/unit_tests/test_multinomial.cpp
-+++ b/unit_tests/test_multinomial.cpp
-@@ -1,4 +1,4 @@
--#include "catch.hpp"
-+#include <catch2/catch_all.hpp>
- 
- #include <iostream>
- #include <vector>
---- a/unit_tests/test_weights.cpp
-+++ b/unit_tests/test_weights.cpp
-@@ -1,4 +1,4 @@
--#include "catch.hpp"
-+#include <catch2/catch_all.hpp>
- 
- #include <vector>
- 
diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch b/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch
deleted file mode 100644
index 6516f162e906..000000000000
--- a/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch
+++ /dev/null
@@ -1,149 +0,0 @@
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -11,9 +11,6 @@
-     add_compile_definitions("USE_HDF5=ON")
- endif(USE_HDF5)
- 
--set(EXT_PROJECTS_DIR ${PROJECT_SOURCE_DIR}/ext)
--set(CMAKE_CXX_FLAGS_PROFILE "-g")
--
- # Set Release type for builds where CMAKE_BUILD_TYPE is unset
- # This is usually a good default as this implictly enables
- #
-@@ -33,44 +30,12 @@
-     set(CMAKE_CXX_EXTENSIONS OFF)
- endif()
- 
--#add_compile_options(-Wall -Wno-unused-function)
--
--if(LINK MATCHES static)
--    message("static build")
--ELSE(LINK MATCHES shared)
--    message("shared build")
--ENDIF(LINK MATCHES static)
--
--
--include(ExternalProject)
--ExternalProject_Add(htslib
--    PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
--    SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib
--    BUILD_IN_SOURCE 1
--    CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure 
--        --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
--    BUILD_COMMAND make lib-static
--    INSTALL_COMMAND ""
--)
--
--include_directories(${htslib_PREFIX}/src/htslib)
--
--
--
--# add_compile_options(-Wdeprecated-register)
--
- add_subdirectory(src)
--include_directories(${EXT_PROJECTS_DIR})
- 
- option(BUILD_TESTING "Build unit tests." OFF)
- include(CTest)
- 
- if (BUILD_TESTING)
--    add_subdirectory(${EXT_PROJECTS_DIR}/catch)
--
--    # Includes Catch in the project:
--    include_directories(${CATCH_INCLUDE_DIR} ${COMMON_INCLUDES})
--
-     add_subdirectory(unit_tests)
- endif(BUILD_TESTING)
- 
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -3,30 +3,17 @@
- 
- list(REMOVE_ITEM sources main.cpp)
- 
--include_directories(../ext/htslib)
--
- add_library(kallisto_core ${sources} ${headers})
- target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
- 
- add_executable(kallisto main.cpp)
- 
--find_package( Threads REQUIRED )
--target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)
--
--if(LINK MATCHES static)
--    set(BUILD_SHARED_LIBS OFF)
--    set(HDF5_USE_STATIC_LIBRARIES 1)
--
--    if (UNIX AND NOT APPLE)
--        #set(CMAKE_EXE_LINKER_FLAGS  "-static -static-libgcc -static-libstdc++")
--        set(CMAKE_EXE_LINKER_FLAGS  "-static -static-libstdc++")
--        SET(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
--        set(CMAKE_EXE_LINKER_FLAGS  "-static -static-libgcc -static-libstdc++")
--    endif(UNIX AND NOT APPLE)
--
--    SET_TARGET_PROPERTIES(kallisto kallisto_core PROPERTIES LINK_SEARCH_END_STATIC 1)
--endif(LINK MATCHES static)
-+find_package( PkgConfig REQUIRED )
-+pkg_check_modules( HTSLIB REQUIRED htslib )
- 
-+find_package( Threads REQUIRED )
-+target_include_directories(kallisto PRIVATE ${HTSLIB_CFLAGS})
-+target_link_libraries(kallisto PRIVATE kallisto_core Threads::Threads ${HTSLIB_LDFLAGS})
- 
- if(USE_HDF5)
-     find_package( HDF5 REQUIRED )
-@@ -36,7 +23,7 @@
- 
- if ( ZLIB_FOUND )
-     include_directories( ${ZLIB_INCLUDE_DIRS} )
--    target_link_libraries(kallisto kallisto_core ${ZLIB_LIBRARIES})
-+    target_link_libraries(kallisto PRIVATE kallisto_core ${ZLIB_LIBRARIES})
- else()
-     message(FATAL_ERROR "zlib not found. Required for to output files" )
- endif( ZLIB_FOUND )
-@@ -44,22 +31,17 @@
- if(USE_HDF5)
-     if(HDF5_FOUND)
-         include_directories( ${HDF5_INCLUDE_DIRS} )
--        target_link_libraries( kallisto_core ${HDF5_LIBRARIES} )
--        target_link_libraries( kallisto ${HDF5_LIBRARIES} )
-+        target_link_libraries( kallisto_core PRIVATE ${HDF5_LIBRARIES} )
-+        target_link_libraries( kallisto PRIVATE ${HDF5_LIBRARIES} )
-     else()
-         message(FATAL_ERROR "HDF5 not found. Required to output files")
-     endif()
- endif(USE_HDF5)
- 
--if(LINK MATCHES static)
--    if (UNIX AND NOT APPLE)
--        target_link_libraries(kallisto librt.a)
--    endif()
--else()
--    if (UNIX AND NOT APPLE)
--        target_link_libraries(kallisto rt)
--    endif()
--endif(LINK MATCHES static)
--
-+target_compile_options( kallisto_core PRIVATE ${HTSLIB_CFLAGS} )
-+target_link_libraries( kallisto_core PRIVATE ${HTSLIB_LDFLAGS} )
- 
--install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
-\ No newline at end of file
-+install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
-+if ( BUILD_SHARED_LIBS )
-+    install(TARGETS kallisto_core DESTINATION "${CMAKE_INSTALL_LIBDIR}")
-+endif()
---- a/unit_tests/CMakeLists.txt
-+++ b/unit_tests/CMakeLists.txt
-@@ -8,6 +8,10 @@
- add_executable(tests ${sources})
- add_test(unittest tests)
- 
-+find_package( Catch2 REQUIRED )
-+include_directories( ${Catch2_INCLUDE_DIRS} )
-+target_link_libraries( tests Catch2::Catch2WithMain )
-+
- find_package( ZLIB REQUIRED )
- if ( ZLIB_FOUND )
-     include_directories( ${ZLIB_INCLUDE_DIRS} )
diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch b/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch
deleted file mode 100644
index 19594f067776..000000000000
--- a/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-From 1d63e9d731bada64f6038818e27f06da63007d73 Mon Sep 17 00:00:00 2001
-From: Nilesh Patra <npatra974@gmail.com>
-Date: Thu, 4 Mar 2021 23:38:30 +0530
-Subject: [PATCH] Fix GCC-11 Build Failure: include limits lib
-
----
- src/MinCollector.h | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/src/MinCollector.h b/src/MinCollector.h
-index a905f1f..c4460fb 100644
---- a/src/MinCollector.h
-+++ b/src/MinCollector.h
-@@ -7,6 +7,7 @@
- #include <sstream>
- #include <vector>
- #include <unordered_map>
-+#include <limits>
- 
- #include "KmerIndex.h"
- #include "weights.h"
diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch b/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch
deleted file mode 100644
index 0e926136261c..000000000000
--- a/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch
+++ /dev/null
@@ -1,52 +0,0 @@
---- a/src/KmerIndex.cpp
-+++ b/src/KmerIndex.cpp
-@@ -4,7 +4,7 @@
- #include <ctype.h>
- #include <zlib.h>
- #include <unordered_set>
--#include "kseq.h"
-+#include <htslib/kseq.h>
- 
- #ifndef KSEQ_INIT_READY
- #define KSEQ_INIT_READY
---- a/src/ProcessReads.cpp
-+++ b/src/ProcessReads.cpp
-@@ -1,6 +1,6 @@
- /*
- #include <zlib.h>
--#include "kseq.h"
-+#include <htslib/kseq.h>
- #include <string>
- #include <vector>
- #include <unordered_map>
-@@ -20,7 +20,7 @@
- #include <iomanip>
- 
- #include "ProcessReads.h"
--#include "kseq.h"
-+#include <htslib/kseq.h>
- #include "PseudoBam.h"
- #include "Fusion.hpp"
- #include "BUSData.h"
---- a/src/ProcessReads.h
-+++ b/src/ProcessReads.h
-@@ -2,7 +2,7 @@
- #define KALLISTO_PROCESSREADS_H
- 
- #include <zlib.h>
--#include "kseq.h"
-+#include <htslib/kseq.h>
- #include <string>
- #include <vector>
- #include <unordered_map>
---- a/unit_tests/test_kmerhashtable.cpp
-+++ b/unit_tests/test_kmerhashtable.cpp
-@@ -13,7 +13,7 @@
- #include "KmerHashTable.h"
- 
- #include <zlib.h>
--#include "kseq.h"
-+#include <htslib/kseq.h>
- 
- #ifndef KSEQ_INIT_READY
- #define KSEQ_INIT_READY
diff --git a/sci-biology/kallisto/kallisto-0.46.2-r1.ebuild b/sci-biology/kallisto/kallisto-0.46.2-r1.ebuild
deleted file mode 100644
index 32a97d6d39df..000000000000
--- a/sci-biology/kallisto/kallisto-0.46.2-r1.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake flag-o-matic
-
-DESCRIPTION="Near-optimal RNA-Seq quantification"
-HOMEPAGE="http://pachterlab.github.io/kallisto/"
-
-if [[ ${PV} == *9999 ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/pachterlab/kallisto.git"
-else
-	SRC_URI="https://github.com/pachterlab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="hdf5 test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
-	sci-libs/htslib:=
-	virtual/zlib:=
-	hdf5? ( sci-libs/hdf5:= )"
-DEPEND="
-	${RDEPEND}
-	test? (
-		>=dev-cpp/catch-3:0
-		sci-libs/hdf5
-	)"
-BDEPEND="virtual/pkgconfig"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-cmake.patch
-	"${FILESDIR}"/${P}-htslib.patch
-	"${FILESDIR}"/${P}-catch2.patch
-	"${FILESDIR}"/${P}-gcc11.patch
-)
-
-src_prepare() {
-	cmake_src_prepare
-	# bundled catch2
-	rm -r ext || die
-	# bundled htslib structs
-	rm src/kseq.h || die
-
-	# the test suite is cheesy and relies on a
-	# specific builddir nesting structure.
-	sed -e "s|../test/input/short_reads.fastq|$(readlink -f unit_tests/input/short_reads.fastq)|g" \
-		-i unit_tests/test_kmerhashtable.cpp || die
-
-	# This randomly hardcodes a particular std, which unfortunately is too old for catch2.
-	sed -i '/CMAKE_CXX_STANDARD/d' CMakeLists.txt || die
-	append-cxxflags -std=c++14
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DUSE_HDF5=$(usex hdf5)
-		-DBUILD_TESTING=$(usex test)
-		# convenience library only
-		-DBUILD_SHARED_LIBS=OFF
-	)
-	cmake_src_configure
-}
diff --git a/sci-biology/kallisto/metadata.xml b/sci-biology/kallisto/metadata.xml
deleted file mode 100644
index 5d84bfa5c986..000000000000
--- a/sci-biology/kallisto/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">pachterlab/kallisto</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/lagan/Manifest b/sci-biology/lagan/Manifest
deleted file mode 100644
index 875b053d65f3..000000000000
--- a/sci-biology/lagan/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST lagan20.tar.gz 589115 BLAKE2B 8aaee40b767d7c1828760449e3bf2718210ad345447524ec2c391eb9f2856023f9258618d3d2625b15c42af814615870082bff6320ba0372dff79221798d2618 SHA512 f77217ab534df33834a725eb6e1b716f7bbffa98768a42c2294a6ab62404192e560bb05ffd41e4cdccb5b96ef9efceb8ecdc06472bbc6a301e1d11572ba29b98
diff --git a/sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch b/sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch
deleted file mode 100644
index 2c9d88111aee..000000000000
--- a/sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch
+++ /dev/null
@@ -1,258 +0,0 @@
---- a/src/fchaos.c
-+++ b/src/fchaos.c
-@@ -985,7 +985,7 @@
-   SLremove(mylist, tbf->mysles[i]);
- }
- 
--inline int CHmatchscore(unsigned char a, unsigned char b) {
-+static inline int CHmatchscore(unsigned char a, unsigned char b) {
-   return substmatrix[a][b];
-   /*
-   if (translated)
---- a/src/multial.c
-+++ b/src/multial.c
-@@ -59,16 +59,16 @@
- int normf;
- int normprev;
- 
--inline int ismatch(char a, char b) {
-+static inline int ismatch(char a, char b) {
-   return (a == b);
- }
- 
--inline int isGap(align* ali, int seqn, int loc) {
-+static inline int isGap(align* ali, int seqn, int loc) {
-   int i = !((ali->algn[loc] >> seqn) & 1);
-   return i;
- }
- 
--inline int scoreLocal(int which, align* ali, int loc) {
-+static inline int scoreLocal(int which, align* ali, int loc) {
-   int i, lets = 0;
-   for (i=0; i < 4; i++)
-     lets += ali->cnts[i][loc];
-@@ -83,7 +83,7 @@
-     return lets+ali->cnts[CNTS_GS][loc] * gapcont;
- }
- 
--inline hll* reverseHLL(hll* tbr) {
-+static inline hll* reverseHLL(hll* tbr) {
-   hll *nn, *prev=0;
-   while (tbr) {
-     nn = tbr->next;
-@@ -171,7 +171,7 @@
-   return res;
- }
- 
--inline void reverse (long long int* a, int length) {
-+static inline void reverse (long long int* a, int length) {
-   long long int lft;
-   int i;
-   for (i=0; i < length/2; i++) {
-@@ -409,7 +409,7 @@
-   */
- }
- 
--inline int scoreGap(int numgs, int numgc, int numge, int numseq) {
-+static inline int scoreGap(int numgs, int numgc, int numge, int numseq) {
-   return (MIN2(numgc, numseq-numgc) * gapcont) +
-     (MIN2(numgs, numseq-numgs) * gapstart) +
-     (MIN2(numge, numseq-numge) * gapend);
-@@ -493,7 +493,7 @@
-   fclose (file);
- }
- 
--inline int chmatchscore (unsigned char a, unsigned char b, int substmatrix[256][256]) {
-+static inline int chmatchscore (unsigned char a, unsigned char b, int substmatrix[256][256]) {
-   return substmatrix[a][b];
- }
- 
-@@ -539,14 +539,14 @@
-   // printcache();
- }
- 
--inline int v (int y){
-+static inline int v (int y){
-   if (y >= 0 && y <= MAX_SEQ) return y;
-   fprintf(stderr, "Got %d in v\n", y);
-   assert (0);
-   return 0;
- }
- 
--inline int matchscore (align*a, int ai, align *b, int bi){
-+static inline int matchscore (align*a, int ai, align *b, int bi){
-   
-   return
-     matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | 
-@@ -559,30 +559,30 @@
- 	    (v(a->numseq + b->numseq - (a->cnts[CNTS_CB][ai] + b->cnts[CNTS_CB][bi])) << 18)];
- }
- 
--inline int scoreOpp (align *other, int ow, int oppnum){
-+static inline int scoreOpp (align *other, int ow, int oppnum){
-   return matchcache[v(other->cnts[0][ow]) | 
- 		   (v(other->cnts[1][ow]) << 6) |
- 		   (v(other->cnts[2][ow]) << 12) |
- 		   (v(other->cnts[3][ow]) << 18)];
- }
- 
--inline int endGap0 (align* a, int ai, align* b, int bi){
-+static inline int endGap0 (align* a, int ai, align* b, int bi){
-   return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | 
- 		  (v(a->numseq + b->numseq-(b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)];
- }
- 
--inline int endGap1 (align* a, int ai, align* b, int bi){
-+static inline int endGap1 (align* a, int ai, align* b, int bi){
- 
-   return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | 
- 		  (v(a->numseq + b->numseq - (b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)];
- }
- 
--inline int endGap2 (align* a, int ai, align* b, int bi){
-+static inline int endGap2 (align* a, int ai, align* b, int bi){
-   return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | 
- 		  (v(a->numseq + b->numseq - (b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)];
- }
- 
--inline int contGap(align* ali, int myw, align* other, int ow, int *sopp) {
-+static inline int contGap(align* ali, int myw, align* other, int ow, int *sopp) {
-   return gapcache[(v(other->cnts[CNTS_GS][ow])) |
- 		  (v(ali->numseq + other->cnts[CNTS_GC][ow]) << 6) |
- 		  (v(other->cnts[CNTS_GE][ow]) << 12) |
-@@ -590,7 +590,7 @@
-     sopp[ow];
- }
- 
--inline int openGap(align* ali, int w, align* other, int ow, int *sopp, char *desc) {
-+static inline int openGap(align* ali, int w, align* other, int ow, int *sopp, char *desc) {
-   int alopen, pen, sav, i;
- 
-   alopen = ali->cnts[CNTS_GC][w] + ali->cnts[CNTS_GE][w];
---- a/src/order.c
-+++ b/src/order.c
-@@ -454,11 +454,11 @@
- }
- 
- 
--inline int ismatch(char a, char b) {
-+static inline int ismatch(char a, char b) {
-   return a == b;
- }
- 
--inline int matchscore (unsigned char a, unsigned char b) {
-+static inline int matchscore (unsigned char a, unsigned char b) {
-   return substmatrix[a][b];
-   /*
-     
---- a/src/utils/cstat.c
-+++ b/src/utils/cstat.c
-@@ -121,7 +121,7 @@
-   return res;
- }
- 
--inline int getScore (align* a, int i){
-+static inline int getScore (align* a, int i){
-   return
-     ((a->cnts[0][i] * (a->cnts[0][i] - 1)) +
-      (a->cnts[1][i] * (a->cnts[1][i] - 1)) +
---- a/src/utils/getbounds.c
-+++ b/src/utils/getbounds.c
-@@ -6,8 +6,8 @@
- 
- #define EXPAND 2
- 
--inline int max (int a, int b){ if (a > b) return a; return b; }
--inline int min (int a, int b){ if (a < b) return a; return b; }
-+static inline int max (int a, int b){ if (a > b) return a; return b; }
-+static inline int min (int a, int b){ if (a < b) return a; return b; }
- 
- int getLength (char *filename){
-   FILE *file;
---- a/src/utils/scorealign.c
-+++ b/src/utils/scorealign.c
-@@ -18,17 +18,17 @@
- int matchscore[256][256];
- int gapopen = -1500, gapcont = -50;
- 
--inline int min (int a, int b){
-+static inline int min (int a, int b){
-   if (a < b) return a;
-   return b;
- }
- 
--inline int max (int a, int b){
-+static inline int max (int a, int b){
-   if (a > b) return a;
-   return b;
- }
- 
--inline int scoreMatch (char c, char d){
-+static inline int scoreMatch (char c, char d){
-   if (c == '-' && d == '-') return 0;
-   if (c == '-' || d == '-') return gapcont;
-   return matchscore[(unsigned char) c][(unsigned char) d];
-@@ -235,7 +235,7 @@
-   }
- }
- 
--inline int issymbol (char ch){
-+static inline int issymbol (char ch){
-   return ch == 'A' || ch == 'C' || ch == 'G' || ch == 'T' || ch == 'N' || ch == '.' || ch == '-';
- }
- 
---- a/src/utils/scorecontigs.c
-+++ b/src/utils/scorecontigs.c
-@@ -133,7 +133,7 @@
-   return res;
- }
- 
--inline int getstate (char c, char d){
-+static inline int getstate (char c, char d){
-   if (c == '-' || d == '-') return 2;
-   if (c == 'N' || d == 'N') return 3;
-   return c == d;
-@@ -235,7 +235,7 @@
-   return r;
- }
- 
--inline int getdata (rangelist **ranges, int *offs, int j, int i){
-+static inline int getdata (rangelist **ranges, int *offs, int j, int i){
-   i -= offs[j];
-   if (i >= 0 && i < ranges[j]->seqlen)
-     return ranges[j]->score[i];
-@@ -243,14 +243,14 @@
- }
- 
- 
--inline int match (rangelist **ranges, int numContigs, int i, int j, int *offs){
-+static inline int match (rangelist **ranges, int numContigs, int i, int j, int *offs){
-   int k;
-   for (k = 0; k < numContigs; k++)
-     if ((getdata (ranges, offs, k, i) != 0) != (getdata (ranges, offs, k, j) != 0)) return 0;
-   return 1;
- }
- 
--inline int allzeroes (rangelist **ranges, int numContigs, int pos, int *offs){
-+static inline int allzeroes (rangelist **ranges, int numContigs, int pos, int *offs){
-   int i;
- 
-   for (i = 0; i < numContigs; i++)
-@@ -258,7 +258,7 @@
-   return 1;
- }
- 
--inline void print (int start, int end, int *score, int numContigs){
-+static inline void print (int start, int end, int *score, int numContigs){
-   int j;
- 
-   printf ("(%7d %7d)", start, end);
-@@ -303,7 +303,7 @@
-   free (pattern);
- }
- 
--inline double scoregap (int gaplen){
-+static inline double scoregap (int gaplen){
-   if (gaplen == 0) return 0;
-   //return (gaplen - 1) * -1 - 50;
-   return (log (gaplen) / log (10) + 1) * scoreGapOpen;
diff --git a/sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch b/sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch
deleted file mode 100644
index 945120b1fc47..000000000000
--- a/sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch
+++ /dev/null
@@ -1,49 +0,0 @@
-Author: Steffen Moeller
-Last-Update: 2018-09-07 15:08:19 +0200
-Description: Fix build issue
-
-Index: lagan/src/glocal/rightinfluence.cpp
-===================================================================
---- lagan.orig/src/glocal/rightinfluence.cpp
-+++ lagan/src/glocal/rightinfluence.cpp
-@@ -1,6 +1,6 @@
- #include <rightinfluence.h>
- 
--Fragment origin, end;
-+static Fragment originFrag, endFrag;
- 
- // Sets the first default owner of the whole region
- void initRI(RI *RightInfluence, long long int scoreIndex) {
-@@ -13,22 +13,22 @@ void initRI(RI *RightInfluence, long lon
- 	}
- 
- 	// will lose to anyone
--	origin.seq1End = 0; origin.seq2End = 0;
--    origin.seq1Start = 0; origin.seq2Start = 0;
-+	originFrag.seq1End = 0; originFrag.seq2End = 0;
-+    originFrag.seq1Start = 0; originFrag.seq2Start = 0;
- 
- 	// hack to aid winner selection
--	origin.score = -1;
--	end.score = -2;
--	origin.totalScore = end.totalScore = 0;
-+	originFrag.score = -1;
-+	endFrag.score = -2;
-+	originFrag.totalScore = endFrag.totalScore = 0;
- 
- 	// will win against anyone
--	end.seq1End = 0; end.seq2End = 0;
--	end.seq1Start = 0; end.seq2Start = 0;
-+	endFrag.seq1End = 0; endFrag.seq2End = 0;
-+	endFrag.seq1Start = 0; endFrag.seq2Start = 0;
- 
--	origin.back = NULL;
-+	originFrag.back = NULL;
- 
--    RightInfluence->act[-INF] = &origin;
--    RightInfluence->act[+INF] = &end;
-+    RightInfluence->act[-INF] = &originFrag;
-+    RightInfluence->act[+INF] = &endFrag;
- }
- 
- 
diff --git a/sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch b/sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch
deleted file mode 100644
index 075753a924c9..000000000000
--- a/sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Author: Andreas Tille <tille@debian.org>
-LastChanged: Fri, 15 Nov 2013 10:31:20 +0100
-Description: Prevent conflicting getline by simply renaming it
-
---- a/src/anchors.c
-+++ b/src/anchors.c
-@@ -225,7 +225,7 @@ char* rolltonum(char* str) {
-   return &str[i];
- }
- 
--int getline(FILE* infile, hll* tt) {
-+int anchors_getline(FILE* infile, hll* tt) {
-   char temp[1024];
-   char* help;
-   int z, h;
-@@ -248,7 +248,7 @@ hll* parseCHAOS(FILE* infile, int* totnu
-   *totnum = 0;
-   while(!feof(infile)) {
-     tt = (hll*) malloc(sizeof(hll));
--    while (!feof(infile) && !getline(infile, tt))
-+    while (!feof(infile) && !anchors_getline(infile, tt))
-       ;
-     if (feof(infile)) break;
-     if (gapfreechunks) {
diff --git a/sci-biology/lagan/files/lagan-2.0-gcc-10.patch b/sci-biology/lagan/files/lagan-2.0-gcc-10.patch
deleted file mode 100644
index bd9824cf2ed0..000000000000
--- a/sci-biology/lagan/files/lagan-2.0-gcc-10.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-Description: Add patch to build with GCC-10
-Bug-Debian: https://bugs.debian.org/957415
-Author: Nilesh Patra <npatra974@gmail.com>
-Date:   Fri Apr 17 21:13:21 2020 +0530
-
---- a/src/fchaos.c
-+++ b/src/fchaos.c
-@@ -29,7 +29,7 @@
-   int offset;
- } match;
- 
--extern int indeces[256];
-+int indeces[256];
- 
- 
- void remElem(LList* tbf, int i);
---- a/src/thrtrie.h
-+++ b/src/thrtrie.h
-@@ -2,7 +2,7 @@
- #define MAX_DEGEN 2
- 
- 
--int indeces[256];
-+extern int indeces[256];
- 
- typedef struct PrevHits {
-   int* inds1;
diff --git a/sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch b/sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch
deleted file mode 100644
index 3d7ed780445f..000000000000
--- a/sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-Author: Andreas Tille <tille@debian.org>
-LastChanged: Fri, 15 Nov 2013 10:31:20 +0100
-Description: Fix some includes to build using gcc-4.8
-
---- a/src/utils/Glue.cpp
-+++ b/src/utils/Glue.cpp
-@@ -6,6 +6,7 @@
- #include <fstream>
- #include <iostream>
- #include <algorithm>
-+#include <string.h>
- 
- #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt"
- #define MAX_LINE_LENGTH 1024
---- a/src/glocal/score.cpp
-+++ b/src/glocal/score.cpp
-@@ -2,7 +2,7 @@
- #include<score.h>
- #include<leftinfluence.h>
- #include<rightinfluence.h>
--#include<fstream.h>
-+#include<fstream>
- 
- extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
- 
diff --git a/sci-biology/lagan/files/lagan-2.0-gcc-9.patch b/sci-biology/lagan/files/lagan-2.0-gcc-9.patch
deleted file mode 100644
index 6ea30e57a854..000000000000
--- a/sci-biology/lagan/files/lagan-2.0-gcc-9.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-# Two patches to bring lagan up to speed with gcc-9
-Index: lagan/src/fchaos.c
-===================================================================
---- lagan.orig/src/fchaos.c
-+++ lagan/src/fchaos.c
-@@ -430,7 +430,7 @@ int chain(LList* second, int off2, LList
- int tc =0;
- int wc = 0;
- 
--inline void findPrev(LList* curr, int position, int offset, float baseval) {
-+void findPrev(LList* curr, int position, int offset, float baseval) {
-   int j,k;
-   LList* temp;
-   sle* iterator;
-Index: lagan/src/filebuffer.c
-===================================================================
---- lagan.orig/src/filebuffer.c
-+++ lagan/src/filebuffer.c
-@@ -1,5 +1,6 @@
- #include "filebuffer.h"
- #include <stdlib.h>
-+#include <ctype.h>
- #include <string.h>
- #include <stdio.h>
- #include <assert.h>
diff --git a/sci-biology/lagan/files/lagan-2.0-makefile.patch b/sci-biology/lagan/files/lagan-2.0-makefile.patch
deleted file mode 100644
index 1bef6721ab9b..000000000000
--- a/sci-biology/lagan/files/lagan-2.0-makefile.patch
+++ /dev/null
@@ -1,120 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -1,5 +1,8 @@
- all:
--	(cd src; $(MAKE))
-+	$(MAKE) -C src
- clean:
- 	rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay
--	(cd src; $(MAKE) clean)
-+	$(MAKE) -C src clean
-+
-+check:	all
-+	(LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]"
---- a/src/glocal/Makefile
-+++ b/src/glocal/Makefile
-@@ -1,19 +1,13 @@
--CC = g++
--OPTFLAGS = 
--CFLAGS = $(OPTFLAGS) -O3
--CLINKER = g++ 
--# LIBDIR = -L/usr/local/lib
-+CXXFLAGS += -Wno-deprecated
-+CPPFLAGS += -I./
-+
- MLIB =  -lm
--INCDIR =   -I./
- TRGT_DIR = ../..
- TRGT = glocal
- OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o
- 
--.cpp.o:
--	$(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp
--
- $(TRGT): $(OBJECTS)
--	$(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
- 
- clean :
- 	rm -f *.o ./*~ *~ core
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -1,54 +1,51 @@
--CC = gcc $(CFLAGS)
--CPP = g++ $(CFLAGS)
--CFLAGS = -O3 # -Wall -W
- TRGT_DIR = ..
- 
- all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay
--	(cd glocal; $(MAKE))
-+	(cd glocal && $(MAKE))
- clean: 
- 	rm -f *.o *~ utils/*~ mlagan.purify core
--	(cd glocal; $(MAKE) clean)
-+	(cd glocal && $(MAKE) clean)
- ../anchors: anchors.c skiplist.c
--	$(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
- ../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c
--	$(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
- ../order: order.c diagmatrix.c filebuffer.c
--	$(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
- ../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
--	$(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
- ../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
--	$(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
- ../utils/bin2mf: utils/bin2mf.c
--	$(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
- ../utils/bin2bl: utils/bin2bl.c
--	$(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
- ../utils/cextract: utils/cextract.c
--	$(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
- ../utils/cstat: utils/cstat.c
--	$(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
- ../utils/contigorder: utils/contigorder.c
--	$(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
- ../utils/getbounds: utils/getbounds.c
--	$(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
- ../utils/getcontigpos: utils/getcontigpos.c
--	$(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
- ../utils/getlength: utils/getlength.c
--	$(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
- ../utils/getoverlap: utils/getoverlap.c
--	$(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
- ../utils/rc: utils/rc.c
--	$(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c
- ../utils/seqmerge: utils/seqmerge.c
--	$(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
- ../utils/scorealign: utils/scorealign.c
--	$(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
- ../utils/scorecontigs: utils/scorecontigs.c
--	$(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
- ../utils/fa2xfa: utils/fa2xfa.c
--	$(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
- ../utils/overlay: utils/overlay.c
--	$(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
- ../utils/Glue: utils/Glue.cpp
--	$(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
- ../utils/dotplot: utils/dotplot.cpp
--	$(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
diff --git a/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch b/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch
deleted file mode 100644
index 29db043d5f34..000000000000
--- a/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch
+++ /dev/null
@@ -1,61 +0,0 @@
---- a/src/mlagan.c
-+++ b/src/mlagan.c
-@@ -46,6 +46,7 @@
-     return 1;
- }
- 
-+int printXMFAAlign(FILE* outfile, align* myalign);
- 
- void usage(void) {
-   printf("mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\n\n",
---- a/src/order.c
-+++ b/src/order.c
-@@ -28,6 +28,8 @@
- 
- align* makeAlign(dmat* mydm, char* seq1, char* seq2);
- 
-+int printMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2);
-+int printXMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2);
- 
- char* alpha = "ATCGN.";
- 
---- a/src/prolagan.c
-+++ b/src/prolagan.c
-@@ -49,6 +49,7 @@
-     return 1;
- }
- 
-+int printXMFAAlign(FILE* outfile, align* myalign);
- 
- void usage(void) {
-   printf("mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\n\n",
---- a/src/utils/cstat.c
-+++ b/src/utils/cstat.c
-@@ -3,6 +3,7 @@
- #include <string.h>
- #include <math.h>
- #include <assert.h>
-+#include <ctype.h>
- 
- #define MAX_SEQ 31
- #define MAX(a,b) ((a)>(b)?(a):(b))
---- a/src/utils/overlay.c
-+++ b/src/utils/overlay.c
-@@ -2,6 +2,7 @@
- #include <stdio.h>
- #include <assert.h>
- #include <string.h>
-+#include <ctype.h>
- 
- #define MAX_SEQS 63
- #define MIN2(y,z)        ((y)<(z))?(y):(z)
---- a/src/utils/scorecontigs.c
-+++ b/src/utils/scorecontigs.c
-@@ -3,6 +3,7 @@
- #include <string.h>
- #include <math.h>
- #include <assert.h>
-+#include <ctype.h>
- 
- #define MAX_SEQ 1024
- #define MAX(a,b) ((a)>(b)?(a):(b))
diff --git a/sci-biology/lagan/lagan-2.0-r4.ebuild b/sci-biology/lagan/lagan-2.0-r4.ebuild
deleted file mode 100644
index 4582d8f1078e..000000000000
--- a/sci-biology/lagan/lagan-2.0-r4.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-MY_P="lagan20"
-
-DESCRIPTION="The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA"
-HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
-SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-lang/perl"
-
-S="${WORKDIR}/${MY_P}"
-PATCHES=(
-	"${FILESDIR}"/${P}-makefile.patch
-	"${FILESDIR}"/${P}-conflicting-getline.patch
-	"${FILESDIR}"/${P}-gcc-4.8.patch
-	"${FILESDIR}"/${P}-ambiguous-end.patch
-	"${FILESDIR}"/${P}-gcc-9.patch
-	"${FILESDIR}"/${P}-gcc-10.patch
-	"${FILESDIR}"/${P}-C99-static-inline.patch
-	"${FILESDIR}"/${P}-qa-implicit-declarations.patch
-)
-
-src_prepare() {
-	default
-	sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/lagan/lib\";" \
-		supermap.pl || die
-}
-
-src_configure() {
-	tc-export CC CXX
-}
-
-src_install() {
-	newbin lagan.pl lagan
-	newbin slagan.pl slagan
-	dobin mlagan
-	rm lagan.pl slagan.pl utils/Utils.pm || die
-
-	insinto /usr/$(get_libdir)/lagan/lib
-	doins Utils.pm
-
-	exeinto /usr/$(get_libdir)/lagan/utils
-	doexe utils/*
-
-	exeinto /usr/$(get_libdir)/lagan
-	doexe *.pl anchors chaos glocal order prolagan
-
-	insinto /usr/$(get_libdir)/lagan
-	doins *.txt
-
-	dosym ../$(get_libdir)/lagan/supermap.pl /usr/bin/supermap
-
-	newenvd - 99lagan <<- _EOF_
-		LAGAN_DIR="${EPREFIX}/usr/$(get_libdir)/lagan"
-	_EOF_
-
-	dodoc Readmes/README.*
-}
diff --git a/sci-biology/lagan/metadata.xml b/sci-biology/lagan/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/lagan/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/libgtextutils/Manifest b/sci-biology/libgtextutils/Manifest
deleted file mode 100644
index 9480b9ec6419..000000000000
--- a/sci-biology/libgtextutils/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST libgtextutils-0.6.1.tar.bz2 273459 BLAKE2B 81b1e9b467287ed9551fc53abddf5757efb2dd1c98f0388e2128535fbe70b706badd5702a5b5c3cb19a34c26ffa218c9c41caf9f17770a015b09fc13fabe4d53 SHA512 0bc392385f9e6c345dff82b3fb04f322e8aceca769e15a3a87da6c718b6e9a7e1de082940d4bb0339a4c3a86f706fde0de047df459682aa9ea216d6e5c17eab6
diff --git a/sci-biology/libgtextutils/files/libgtextutils-0.6.1-fix-build-system.patch b/sci-biology/libgtextutils/files/libgtextutils-0.6.1-fix-build-system.patch
deleted file mode 100644
index f7f608b792d2..000000000000
--- a/sci-biology/libgtextutils/files/libgtextutils-0.6.1-fix-build-system.patch
+++ /dev/null
@@ -1,61 +0,0 @@
---- a/configure.ac
-+++ b/configure.ac
-@@ -15,7 +15,7 @@
- 
- AC_CONFIG_AUX_DIR(config)
- AC_CONFIG_MACRO_DIR([m4])
--AM_CONFIG_HEADER(config.h)
-+AC_CONFIG_HEADERS([config.h])
- AM_INIT_AUTOMAKE([dist-bzip2])
- 
- # dynamic library version
-@@ -25,12 +25,12 @@
- 
- AC_PROG_CC
- AC_PROG_CXX
--AC_PROG_LIBTOOL
-+LT_INIT
- 
- dnl --enable-wall
--EXTRA_CHECKS="-Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror"
-+EXTRA_CHECKS="-Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal"
- AC_ARG_ENABLE(wall,
--[  --enable-wall          Enable many common GCC warnings (-Wall,-Wextra, -Werror etc., default enabled)],
-+[  --enable-wall          Enable many common GCC warnings (-Wall,-Wextra etc., default enabled)],
- [case "${enableval}" in
-   yes) wall=true ;;
-   no)  wall=false ;;
-@@ -42,22 +42,6 @@
-   CXXFLAGS="${CXXFLAGS} ${EXTRA_CHECKS}"
- fi
- 
--dnl --enable-debug
--AC_ARG_ENABLE(debug,
--[  --enable-debug          Enable debug mode (default enabled)],
--[case "${enableval}" in
--  yes) debug=true ;;
--  no)  debug=false ;;
--  *) AC_MSG_ERROR(bad value ${enableval} for --enable-debug) ;;
--esac],[debug=true])
--if test "$debug" = "true"
--then
--  CFLAGS="${CFLAGS} -DDEBUG -g -O1"
--  CXXFLAGS="${CFLAGS} -DDEBUG -g -O1"
--else
--  CFLAGS="${CFLAGS} -O3"
--  CXXFLAGS="${CFLAGS} -O3"
--fi
- 
- 
- dnl --enable-tuple-parser-check
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -9,7 +9,7 @@
- # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
- 
- EXTRA_DIST = reconf configure
--SUBDIRS = m4 src doc tests
-+SUBDIRS = src doc tests
- 
- pkgconfigdir = $(libdir)/pkgconfig
- pkgconfig_DATA = gtextutils.pc
diff --git a/sci-biology/libgtextutils/files/libgtextutils-0.6.1-gcc6.patch b/sci-biology/libgtextutils/files/libgtextutils-0.6.1-gcc6.patch
deleted file mode 100644
index 490b4be9b91b..000000000000
--- a/sci-biology/libgtextutils/files/libgtextutils-0.6.1-gcc6.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From d8bb66d26288293ebde7f8d88979c13c208ffce5 Mon Sep 17 00:00:00 2001
-From: Assaf Gordon <assafgordon@gmail.com>
-Date: Mon, 14 Aug 2017 11:52:09 -0600
-Subject: [PATCH] text_line_reader: adjust to new compilers
-
-Fixes https://github.com/agordon/libgtextutils/issues/10 .
----
- src/gtextutils/text_line_reader.cpp | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/gtextutils/text_line_reader.cpp b/src/gtextutils/text_line_reader.cpp
-index fede933..f0984d5 100644
---- a/src/gtextutils/text_line_reader.cpp
-+++ b/src/gtextutils/text_line_reader.cpp
-@@ -44,6 +44,6 @@ bool TextLineReader::next_line()
- 	if (input_stream.eof())
- 		return false;
- 
--	return input_stream ;
-+	return input_stream.good() ;
- }
- 
diff --git a/sci-biology/libgtextutils/libgtextutils-0.6.1-r1.ebuild b/sci-biology/libgtextutils/libgtextutils-0.6.1-r1.ebuild
deleted file mode 100644
index 2ffb1c3338b8..000000000000
--- a/sci-biology/libgtextutils/libgtextutils-0.6.1-r1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools
-
-DESCRIPTION="Gordon Text utils Library"
-HOMEPAGE="http://hannonlab.cshl.edu/fastx_toolkit/"
-SRC_URI="http://hannonlab.cshl.edu/fastx_toolkit/${P}.tar.bz2"
-
-LICENSE="AGPL-3"
-SLOT="0/0"
-KEYWORDS="~amd64 ~x86"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-fix-build-system.patch
-	"${FILESDIR}"/${P}-gcc6.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_install() {
-	default
-
-	find "${ED}" -name '*.la' -delete || die
-}
diff --git a/sci-biology/libgtextutils/metadata.xml b/sci-biology/libgtextutils/metadata.xml
deleted file mode 100644
index 2de5d595743e..000000000000
--- a/sci-biology/libgtextutils/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person" proxied="yes">
-		<email>mmokrejs@gmail.com</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
deleted file mode 100644
index 0cf31ad3c018..000000000000
--- a/sci-biology/mafft/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mafft-7.525-without-extensions-src.tgz 622798 BLAKE2B d1c58a2f44aacf00917351a5118b694684c64f128a777096a56904acb0c4ed728408fa58399c8d1dfcd38cb0733dc86b830b5b5bec582875577796f5aa75a811 SHA512 84b3ae1cabca0af0286713bfcfc1de3fd912214106c3b836e465d643d3a68dd6c8df697e424a82c324936b4d448c73e465fb16bcf3fc44e98270c16580e9dbb3
diff --git a/sci-biology/mafft/files/mafft-7.525-c23.patch b/sci-biology/mafft/files/mafft-7.525-c23.patch
deleted file mode 100644
index 3fa9a829faae..000000000000
--- a/sci-biology/mafft/files/mafft-7.525-c23.patch
+++ /dev/null
@@ -1,126 +0,0 @@
-https://salsa.debian.org/med-team/mafft/-/commit/73d7be1d2ee617b3cd533e62adc2536b5c8330a9
-
-From: Michael R. Crusoe <crusoe@debian.org>
-Subject: Add GCC-16 compatibility
-Forwarded: katoh@ifrec.osaka-u.ac.jp
-
---- a/core/constants.c
-+++ b/core/constants.c
-@@ -1537,7 +1537,7 @@
- 	}
- }
- 
--void freeconstants()
-+void freeconstants(void)
- {
- 	if( n_disLN ) FreeDoubleMtx( n_disLN ); n_disLN = NULL;
- 	if( n_dis ) FreeIntMtx( n_dis ); n_dis = NULL;
---- a/core/defs.c
-+++ b/core/defs.c
-@@ -139,7 +139,7 @@
- int terminalmargin = 100;
- 
- 
--void initglobalvariables()
-+void initglobalvariables(void)
- {
- 	commonAlloc1 = 0;
- 	commonAlloc2 = 0;
---- a/core/io.c
-+++ b/core/io.c
-@@ -1063,8 +1063,7 @@
-      return( !noteofflag );
- }
- 
--int getaline_fp_eof_new(s, l, fp)  /* end of file -> return 1 */
--char    s[] ; int l ; FILE *fp ;
-+int getaline_fp_eof_new( char s[], int l, FILE *fp )  /* end of file -> return 1 */
- {
-         int c = 0, i = 0 ;
- 		int noteofflag = 0;
-@@ -1079,8 +1078,7 @@
- 		return( !noteofflag );
- }
- 
--int myfgets(s, l, fp)  /* l�ʾ�ϡ������ޤ��ɤ����Ф� */
--char    s[] ; int l ; FILE *fp ;
-+int myfgets( char s[], int l, FILE *fp )  /* l�ʾ�ϡ������ޤ��ɤ����Ф� */
- {
-         int     c = 0, i = 0 ;
- 
-@@ -5505,7 +5503,7 @@
- 		}
- 	}
- }
--static void showaamtxexample()
-+static void showaamtxexample(void)
- {
- 	fprintf( stderr, "Format error in aa matrix\n" );
- 	fprintf( stderr, "# Example:\n" );
---- a/core/mltaln.h
-+++ b/core/mltaln.h
-@@ -166,7 +166,7 @@
- extern char rnaprediction;
- 
- /* sengen no ichi ha koko dake de ha nai */
--extern void constants();
-+extern void constants( int nseq, char **seq );
- extern char **Calignm1();
- extern char **Dalignm1();
- extern char **align0();
-@@ -179,24 +179,24 @@
- extern double substitution_nid( char *, char * );
- extern double substitution_hosei( char *, char * );
- extern double ipower( double, int );
--extern double translate_and_Calign();
--extern double A__align();
-+extern double translate_and_Calign( char **mseq1, char **mseq2, double *effarr1, double *effarr2, int clus1, int clus2, int alloclen );
-+extern double A__align( double **scoringmtx, int penalty, int penalty_ex, char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, char *gs1, char *gs2, char *ge1, char *ge2, int *, int, int *, int headgp, int tailgp, int firstmem, int calledby, double ***cpmxchild0, double ***cpmxchild1, double ***cpmxresult, double orieff1, double orieff2 );
- extern double A__align11();
--extern double A__align_gapmap();
--extern double partA__align();
-+extern double A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, int *gapmap1, int *gapmap2 );
-+extern double partA__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *, char *, char *, char *, int *, int, int * );
- extern double L__align11( double **scoringmtx, double scoreoffset, char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt );
--extern double G__align11();
--extern double Falign();
--extern double Falign_localhom();
-+extern double G__align11( double **scoringmtx, char **seq1, char **seq2, int alloclen, int headgp, int tailgp  );
-+extern double Falign( int **whichmtx, double ***scoringmatrices, double **scoreingmtx, char  **seq1, char  **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int    clus1, int    clus2, int alloclen, int *fftlog, int *, int, int * );
-+extern double Falign_localhom( int **which, double ***scoringmatrices, double **scoreingmtx, char  **seq1, char  **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int    clus1, int    clus2, int alloclen, int constraint, double *totalimpmatch, int *gapmap1, int *gapmap2, int *chudanpt, int chudanref, int *chudanres );
- extern double Conalign();
- extern double Aalign();
- extern double imp_match_out_sc( int, int );
- extern double part_imp_match_out_sc( int, int );
--extern void ErrorExit();
--extern void cpmx_calc();
-+extern void ErrorExit( char *message );
-+extern void cpmx_calc( char **seq, double **cpmx, double *eff, int lgth, int clus );
- extern void intergroup_score( char **, char **, double *, double *, int, int, int, double * );
- extern int conjuctionfortbfast();
--extern int fastconjuction();
-+extern int fastconjuction( int *memlist, char **seq, char **aseq, double *peff, double *eff, char name[M][B], char aname[M][B], char *d );
- extern char seqcheck( char ** );
- 
- typedef struct _LocalHom
---- a/core/mltaln9.c
-+++ b/core/mltaln9.c
-@@ -15232,7 +15232,7 @@
- 		}
- 	}
- }
--void FreeCommonIP()
-+void FreeCommonIP(void)
- {
- 	if( commonIP ) FreeIntMtx( commonIP ); 
- 	commonIP = NULL;
---- a/core/version.c
-+++ b/core/version.c
-@@ -1,6 +1,6 @@
- #include "mltaln.h"
- 
--int main()
-+int main(void)
- {
- 	fprintf( stdout, VERSION );
- 	return( 0 );
diff --git a/sci-biology/mafft/mafft-7.525.ebuild b/sci-biology/mafft/mafft-7.525.ebuild
deleted file mode 100644
index 5be0faf00dd7..000000000000
--- a/sci-biology/mafft/mafft-7.525.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit flag-o-matic toolchain-funcs
-
-EXTENSIONS="-without-extensions"
-
-DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="https://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
-S="${WORKDIR}/${P}${EXTENSIONS}"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-7.525-c23.patch
-)
-
-src_prepare() {
-	default
-
-	sed \
-		-e 's/(PREFIX)\/man/(PREFIX)\/share\/man/' \
-		-e 's:$(LDFLAGS)::g' \
-		-e 's:$(CC) -o $@:$(CC) $(LDFLAGS) -o $@:g' \
-		-e 's:$(CC) -shared -o $@:$(CC) $(LDFLAGS) -shared -o $@:g' \
-		-e '/INSTALL/s: -s : :g' \
-		-i core/Makefile || die
-}
-
-src_configure() {
-	append-cflags -Wno-unused-result
-}
-
-src_compile() {
-	emake -C core \
-		PREFIX="${EPREFIX}"/usr \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS}"
-}
-
-src_test() {
-	export MAFFT_BINARIES="${S}"/core
-	cd test || die
-	bash ../core/mafft sample > test.fftns2 || die "Tests failed"
-	bash ../core/mafft --maxiterate 100  sample > test.fftnsi || die "Tests failed"
-	bash ../core/mafft --globalpair sample > test.gins1 || die "Tests failed"
-	bash ../core/mafft --globalpair --maxiterate 100  sample > test.ginsi || die "Tests failed"
-	bash ../core/mafft --localpair sample > test.lins1 || die "Tests failed"
-	bash ../core/mafft --localpair --maxiterate 100  sample > test.linsi || die "Tests failed"
-
-	diff test.fftns2 sample.fftns2 || die "Tests failed"
-	diff test.fftnsi sample.fftnsi || die "Tests failed"
-	diff test.gins1 sample.gins1 || die "Tests failed"
-	diff test.ginsi sample.ginsi || die "Tests failed"
-	diff test.lins1 sample.lins1 || die "Tests failed"
-}
-
-src_install() {
-	emake -C core DESTDIR="${D}" STRIP=":" PREFIX="${EPREFIX}"/usr install
-	dodoc README.md
-}
diff --git a/sci-biology/mafft/metadata.xml b/sci-biology/mafft/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/mafft/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/maq/Manifest b/sci-biology/maq/Manifest
deleted file mode 100644
index 3838b916cf64..000000000000
--- a/sci-biology/maq/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST calib-36.dat.gz 196371 BLAKE2B e4dab71e0830603a7c25bb4c8e15f92e4a5068eeeece451a3e0a2a9e2c4f65b87325e7ff4e4e5543b79f2c3d9dd43c9398cdb32241535bf44e66705bfdf683f7 SHA512 1033ad47b31882823f71f16054f366a6853b4b5e1fb286ab2c5f62c1409ed20e6dc0faec7e356350e91c71d25a198d8e0d7a521b3662b5e2fae22af44098e8b7
-DIST maq-0.7.1.tar.bz2 368645 BLAKE2B a7989ae2348a7332f17a75c6fccba55deb8bd9330863d0c5ab3bf997f2f07abd1ca89ebb41d034902f6571ee36365f63db9c8c84c1e5d3d788236279581b989e SHA512 acaba2d172f8f4ef7a2b1254bd220f134a5eb8e4936af16bf7fa6695d016e6b6fa9a5b00d073ec1ecc0ecc39dfb1c9700c38fd017edb5bd49a83de383cb0d30c
diff --git a/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch b/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch
deleted file mode 100644
index 9f4247d441f5..000000000000
--- a/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- simulate.c |    2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/simulate.c b/simulate.c
-index 788c440..67ba2ba 100644
---- a/simulate.c
-+++ b/simulate.c
-@@ -383,7 +383,7 @@ static void simustat_core(gzFile fp, int Q_thres)
- 	memset(wc_single, 0, 40); memset(tot_single, 0, 40);
- 	memset(wc_pair, 0, 40); memset(tot_pair, 0, 40);
- 	memset(abpair, 0, 4 * 256 * 10);
--	memset(tc[2], 0, 4 * sizeof(int));
-+	memset(tc, 0, 4 * sizeof(int));
- 	while (maqmap_read1(fp, m1)) {
- 		int is_correct;
- 		bit32_t p1, p2;
diff --git a/sci-biology/maq/files/maq-0.7.1-flags.patch b/sci-biology/maq/files/maq-0.7.1-flags.patch
deleted file mode 100644
index 721e53248b7a..000000000000
--- a/sci-biology/maq/files/maq-0.7.1-flags.patch
+++ /dev/null
@@ -1,24 +0,0 @@
- configure.ac |    3 ++-
- 1 files changed, 2 insertions(+), 1 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index ad2f1e6..4f9d7be 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -8,6 +8,7 @@ AC_PROG_CXX
- 
- # set CFLAGS and CXXFLAGS
- user_CFLAGS=${CFLAGS}
-+user_CXXFLAGS=${CXXFLAGS}
- generic_CFLAGS="-Wall"
- ext_CFLAGS=""
- case "${host_cpu}-${host_os}" in
-@@ -37,7 +38,7 @@ AC_ARG_ENABLE(shortread,    [  --enable-shortreads     use shortread mode],
- AC_ARG_ENABLE(intel64,      [  --enable-intel64        optimize for Intel64 CPU such as Xeon and Core2],
- 			  [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], [])
- CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS}"
--CXXFLAGS=$CFLAGS
-+CXXFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CXXFLAGS}"
- 
- AC_STDC_HEADERS
- AC_CHECK_HEADER(zlib.h)
diff --git a/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch b/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch
deleted file mode 100644
index 4b97da89be48..000000000000
--- a/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch
+++ /dev/null
@@ -1,34 +0,0 @@
- stdhash.hh |    6 +++---
- 1 files changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/stdhash.hh b/stdhash.hh
-index eaf98af..16cd1a3 100644
---- a/stdhash.hh
-+++ b/stdhash.hh
-@@ -412,7 +412,7 @@ public:
- 	inline bool insert(const keytype_t &key) {
- 		__lh3_hash_base_class<keytype_t>::rehash();
- 		hashint_t i;
--		int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
-+		int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
- 		if (ret == 0) return true;
- 		if (ret == 1) { ++(this->n_size); ++(this->n_occupied); }
- 		else ++(this->n_size); // then ret == 2
-@@ -493,7 +493,7 @@ public:
- 	inline bool insert(const keytype_t &key, const valtype_t &val) {
- 		rehash();
- 		hashint_t i;
--		int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
-+		int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
- 		vals[i] = val;
- 		if (ret == 0) return true;
- 		if (ret == 1) { ++(this->n_size); ++(this->n_occupied); }
-@@ -503,7 +503,7 @@ public:
- 	inline bool insert(const keytype_t &key, valtype_t **q) {
- 		rehash();
- 		hashint_t i;
--		int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
-+		int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
- 		*q = vals + i;
- 		if (ret == 0) return true;
- 		if (ret == 1) { ++(this->n_size); ++(this->n_occupied); }
diff --git a/sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch b/sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch
deleted file mode 100644
index b92b7711bfe0..000000000000
--- a/sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-Bug: https://bugs.gentoo.org/921137
---- a/fastq2bfq.c
-+++ b/fastq2bfq.c
-@@ -15,7 +15,7 @@ int64_t fastq2bfq(FILE *fp_fq, const char *fn_bfq, int n_reads)
- 	char name[256], str[1024];
- 	int l, is_new = 0, l_prefix = 0;
- 	bit64_t n;
--	gzFile *fp = 0;
-+	gzFile fp = 0;
- 	INIT_SEQ(seq); INIT_SEQ(qual);
- 	seq_set_block_size(256);
- 	n = 0;
---- a/simulate.c
-+++ b/simulate.c
-@@ -74,7 +74,7 @@ int maq_simutrain(int argc, char *argv[])
- {
- 	fqc_t *fqc;
- 	FILE *fp;
--	gzFile *fpout;
-+	gzFile fpout;
- 	if (argc < 3) {
- 		fprintf(stderr, "Usage: maq simutrain <simupars.dat> <known_reads.fastq>\n");
- 		return 1;
diff --git a/sci-biology/maq/files/maq-0.7.1-remove-64bit-flag.patch b/sci-biology/maq/files/maq-0.7.1-remove-64bit-flag.patch
deleted file mode 100644
index 3bcbc2b5fd51..000000000000
--- a/sci-biology/maq/files/maq-0.7.1-remove-64bit-flag.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-Do not hardcode -m64 into the build system
-
---- a/configure.ac
-+++ b/configure.ac
-@@ -21,12 +21,12 @@
- 						   [ext_CFLAGS="-arch x86_64 -arch i386 -arch ppc64 -arch ppc"],
- 						   [ext_CFLAGS="-arch i386 -arch ppc"]);;
- 	  0) CFLAGS="-m64"
--	  	 AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"], []);;
-+	  	 AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS=""], []);;
- 	esac;;
-   *)
-     AC_MSG_CHECKING([if gcc accepts -m64])
-     CFLAGS="-m64"
--    AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"; AC_MSG_RESULT([yes])],
-+    AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS=""; AC_MSG_RESULT([yes])],
- 					  [ext_CFLAGS="-D_FILE_OFFSET_BITS=64"; AC_MSG_RESULT([no])]);;
- esac
- AC_ARG_ENABLE(experimental, [  --enable-experimental   enable experimental features],
diff --git a/sci-biology/maq/maq-0.7.1-r4.ebuild b/sci-biology/maq/maq-0.7.1-r4.ebuild
deleted file mode 100644
index 63c8ae46d650..000000000000
--- a/sci-biology/maq/maq-0.7.1-r4.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools
-
-DESCRIPTION="Mapping and Assembly with Qualities, mapping NGS reads to reference genomes"
-HOMEPAGE="https://maq.sourceforge.net/"
-SRC_URI="
-	https://downloads.sourceforge.net/${PN}/${P}.tar.bz2
-	https://downloads.sourceforge.net/${PN}/calib-36.dat.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="virtual/zlib:="
-DEPEND="${RDEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-flags.patch
-	"${FILESDIR}"/${P}-bfr-overfl.patch
-	"${FILESDIR}"/${P}-gcc-4.7.patch
-	"${FILESDIR}"/${P}-remove-64bit-flag.patch
-	"${FILESDIR}"/${P}-gcc14-build-fix.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_install() {
-	default
-
-	insinto /usr/share/maq
-	doins "${WORKDIR}"/*.dat
-
-	doman maq.1
-	dodoc maq.pdf
-}
diff --git a/sci-biology/maq/metadata.xml b/sci-biology/maq/metadata.xml
deleted file mode 100644
index c555decd8d6f..000000000000
--- a/sci-biology/maq/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">maq</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/maqview/Manifest b/sci-biology/maqview/Manifest
deleted file mode 100644
index 31c58c4bc639..000000000000
--- a/sci-biology/maqview/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST maqview-0.2.5.tar.gz 383410 BLAKE2B 7058f32e49267dfcc8b25da2ca2bbbd5134f66f0f9cbd10de7e876365d955d2e51cbab342af817f13018b7b1903872033c363fe077f10ce76e5fcc87da568dc1 SHA512 40bed0a1005ca96fdb12773cd9c22ddc926fe722c64652031609a17a50ff725a3dc117d51f4f27eda68b48861da78427469aaedff744f29921236b486396aed6
diff --git a/sci-biology/maqview/files/0.2.5-ldflags.patch b/sci-biology/maqview/files/0.2.5-ldflags.patch
deleted file mode 100644
index 92b9a3ed58ac..000000000000
--- a/sci-biology/maqview/files/0.2.5-ldflags.patch
+++ /dev/null
@@ -1,46 +0,0 @@
- configure.ac |   18 +++---------------
- 1 files changed, 3 insertions(+), 15 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index 90e612b..5a00d15 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -9,17 +9,10 @@ AC_PROG_INSTALL
- AC_STDC_HEADERS
- 
- is_static=0
--case ${prefix} in
--  NONE);;
--  *) is_static=1
--     AC_MSG_WARN([Library libglut will be statically linked.])
--     LDFLAGS="-L${prefix}/lib"
--     CPPFLAGS="-I${prefix}/include";;
--esac
- 
- # set CFLAGS and LDFLAGS
- 
--true_CFLAGS="-g -O2 -Wall -W -DMAQ_LONGREADS"
-+true_CFLAGS="-DMAQ_LONGREADS"
- case "${host_os}" in
-   darwin*)
-     GLLIBS="-framework OpenGL -framework GLUT"
-@@ -30,17 +23,12 @@ case "${host_os}" in
- 	  i?86) CPPFLAGS="$CPPFLAGS -D_FILE_OFFSET_BITS=64";;
- 	esac
- 	AC_CHECK_LIB([glut], [glutMouseWheelFunc], [CPPFLAGS="$CPPFLAGS -DHAVE_FREEGLUT"])
--    AC_ARG_ENABLE(static, [  --enable-static         statically link GLUT (Linux Only)],
--				  [is_static=1])
--    case $is_static in
--      1) GLLIBS="-Wl,-Bstatic -lglut -Wl,-Bdynamic -lGL -lGLU -lm";;
--	  0) GLLIBS="-lGL -lglut -lm";;
--    esac
-+	GLLIBS="-lGL -lglut -lm -lGLU"
- 	AC_SUBST([GLLIBS]);;
- #  *) AC_MSG_ERROR([OS is not supported]);;
- esac
- AM_CONDITIONAL([HAVE_GL], [test "$isgl" = 1])
--CFLAGS=$true_CFLAGS
-+CFLAGS="${CFLAGS} $true_CFLAGS"
- 
- AC_CONFIG_FILES([Makefile])
- AC_OUTPUT
diff --git a/sci-biology/maqview/files/0.2.5-zlib.patch b/sci-biology/maqview/files/0.2.5-zlib.patch
deleted file mode 100644
index cd35273de66b..000000000000
--- a/sci-biology/maqview/files/0.2.5-zlib.patch
+++ /dev/null
@@ -1,33 +0,0 @@
- Makefile.am |    6 +++---
- zrio.c      |    2 +-
- 2 files changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/Makefile.am b/Makefile.am
-index dad515a..9617eb7 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -1,8 +1,8 @@
- bin_PROGRAMS = zrio maqindex maqview maqindex_socks
--zlib_src = adler32.c compress.c crc32.c deflate.c gzio.c inffast.c inflate.c \
--		   infback.c inftrees.c trees.c uncompr.c zutil.c
--generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c $(zlib_src)
-+generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c
-+LIBS = -lz
- zrio_SOURCES = zrio_main.c $(generic_src)
-+zrio_LDADD = -lz
- maqindex_SOURCES = maqmap_index_main.c $(generic_src)
- maqview_SOURCES = read_cache.c view_goto.c view_panel.c gl_gui.c MainFrame.c \
- 				  $(generic_src)				  
-diff --git a/zrio.c b/zrio.c
-index ffed00a..fe744df 100644
---- a/zrio.c
-+++ b/zrio.c
-@@ -506,7 +506,7 @@ int build_index(int in, int64_t span, struct access **built, void (*notify)(void
-             totin += strm.avail_in;
-             totout += strm.avail_out;
- 			tmp = strm.avail_out;
--            ret = inflate_zr(&strm, Z_BLOCK);      /* return at end of block */
-+            ret = inflate(&strm, Z_BLOCK);      /* return at end of block */
-             totin -= strm.avail_in;
-             totout -= strm.avail_out;
- 			if(notify) notify(obj, window + WINSIZE - tmp, tmp - strm.avail_out, totout);
diff --git a/sci-biology/maqview/files/maqview-0.2.5-gcc14-build-fix.patch b/sci-biology/maqview/files/maqview-0.2.5-gcc14-build-fix.patch
deleted file mode 100644
index 8f973f38a272..000000000000
--- a/sci-biology/maqview/files/maqview-0.2.5-gcc14-build-fix.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-Bug: https://bugs.gentoo.org/930767
---- a/socket_view.c
-+++ b/socket_view.c
-@@ -267,7 +267,7 @@ int service_core(ViewServer *server, int sock){
- 
- int runViewServer(ViewServer *server){
- 	int i, sock, state;
--	size_t size;
-+	socklen_t size;
- 	fd_set active_fd_set, read_fd_set;
- 	struct timeval timeout;
- 	struct sockaddr_in clientname;
diff --git a/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch
deleted file mode 100644
index 043208bb79b5..000000000000
--- a/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- stdhash.hh | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/stdhash.hh b/stdhash.hh
-index eaf98af..f22c5a6 100644
---- a/stdhash.hh
-+++ b/stdhash.hh
-@@ -493,7 +493,7 @@ public:
- 	inline bool insert(const keytype_t &key, const valtype_t &val) {
- 		rehash();
- 		hashint_t i;
--		int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
-+		int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i);
- 		vals[i] = val;
- 		if (ret == 0) return true;
- 		if (ret == 1) { ++(this->n_size); ++(this->n_occupied); }
diff --git a/sci-biology/maqview/maqview-0.2.5-r5.ebuild b/sci-biology/maqview/maqview-0.2.5-r5.ebuild
deleted file mode 100644
index 2d4e50382027..000000000000
--- a/sci-biology/maqview/maqview-0.2.5-r5.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools
-
-DESCRIPTION="GUI for sci-biology/maq, a short read mapping assembler"
-HOMEPAGE="https://maq.sourceforge.net/"
-SRC_URI="https://downloads.sourceforge.net/maq/${P}.tar.gz"
-S="${WORKDIR}/${PN}"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
-	media-libs/freeglut
-	virtual/zlib:="
-RDEPEND="${DEPEND}
-	sci-biology/maq"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-ldflags.patch
-	"${FILESDIR}"/${PV}-zlib.patch
-	"${FILESDIR}"/${P}-gcc4.7.patch
-	"${FILESDIR}"/${P}-gcc14-build-fix.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-biology/maqview/metadata.xml b/sci-biology/maqview/metadata.xml
deleted file mode 100644
index c555decd8d6f..000000000000
--- a/sci-biology/maqview/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">maq</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/metadata.xml b/sci-biology/metadata.xml
deleted file mode 100644
index 6b9dcbff3e29..000000000000
--- a/sci-biology/metadata.xml
+++ /dev/null
@@ -1,45 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE catmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<catmetadata>
-	<longdescription lang="en">
-		The sci-biology category contains software that can be used
-		in biological and related scientific environments.
-	</longdescription>
-	<longdescription lang="de">
-		Die Kategorie sci-biology enthält Software, die in biologischen
-		und verwandten wissenschaftlichen Umgebungen genutzt werden kann.
-	</longdescription>
-	<longdescription lang="es">
-		La categoría sci-biology contiene programas que pueden ser utilizados en
-		entornos relacionados con la biología.
-	</longdescription>
-	<longdescription lang="ja">
-		sci-biologyカテゴリーには生物学の科学的な分野に利用される
-		ソフトウェアが含まれています。
-	</longdescription>
-	<longdescription lang="nl">
-		De sci-biology categorie bevat software, die in biologische en gerelateerde
-		wetenschappelijke omgevingen gebruikt kan worden.
-	</longdescription>
-	<longdescription lang="fr">
-		La catégorie sci-biology contient des logiciels pour les sciences
-		biologiques et les disciplines connexes.
-	</longdescription>
-	<longdescription lang="vi">
-		Nhóm sci-biology chứa các phần mềm sinh học và liên quan đến khoa học.
-	</longdescription>
-	<longdescription lang="sk">
-		Kategória sci-biology obsahuje programy, ktoré sa používajú pri
-		biologickom výskume.
-	</longdescription>
-	<longdescription lang="it">
-		La categoria sci-biology contiene programmi per la biologia.
-	</longdescription>
-	<longdescription lang="pt">
-		A categoria sci-biology contém programas que podem ser usados
-		em ambientes relacionados a biologia.
-	</longdescription>
-	<longdescription lang="pl">
-		Kategoria sci-biology zawiera programy naukowe związane z biologią.
-	</longdescription>
-</catmetadata>
diff --git a/sci-biology/mosaik/Manifest b/sci-biology/mosaik/Manifest
deleted file mode 100644
index 991bb79876e6..000000000000
--- a/sci-biology/mosaik/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mosaik-2.2.30.tar.gz 4387062 BLAKE2B 6f373aeae4f68be2455556e7f79a5850e25d804bd482d85a846b44f8adaabb2513ffc7ced774f5ead6dbc8fc9dca9d64f76f83bc5b55b1be4073a8cf309e121b SHA512 1acf534e6defc927fc22937a7bae6786e85ab7aa234b4209169f1267f1a9bd68415b441c6aed2e7cd667f694a562017ebc9457251958f77386259ffce9812b10
diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-Wformat-security.patch b/sci-biology/mosaik/files/mosaik-2.2.30-Wformat-security.patch
deleted file mode 100644
index 9f7271860229..000000000000
--- a/sci-biology/mosaik/files/mosaik-2.2.30-Wformat-security.patch
+++ /dev/null
@@ -1,84 +0,0 @@
-- Fix incorrect printf format specifier (-Wformat)
-* fann.c: In function ‘fann_print_connections’:
-* fann.c:889:11: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=]
-*     printf("L %3d / N %4d %s\n", layer_it - ann->first_layer,
-
-- Fix erroneous memset call
-* md5.c: In function ‘MD5Final’:
-* md5.c:152:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess]
-*      memset(ctx, 0, sizeof(ctx));        /* In case it's sensitive */
-
---- a/fann-2.1.0/fann.c
-+++ b/fann-2.1.0/fann.c
-@@ -886,7 +886,7 @@
- 					neurons[ann->connections[i] - ann->first_layer->first_neuron] = (char)('A' + value);
- 				}
- 			}
--			printf("L %3d / N %4d %s\n", layer_it - ann->first_layer,
-+			printf("L %3ld / N %4ld %s\n", layer_it - ann->first_layer,
- 				   neuron_it - ann->first_layer->first_neuron, neurons);
- 		}
- 	}
-@@ -987,12 +987,12 @@
- 	{
- 		if(ann->network_type == FANN_NETTYPE_SHORTCUT)
- 		{
--			printf("  Hidden layer                       :%4d neurons, 0 bias\n",
-+			printf("  Hidden layer                       :%4ld neurons, 0 bias\n",
- 				   layer_it->last_neuron - layer_it->first_neuron);
- 		}
- 		else
- 		{
--			printf("  Hidden layer                       :%4d neurons, 1 bias\n",
-+			printf("  Hidden layer                       :%4ld neurons, 1 bias\n",
- 				   layer_it->last_neuron - layer_it->first_neuron - 1);
- 		}
- 	}
---- a/fann-2.1.0/fann_io.c
-+++ b/fann-2.1.0/fann_io.c
-@@ -174,7 +174,7 @@
- #endif
- 
- 	/* Save network parameters */
--	fprintf(conf, "num_layers=%u\n", ann->last_layer - ann->first_layer);
-+	fprintf(conf, "num_layers=%ld\n", ann->last_layer - ann->first_layer);
- 	fprintf(conf, "learning_rate=%f\n", ann->learning_rate);
- 	fprintf(conf, "connection_rate=%f\n", ann->connection_rate);
- 	fprintf(conf, "network_type=%u\n", ann->network_type);
-@@ -236,7 +236,7 @@
- 	for(layer_it = ann->first_layer; layer_it != ann->last_layer; layer_it++)
- 	{
- 		/* the number of neurons in the layers (in the last layer, there is always one too many neurons, because of an unused bias) */
--		fprintf(conf, "%u ", layer_it->last_neuron - layer_it->first_neuron);
-+		fprintf(conf, "%ld ", layer_it->last_neuron - layer_it->first_neuron);
- 	}
- 	fprintf(conf, "\n");
- 
-@@ -316,14 +316,14 @@
- 		if(save_as_fixed)
- 		{
- 			/* save the connection "(source weight) " */
--			fprintf(conf, "(%u, %d) ",
-+			fprintf(conf, "(%ld, %d) ",
- 					connected_neurons[i] - first_neuron,
- 					(int) floor((weights[i] * fixed_multiplier) + 0.5));
- 		}
- 		else
- 		{
- 			/* save the connection "(source weight) " */
--			fprintf(conf, "(%u, " FANNPRINTF ") ", connected_neurons[i] - first_neuron, weights[i]);
-+			fprintf(conf, "(%ld, " FANNPRINTF ") ", connected_neurons[i] - first_neuron, weights[i]);
- 		}
- #else
- 		/* save the connection "(source weight) " */
---- a/CommonSource/Utilities/md5.c
-+++ b/CommonSource/Utilities/md5.c
-@@ -149,7 +149,7 @@
-     MD5Transform(ctx->buf, (uint32 *) ctx->in);
-     byteReverse((unsigned char *) ctx->buf, 4);
-     memcpy(digest, ctx->buf, 16);
--    memset(ctx, 0, sizeof(ctx));        /* In case it's sensitive */
-+    memset(ctx, 0, sizeof(*ctx));        /* In case it's sensitive */
- }
- 
- 
diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-fix-build-system.patch b/sci-biology/mosaik/files/mosaik-2.2.30-fix-build-system.patch
deleted file mode 100644
index 00a9bec3ae4d..000000000000
--- a/sci-biology/mosaik/files/mosaik-2.2.30-fix-build-system.patch
+++ /dev/null
@@ -1,226 +0,0 @@
-- Make build system verbose by default, as required by Gentoo policy
-  See also: https://bugs.gentoo.org/show_bug.cgi?id=429308
-- Remove CFLAGS and CXXFLAGS defaults
-- Fix order of flags and honour CPPFLAGS for LFS support
-  and LDFLAGS for --as-needed, respectively
-
---- a/CommonSource/DataStructures/Makefile
-+++ b/CommonSource/DataStructures/Makefile
-@@ -22,7 +22,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/CommonSource/ExternalReadFormats/Makefile
-+++ b/CommonSource/ExternalReadFormats/Makefile
-@@ -22,7 +22,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/CommonSource/MosaikReadFormat/Makefile
-+++ b/CommonSource/MosaikReadFormat/Makefile
-@@ -22,7 +22,7 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- clean:
- 	@echo "Cleaning up."
---- a/CommonSource/PairwiseAlignment/Makefile
-+++ b/CommonSource/PairwiseAlignment/Makefile
-@@ -26,11 +26,11 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(CBUILT_OBJECTS): $(CSOURCES)
- 	@echo "  * compiling" $(*F).c
--	@$(CC) -c -o $@ $(*F).c -O3 $(PLATFORM_FLAGS) $(INCLUDES)
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).c
- 
- clean:
- 	@echo "Cleaning up."
---- a/CommonSource/Utilities/Makefile
-+++ b/CommonSource/Utilities/Makefile
-@@ -48,11 +48,11 @@
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(CBUILT_OBJECTS): $(CSOURCES)
- 	@echo "  * compiling" $(*F).c
--	@$(CC) -c -o $@ $(*F).c -O3 -w -DSQLITE_OMIT_LOAD_EXTENSION $(PLATFORM_FLAGS) $(INCLUDES)
-+	$(CC) $(CFLAGS) $(CPPFLAGS) -DSQLITE_OMIT_LOAD_EXTENSION $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).c
- 
- clean:
- 	@echo "Cleaning up."
---- a/fann-2.1.0/Makefile
-+++ b/fann-2.1.0/Makefile
-@@ -12,7 +12,7 @@
- 
- $(CBUILT_OBJECTS): $(CSOURCES)
- 	@echo "  * compiling" $(*F).c
--	@$(CC) -c -o $@ $(*F).c -O3 $(PLATFORM_FLAGS) -I$(INCLUDES) 
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) -I$(INCLUDES) -c -o $@ $(*F).c
- 
- clean:
- 	@echo "Cleaning up."
---- a/Makefile
-+++ b/Makefile
-@@ -4,8 +4,8 @@
- # ==========================
- 
- # define our object and binary directories
--export OBJ_DIR = ../obj
--export BIN_DIR = ../bin
-+export OBJ_DIR = ./obj
-+export BIN_DIR = ./bin
- 
- # define our common source directories
- export ASSEMBLY_DIR = CommonSource/AssemblyFormats
-@@ -16,20 +16,6 @@
- export PAIRWISE_DIR = CommonSource/PairwiseAlignment
- export UTILITIES_DIR = CommonSource/Utilities
- 
--# define some default flags
--FLAGS = -Wall -Wno-char-subscripts -ansi -O3
--#FLAGS = -Wall -Wno-char-subscripts -ansi -g -D VERBOSE_DEBUG #gdb debugging
--#FLAGS = -Wall -Wno-char-subscripts -ansi -O3 -D VERBOSE_DEBUG #enables verbose debugging
--CFLAGS =
--CXXFLAGS =
--#CXXFLAGS = -ansi -pedantic -Wextra -Weffc++
--CFLAGS += $(FLAGS)
--CXXFLAGS += $(FLAGS)
--export CFLAGS
--export CXXFLAGS
--#export LDFLAGS = -Wl
--export CXX ?= g++
--
- # define our platform
- export BLD_PLATFORM ?= linux
- include includes/$(BLD_PLATFORM).inc
---- a/MosaikAligner/Makefile
-+++ b/MosaikAligner/Makefile
-@@ -68,11 +68,11 @@
- 
- $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
- 	@echo "  * linking $(PROGRAM)"
--	@$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(TD)$(DATA_STRUCT_DIR)
---- a/MosaikBuild/Makefile
-+++ b/MosaikBuild/Makefile
-@@ -26,11 +26,11 @@
- 
- $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
- 	@echo "  * linking $(PROGRAM)"
--	@$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(TD)$(DATA_STRUCT_DIR)
---- a/MosaikJump/Makefile
-+++ b/MosaikJump/Makefile
-@@ -26,11 +26,11 @@
- 
- $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
- 	@echo "  * linking $(PROGRAM)"
--	@$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(TD)$(MOSAIKREAD_DIR)
---- a/MosaikText/Makefile
-+++ b/MosaikText/Makefile
-@@ -26,11 +26,11 @@
- 
- $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
- 	@echo "  * linking $(PROGRAM)"
--	@$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
- 
- $(BUILT_OBJECTS): $(SOURCES)
- 	@echo "  * compiling" $(*F).cpp
--	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
- 
- $(EXT_OBJECTS):
- 	@$(MAKE) --no-print-directory -C $(TD)$(MOSAIKREAD_DIR)
---- a/networkFile/retrainCode/attachXC/Makefile
-+++ b/networkFile/retrainCode/attachXC/Makefile
-@@ -3,12 +3,11 @@
- # (c) 2012 Wan-Ping Lee
- # ==========================
- 
--FLAGS = -Wall -O3
- 
- 
- all: xc_pe.cpp xc_se.cpp
--	@$(CXX) $(FLAGS) xc_pe.cpp -o xc_pe
--	@$(CXX) $(FLAGS) xc_se.cpp -o xc_se
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) xc_pe.cpp -o xc_pe
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) xc_se.cpp -o xc_se
- 
- .PHONY: all
- 
---- a/networkFile/retrainCode/trainNetwork/Makefile
-+++ b/networkFile/retrainCode/trainNetwork/Makefile
-@@ -5,8 +5,6 @@
- 
- OBJ_DIR = ./obj
- 
--FLAGS =  -Wall -O3
--CFLAGS = -O3
- FANN=../../../fann-2.1.0
- 
- SOURCES = sam_parser_float.cpp parameter_parser_float.cpp mq_train_float.cpp
-@@ -15,12 +13,12 @@
- all: $(FANN)/floatfann.c $(SOURCES)
- 	@test -d $(OBJ_DIR) || mkdir $(OBJ_DIR)
- 	@echo "  * compiling ......"
--	@$(CC) $(CFLAGS) -c -o $(OBJ_DIR)/floatfann.o $(FANN)/floatfann.c -I$(FANN)/include
--	@$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/sam_parser_float.o sam_parser_float.cpp
--	@$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/parameter_parser_float.o parameter_parser_float.cpp
--	@$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/mq_train_float.o mq_train_float.cpp -I$(FANN)/include
-+	$(CC)  $(CFLAGS)   $(CPPFLAGS) -c -o $(OBJ_DIR)/floatfann.o $(FANN)/floatfann.c -I$(FANN)/include
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/sam_parser_float.o sam_parser_float.cpp
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/parameter_parser_float.o parameter_parser_float.cpp
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/mq_train_float.o mq_train_float.cpp -I$(FANN)/include
- 	@echo "  * linking ......"
--	@$(CXX) $(FLAGS) $(OBJ_DIR)/*.o -o $(PROGRAM)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) $(OBJ_DIR)/*.o -o $(PROGRAM)
- 
- .PHONY: all
- 
diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-gcc11.patch b/sci-biology/mosaik/files/mosaik-2.2.30-gcc11.patch
deleted file mode 100644
index 918d882983a3..000000000000
--- a/sci-biology/mosaik/files/mosaik-2.2.30-gcc11.patch
+++ /dev/null
@@ -1,60 +0,0 @@
---- a/CommonSource/DataStructures/UnorderedMap.h
-+++ b/CommonSource/DataStructures/UnorderedMap.h
-@@ -42,13 +42,9 @@
- 
- #else // all decent C++ compilers
- 
--#ifdef WIN32
- #include <unordered_map>
--#else // Linux
--#include <tr1/unordered_map>
--#endif
- 
--using namespace std::tr1;
-+using namespace std;
- 
- #endif
- 
---- a/CommonSource/DataStructures/UnorderedSet.h
-+++ b/CommonSource/DataStructures/UnorderedSet.h
-@@ -42,13 +42,9 @@
- 
- #else // all decent C++ compilers
- 
--#ifdef WIN32
- #include <unordered_set>
--#else // Linux
--#include <tr1/unordered_set>
--#endif
- 
--using namespace std::tr1;
-+using namespace std;
- 
- #endif
- 
---- a/CommonSource/Utilities/RegexUtilities.h
-+++ b/CommonSource/Utilities/RegexUtilities.h
-@@ -12,10 +12,7 @@
- #define REGEXUTILITIES_H_
- 
- #include <iostream>
--#ifdef WIN32
- #include <regex>
--using namespace std::tr1;
--#endif
- #include <string>
- #include <vector>
- #include <cstdlib>
---- a/MosaikBuild/MosaikBuild.h
-+++ b/MosaikBuild/MosaikBuild.h
-@@ -15,10 +15,7 @@
- #include <iostream>
- #include <fstream>
- #include <map>
--#ifdef WIN32
- #include <regex>
--using namespace std::tr1;
--#endif
- #include <set>
- #include <sstream>
- #include "ColorspaceUtilities.h"
diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-gcc12-time.patch b/sci-biology/mosaik/files/mosaik-2.2.30-gcc12-time.patch
deleted file mode 100644
index 1bc63bfd4776..000000000000
--- a/sci-biology/mosaik/files/mosaik-2.2.30-gcc12-time.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-https://bugs.gentoo.org/851669
---- a/CommonSource/Utilities/SafeFunctions.h
-+++ b/CommonSource/Utilities/SafeFunctions.h
-@@ -17,6 +17,7 @@
- #include <cstdio>
- #include <cstdarg>
- #include <cstring>
-+#include <ctime>
- #include <stdio.h>
- #include <stdlib.h>
- #include <errno.h>
diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch b/sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch
deleted file mode 100644
index ebf925a0cbb7..000000000000
--- a/sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch
+++ /dev/null
@@ -1,40 +0,0 @@
---- a/CommonSource/ExternalReadFormats/BamWriter.cpp
-+++ b/CommonSource/ExternalReadFormats/BamWriter.cpp
-@@ -496,7 +496,7 @@
- 	buffer[6] = 0xffffffff;  // mate_pos
- 	buffer[7] = 0;           // ins_size
- 
--	const char* startChar = '\0';
-+	const char* startChar = NULL;
- 	
- 	// write the block size
- 	const unsigned int dataBlockSize = nameLen + packedCigarLen + encodedQueryLen + queryLen;
-@@ -652,7 +652,7 @@
- 	unsigned int zaTagLen = 0;
- 	string zaTag;
- 	char* pZaTag;
--	if ((zaString != 0) && (zaString != (char)0)) {
-+	if ((zaString != 0) && (zaString[0] != '\0')) {
- 		zaTagLen = 3 + strlen( zaString ) + 1;
- 		zaTag.resize( zaTagLen );
- 		pZaTag = (char*)zaTag.data();
-@@ -776,7 +776,7 @@
- 	BgzfWrite(mdTag.data(), mdTagLen);
- 
- 	// write the ZA tag
--	if ( zaString != 0 && (zaString != (char)0))
-+	if ( zaString != 0 && (zaString[0] != '\0'))
- 		BgzfWrite(zaTag.data(), zaTagLen);
- 	
- 	// write the ZN tag
---- a/MosaikAligner/AlignmentThread.cpp
-+++ b/MosaikAligner/AlignmentThread.cpp
-@@ -591,7 +591,7 @@
- 	buffer.al              = al;
- 	buffer.noCigarMdNm     = noCigarMdNm;
- 	buffer.notShowRnamePos = notShowRnamePos;
--	if ( zaString == (char)0 ) 
-+	if ( zaString == NULL ) 
- 		buffer.zaString.clear();
- 	else
- 		buffer.zaString = zaString;
diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-remove-platform-code.patch b/sci-biology/mosaik/files/mosaik-2.2.30-remove-platform-code.patch
deleted file mode 100644
index 8573573ec125..000000000000
--- a/sci-biology/mosaik/files/mosaik-2.2.30-remove-platform-code.patch
+++ /dev/null
@@ -1,10 +0,0 @@
-- Remove macro for enabling large file support, this is better handled at an
-  ebuild level, where the LFS flags can be handled for multiple architectures
-- Remove static flag, which is contrary to Gentoo policy
-
---- a/includes/linux.inc
-+++ b/includes/linux.inc
-@@ -1,2 +1,2 @@
- # define our processor specific flags
--export PLATFORM_FLAGS = -D_FILE_OFFSET_BITS=64 -static
-+export PLATFORM_FLAGS =
diff --git a/sci-biology/mosaik/metadata.xml b/sci-biology/mosaik/metadata.xml
deleted file mode 100644
index cbe93c59213f..000000000000
--- a/sci-biology/mosaik/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="google-code">mosaik-aligner</remote-id>
-    <remote-id type="github">wanpinglee/MOSAIK</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/mosaik/mosaik-2.2.30.ebuild b/sci-biology/mosaik/mosaik-2.2.30.ebuild
deleted file mode 100644
index a929f1160f67..000000000000
--- a/sci-biology/mosaik/mosaik-2.2.30.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic toolchain-funcs vcs-snapshot
-
-DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
-HOMEPAGE="https://github.com/wanpinglee/MOSAIK"
-SRC_URI="https://github.com/wanpinglee/MOSAIK/archive/5c25216d3522d6a33e53875cd76a6d65001e4e67.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${P}/src"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-remove-platform-code.patch
-	"${FILESDIR}"/${P}-fix-build-system.patch
-	"${FILESDIR}"/${P}-Wformat-security.patch
-	"${FILESDIR}"/${P}-gcc7.patch
-	"${FILESDIR}"/${P}-gcc11.patch
-	"${FILESDIR}"/${P}-gcc12-time.patch
-)
-
-src_configure() {
-	# readd default warning flags from build system
-	append-flags -Wall -Wno-char-subscripts
-	append-lfs-flags
-	export BLD_PLATFORM=linux
-}
-
-src_compile() {
-	emake \
-		CC="$(tc-getCC)" \
-		CXX="$(tc-getCXX)" \
-		CFLAGS="${CFLAGS}" \
-		CXXFLAGS="${CXXFLAGS}" \
-		CPPFLAGS="${CPPFLAGS}" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dobin bin/Mosaik*
-
-	dodoc ../README
-
-	insinto /usr/share/${PN}/examples
-	doins -r ../demo/.
-}
diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest
deleted file mode 100644
index f553bac75ba0..000000000000
--- a/sci-biology/mothur/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mothur-1.48.2.tar.gz 24702253 BLAKE2B 4342640e70f08763c4bc1605441a9526ef967bd5832d103db3095c470ea82c2c554dd03775e8ffdf02a983ee4dfdb43ba008dcf7ff19b99321a0204843f98710 SHA512 0c3496d08131d15db3933165eba832a135ca3bce8010e7a2b4a84802c91d6f5efa54711498148d7cc190420b75a94babf20d6c435a5e07c730924f1f3f966586
diff --git a/sci-biology/mothur/files/mothur-1.48.0-build.patch b/sci-biology/mothur/files/mothur-1.48.0-build.patch
deleted file mode 100644
index da9784e20dd8..000000000000
--- a/sci-biology/mothur/files/mothur-1.48.0-build.patch
+++ /dev/null
@@ -1,79 +0,0 @@
-Fix building and don't use bundled uchime.
---- a/Makefile
-+++ b/Makefile
-@@ -104,12 +104,19 @@ endif
- # INCLUDE directories for mothur
- #
- #
--	VPATH=source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/engines:source/metastats:source/read:source/svm:source/
-+	VPATH=source:source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/engines:source/metastats:source/read:source/svm:source/
-+    source := source
-     skipUchime := source/uchime_src/
-+    skipTestMothur := source/TestMothur/
-+    skipSeqnoise := seqnoise.cpp
-     subdirs :=  $(sort $(dir $(filter-out  $(skipUchime), $(wildcard source/*/))))
-+    subdirs :=  $(filter-out  $(skipTestMothur), $(subdirs))
-     subDirIncludes = $(patsubst %, -I %, $(subdirs))
-+    subDirIncludes += $(patsubst %, -I %, $(source))
-     subDirLinking =  $(patsubst %, -L%, $(subdirs))
--    CXXFLAGS += -I. $(subDirIncludes)
-+    subDirLinking +=  $(patsubst %, -L%, $(source))
-+    subdirs :=  $(dir source) $(sort $(dir $(filter-out  $(skipUchime), $(wildcard source/*/))))
-+    CXXFLAGS += -Isource -I. $(subDirIncludes)
-     LDFLAGS += $(subDirLinking)
- 
- 
-@@ -118,15 +125,14 @@ endif
- #
-     OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))
-     OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))
-+    OBJECTS+=$(patsubst %.cpp,%.o,$(filter-out $(skipSeqnoise), $(wildcard source/*.cpp)))
-+    OBJECTS+=$(patsubst %.cpp,%.o,$(filter-out $(skipSeqnoise), $(wildcard source/*.c)))
-     OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
-     OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
- 
--mothur : $(OBJECTS) uchime
-+mothur : $(OBJECTS)
- 	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
- 
--uchime :
--	cd source/uchime_src && export CXX=$(CXX) && make clean && make && mv uchime ../../ && cd ..
--
- install : mothur
- 
- ifeq  ($(strip $(INSTALL_DIR)),"\"Enter_your_mothur_install_path_here\"")
---- a/makefile-internal
-+++ b/makefile-internal
-@@ -115,7 +115,6 @@ endif
- 
- mothur : $(OBJECTS)
-     $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
--    strip mothur
- 
- %.o : %.c %.h
-     $(COMPILE.c) $(OUTPUT_OPTION) $<
---- a/source/uchime_src/makefile
-+++ b/source/uchime_src/makefile
-@@ -1,4 +1,4 @@
--CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
-+CXXFLAGS = -std=c++11 -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
- LDFLAGS = -g
- 
- #
-@@ -26,4 +26,4 @@ install : uchime
- 
- clean :
- 	@rm -f $(OBJECTS)
--	
-\ No newline at end of file
-+	
---- a/source/writer.h
-+++ b/source/writer.h
-@@ -9,6 +9,7 @@
- #ifndef writer_h
- #define writer_h
- 
-+#include <memory>
- #include "sharedwriter.hpp"
- 
- /***********************************************************************/
diff --git a/sci-biology/mothur/files/mothur-1.48.2-boost-1.89.patch b/sci-biology/mothur/files/mothur-1.48.2-boost-1.89.patch
deleted file mode 100644
index 26417a05992b..000000000000
--- a/sci-biology/mothur/files/mothur-1.48.2-boost-1.89.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -78,7 +78,7 @@
- 
-     LDFLAGS += -L ${BOOST_LIBRARY_DIR}
- 
--    LIBS += -lboost_iostreams -lboost_system -lboost_filesystem -lz
-+    LIBS += -lboost_iostreams -lboost_filesystem -lz
-     CXXFLAGS += -DUSE_BOOST -I ${BOOST_INCLUDE_DIR}
- endif
- 
diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml
deleted file mode 100644
index 15fc0072ba17..000000000000
--- a/sci-biology/mothur/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<use>
-		<flag name="boost">Depend on <pkg>dev-libs/boost</pkg> for make.contigs to read .gz compressed files.</flag>
-		<flag name="gsl">Use <pkg>sci-libs/gsl</pkg> to support diversity estimates for estimiator.single.</flag>
-		<flag name="hdf5">Support Biom format 2.0 for the biom.info command via <pkg>sci-libs/hdf5</pkg>.</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">mothur/mothur</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/mothur/mothur-1.48.2.ebuild b/sci-biology/mothur/mothur-1.48.2.ebuild
deleted file mode 100644
index 0e9ede44d6a3..000000000000
--- a/sci-biology/mothur/mothur-1.48.2.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit flag-o-matic toolchain-funcs
-
-DESCRIPTION="Suite of algorithms for ecological bioinformatics"
-HOMEPAGE="https://mothur.org/"
-SRC_URI="https://github.com/mothur/mothur/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-IUSE="boost gsl hdf5 mpi +readline"
-
-RDEPEND="
-	sci-biology/uchime
-	boost? ( dev-libs/boost:=[zlib] )
-	gsl? ( sci-libs/gsl:= )
-	hdf5? ( sci-libs/hdf5:=[cxx] )
-	mpi? ( virtual/mpi )
-"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.48.0-build.patch
-	"${FILESDIR}"/${P}-boost-1.89.patch # bug 965517
-)
-
-src_configure() {
-	use mpi && export CXX=mpicxx || tc-export CXX
-	use amd64 && append-cppflags -DBIT_VERSION
-}
-
-src_compile() {
-	# bug #862273
-	append-flags -fno-strict-aliasing
-	filter-lto
-
-	# USEBOOST - link with boost libraries. Must install boost. Allows the make.contigs command to read .gz files.
-	# USEHDF5 - link with HDF5cpp libraries. Must install HDF5. Allows the biom.info command to read Biom format 2.0.
-	# USEGSL - link with GNU Scientific libraries. Must install GSL. Allows the estimiator.single command to find diversity estimates.
-	emake \
-		USEBOOST=$(usex boost) \
-		USEHDF5=$(usex hdf5) \
-		USEGSL=$(usex gsl) \
-		USEMPI=$(usex mpi) \
-		USEREADLINE=$(usex readline) \
-		OPTIMIZE=no
-}
-
-src_install() {
-	dobin mothur
-}
diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest
deleted file mode 100644
index 3d68a52ee87a..000000000000
--- a/sci-biology/mrbayes/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST mrbayes-3.1.2.tar.gz 545968 BLAKE2B f4c5bbdde765fb9e596c17d5fd890b168c22cefb0d24b67c1c68623e1dcfa4df716a896fe120f7a1cac4234125b6ed524973506e47492ba3ec26e389783d618a SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14
-DIST mrbayes-3.2.7.tar.gz 9787214 BLAKE2B 2d0ebbc376712e15fc1ed146053d977ad1af96f44c31b8fd0fdbd47ef9bafc41cbb8904db94bc8d30c753c0267a1dcce0d08c73d8b35c20e0f15206bc8fef6ff SHA512 4dc869cd07cf384b3a3945ac8d91a7cc2982e8c5cd8d1f097b46a479a071cb71e71c60e152aa4fc01b0bb296295c5fa9f5a48aa8e913b920c33e30cbb3a6ed37
diff --git a/sci-biology/mrbayes/files/mb_readline_312.patch b/sci-biology/mrbayes/files/mb_readline_312.patch
deleted file mode 100644
index d41986704708..000000000000
--- a/sci-biology/mrbayes/files/mb_readline_312.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -50,4 +50,5 @@
- ifeq  ($(strip $(USEREADLINE)),yes)
-     CFLAGS += -DUSE_READLINE
-+#   CFLAGS += -DCOMPLETIONMATCHES
- 	LIBS += -lncurses -lreadline 
- endif
---- a/bayes.c
-+++ b/bayes.c
-@@ -382,9 +382,11 @@
- char **readline_completion(const char *text, int start, int stop) {
- 	char **matches = (char **) NULL;
--	
-+
-+#ifdef COMPLETIONMATCHES	
- 	if(start == 0)
--    	matches = rl_completion_matches (text, command_generator);
-+    		matches = rl_completion_matches (text, command_generator);
-+#endif
- 
--  return (matches);	
-+	return (matches);	
- }
- #endif
diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml
deleted file mode 100644
index 2fbcd4fa4f98..000000000000
--- a/sci-biology/mrbayes/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-MrBayes is a program for the Bayesian estimation of phylogeny.
-Bayesian inference of phylogeny is based upon a quantity called the
-posterior probability distribution of trees, which is the probability of a
-tree conditioned on the observations. The conditioning is accomplished using
-Bayes's theorem. The posterior probability distribution of trees is
-impossible to calculate analytically; instead, MrBayes uses a simulation
-technique called Markov chain Monte Carlo (or MCMC) to approximate the
-posterior probabilities of trees.
-	</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">mrbayes</remote-id>
-		<remote-id type="github">NBISweden/MrBayes</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
deleted file mode 100644
index 90f8f1d407b5..000000000000
--- a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Bayesian Inference of Phylogeny"
-HOMEPAGE="http://mrbayes.csit.fsu.edu/"
-SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug mpi readline"
-
-DEPEND="
-	sys-libs/ncurses:=
-	mpi? ( virtual/mpi )
-	readline? ( sys-libs/readline:= )
-"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
-	default
-
-	if use mpi; then
-		sed -e "s:MPI ?= no:MPI=yes:" -i Makefile || die "Patching MPI support."
-	fi
-	if ! use readline; then
-		sed -e "s:USEREADLINE ?= yes:USEREADLINE=no:" \
-			-i Makefile || die "Patching readline support."
-	else
-		# Only needed for OSX with an old (4.x) version of
-		# libreadline, but it doesn't hurt for other distributions.
-		eapply "${FILESDIR}"/mb_readline_312.patch
-	fi
-	sed -e 's:-ggdb::g' -i Makefile || die
-}
-
-src_compile() {
-	local myconf mycc
-
-	if use mpi; then
-		mycc=mpicc
-	else
-		mycc="$(tc-getCC)"
-	fi
-
-	use mpi && myconf="MPI=yes"
-	use readline || myconf="${myconf} USEREADLINE=no"
-	use debug && myconf="${myconf} DEBUG=yes"
-	emake \
-		OPTFLAGS="${CFLAGS}" \
-		LDFLAGS="${LDFLAGS}" \
-		CC=${mycc} \
-		${myconf}
-}
-
-src_install() {
-	dobin mb
-	insinto /usr/share/${PN}
-	doins *.nex
-}
diff --git a/sci-biology/mrbayes/mrbayes-3.2.7.ebuild b/sci-biology/mrbayes/mrbayes-3.2.7.ebuild
deleted file mode 100644
index 9f3f61c7af89..000000000000
--- a/sci-biology/mrbayes/mrbayes-3.2.7.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="Bayesian Inference of Phylogeny"
-HOMEPAGE="https://nbisweden.github.io/MrBayes/"
-SRC_URI="https://github.com/NBISweden/MrBayes/releases/download/v${PV}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug mpi readline"
-# --with-readline was given, but MPI support requires readline to be disabled.
-REQUIRED_USE="mpi? ( !readline )"
-
-DEPEND="
-	sys-libs/ncurses:=
-	mpi? ( virtual/mpi )
-	readline? ( sys-libs/readline:= )
-"
-RDEPEND="${DEPEND}"
-
-src_configure() {
-	econf \
-		"$(use_with mpi)" \
-		"$(use_with readline)" \
-		"$(use_enable debug )" \
-		# configure checks cpuid and enables fma{3,4}, sse{1..4} if detected.
-		# Configure options only allow disabling the auto-detection, but do not
-		# actually allow toggling the individual cpu instruction sets. The only
-		# way to guarantee that cross-compiling and binpkgs will work on machines
-		# other than the host is to unconditionally disable sse/fma/avx.
-		#"$(use_enable cpu_flags_x86_sse sse )" \
-		#"$(use_enable cpu_flags_x86_avx avx )" \
-		#"$(use_enable cpu_flags_x86_fma3 fma )" \
-		# Has optional support for sci-biology/beagle::science
-		# "$(use_with beagle)"
-}
-
-src_compile() {
-	# The --disable options for the cpu instruction sets don't actually work so
-	# we override it here and also set the user specified CFLAGS.
-	emake SIMD_FLAGS= CPUEXT_FLAGS= CFLAGS="${CFLAGS}"
-}
diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest
deleted file mode 100644
index 3eb00f919628..000000000000
--- a/sci-biology/mummer/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST MUMmer3.23.tar.gz 3160143 BLAKE2B 5be613e0b7bcdbd0c38bb6dd7ff8d5c220ceb596582d89e0c1b62bbb2b289ce3a1842cd7e335a62d612af55388e21b6f780254de06f59e9e49a7eeadd04b6d8e SHA512 f31d36ef3e07fa4ac017c76c1c8d5f53882a59b061742d201f1f7aafb29d16af8268985285398dd90e98d276b2513d2c611f9876069b23fe82b5da1d3ebc04d3
diff --git a/sci-biology/mummer/files/mummer-3.23-fix-build-system.patch b/sci-biology/mummer/files/mummer-3.23-fix-build-system.patch
deleted file mode 100644
index b92f75c07719..000000000000
--- a/sci-biology/mummer/files/mummer-3.23-fix-build-system.patch
+++ /dev/null
@@ -1,397 +0,0 @@
-Fix build system to restore some sanity
-
---- a/Makefile
-+++ b/Makefile
-@@ -27,31 +27,27 @@
- 
- 
- TOP_DIR     := $(CURDIR)
--BIN_DIR     := $(TOP_DIR)
--AUX_BIN_DIR := $(TOP_DIR)/aux_bin
-+
-+BIN_DIR     = $(EPREFIX)/usr/bin
-+SCRIPT_DIR  = $(EPREFIX)/usr/share/mummer/scripts
-+AUX_BIN_DIR = $(EPREFIX)/usr/bin
- 
- DOC_DIR       := $(TOP_DIR)/docs
- SCRIPT_DIR    := $(TOP_DIR)/scripts
- TIGR_SRC_DIR  := $(TOP_DIR)/src/tigr
- KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz
- 
--CC   := $(filter /%,$(shell /bin/sh -c 'type gcc'))
--CXX  := $(filter /%,$(shell /bin/sh -c 'type g++'))
- SED  := $(filter /%,$(shell /bin/sh -c 'type sed'))
- CSH  := $(filter /%,$(shell /bin/sh -c 'type csh'))
- PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
--AR   := $(filter /%,$(shell /bin/sh -c 'type ar'))
- 
--CXXFLAGS = -O3
--CFLAGS = -O3
--LDFLAGS  =
- 
- FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README ChangeLog
- 
- 
- 
- #-- EXPORT THESE VARIABLES TO OTHER MAKEFILES
--export BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
-+export BIN_DIR SCRIPT_DIR AUX_BIN_DIR
- 
- 
- 
-@@ -114,15 +110,15 @@
- 
- 
- kurtz:
--	cd $(KURTZ_SRC_DIR); $(MAKE) mummer
-+	$(MAKE) -C $(KURTZ_SRC_DIR) mummer
- 
- 
- scripts:
--	cd $(SCRIPT_DIR); $(MAKE) all
-+	$(MAKE) -C $(SCRIPT_DIR) all
- 
- 
- tigr:
--	cd $(TIGR_SRC_DIR); $(MAKE) all
-+	$(MAKE) -C $(TIGR_SRC_DIR) all
- 
- 
- uninstall: clean
---- a/scripts/Makefile
-+++ b/scripts/Makefile
-@@ -1,21 +1,10 @@
--#-- Imported variables from top level makefile
--# BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
-+BIN_DIR     = $(EPREFIX)/usr/bin
-+SCRIPT_DIR  = $(EPREFIX)/usr/share/mummer/scripts
-+AUX_BIN_DIR = $(EPREFIX)/usr/bin
- 
--ifndef BIN_DIR
--BIN_DIR := $(CURDIR)
--endif
--ifndef AUX_BIN_DIR
--AUX_BIN_DIR := $(CURDIR)
--endif
--ifndef SCRIPT_DIR
--SCRIPT_DIR := $(CURDIR)
--endif
--
--SCRIPT_DIR := $(CURDIR)
- SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
- CSH := $(filter /%,$(shell /bin/sh -c 'type csh'))
- PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
--VPATH := $(BIN_DIR)
- 
- ALL := exact-tandems mapview mummerplot nucmer promer \
-        run-mummer1 run-mummer3 nucmer2xfig dnadiff
-@@ -39,58 +28,49 @@
- 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
- 		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
- 		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
--		exact-tandems.csh > $(BIN_DIR)/exact-tandems
--	chmod 755 $(BIN_DIR)/exact-tandems
-+		exact-tandems.csh > exact-tandems
- 
- mapview: mapview.pl
- 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
- 		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
--                mapview.pl > $(BIN_DIR)/mapview
--	chmod 755 $(BIN_DIR)/mapview
-+                mapview.pl > mapview
- 
- mummerplot: mummerplot.pl Foundation.pm
- 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
-                 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
-                 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
--                mummerplot.pl > $(BIN_DIR)/mummerplot
--	chmod 755 $(BIN_DIR)/mummerplot
-+                mummerplot.pl > mummerplot
- 
- dnadiff: dnadiff.pl Foundation.pm
- 	$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
-                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
-                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
--                 dnadiff.pl > $(BIN_DIR)/dnadiff
--	chmod 755 $(BIN_DIR)/dnadiff
-+                 dnadiff.pl > dnadiff
- 
- nucmer: nucmer.pl Foundation.pm
- 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
-                 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
-                 -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
-                 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
--                 nucmer.pl > $(BIN_DIR)/nucmer
--	chmod 755 $(BIN_DIR)/nucmer
-+                 nucmer.pl > nucmer
- 
- promer: promer.pl Foundation.pm
- 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
-                 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
-                 -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
-                 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
--                promer.pl > $(BIN_DIR)/promer
--	chmod 755 $(BIN_DIR)/promer
-+                promer.pl > promer
- 
- run-mummer1: run-mummer1.csh
- 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
- 		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
--		run-mummer1.csh > $(BIN_DIR)/run-mummer1
--	chmod 755 $(BIN_DIR)/run-mummer1
-+		run-mummer1.csh > run-mummer1
- 
- run-mummer3: run-mummer3.csh
- 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
- 		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
--		run-mummer3.csh > $(BIN_DIR)/run-mummer3
--	chmod 755 $(BIN_DIR)/run-mummer3
-+		run-mummer3.csh > run-mummer3
- 
- nucmer2xfig: nucmer2xfig.pl
- 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
--		nucmer2xfig.pl > $(BIN_DIR)/nucmer2xfig
--	chmod 755 $(BIN_DIR)/nucmer2xfig
-+		nucmer2xfig.pl > nucmer2xfig
---- a/src/kurtz/libbasedir/Makefile
-+++ b/src/kurtz/libbasedir/Makefile
-@@ -5,8 +5,6 @@
- 
- SPLINTFLAGS=-f ../Splintoptions -DDEBUG
- 
--LD=$(CC)
--
- ##CFLAGS=${DEFINECFLAGS}
- 
- LIBBASE=libbase.a
-@@ -24,14 +22,14 @@
- 
- 
- $(LIBBASE): $(LIBOBJECTS)
--	ar sruv $@ $(LIBOBJECTS)
-+	$(AR) sruv $@ $(LIBOBJECTS)
- 
- 
- include Filegoals.mf
- 
- 
- $(LIBBASEDBG): $(LIBDEBUGOBJECTS)
--	ar sruv $@ $(LIBDEBUGOBJECTS)
-+	$(AR) sruv $@ $(LIBDEBUGOBJECTS)
- 
- 
- .PHONY:clean
---- a/src/kurtz/Makefile
-+++ b/src/kurtz/Makefile
-@@ -1,7 +1,7 @@
- all:
--	cd libbasedir; $(MAKE) all
--	cd streesrc; $(MAKE) all
--	cd mm3src; $(MAKE) all
-+	$(MAKE) -C libbasedir all
-+	$(MAKE) -C streesrc all
-+	$(MAKE) -C mm3src all
- 
- clean:
- 	rm -f *~
-@@ -10,11 +10,11 @@
- 	cd mm3src; $(MAKE) clean
- 
- mummer:
--	cd libbasedir; $(MAKE) libbase.a
--	cd streesrc; $(MAKE) libstree.a
--	cd mm3src; $(MAKE) mummer
-+	$(MAKE) -C libbasedir libbase.a
-+	$(MAKE) -C streesrc libstree.a
-+	$(MAKE) -C mm3src mummer
- 
- splintall:
--	cd libbasedir; ${MAKE} splintall
--	cd streesrc; ${MAKE} splintall
--	cd mm3src; ${MAKE} splintall
-+	$(MAKE) -C libbasedir splintall
-+	$(MAKE) -C streesrc splintall
-+	$(MAKE) -C mm3src splintall
---- a/src/kurtz/mm3src/Makefile
-+++ b/src/kurtz/mm3src/Makefile
-@@ -3,11 +3,7 @@
- 
- ##include ../Makedef
- 
--ifndef BIN_DIR
--BIN_DIR := $(CURDIR)
--endif
--
--VPATH := $(BIN_DIR)
-+BIN_DIR     = $(EPREFIX)/usr/bin
- 
- ALL := maxmat3.x maxmat3.dbg.x
- 
-@@ -15,11 +11,8 @@
- LIBSTREEDIR=../streesrc
- INCLUDEDIR=-I${LIBBASEDIR} -I${LIBSTREEDIR}
- 
--override CFLAGS+=$(INCLUDEDIR)
--##CFLAGS=${DEFINECFLAGS} $(INCLUDEDIR)
--##LDFLAGS=${DEFINELDFLAGS}
-+override CPPFLAGS+=$(INCLUDEDIR)
- SPLINTFLAGS=${INCLUDEDIR} -f ../Splintoptions -DDEBUG
--LD=$(CC)
- 
- LIBBASE=$(LIBBASEDIR)/libbase.a
- LIBBASEDBG=$(LIBBASEDIR)/libbase.dbg.a
-@@ -40,16 +33,16 @@
- all: $(ALL)
- 
- mummer: $(MUM3OBJECTS) $(LIBSTREE)
--	$(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
--	-o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
-+	$(CC) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
-+	-o $@
- 
- maxmat3.x: $(MUM3OBJECTS) $(LIBSTREE)
--	$(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
--	-o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
-+	$(CC) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
-+	-o $@
- 
- maxmat3.dbg.x: ${MUM3DBGOBJECTS} $(LIBSTREEDBG)
--	$(LD) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \
--	-lm -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
-+	$(CC) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \
-+	-lm -o $@
- 
- include Filegoals.mf
- 
---- a/src/kurtz/streesrc/Makefile
-+++ b/src/kurtz/streesrc/Makefile
-@@ -23,8 +23,6 @@
- 
- #-DSTARTFACTOR=0.5
- 
--LD=${CC}
--
- LIBBASE=${LIBBASEDIR}/libbase.a
- LIBBASEDBG=${LIBBASEDIR}/libbase.dbg.a
- 
-@@ -65,29 +63,29 @@
- include Filegoals.mf
- 
- libstree.4.a: $(OBJECTS4)
--	ar sruv $@ $(OBJECTS4)
-+	$(AR) sruv $@ $(OBJECTS4)
- 
- libstree.a: $(OBJECTS)
--	ar sruv $@ $(OBJECTS)
-+	$(AR) sruv $@ $(OBJECTS)
- 
- libstree.dbg.4.a: $(DBGOBJECTS4)
--	ar sruv $@ $(DBGOBJECTS4)
-+	$(AR) sruv $@ $(DBGOBJECTS4)
- 
- libstree.dbg.a: $(DBGOBJECTS)
--	ar sruv $@ $(DBGOBJECTS)
-+	$(AR) sruv $@ $(DBGOBJECTS)
- 
- 
- stree.x: stree.o libstree.a
--	$(LD) $(LDFLAGS) stree.o libstree.a $(LIBBASE) -o $@
-+	$(CC) $(LDFLAGS) stree.o libstree.a $(LIBBASE) -o $@
- 
- loc.x: loc.o libstree.a
--	$(LD) $(LDFLAGS) loc.o libstree.a $(LIBBASE) -o $@
-+	$(CC) $(LDFLAGS) loc.o libstree.a $(LIBBASE) -o $@
- 
- stree.dbg.x: stree.dbg.o libstree.dbg.a 
--	$(LD) $(LDFLAGS) stree.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@
-+	$(CC) $(LDFLAGS) stree.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@
- 
- loc.dbg.x: loc.dbg.o libstree.dbg.a 
--	$(LD) $(LDFLAGS) loc.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@
-+	$(CC) $(LDFLAGS) loc.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@
- 
- streeproto.h: $(PROTOFILES) Mkstreeproto.sh
- 	@echo "make $@"
---- a/src/tigr/Makefile
-+++ b/src/tigr/Makefile
-@@ -1,20 +1,3 @@
--#-- Imported variables from top level makefile
--# BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
--
--ifndef BIN_DIR
--BIN_DIR := $(CURDIR)
--endif
--ifndef AUX_BIN_DIR
--AUX_BIN_DIR := $(CURDIR)
--endif
--
--OBJ_RULE = $(CXX) $(CXXFLAGS) $< -c -o $@
--BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \
--           chmod 755 $(BIN_DIR)/$@
--AUX_BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
--           chmod 755 $(AUX_BIN_DIR)/$@
--VPATH := $(AUX_BIN_DIR):$(BIN_DIR)
--
- ALL := annotate combineMUMs delta-filter gaps mgaps \
-      postnuc postpro prenuc prepro repeat-match \
-      show-aligns show-coords show-tiling show-snps \
-@@ -38,59 +21,22 @@
- 
- #-- not so PHONY rules --#
- delta.o: delta.cc delta.hh
--	$(OBJ_RULE)
--
- tigrinc.o: tigrinc.cc tigrinc.hh
--	$(OBJ_RULE)
--
- sw_align.o: sw_align.cc sw_align.hh tigrinc.hh
--	$(OBJ_RULE)
--
- translate.o: translate.cc translate.hh
--	$(OBJ_RULE)
--
- 
- annotate: annotate.cc tigrinc.o
--	$(BIN_RULE)
--
- combineMUMs: combineMUMs.cc tigrinc.o
--	$(BIN_RULE)
--
- delta-filter: delta-filter.cc tigrinc.o delta.o
--	$(BIN_RULE)
--
- gaps: gaps.cc tigrinc.o
--	$(BIN_RULE)
--
- mgaps: mgaps.cc tigrinc.o
--	$(BIN_RULE)
--
- postnuc: postnuc.cc tigrinc.o sw_align.o
--	$(AUX_BIN_RULE)
--
- postpro: postpro.cc tigrinc.o sw_align.o translate.o
--	$(AUX_BIN_RULE)
--
- prenuc: prenuc.cc tigrinc.o
--	$(AUX_BIN_RULE)
--
- prepro: prepro.cc tigrinc.o translate.o
--	$(AUX_BIN_RULE)
--
- repeat-match: repeat-match.cc tigrinc.o
--	$(BIN_RULE)
--
- show-aligns: show-aligns.cc tigrinc.o translate.o delta.o
--	$(BIN_RULE)
--
- show-coords: show-coords.cc tigrinc.o delta.o
--	$(BIN_RULE)
--
- show-tiling: show-tiling.cc tigrinc.o delta.o
--	$(BIN_RULE)
--
- show-snps: show-snps.cc tigrinc.o translate.o delta.o
--	$(BIN_RULE)
--
- show-diff: show-diff.cc tigrinc.o delta.o
--	$(BIN_RULE)
diff --git a/sci-biology/mummer/files/mummer-3.23-fix-c++-qa.patch b/sci-biology/mummer/files/mummer-3.23-fix-c++-qa.patch
deleted file mode 100644
index d6926c913d4a..000000000000
--- a/sci-biology/mummer/files/mummer-3.23-fix-c++-qa.patch
+++ /dev/null
@@ -1,83 +0,0 @@
---- a/src/kurtz/libbasedir/space.c
-+++ b/src/kurtz/libbasedir/space.c
-@@ -379,7 +379,7 @@
-   }
-   if(numberofblocks > 0)
-   {
--    fprintf(stderr,"space leak: number of blocks = %u\n",numberofblocks);
-+    fprintf(stderr,"space leak: number of blocks = %lu\n",numberofblocks);
-     exit(EXIT_FAILURE);
-   } 
-   free(blocks);
---- a/src/tigr/combineMUMs.cc
-+++ b/src/tigr/combineMUMs.cc
-@@ -106,7 +106,7 @@
-     //  This array [i]  is the maximum number of errors allowed
-     //  in a match between sequences of length  i , which is
-     //  i * MAXERROR_RATE .
--char  * Error_File_Name = DEFAULT_ERROR_FILE_NAME;
-+const char  * Error_File_Name = DEFAULT_ERROR_FILE_NAME;
-     // Name of file to write gaps listing with # errors in each gap
- int  Fill_Ct = 0;
-     // Number of non-acgt bases in ref sequence
-@@ -132,7 +132,7 @@
-     // The query sequence
- long int  Query_Len;
-     // The length of the query sequence
--char  * Query_Suffix = "Query";
-+const char  * Query_Suffix = "Query";
-     // Suffix for query tag
- char  * Ref = NULL;
-     // The reference sequence
-@@ -142,7 +142,7 @@
-     // The length of the reference sequence
- long int  Ref_Size;
-     // The size of the reference sequence buffer
--char  * Ref_Suffix = "Ref";
-+const char  * Ref_Suffix = "Ref";
-     // Suffix for reference tag
- int  Show_Differences = FALSE;
-     // If  TRUE  then show differences in all alignments
---- a/src/tigr/mgaps.cc
-+++ b/src/tigr/mgaps.cc
-@@ -64,9 +64,9 @@
- static void  Parse_Command_Line
-     (int argc, char * argv []);
- static void  Process_Matches
--    (Match_t * A, int N, char * label);
-+    (Match_t * A, int N, const char * label);
- static int  Process_Cluster
--    (Match_t * A, int N, char * label);
-+    (Match_t * A, int N, const char * label);
- static void  Union
-     (int a, int b);
- static void  Usage
-@@ -438,7 +438,7 @@
- 
- 
- static int  Process_Cluster
--    (Match_t * A, int N, char * label)
-+    (Match_t * A, int N, const char * label)
- 
- //  Process the cluster of matches in  A [0 .. (N - 1)]  and output them
- //  after a line containing  label .  Return the number of clusters
-@@ -552,7 +552,7 @@
- 
- 
- static void  Process_Matches
--    (Match_t * A, int N, char * label)
-+    (Match_t * A, int N, const char * label)
- 
- //  Process matches  A [1 .. N]  and output them after
- //  a line containing  label .
---- a/src/tigr/show-coords.cc
-+++ b/src/tigr/show-coords.cc
-@@ -788,7 +788,7 @@
-      (vector<AlignStats> Stats)
- {
-   time_t currtime;
--  char * type;
-+  const char * type;
-   char date[MAX_LINE];
-   long int len;
-   vector<AlignStats>::iterator Sip;
diff --git a/sci-biology/mummer/files/mummer-3.23-fix-shebangs.patch b/sci-biology/mummer/files/mummer-3.23-fix-shebangs.patch
deleted file mode 100644
index 97f1dd843aca..000000000000
--- a/sci-biology/mummer/files/mummer-3.23-fix-shebangs.patch
+++ /dev/null
@@ -1,75 +0,0 @@
-Use portable shebangs instead of hardcoding interpreters
-See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/
-
---- a/scripts/dnadiff.pl
-+++ b/scripts/dnadiff.pl
-@@ -1,4 +1,4 @@
--#!__PERL_PATH -w
-+#!/usr/bin/env perl
- 
- #-------------------------------------------------------------------------------
- #   Programmer: Adam M Phillippy, University of Maryland
---- a/scripts/exact-tandems.csh
-+++ b/scripts/exact-tandems.csh
-@@ -1,4 +1,4 @@
--#!__CSH_PATH -f
-+#!/usr/bin/env csh
- #
- # Find exact tandem repeats in specified file involving an
- # exact duplicate of at least the specified length
---- a/scripts/mapview.pl
-+++ b/scripts/mapview.pl
-@@ -1,4 +1,4 @@
--#!__PERL_PATH
-+#!/usr/bin/env perl
- 
- use lib "__SCRIPT_DIR";
- use Foundation;
---- a/scripts/mummerplot.pl
-+++ b/scripts/mummerplot.pl
-@@ -1,4 +1,4 @@
--#!__PERL_PATH
-+#!/usr/bin/env perl
- 
- ################################################################################
- #   Programmer: Adam M Phillippy, The Institute for Genomic Research
---- a/scripts/nucmer2xfig.pl
-+++ b/scripts/nucmer2xfig.pl
-@@ -1,4 +1,4 @@
--#!__PERL_PATH
-+#!/usr/bin/env perl
- # (c) Steven Salzberg 2001
- # Make an xfig plot for a comparison of a reference chromosome (or single
- # molecule) versus a multifasta file of contigs from another genome.  
---- a/scripts/nucmer.pl
-+++ b/scripts/nucmer.pl
-@@ -1,4 +1,4 @@
--#!__PERL_PATH
-+#!/usr/bin/env perl
- 
- #-------------------------------------------------------------------------------
- #   Programmer: Adam M Phillippy, The Institute for Genomic Research
---- a/scripts/promer.pl
-+++ b/scripts/promer.pl
-@@ -1,4 +1,4 @@
--#!__PERL_PATH
-+#!/usr/bin/env perl
- 
- #-------------------------------------------------------------------------------
- #   Programmer: Adam M Phillippy, The Institute for Genomic Research
---- a/scripts/run-mummer1.csh
-+++ b/scripts/run-mummer1.csh
-@@ -1,4 +1,4 @@
--#!__CSH_PATH -f
-+#!/usr/bin/env csh
- #
- # **SEVERELY** antiquated script for running the mummer 1 suite
- # -r option reverse complements the query sequence, coordinates of the reverse
---- a/scripts/run-mummer3.csh
-+++ b/scripts/run-mummer3.csh
-@@ -1,4 +1,4 @@
--#!__CSH_PATH -f
-+#!/usr/bin/env csh
- #
- # for running the basic mummer 3 suite, should use nucmer instead when possible
- # to avoid the confusing reverse coordinate system of the raw programs.
diff --git a/sci-biology/mummer/metadata.xml b/sci-biology/mummer/metadata.xml
deleted file mode 100644
index 16d1e87a1b24..000000000000
--- a/sci-biology/mummer/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">mummer</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/mummer/mummer-3.23-r1.ebuild b/sci-biology/mummer/mummer-3.23-r1.ebuild
deleted file mode 100644
index 1359833dc21d..000000000000
--- a/sci-biology/mummer/mummer-3.23-r1.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit flag-o-matic toolchain-funcs
-
-DESCRIPTION="A rapid whole genome aligner"
-HOMEPAGE="http://mummer.sourceforge.net/"
-SRC_URI="https://downloads.sourceforge.net/mummer/MUMmer${PV}.tar.gz"
-S="${WORKDIR}/MUMmer${PV}"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc"
-
-RDEPEND="
-	app-shells/tcsh
-	dev-lang/perl"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-3.23-fix-build-system.patch
-	"${FILESDIR}"/${PN}-3.23-fix-c++-qa.patch
-	"${FILESDIR}"/${PN}-3.23-fix-shebangs.patch
-)
-
-src_configure() {
-	use amd64 && append-cppflags -DSIXTYFOURBITS
-	tc-export AR CC CXX
-}
-
-src_install() {
-	dobin src/kurtz/mm3src/mummer
-	dobin src/tigr/{combineMUMs,delta-filter,gaps,mgaps,postnuc,postpro,prenuc,prepro,repeat-match,show-aligns,show-coords,show-tiling,show-snps,show-diff}
-	dobin scripts/{exact-tandems,mapview,mummerplot,dnadiff,nucmer,promer,run-mummer1,run-mummer3,nucmer2xfig}
-	newbin src/tigr/annotate mummer-annotate
-
-	insinto /usr/share/mummer/lib
-	doins scripts/Foundation.pm
-
-	einstalldocs
-	use doc && dodoc -r docs/.
-}
diff --git a/sci-biology/muscle/Manifest b/sci-biology/muscle/Manifest
deleted file mode 100644
index 47000518089c..000000000000
--- a/sci-biology/muscle/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST muscle-5.1.0.tar.gz 185437 BLAKE2B b3742c37179fc8c36fb6160be4c3a8b4afa2f686bc018ec8e97a10834c1f1901b54b489faa9c365aa65c8514f378b7b5518d91a4e2fb067492e32202a06c4f64 SHA512 0cafc7ce07e5d0c261811e085e0fec8e44318a3d2604ad530ad95b370d6386143a4eeb59012e17cfc703f54bde5ee0752c3ce7fc8bb489748dbe89b2229dd6eb
diff --git a/sci-biology/muscle/files/0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch b/sci-biology/muscle/files/0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch
deleted file mode 100644
index a8604239105b..000000000000
--- a/sci-biology/muscle/files/0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch
+++ /dev/null
@@ -1,49 +0,0 @@
-From 9ef231e4612263524a4c41ecb841cdcf0e17d011 Mon Sep 17 00:00:00 2001
-From: Eli Schwartz <eschwartz93@gmail.com>
-Date: Tue, 19 Mar 2024 23:44:43 -0400
-Subject: [PATCH] Makefile: fix horribleness so that it respects build system
- environment
-
-Do not strip, that is portage's job. Respect $CXX, don't override use
--O.
----
- Makefile | 15 ++++-----------
- 1 file changed, 4 insertions(+), 11 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index df16673..086aba3 100644
---- a/Makefile
-+++ b/Makefile
-@@ -19,14 +19,10 @@ OS := $(shell uname)
- 
- CPPFLAGS := $(CPPFLAGS) -DNDEBUG -pthread
- 
--CXX := g++
--ifeq ($(OS),Darwin)
--	CXX := g++-11
--endif
-+CXX ?= g++
-+CXXFLAGS := $(CXXFLAGS) -fopenmp -ffast-math
- 
--CXXFLAGS := $(CXXFLAGS) -O3 -fopenmp -ffast-math
--
--LDFLAGS := $(LDFLAGS) -O3 -fopenmp -pthread -lpthread ${LDFLAGS2}
-+LDFLAGS := $(LDFLAGS) -fopenmp -pthread -lpthread ${LDFLAGS2}
- 
- HDRS := $(shell echo *.h)
- OBJS := $(shell echo *.cpp | sed "-es/^/$(OS)\//" | sed "-es/ / $(OS)\//g" | sed "-es/\.cpp/.o/g")
-@@ -35,10 +31,7 @@ SRCS := $(shell ls *.cpp *.h)
- .PHONY: clean
- 
- $(OS)/muscle : gitver.txt $(OS)/ $(OBJS)
--	$(CXX) $(LDFLAGS) $(OBJS) -o $@
--
--	# Warning: do not add -d option to strip, this is not portable
--	strip $(OS)/muscle
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) $(OBJS) -o $@
- 
- gitver.txt : $(SRCS)
- 	bash ./gitver.bash
--- 
-2.43.2
-
diff --git a/sci-biology/muscle/metadata.xml b/sci-biology/muscle/metadata.xml
deleted file mode 100644
index adacdd12bcf1..000000000000
--- a/sci-biology/muscle/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">rcedgar/muscle</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/muscle/muscle-5.1.0.ebuild b/sci-biology/muscle/muscle-5.1.0.ebuild
deleted file mode 100644
index 7f61b0702052..000000000000
--- a/sci-biology/muscle/muscle-5.1.0.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Multiple sequence comparison by log-expectation"
-HOMEPAGE="https://www.drive5.com/muscle/"
-SRC_URI="https://github.com/rcedgar/muscle/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}"/${P}/src
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86"
-
-RDEPEND="!sci-libs/libmuscle"
-
-PATCHES=(
-	"${FILESDIR}"/0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch
-)
-
-src_configure() {
-	tc-export CXX
-	printf '"%s"\n' "${PV}" > gitver.txt
-}
-
-src_install() {
-	local OS=$(uname) || die
-	dobin ${OS}/muscle
-	dodoc *.txt
-}
diff --git a/sci-biology/newick-utils/Manifest b/sci-biology/newick-utils/Manifest
deleted file mode 100644
index da3e87391d6d..000000000000
--- a/sci-biology/newick-utils/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST newick-utils-1.6.tar.gz 7518535 BLAKE2B 6b5456be6fec4311e40b19972736194a3f2eb51e8efc4a97cdcf027838459a8f22f41d10e49e7ac3e6461aa290aeed1813baeffcb5706749ebf1bf4333e28047 SHA512 1e327f9a32b5b0df097bcb63f933f9073a85f0499a2a48be122f4affca52ae1541e1a6e0cca7420447aa8fe8d10d6e76e8d89933b2f84e023d6c87b50808d96c
diff --git a/sci-biology/newick-utils/files/newick-utils-1.6-deduplicate-libnw.patch b/sci-biology/newick-utils/files/newick-utils-1.6-deduplicate-libnw.patch
deleted file mode 100644
index ca997830aced..000000000000
--- a/sci-biology/newick-utils/files/newick-utils-1.6-deduplicate-libnw.patch
+++ /dev/null
@@ -1,153 +0,0 @@
-Don't rebuild all of libnw.la pointlessly
-
---- a/tests/Makefile.am
-+++ b/tests/Makefile.am
-@@ -8,6 +8,8 @@
- showsrc:
- 	@echo $(srcdir)
- 
-+LDADD = $(top_builddir)/src/libnw.la
-+
- TESTS = test_newick_scanner test_newick_parser test_rnode test_list \
- 	test_link test_masprintf test_svg_graph_radial \
- 	test_canvas test_concat test_hash test_lca test_enode \
-@@ -37,100 +39,57 @@
- 
- SRC = $(top_builddir)/src
- 
--test_newick_scanner_SOURCES = test_newick_scanner.c $(SRC)/newick_scanner.c \
--	$(SRC)/newick_parser.c $(SRC)/rnode.c $(SRC)/rnode_iterator.c \
--	$(SRC)/list.c $(SRC)/hash.c $(SRC)/masprintf.c $(SRC)/link.c
--
--test_newick_parser_SOURCES = test_newick_parser.c $(SRC)/parser.c \
--	$(SRC)/newick_scanner.c $(SRC)/newick_parser.c $(SRC)/list.c \
--	$(SRC)/rnode.c $(SRC)/link.c $(SRC)/hash.c $(SRC)/rnode_iterator.c \
--	$(SRC)/masprintf.c $(SRC)/to_newick.c $(SRC)/concat.c
--
--test_rnode_SOURCES = test_rnode.c $(SRC)/rnode.c $(SRC)/list.c \
--	$(SRC)/rnode_iterator.c $(SRC)/hash.c $(SRC)/masprintf.c \
--	tree_stubs.c $(SRC)/nodemap.c $(SRC)/link.c
--
--test_list_SOURCES = test_list.c $(SRC)/list.c
--
--test_link_SOURCES = test_link.c $(SRC)/link.c $(SRC)/nodemap.c \
--	$(SRC)/list.c $(SRC)/to_newick.c $(SRC)/rnode.c \
--	$(SRC)/concat.c $(SRC)/hash.c tree_stubs.c \
--	$(SRC)/rnode_iterator.c $(SRC)/masprintf.c
-+test_newick_scanner_SOURCES = test_newick_scanner.c
-+
-+test_newick_parser_SOURCES = test_newick_parser.c
-+
-+test_rnode_SOURCES = test_rnode.c tree_stubs.c
-+
-+test_list_SOURCES = test_list.c
-+
-+test_link_SOURCES = test_link.c tree_stubs.c
- 
- test_canvas_SOURCES = test_canvas.c $(SRC)/canvas.c
- 
--test_concat_SOURCES = test_concat.c $(SRC)/concat.c
-+test_concat_SOURCES = test_concat.c
-+
-+test_hash_SOURCES = test_hash.c
-+
-+test_lca_SOURCES = test_lca.c tree_stubs.c
-+
-+test_nodemap_SOURCES = test_nodemap.c tree_stubs.c
- 
--test_hash_SOURCES = test_hash.c $(SRC)/hash.c $(SRC)/list.c $(SRC)/masprintf.c
-+test_to_newick_SOURCES = test_to_newick.c tree_stubs.c
- 
--test_lca_SOURCES = test_lca.c $(SRC)/lca.c $(SRC)/list.c $(SRC)/nodemap.c \
--	$(SRC)/link.c $(SRC)/rnode.c $(SRC)/hash.c \
--	$(SRC)/rnode_iterator.c tree_stubs.c $(SRC)/masprintf.c \
--	$(SRC)/error.c
--
--test_nodemap_SOURCES = test_nodemap.c $(SRC)/nodemap.c \
--	$(SRC)/rnode.c $(SRC)/list.c $(SRC)/hash.c $(SRC)/link.c \
--	$(SRC)/rnode_iterator.c $(SRC)/masprintf.c tree_stubs.c
--
--test_to_newick_SOURCES = test_to_newick.c $(SRC)/to_newick.c \
--	$(SRC)/rnode.c $(SRC)/link.c $(SRC)/concat.c \
--	$(SRC)/list.c $(SRC)/rnode_iterator.c $(SRC)/hash.c \
--	$(SRC)/masprintf.c $(SRC)/parser.c $(SRC)/newick_scanner.c \
--	$(SRC)/newick_parser.c tree_stubs.c
--
--test_tree_SOURCES = test_tree.c $(SRC)/tree.c $(SRC)/rnode.c $(SRC)/list.c \
--	$(SRC)/to_newick.c $(SRC)/nodemap.c $(SRC)/link.c $(SRC)/concat.c \
--	$(SRC)/hash.c tree_stubs.c $(SRC)/rnode_iterator.c \
--	$(SRC)/masprintf.c
--
--test_node_set_SOURCES = test_node_set.c tree_stubs.c $(SRC)/node_set.c \
--	$(SRC)/hash.c $(SRC)/rnode.c $(SRC)/list.c $(SRC)/link.c \
--	$(SRC)/rnode_iterator.c $(SRC)/masprintf.c
--
--test_enode_SOURCES = test_enode.c $(SRC)/enode.c $(SRC)/rnode.c \
--	$(SRC)/link.c $(SRC)/list.c $(SRC)/rnode_iterator.c \
--	$(SRC)/hash.c $(SRC)/masprintf.c
--
--test_rnode_iterator_SOURCES = test_rnode_iterator.c $(SRC)/rnode_iterator.c \
--  	$(SRC)/list.c $(SRC)/link.c $(SRC)/rnode.c $(SRC)/to_newick.c \
--       	$(SRC)/hash.c $(SRC)/nodemap.c tree_stubs.c $(SRC)/masprintf.c \
--	$(SRC)/parser.c $(SRC)/newick_scanner.c $(SRC)/newick_parser.c \
--	$(SRC)/concat.c
-+test_tree_SOURCES = test_tree.c tree_stubs.c
-+
-+test_node_set_SOURCES = test_node_set.c tree_stubs.c $(SRC)/node_set.c
-+
-+test_enode_SOURCES = test_enode.c $(SRC)/enode.c
-+
-+test_rnode_iterator_SOURCES = test_rnode_iterator.c tree_stubs.c
- 
- test_readline_SOURCES = test_readline.c $(SRC)/readline.c
- 
--test_tree_models_SOURCES = test_tree_models.c $(SRC)/tree_models.c \
--	$(SRC)/rnode.c $(SRC)/list.c $(SRC)/to_newick.c $(SRC)/link.c \
--	$(SRC)/concat.c $(SRC)/rnode_iterator.c \
--	$(SRC)/hash.c $(SRC)/masprintf.c
--
--test_xml_utils_SOURCES = test_xml_utils.c $(SRC)/xml_utils.c \
--	$(SRC)/masprintf.c
--
--test_masprintf_SOURCES = test_masprintf.c $(SRC)/masprintf.c
--
--test_error_SOURCES = test_error.c $(SRC)/error.c
--
--test_order_tree_SOURCES = test_order_tree.c $(SRC)/order_tree.c tree_stubs.c \
--	$(SRC)/link.c $(SRC)/to_newick.c $(SRC)/rnode.c $(SRC)/list.c \
--	$(SRC)/masprintf.c $(SRC)/concat.c $(SRC)/hash.c $(SRC)/nodemap.c \
--	$(SRC)/rnode_iterator.c
--
--test_graph_common_SOURCES = test_graph_common.c $(SRC)/graph_common.c \
--	tree_stubs.c $(SRC)/link.c $(SRC)/list.c $(SRC)/tree.c \
--	$(SRC)/rnode_iterator.c $(SRC)/hash.c $(SRC)/masprintf.c \
--	$(SRC)/rnode.c $(SRC)/nodemap.c
-+test_tree_models_SOURCES = test_tree_models.c $(SRC)/tree_models.c
-+
-+test_xml_utils_SOURCES = test_xml_utils.c $(SRC)/xml_utils.c
-+
-+test_masprintf_SOURCES = test_masprintf.c
-+
-+test_error_SOURCES = test_error.c
-+
-+test_order_tree_SOURCES = test_order_tree.c tree_stubs.c $(SRC)/order_tree.c
-+
-+test_graph_common_SOURCES = test_graph_common.c tree_stubs.c $(SRC)/graph_common.c
- 
- test_svg_graph_radial_SOURCES = test_svg_graph_radial.c \
--	$(SRC)/svg_graph_radial.c $(SRC)/tree.c $(SRC)/svg_graph.c \
--	$(SRC)/rnode.c $(SRC)/hash.c $(SRC)/list.c $(SRC)/masprintf.c \
--	$(SRC)/rnode_iterator.c $(SRC)/svg_graph_ortho.c $(SRC)/error.c \
-+	$(SRC)/svg_graph_radial.c $(SRC)/svg_graph.c \
-+	$(SRC)/svg_graph_ortho.c \
- 	$(SRC)/readline.c $(SRC)/xml_utils.c $(SRC)/graph_common.c \
--	$(SRC)/node_pos_alloc.c $(SRC)/nodemap.c $(SRC)/lca.c $(SRC)/link.c
-+	$(SRC)/node_pos_alloc.c
- 
--test_subtree_SOURCES = test_subtree.c $(SRC)/subtree.c $(SRC)/rnode.c \
--	$(SRC)/list.c $(SRC)/hash.c $(SRC)/link.c $(SRC)/rnode_iterator.c \
--	$(SRC)/masprintf.c $(SRC)/nodemap.c
-+test_subtree_SOURCES = test_subtree.c $(SRC)/subtree.c
- 
- clean-local:
- 	$(RM) *.out
diff --git a/sci-biology/newick-utils/files/newick-utils-1.6-fno-common.patch b/sci-biology/newick-utils/files/newick-utils-1.6-fno-common.patch
deleted file mode 100644
index 15847a52c480..000000000000
--- a/sci-biology/newick-utils/files/newick-utils-1.6-fno-common.patch
+++ /dev/null
@@ -1,41 +0,0 @@
---- a/src/address_parser.c
-+++ b/src/address_parser.c
-@@ -83,6 +83,8 @@
- #include "enode.h"
- #include "address_parser_status.h"
- 
-+enum address_parser_status_type address_parser_status;
-+
- extern int adslex (void);
- 
- /* The root of the expression (when represented as a parse tree) */
---- a/src/address_parser_status.h
-+++ b/src/address_parser_status.h
-@@ -13,4 +13,4 @@
-  * returns either \c NULL or the top-level enode of the address, so we need to
-  * use an extern variable to convey its status. */
- 
--enum address_parser_status_type address_parser_status;
-+extern enum address_parser_status_type address_parser_status;
---- a/tests/test_newick_parser.c
-+++ b/tests/test_newick_parser.c
-@@ -11,7 +11,7 @@
- int nwslex (void);
- struct rnode *root;
- struct llist *nodes_in_order;
--enum parser_status_type newick_parser_status;
-+extern enum parser_status_type newick_parser_status;
- void newick_scanner_set_string_input(char *);
- 
- /* NOTE: we can use to_newick() to check the parser's output because this
---- a/tests/test_newick_scanner.c
-+++ b/tests/test_newick_scanner.c
-@@ -20,7 +20,7 @@
- int nwslex (void);
- struct rnode *root;
- struct llist *nodes_in_order;
--enum parser_status_type newick_parser_status;
-+extern enum parser_status_type newick_parser_status;
- void newick_scanner_set_string_input(char *);
- void newick_scanner_set_file_input(FILE *);
- 
diff --git a/sci-biology/newick-utils/metadata.xml b/sci-biology/newick-utils/metadata.xml
deleted file mode 100644
index 9ba134125d0c..000000000000
--- a/sci-biology/newick-utils/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<use>
-		<flag name="xml">Uses <pkg>dev-libs/libxml2</pkg> to handle ornaments</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">tjunier/newick_utils</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/newick-utils/newick-utils-1.6-r3.ebuild b/sci-biology/newick-utils/newick-utils-1.6-r3.ebuild
deleted file mode 100644
index 267cf5da476f..000000000000
--- a/sci-biology/newick-utils/newick-utils-1.6-r3.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools flag-o-matic
-
-DESCRIPTION="Tools for processing phylogenetic trees"
-HOMEPAGE="https://web.archive.org/web/20120206012743/http://cegg.unige.ch/newick_utils"
-SRC_URI="https://web.archive.org/web/20120126210029if_/http://cegg.unige.ch/pub/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="xml"
-
-DEPEND="
-	xml? ( dev-libs/libxml2:= )"
-RDEPEND="
-	${DEPEND}
-	!dev-games/libnw"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-deduplicate-libnw.patch
-	"${FILESDIR}"/${P}-fno-common.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	# -Werror=lto-type-mismatch
-	# https://bugs.gentoo.org/862279
-	# https://github.com/tjunier/newick_utils/issues/34
-	filter-lto
-
-	econf \
-		--disable-static \
-		--without-guile \
-		--without-lua \
-		$(use_with xml libxml)
-}
-
-src_install() {
-	default
-	find "${ED}" -name '*.la' -delete || die
-}
diff --git a/sci-biology/pals/Manifest b/sci-biology/pals/Manifest
deleted file mode 100644
index 5353f14a9f31..000000000000
--- a/sci-biology/pals/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pals-1.0.tar.gz 24895 BLAKE2B 09a24b3a2e99471378f33a84c447dea9153ddedd502de4e6b771c85ef99df5ca30f687b58d1d9d4726b29345215b617f1dc93a71b8be417d8c0c03e8ecd71015 SHA512 655e3311c63709dab1f8a13b193ed30a5ee97c04757a1e8408a74f6110ff3bdd96ba9eb07f4987ed5b83790ffa8cec67f722fee783c4ab4120483a683ebb9b8f
diff --git a/sci-biology/pals/files/pals-1.0-fix-build-system.patch b/sci-biology/pals/files/pals-1.0-fix-build-system.patch
deleted file mode 100644
index a020a697f85b..000000000000
--- a/sci-biology/pals/files/pals-1.0-fix-build-system.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-Make build system honour user variables
-
---- a/Makefile
-+++ b/Makefile
-@@ -1,6 +1,4 @@
--CFLAGS = -O3 -march=pentiumpro -mcpu=pentiumpro -funroll-loops -Winline -DNDEBUG=1
--LDLIBS = -lm -static
--# LDLIBS = -lm
-+LDLIBS = -lm
- 
- OBJ = .o
- EXE =
-@@ -8,18 +6,13 @@
- RM = rm -f
- CP = cp
- 
--GPP = g++
--LD = $(GPP) $(CFLAGS)
--CPP = $(GPP) -c $(CFLAGS) 
--CC = gcc -c $(CFLAGS) 
--
- all: pals
- 
- CPPSRC = $(sort $(wildcard *.cpp))
- CPPOBJ	= $(subst .cpp,.o,$(CPPSRC))
- 
--$(CPPOBJ): %.o: %.cpp
--	$(CPP) $< -o $@
-+%.o: %.cpp
-+	$(CXX) $(CXXFLAGS) -DNDEBUG $(CPPFLAGS) -c $< -o $@
- 
- pals: $(CPPOBJ)
--	$(LD) -o pals $(CPPOBJ) $(LDLIBS)
-+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o pals $(CPPOBJ) $(LDLIBS)
diff --git a/sci-biology/pals/metadata.xml b/sci-biology/pals/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/pals/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/pals/pals-1.0-r2.ebuild b/sci-biology/pals/pals-1.0-r2.ebuild
deleted file mode 100644
index 94f972567ea7..000000000000
--- a/sci-biology/pals/pals-1.0-r2.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Pairwise Aligner for Long Sequences"
-HOMEPAGE="https://www.drive5.com/pals/"
-SRC_URI="https://www.drive5.com/pals/pals_source.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-PATCHES=( "${FILESDIR}"/${PN}-1.0-fix-build-system.patch )
-
-src_configure() {
-	tc-export CXX
-}
-
-src_install() {
-	dobin pals
-}
diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest
deleted file mode 100644
index afb22bd8917b..000000000000
--- a/sci-biology/paml/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST paml-4.10.10.tar.gz 3835148 BLAKE2B 170915e094bd7f4c95895b4cb56e31d4e11f7b70c0f4b8c5c9104a88c68af62c635e18b36a7f56c96170e7eb490966d9ece0ab0e73aa42142def867a1bdce0bc SHA512 e3a3a0f2300213823f4126914073f538fc9859a2378a8494303c3b5fedf935e42c44311e9a89dac4eebc97fdd5653aa95c4d20e1b3ec62866f3bffffcbc9689c
-DIST paml-4.10.7.tar.gz 5250841 BLAKE2B 4d2a7fdc8eb93abe200165f7805520a02f4251dc651f26c4e1bf6fb11eee3d0721fd9d6f3c96979bae0f51b77f168e8d8a12f3dd3cbbfec7e8210a70b7c4bb9e SHA512 e450c0a28ecef946279fd92834eb5ddfb50805167655364cc959ef21839a75280a37d79209918373e80dacb0fc35decaccdb1477e53a81fd99fb140a0ce839fe
diff --git a/sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch b/sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch
deleted file mode 100644
index 492396a0fd83..000000000000
--- a/sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch
+++ /dev/null
@@ -1,60 +0,0 @@
-https://github.com/abacus-gene/paml/pull/46
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -9,39 +9,39 @@ LIBS = -lm # -lM
- all : $(PRGS)
- 
- baseml : baseml.o tools.o treesub.c treespace.c paml.h
--	$(CC) $(CFLAGS) -o $@ baseml.o tools.o $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ baseml.o tools.o $(LIBS)
- basemlg : basemlg.o tools.o treesub.c treespace.c paml.h
--	$(CC) $(CFLAGS) -o $@ basemlg.o tools.o $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ basemlg.o tools.o $(LIBS)
- codeml : codeml.o tools.o treesub.c treespace.c paml.h
--	$(CC) $(CFLAGS) -o $@ codeml.o tools.o $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ codeml.o tools.o $(LIBS)
- evolver : evolver.o tools.o treesub.c treespace.c paml.h
--	$(CC) $(CFLAGS) -o $@ evolver.o tools.o $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ evolver.o tools.o $(LIBS)
- pamp : pamp.o tools.o treesub.c treespace.c paml.h
--	$(CC) $(CFLAGS) -o $@ pamp.o tools.o $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ pamp.o tools.o $(LIBS)
- mcmctree : mcmctree.o tools.o treesub.c treespace.c paml.h
--	$(CC) $(CFLAGS) -o $@ mcmctree.c tools.o $(LIBS)
--	$(CC) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.o $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ mcmctree.c tools.o $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.o $(LIBS)
- yn00: yn00.o tools.o paml.h
--	$(CC) $(CFLAGS) -o $@ yn00.o tools.o $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ yn00.o tools.o $(LIBS)
- chi2 : chi2.o
--	$(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ chi2.c $(LIBS)
- 
- tools.o : paml.h tools.c
--	$(CC) $(CFLAGS) -c tools.c
-+	$(CC) $(CPPFLAGS) $(CFLAGS) -c tools.c
- baseml.o : paml.h baseml.c treesub.c treespace.c
--	$(CC) $(CFLAGS) -c baseml.c
-+	$(CC) $(CPPFLAGS) $(CFLAGS) -c baseml.c
- basemlg.o : paml.h basemlg.c treesub.c
--	$(CC) $(CFLAGS) -c basemlg.c
-+	$(CC) $(CPPFLAGS) $(CFLAGS) -c basemlg.c
- codeml.o : paml.h codeml.c treesub.c treespace.c
--	$(CC) $(CFLAGS) -c codeml.c
-+	$(CC) $(CPPFLAGS) $(CFLAGS) -c codeml.c
- evolver.o: evolver.c treesub.c treespace.c
--	$(CC) $(CFLAGS) -c evolver.c
-+	$(CC) $(CPPFLAGS) $(CFLAGS) -c evolver.c
- mcmctree.o : paml.h mcmctree.c treesub.c treespace.c
--	$(CC) $(CFLAGS) -c mcmctree.c
-+	$(CC) $(CPPFLAGS) $(CFLAGS) -c mcmctree.c
- pamp.o : paml.h pamp.c treesub.c treespace.c
--	$(CC) $(CFLAGS) -c pamp.c
-+	$(CC) $(CPPFLAGS) $(CFLAGS) -c pamp.c
- yn00.o : paml.h yn00.c
--	$(CC) $(CFLAGS) -c yn00.c
-+	$(CC) $(CPPFLAGS) $(CFLAGS) -c yn00.c
- 
- clean :
- 	-rm *.o $(PRGS)
diff --git a/sci-biology/paml/metadata.xml b/sci-biology/paml/metadata.xml
deleted file mode 100644
index 1407729820e0..000000000000
--- a/sci-biology/paml/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="github">abacus-gene/paml</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/paml/paml-4.10.10.ebuild b/sci-biology/paml/paml-4.10.10.ebuild
deleted file mode 100644
index 068e46ee72dd..000000000000
--- a/sci-biology/paml/paml-4.10.10.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
-HOMEPAGE="https://github.com/abacus-gene/paml/wiki"
-SRC_URI="https://github.com/abacus-gene/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-src_compile() {
-	emake -C src CC="$(tc-getCC)" CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dobin src/{baseml,basemlg,codeml,evolver,pamp,mcmctree,infinitesites,yn00,chi2}
-
-	dodoc -r README.md doc/.
-
-	insinto /usr/share/${PN}/control
-	doins examples/*.ctl
-
-	insinto /usr/share/${PN}/dat
-	doins -r examples/stewart* examples/*.dat dat/.
-
-	insinto /usr/share/${PN}
-	doins -r examples
-}
diff --git a/sci-biology/paml/paml-4.10.7.ebuild b/sci-biology/paml/paml-4.10.7.ebuild
deleted file mode 100644
index 3291f74efcad..000000000000
--- a/sci-biology/paml/paml-4.10.7.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
-HOMEPAGE="https://abacus.gene.ucl.ac.uk/software/paml.html"
-SRC_URI="https://github.com/abacus-gene/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="free-noncomm"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-4.10.7-LDFLAGS.patch
-)
-
-src_compile() {
-	emake -C src CC="$(tc-getCC)" CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dobin src/{baseml,basemlg,codeml,evolver,pamp,mcmctree,infinitesites,yn00,chi2}
-
-	dodoc -r README.md doc/.
-
-	insinto /usr/share/${PN}/control
-	doins examples/*.ctl
-
-	insinto /usr/share/${PN}/dat
-	doins -r examples/stewart* examples/*.dat dat/.
-
-	insinto /usr/share/${PN}
-	doins -r examples
-}
diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest
deleted file mode 100644
index 444e3d45e356..000000000000
--- a/sci-biology/phylip/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST phylip-3.698.zip 9675991 BLAKE2B 8d020cf17b3245b9827af4bdd1d17167c3e1a41ae805766c4b72f09de107775314a2a296c00f84f928487403cc02741fd46ae73585d0dba143f4b926777e9add SHA512 7f822dabd1ffdb6a689e0c308f5a3ae129bd86e305086a18c0c755ac3c6ca28a4337d52ced76b280706926370e23f19f304851ef82e32833d1945ed277f7d70d
diff --git a/sci-biology/phylip/files/README.Gentoo b/sci-biology/phylip/files/README.Gentoo
deleted file mode 100644
index 3b2062003996..000000000000
--- a/sci-biology/phylip/files/README.Gentoo
+++ /dev/null
@@ -1,15 +0,0 @@
-Using the PHYlogeny Inference Package on Gentoo systems
-
-Location of the factor program
-
-On Gentoo systems, the PHYLIP program "factor" is named "factor-phylip", in
-order to avoid a file collision with the program of the same name provided by
-the "sys-apps/coreutils" package.
-
-Location of the font files
-
-PHYLIP programs will find font files only if they are in a directory
-referenced by the "PATH" variable or if they are in the current working
-directory. When working with PHYLIP programs that need these files, either
-copy or symlink the fonts you need to your working directory, or add
-"/usr/share/phylip/fonts/" to your "PATH" variable.
diff --git a/sci-biology/phylip/files/phylip-3.698-fno-common.patch b/sci-biology/phylip/files/phylip-3.698-fno-common.patch
deleted file mode 100644
index 986b1d9650ab..000000000000
--- a/sci-biology/phylip/files/phylip-3.698-fno-common.patch
+++ /dev/null
@@ -1,70 +0,0 @@
---- a/src/draw.c
-+++ b/src/draw.c
-@@ -34,6 +34,11 @@
- 
- char fontname[LARGE_BUF_LENGTH];
- 
-+long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
-+     vrmlgroundcolornear, vrmlgroundcolorfar, vrmlplotcolor;
-+
-+char afmfile[FNMLNGTH];
-+
- /* format of matrix: capheight,  length[32],length[33],..length[256]*/
- 
- byte *full_pic ;
---- a/src/draw.h
-+++ b/src/draw.h
-@@ -52,10 +52,10 @@
-   double intensity, x, y, z;
- } vrmllighttype;
- 
--long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
-+extern long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
-      vrmlgroundcolornear, vrmlgroundcolorfar, vrmlplotcolor;
-      
--char afmfile[FNMLNGTH];
-+extern char afmfile[FNMLNGTH];
- 
- double lengthtext(char *, long, char *, fonttype);
- double heighttext(fonttype, char *);
---- a/src/drawtree.c
-+++ b/src/drawtree.c
-@@ -69,7 +69,7 @@
-              uselengths, regular, rotate, empty, rescaled,
-              notfirst, improve, nbody, firstscreens, labelavoid;
- boolean     pictbold,pictitalic,pictshadow,pictoutline;
--boolean javarun;
-+extern boolean javarun;
- 
- striptype stripe;
- plottertype plotter, oldplotter;
---- a/src/phylip.c
-+++ b/src/phylip.c
-@@ -34,6 +34,8 @@
- 
- #include "phylip.h"
- 
-+boolean javarun;
-+
- #ifdef WIN32
- #include <windows.h>
- /* for console code (clear screen, text color settings) */
---- a/src/phylip.h
-+++ b/src/phylip.h
-@@ -331,7 +331,7 @@
- /* Lower-triangular format. */
- #define MAT_LOWERTRI    (MAT_LOWER | MAT_MACHINE)
- 
--boolean javarun;
-+extern boolean javarun;
- 
- typedef long *steptr;
- typedef long longer[6];
-@@ -351,7 +351,6 @@
- extern long spp, words, bits;
- extern boolean ibmpc, ansi, tranvsp;
- extern naym *nayme;                     /* names of species */
--boolean firstplotblock; // for debugging BMP output
- 
- #define ebcdic          EBCDIC
- 
diff --git a/sci-biology/phylip/files/phylip-3.698-makefile.patch b/sci-biology/phylip/files/phylip-3.698-makefile.patch
deleted file mode 100644
index f55ab98dd9cb..000000000000
--- a/sci-biology/phylip/files/phylip-3.698-makefile.patch
+++ /dev/null
@@ -1,266 +0,0 @@
---- a/src/Makefile.unx
-+++ b/src/Makefile.unx
-@@ -81,7 +81,6 @@
- #CC        = cc
- #
- #  To use GCC instead:
--CC        = gcc
- #
- # ----------------------------------------------------------------------------
- #
-@@ -91,7 +90,6 @@
- #
- #
- #A minimal one
--CFLAGS = 
- #
- # A basic one for debugging
- #CFLAGS  = -g 
-@@ -220,7 +218,7 @@
- 	@echo "Done."
- 	@echo ""
- 
--put:
-+put: all
- 	@echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)"
- 	@mkdir -p $(EXEDIR)
- 	@cp $(PROGS) $(EXEDIR)
-@@ -270,195 +268,195 @@
- clique.o:       clique.c disc.h phylip.h
- 
- clique:         clique.o disc.o phylip.o
--	$(CC) $(CFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique
-+	$(CC) $(LDFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique
- 
- cons.o:         cons.c cons.h phylip.h 
- 
- consense.o:     consense.c cons.h phylip.h
- 
- consense:       consense.o phylip.o cons.o
--	$(CC) $(CFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense
-+	$(CC) $(LDFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense
- 
- contml.o:       contml.c cont.h phylip.h
- 
- contml:       contml.o cont.o phylip.o
--	$(CC) $(CFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml
-+	$(CC) $(LDFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml
- 
- contrast.o:       contrast.c cont.h phylip.h
- 
- contrast:       contrast.o cont.o phylip.o
--	$(CC) $(CFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast
-+	$(CC) $(LDFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast
- 
- dnacomp.o:      dnacomp.c seq.h phylip.h
- 
- dnacomp:      dnacomp.o seq.o phylip.o
--	$(CC) $(CFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp
-+	$(CC) $(LDFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp
- 
- dnadist.o:      dnadist.c seq.h phylip.h
- 
- dnadist:      dnadist.o seq.o phylip.o
--	$(CC) $(CFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist
-+	$(CC) $(LDFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist
- 
- dnainvar.o:      dnainvar.c seq.h phylip.h
- 
- dnainvar:      dnainvar.o seq.o phylip.o
--	$(CC) $(CFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar
-+	$(CC) $(LDFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar
- 
- dnaml.o:      dnaml.c seq.h phylip.h
- 
- dnaml:      dnaml.o seq.o phylip.o
--	$(CC) $(CFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml
-+	$(CC) $(LDFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml
- 
- dnamlk.o:      dnamlk.c seq.h phylip.h mlclock.h printree.h
- 
- dnamlk:      dnamlk.o seq.o phylip.o mlclock.o printree.o
--	$(CC) $(CFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk
-+	$(CC) $(LDFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk
- 
- dnamove.o:      dnamove.c seq.h moves.h phylip.h
- 
- dnamove:      dnamove.o seq.o moves.o phylip.o
--	$(CC) $(CFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove
-+	$(CC) $(LDFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove
- 
- dnapenny.o:      dnapenny.c seq.h phylip.h
- 
- dnapenny:      dnapenny.o seq.o phylip.o
--	$(CC) $(CFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny
-+	$(CC) $(LDFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny
- 
- dnapars.o:      dnapars.c seq.h phylip.h
- 
- dnapars:      dnapars.o seq.o phylip.o
--	$(CC) $(CFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars
-+	$(CC) $(LDFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars
- 
- dolmove.o:       dolmove.c disc.h moves.h dollo.h phylip.h
- 
- dolmove:       dolmove.o disc.o moves.o dollo.o phylip.o
--	$(CC) $(CFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove
-+	$(CC) $(LDFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove
- 
- dollop.o:       dollop.c disc.h dollo.h phylip.h
- 
- dollop:       dollop.o disc.o dollo.o phylip.o
--	$(CC) $(CFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop
-+	$(CC) $(LDFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop
- 
- dolpenny.o:       dolpenny.c disc.h dollo.h phylip.h
- 
- dolpenny:       dolpenny.o disc.o dollo.o phylip.o
--	$(CC) $(CFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny
-+	$(CC) $(LDFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny
- 
- draw.o:   draw.c draw.h phylip.h 
--	$(CC) $(DFLAGS) -c draw.c
-+	$(CC) $(DFLAGS) $(CPPFLAGS) -c draw.c
- 
- draw2.o:   draw2.c draw.h phylip.h 
--	$(CC) $(DFLAGS) -c draw2.c
-+	$(CC) $(DFLAGS) $(CPPFLAGS) -c draw2.c
- 
- drawgram.o:     drawgram.c draw.h phylip.h
--	$(CC) $(DFLAGS) -c drawgram.c
-+	$(CC) $(DFLAGS) $(CPPFLAGS) -c drawgram.c
- 
- drawgram:     drawgram.o draw.o draw2.o phylip.o
--	$(CC) $(DFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram
-+	$(CC) $(LDFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram
- 	
- # needed by java	
--libdrawgram.so:   drawgram.o draw.o draw2.o phylip.o
--	$(CC) $(CFLAGS) -o libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS)
-+libdrawgram.so:
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawgram.so -Wl,-soname,libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS)
- 
- drawtree.o:     drawtree.c draw.h phylip.h
--	$(CC) $(DFLAGS)  -shared -fPIC -c drawtree.c
-+	$(CC) $(DFLAGS) $(CPPFLAGS) -c drawtree.c
- 
- drawtree:     drawtree.o draw.o draw2.o phylip.o
--	$(CC) $(DFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree
-+	$(CC) $(LDFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree
- 
- # needed by java	
--libdrawtree.so:     drawtree.o draw.o draw2.o phylip.o
--	$(CC) $(CFLAGS) -o libdrawtree.so  -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS)
-+libdrawtree.so:
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawtree.so -Wl,-soname,libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS)
- 
- factor.o:       factor.c phylip.h
- 
- factor:       factor.o phylip.o
--	$(CC) $(CFLAGS) factor.o phylip.o $(LIBS) -o factor
-+	$(CC) $(LDFLAGS) factor.o phylip.o $(LIBS) -o factor
- 
- fitch.o:        fitch.c dist.h phylip.h
- 
- fitch:        fitch.o dist.o phylip.o
--	$(CC) $(CFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch
-+	$(CC) $(LDFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch
- 
- gendist.o:      gendist.c phylip.h
- 
- gendist:      gendist.o phylip.o
--	$(CC) $(CFLAGS) gendist.o phylip.o $(LIBS) -o gendist
-+	$(CC) $(LDFLAGS) gendist.o phylip.o $(LIBS) -o gendist
- 
- kitsch.o:        kitsch.c dist.h phylip.h
- 
- kitsch:        kitsch.o dist.o phylip.o
--	$(CC) $(CFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch
-+	$(CC) $(LDFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch
- 
- mix.o:        mix.c disc.h wagner.h phylip.h
- 
- mix:        mix.o disc.o wagner.o phylip.o
--	$(CC) $(CFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix
-+	$(CC) $(LDFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix
- 
- move.o:        move.c disc.h moves.h wagner.h phylip.h
- 
- move:        move.o disc.o moves.o wagner.o phylip.o
--	$(CC) $(CFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move
-+	$(CC) $(LDFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move
- 
- neighbor.o:        neighbor.c dist.h phylip.h
- 
- neighbor:        neighbor.o dist.o phylip.o
--	$(CC) $(CFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor
-+	$(CC) $(LDFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor
- 
- pars.o:   pars.c discrete.h phylip.h
- 
- pars: pars.o discrete.o phylip.o
--	$(CC) $(CFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars
-+	$(CC) $(LDFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars
- 
- penny.o:  penny.c disc.h wagner.h phylip.h
- 
- penny:  penny.o disc.o wagner.o phylip.o
--	$(CC) $(CFLAGS) penny.o disc.o wagner.o  phylip.o $(LIBS) -o penny
-+	$(CC) $(LDFLAGS) penny.o disc.o wagner.o phylip.o $(LIBS) -o penny
- 
- proml.o:      proml.c seq.h phylip.h
- 
- proml:      proml.o seq.o phylip.o
--	$(CC) $(CFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml
-+	$(CC) $(LDFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml
- 
- promlk.o:      promlk.c seq.h phylip.h mlclock.h printree.h
- 
- promlk:      promlk.o seq.o phylip.o mlclock.o printree.o
--	$(CC) $(CFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk
-+	$(CC) $(LDFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk
- 
- protdist.o:      protdist.c seq.h phylip.h
- 
- protdist:      protdist.o seq.o phylip.o
--	$(CC) $(CFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist
-+	$(CC) $(LDFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist
- 
- protpars.o: protpars.c seq.h phylip.h
- 
- protpars: protpars.o seq.o phylip.o
--	$(CC) $(CFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars
-+	$(CC) $(LDFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars
- 
- restdist.o: restdist.c seq.h phylip.h
- 
- restdist: restdist.o seq.o phylip.o
--	$(CC) $(CFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist
-+	$(CC) $(LDFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist
- 
- restml.o: restml.c seq.h phylip.h
- 
- restml: restml.o seq.o phylip.o
--	$(CC) $(CFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml
-+	$(CC) $(LDFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml
- 
- retree.o:       retree.c moves.h phylip.h
- 
- retree:       retree.o moves.o phylip.o
--	$(CC) $(CFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree
-+	$(CC) $(LDFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree
- 
- seqboot.o:      seqboot.c phylip.h
- 
- seqboot:      seqboot.o seq.o phylip.o
--	$(CC) $(CFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot
-+	$(CC) $(LDFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot
- 
- treedist.o:     treedist.c cons.h phylip.h
- 
- treedist:     treedist.o phylip.o cons.o
--	$(CC) $(CFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist
-+	$(CC) $(LDFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist
- 
- 
- # ----------------------------------------------------------------------------
diff --git a/sci-biology/phylip/metadata.xml b/sci-biology/phylip/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/phylip/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/phylip/phylip-3.698.ebuild b/sci-biology/phylip/phylip-3.698.ebuild
deleted file mode 100644
index 8c425b1d5add..000000000000
--- a/sci-biology/phylip/phylip-3.698.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic toolchain-funcs
-
-DESCRIPTION="The PHYLogeny Inference Package"
-HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
-SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.zip"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-
-# 'mix' tool collides with dev-lang/elixir, bug #537514
-RDEPEND="
-	x11-libs/libXaw
-	!dev-lang/elixir"
-DEPEND="${RDEPEND}
-	x11-base/xorg-proto"
-BDEPEND="app-arch/unzip"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-makefile.patch
-	"${FILESDIR}"/${P}-fno-common.patch
-)
-
-src_prepare() {
-	default
-
-	mkdir fonts || die
-	# clear out old binaries
-	rm -r exe || die
-}
-
-src_configure() {
-	tc-export CC
-	append-cflags -Wno-unused-result
-}
-
-src_compile() {
-	emake -C src -f Makefile.unx all put
-}
-
-src_install() {
-	mv exe/font* fonts || die "Font move failed"
-	mv exe/factor exe/factor-${PN} || die "Renaming factor failed"
-
-	dolib.so exe/*so
-	rm exe/*so || die
-	dobin exe/*
-
-	dodoc "${FILESDIR}"/README.Gentoo
-	docinto html
-	dodoc -r phylip.html doc
-
-	insinto /usr/share/phylip
-	doins -r fonts
-}
diff --git a/sci-biology/phyml/Manifest b/sci-biology/phyml/Manifest
deleted file mode 100644
index 9f0a281cf0c4..000000000000
--- a/sci-biology/phyml/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST phyml_v2.4.5.tar.gz 92143 BLAKE2B f95b6b5023cd9b68e92e600edd9ee404bdec717d0b1e748c9e4f4667d732a23469762b847e4aa3c36e5cea7ce1d663ade031ec996cd6449ef1cf2fd55b96b2c8 SHA512 119716290eca0de4da05b0bacbec96139f4c89f6a033b861d1cb2655a620766bd0bea0675c4d7722a31d888652a28bf3544a643f39f11682982ede80dc5928c3
diff --git a/sci-biology/phyml/files/phyml-2.4.5-fix-build-system.patch b/sci-biology/phyml/files/phyml-2.4.5-fix-build-system.patch
deleted file mode 100644
index 9b1d9e03ca14..000000000000
--- a/sci-biology/phyml/files/phyml-2.4.5-fix-build-system.patch
+++ /dev/null
@@ -1,67 +0,0 @@
-Fix build system to honour user flags.
-
---- a/Makefile
-+++ b/Makefile
-@@ -1,10 +1,4 @@
--hello !!!
--
--CC = gcc #cc
--CFLAGS = -O4 -fomit-frame-pointer -Wall -static
--# CFLAGS = -Wall
--# CFLAGS = -g -Wall
--# CFLAGS = -pg -Wall -fprofile-arcs -static
-+CC ?= gcc
- LIBS = -lm
- 
- PROG = PHYML
-@@ -23,39 +17,39 @@
- 
- 
- $(EXEC) : $(OBJS)
--	$(CC) -o $(EXEC) $(OBJS) $(LIBS) $(CFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(EXEC) $(OBJS) $(LIBS)
- 
- clean :
- 	@rm *.o
- ######################################################################################################
- 
- eigen.o : eigen.c eigen.h
--	$(CC) $(CFLAGS) $(DFLAG) -c eigen.c
-+	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c eigen.c
- 
- simu.o : simu.c simu.h
--	$(CC) $(CFLAGS) $(DFLAG) -c simu.c
-+	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c simu.c
- 
- lk.o : lk.c lk.h
--	$(CC) $(CFLAGS) $(DFLAG) -c lk.c
-+	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c lk.c
- 
- utilities.o : utilities.c utilities.h
--	$(CC) $(CFLAGS) $(DFLAG) -c utilities.c
-+	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c utilities.c
- 
- optimiz.o : optimiz.c optimiz.h
--	$(CC) $(CFLAGS) $(DFLAG) -c optimiz.c
-+	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c optimiz.c
- 
- bionj.o : bionj.c bionj.h
--	$(CC) $(CFLAGS) $(DFLAG) -c bionj.c
-+	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c bionj.c
- 
- main.o : main.c
--	$(CC) $(CFLAGS) $(DFLAG) -c main.c
-+	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c main.c
- 
- models.o : models.c models.h
--	$(CC) $(CFLAGS) $(DFLAG) -c models.c
-+	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c models.c
- 
- free.o : free.c free.h
--	$(CC) $(CFLAGS) $(DFLAG) -c free.c
-+	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c free.c
- 
- options.o : options.c options.h
--	$(CC) $(CFLAGS) $(DFLAG) -c options.c
-+	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c options.c
- 
diff --git a/sci-biology/phyml/metadata.xml b/sci-biology/phyml/metadata.xml
deleted file mode 100644
index e8a2d7c4a3b0..000000000000
--- a/sci-biology/phyml/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription lang="en">
-		Phyml is a simple, fast, and accurate algorithm to estimate large
-		phylogenies by maximum likelihood. Given input sequence files, it
-		estimates phylogenies using maximum likelihood, and is capable of
-		processing large amounts of phylogenetic data.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/phyml/phyml-2.4.5-r4.ebuild b/sci-biology/phyml/phyml-2.4.5-r4.ebuild
deleted file mode 100644
index c0e9c38caf92..000000000000
--- a/sci-biology/phyml/phyml-2.4.5-r4.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-MY_P="${PN}_v${PV}"
-
-DESCRIPTION="Estimation of large phylogenies by maximum likelihood"
-HOMEPAGE="http://atgc.lirmm.fr/phyml/"
-SRC_URI="http://www.lirmm.fr/~guindon/${MY_P}.tar.gz"
-S="${WORKDIR}/${MY_P}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.4.5-fix-build-system.patch )
-
-src_configure() {
-	tc-export CC
-}
-
-src_install() {
-	dobin phyml
-}
diff --git a/sci-biology/piler/Manifest b/sci-biology/piler/Manifest
deleted file mode 100644
index 8f97ae8d5ad2..000000000000
--- a/sci-biology/piler/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST piler-1.0.tar.gz 35220 BLAKE2B a3a5d9ab6885e0900c523db9d1248888cd3de50b18c2c4ae110a13d792a0faa60eefffbac4526df96b482b4fe6ed8bd19299eb96380332a57f2d60330ca40037 SHA512 35be1b445f1eaf26f96d0356a04d985fb528754677403df2061c0872107d31819c5fb355e7f616e953a997e67ce781846acaf3cc2a016097aca785b6a26de3d4
diff --git a/sci-biology/piler/files/piler-1.0-fix-build-system.patch b/sci-biology/piler/files/piler-1.0-fix-build-system.patch
deleted file mode 100644
index 78a72f1b4850..000000000000
--- a/sci-biology/piler/files/piler-1.0-fix-build-system.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-Make build system honour user variables
-
---- a/Makefile
-+++ b/Makefile
-@@ -1,6 +1,4 @@
--CFLAGS = -O3 -march=pentiumpro -mcpu=pentiumpro -funroll-loops -Winline -DNDEBUG=1
--LDLIBS = -lm -static
--# LDLIBS = -lm
-+LDLIBS = -lm
- 
- OBJ = .o
- EXE =
-@@ -8,18 +6,13 @@
- RM = rm -f
- CP = cp
- 
--GPP = g++
--LD = $(GPP) $(CFLAGS)
--CPP = $(GPP) -c $(CFLAGS) 
--CC = gcc -c $(CFLAGS) 
--
- all: piler
- 
- CPPSRC = $(sort $(wildcard *.cpp))
- CPPOBJ	= $(subst .cpp,.o,$(CPPSRC))
- 
--$(CPPOBJ): %.o: %.cpp
--	$(CPP) $< -o $@
-+%.o: %.cpp
-+	$(CXX) $(CXXFLAGS) -DNDEBUG $(CPPFLAGS) -c $< -o $@
- 
- piler: $(CPPOBJ)
--	$(LD) -o piler $(CPPOBJ) $(LDLIBS)
-+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o piler $(CPPOBJ) $(LDLIBS)
diff --git a/sci-biology/piler/files/piler-1.0-glibc-2.10.patch b/sci-biology/piler/files/piler-1.0-glibc-2.10.patch
deleted file mode 100644
index 4c7f124c5e3d..000000000000
--- a/sci-biology/piler/files/piler-1.0-glibc-2.10.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -ur piler.orig/gff.cpp piler/gff.cpp
---- piler.orig/gff.cpp	2004-12-18 01:25:29.000000000 +0200
-+++ piler/gff.cpp	2009-08-09 17:22:33.000000000 +0300
-@@ -70,7 +70,7 @@
- 		const char *Attrs = Fields[8];
- 
- 	// Truncate attrs if comment found
--		char *Pound = strchr(Attrs, '#');
-+		char *Pound = const_cast <char*> (strchr(Attrs, '#'));
- 		if (0 != Pound)
- 			*Pound = 0;
- 
diff --git a/sci-biology/piler/metadata.xml b/sci-biology/piler/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/piler/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/piler/piler-1.0-r2.ebuild b/sci-biology/piler/piler-1.0-r2.ebuild
deleted file mode 100644
index 6f419d040b89..000000000000
--- a/sci-biology/piler/piler-1.0-r2.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Analysis of repetitive DNA found in genome sequences"
-HOMEPAGE="http://www.drive5.com/piler/"
-SRC_URI="http://www.drive5.com/piler/piler_source.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-RDEPEND="
-	|| (
-		sci-biology/muscle
-		sci-libs/libmuscle
-	)
-	sci-biology/pals"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.0-fix-build-system.patch
-	"${FILESDIR}"/${PN}-1.0-glibc-2.10.patch
-)
-
-src_configure() {
-	tc-export CXX
-}
-
-src_install() {
-	dobin piler
-}
diff --git a/sci-biology/pilercr/Manifest b/sci-biology/pilercr/Manifest
deleted file mode 100644
index 1b378eef8ef2..000000000000
--- a/sci-biology/pilercr/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pilercr-1.0.tar.gz 1709144 BLAKE2B 59aef12a10d168c8cbf4d3b3eec95dd4cd47b0ba073f19bd9f3954e6fab088af1c9f0328b0120c219034be07e4d13af4df17ca3eb7f40c19ff2a13d72000251a SHA512 c262ceef1d1af9e71f454809e940c2ad6d835a8404daa51ccef698b8348a504c697f5b5c268ec24df611f5adda2932e4982bcdabe4fbdf99d8c204f0f77f1be5
diff --git a/sci-biology/pilercr/files/pilercr-1.0-drop-registers.patch b/sci-biology/pilercr/files/pilercr-1.0-drop-registers.patch
deleted file mode 100644
index ab1535b4a767..000000000000
--- a/sci-biology/pilercr/files/pilercr-1.0-drop-registers.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- a/comp.cpp
-+++ b/comp.cpp
-@@ -28,7 +28,7 @@ void Complement(char *seq, int len)
-   /* Complement and reverse sequence */
- 
- 
--  { register unsigned char *s, *t;
-+  { unsigned char *s, *t;
-     int c;
- 
- 
-old mode 100644
-new mode 100755
-Binary files a/pilercr and b/pilercr differ
diff --git a/sci-biology/pilercr/files/pilercr-1.0-fix-build-system.patch b/sci-biology/pilercr/files/pilercr-1.0-fix-build-system.patch
deleted file mode 100644
index 3754f80a9346..000000000000
--- a/sci-biology/pilercr/files/pilercr-1.0-fix-build-system.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-Make build system honour user variables
-
---- a/Makefile
-+++ b/Makefile
-@@ -1,7 +1,4 @@
--CFLAGS = -O3 -funroll-loops -Winline -DNDEBUG=1
--#CFLAGS = -O3 -funroll-loops -Winline
--LDLIBS = -lm -static
--# LDLIBS = -lm
-+LDLIBS = -lm
- 
- OBJ = .o
- EXE =
-@@ -9,17 +6,13 @@
- RM = rm -f
- CP = cp
- 
--GPP = g++
--LD = $(GPP) $(CFLAGS)
--CPP = $(GPP) -c $(CFLAGS) 
--
- all: pilercr
- 
- CPPSRC = $(sort $(wildcard *.cpp))
- CPPOBJ	= $(subst .cpp,.o,$(CPPSRC))
- 
--$(CPPOBJ): %.o: %.cpp
--	$(CPP) $< -o $@
-+%.o: %.cpp
-+	$(CXX) $(CXXFLAGS) -DNDEBUG $(CPPFLAGS) -c $< -o $@
- 
- pilercr: $(CPPOBJ)
--	$(LD) -o pilercr $(CPPOBJ) $(LDLIBS)
-+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o pilercr $(CPPOBJ) $(LDLIBS)
diff --git a/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch b/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch
deleted file mode 100644
index 7b49df872e27..000000000000
--- a/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-diff -dur work/multaln.h work-orig/multaln.h
---- work/multaln.h	2007-04-17 19:02:18.000000000 +0000
-+++ work-orig/multaln.h	2009-02-18 21:25:26.166333299 +0000
-@@ -6,6 +6,7 @@
- #define _CRT_SECURE_NO_DEPRECATE	1
- #endif
- 
-+#include <cstring>
- #include <vector>
- #include <limits.h>
- #include <ctype.h>
-diff -dur work/seqvect.h work-orig/seqvect.h
---- work/seqvect.h	2006-04-06 23:36:18.000000000 +0000
-+++ work-orig/seqvect.h	2009-02-18 21:25:26.171090246 +0000
-@@ -1,6 +1,7 @@
- #ifndef SeqVect_h
- #define SeqVect_h
- 
-+#include <stdio.h>
- #include <vector>
- #include "seq.h"
- 
-diff -dur work/tree.h work-orig/tree.h
---- work/tree.h	2006-04-05 23:52:42.000000000 +0000
-+++ work-orig/tree.h	2009-02-18 21:25:26.171090246 +0000
-@@ -1,6 +1,7 @@
- #ifndef tree_h
- #define tree_h
- 
-+#include <stdlib.h>
- #include <limits.h>
- 
- class Clust;
diff --git a/sci-biology/pilercr/metadata.xml b/sci-biology/pilercr/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/pilercr/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/pilercr/pilercr-1.0-r2.ebuild b/sci-biology/pilercr/pilercr-1.0-r2.ebuild
deleted file mode 100644
index 46c5dbc2b944..000000000000
--- a/sci-biology/pilercr/pilercr-1.0-r2.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)"
-HOMEPAGE="http://www.drive5.com/pilercr/"
-SRC_URI="http://www.drive5.com/pilercr/pilercr1.06.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.0-fix-build-system.patch
-	"${FILESDIR}"/${PN}-1.0-gcc43.patch
-)
-
-src_configure() {
-	tc-export CXX
-}
-
-src_install() {
-	dobin pilercr
-}
diff --git a/sci-biology/pilercr/pilercr-1.0-r3.ebuild b/sci-biology/pilercr/pilercr-1.0-r3.ebuild
deleted file mode 100644
index 3a2ee27a3379..000000000000
--- a/sci-biology/pilercr/pilercr-1.0-r3.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)"
-HOMEPAGE="https://www.drive5.com/pilercr/"
-SRC_URI="https://www.drive5.com/pilercr/pilercr1.06.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.0-fix-build-system.patch
-	"${FILESDIR}"/${PN}-1.0-gcc43.patch
-	"${FILESDIR}"/${PN}-1.0-drop-registers.patch
-)
-
-src_configure() {
-	tc-export CXX
-}
-
-src_install() {
-	dobin pilercr
-}
diff --git a/sci-biology/plink/Manifest b/sci-biology/plink/Manifest
deleted file mode 100644
index 75806d2b2477..000000000000
--- a/sci-biology/plink/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST plink-1.90_pre140514.zip 822157 BLAKE2B 3c29670862de99c9715bc37d8cffc2b02c0cb25ad746975f253ca1e8094b24668cc6739943c68bfa407471f30835a74c6ad027eaa56a92f13445e0a02854cad3 SHA512 679f1e136b11f35f1d49636bc44ffd17e72e4e38edc5daa270cd963ca39f7b8a80f31905a94de517059e5b3ea7a6bf518ae34a5c2af8a05c530bd6df771606c4
diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml
deleted file mode 100644
index bdabd1d83788..000000000000
--- a/sci-biology/plink/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/plink/plink-1.90_pre140514.ebuild b/sci-biology/plink/plink-1.90_pre140514.ebuild
deleted file mode 100644
index 63bda6c59a48..000000000000
--- a/sci-biology/plink/plink-1.90_pre140514.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Whole genome association analysis toolset"
-HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/"
-SRC_URI="http://pngu.mgh.harvard.edu/~purcell/static/bin/plink140514/plink_src.zip -> ${P}.zip"
-S="${WORKDIR}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	virtual/zlib:=
-	virtual/cblas
-	virtual/lapack
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	app-arch/unzip
-	virtual/pkgconfig
-"
-
-# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian.
-# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
-
-src_prepare() {
-	default
-
-	sed \
-		-e 's:zlib-1.2.8/zlib.h:zlib.h:g' \
-		-i *.{c,h} || die
-
-	sed \
-		-e 's:g++:$(CXX):g' \
-		-e 's:gcc:$(CC):g' \
-		-e 's:gfortran:$(FC):g' \
-		-i Makefile || die
-	tc-export PKG_CONFIG
-}
-
-src_compile() {
-	emake \
-		CXX="$(tc-getCXX)" \
-		CFLAGS="${CFLAGS}" \
-		LDFLAGS="${LDFLAGS}" \
-		ZLIB="$($(tc-getPKG_CONFIG) --libs zlib)" \
-		BLASFLAGS="$($(tc-getPKG_CONFIG) --libs lapack cblas)"
-}
-
-src_install() {
-	newbin plink p-link
-}
diff --git a/sci-biology/poa/Manifest b/sci-biology/poa/Manifest
deleted file mode 100644
index 91561875b9a3..000000000000
--- a/sci-biology/poa/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST poaV2.tar.gz 62612 BLAKE2B 92f7b2926dd7fc93745411fc04c8dd3380c32e3e87cf89afa81aefe787a1aa0e7a416d08809cce531a21d5118398a9474a751a742ee1fca47e83bd907444e9c0 SHA512 2a54b025f0a74ff4c01828f3e4b9e8e135bffe26d08f651f981bc95a64196173b5d887ef988a25c1f5fbf89333b4771622d5dc93946d66e7ec9abacb6167595c
diff --git a/sci-biology/poa/files/poa-2-clang16.patch b/sci-biology/poa/files/poa-2-clang16.patch
deleted file mode 100644
index 5399dd631f48..000000000000
--- a/sci-biology/poa/files/poa-2-clang16.patch
+++ /dev/null
@@ -1,74 +0,0 @@
---- a/black_flag.c
-+++ b/black_flag.c
-@@ -82,7 +82,7 @@
- 
- 
- 
--int handle_crash_init(void (*crash_fun)())
-+int handle_crash_init(void (*crash_fun)(int))
- {
- #define HANDLE_CRASH_MAX 5
-   int i,signal_type[HANDLE_CRASH_MAX]
---- a/black_flag.h
-+++ b/black_flag.h
-@@ -230,7 +230,7 @@
- ((INDEX)<(MINIMUM_BOUND) || (INDEX)>=(MAXIMUM_BOUND))
- 
- void handle_crash(int sigcode);
--int handle_crash_init(void (*crash_fun)());
-+int handle_crash_init(void (*crash_fun)(int));
- int black_flag(int bug_level,
- 	       char sourcefile[],
- 	       int sourceline,
---- a/default.h
-+++ b/default.h
-@@ -19,7 +19,6 @@
- 
- typedef void *voidptr;  /* ~~e: should be moved out to generic typing header
- 			   --- */
--typedef int (*funptr)();
- 
- #define LOOPB(i,size) for ((i)=(size);(i)-- >0;)
- #define LOOP(i,size) for ((i)=(size);(i)-- >0;)
-@@ -152,7 +151,7 @@
-   else if (NULL == ((memptr)=(ATYPE *)calloc((size_t)(N),sizeof(ATYPE))))  { \
-     fprintf(stderr,"%s, line %d: *** out of memory \n",__FILE__,__LINE__);                \
-     fprintf(stderr,"Unable to meet request: %s[%d]\n",STRINGIFY(memptr),(N));    \
--    fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE));   \
-+    fprintf(stderr,"requested %d x %zu bytes \n",(N),sizeof(ATYPE));   \
-     MALLOC_FAILURE_ACTION;                                            \
-   }
- 
-@@ -193,7 +192,7 @@
-     else { \
-       fprintf(stderr,"%s, line %d: *** out of memory \n",__FILE__,__LINE__); \
-       fprintf(stderr,"Unable to meet request: %s\n",STRINGIFY(memptr));  \
--      fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE));   \
-+      fprintf(stderr,"requested %d x %zu bytes \n",(NUM),sizeof(ATYPE));   \
-       REALLOC_FAILURE_ACTION;                                             \
-     } \
-   }
---- a/fasta_format.c
-+++ b/fasta_format.c
-@@ -2,6 +2,7 @@
- #include "default.h"
- #include "seq_util.h"
- 
-+char *stringptr_cat_pos(stringptr *s1,const char s2[],int *pos);
- 
- 
- /** reads FASTA formatted sequence file, and saves the sequences to
---- a/msa_format.c
-+++ b/msa_format.c
-@@ -16,6 +16,11 @@
- 
- #include "msa_format.h"
- 
-+void fuse_ring_identities(int len_x,LPOLetter_T seq_x[],
-+        int len_y,LPOLetter_T seq_y[],
-+        LPOLetterRef_T al_x[],
-+        LPOLetterRef_T al_y[]);
-+void build_seq_to_po_index(LPOSequence_T *seq);
- 
- /** is `ch' an allowed residue? (a-z OR A-Z OR ? OR [ OR ]) */
- static int is_residue_char (char ch);
diff --git a/sci-biology/poa/files/poa-2-fno-common.patch b/sci-biology/poa/files/poa-2-fno-common.patch
deleted file mode 100644
index ddd738a5524c..000000000000
--- a/sci-biology/poa/files/poa-2-fno-common.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- a/black_flag.h
-+++ b/black_flag.h
-@@ -236,8 +236,8 @@
- 	       int sourceline,
- 	       char sourcefile_revision[]);
- 
--char *Program_name;
--char *Program_version;
-+extern char *Program_name;
-+extern char *Program_version;
- 
- void black_flag_init(char progname[],char progversion[]);
- void black_flag_init_args(int narg,char *arg[],char progversion[]);
diff --git a/sci-biology/poa/files/poa-2-respect-flags.patch b/sci-biology/poa/files/poa-2-respect-flags.patch
deleted file mode 100644
index fb01f0b5f934..000000000000
--- a/sci-biology/poa/files/poa-2-respect-flags.patch
+++ /dev/null
@@ -1,38 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -1,6 +1,3 @@
--
--AR=ar rc
--
- TARGETS=poa liblpo.a poa_doc libbflag.a
- 
- # align_score.c CAN BE USED TO ADD CUSTOMIZED SCORING FUNCTIONS
-@@ -26,9 +23,8 @@
- 	stringptr.o
- 
- 
--CC = gcc
- #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
--CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
-+CPPFLAGS+= -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
- # -I$(HOME)/lib/include
- # -DREPORT_MAX_ALLOC
- 
-@@ -37,14 +33,14 @@
- 
- liblpo.a: $(LIBOBJECTS)
- 	rm -f $@
--	$(AR) $@ $(LIBOBJECTS)
--	ranlib $@
-+	$(AR) rc $@ $(LIBOBJECTS)
-+	$(RANLIB) $@
- 
- 
- 
- # NB: LIBRARY MUST FOLLOW OBJECTS OR LINK FAILS WITH UNRESOLVED REFERENCES!!
- poa: $(OBJECTS) liblpo.a
--	$(CC) -o $@ $(OBJECTS) -lm liblpo.a
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a
- 
- what:
- 	@echo poa: partial-order based sequence alignment program
diff --git a/sci-biology/poa/metadata.xml b/sci-biology/poa/metadata.xml
deleted file mode 100644
index 1029a137f48b..000000000000
--- a/sci-biology/poa/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">poamsa</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/poa/poa-2-r1.ebuild b/sci-biology/poa/poa-2-r1.ebuild
deleted file mode 100644
index 8044b8f822bf..000000000000
--- a/sci-biology/poa/poa-2-r1.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-MY_P="${PN}V${PV}"
-
-DESCRIPTION="Fast multiple sequence alignments using partial-order graphs"
-HOMEPAGE="http://bioinfo.mbi.ucla.edu/poa/"
-SRC_URI="https://downloads.sourceforge.net/poamsa/${MY_P}.tar.gz"
-
-# According to SF project page
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-respect-flags.patch
-	"${FILESDIR}"/${P}-fno-common.patch
-	"${FILESDIR}"/${P}-clang16.patch
-)
-
-src_configure() {
-	tc-export AR CC RANLIB
-}
-
-src_compile() {
-	emake poa
-}
-
-src_install() {
-	dobin poa make_pscores.pl
-	dodoc README multidom.*
-	insinto /usr/share/poa
-	doins *.mat
-}
-
-pkg_postinst() {
-	elog "poa requires a score matrix as the first argument."
-	elog "This package installs two examples to ${EROOT}/usr/share/poa/."
-}
diff --git a/sci-biology/prank/Manifest b/sci-biology/prank/Manifest
deleted file mode 100644
index c56430ac3338..000000000000
--- a/sci-biology/prank/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST prank.source.140603.tgz 150346 BLAKE2B 4bd5ba1d2f5106a20f51be359ddfc2421ef6c5ae235bf14dddf6fe82745d3375074ee213e957ef290edeae124c070cf14d6674765ebebdafc0a726a037ed269f SHA512 25e5f99a3822ff31436406f9ba1c781ba375959e1ed452c1e7416898d5246183510ec6d2bc715ff1495a779e42d7bd1d49ad1c332e1bd5982dad8c744ad999c7
diff --git a/sci-biology/prank/files/prank-140603-fix-c++14.patch b/sci-biology/prank/files/prank-140603-fix-c++14.patch
deleted file mode 100644
index 211e377d798a..000000000000
--- a/sci-biology/prank/files/prank-140603-fix-c++14.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Fix building with C++14, which errors out due to changing operator void* -> operator bool.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=594060
-
---- a/hmmodel.cpp
-+++ b/hmmodel.cpp
-@@ -1499,7 +1499,7 @@
-     }
-     else
-     {
--        cout<<"HMModel::alignmentModel: impossible 'as'"<<cout;
-+        cout<<"HMModel::alignmentModel: impossible 'as'";
-         exit(-1);
-     }
- 
diff --git a/sci-biology/prank/files/prank-140603-makefile.patch b/sci-biology/prank/files/prank-140603-makefile.patch
deleted file mode 100644
index eeb74df89b4c..000000000000
--- a/sci-biology/prank/files/prank-140603-makefile.patch
+++ /dev/null
@@ -1,28 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -4,14 +4,8 @@
- 
- ####### Compiler, tools and options
- 
--CC            = gcc
--CXX           = g++
--DEFINES       = 
--CFLAGS        = -m64 -pipe -O3 $(DEFINES)
--CXXFLAGS      = -m64 -pipe -O3 $(DEFINES)
--INCPATH       = -I. -I/usr/include
--LINK          = g++
--LFLAGS        = -m64
-+INCPATH       = $(CPPFLAGS) -I.
-+LINK          = $(CXX)
- LIBS          = $(SUBLIBS)    
- AR            = ar cqs
- RANLIB        = 
-@@ -136,7 +130,7 @@
- all: Makefile $(TARGET) $(MANPAGES)
- 
- $(TARGET):  $(OBJECTS)  
--	$(LINK) $(LFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS)
-+	$(LINK) $(LDFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS)
- 
- 
- clean:compiler_clean 
diff --git a/sci-biology/prank/metadata.xml b/sci-biology/prank/metadata.xml
deleted file mode 100644
index 2a0345f8b0ad..000000000000
--- a/sci-biology/prank/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="google-code">prank-msa</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/prank/prank-140603-r1.ebuild b/sci-biology/prank/prank-140603-r1.ebuild
deleted file mode 100644
index 9128cf9cf99b..000000000000
--- a/sci-biology/prank/prank-140603-r1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Probabilistic Alignment Kit"
-HOMEPAGE="http://wasabiapp.org/software/prank/"
-SRC_URI="http://wasabiapp.org/download/${PN}/${PN}.source.${PV}.tgz"
-S="${WORKDIR}/${PN}-msa/src"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-makefile.patch
-	"${FILESDIR}"/${P}-fix-c++14.patch
-)
-
-src_configure() {
-	tc-export CXX
-}
-
-src_install() {
-	dobin prank
-}
diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest
deleted file mode 100644
index e508ab6b47a8..000000000000
--- a/sci-biology/primer3/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST primer3-2.3.7.tar.gz 1658090 BLAKE2B 0bc9a0faa19c4ac3b48680d65b0d91a13d8bdd651ad3a0d344b4f50ce8dc510fe7a22665192751fb2c8ff6282b560daf4540a02cc70482dba0fcc344f7727e37 SHA512 f227f80d395cb682a9d65e0ac3afdcacb8385d66e721b9163fda939a9c788a7c6907273f6223782702b48d7df66ea2331114f6303fcd29e3b3c50a2717da2fa7
diff --git a/sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch b/sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch
deleted file mode 100644
index 8f9bf4042758..000000000000
--- a/sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch
+++ /dev/null
@@ -1,173 +0,0 @@
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -52,15 +52,13 @@
- WINMAKE=mingw32-make
- 
- LDLIBS     = -lm
--AR         = ar
--CC         = gcc
--CPP        = g++
--O_OPTS     = -O2
--CC_OPTS    = -g -Wall -D__USE_FIXED_PROTOTYPES__
--P_DEFINES  =
--
--CFLAGS  = $(CC_OPTS) $(O_OPTS)
--LDFLAGS = -g
-+O_OPTS     ?= 
-+CC_OPTS    ?= -Wall -D__USE_FIXED_PROTOTYPES__
-+P_DEFINES  ?=
-+
-+CFLAGS    += $(CC_OPTS) $(O_OPTS)
-+CXXFLAGS  += $(CC_OPTS) $(O_OPTS)
-+LDFLAGS   +=
- # Note, for profiling, use
- # make O_OPTS='-pg -O0' LDFLAGS='-g -pg'
- 
-@@ -92,7 +90,6 @@
- LIBPRIMER3_DYN  = libprimer3.so.1.0.0
- LIBRARIES       = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM) 
- DYNLIBS         = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN)
--RANLIB          = ranlib
- 
- PRIMER_OBJECTS1=primer3_boulder_main.o\
-                 format_output.o\
-@@ -119,93 +116,89 @@
- ifeq ($(TESTOPTS),--windows)
- 	cd ..\test & $(WINMAKE) clean TESTOPTS=$(TESTOPTS)
- else
--	cd ../test/; make clean
-+	cd ../test/ && $(MAKE) clean
- endif
- 
- $(LIBOLIGOTM): oligotm.o
--	$(AR) rv $@ oligotm.o
--	$(RANLIB) $@
-+	$(AR) rcs $@ oligotm.o
- 
- $(LIBOLIGOTM_LIB): oligotm.o
--	$(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
-+	$(CC) $(LDFLAGS) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
- 
- $(LIBDPAL): dpal_primer.o
--	$(AR) rv $@ dpal_primer.o
--	$(RANLIB) $@
-+	$(AR) rcs $@ dpal_primer.o
- 
- $(LIBDPAL_DYN): dpal_primer.o
--	$(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
-+	$(CC) $(LDFLAGS) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
- 
- $(LIBTHAL): thal_primer.o
--	$(AR) rv $@ thal_primer.o
--	$(RANLIB) $@
-+	$(AR) rcs $@ thal_primer.o
- 
- $(LIBTHAL_DYN): thal_primer.o
--	$(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
-+	$(CC) $(LDFLAGS) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
- 
- $(LIBPRIMER3): libprimer3.o p3_seq_lib.o
--	$(AR) rv $@ libprimer3.o p3_seq_lib.o
--	$(RANLIB) $@
-+	$(AR) rcs $@ libprimer3.o p3_seq_lib.o
- 
- $(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o
--	$(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
-+	$(CC) $(LDFLAGS) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
- 
- $(PRIMER_EXE): $(PRIMER_OBJECTS)
--	$(CPP) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
-+	$(CXX) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
- 
- libprimer3.o: libprimer3.c libprimer3.h p3_seq_lib.h dpal.h thal.h oligotm.h
--	$(CPP) -c $(CFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c
-+	$(CXX) -c $(CXXFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c
- 
- $(NTDPAL_EXE): ntdpal_main.o dpal.o
--	$(CPP) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
-+	$(CXX) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
- 
- $(NTTHAL_EXE): thal_main.o thal.o
--	$(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
-+	$(CXX) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
- 
- $(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM)
--	$(CPP) $(CFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
- 
- $(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o
--	$(CPP) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
- 
- read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h p3_seq_lib.h 
--	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c
-+	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ read_boulder.c
- 
- print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h 
--	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ print_boulder.c
-+	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ print_boulder.c
- 
- dpal.o: dpal.c dpal.h
--	$(CPP) -c $(CFLAGS) -o $@ dpal.c
-+	$(CXX) -c $(CXXFLAGS) -o $@ dpal.c
- 
- # We use '-ffloat-store' on windows to prevent undesirable
- # precision which may lead to differences in floating point results.
- thal.o: thal.c thal.h
--	$(CPP) -c $(CFLAGS) -ffloat-store -o $@ thal.c
-+	$(CXX) -c $(CXXFLAGS) -ffloat-store -o $@ thal.c
- 
- p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h
--	$(CPP) -c $(CFLAGS) -o $@ p3_seq_lib.c
-+	$(CXX) -c $(CXXFLAGS) -o $@ p3_seq_lib.c
- 
- dpal_primer.o: dpal.c dpal.h
--	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c
-+	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ dpal.c
- 
- thal_primer.o: thal.c thal.h
--	$(CPP) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
-+	$(CXX) -c $(CXXFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
- 
- format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h 
--	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c
-+	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ format_output.c
- 
- ntdpal_main.o: ntdpal_main.c dpal.h
--	$(CPP) -c $(CC_OPTS) -o $@ ntdpal_main.c
-+	$(CXX) -c $(CXXFLAGS) -o $@ ntdpal_main.c
- 
- thal_main.o: thal_main.c thal.h
--	$(CPP) -c $(CFLAGS) -o $@ thal_main.c
-+	$(CXX) -c $(CXXFLAGS) -o $@ thal_main.c
- # We use CC_OPTS above rather than CFLAGS because
- # gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2
- 
- oligotm.o: oligotm.c oligotm.h
- 
- primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h oligotm.h format_output.h print_boulder.h read_boulder.h
--	$(CPP) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c
-+	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) primer3_boulder_main.c
- 
- primer_test: test
- 
-@@ -213,7 +206,7 @@
- ifeq ($(TESTOPTS),--windows)
- 	cd ..\test & $(WINMAKE) TESTOPTS=$(TESTOPTS)
- else
--	cd ../test; make test
-+	cd ../test && $(MAKE) test
- endif
- 
- # ======================================================================
---- a/test/Makefile
-+++ b/test/Makefile
-@@ -86,7 +86,7 @@
- ifeq ($(TESTOPTS),--windows)
- 	cd ..\src & $(WINMAKE)
- else
--	cd ../src; make
-+	cd ../src && $(MAKE)
- endif
- 
- clean:
diff --git a/sci-biology/primer3/files/primer3-2.3.7-gcc7.patch b/sci-biology/primer3/files/primer3-2.3.7-gcc7.patch
deleted file mode 100644
index a04ee1ac3b12..000000000000
--- a/sci-biology/primer3/files/primer3-2.3.7-gcc7.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- a/src/thal.c
-+++ b/src/thal.c
-@@ -426,12 +426,12 @@
- 	       "Illegal type");
-    o->align_end_1 = -1;
-    o->align_end_2 = -1;
--   if ('\0' == oligo_f) {
-+   if ('\0' == oligo_f[0]) {
-       strcpy(o->msg, "Empty first sequence");
-       o->temp = 0.0;
-       return;
-    }
--   if ('\0' == oligo_r) {
-+   if ('\0' == oligo_r[0]) {
-       strcpy(o->msg, "Empty second sequence");
-       o->temp = 0.0;
-       return;
diff --git a/sci-biology/primer3/metadata.xml b/sci-biology/primer3/metadata.xml
deleted file mode 100644
index af82be55b453..000000000000
--- a/sci-biology/primer3/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		Primer3 picks primers for PCR reactions, considering: oligonucleotide
-		melting temperature, size, GC content, and primer-dimer possibilities;
-		PCR product size; positional constraints within the source sequence;
-		and miscellaneous other constraints. All of these criteria are
-		user-specifiable as constraints, and some are specifiable as terms in
-		an objective function that characterizes an optimal primer pair.
-	</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">primer3</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/primer3/primer3-2.3.7-r1.ebuild b/sci-biology/primer3/primer3-2.3.7-r1.ebuild
deleted file mode 100644
index 833db50b0ca3..000000000000
--- a/sci-biology/primer3/primer3-2.3.7-r1.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Primer Design for PCR reactions"
-HOMEPAGE="http://primer3.sourceforge.net/"
-SRC_URI="https://downloads.sourceforge.net/project/${PN}/${PN}/${PV}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86"
-
-BDEPEND="dev-lang/perl"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-buildsystem.patch
-	"${FILESDIR}"/${P}-gcc7.patch
-)
-
-src_prepare() {
-	default
-	if [[ ${CHOST} == *-darwin* ]]; then
-		sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die
-	fi
-}
-
-src_configure() {
-	tc-export AR CC CXX
-}
-
-src_compile() {
-	emake -C src
-}
-
-src_test() {
-	emake -C test | tee "${T}"/test.log
-	grep -q "\[FAILED\]" && die "test failed. See ${T}/test.log"
-}
-
-src_install() {
-	dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core}
-
-	insinto /opt/primer3_config
-	doins -r src/primer3_config/. primer3*settings.txt
-
-	dodoc src/release_notes.txt example
-	docinto html
-	dodoc primer3_manual.htm
-}
diff --git a/sci-biology/prints/Manifest b/sci-biology/prints/Manifest
deleted file mode 100644
index eaf85ea2bb32..000000000000
--- a/sci-biology/prints/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST prints-39.0.tar.bz2 26277011 BLAKE2B a815e93f41694c76d62c6809f05457b286333ad103852eb493b0e723c54a088825f262a64ff8db0e47ff8a97c37fbf670c6c7967aabb303fd7d454982e4dff5e SHA512 4ea48a2a0892739ac4e32a6309922b7b4ad01f9d2f847f7c42c7e6a00e8f56bab0771d272adcaed1f85516ea93245fb8c7864762c4699023a8d85d61c012bdc7
diff --git a/sci-biology/prints/metadata.xml b/sci-biology/prints/metadata.xml
deleted file mode 100644
index 720b31a11b56..000000000000
--- a/sci-biology/prints/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		A protein motif fingerprint database maintained at the University of
-		Manchester. A fingerprint is a group of conserved motifs used to
-		characterise a protein family; its diagnostic power is refined by
-		iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs
-		do not overlap, but are separated along a sequence, though they may be
-		contiguous in 3D-space. Fingerprints can encode protein folds and
-		functionalities more flexibly and powerfully than can single motifs,
-		full diagnostic potency deriving from the mutual context provided by
-		motif neighbours.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/prints/prints-39.0-r2.ebuild b/sci-biology/prints/prints-39.0-r2.ebuild
deleted file mode 100644
index ee8a307e0cdb..000000000000
--- a/sci-biology/prints/prints-39.0-r2.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-MY_PV="${PV/./_}"
-
-DESCRIPTION="A protein motif fingerprint database"
-HOMEPAGE="http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/"
-SRC_URI="mirror://gentoo/${P}.tar.bz2"
-
-LICENSE="public-domain"
-SLOT="0"
-# Minimal build keeps only the indexed files (if applicable) and the
-# documentation. The non-indexed database is not installed.
-KEYWORDS="~amd64 ~x86"
-IUSE="emboss minimal"
-
-BDEPEND="emboss? ( sci-biology/emboss )"
-RDEPEND="${BDEPEND}"
-
-src_compile() {
-	if use emboss; then
-		mkdir PRINTS || die
-		einfo
-		einfo "Indexing PRINTS for usage with EMBOSS"
-		EMBOSS_DATA="." printsextract -auto -infile prints${MY_PV}.dat || die "Indexing PRINTS failed"
-		einfo
-	fi
-}
-
-src_install() {
-	dodoc README
-
-	if ! use minimal; then
-		insinto /usr/share/${PN}
-		doins newpr.lis ${PN}${MY_PV}.{all.fasta,dat,kdat,lis,nam,vsn}
-	fi
-
-	if use emboss; then
-		insinto /usr/share/EMBOSS/data/${PN^^}
-		doins -r ${PN^^}/.
-	fi
-}
diff --git a/sci-biology/probcons/Manifest b/sci-biology/probcons/Manifest
deleted file mode 100644
index 713b675d6937..000000000000
--- a/sci-biology/probcons/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST probcons_v1_12.tar.gz 43200 BLAKE2B db59a4472e5ea4ce1801ca74807aa1b1bdb2861a9e52f9b3a4297b37d048ecd6e34298cfd181523093f8fb1cd9a81285e58098bcdec6ffa32caa9cc1117b8b8f SHA512 ce061ea5cca4204d6e66beb893c1ba508f094b7ea3ee08196dc75a5443ebd0afca14dc8d7cd6c8da4ce1578b8750ea1981e5815408c0b122e8f97ec27b3bf008
diff --git a/sci-biology/probcons/files/gcc-4.3.patch b/sci-biology/probcons/files/gcc-4.3.patch
deleted file mode 100644
index 37c45c03a98f..000000000000
--- a/sci-biology/probcons/files/gcc-4.3.patch
+++ /dev/null
@@ -1,44 +0,0 @@
-diff -u probcons.orig/CompareToRef.cc probcons/CompareToRef.cc
---- probcons.orig/CompareToRef.cc	2008-04-08 16:38:46.000000000 -0700
-+++ probcons/CompareToRef.cc	2008-04-08 16:39:41.000000000 -0700
-@@ -16,6 +16,7 @@
- #include <limits>
- #include <cstdio>
- #include <cstdlib>
-+#include <cstring>
- #include <cerrno>
- #include <iomanip>
- 
-diff -u probcons.orig/FixRef.cc probcons/FixRef.cc
---- probcons.orig/FixRef.cc	2008-04-08 16:38:46.000000000 -0700
-+++ probcons/FixRef.cc	2008-04-08 16:39:33.000000000 -0700
-@@ -17,6 +17,7 @@
- #include <algorithm>
- #include <cstdio>
- #include <cstdlib>
-+#include <cstring>
- #include <cerrno>
- #include <iomanip>
- 
-diff -u probcons.orig/Main.cc probcons/Main.cc
---- probcons.orig/Main.cc	2008-04-08 16:38:46.000000000 -0700
-+++ probcons/Main.cc	2008-04-08 16:39:14.000000000 -0700
-@@ -21,6 +21,7 @@
- #include <climits>
- #include <cstdio>
- #include <cstdlib>
-+#include <cstring>
- #include <cerrno>
- #include <iomanip>
- 
-diff -u probcons.orig/ProjectPairwise.cc probcons/ProjectPairwise.cc
---- probcons.orig/ProjectPairwise.cc	2008-04-08 16:38:46.000000000 -0700
-+++ probcons/ProjectPairwise.cc	2008-04-08 16:39:25.000000000 -0700
-@@ -16,6 +16,7 @@
- #include <limits>
- #include <cstdio>
- #include <cstdlib>
-+#include <cstring>
- #include <cerrno>
- #include <iomanip>
- 
diff --git a/sci-biology/probcons/files/probcons-1.12-cxxflags.patch b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch
deleted file mode 100644
index e07ebe1a613f..000000000000
--- a/sci-biology/probcons/files/probcons-1.12-cxxflags.patch
+++ /dev/null
@@ -1,47 +0,0 @@
-diff --git a/Makefile b/Makefile
-index 75fc47a..4a19140 100644
---- a/Makefile
-+++ b/Makefile
-@@ -15,6 +15,8 @@ CXX = g++
- #    c) RELEASE mode
- ################################################################################
- 
-+OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops
-+
- OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
- 
- # debug mode    
-@@ -25,7 +27,7 @@ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
- 
- # release mode
- #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer 
--CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
-+CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS)
- 
- ################################################################################
- # 3) Dependencies
-@@ -37,19 +39,19 @@ TARGETS = probcons compare project makegnuplot
- all : $(TARGETS)
- 
- probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc
--	$(CXX) $(CXXFLAGS) -lm -o probcons Main.cc 
-+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o probcons Main.cc -lm
- 
- compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
--	$(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
-+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o compare CompareToRef.cc
- 
- fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
--	$(CXX) $(CXXFLAGS) -o fixref FixRef.cc
-+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o fixref FixRef.cc
- 
- project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
--	$(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc
-+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o project ProjectPairwise.cc
- 
- makegnuplot : MakeGnuPlot.cc
--	$(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
-+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
- 
- .PHONY : clean
- clean:
diff --git a/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch b/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch
deleted file mode 100644
index 1596f3b31916..000000000000
--- a/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- SafeVector.h |    1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/SafeVector.h b/SafeVector.h
-index abf4b64..9c3292e 100644
---- a/SafeVector.h
-+++ b/SafeVector.h
-@@ -8,6 +8,7 @@
- #ifndef SAFEVECTOR_H
- #define SAFEVECTOR_H
- 
-+#include <cstddef>
- #include <cassert>
- #include <vector>
- 
diff --git a/sci-biology/probcons/metadata.xml b/sci-biology/probcons/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/probcons/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/probcons/probcons-1.12-r1.ebuild b/sci-biology/probcons/probcons-1.12-r1.ebuild
deleted file mode 100644
index 0a1d9b2c1efb..000000000000
--- a/sci-biology/probcons/probcons-1.12-r1.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-MY_P="${PN}_v${PV/./_}"
-
-DESCRIPTION="Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences"
-HOMEPAGE="http://probcons.stanford.edu/"
-SRC_URI="http://probcons.stanford.edu/${MY_P}.tar.gz"
-S="${WORKDIR}/${PN}"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-# Gnuplot is explicitly runtime-only, it's run using system()
-RDEPEND="
-	!sci-geosciences/gmt
-	sci-visualization/gnuplot"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-cxxflags.patch
-	"${FILESDIR}"/gcc-4.3.patch
-	"${FILESDIR}"/${P}-gcc-4.6.patch
-)
-
-src_compile() {
-	emake \
-		CXX="$(tc-getCXX)" \
-		OPT_CXXFLAGS="${CXXFLAGS}"
-}
-
-src_install() {
-	dobin probcons project makegnuplot
-	# Overlap with imagemagick
-	newbin compare compare-probcons
-	dodoc README
-}
-
-pkg_postinst() {
-	ewarn "The 'compare' binary is installed as 'compare-probcons'"
-	ewarn "to avoid overlap with other packages."
-	einfo "You may also want to download the user manual"
-	einfo "from http://probcons.stanford.edu/manual.pdf"
-}
diff --git a/sci-biology/prodigal/Manifest b/sci-biology/prodigal/Manifest
deleted file mode 100644
index 4157a49cb60c..000000000000
--- a/sci-biology/prodigal/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST prodigal-2.6.3.tar.gz 610934 BLAKE2B 54a75a694aec216da411717c29c8e896f064b4893d74fa1c736fdea3cd7bff98cb8d597cdbb96dd4cb2f0e82972c99b43eee8f2ddd8678535dc68c831dfd4e08 SHA512 6d6ec310143c50c0d65dbdbd26d6d271839bb23b1da376ecef20059731a9e643d631613eccaac2eb548b295264b9fe58c21b083f1511a6554912cb7d5351d541
diff --git a/sci-biology/prodigal/files/prodigal-2.6.3-fix-build-system.patch b/sci-biology/prodigal/files/prodigal-2.6.3-fix-build-system.patch
deleted file mode 100644
index b6d92392d179..000000000000
--- a/sci-biology/prodigal/files/prodigal-2.6.3-fix-build-system.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-Fix build system to honour user variables.
-
---- a/Makefile
-+++ b/Makefile
-@@ -19,32 +19,31 @@
- ##############################################################################
- 
- SHELL   = /bin/sh
--CC      = gcc
-+CC     ?= gcc
- 
--CFLAGS  += -pedantic -Wall -O3
--LFLAGS = -lm $(LDFLAGS)
-+LIBS    = -lm
- 
- TARGET  = prodigal
- SOURCES = $(shell echo *.c)
- HEADERS = $(shell echo *.h)
- OBJECTS = $(SOURCES:.c=.o)
- 
--INSTALLDIR  = /usr/local/bin
-+BINDIR = $(EPREFIX)/usr/bin
- 
- all: $(TARGET)
- 
- $(TARGET): $(OBJECTS)
--	$(CC) $(CFLAGS) -o $@ $^ $(LFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS)
- 
- %.o: %.c $(HEADERS)
--	$(CC) $(CFLAGS) -c -o $@ $<
-+	$(CC) -Wall -pedantic $(CFLAGS) $(CPPFLAGS) -c -o $@ $<
- 
- install: $(TARGET)
--	install -d -m 0755 $(INSTALLDIR)
--	install -m 0755 $(TARGET) $(INSTALLDIR)
-+	install -d -m 0755 $(DESTDIR)$(BINDIR)
-+	install -m 0755 $(TARGET) $(DESTDIR)$(BINDIR)
-  
- uninstall:
--	-rm $(INSTALLDIR)/$(TARGET)
-+	-rm $(DESTDIR)$(BINDIR)/$(TARGET)
- 
- clean:
- 	-rm -f $(OBJECTS)
diff --git a/sci-biology/prodigal/metadata.xml b/sci-biology/prodigal/metadata.xml
deleted file mode 100644
index 657774f9a8ec..000000000000
--- a/sci-biology/prodigal/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="google-code">prodigal</remote-id>
-		<remote-id type="github">hyattpd/Prodigal</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/prodigal/prodigal-2.6.3-r1.ebuild b/sci-biology/prodigal/prodigal-2.6.3-r1.ebuild
deleted file mode 100644
index 8428da82c5e7..000000000000
--- a/sci-biology/prodigal/prodigal-2.6.3-r1.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Prokaryotic Dynamic Programming Genefinding Algorithm"
-HOMEPAGE="http://prodigal.ornl.gov/"
-SRC_URI="https://github.com/hyattpd/${PN^}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${P^}"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.6.3-fix-build-system.patch )
-
-src_configure() {
-	tc-export CC
-}
diff --git a/sci-biology/profphd/Manifest b/sci-biology/profphd/Manifest
deleted file mode 100644
index 9aa5af5a04db..000000000000
--- a/sci-biology/profphd/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST profphd-1.0.40.tar.xz 4491592 BLAKE2B 2aa1e091c0674fa5318a075148a63b15354ecb6d8d6f7ac41d1d05f8bea17c47b6f37be707cc1c738e22342c26ae9be59cabf919610e5bffd5028fc587b2995b SHA512 287f1a548030e7978119788dffdf2529e0018cd772bc820e116f79ed10cefd440645424b56415333362098a1ed32f4841d3fd4069adede2a95968f81c63956e3
diff --git a/sci-biology/profphd/files/profphd-1.0.39-perl.patch b/sci-biology/profphd/files/profphd-1.0.39-perl.patch
deleted file mode 100644
index 10682271601c..000000000000
--- a/sci-biology/profphd/files/profphd-1.0.39-perl.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/prof/prof | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/prof/prof b/src/prof/prof
-index 4f26024..356442d 100755
---- a/src/prof/prof
-+++ b/src/prof/prof
-@@ -238,7 +238,7 @@ See each keyword for more help.  Most of these are likely to be broken.
- 
- alternative connectivity patterns (default=3)
- 
--=item 3
-+=item C<3>
- 
- predict sec + acc + htm
- 
diff --git a/sci-biology/profphd/files/profphd-1.0.40-symlink.patch b/sci-biology/profphd/files/profphd-1.0.40-symlink.patch
deleted file mode 100644
index 7733d55af4a6..000000000000
--- a/sci-biology/profphd/files/profphd-1.0.40-symlink.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/src/prof/Makefile
-+++ b/src/prof/Makefile
-@@ -40,7 +40,7 @@
- 		./. $(DESTDIR)$(prefix)/share/profphd/prof/.
- 	find $(DESTDIR)$(prefix)/share/profphd/prof/embl/phd.pl $(DESTDIR)$(prefix)/share/profphd/prof/scr/CONFprof.pl $(DESTDIR)$(prefix)/share/profphd/prof/prof $(DESTDIR)$(prefix)/share/profphd/prof/scr/lib/prof.pm \
- 		-type f -exec sed -i -e 's|__PREFIX__|$(prefix)|g;s|__VERSION__|$(VERSION)|;' {} \;
--	rm -rf $(DESTDIR)$(prefix)/bin/prof && mkdir -p $(DESTDIR)$(prefix)/bin && ln -s ../share/profphd/prof/prof $(DESTDIR)$(prefix)/bin/prof
-+	rm -rf $(DESTDIR)$(prefix)/bin/prof && mkdir -p $(DESTDIR)$(prefix)/bin && ln -s ../share/profphd/prof/prof $(DESTDIR)$(prefix)/bin/profphd
- 
- install-neuralnet:
- 	mkdir -p $(DESTDIR)$(prefix)/share/profphd/prof/embl/para && rsync -aC \
diff --git a/sci-biology/profphd/metadata.xml b/sci-biology/profphd/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/profphd/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/profphd/profphd-1.0.40.ebuild b/sci-biology/profphd/profphd-1.0.40.ebuild
deleted file mode 100644
index af3d03321616..000000000000
--- a/sci-biology/profphd/profphd-1.0.40.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Secondary structure and solvent accessibility predictor"
-HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction"
-SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="dev-lang/perl"
-RDEPEND="
-	${DEPEND}
-	dev-perl/librg-utils-perl
-	sci-libs/profnet
-	sci-libs/profphd-utils"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.0.39-perl.patch
-	"${FILESDIR}"/${PN}-1.0.40-symlink.patch
-)
-
-src_compile() {
-	emake prefix="${EPREFIX}"/usr
-}
-
-src_install() {
-	emake prefix="${EPREFIX}"/usr DESTDIR="${D}" install
-	einstalldocs
-}
diff --git a/sci-biology/prosite/Manifest b/sci-biology/prosite/Manifest
deleted file mode 100644
index a5a3248e6f54..000000000000
--- a/sci-biology/prosite/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST prosite2017_02.tar.bz2 9234253 BLAKE2B e818ba766a0761336b3f06b173fe98133e3c6fd9ee21198234fdfaf711ac2bf6ee68513c073a09765b050ffdcfe8c8d83a2ae91b89558db18ac6039798201c68 SHA512 2b8a26a44d62d17108afc43a3ab65d024f76e41ea9c9f477024700621323d2606fcaec54411e1d3f4ddad40717ad9ce3a1989ffd92220e0d3c2acf70400d2e43
diff --git a/sci-biology/prosite/metadata.xml b/sci-biology/prosite/metadata.xml
deleted file mode 100644
index 496029464135..000000000000
--- a/sci-biology/prosite/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		A protein families and domains database maintained at the Swiss
-		Institude for Bioinformatics. It consists of biologically significant
-		sites, patterns and profiles that help to reliably identify to which
-		known protein family (if any) a new sequence belongs. PROSITE currently
-		contains patterns and profiles specific for more than a thousand
-		protein families or domains. Each of these signatures comes with
-		documentation providing background information on the structure and
-		function of these proteins.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/prosite/prosite-2017.02-r1.ebuild b/sci-biology/prosite/prosite-2017.02-r1.ebuild
deleted file mode 100644
index e64701106888..000000000000
--- a/sci-biology/prosite/prosite-2017.02-r1.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="A protein families and domains database"
-HOMEPAGE="https://prosite.expasy.org/"
-SRC_URI="ftp://ftp.expasy.org/databases/prosite/old_releases/prosite${PV//./_}.tar.bz2"
-S="${WORKDIR}"
-
-LICENSE="swiss-prot"
-SLOT="0"
-# Minimal build keeps only the indexed files (if applicable).
-# The non-indexed database is not installed.
-KEYWORDS="~amd64 ~x86"
-IUSE="emboss minimal"
-
-BDEPEND="emboss? ( sci-biology/emboss )"
-RDEPEND="${BDEPEND}"
-
-src_compile() {
-	if use emboss; then
-		mkdir PROSITE || die
-		einfo
-		einfo "Indexing PROSITE for usage with EMBOSS"
-		EMBOSS_DATA="." prosextract -auto -prositedir "${S}" || die "Indexing PROSITE failed"
-		einfo
-	fi
-}
-
-src_install() {
-	if ! use minimal; then
-		insinto /usr/share/${PN}
-		doins *.{doc,dat}
-	fi
-
-	if use emboss; then
-		insinto /usr/share/EMBOSS/data/PROSITE
-		doins -r PROSITE/.
-	fi
-}
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
deleted file mode 100644
index 48717af7c11f..000000000000
--- a/sci-biology/pysam/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pysam-0.23.3.gh.tar.gz 4077706 BLAKE2B 52ea1866188374b6d832113f49de88b9b4fe1f777f0c81184aadfa5acd1f0e3048996e31a384061f0d1f9a289574c12e3e0a1c28a960e1e2f3f7af0c4e2b8d9a SHA512 e259a64ed722b72309827695585f429a6e59641223f5432c9cd7e673fd04fcbd5963618e9145315373e557edce532bf1a312db185bcc4235ff699357e453e07b
diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml
deleted file mode 100644
index 734257e94f10..000000000000
--- a/sci-biology/pysam/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="google-code">pysam</remote-id>
-		<remote-id type="github">pysam-developers/pysam</remote-id>
-		<remote-id type="pypi">pysam</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/pysam/pysam-0.23.3.ebuild b/sci-biology/pysam/pysam-0.23.3.ebuild
deleted file mode 100644
index 4e0b6f6e6b78..000000000000
--- a/sci-biology/pysam/pysam-0.23.3.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-DISTUTILS_EXT=1
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{13..14} )
-
-inherit distutils-r1
-
-if [[ ${PV} == *9999 ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/pysam-developers/pysam.git"
-else
-	SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
-HOMEPAGE="
-	https://github.com/pysam-developers/pysam
-	https://pypi.org/project/pysam/"
-
-LICENSE="MIT"
-SLOT="0"
-
-RDEPEND="=sci-libs/htslib-1.21*:="
-DEPEND="${RDEPEND}"
-BDEPEND="
-	test? (
-		=sci-biology/bcftools-1.21*
-		=sci-biology/samtools-1.21*
-	)"
-
-distutils_enable_tests pytest
-
-EPYTEST_DESELECT=(
-	# only work with bundled htslib
-	'tests/tabix_test.py::TestRemoteFileHTTP'
-	'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
-
-	'tests/AlignedSegment_test.py::TestBaseModifications'
-)
-
-python_prepare_all() {
-
-	# unbundle htslib
-	export HTSLIB_MODE="external"
-	export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include
-	export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir)
-	rm -r htslib || die
-
-	if use test; then
-		einfo "Building test data"
-		emake -C tests/pysam_data
-		emake -C tests/cbcf_data
-	fi
-
-	# breaks with parallel build
-	# need to avoid dropping .so plugins into
-	# build-lib, which breaks tests
-	DISTUTILS_ARGS=(
-		build_ext
-		--inplace
-		-j1
-	)
-	distutils-r1_python_prepare_all
-}
-
-python_test() {
-	rm -rf pysam || die
-	epytest
-}
diff --git a/sci-biology/pysam/pysam-9999.ebuild b/sci-biology/pysam/pysam-9999.ebuild
deleted file mode 100644
index 05dccff44ea8..000000000000
--- a/sci-biology/pysam/pysam-9999.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-DISTUTILS_EXT=1
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{13..14} )
-
-inherit distutils-r1
-
-if [[ ${PV} == *9999 ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/pysam-developers/pysam.git"
-else
-	SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
-HOMEPAGE="
-	https://github.com/pysam-developers/pysam
-	https://pypi.org/project/pysam/"
-
-LICENSE="MIT"
-SLOT="0"
-
-RDEPEND=">=sci-libs/htslib-1.21"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	test? (
-		>=sci-biology/bcftools-1.21
-		>=sci-biology/samtools-1.21
-	)"
-
-distutils_enable_tests pytest
-
-EPYTEST_DESELECT=(
-	# only work with bundled htslib
-	'tests/tabix_test.py::TestRemoteFileHTTP'
-	'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
-
-	'tests/AlignedSegment_test.py::TestBaseModifications'
-)
-
-python_prepare_all() {
-	# unbundle htslib
-	export HTSLIB_MODE="external"
-	export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include
-	export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir)
-	rm -r htslib || die
-
-	if use test; then
-		einfo "Building test data"
-		emake -C tests/pysam_data
-		emake -C tests/cbcf_data
-	fi
-
-	# breaks with parallel build
-	# need to avoid dropping .so plugins into
-	# build-lib, which breaks tests
-	DISTUTILS_ARGS=(
-		build_ext
-		--inplace
-		-j1
-	)
-	distutils-r1_python_prepare_all
-}
-
-python_test() {
-	rm -rf pysam || die
-	epytest
-}
diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest
deleted file mode 100644
index 56416ac10d7f..000000000000
--- a/sci-biology/raxml/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST raxml-8.2.13.tar.gz 10201721 BLAKE2B ee48dc599947619d12a54cafef1eee554abc0df30a31ba2fdb501b228dadec9f137acff8f472047f4686304f74d27893696c95ff808baa128c2c3d83539366a1 SHA512 c99dc3f8c8798cda38c644501f474c0261e72c1f3b64d594d5006fa03e8d8c4da3bdf20b8e3c6c9f669c9509d5af27a0c286a2570a54c8ff7df7cd63c1f78885
diff --git a/sci-biology/raxml/files/raxml-8.2.13-c23.patch b/sci-biology/raxml/files/raxml-8.2.13-c23.patch
deleted file mode 100644
index b0ce95bf2ae8..000000000000
--- a/sci-biology/raxml/files/raxml-8.2.13-c23.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- a/rmq.h
-+++ b/rmq.h
-@@ -2,15 +2,12 @@
- #define _rmq_h_
- 
- #include <math.h>
--
--#define false 0
--#define true 1
-+#include <stdbool.h>
- 
- typedef int DT;                 // use long for 64bit-version (but take care of fast log!)
- typedef unsigned int DTidx;     // for indexing in arrays
- typedef unsigned char DTsucc;
- typedef unsigned short DTsucc2;
--typedef int bool;
- DTidx query(DTidx, DTidx);
- void RMQ_succinct(DT* a, DTidx n);
- void RMQ_succinct_destroy(void);
diff --git a/sci-biology/raxml/files/raxml-8.2.13-makefile.patch b/sci-biology/raxml/files/raxml-8.2.13-makefile.patch
deleted file mode 100644
index d774b1fb824d..000000000000
--- a/sci-biology/raxml/files/raxml-8.2.13-makefile.patch
+++ /dev/null
@@ -1,37 +0,0 @@
---- a/Makefile.gcc
-+++ b/Makefile.gcc
-@@ -1,7 +1,6 @@
- # Makefile August 2006 by Alexandros Stamatakis
- # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>
- 
--CC = gcc 
- 
- ARCH := $(shell uname -m)
- ifeq ($(ARCH), x86_64)
-@@ -10,7 +9,7 @@
- ARCH_CFLAGS=
- endif
- 
--CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 $(ARCH_CFLAGS) #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
-+CFLAGS += -D_GNU_SOURCE #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
- 
- LIBRARIES = -lm
- 
-@@ -23,7 +22,7 @@
- GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h
- 
- raxmlHPC : $(objs)
--	$(CC) -o raxmlHPC $(objs) $(LIBRARIES) $(LDFLAGS) 
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES)
- 
- rmqs.o : rmqs.c $(GLOBAL_DEPS)
- classify.o : classify.c $(GLOBAL_DEPS)
-@@ -51,8 +50,6 @@
- 
- 
- 
--eigen.o : eigen.c $(GLOBAL_DEPS)
--	$(CC) -c -o eigen.o eigen.c 
- clean : 
- 	$(RM) *.o raxmlHPC
- 
diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml
deleted file mode 100644
index dd68d972db31..000000000000
--- a/sci-biology/raxml/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">stamatak/standard-RAxML</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/raxml/raxml-8.2.13.ebuild b/sci-biology/raxml/raxml-8.2.13.ebuild
deleted file mode 100644
index 0aa191b50785..000000000000
--- a/sci-biology/raxml/raxml-8.2.13.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit flag-o-matic toolchain-funcs
-
-DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees"
-HOMEPAGE="https://github.com/stamatak/standard-RAxML"
-SRC_URI="https://github.com/stamatak/standard-RAxML/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/standard-RAxML-${PV}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="cpu_flags_x86_sse3 +threads"
-
-# mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS
-PATCHES=(
-	"${FILESDIR}"/${P}-makefile.patch
-	"${FILESDIR}"/${P}-c23.patch
-)
-
-src_configure() {
-	use cpu_flags_x86_sse3 &&
-		append-cppflags -D__SIM_SSE3 &&
-		append-cflags -msse3
-	use threads &&
-		append-cppflags -D_USE_PTHREADS &&
-		append-cflags -pthread
-
-	tc-export CC
-}
-
-src_compile() {
-	emake -f Makefile.gcc
-}
-
-src_install() {
-	dobin raxmlHPC
-}
diff --git a/sci-biology/rebase/Manifest b/sci-biology/rebase/Manifest
deleted file mode 100644
index b383cb20278f..000000000000
--- a/sci-biology/rebase/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST rebase-1901.tar.xz 182532548 BLAKE2B 5ac8d26ab057bcd21dc9c57abeb226ac70cfabb156b48a51f820789626257be55bb21c9eb2099e6e55b1cfe3691480df0ec9b3f4b18b50ba2712b986c6d057b4 SHA512 1e3553e59c3520190754cb40bb0900e466d9ffd206e6460d3262a7d7d2af8aab0e28f3e60187665362824fa3730211c0e2119016ce5fed49095f9de46c7f25d4
diff --git a/sci-biology/rebase/metadata.xml b/sci-biology/rebase/metadata.xml
deleted file mode 100644
index e4403acacd03..000000000000
--- a/sci-biology/rebase/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		The Restriction Enzyme data BASE is a collection of information about
-		restriction enzymes and related proteins. It is maintained by New
-		England Biolabs. It contains published and unpublished references,
-		recognition and cleavage sites, isoschizomers, commercial availability,
-		methylation sensitivity, crystal and sequence data. DNA
-		methyltransferases, homing endonucleases, nicking enzymes, specificity
-		subunits and control proteins are also included. More recently,
-		putative DNA methyltransferases and restriction enzymes, as predicted
-		from analysis of genomic sequences, are also listed.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/rebase/rebase-1901-r2.ebuild b/sci-biology/rebase/rebase-1901-r2.ebuild
deleted file mode 100644
index f2a3d9c9988f..000000000000
--- a/sci-biology/rebase/rebase-1901-r2.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-MY_PV="${PV#1}"
-
-DESCRIPTION="A restriction enzyme database"
-HOMEPAGE="http://rebase.neb.com"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="emboss minimal"
-RESTRICT="binchecks strip"
-
-BDEPEND="emboss? ( sci-biology/emboss )"
-RDEPEND="${BDEPEND}"
-
-src_compile() {
-	if use emboss; then
-		einfo
-		einfo "Indexing Rebase for usage with EMBOSS"
-		mkdir REBASE || die
-		EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \
-				-protofile proto.${MY_PV} -equivalences \
-				|| die "Indexing Rebase failed"
-		einfo
-	fi
-}
-
-src_install() {
-	if ! use minimal; then
-		insinto /usr/share/${PN}
-		doins withrefm.${MY_PV} proto.${MY_PV}
-	fi
-	newdoc REBASE.DOC README
-	if use emboss; then
-		insinto /usr/share/EMBOSS/data/REBASE
-		doins REBASE/embossre.{enz,ref,sup}
-		insinto /usr/share/EMBOSS/data
-		doins REBASE/embossre.equ
-	fi
-}
diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest
deleted file mode 100644
index 8ee80f1aa469..000000000000
--- a/sci-biology/recon/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST RECON-1.08.tar.gz 108477 BLAKE2B 155a740056e876f5aa2279ca0572fe151a52a2db5ac43af9b902ea4c099727f3274dd58abec59b74c13605ccd37ad9b3cd80379f79cb976c4bb677f661fd6273 SHA512 68672312f31751fa93250bbe337ae57f11dc4b1994c7dd5249dca916012c2df83a03c925cb631709e081c72055ef5bffd0846bc252d8c3c6247ae5ef61b160c9
diff --git a/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch b/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch
deleted file mode 100644
index 9eba16e4a410..000000000000
--- a/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- a/src/bolts.h
-+++ b/src/bolts.h
-@@ -3,6 +3,7 @@
- #include <stdio.h>
- #include <math.h>
- #include <stdlib.h>
-+#include <stdint.h>
- 
- 
- #define NAME_LEN 50
---- a/src/seqlist.h
-+++ b/src/seqlist.h
-@@ -1,6 +1,7 @@
- 
- #include "bolts.h"
- #include "string.h"
-+#include <ctype.h>
- 
- #ifndef _seqlist_h
- #define _seqlist_h
diff --git a/sci-biology/recon/files/recon-1.08-buffer-overflow.patch b/sci-biology/recon/files/recon-1.08-buffer-overflow.patch
deleted file mode 100644
index e6bf54e7c2f2..000000000000
--- a/sci-biology/recon/files/recon-1.08-buffer-overflow.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/src/eledef.c
-+++ b/src/eledef.c
-@@ -385,7 +385,7 @@ void ele_def(int method, FILE *frags, float cutoff, EPROT_t **all_epp, int *ecp,
- 
- void img_charge(IPROT_t **shadow, int ct, FILE *input) {
-   int i=0, pos=0;
--  char line[151];
-+  char line[256];
-   int scan_flag;
-   MSP_t msp;
- 
diff --git a/sci-biology/recon/files/recon-1.08-perl-shebangs.patch b/sci-biology/recon/files/recon-1.08-perl-shebangs.patch
deleted file mode 100644
index 769fe4a93c65..000000000000
--- a/sci-biology/recon/files/recon-1.08-perl-shebangs.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-Make Perl shebangs Prefix friendly
-See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/
-
---- a/scripts/MSPCollect.pl
-+++ b/scripts/MSPCollect.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- if (!@ARGV) {
-     die "usage: MSPCollect BLAST_output_file\n";
---- a/scripts/recon.pl
-+++ b/scripts/recon.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- $path = "";
- 
diff --git a/sci-biology/recon/metadata.xml b/sci-biology/recon/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/recon/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/recon/recon-1.08-r1.ebuild b/sci-biology/recon/recon-1.08-r1.ebuild
deleted file mode 100644
index dd79dd43c496..000000000000
--- a/sci-biology/recon/recon-1.08-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Automated de novo identification of repeat families from genomic sequences"
-HOMEPAGE="http://www.repeatmasker.org/RepeatModeler.html"
-SRC_URI="http://www.repeatmasker.org/${P^^}.tar.gz"
-S="${WORKDIR}/${P^^}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples"
-
-RDEPEND="dev-lang/perl"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.08-buffer-overflow.patch
-	"${FILESDIR}"/${PN}-1.08-perl-shebangs.patch
-	"${FILESDIR}"/${PN}-1.08-Wimplicit-function-declaration.patch
-)
-
-src_prepare() {
-	default
-	sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/recon\";|" scripts/recon.pl || die
-}
-
-src_compile() {
-	emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}" -C src
-}
-
-src_install() {
-	dobin scripts/*
-
-	exeinto /usr/libexec/recon
-	doexe src/{edgeredef,eledef,eleredef,famdef,imagespread}
-
-	newdoc {00,}README
-
-	if use examples; then
-		insinto /usr/share/recon
-		doins -r Demos
-	fi
-}
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
deleted file mode 100644
index 43a41ae4a17b..000000000000
--- a/sci-biology/samtools/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST samtools-1.20.tar.bz2 9179938 BLAKE2B b534e659899a822e191c779a6ce9247854036da3435a0b63748783edc96d610ff0f02f73bbb5c1eab3ff86dbcca331113f3312a7c3376141ef89b6a8684446e4 SHA512 8526286243d057758cb846311d0a8c728026d31438e87fcc03e0df576f33bcc6da0e18bce141dbdc438a116341c94aa92701cdf10ba6b1301eadedbb34120822
-DIST samtools-1.21.tar.bz2 9149284 BLAKE2B f4e0b155b0bc8aaea81835e751d94c121f6256340e2db3a809d1ee46bed16168a0fb43d9359bf4c3967d0b77ab1151e105107c47eb0481a2c49414ffd5f1faa2 SHA512 4f80a4333ebb4dc0eb5f38f29474424b1acca9b677aa206b111c7a638b8ae924ab2dcdc9de15eb1b849576d0158579a476a7b78ccd73e7d2baafc3bbb88c6103
-DIST samtools-1.22.1.tar.bz2 9269357 BLAKE2B 240b2166a548d398af18e5c5b1897988e4a1267988e1c3f508c990b05cfa684ca631336971d28ce08581b9d65c3b33cdb1be4cfabc5b65e210c3ae0a57215881 SHA512 31d05490f3b5d8879b7cdfe16bb628e2a1c42fdfd98873f55796b94e2d59a86cd58d7a820758d368998f0c013a26da838a7b051c01f0f22d38362ae13d069600
-DIST samtools-1.22.tar.bz2 9292743 BLAKE2B 74805efe6035d4987762c5d9c5fc1ede217f8c67e1778767c2e611c0844639149c73b7cef40649212ba3dcd11f089d0ede91f6127df31433d4e33c8f22378b93 SHA512 8bb4d68ac5f819d6e175f43d8719402f17636b958ed016a943dc6c1971704f405908562ff9fe8f3c7c8725f729057024b305a6ca428a09be8b1e63a1df1cd578
-DIST samtools-1.23.tar.bz2 9357675 BLAKE2B 253ded3935bce0f8d7329fd1d6bafb194bf2c0821bdd378a31b0e0646f53940df252df69cc830ea4bef360285349c07cb6b13f3c1a0c8e4e1321feeb21500a84 SHA512 cf3442cd731729b5a9f9487843ea98bbb31db853c253109a97dec6e609d0df9095223ab47d8ce3cb8b3536a8d26e2f616e732d115b1340247873f41659688bac
diff --git a/sci-biology/samtools/metadata.xml b/sci-biology/samtools/metadata.xml
deleted file mode 100644
index ddf4bb2590f4..000000000000
--- a/sci-biology/samtools/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">samtools</remote-id>
-    <remote-id type="github">samtools/samtools</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/samtools/samtools-1.20.ebuild b/sci-biology/samtools/samtools-1.20.ebuild
deleted file mode 100644
index a8ef4fe964ff..000000000000
--- a/sci-biology/samtools/samtools-1.20.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="amd64 ~x86 ~x64-macos"
-
-RDEPEND="
-	dev-lang/perl
-	=sci-libs/htslib-$(ver_cut 1-2)*:=
-	sys-libs/ncurses:=[unicode(+)]
-	virtual/zlib:="
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-	default
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-}
-
-src_configure() {
-	econf \
-		--with-ncurses \
-		--with-htslib=system \
-		CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
-	emake AR="$(tc-getAR)"
-}
-
-src_install() {
-	default
-
-	dodoc -r examples
-	docompress -x /usr/share/doc/${PF}/examples
-}
diff --git a/sci-biology/samtools/samtools-1.21.ebuild b/sci-biology/samtools/samtools-1.21.ebuild
deleted file mode 100644
index f11e9e81198b..000000000000
--- a/sci-biology/samtools/samtools-1.21.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-RDEPEND="
-	dev-lang/perl
-	=sci-libs/htslib-$(ver_cut 1-2)*:=
-	sys-libs/ncurses:=[unicode(+)]
-	virtual/zlib:="
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-	default
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-}
-
-src_configure() {
-	econf \
-		--with-ncurses \
-		--with-htslib=system \
-		CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
-	emake AR="$(tc-getAR)"
-}
-
-src_install() {
-	default
-
-	dodoc -r examples
-	docompress -x /usr/share/doc/${PF}/examples
-}
diff --git a/sci-biology/samtools/samtools-1.22.1.ebuild b/sci-biology/samtools/samtools-1.22.1.ebuild
deleted file mode 100644
index f11e9e81198b..000000000000
--- a/sci-biology/samtools/samtools-1.22.1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-RDEPEND="
-	dev-lang/perl
-	=sci-libs/htslib-$(ver_cut 1-2)*:=
-	sys-libs/ncurses:=[unicode(+)]
-	virtual/zlib:="
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-	default
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-}
-
-src_configure() {
-	econf \
-		--with-ncurses \
-		--with-htslib=system \
-		CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
-	emake AR="$(tc-getAR)"
-}
-
-src_install() {
-	default
-
-	dodoc -r examples
-	docompress -x /usr/share/doc/${PF}/examples
-}
diff --git a/sci-biology/samtools/samtools-1.22.ebuild b/sci-biology/samtools/samtools-1.22.ebuild
deleted file mode 100644
index f11e9e81198b..000000000000
--- a/sci-biology/samtools/samtools-1.22.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-RDEPEND="
-	dev-lang/perl
-	=sci-libs/htslib-$(ver_cut 1-2)*:=
-	sys-libs/ncurses:=[unicode(+)]
-	virtual/zlib:="
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-	default
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-}
-
-src_configure() {
-	econf \
-		--with-ncurses \
-		--with-htslib=system \
-		CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
-	emake AR="$(tc-getAR)"
-}
-
-src_install() {
-	default
-
-	dodoc -r examples
-	docompress -x /usr/share/doc/${PF}/examples
-}
diff --git a/sci-biology/samtools/samtools-1.23.ebuild b/sci-biology/samtools/samtools-1.23.ebuild
deleted file mode 100644
index 1c202445e9de..000000000000
--- a/sci-biology/samtools/samtools-1.23.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-
-RDEPEND="
-	dev-lang/perl
-	=sci-libs/htslib-$(ver_cut 1-2)*:=
-	sys-libs/ncurses:=[unicode(+)]
-	virtual/zlib:="
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-	default
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-}
-
-src_configure() {
-	econf \
-		--with-ncurses \
-		--with-htslib=system \
-		CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)"
-}
-
-src_compile() {
-	emake AR="$(tc-getAR)"
-}
-
-src_install() {
-	default
-
-	dodoc -r examples
-	docompress -x /usr/share/doc/${PF}/examples
-}
diff --git a/sci-biology/seaview/Manifest b/sci-biology/seaview/Manifest
deleted file mode 100644
index 2b43f22a2ea3..000000000000
--- a/sci-biology/seaview/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST seaview_4.6.tar.gz 424258 BLAKE2B e958ff4b1f6bb283a2122d65917a352914f33e5c9593c34c449800fbcac74b0dd4fa98bb1f47c45e11f24e07dfebb3ced54fbd8440b2bcd2b1df32dc398d5892 SHA512 e005d9dcc9e03c5636404e94f0059f7d4a9289fe77ecdab765e3ca2b59d826b8711a344f3824d079383a7ede0fe17b3b06694dfb7b709bb6a0a1e38cef6ee1d6
diff --git a/sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch b/sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch
deleted file mode 100644
index c9595748e901..000000000000
--- a/sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch
+++ /dev/null
@@ -1,76 +0,0 @@
---- a/align.cxx
-+++ b/align.cxx
-@@ -754,7 +754,7 @@
-   alignitems[clustalopt + MAX_MSA_ALGOS].label(strdup(options));
-   alignitems[clustalopt + MAX_MSA_ALGOS].flags = attr;
-   if (view->alignment_algorithm < 2) alignitems[clustalopt + MAX_MSA_ALGOS + 3].flags = FL_MENU_INACTIVE;
--  delete options;
-+  delete[] options;
-   view->menu_align = alignitems;
-   view->menubar->add("Align", 0, NULL, (void*)view->menu_align, FL_SUBMENU_POINTER);
-   if (view->count_msa_algos >= MAX_MSA_ALGOS) (alignitems + clustalopt + MAX_MSA_ALGOS + 2)->deactivate();
---- a/seaview.cxx
-+++ b/seaview.cxx
-@@ -3314,7 +3314,7 @@
- 	if(p != NULL) *p = 0;
- 	if(printout_black == TEXT_ONLY) strcat(suggested, ".txt");
- 	else {
--		strcat(suggested, "."PDF_OR_PS_EXT);
-+		strcat(suggested, "." PDF_OR_PS_EXT);
- 		}
- if( view->alt_col_rank != NULL ) {
- 		for(anerr = 0; anerr < view->tot_seqs; anerr++)
-@@ -3424,7 +3424,7 @@
- 
- pdf_form = new Fl_Window(415, 90);
- pdf_form->box(FL_FLAT_BOX);
--pdf_form->label("Set "PDF_OR_PS" output options");
-+pdf_form->label("Set " PDF_OR_PS " output options");
- 
- x = 5 + (int)fl_width("block size:"); y = 5; w = 50; h = 25;
- sizeinput = new Fl_Input(x, y, w, h, "font size:");
-@@ -5000,10 +5000,10 @@
-     {"Save prot alignmt", 0,file_menu_callback, 0, FL_MENU_INACTIVE},
-     {"Save bootstrap replicates", 0,file_menu_callback, 0, FL_MENU_INACTIVE | FL_MENU_DIVIDER},
- #if !defined(__APPLE__)
--    {"Prepare "PDF_OR_PS"", 0, file_menu_callback, 0, 0},
--    {""PDF_OR_PS" options...", 0, file_menu_callback, 0, FL_MENU_DIVIDER},
-+    {"Prepare " PDF_OR_PS "", 0, file_menu_callback, 0, 0},
-+    {"" PDF_OR_PS " options...", 0, file_menu_callback, 0, FL_MENU_DIVIDER},
- #else
--    {"Prepare "PDF_OR_PS"", 0, file_menu_callback, 0, FL_MENU_DIVIDER},
-+    {"Prepare " PDF_OR_PS "", 0, file_menu_callback, 0, FL_MENU_DIVIDER},
- #endif
-     {"Concatenate", 0,file_menu_callback, 0, FL_MENU_DIVIDER},
-     {"New window", FL_COMMAND | 'n', file_menu_callback, 0, 0},
---- a/treedraw.cxx
-+++ b/treedraw.cxx
-@@ -210,7 +210,7 @@
-     {"Save all trees", 0, file_callback, NULL, 0},
-     {"Save patristic distances", 0, patristic_callback, NULL, FL_MENU_DIVIDER},
-     {"Print", FL_COMMAND | 'p', file_callback, NULL, 0},
--    {"Save as "PDF_OR_PS"", 0, file_callback, NULL, 0},
-+    {"Save as " PDF_OR_PS "", 0, file_callback, NULL, 0},
-     {"Save as SVG", 0, file_callback, NULL, 0},
-     {"A4", 0, file_callback, NULL, FL_MENU_RADIO | 0},
-     {"Letter", 0, file_callback, NULL, FL_MENU_RADIO | 0},
---- a/xfmatpt.cxx
-+++ b/xfmatpt.cxx
-@@ -205,7 +205,7 @@
- compute->callback(compute_proc, fdui);
- fdui->compute_butt = compute;
- 
--Fl_Widget *postscript = cre_button(fin, curr_y, &width, but_height, fontsize, "Write "PDF_OR_PS);
-+Fl_Widget *postscript = cre_button(fin, curr_y, &width, but_height, fontsize, "Write " PDF_OR_PS);
- fin += width;
- postscript->callback(plot_button_proc, fdui);
- 
-@@ -870,7 +870,7 @@
- #ifndef MICRO
-   matpt->form->hide(); Fl::flush(); // because of strange bug on 32-bit Linux only
- #endif
--  fl_message("Dot plot is now in file\n%s\nin "PDF_OR_PS" format", surface->outfname());
-+  fl_message("Dot plot is now in file\n%s\nin " PDF_OR_PS " format", surface->outfname());
-   delete surface;
- #ifndef MICRO
-   matpt->form->show(); Fl::flush();
diff --git a/sci-biology/seaview/files/seaview-4.6-fno-common.patch b/sci-biology/seaview/files/seaview-4.6-fno-common.patch
deleted file mode 100644
index 24cc28dfb3b7..000000000000
--- a/sci-biology/seaview/files/seaview-4.6-fno-common.patch
+++ /dev/null
@@ -1,110 +0,0 @@
---- a/csrc/dnapars.c
-+++ b/csrc/dnapars.c
-@@ -77,41 +77,43 @@
- /* function prototypes */
- 
- 
--Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename,
-+extern Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename,
-      weightfilename[FNMLNGTH];
- char basechar[32]="ACMGRSVTWYHKDBNO???????????????";
--node *root;
--long chars, col, msets, ith, njumble, jumb, maxtrees;
-+extern node *root;
-+extern long chars, col, msets, ith, njumble, jumb;
-+long maxtrees;
- /*   chars = number of sites in actual sequences */
--long inseed, inseed0;
--double threshold;
--boolean jumble, usertree, thresh, weights, thorough, rearrfirst,
--          trout, progress, stepbox, ancseq, mulsets, justwts, firstset, mulf,
--          multf;
-+extern long inseed, inseed0;
-+extern double threshold;
-+boolean thorough, rearrfirst, mulf, multf;
-+extern boolean justwts, ancseq, weights, thresh, jumble, usertree, trout, mulsets, progress, stepbox, firstset;
- steptr oldweight;
--longer seed;
--pointarray treenode;            /* pointers to all nodes in tree */
--long *enterorder;
-+extern longer seed;
-+extern pointarray treenode;            /* pointers to all nodes in tree */
-+extern long *enterorder;
- long *zeros;
- 
- /* local variables for Pascal maketree, propagated globally for C version: */
- 
--long minwhich;
-+extern long minwhich;
- static double like, minsteps, bestyet, bestlike, bstlike2;
--boolean lastrearr, recompute;
--double nsteps[maxuser];
--long **fsteps;
--node *there, *oldnufork;
--long *place;
--bestelm *bestrees;
--long *threshwt;
-+extern boolean lastrearr, recompute;
-+extern double nsteps[maxuser];
-+extern long **fsteps;
-+extern node *there;
-+node *oldnufork;
-+extern long *place;
-+extern bestelm *bestrees;
-+extern long *threshwt;
- baseptr nothing;
--gbases *garbage;
--node *temp, *temp1, *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1,
-+extern gbases *garbage;
-+extern node *temp, *temp1;
-+node *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1,
-        *tmp2, *tmp3, *tmprm, *tmpadd;
--boolean *names;
-+extern boolean *names;
- node *grbg;
--char *progname;
-+extern char *progname;
- 
- 
- static void getoptions(int arg_maxtrees, dnapars_S_option s_option)
---- a/csrc/phylip.c
-+++ b/csrc/phylip.c
-@@ -35,6 +35,8 @@
- 
- #include "phylip.h"
- 
-+boolean javarun;
-+
- #ifdef WIN32
- #include <windows.h>
- /* for console code (clear screen, text color settings) */
---- a/csrc/phylip.h
-+++ b/csrc/phylip.h
-@@ -342,7 +342,7 @@
- /* Lower-triangular format. */
- #define MAT_LOWERTRI    (MAT_LOWER | MAT_MACHINE)
- 
--boolean javarun;
-+extern boolean javarun;
- 
- typedef long *steptr;
- typedef long longer[6];
-@@ -363,7 +363,6 @@
- extern boolean ibmpc, ansi, tranvsp;
- //extern naym *nayme;                     /* names of species */
- extern char* *nayme;                     /* names of species */
--boolean firstplotblock; // for debugging BMP output
- 
- #define ebcdic          EBCDIC
- 
---- a/csrc/protpars.c
-+++ b/csrc/protpars.c
-@@ -127,7 +127,7 @@
- node *temp, *temp1;
- Char ch;
- aas tmpa;
--char *progname;
-+extern char *progname;
- 
- /* Local variables for maketree, propagated globally for c version: */
- long minwhich;
diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml
deleted file mode 100644
index a01c6174c4ce..000000000000
--- a/sci-biology/seaview/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		SeaView is a graphical multiple sequence alignment editor developped by
-		Manolo Gouy. SeaView is able to read and write various alignment
-		formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to
-		manually edit the alignment, and also to run DOT-PLOT or CLUSTALW
-		programs to locally improve the alignment.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/seaview/seaview-4.6-r2.ebuild b/sci-biology/seaview/seaview-4.6-r2.ebuild
deleted file mode 100644
index d95d0b842eef..000000000000
--- a/sci-biology/seaview/seaview-4.6-r2.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit desktop toolchain-funcs
-
-DESCRIPTION="A graphical multiple sequence alignment editor"
-HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html"
-SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+xft"
-
-RDEPEND="
-	sci-biology/clustalw:2
-	sci-biology/phyml
-	|| (
-		sci-libs/libmuscle
-		sci-biology/muscle
-	)
-	virtual/zlib:=
-	x11-libs/fltk:1=[xft(+)?]
-	x11-libs/libX11
-	xft? ( x11-libs/libXft )"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-S="${WORKDIR}/${PN}"
-PATCHES=(
-	"${FILESDIR}"/${PN}-4.6-fno-common.patch
-	"${FILESDIR}"/${PN}-4.6-Wreserved-user-defined-literal.patch
-)
-
-src_prepare() {
-	default
-
-	# respect CXXFLAGS (package uses them as CFLAGS)
-	sed \
-		-e "s:^CC.*:CC = $(tc-getCC):" \
-		-e "s:^CXX.*:CXX = $(tc-getCXX):" \
-		-e "s:\$(OPT):${CXXFLAGS}:" \
-		-e "s:^OPT:#OPT:" \
-		-e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \
-		-e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \
-		-e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \
-		-e "s:^USE_XFT:#USE_XFT:" \
-		-e "s:^#HELPFILE:HELPFILE:" \
-		-e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \
-		-e "s:^#PHYMLNAME:PHYMLNAME:" \
-		-e 's:-lXinerama::g' \
-		-e 's:-lpng::g' \
-		-e 's:-ljpeg::g' \
-		-e 's:-lfontconfig::g' \
-		-i Makefile || die "sed failed while editing Makefile"
-
-	if use xft; then
-		sed \
-			-e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \
-			-e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \
-			-i Makefile || die "sed failed while editing Makefile to enable xft"
-	else
-		sed -i -e "s:-lXft::" Makefile || die
-	fi
-}
-
-src_install() {
-	dobin seaview
-
-	# /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile
-	insinto /usr/share/seaview
-	doins example.nxs seaview.html
-
-	insinto /usr/share/seaview/images
-	doins seaview.xpm
-
-	make_desktop_entry seaview Seaview
-
-	doman seaview.1
-}
diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
deleted file mode 100644
index ed2aa485711a..000000000000
--- a/sci-biology/seqan/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST seqan3-3.1.0-Source.tar.xz 2656120 BLAKE2B 6a18844f62d935fdbd7008822f83ffeefd596e93b704a8c7b0f478dec87b2265ff532be107ebfd1adc248e2b1db65e4b86cdce2e989c7ac097054d43633a24bd SHA512 686d0ffbe32951e7f831e399a3eab35b7249f45408b7de27ee9cfd6a012215603f033afa6082c8a81783de1cc7c93d3ffbae42cabc122d3b77988c236a049ffd
diff --git a/sci-biology/seqan/metadata.xml b/sci-biology/seqan/metadata.xml
deleted file mode 100644
index bdabd1d83788..000000000000
--- a/sci-biology/seqan/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/seqan/seqan-3.1.0.ebuild b/sci-biology/seqan/seqan-3.1.0.ebuild
deleted file mode 100644
index b5a97f2052eb..000000000000
--- a/sci-biology/seqan/seqan-3.1.0.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake
-
-DESCRIPTION="C++ Sequence Analysis Library"
-HOMEPAGE="https://www.seqan.de/"
-SRC_URI="https://github.com/seqan/seqan3/releases/download/${PV}/seqan3-${PV}-Source.tar.xz"
-S="${WORKDIR}/seqan3-${PV}-Source"
-
-LICENSE="BSD GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_x86_sse4_2"
-REQUIRED_USE="cpu_flags_x86_sse4_2"
-
-RDEPEND="
-	app-arch/bzip2:=
-	dev-cpp/range-v3
-	dev-libs/cereal
-	sci-libs/lemon
-	virtual/zlib:=
-"
-DEPEND="${RDEPEND}"
-
-src_install() {
-	cmake_src_install
-	dodoc -r doc/*
-}
diff --git a/sci-biology/sibsim4/Manifest b/sci-biology/sibsim4/Manifest
deleted file mode 100644
index 378e871a0110..000000000000
--- a/sci-biology/sibsim4/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST SIBsim4-0.20.tar.gz 32118 BLAKE2B 79b1f080d547732ee6a5996885c26f422f8a1590fa37d525f35cfa3dee353fd36ce9aa4677fe7e570f43e8283c26541c8c9e76ca03788a66d1c356adb3d649d5 SHA512 3802520095e83d3c691804b661696095a4198c4b2a16385c55ccdc8e4e836f82cc9c2251a5d37cb5918c2ee80aeb81737d751e6b065fbfe9c64f1aee3e0ea0c8
diff --git a/sci-biology/sibsim4/files/sibsim4-0.20-makefile.patch b/sci-biology/sibsim4/files/sibsim4-0.20-makefile.patch
deleted file mode 100644
index 6436747e3dd9..000000000000
--- a/sci-biology/sibsim4/files/sibsim4-0.20-makefile.patch
+++ /dev/null
@@ -1,26 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -21,13 +21,12 @@
- # to change it to this:
- # CFLAGS = -Xc
- 
--CFLAGS = -std=gnu99 -W -Wall -Wconversion -pedantic $(DEBUG) $(OPT)
-+CFLAGS += -std=gnu99 -Wall -Wconversion -pedantic
- 
- 
- # The default is GCC.  On Solaris, you might put:
- # CC = /opt/SUNWspro/bin/cc
- 
--CC = gcc
- 
- 
- # Depending on the compile flags you use, you might need to explicitly use the
-@@ -42,7 +41,7 @@
- OBJS = sim4b1.o align.o misc.o sim4.init.o
- 
- sim4: $(OBJS)
--	$(CC) -o SIBsim4 $(CFLAGS) $(OBJS) $(LIBS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o SIBsim4 $(OBJS) $(LIBS)
- 
- clean:
- 	rm -f SIBsim4 *.o
diff --git a/sci-biology/sibsim4/metadata.xml b/sci-biology/sibsim4/metadata.xml
deleted file mode 100644
index 149d1330aaf9..000000000000
--- a/sci-biology/sibsim4/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">sibsim4</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/sibsim4/sibsim4-0.20.ebuild b/sci-biology/sibsim4/sibsim4-0.20.ebuild
deleted file mode 100644
index 2c9d69ada02c..000000000000
--- a/sci-biology/sibsim4/sibsim4-0.20.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="A rewrite and improvement upon sim4, a DNA-mRNA aligner"
-HOMEPAGE="http://sibsim4.sourceforge.net/"
-SRC_URI="https://downloads.sourceforge.net/${PN}/SIBsim4-${PV}.tar.gz"
-S="${WORKDIR}/SIBsim4-${PV}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-PATCHES=( "${FILESDIR}"/${P}-makefile.patch )
-
-src_configure() {
-	tc-export CC
-}
-
-src_install() {
-	dobin SIBsim4
-	doman SIBsim4.1
-}
diff --git a/sci-biology/sim4/Manifest b/sci-biology/sim4/Manifest
deleted file mode 100644
index a9548f107ec7..000000000000
--- a/sci-biology/sim4/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST sim4-20030921.tar.gz 60814 BLAKE2B 2a6aeaf56cbec7b3d5e8cb0c0405afd3b1325977d1b68ba319347dbc38461bde9bdb028e92d8b463a593a2fdc8d72d65db27c8e30462901ce8921632201ad038 SHA512 de7ee4094830262cb7ea8ed2f4573beed96df4b12f2915f669c52fd3fa40f5a4894cd94224e575bfb2588f9a6f19c0b73a38d6209d92a1dc644639a4927aa6b5
diff --git a/sci-biology/sim4/files/sim4-20030921-fix-build-system.patch b/sci-biology/sim4/files/sim4-20030921-fix-build-system.patch
deleted file mode 100644
index 8fd50fe9cfae..000000000000
--- a/sci-biology/sim4/files/sim4-20030921-fix-build-system.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-Fix build system to honour user flags.
-
---- a/Makefile
-+++ b/Makefile
-@@ -1,13 +1,11 @@
--
- # For better performance, replace ``-O'' with whatever
- # the best optimization flag is for your computer.
- # For Sun's compilers under Solaris, ``-fast'' works well.
- # For gcc, ``-O2'' works well.
--CC=cc
--CFLAGS=-O
--LDLIBS=-lm
-+CC ?= gcc
-+LDLIBS = -lm
-  
- sim4:
--	$(CC) -o sim4 -I. $(CFLAGS) *.c $(LDLIBS)
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o sim4 -I. *.c $(LDLIBS)
- clean:
- 	rm -f sim4 *.o
diff --git a/sci-biology/sim4/metadata.xml b/sci-biology/sim4/metadata.xml
deleted file mode 100644
index 1e40799f38d9..000000000000
--- a/sci-biology/sim4/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		sim4 is a similarity-based tool for aligning an expressed DNA sequence
-		(EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects
-		end matches when the two input sequences overlap at one end (i.e., the
-		start of one sequence overlaps the end of the other).sim4 employs a
-		blast-based technique to first determine the basic matching blocks
-		representing the "exon cores". In this first stage, it detects all
-		possible exact matches of W-mers (i.e., DNA words of size W) between
-		the two sequences and extends them to maximal scoring gap-free
-		segments. In the second stage, the exon cores are extended into the
-		adjacent as-yet-unmatched fragments using greedy alignment algorithms,
-		and heuristics are used to favor configurations that conform to the
-		splice-site recognition signals (GT-AG, CT-AC). If necessary, the
-		process is repeated with less stringent parameters on the unmatched
-		fragments.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/sim4/sim4-20030921-r2.ebuild b/sci-biology/sim4/sim4-20030921-r2.ebuild
deleted file mode 100644
index 64c0e64d19ef..000000000000
--- a/sci-biology/sim4/sim4-20030921-r2.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="A program to align cDNA and genomic DNA"
-HOMEPAGE="http://globin.cse.psu.edu/html/docs/sim4.html"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-S="${WORKDIR}/${PN}.2003-09-21"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-
-PATCHES=( "${FILESDIR}"/${PN}-20030921-fix-build-system.patch )
-
-src_configure() {
-	tc-export CC
-}
-
-src_install() {
-	dobin ${PN}
-	einstalldocs
-}
diff --git a/sci-biology/stride/Manifest b/sci-biology/stride/Manifest
deleted file mode 100644
index bfd0e48635ba..000000000000
--- a/sci-biology/stride/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST stride-20011129.tar.gz 56441 BLAKE2B 4d4cd3f9f6cef997fff10571aecb70cb21056e88c5130e7dfdafe15a6fb353656d0635b4d65895ef115479a87dcf600b659455d15460344c838543a2e356bfae SHA512 cbd40fce4684728f363520540132fc1a0003126954a145d59aeff48adb20fdaa66520bd12b56ee5d2906e8ea97bf78a225204105b820f7f368aee5e790a6471b
-DIST stride-20030408.tar.gz 318997 BLAKE2B 0a6fbb7da0a18cc9fbc4beb3214488080e5f6b85b93f87a33f3d6c38385da12707ee0eb2a10a86c9f6dd3884bd043e3f7f36c6aac797da7dc4f351fab047a950 SHA512 50d71c053118ca078dd9a4659d9b0f62d1f1101519e01b258a088e229ad2062bec917160c7794f18c96d982992d5571f93508365ff4f6e76438da8183390b498
-DIST stride-20060723-update-r1.patch.xz 5888 BLAKE2B 6f477787004fd962b2faf5f0dd1a497067608eb8fcc5d16e161d918ecff7a6b86184eeb5f97ece4465d7595dd64fd0958a6bcedb76f2b666bdc4d0947e51eda0 SHA512 5ecaa5c262856009e188c00a9cf75765fcd7988ebe3cf0389101a4c281fdbc8d085a024fa78b6c88916528d1158133873ebf38a070a66b7e76f842586646ba2d
-DIST stride-20060723-update.patch.bz2 5621 BLAKE2B 266a7371c0963a996430c1f809b46196e8bf179fcf2afb4380f6eccd092c03b29d5b09b8a8438ee7848d0f411920db2e4465ef646c75a406197412f35e880179 SHA512 e06eb68b907615e12dc1a9981be157400e9ffed9391a906cb4eb3ef4067b7027c26cc600298053bfc5d2bbbebbbfefe0e6b18d0e4f6fef2172768e6f95498af1
diff --git a/sci-biology/stride/files/stride-20011129-clang16.patch b/sci-biology/stride/files/stride-20011129-clang16.patch
deleted file mode 100644
index e1e4383a3281..000000000000
--- a/sci-biology/stride/files/stride-20011129-clang16.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-https://bugs.gentoo.org/874069
---- a/hydrbond.c
-+++ b/hydrbond.c
-@@ -293,3 +293,3 @@
-   int dc, ac, ccd, cca, cc, hc=0, i;
--  void (*HBOND_Energy)();
-+  void (*HBOND_Energy)(float*, float*, float*, float*, float*, COMMAND*, HBOND*);
-   BUFFER Text;
---- a/p_atom.c
-+++ b/p_atom.c
-@@ -11,3 +11,3 @@
-   RESIDUE *r;
--  register i;
-+  register int i;
- 
diff --git a/sci-biology/stride/files/stride-20011129-fix-buildsystem.patch b/sci-biology/stride/files/stride-20011129-fix-buildsystem.patch
deleted file mode 100644
index ec4415ec45d4..000000000000
--- a/sci-biology/stride/files/stride-20011129-fix-buildsystem.patch
+++ /dev/null
@@ -1,21 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -1,4 +1,3 @@
--CC = gcc -g
- FLAGS = -lm  -o
- 
- SOURCE = stride.c splitstr.c rdpdb.c initchn.c geometry.c thr2one.c one2thr.c filename.c tolostr.c strutil.c place_h.c hbenergy.c memory.c helix.c sheet.c rdmap.c phipsi.c command.c molscr.c die.c hydrbond.c mergepat.c fillasn.c escape.c p_jrnl.c p_rem.c p_atom.c p_helix.c p_sheet.c p_turn.c p_ssbond.c p_expdta.c p_model.c p_compnd.c report.c nsc.c area.c ssbond.c chk_res.c chk_atom.c turn.c pdbasn.c dssp.c outseq.c chkchain.c elem.c measure.c asngener.c p_endmdl.c stred.c contact_order.c contact_map.c
-@@ -7,12 +6,9 @@
- 
- BINDIR = .
- 
--.c.o: 
--	$(CC) -c $< -o $@
--
- 
- stride : $(OBJECT)
--	$(CC) $(OBJECT) $(FLAGS)  $(BINDIR)/stride
-+	$(CC) $(LDFLAGS) $(OBJECT) $(FLAGS) $(BINDIR)/stride
- 
- $(OBJECT) : stride.h protot.h
- 
diff --git a/sci-biology/stride/metadata.xml b/sci-biology/stride/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/stride/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/stride/stride-20011129-r1.ebuild b/sci-biology/stride/stride-20011129-r1.ebuild
deleted file mode 100644
index a2cda0fa34e3..000000000000
--- a/sci-biology/stride/stride-20011129-r1.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Protein secondary structure assignment from atomic coordinates"
-HOMEPAGE="http://webclu.bio.wzw.tum.de/stride/"
-SRC_URI="
-	ftp://ftp.ebi.ac.uk/pub/software/unix/${PN}/src/${PN}.tar.gz -> ${P}.tar.gz
-	https://dev.gentoo.org/~pacho/${PN}/${PN}-20060723-update.patch.bz2"
-
-LICENSE="STRIDE"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86"
-RESTRICT="mirror bindist"
-
-S="${WORKDIR}"
-PATCHES=(
-	# this patch updates the source to the most recent
-	# version which was kindly provided by the author
-	"${S}"/${PN}-20060723-update.patch
-	"${FILESDIR}"/${PN}-20011129-fix-buildsystem.patch
-	"${FILESDIR}"/${PN}-20011129-clang16.patch
-)
-
-src_configure() {
-	tc-export CC
-}
-
-src_install() {
-	dobin ${PN}
-}
diff --git a/sci-biology/stride/stride-20060723.ebuild b/sci-biology/stride/stride-20060723.ebuild
deleted file mode 100644
index 5938a8bfda5f..000000000000
--- a/sci-biology/stride/stride-20060723.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit toolchain-funcs
-
-DESCRIPTION="Protein secondary structure assignment from atomic coordinates"
-HOMEPAGE="http://webclu.bio.wzw.tum.de/stride/"
-# Version 20030408 per dates in upstream tarball
-UPSTREAM_VER="20030408"
-SRC_URI="https://webclu.bio.wzw.tum.de/stride/${PN}.tar.gz -> ${PN}-${UPSTREAM_VER}.tar.gz
-	https://dev.gentoo.org/~pacho/${PN}/${PN}-20060723-update-r1.patch.xz"
-
-LICENSE="STRIDE"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86"
-RESTRICT="mirror bindist"
-
-S="${WORKDIR}"
-PATCHES=(
-	# This patch updates the source to the most recent
-	# version which was kindly provided by the author
-	"${S}"/${P}-update-r1.patch
-
-	"${FILESDIR}"/${PN}-20011129-fix-buildsystem.patch
-	"${FILESDIR}"/${PN}-20011129-clang16.patch
-)
-
-src_configure() {
-	tc-export CC
-}
-
-src_install() {
-	dobin ${PN}
-}
diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest
deleted file mode 100644
index 447e11259498..000000000000
--- a/sci-biology/t-coffee/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST T-COFFEE_distribution_Version_11.00.4466924.tar.gz 3502302 BLAKE2B 0d8087eb219ff72e6f478a779ccdb51e7aee861236c522dec5391e854b0b0bf6eab324009686237e6d334d2e13e17700f6692333060a2ed55711380ef2ab2cdb SHA512 c6c1a7b768156f8457dc4c53a77b14ce0b85e591d60762faf6e6f6f3b60dab75e99449d55b42ef3af1c90e244f735e19abb72d0ce871bb9fbfbb8d1641531293
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-cxx11.patch b/sci-biology/t-coffee/files/t-coffee-11.00-cxx11.patch
deleted file mode 100644
index 17817d30eca2..000000000000
--- a/sci-biology/t-coffee/files/t-coffee-11.00-cxx11.patch
+++ /dev/null
@@ -1,21 +0,0 @@
---- a/t_coffee_source/programmes_define.h
-+++ b/t_coffee_source/programmes_define.h
-@@ -390,12 +390,12 @@
- #define XMLSIMPLE_language2 "Perl"
- #define XMLSIMPLE_source "empty"
- #define XMLSIMPLE_mode "psicoffee,expresso,accurate"
--#define x3dna-ssr_4_TCOFFEE "x3dna"
--#define x3dna-ssr_type "RNA_secondarystructure_predictor"
--#define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/"
--#define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz"
--#define x3dna-ssr_mode "saracoffee"
--#define x3dna-ssr_update_action "never"
-+#define x3dna_ssr_4_TCOFFEE "x3dna"
-+#define x3dna_ssr_type "RNA_secondarystructure_predictor"
-+#define x3dna_ssr_ADDRESS "http://x3dna.bio.columbia.edu/"
-+#define x3dna_ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz"
-+#define x3dna_ssr_mode "saracoffee"
-+#define x3dna_ssr_update_action "never"
- //TclinkdbEnd
- /*New Methods*/
- /********************************************/
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-gcc7.patch b/sci-biology/t-coffee/files/t-coffee-11.00-gcc7.patch
deleted file mode 100644
index 64afc04a4b50..000000000000
--- a/sci-biology/t-coffee/files/t-coffee-11.00-gcc7.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- a/t_coffee_source/util_lib/aln_convertion_util.c
-+++ b/t_coffee_source/util_lib/aln_convertion_util.c
-@@ -5592,7 +5592,7 @@
- 
- 	     list=string2list (H->seq_comment[n]);
- 	     if ( list==NULL || atoi(list[0])==1)continue;
--	     S->seq_comment[a]='\0';
-+	     S->seq_comment[a]=NULL;
- 	     sprintf (S->name[a], "%s%s%s",H->name[n], list[1], list[2]);
- 	     vfree ( S->seq_comment[a]);S->seq_comment[a]=(char*)vcalloc ( strlen (H->seq_comment[n])+1, sizeof (char));
- 	     for (b=3; b< atoi(list[0]); b++)S->seq_comment[a]=strcat (S->seq_comment[a], list[b]);
---- a/t_coffee_source/util_lib/util.c
-+++ b/t_coffee_source/util_lib/util.c
-@@ -5946,7 +5946,7 @@
- 		  val_array[a]=(char*)vrealloc (val_array[a], strlen (v)+1);
- 		  sprintf (val_array[a],"%s",v);
- 		}
--	      else val_array[a]='\0';
-+	      else val_array[a]=NULL;
- 	      return v;
- 	    }
- 	}
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch b/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch
deleted file mode 100644
index b7a6d9e17a5e..000000000000
--- a/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- a/t_coffee_source/makefile
-+++ b/t_coffee_source/makefile
-@@ -1,14 +1,12 @@
--CC=g++
--CFLAGS=-O3 -Wno-write-strings
- SOURCES := $(shell find . -type f -name *.c)
- OBJECTS := $(SOURCES:.c=.o)
- DEPS := $(OBJECTS:.o=.deps)
-  
- t_coffee: $(OBJECTS)
--	@echo " Linking..."; $(CC) $^ -o t_coffee -lm
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) $^ -o t_coffee -lm $(LIBS)
-  
- %.o: %.c
--	@echo " CC $<"; $(CC) $(CFLAGS) -I. -MD -MF $(@:.o=.deps) -c -o $@ $<
-+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -I. -MD -MF $(@:.o=.deps) -c -o $@ $<
-  
- -include $(DEPS)
-  
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch b/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch
deleted file mode 100644
index cbfeeabc181b..000000000000
--- a/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Mon, 21 Dec 2015 21:30:36 +0100
-Bug-Debian: https://bugs.debian.org/716373
-Description: Fix Mayhem issue
- The idea behind this patch is that if there is a problem to set the HOME
- directories no additional processes can exist and so we should *really*
- exit.  Somehow the printf_exit() function does some logic which ends up
- in an endless loop and thus forcing the exit will help here.
- .
- Unfortunately this does not solve the issue completely since inside the
- Exit call a "Segmentation fault" happens - so some broken pointer handling
- seems to happen somewhere before.
-
---- a/t_coffee_source/util_lib/util.c
-+++ b/t_coffee_source/util_lib/util.c
-@@ -4642,7 +4642,8 @@ char *get_home_4_tcoffee ()
-     }
-   else
-     {
--      printf_exit (EXIT_FAILURE, stderr, "ERROR: Could not set a HOME directory.\nSet any of the following environement variables to some suitable location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:%s]\n", PROGRAM);
-+      fprintf(stderr, "ERROR: Could not set a HOME directory.\nSet any of the following environement variables to some suitable location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:%s]\n", PROGRAM);
-+      exit(EXIT_FAILURE);
-     }
- 
- 
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch b/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch
deleted file mode 100644
index a3f47cd9fce2..000000000000
--- a/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Mon, 21 Dec 2015 21:30:36 +0100
-Bug-Debian: https://bugs.debian.org/751579
-Description: When creating subdirectories in $HOME do not
- make these world writable but keep users umask
-
---- a/t_coffee_source/util_lib/util.c
-+++ b/t_coffee_source/util_lib/util.c
-@@ -7714,6 +7714,10 @@ int my_mkdir ( char *dir_in)
-   int a, buf;
-   char *dir;
- 
-+  static char *home = getenv ("HOME");
-+  static mode_t oldmask = umask(0);
-+  int change_umask = 0;
-+  if (strncmp (dir_in, home, strlen(home))==0) change_umask = 1;
- 
-   dir=(char*)vcalloc ( strlen (dir_in)+strlen (get_home_4_tcoffee())+100, sizeof (char));
-   sprintf ( dir, "%s", dir_in);
-@@ -7733,10 +7737,11 @@ int my_mkdir ( char *dir_in)
- 
- 	  if (access(dir, F_OK)==-1)
- 	    {
--		  mode_t oldmask = umask(0);
--	      mkdir (dir, S_IRWXU | S_IRWXG | S_IRWXO);
--	      umask(oldmask);
--
-+	      if ( change_umask == 1 ) mkdir (dir, 0777-oldmask);
-+	      else {
-+	        mkdir (dir, S_IRWXU | S_IRWXG | S_IRWXO);
-+	        umask(oldmask);
-+	      }
- 	      if ( access (dir, F_OK)==-1)
- 		{
- 		  myexit(fprintf_error ( stderr, "\nERROR: Could Not Create Directory %s [FATAL:%s]", dir, PROGRAM));	}
diff --git a/sci-biology/t-coffee/metadata.xml b/sci-biology/t-coffee/metadata.xml
deleted file mode 100644
index bc6621eb034f..000000000000
--- a/sci-biology/t-coffee/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		T-Coffee is a multiple sequence alignment package. Given a set of
-		sequences (Proteins or DNA), T-Coffee generates a multiple sequence
-		alignment. Version 2.00 and higher can mix sequences and structures.
-		T-Coffee allows the combination of a collection of multiple/pairwise,
-		global or local alignments into a single model. It also allows to
-		estimate the level of consistency of each position within the new
-		alignment with the rest of the alignments.
-	</longdescription>
-	<upstream>
-		<remote-id type="github">cbcrg/tcoffee</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/t-coffee/t-coffee-11.00-r3.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r3.ebuild
deleted file mode 100644
index 94ed806184d3..000000000000
--- a/sci-biology/t-coffee/t-coffee-11.00-r3.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit flag-o-matic toolchain-funcs
-
-MY_HASH="4466924"
-MY_PV="${PV}.${MY_HASH}"
-MY_P="${PN^^}_distribution_Version_${MY_PV}"
-
-DESCRIPTION="A multiple sequence alignment package"
-HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
-SRC_URI="http://www.tcoffee.org/Packages/Beta/Latest/${MY_P}.tar.gz"
-S="${WORKDIR}/${MY_P}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
-
-RDEPEND="
-	sci-biology/clustalw
-	sci-chemistry/tm-align"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-mayhem.patch
-	"${FILESDIR}"/${P}-set_proper_dir_permissions.patch
-	"${FILESDIR}"/${P}-cxx11.patch
-	"${FILESDIR}"/${P}-gcc7.patch
-	"${FILESDIR}"/${P}-makefile.patch
-)
-
-src_configure() {
-	# -Werror=strict-aliasing
-	# https://bugs.gentoo.org/862327
-	# https://github.com/cbcrg/tcoffee/issues/60
-	#
-	# Do not trust with LTO either
-	append-flags -fno-strict-aliasing
-	filter-lto
-
-	tc-export CXX
-	append-cxxflags -Wno-write-strings -Wno-unused-result
-}
-
-src_compile() {
-	emake -C t_coffee_source t_coffee
-}
-
-src_install() {
-	dobin t_coffee_source/t_coffee
-
-	insinto /usr/share/t-coffee
-	doins -r example
-}
diff --git a/sci-biology/tree-puzzle/Manifest b/sci-biology/tree-puzzle/Manifest
deleted file mode 100644
index f64cd3fa4adf..000000000000
--- a/sci-biology/tree-puzzle/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST tree-puzzle-5.2.tar.gz 875142 BLAKE2B aa13e9a7aa403c12aebefb94a1931baa8b17cbee56d20011cb06db5a7b1b7f78c719ed6c6bfb0b79e47dc652d7b984415694907fc6cd56bdbe9eebca4aaa96a8 SHA512 5b9a729b120cba59f59ba426acd439cf396826ea01e75361b23387ccb9baf295d2512f21af96071a5f7b7507db4ff4d6b135cf6c5b6233a8b438532d31abe751
diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-5.2-C99-decls.patch b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-C99-decls.patch
deleted file mode 100644
index 98456c0dacc1..000000000000
--- a/sci-biology/tree-puzzle/files/tree-puzzle-5.2-C99-decls.patch
+++ /dev/null
@@ -1,360 +0,0 @@
---- a/src/consensus.c
-+++ b/src/consensus.c
-@@ -32,7 +32,7 @@
- /******************************************************************************/
- 
- /* prepare for consensus tree analysis */
--void initconsensus()
-+void initconsensus(void)
- {
- #	if ! PARALLEL
- 		biparts = new_cmatrix(Maxspc-3, Maxspc);
---- a/src/consensus.h
-+++ b/src/consensus.h
-@@ -65,7 +65,7 @@
- /******************************************************************************/
- 
- /* prepare for consensus tree analysis */
--void initconsensus();
-+void initconsensus(void);
- 
- /* recursive function to get bipartitions */
- /* traversal should be optimazable (HAS) */
---- a/src/ml1.c
-+++ b/src/ml1.c
-@@ -244,7 +244,7 @@
- /***************************** exported functions *****************************/
- 
- 
--void evaluateseqs()
-+void evaluateseqs(void)
- {	
- 	ivector ali;
- 
-@@ -1018,7 +1018,7 @@
- 
- 
- /* compute 1 PAM rate matrix, its eigensystem, and the inverse matrix thereof */
--void tranprobmat()
-+void tranprobmat(void)
- {
- 	eigensystem(Eval, Evec); /* eigensystem of 1 PAM rate matrix */
- 	luinverse(Evec, Ievc, tpmradix); /* inverse eigenvectors are in Ievc */
-@@ -1324,7 +1324,7 @@
- 
- 
- /* initialize distance matrix */
--void initdistan()
-+void initdistan(void)
- {
- 	int i, j, k, diff, x, y;
- 	double obs, temp;
-@@ -1478,7 +1478,7 @@
- 
- #else /* not PARALLEL */
- 
--void computedistan()
-+void computedistan(void)
- {
- 	int i, j;
- 
---- a/src/ml2.c
-+++ b/src/ml2.c
-@@ -1036,7 +1036,7 @@
- 
- 
- /* preparation for ML analysis */
--void mlstart()
-+void mlstart(void)
- {
- 	/* number of states and code length */
- 	tpmradix = gettpmradix();
-@@ -1098,7 +1098,7 @@
- 
- 
- /* cleanup after ML analysis */
--void mlfinish()
-+void mlfinish(void)
- {
- 	if (Ctree != NULL)
- 		free_tree(Ctree, Numspc);
-@@ -1566,7 +1566,7 @@
-                              int bestratefound,
-                              int ncats)    /* numcats */
- #endif
--void findbestratecombination()
-+void findbestratecombination(void)
- {
- 	int k, u;
- 	double bestvalue, fv2;
-@@ -2147,7 +2147,7 @@
- } /* clock_lklhd */
- 
- /* find out the edge containing the root */
--int findrootedge()
-+int findrootedge(void)
- {
- 	int e, ebest;
- 	double logbest, logtest;
---- a/src/mlparam.c
-+++ b/src/mlparam.c
-@@ -70,7 +70,7 @@
- }
- 
- /* compute rates of each category when rates are Gamma-distributed */
--void updaterates()
-+void updaterates(void)
- {
- 	int i;
- 	double alpha;
-@@ -190,7 +190,7 @@
- }
- 
- /* estimate substitution process parameters - random quartets */
--void optimseqevolparamsquart()
-+void optimseqevolparamsquart(void)
- {
- 	double tsmeanold, yrmeanold;
- 	dvector tslist, yrlist;
-@@ -320,7 +320,7 @@
- 
- 
- /* optimize substitution process parameters - tree */
--void optimseqevolparamstree()
-+void optimseqevolparamstree(void)
- {
- 	twodimenmin(EPSILON_SUBSTPARAM,
- 		(SH_optn || nuc_optn) && optim_optn && (data_optn == 0),
-@@ -379,7 +379,7 @@
- 
- 
- /* optimize rate heterogeneity parameters */
--void optimrateparams()
-+void optimrateparams(void)
- {	
- 	twodimenmin(EPSILON_RATEPARAM,
- 		fracinv_optim,
-@@ -396,7 +396,7 @@
- 
- /* estimate parameters of substitution process and rate heterogeneity - no tree
-    n-taxon tree is not needed because of quartet method or NJ tree topology */
--void estimateparametersnotree()
-+void estimateparametersnotree(void)
- {
- 	int it, nump, change;
- 	double TSold, YRold, FIold, GEold;
-@@ -495,7 +495,7 @@
- 
- /* estimate parameters of substitution process and rate heterogeneity - tree
-    same as above but here the n-taxon tree is already in memory */
--void estimateparameterstree()
-+void estimateparameterstree(void)
- {
- 	int it, nump, change;
- 	double TSold, YRold, FIold, GEold;
---- a/src/model1.c
-+++ b/src/model1.c
-@@ -31,7 +31,7 @@
- #include "ml.h"
- 
- /* number of states of the selected model */ 
--int gettpmradix()
-+int gettpmradix(void)
- {
- 	if (data_optn == 0) { /* nucleotides */
- 		if (nuc_optn) return 4;
---- a/src/puzzle1.c
-+++ b/src/puzzle1.c
-@@ -345,7 +345,7 @@
- /******************************************************************************/
- 
- /* compute TN parameters according to F84 Ts/Tv ratio */
--void makeF84model()
-+void makeF84model(void)
- {
- 	double rho, piA, piC, piG, piT, piR, piY, ts, yr;
- 	
-@@ -390,7 +390,7 @@
- } /* makeF84model */
- 
- /* compute number of quartets used in LM analysis */
--void compnumqts()
-+void compnumqts(void)
- {
- 	if (lmqts == 0) {
- 		if (numclust == 4)
-@@ -407,7 +407,7 @@
- } /* compnumqts */
- 
- /* set options interactively */
--void setoptions()
-+void setoptions(void)
- {	
- 	int i, valid;
- 	double sumfreq;
-@@ -1718,7 +1718,7 @@
- } /* closefile */
- 
- /* symmetrize doublet frequencies */
--void symdoublets()
-+void symdoublets(void)
- {
- 	int i, imean;
- 	double mean;
-@@ -1769,7 +1769,7 @@
- } /* symdoublets */
- 
- /* show Ts/Tv ratio and Ts Y/R ratio */
--void computeexpectations()
-+void computeexpectations(void)
- {
- 	double AlphaYBeta, AlphaRBeta, piR, piY, num, denom, pyr, pur;
- 	
-@@ -4604,7 +4604,7 @@
- /* Reconstruct a tree with QP */
- /* (parameter estimation already done) */
- 
--void recon_tree()
-+void recon_tree(void)
- {
- 	int i;
- 	unsigned char tmpweight;
-@@ -4848,7 +4848,7 @@
- 
- /***************************************************************/ 
- 
--void map_lklhd()
-+void map_lklhd(void)
- {	
- 	int i, a, a1, a2, b, b1, b2, c, c1, c2, d;
- 	uli nq;
-@@ -5101,7 +5101,7 @@
- 
- /***************************************************************/ 
- 
--void setdefaults() {
-+void setdefaults(void) {
- 
-   strcpy(INFILE,     INFILEDEFAULT);
-   strcpy(OUTFILE,    OUTFILEDEFAULT);
-@@ -6027,7 +6027,7 @@
- 
- /***************************************************************/ 
- 
--void memcleanup() { 
-+void memcleanup(void) { 
- 	if (puzzlemode == QUARTPUZ && typ_optn == TREERECON_OPTN) {
- 		free(splitfreqs);
- 		free(splitpatterns);
---- a/src/puzzle2.c
-+++ b/src/puzzle2.c
-@@ -860,7 +860,7 @@
- 
- 
- /* estimate mean base frequencies from translated data set */
--void estimatebasefreqs()
-+void estimatebasefreqs(void)
- {
- 	int tpmradix, i, j;
- 	uli all, *gene;
-@@ -903,7 +903,7 @@
- 
- 
- /* guess model of substitution */
--void guessmodel()
-+void guessmodel(void)
- {
- 	double c1, c2, c3, c4, c5, c6;
- 	dvector f;
-@@ -1160,7 +1160,7 @@
- } /* callocquartets */
- 
- /* free quartet memory */
--void freequartets()
-+void freequartets(void)
- {	
- 	free(quartetinfo);
- } /* freequartets */
-@@ -1357,7 +1357,7 @@
- /*************************/
- 
- /* checks out all possible quartets */
--void computeallquartets()
-+void computeallquartets(void)
- {	
- 	double onethird;
- 	uli nq;
---- a/src/sprng/makeseed.c
-+++ b/src/sprng/makeseed.c
-@@ -1,10 +1,6 @@
- #include <time.h>
- 
--#ifdef __STDC__
--int make_new_seed()
--#else
--int make_new_seed()
--#endif
-+int make_new_seed(void)
- {
-   time_t tp;
-   struct tm *temp;
---- a/src/sprng/primes-lcg64.c
-+++ b/src/sprng/primes-lcg64.c
-@@ -1,5 +1,6 @@
- #include <stdio.h>
- #include <stdlib.h>
-+#include <string.h>
- #include "primes-lcg64.h"
- #include "primelist-lcg64.h"
- 
---- a/src/treesort.c
-+++ b/src/treesort.c
-@@ -487,7 +487,7 @@
- /**********/
- 
- /* malloc new tree list item */
--treelistitemtype *gettreelistitem()
-+treelistitemtype *gettreelistitem(void)
- {
- 	treelistitemtype *tmpptr;
- 	tmpptr = (treelistitemtype *)calloc((size_t) 1, sizeof(treelistitemtype));
---- a/src/treesort.h
-+++ b/src/treesort.h
-@@ -84,7 +84,7 @@
- /**********/
- 
- /* allocate memory for ctree 3 ints pointer plus 1 check byte */
--int *initctree();
-+int *initctree(void);
- 
- /**********/
- 
-@@ -174,7 +174,7 @@
- /**********/
- 
- /* malloc new tree list item */
--treelistitemtype *gettreelistitem();
-+treelistitemtype *gettreelistitem(void);
- 
- /**********/
- 
---- a/src/util.c
-+++ b/src/util.c
-@@ -507,7 +507,7 @@
- #define EPS 1.2e-7
- #define RNMX (1.0-EPS)
- 
--double randomunitintervall()
-+double randomunitintervall(void)
- /* Long period (> 2e18) random number generator. Returns a uniform random
-    deviate between 0.0 and 1.0 (exclusive of endpoint values).
- 
-@@ -734,7 +734,7 @@
- /* Reads characters from stdin until a newline character or EOF
-    is received.  The newline is not made part of the string.
-    If an error occurs a null string \0 is returned */
--cvector mygets()
-+cvector mygets(void)
- {
- 	int c, n;
- 	cvector str;
diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch
deleted file mode 100644
index 66e3e6482338..000000000000
--- a/sci-biology/tree-puzzle/files/tree-puzzle-5.2-MPI-3.0.patch
+++ /dev/null
@@ -1,362 +0,0 @@
-https://bugs.gentoo.org/690900
-rename MPI 1.0 to 3.0+ functions:
-- MPI_Address -> MPI_Get_address
-- MPI_Type_struct -> MPI_Type_create_struct
-
---- a/src/ppuzzle.c
-+++ b/src/ppuzzle.c
-@@ -297,13 +297,13 @@
- 	else	MPI_Recv(&dummy, 0, MPI_INT, PP_MyMaster, PP_UPDATEEEI, PP_Comm, &stat);
- 
- 	Dtypes[0] = MPI_DOUBLE; Dtypelens[0] = tpmradix;
--	MPI_Address(&(Eval[0]), &(Dtypeaddr[0]));
-+	MPI_Get_address(&(Eval[0]), &(Dtypeaddr[0]));
- 	Dtypes[1] = MPI_DOUBLE; Dtypelens[1] = tpmradix * tpmradix;
--	MPI_Address(&(Evec[0][0]), &(Dtypeaddr[1]));
-+	MPI_Get_address(&(Evec[0][0]), &(Dtypeaddr[1]));
- 	Dtypes[2] = MPI_DOUBLE; Dtypelens[2] = tpmradix * tpmradix;
--	MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[2]));
-+	MPI_Get_address(&(Ievc[0][0]), &(Dtypeaddr[2]));
- 
--	MPI_Type_struct(3, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
-+	MPI_Type_create_struct(3, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
- 	MPI_Type_commit(&PP_Data);
- 
- 	MPI_Bcast (MPI_BOTTOM, 1, PP_Data, PP_MyMaster, PP_Comm);
-@@ -341,19 +341,19 @@
- 	double*      DMVector = new_dvector(jobs);
- 
- 	Dtypes[0] = MPI_DOUBLE; Dtypelens[0] = jobs;
--	MPI_Address(&(DMVector[0]), &(Dtypeaddr[0]));
-+	MPI_Get_address(&(DMVector[0]), &(Dtypeaddr[0]));
- 	Dtypes[1] = MPI_DOUBLE; Dtypelens[1] = numcats;
--	MPI_Address(&(Rates[0]), &(Dtypeaddr[1]));
-+	MPI_Get_address(&(Rates[0]), &(Dtypeaddr[1]));
- 	Dtypes[2] = MPI_DOUBLE; Dtypelens[2] = 1;
--	MPI_Address(&(fracinv), &(Dtypeaddr[2]));
-+	MPI_Get_address(&(fracinv), &(Dtypeaddr[2]));
- 	Dtypes[3] = MPI_DOUBLE; Dtypelens[3] = tpmradix;
--	MPI_Address(&(Eval[0]), &(Dtypeaddr[3]));
-+	MPI_Get_address(&(Eval[0]), &(Dtypeaddr[3]));
- 	Dtypes[4] = MPI_DOUBLE; Dtypelens[4] = tpmradix * tpmradix;
--	MPI_Address(&(Evec[0][0]), &(Dtypeaddr[4]));
-+	MPI_Get_address(&(Evec[0][0]), &(Dtypeaddr[4]));
- 	Dtypes[5] = MPI_DOUBLE; Dtypelens[5] = tpmradix * tpmradix;
--	MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[5]));
-+	MPI_Get_address(&(Ievc[0][0]), &(Dtypeaddr[5]));
- 
--	MPI_Type_struct(6, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
-+	MPI_Type_create_struct(6, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
- 	MPI_Type_commit(&PP_Data);
- 
- 	if (PP_IamMaster) {
-@@ -719,10 +719,10 @@
- #endif
-   doubles[0] = frconst;
- 
--  MPI_Address(ints,     Dtypeaddr);
--  MPI_Address(doubles, (Dtypeaddr+1));
-+  MPI_Get_address(ints,     Dtypeaddr);
-+  MPI_Get_address(doubles, (Dtypeaddr+1));
-   
--  MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes);
-+  MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes);
-   MPI_Type_commit(&PP_Sizes);
- 
-   for (dest=1; dest<PP_NumProcs; dest++) {
-@@ -797,10 +797,10 @@
-     fprintf(STDOUT, "(%2d) Receiving Sizes ...\n", PP_Myid);
- # endif /* PVERBOSE3 */
- 
--  MPI_Address(ints,     Dtypeaddr);
--  MPI_Address(doubles, (Dtypeaddr+1));
-+  MPI_Get_address(ints,     Dtypeaddr);
-+  MPI_Get_address(doubles, (Dtypeaddr+1));
- 
--  MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes);
-+  MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes);
-   MPI_Type_commit(&PP_Sizes);
-  
-   error = MPI_Probe(PP_MyMaster, MPI_ANY_TAG, PP_Comm, &stat);
-@@ -889,31 +889,31 @@
- # endif /* PVERBOSE2 */
- 
-   Dtypes  [0] = MPI_CHAR; Dtypelens [0] = Maxspc * Numptrn;
--  MPI_Address(&(Seqpat[0][0]), &(Dtypeaddr[0]));
-+  MPI_Get_address(&(Seqpat[0][0]), &(Dtypeaddr[0]));
-   Dtypes  [1] = MPI_INT; Dtypelens  [1] = Maxsite ;
--  MPI_Address(&(Alias[0]), &(Dtypeaddr[1]));
-+  MPI_Get_address(&(Alias[0]), &(Dtypeaddr[1]));
-   Dtypes  [2] = MPI_INT; Dtypelens  [2] = Numptrn ;
--  MPI_Address(&(Weight[0]), &(Dtypeaddr[2]));
-+  MPI_Get_address(&(Weight[0]), &(Dtypeaddr[2]));
-   Dtypes  [3] = MPI_INT; Dtypelens  [3] = Numptrn ;
--  MPI_Address(&(constpat[0]), &(Dtypeaddr[3]));
-+  MPI_Get_address(&(constpat[0]), &(Dtypeaddr[3]));
-   Dtypes  [4] = MPI_DOUBLE; Dtypelens  [4] = numcats ;
--  MPI_Address(&(Rates[0]), &(Dtypeaddr[4]));
-+  MPI_Get_address(&(Rates[0]), &(Dtypeaddr[4]));
-   Dtypes  [5] = MPI_DOUBLE; Dtypelens  [5] = tpmradix ;
--  MPI_Address(&(Eval[0]), &(Dtypeaddr[5]));
-+  MPI_Get_address(&(Eval[0]), &(Dtypeaddr[5]));
-   Dtypes  [6] = MPI_DOUBLE; Dtypelens  [6] = tpmradix ;
--  MPI_Address(&(Freqtpm[0]), &(Dtypeaddr[6]));
-+  MPI_Get_address(&(Freqtpm[0]), &(Dtypeaddr[6]));
-   Dtypes  [7] = MPI_DOUBLE; Dtypelens  [7] = tpmradix * tpmradix ;
--  MPI_Address(&(Evec[0][0]), &(Dtypeaddr[7]));
-+  MPI_Get_address(&(Evec[0][0]), &(Dtypeaddr[7]));
-   Dtypes  [8] = MPI_DOUBLE; Dtypelens  [8] = tpmradix * tpmradix ;
--  MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[8]));
-+  MPI_Get_address(&(Ievc[0][0]), &(Dtypeaddr[8]));
-   Dtypes  [9] = MPI_DOUBLE; Dtypelens [9] = tpmradix * tpmradix ;
--  MPI_Address(&(iexp[0][0]), &(Dtypeaddr[9]));
-+  MPI_Get_address(&(iexp[0][0]), &(Dtypeaddr[9]));
-   Dtypes [10] = MPI_DOUBLE; Dtypelens [10] = Maxspc * Maxspc ;
--  MPI_Address(&(Distanmat[0][0]), &(Dtypeaddr[10]));
-+  MPI_Get_address(&(Distanmat[0][0]), &(Dtypeaddr[10]));
-   Dtypes [11] = MPI_DOUBLE; Dtypelens [11] = numcats * tpmradix * tpmradix ;
--  MPI_Address(&(ltprobr[0][0][0]), &(Dtypeaddr[11]));
-+  MPI_Get_address(&(ltprobr[0][0][0]), &(Dtypeaddr[11]));
-  
--  MPI_Type_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
-+  MPI_Type_create_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
-   MPI_Type_commit(&PP_Data);
-  
- 
-@@ -984,31 +984,31 @@
- # endif /* PVERBOSE2 */
-  
-   Dtypes  [0] = MPI_CHAR; Dtypelens [0] = Maxspc * Numptrn;
--  MPI_Address(&(Seqpat[0][0]), &(Dtypeaddr[0]));
-+  MPI_Get_address(&(Seqpat[0][0]), &(Dtypeaddr[0]));
-   Dtypes  [1] = MPI_INT; Dtypelens  [1] = Maxsite ;
--  MPI_Address(&(Alias[0]), &(Dtypeaddr[1]));
-+  MPI_Get_address(&(Alias[0]), &(Dtypeaddr[1]));
-   Dtypes  [2] = MPI_INT; Dtypelens  [2] = Numptrn ;
--  MPI_Address(&(Weight[0]), &(Dtypeaddr[2]));
-+  MPI_Get_address(&(Weight[0]), &(Dtypeaddr[2]));
-   Dtypes  [3] = MPI_INT; Dtypelens  [3] = Numptrn ;
--  MPI_Address(&(constpat[0]), &(Dtypeaddr[3]));
-+  MPI_Get_address(&(constpat[0]), &(Dtypeaddr[3]));
-   Dtypes  [4] = MPI_DOUBLE; Dtypelens  [4] = numcats ;
--  MPI_Address(&(Rates[0]), &(Dtypeaddr[4]));
-+  MPI_Get_address(&(Rates[0]), &(Dtypeaddr[4]));
-   Dtypes  [5] = MPI_DOUBLE; Dtypelens  [5] = tpmradix ;
--  MPI_Address(&(Eval[0]), &(Dtypeaddr[5]));
-+  MPI_Get_address(&(Eval[0]), &(Dtypeaddr[5]));
-   Dtypes  [6] = MPI_DOUBLE; Dtypelens  [6] = tpmradix ;
--  MPI_Address(&(Freqtpm[0]), &(Dtypeaddr[6]));
-+  MPI_Get_address(&(Freqtpm[0]), &(Dtypeaddr[6]));
-   Dtypes  [7] = MPI_DOUBLE; Dtypelens  [7] = tpmradix * tpmradix ;
--  MPI_Address(&(Evec[0][0]), &(Dtypeaddr[7]));
-+  MPI_Get_address(&(Evec[0][0]), &(Dtypeaddr[7]));
-   Dtypes  [8] = MPI_DOUBLE; Dtypelens  [8] = tpmradix * tpmradix ;
--  MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[8]));
-+  MPI_Get_address(&(Ievc[0][0]), &(Dtypeaddr[8]));
-   Dtypes  [9] = MPI_DOUBLE; Dtypelens  [9] = tpmradix * tpmradix ;
--  MPI_Address(&(iexp[0][0]), &(Dtypeaddr [9]));
-+  MPI_Get_address(&(iexp[0][0]), &(Dtypeaddr [9]));
-   Dtypes [10] = MPI_DOUBLE; Dtypelens [10] = Maxspc * Maxspc ;
--  MPI_Address(&(Distanmat[0][0]), &(Dtypeaddr[10]));
-+  MPI_Get_address(&(Distanmat[0][0]), &(Dtypeaddr[10]));
-   Dtypes [11] = MPI_DOUBLE; Dtypelens [11] = numcats * tpmradix * tpmradix ;
--  MPI_Address(&(ltprobr[0][0][0]), &(Dtypeaddr[11]));
-+  MPI_Get_address(&(ltprobr[0][0][0]), &(Dtypeaddr[11]));
-  
--  MPI_Type_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
-+  MPI_Type_create_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data);
-   MPI_Type_commit(&PP_Data);
-  
-   for (dest=1; dest<PP_NumProcs; dest++) {
-@@ -1150,10 +1150,10 @@
-   ints[4] = usebestq;
-   ints[5] = approx;
-  
--  MPI_Address(ints,     Dtypeaddr);
--  MPI_Address(doubles, (Dtypeaddr+1));
-+  MPI_Get_address(ints,     Dtypeaddr);
-+  MPI_Get_address(doubles, (Dtypeaddr+1));
-   
--  MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart);
-+  MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart);
-   MPI_Type_commit(&PP_Quart);
-  
- # ifdef PVERBOSE2
-@@ -1201,10 +1201,10 @@
-  
-   PP_quartrecved++;
-   PP_quartrecvedn++;
--  MPI_Address(ints,     Dtypeaddr);
--  MPI_Address(doubles, (Dtypeaddr+1));
-+  MPI_Get_address(ints,     Dtypeaddr);
-+  MPI_Get_address(doubles, (Dtypeaddr+1));
-   
--  MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart);
-+  MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart);
-   MPI_Type_commit(&PP_Quart);
-  
-   error = MPI_Recv(MPI_BOTTOM, 1, PP_Quart, MPI_ANY_SOURCE, PP_QUART, PP_Comm, &stat);
-@@ -1368,10 +1368,10 @@
-   ulis[5] = fullresqs; /* number of fully resolved quartets */
-   ulis[6] = missingqs; /* number of missing quartets */
- 
--  MPI_Address(ulis,  Dtypeaddr);
--  MPI_Address(ints, (Dtypeaddr+1));
-+  MPI_Get_address(ulis,  Dtypeaddr);
-+  MPI_Get_address(ints, (Dtypeaddr+1));
-   
--  MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs);
-+  MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs);
-   MPI_Type_commit(&PP_QBlockSpecs);
-  
- # ifdef PVERBOSE2
-@@ -1384,12 +1384,12 @@
-     fprintf(STDOUT, "(%2d) ... Sent QuartBlockSpecs (%ld, %ld, %ld, %d)\n", PP_Myid, ulis[0], ulis[1], ulis[2], ints[0]);
- # endif /* PVERBOSE3 */
- 
--  MPI_Address(trueaddr, DtypeaddrRes);
-+  MPI_Get_address(trueaddr, DtypeaddrRes);
-   DtypelensRes[0] = truenum;
- 
--  MPI_Address(bq, (DtypeaddrRes + 1));
-+  MPI_Get_address(bq, (DtypeaddrRes + 1));
-   DtypelensRes[1] = numofbq;
--  MPI_Type_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes);
-+  MPI_Type_create_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes);
-   MPI_Type_commit(&PP_QBlockRes);
- 
-   error = MPI_Ssend(MPI_BOTTOM, 1, PP_QBlockRes, PP_MyMaster, PP_QUARTBLOCK, PP_Comm);
-@@ -1455,10 +1455,10 @@
- #	ifdef PVERBOSE3
- 	    fprintf(STDOUT, "(%2d) Receiving QuartBlock ...\n", PP_Myid);
- #	endif /* PVERBOSE3 */
--	MPI_Address(ulis,  Dtypeaddr);
--	MPI_Address(ints, (Dtypeaddr+1));
-+	MPI_Get_address(ulis,  Dtypeaddr);
-+	MPI_Get_address(ints, (Dtypeaddr+1));
-  
--	MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs);
-+	MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs);
- 	MPI_Type_commit(&PP_QBlockSpecs);
-  
- 	MPI_Probe(MPI_ANY_SOURCE, PP_QUARTBLOCKSPECS, PP_Comm, &stat);
-@@ -1486,13 +1486,13 @@
- #       endif /* PVERBOSE3 */
- 
- 	DtypelensRes[0] =  truenum;
--	MPI_Address(trueaddr,  DtypeaddrRes);
-+	MPI_Get_address(trueaddr,  DtypeaddrRes);
- 
- 	bq = calloc((size_t) *numofbq, sizeof(uli));
- 
- 	DtypelensRes[1] = *numofbq;
--	MPI_Address(bq, (DtypeaddrRes+1));
--	MPI_Type_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes);
-+	MPI_Get_address(bq, (DtypeaddrRes+1));
-+	MPI_Type_create_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes);
- 	MPI_Type_commit(&PP_QBlockRes);
-  
- 	error = MPI_Recv(MPI_BOTTOM, 1, PP_QBlockRes, dest, PP_QUARTBLOCK, PP_Comm, &stat);
-@@ -1637,8 +1637,8 @@
-      Dtypelens[0] = (Numquartets + 1)/2;
-   }
- 
--  MPI_Address(&(quartetinfo[0]), Dtypeaddr);
--  MPI_Type_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts);
-+  MPI_Get_address(&(quartetinfo[0]), Dtypeaddr);
-+  MPI_Type_create_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts);
-   MPI_Type_commit(&PP_AllQuarts);
-  
-   for (dest=1; dest<PP_NumProcs; dest++) {
-@@ -1686,8 +1686,8 @@
-     Dtypelens[0] = (*Numquartets + 1)/2;
-   }
-  
--  MPI_Address(&(quartetinfo[0]), Dtypeaddr);
--  MPI_Type_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts);
-+  MPI_Get_address(&(quartetinfo[0]), Dtypeaddr);
-+  MPI_Type_create_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts);
-   MPI_Type_commit(&PP_AllQuarts);
-  
-   error = MPI_Recv(MPI_BOTTOM, 1, PP_AllQuarts, PP_MyMaster, PP_ALLQUARTS, PP_Comm, &stat);
-@@ -1748,13 +1748,13 @@
-   for (n=0; n<(int)blocksize; n++) {
-     Dtypes[n]    = MPI_CHAR;
-     Dtypelens[n] = (taxa - 3) * taxa;
--    MPI_Address(&(biparts[n][0][0]), &(Dtypeaddr[n]));
-+    MPI_Get_address(&(biparts[n][0][0]), &(Dtypeaddr[n]));
-   }
-   pstptr = pstlist;
-   for (n=0; n<pstnum; n++) {
-     Dtypes[(int)blocksize + n]    = MPI_CHAR;
-     Dtypelens[(int)blocksize + n] = psteptreestrlen;
--    MPI_Address((*pstptr).tree, &(Dtypeaddr[(int)blocksize + n]));
-+    MPI_Get_address((*pstptr).tree, &(Dtypeaddr[(int)blocksize + n]));
-     pstnumarr[n] = (*pstptr).count;
- #   ifdef PVERBOSE3
-        fprintf(STDOUT, "(%2d) Sent tree item ->%d: [%d/%d] #=%d  \"%s\"\n",
-@@ -1764,9 +1764,9 @@
-   }
-   Dtypes[((int)blocksize + pstnum)]    = MPI_INT;
-   Dtypelens[((int)blocksize + pstnum)] = pstnum;
--  MPI_Address(&(pstnumarr[0]), &(Dtypeaddr[((int)blocksize + pstnum)]));
-+  MPI_Get_address(&(pstnumarr[0]), &(Dtypeaddr[((int)blocksize + pstnum)]));
- 
--  MPI_Type_struct(((int)blocksize + pstnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts);
-+  MPI_Type_create_struct(((int)blocksize + pstnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts);
-   MPI_Type_commit(&PP_Biparts);
-  
-   error = MPI_Ssend(MPI_BOTTOM, 1, PP_Biparts, PP_MyMaster, PP_PUZZLEBLOCK, PP_Comm);
-@@ -1843,20 +1843,20 @@
-     (*bip)[n]        = new_cmatrix(*taxa - 3, *taxa);
-     Dtypes[n]    = MPI_CHAR;
-     Dtypelens[n] = (*taxa - 3) * *taxa;
--    MPI_Address(&((*bip)[n][0][0]), &(Dtypeaddr[n]));
-+    MPI_Get_address(&((*bip)[n][0][0]), &(Dtypeaddr[n]));
-   }
-   for (n=0; n<pstlistnum; n++) {
-     pstarr[n]        = (char *)calloc((size_t) psteptreestrlen, sizeof(char)); 
-     Dtypes[(int)*blocksize + n]    = MPI_CHAR;
-     Dtypelens[(int)*blocksize + n] = psteptreestrlen;
--    MPI_Address(&(pstarr[n][0]), &(Dtypeaddr[(int)*blocksize + n]));
-+    MPI_Get_address(&(pstarr[n][0]), &(Dtypeaddr[(int)*blocksize + n]));
-   }
-   
-   Dtypes[(int)*blocksize + pstlistnum]    = MPI_INT;
-   Dtypelens[(int)*blocksize + pstlistnum] = pstlistnum;
--  MPI_Address(&(pstnumarr[0]), &(Dtypeaddr[(int)*blocksize + pstlistnum]));
-+  MPI_Get_address(&(pstnumarr[0]), &(Dtypeaddr[(int)*blocksize + pstlistnum]));
- 
--  MPI_Type_struct(((int)*blocksize + pstlistnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts);
-+  MPI_Type_create_struct(((int)*blocksize + pstlistnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts);
-   MPI_Type_commit(&PP_Biparts);
-  
-   error = MPI_Recv(MPI_BOTTOM, 1, PP_Biparts, dest, PP_PUZZLEBLOCK, PP_Comm, &stat);
-@@ -2053,10 +2053,10 @@
-     fprintf(STDOUT, "(%2d) ... Sent DONE Signal\n", PP_Myid);
- # endif /* PVERBOSE3 */
-  
--  MPI_Address(ints,     Dtypeaddr);
--  MPI_Address(doubles, (Dtypeaddr+1));
-+  MPI_Get_address(ints,     Dtypeaddr);
-+  MPI_Get_address(doubles, (Dtypeaddr+1));
- 
--  MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Stats);
-+  MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Stats);
-   MPI_Type_commit(&PP_Stats);
- 
-   doquartrecved[0]  = 0;
-@@ -2173,10 +2173,10 @@
-   doubles[4] = tarr.cpu;
-   doubles[5] = tarr.time;
- 
--  MPI_Address(ints,     Dtypeaddr);
--  MPI_Address(doubles, (Dtypeaddr+1));
-+  MPI_Get_address(ints,     Dtypeaddr);
-+  MPI_Get_address(doubles, (Dtypeaddr+1));
- 
--  MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Stats);
-+  MPI_Type_create_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Stats);
-   MPI_Type_commit(&PP_Stats);
- 
-   error = MPI_Ssend(MPI_BOTTOM, 1, PP_Stats, PP_MyMaster, PP_STATS, PP_Comm);
diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-5.2-configure-c99.patch b/sci-biology/tree-puzzle/files/tree-puzzle-5.2-configure-c99.patch
deleted file mode 100644
index 8c3834136af1..000000000000
--- a/sci-biology/tree-puzzle/files/tree-puzzle-5.2-configure-c99.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- a/configure.ac
-+++ b/configure.ac
-@@ -33,7 +33,7 @@ int main (int argc, char **argv)
- {
- MPI_Init(&argc,&argv);
- MPI_Finalize();
--exit(0);
-+return 0;
- }
- EOF
- 
-@@ -105,7 +105,7 @@ cat > conftest.c <<EOF
- int main (int argc, char **argv)
- {
- printf ("%s-%s", PACKAGE, VERSION);
--exit(0);
-+return 0;
- }
- EOF
- 
diff --git a/sci-biology/tree-puzzle/metadata.xml b/sci-biology/tree-puzzle/metadata.xml
deleted file mode 100644
index 8e14900c2855..000000000000
--- a/sci-biology/tree-puzzle/metadata.xml
+++ /dev/null
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		TREE-PUZZLE is a computer program to reconstruct phylogenetic trees
-		from molecular sequence data by maximum likelihood. It implements a
-		fast tree search algorithm, quartet puzzling, that allows analysis of
-		large data sets and automatically assigns estimations of support to
-		each internal branch. TREE-PUZZLE also computes pairwise maximum
-		likelihood distances as well as branch lengths for user specified
-		trees. Branch lengths can be calculated under the clock-assumption. In
-		addition, TREE-PUZZLE offers a novel method, likelihood mapping, to
-		investigate the support of a hypothesized internal branch without
-		computing an overall tree and to visualize the phylogenetic content of
-		a sequence alignment. TREE-PUZZLE also conducts a number of statistical
-		tests on the data set (chi-square test for homogeneity of base
-		composition, likelihood ratio clock test, Kishino-Hasegawa test). The
-		models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for
-		nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids,
-		and F81 for two-state data. Rate heterogeneity is modeled by a discrete
-		Gamma distribution and by allowing invariable sites. The corresponding
-		parameters can be inferred from the data set.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/tree-puzzle/tree-puzzle-5.2-r1.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.2-r1.ebuild
deleted file mode 100644
index f92bac116720..000000000000
--- a/sci-biology/tree-puzzle/tree-puzzle-5.2-r1.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools
-
-DESCRIPTION="Maximum likelihood analysis for nucleotide, amino acid, and two-state data"
-HOMEPAGE="http://www.tree-puzzle.de"
-SRC_URI="http://www.tree-puzzle.de/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE="mpi"
-RESTRICT="test"
-
-DEPEND="mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-C99-decls.patch
-	"${FILESDIR}"/${P}-MPI-3.0.patch
-	"${FILESDIR}"/${P}-configure-c99.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	default
-
-	if ! use mpi; then
-		sed \
-			-e 's:bin_PROGRAMS = puzzle$(EXEEXT) ppuzzle:bin_PROGRAMS = puzzle :' \
-			-e 's:DIST_SOURCES = $(ppuzzle_SOURCES) $(puzzle_SOURCES):DIST_SOURCES = $(puzzle_SOURCES):' \
-			-i src/Makefile || die
-	fi
-}
-
-src_compile() {
-	# hopelessly terrible build system, abuses Automake
-	emake -j1
-}
-
-src_install() {
-	dobin src/puzzle $(usev mpi src/ppuzzle)
-
-	einstalldocs
-
-	# User manual
-	dodoc doc/tree-puzzle.pdf
-
-	# Example data files
-	insinto /usr/share/${PN}/data
-	rm data/Makefile* || die
-	doins -r data/.
-}
diff --git a/sci-biology/trf/Manifest b/sci-biology/trf/Manifest
deleted file mode 100644
index a2d958884254..000000000000
--- a/sci-biology/trf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST trf404.linux 89853 BLAKE2B 36abf95c88a5b8793e875a276f1494af4df48ff3b3f095e07683589d84eaadfb54099c1764dcd437158c356dcd9d55dd274e7e41515ef098ee2a929493cc0d83 SHA512 c1aa05e394d47ea153df3082258f9a089aa59976963e9ac5d5816ef9dcd95c47e2e46861d1b2aae52b5ea9950a823a2449dd0d8426b04f2b738f5552c319393e
diff --git a/sci-biology/trf/metadata.xml b/sci-biology/trf/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/trf/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/trf/trf-4.04-r2.ebuild b/sci-biology/trf/trf-4.04-r2.ebuild
deleted file mode 100644
index 79558a9d9f11..000000000000
--- a/sci-biology/trf/trf-4.04-r2.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-MY_P="${PN}404"
-
-DESCRIPTION="Tandem Repeats Finder"
-HOMEPAGE="https://tandem.bu.edu/trf/trf.html"
-SRC_URI="https://tandem.bu.edu/trf/downloads/${MY_P}.linux"
-S="${WORKDIR}"
-
-LICENSE="trf"	# http://tandem.bu.edu/trf/trf.license.html
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-RESTRICT="mirror bindist"
-
-QA_PREBUILT="opt/trf/.*"
-
-src_unpack() {
-	cp "${DISTDIR}"/${MY_P}.linux "${S}"/${MY_P}.linux.exe || die
-}
-
-src_install() {
-	exeinto /opt/trf
-	doexe trf404.linux.exe
-	dosym ../trf/${MY_P}.linux.exe /opt/bin/trf
-}
diff --git a/sci-biology/trnascan-se/Manifest b/sci-biology/trnascan-se/Manifest
deleted file mode 100644
index 69853b0907be..000000000000
--- a/sci-biology/trnascan-se/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST trnascan-se-1.31.tar.gz 740960 BLAKE2B 995bfb7ad9f9d46543f15a36134aaec6c27921144c8900a323dbd6152f25e1faa587b5c817dcb8cb838dc1fde8ec7537e5fd6ca8930a4dd1aaadce41c575d651 SHA512 ba55bc8dfa7e5aee9c9a86c135a55b767cda083b74668bd9af4aaaeb693f9c3a17dc8bade5793de12b775564f09fbb861b0ab4f25bf83ccb0954fecd01bb328d
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch
deleted file mode 100644
index 33889c90cf69..000000000000
--- a/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch
+++ /dev/null
@@ -1,62 +0,0 @@
-https://bugs.gentoo.org/874477
---- a/eufind_main.c
-+++ b/eufind_main.c
-@@ -23,4 +23,5 @@
- #include <stdlib.h>
- #include <string.h>
-+#include <unistd.h>
- #include "squid.h"
- #include "sqfuncs.h"
-@@ -47,4 +48,14 @@
- -i <integer>   : start nucleotide numbering at <integer> (def=1)\n\n";
- 
-+int GetBbox(float*, int*, char*, int, int, int);
-+int GetBestABox(TRNA_TYPE*, char*, char*, int, int, int, int, int);
-+int GetBestTrxTerm(TRNA_TYPE*, char*, int, float);
-+int GetSecABox(TRNA_TYPE*, char*);
-+void Get_tRNA_stats(TRNA_TYPE*, char*, int, int);
-+int Init_tRNA(TRNA_TYPE*);
-+int IntEncodeSeq(char*, char*, int);
-+void Save_tRNA(TRNA_TYPE*, SQINFO*, char*, int, int, long int);
-+int tRNAOverlap(TRNA_TYPE*, TRNA_TYPE*, int);
-+
- int
- main (int argc, char **argv)
---- a/scan_main.c
-+++ b/scan_main.c
-@@ -8,4 +8,5 @@
- #include <stdlib.h>
- #include <string.h>
-+#include <unistd.h>
- #include <time.h>
- #include <math.h>
---- a/score_main.c
-+++ b/score_main.c
-@@ -10,4 +10,5 @@
- #include <stdlib.h>
- #include <string.h>
-+#include <unistd.h>
- #include <time.h>
- #include <math.h>
---- a/trnascan.c
-+++ b/trnascan.c
-@@ -69,4 +69,5 @@
- #include <stdio.h>
- #include <stdlib.h>
-+#include <unistd.h>
- #include <ctype.h>
- 
-@@ -333,5 +334,5 @@
- 	    );
- 
--main(int argc, char **argv)
-+int main(int argc, char **argv)
- {
-   /* pointers to the different files fpi=input file, fpo=output file, 
-@@ -1419,5 +1420,5 @@
- /* Calls to this function eliminated for efficiency  T. Lowe  11/95  */
- 
--myindex (char *s, char *t)
-+int myindex (char *s, char *t)
- {
- int i, j, k;
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch
deleted file mode 100644
index acf3c2a6d862..000000000000
--- a/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch
+++ /dev/null
@@ -1,140 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -20,9 +20,9 @@
- PERLBIN = perl
- 
- ## where you want things installed
--BINDIR  = $(HOME)/bin
--LIBDIR  = $(HOME)/lib/tRNAscan-SE
--MANDIR  = $(HOME)/man
-+BINDIR = $(EPREFIX)/usr/bin
-+LIBDIR = $(EPREFIX)/usr/share/trnascan-se
-+MANDIR = $(EPREFIX)/usr/share/man
- 
- ## NOTE !!  If you later manually move the location of 
- ## binaries or data files in the BINDIR or LIBDIR directories,
-@@ -33,10 +33,8 @@
- TEMPDIR = /tmp
- 
- ## your compiler
--CC = gcc	  # GNU cc (if available) otherwise use vendor's cc
- 
- ## any special compiler flags you want
--CFLAGS = -O    # ok for most machines (remove -O for DEC OSF/1 cc compiler)
- 
- ## machine specific definitions
- #  You shouldn't need any. The specific #define's in squid are historical.
-@@ -58,7 +56,7 @@
- #######
- 
- SHELL  = /bin/sh
--LIBS   = -lm
-+LIBS   += -lm
- .SUFFIXES : .c .o
- 
- DOCS = README MANUAL INSTALL COPYING GNULICENSE FILES Release.history
-@@ -109,20 +107,20 @@
- all: 	$(PROGS) tRNAscan-SE setpaths
- 
- covels-SE:  $(OBJ) scan_main.o
--	$(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
- 
- coves-SE: $(OBJ) score_main.o
--	$(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
- 
- eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o
--	$(CC) $(CFLAGS)  -o eufindtRNA eufind_main.o \
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA eufind_main.o \
- 	pavesi.o $(SQUIDOBJ) $(LIBS)
- 
--trnascan-1.4: trnascan.o
--	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
-+trnascan-1.4: trnascan.c
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
- 
- tRNAscan-SE:
--	$(PERLDIR)/$(PERLBIN) checkversion.pl
-+	$(PERLBIN) checkversion.pl
- 	sed 's#/tmp#$(TEMPDIR)#g' tRNAscan-SE.src | \
- 	sed 's#bindir = ""#bindir =\"$(BINDIR)/"#g' | \
- 	sed 's#/usr/local/lib/tRNAscanSE#$(LIBDIR)#g' | \
-@@ -200,11 +198,11 @@
- noambig: trnascan-1.4-NA eufindtRNA-NA
- 
- trnascan-1.4-NA:  trnascan.o
--	$(CC) $(CFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c
- 
- eufindtRNA-NA: $(SQUIDOBJ) eufind_main.o
--	$(CC) $(CFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c 
--	$(CC) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \
-+	$(CC) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c 
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \
- 	pavesi-NA.o $(SQUIDOBJ) $(LIBS)	
- 
- 
-@@ -220,7 +218,7 @@
- 	rmdir -ps $(MANDIR)
- 
- .c.o:
--	$(CC) $(CFLAGS) $(MDEFS) -c $<		
-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $<		
- 
- ## programs from Sean Eddy's sequence i/o function library not
- ## needed for tRNAscan-SE but included for their utility
-@@ -233,16 +231,16 @@
- 	cp $(UTILS) $(BINDIR)/.
- 
- reformat: $(SQUIDOBJ) reformat_main.o
--	$(CC) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS)
- 
- revcomp: $(SQUIDOBJ) revcomp_main.o
--	$(CC) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS)
- 
- seqstat: $(SQUIDOBJ) seqstat_main.o
--	$(CC) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS)
- 
- shuffle: $(SQUIDOBJ) shuffle_main.o
--	$(CC) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS)
- 
- ## other programs in Cove package (below) not needed for
- ## tRNAscan-SE, but are included for users who wish to apply
-@@ -255,25 +253,25 @@
- 	cp $(COVE_SUITE) $(BINDIR)/.
- 
- covea: $(OBJ) align_main.o
--	$(CC) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS)
- 
- coveb: $(OBJ) build_main.o
--	$(CC) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS)
- 
- covee: $(OBJ) emit_main.o
--	$(CC) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS)
- 
- covet: $(OBJ) train_main.o
--	$(CC) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS)
- 
- covels:  $(OBJ) scan_main.o
--	$(CC) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS)
- 
- coves: $(OBJ) score_main.o
--	$(CC) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS)
- 
- structcheck: $(OBJ) structcheck_main.o
--	$(CC) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS)
- 
- 
- ## Maspar memory limits
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch
deleted file mode 100644
index 187705e8b3a0..000000000000
--- a/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- a/fasta2gsi.pl
-+++ b/fasta2gsi.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Usage: fasta2gsi.perl <seqfile>
- # Creates seqfile.gsi
---- a/instman.pl
-+++ b/instman.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- # Sean Eddy, Wed Jul 29 15:24:43 1992
- 
---- a/sstofa.pl
-+++ b/sstofa.pl
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- 
- 
- if ($#ARGV < 0) {
---- a/tRNAscan-SE.src
-+++ b/tRNAscan-SE.src
-@@ -1,4 +1,4 @@
--#! /usr/bin/perl
-+#!/usr/bin/env perl
- #
- # --------------------------------------------------------------------
- # tRNAscan-SE: a program for improved detection of transfer RNA
diff --git a/sci-biology/trnascan-se/metadata.xml b/sci-biology/trnascan-se/metadata.xml
deleted file mode 100644
index 00b47df661a7..000000000000
--- a/sci-biology/trnascan-se/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA
-		genes, with a false positive rate of less than one per 15 gigabases,
-		and with a search speed of about 30 kb/second. It was implemented for
-		large-scale human genome sequence analysis, but is applicable to
-		other DNAs as well.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild
deleted file mode 100644
index f43243921f2f..000000000000
--- a/sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit flag-o-matic perl-functions toolchain-funcs
-
-DESCRIPTION="tRNA detection in large-scale genome sequences"
-HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/"
-SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}"/tRNAscan-SE-1.3.1/
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-lang/perl:="
-BDEPEND="${RDEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-makefile.patch
-	"${FILESDIR}"/${P}-portable-perl-shebangs.patch
-	"${FILESDIR}"/${P}-clang16.patch
-)
-
-src_configure() {
-	tc-export CC
-	append-cflags -std=gnu89 # mid-migration from K&R C, incompatible with c2x
-}
-
-src_test() {
-	emake PATH="${S}:${PATH}" testrun
-}
-
-src_install() {
-	dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4
-
-	newman tRNAscan-SE.man tRNAscan-SE.man.1
-	dodoc MANUAL Manual.ps README Release.history
-
-	insinto /usr/share/trnascan-se
-	doins *.cm gcode.* Dsignal TPCsignal
-
-	perl_domodule -r tRNAscanSE
-}
diff --git a/sci-biology/uchime/Manifest b/sci-biology/uchime/Manifest
deleted file mode 100644
index 00657cd50aa2..000000000000
--- a/sci-biology/uchime/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST uchime4.2.40_src.tar.gz 66772 BLAKE2B 9133853d616ab6e1e6a397da78fc846ba00fc70c2c375eb16a98fbdec25ba6034bd1c876b7ec4a99305e76e47cf7984c1aa30b64bdc96e125f661a0150bae060 SHA512 c3afecb23d164d9c3db6229f54faa13120ac4d88132d9aef707f8d043091099db4205ac80f60242920af6efc23813b3e7e4966d562bdb75ff53244fd525e656b
diff --git a/sci-biology/uchime/files/CMakeLists.patch b/sci-biology/uchime/files/CMakeLists.patch
deleted file mode 100644
index 36b2b39ca5c6..000000000000
--- a/sci-biology/uchime/files/CMakeLists.patch
+++ /dev/null
@@ -1,21 +0,0 @@
---- /dev/null
-+++ b/CMakeLists.txt
-@@ -0,0 +1,18 @@
-+cmake_minimum_required(VERSION 3.31)
-+project(UCHIME LANGUAGES CXX)
-+
-+include(GNUInstallDirs)
-+
-+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FILE_OFFSET_BITS=64 -DUCHIMES=1")
-+
-+# "myutils.h: error: reference to byte is ambiguous""
-+# bug #786297
-+set(CMAKE_CXX_STANDARD 14)
-+set(CMAKE_CXX_STANDARD_REQUIRED ON)
-+set(CMAKE_CXX_EXTENSIONS OFF)
-+
-+# Simply copy the source files from the mk script
-+add_executable(uchime
-+				addtargets2.cpp alignchime.cpp alignchimel.cpp alnparams.cpp alpha.cpp alpha2.cpp fractid.cpp getparents.cpp globalalign2.cpp make3way.cpp mx.cpp myutils.cpp path.cpp searchchime.cpp seqdb.cpp setnucmx.cpp sfasta.cpp tracebackbit.cpp uchime_main.cpp usort.cpp viterbifast.cpp writechhit.cpp)
-+
-+INSTALL(TARGETS uchime DESTINATION ${CMAKE_INSTALL_BINDIR})
diff --git a/sci-biology/uchime/metadata.xml b/sci-biology/uchime/metadata.xml
deleted file mode 100644
index 0e6b9a493f29..000000000000
--- a/sci-biology/uchime/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-	UCHIME is a new algorithm for detecting chimeric sequences. It was developed in
-	collaboration with Brian Haas, Jose Carlos Clemente, Chris Quince and Rob
-	Knight. Chimeras are commonly created during DNA sample amplification by
-	PCR, especially in community sequencing experiments using single regions
-	such as the 16S rRNA gene in bacteria or the fungal ITS region. UCHIME can
-	detect chimeras using a reference database or de novo using abundance
-	information on the assumption that chimeras are less abundant than their
-	parents because they must have undergone fewer rounds of amplification.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/uchime/uchime-4.2.40-r1.ebuild b/sci-biology/uchime/uchime-4.2.40-r1.ebuild
deleted file mode 100644
index 4ef6189ea65b..000000000000
--- a/sci-biology/uchime/uchime-4.2.40-r1.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-MY_P="${PN}${PV}_src"
-inherit cmake
-
-DESCRIPTION="Fast, accurate chimera detection"
-HOMEPAGE="https://www.drive5.com/usearch/manual/uchime_algo.html"
-SRC_URI="https://www.drive5.com/${PN}/${MY_P}.tar.gz"
-S="${WORKDIR}/${MY_P}"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-BDEPEND=">=dev-build/cmake-3.31"
-
-PATCHES=( "${FILESDIR}"/CMakeLists.patch )
diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest
deleted file mode 100644
index 1491362f11d1..000000000000
--- a/sci-biology/ucsc-genome-browser/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jksrc.v260.zip 59090224 BLAKE2B 755bb97f50cde97e7634f38aa81f0843de52710cac78f5b0a2ee6129cffc99f730b8e1ab41d24e2faebb3c0a3e1d1309c84307e2dc4af1efe9a30fb0b9ae1670 SHA512 48aa964ab3ae456ab7e7ddc5d73b91774bd4892f21f1498578a5de38d3a07e4684778ddb1ac1ae389d5bbb3586f9b8506ca3697acca1f6777b85d343cf5d9485
diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml
deleted file mode 100644
index 6cc5e40e4d6c..000000000000
--- a/sci-biology/ucsc-genome-browser/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <use>
-    <flag name="server">Install genome browser Web application. If this flag is off, only libraries and utilities from the suite are installed.</flag>
-  </use>
-</pkgmetadata>
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild
deleted file mode 100644
index ef96f491fb51..000000000000
--- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild
+++ /dev/null
@@ -1,123 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-WEBAPP_MANUAL_SLOT="yes"
-# TODO: use WEBAPP_OPTIONAL?
-inherit toolchain-funcs flag-o-matic webapp
-
-DESCRIPTION="The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath"
-HOMEPAGE="http://genome.ucsc.edu/"
-SRC_URI="http://hgdownload.cse.ucsc.edu/admin/jksrc.v${PV}.zip"
-S="${WORKDIR}/kent"
-
-LICENSE="blat"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+mysql +server static-libs"
-REQUIRED_USE="server? ( mysql )"
-
-# TODO: test with other webservers
-RDEPEND="
-	dev-libs/openssl:=
-	media-libs/libpng:=
-	!<sci-biology/ucsc-genome-browser-223
-	mysql? ( dev-db/mysql-connector-c:= )
-	server? ( virtual/httpd-cgi )
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	app-alternatives/cpio
-	app-arch/unzip
-"
-
-pkg_setup() {
-	use server && webapp_pkg_setup
-}
-
-src_prepare() {
-	default
-
-	use server && webapp_src_preinst
-
-	# bug #708064
-	append-flags -fcommon
-	# bug #831491, bug #919200, bug #921261
-	append-flags -std=gnu89
-
-	sed \
-		-e 's/-Werror//' \
-		-e "/COPT/s:=.*$:=${LDFLAGS}:g" \
-		-e "s/CC=gcc/CC=$(tc-getCC) ${CFLAGS}/" \
-		-e 's:${CC} ${COPT} ${CFLAGS}:${CC} ${CFLAGS}:g' \
-		-i src/inc/common.mk src/hg/lib/makefile || die
-	find -name makefile -or -name cgi_build_rules.mk \
-		| xargs sed -i \
-			-e 's/-${USER}//g' \
-			-e 's/-$(USER)//g' \
-			-e 's:-O2::g' \
-			-e 's:-ggdb::g' \
-			-e 's:-pipe::g' || die
-	sed \
-		-e 's:${DISTDIR}${BINDIR}:${BINDIR}:g' \
-		-i src/hg/genePredToMafFrames/makefile || die
-}
-
-src_compile() {
-	export MACHTYPE=${MACHTYPE/-*/} \
-		BINDIR="${WORKDIR}/destdir/opt/${PN}/bin" \
-		SCRIPTS="${WORKDIR}/destdir/opt/${PN}/cluster/scripts" \
-		ENCODE_PIPELINE_BIN="${WORKDIR}/destdir/opt/${PN}/cluster/data/encode/pipeline/bin" \
-		PATH="${BINDIR}:${PATH}" \
-		STRIP="echo 'skipping strip' "
-
-	export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none"
-
-	# TODO: use pkg-config here
-	use mysql && export MYSQLLIBS="-L${ESYSROOT}/usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \
-		MYSQLINC="${ESYSROOT}/usr/include/mysql"
-
-	use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \
-		CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin"
-
-	mkdir -p "${BINDIR}" "${SCRIPTS}" "${ENCODE_PIPELINE_BIN}" || die
-	use server && mkdir -p "${CGI_BIN}" "${DOCUMENTROOT}"
-
-	emake -C src clean
-	emake -C src/lib
-	emake -C src/jkOwnLib
-	emake -C src/utils/stringify
-	emake -C src blatSuite
-	if use mysql; then
-		emake -j1 -C src/hg utils
-		emake -j1 -C src utils
-		emake -C src libs userApps
-		if use server; then
-			emake -j1 -C src/hg
-			emake -j1 -C src
-		fi
-	fi
-}
-
-src_install() {
-	use server && webapp_src_preinst
-	cp -ad "${WORKDIR}"/destdir/* "${D}" || die
-	use static-libs && dolib.a src/lib/${MACHTYPE/-*/}/*.a
-	echo "PATH=${EPREFIX}/opt/${PN}/bin" > "${S}/98${PN}"
-	doenvd "${S}/98${PN}"
-
-	use server && webapp_postinst_txt en src/product/README.QuickStart
-	use server && webapp_src_install
-
-	insinto "/usr/include/${PN}"
-	doins src/inc/*.h
-	insinto "/usr/share/${PN}"
-	doins -r src/product
-	keepdir "/usr/share/doc/${PF}"
-	find -name 'README*' -or -name '*.doc' | grep -v test | cpio -padv "${ED}/usr/share/doc/${PF}" || die
-}
-
-pkg_postinst() {
-	use server && webapp_pkg_postinst
-}
diff --git a/sci-biology/unafold/Manifest b/sci-biology/unafold/Manifest
deleted file mode 100644
index 22df6cae4441..000000000000
--- a/sci-biology/unafold/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST unafold-3.8.tar.bz2 282418 BLAKE2B 0dddff9dc440362ce3b24d18f42aa47d2dc817de93eba900de76dc73393feabb09ac57cb77af6c8db0ab8c0958f0fd459911fd813fa004b616fedffe9aebd069 SHA512 4c83cf0122e4d4ec2b713833adb11eb608b0f880f5b68114aefd8c7fa980c8d02f9a6cfc0c88cd640b4457e65954b05189118e8ac5ed207b2f9910738ca71a6c
diff --git a/sci-biology/unafold/files/unafold-3.8-autotools.patch b/sci-biology/unafold/files/unafold-3.8-autotools.patch
deleted file mode 100644
index ecf29b470c2c..000000000000
--- a/sci-biology/unafold/files/unafold-3.8-autotools.patch
+++ /dev/null
@@ -1,41 +0,0 @@
---- a/configure.ac
-+++ b/configure.ac
-@@ -2,7 +2,7 @@
- AC_INIT(UNAFold, 3.8, markhn@rpi.edu)
- AC_CONFIG_SRCDIR(src/hybrid.c)
- AC_CONFIG_AUX_DIR(config)
--AM_CONFIG_HEADER(config.h:config.in)
-+AC_CONFIG_HEADERS(config.h:config.in)
- AM_INIT_AUTOMAKE
- AC_CANONICAL_BUILD
- AC_PROG_CC
-@@ -12,7 +12,6 @@
- if test -z "$PERL"; then
-    AC_MSG_ERROR(Perl not found)
- fi
--AC_PROG_PERL_VERSION(5.6.1, , AC_MSG_ERROR(Perl 5.6.1 or better is required))
- AC_CHECK_PROG(GNUPLOT, gnuplot, [system('gnuplot', \"\$prefix.gp\") == 0 or die $!;])
- 
- AC_MSG_CHECKING(whether compiler needs -mieee)
-@@ -28,6 +27,7 @@
- 
- 
- # Checks for libraries.
-+AX_CHECK_GL
- AX_CHECK_GLUT
- AM_CONDITIONAL(GLUT, test -n "$GLUT_LIBS")
- AX_CHECK_GD
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -33,9 +33,9 @@
- endif GLUT
- 
- hybrid_plot_ng_SOURCES = hybrid-plot-ng.c getopt.h util.h xmalloc.h
--hybrid_plot_ng_CFLAGS = @GD_CFLAGS@
-+hybrid_plot_ng_CFLAGS = @GD_CFLAGS@ $(GL_CFLAGS)
- hybrid_plot_ng_LDFLAGS = @GD_LDFLAGS@
--hybrid_plot_ng_LDADD = getopt.$(OBJEXT) getopt1.$(OBJEXT) xmalloc.$(OBJEXT) @GD_LIBS@ -lm
-+hybrid_plot_ng_LDADD = getopt.$(OBJEXT) getopt1.$(OBJEXT) xmalloc.$(OBJEXT) @GD_LIBS@ $(GL_LIBS) -lm
- 
- sbs_SOURCES = getopt.c getopt1.c energy.c xmalloc.c sbs.c energy.h getopt.h xmalloc.h
- sbs_LDADD = -lm
diff --git a/sci-biology/unafold/files/unafold-3.8-clang16.patch b/sci-biology/unafold/files/unafold-3.8-clang16.patch
deleted file mode 100644
index fabc28e1fd88..000000000000
--- a/sci-biology/unafold/files/unafold-3.8-clang16.patch
+++ /dev/null
@@ -1,775 +0,0 @@
---- a/src/ct-energy.c
-+++ b/src/ct-energy.c
-@@ -24,8 +24,8 @@
- double auPenalty(int, int);
- double chooseDangle(int, int);
- double tstackOrDangle(int, int, int);
--int isHomodimer();
--int isCircular();
-+int isHomodimer(void);
-+int isCircular(void);
- 
- int readStructure(FILE* file);
- 
-@@ -87,7 +87,7 @@
-   {NULL, 0, NULL, 0}
- };
- 
--void usage()
-+void usage(void)
- {
-   puts("Usage: ct-energy [OPTION] [FILE]...");
-   puts("");
-@@ -1247,7 +1247,7 @@
-   return 1;
- }
- 
--int isHomodimer()
-+int isHomodimer(void)
- {
-   int i;
- 
-@@ -1272,7 +1272,7 @@
-   return 1;
- }
- 
--int isCircular()
-+int isCircular(void)
- {
-   return g_prev[0] == g_len && g_next[g_len - 1] % g_len == 1;
- }
---- a/src/energy.c
-+++ b/src/energy.c
-@@ -15,6 +15,7 @@
- #endif
- 
- #include "energy.h"
-+#include "util.h"
- #include "xmalloc.h"
- 
- #ifndef isinf
---- a/src/hybrid.c
-+++ b/src/hybrid.c
-@@ -39,10 +39,10 @@
- #endif
- 
- void initializeMatrix(double**, int, double);
--void limitBasePairs();
--void prohibit();
--void force();
--void prefilter();
-+void limitBasePairs(void);
-+void prohibit(void);
-+void force(void);
-+void prefilter(void);
- void fillMatrix(double**, int, double);
- void fillMatrix_noI(double**, int, double);
- void calculateProb(double**, double*, double*, double**, double**, double, double, int, double);
-@@ -706,7 +706,7 @@
-       matrix[i - 1][n - 1] = (reverse ? R0(n, i) : L0(i, n));
- }
- 
--void limitBasePairs()
-+void limitBasePairs(void)
- {
-   if (g_bpFile)
-     {
-@@ -740,7 +740,7 @@
-     }
- }
- 
--void prohibit()
-+void prohibit(void)
- {
-   int i, j, k;
-   struct constraintListNode *top, *newTop;
-@@ -788,7 +788,7 @@
- }
- 
- #if ENABLE_FORCE
--void force()
-+void force(void)
- {
-   int i, j, k;
-   struct constraintListNode *top, *newTop;
-@@ -880,7 +880,7 @@
- 	}
- } */
- 
--void prefilter()
-+void prefilter(void)
- {
-   char** in;
-   int i, j, k, count;
---- a/src/hybrid-min.c
-+++ b/src/hybrid-min.c
-@@ -53,10 +53,10 @@
- } *pairList;
- 
- void initializeMatrices(double);
--void limitBasePairs();
--void prohibit();
--void force();
--void prefilter();
-+void limitBasePairs(void);
-+void prohibit(void);
-+void force(void);
-+void prefilter(void);
- void fillMatrixL(double);
- void fillMatrixR(double);
- void fillMatrixL_noI(double);
-@@ -88,7 +88,7 @@
- #define min2(a, b) ((a) < (b) ? (a) : (b))
- ENERGY min4(ENERGY, ENERGY, ENERGY, ENERGY);
- void pushPairList(int, int, int, ENERGY);
--void sortPairList();
-+void sortPairList(void);
- 
- ENERGY *lprime, *rprime;
- 
-@@ -885,7 +885,7 @@
- 	}
- }
- 
--void limitBasePairs()
-+void limitBasePairs(void)
- {
-   if (g_bpFile)
-     {
-@@ -919,7 +919,7 @@
-     }
- }
- 
--void prohibit()
-+void prohibit(void)
- {
-   int i, j, k;
-   struct constraintListNode* top;
-@@ -965,7 +965,7 @@
- }
- 
- #if ENABLE_FORCE
--void force()
-+void force(void)
- {
-   int i, j, k;
-   struct constraintListNode* top;
-@@ -1041,7 +1041,7 @@
-   return length;
- }
- 
--void prefilter()
-+void prefilter(void)
- {
-   int i, j;
- 
-@@ -1055,7 +1055,7 @@
- 	}
- } */
- 
--void prefilter()
-+void prefilter(void)
- {
-   char** in;
-   int i, j, k, count;
-@@ -2235,7 +2235,7 @@
-   pairList = node;
- }
- 
--void sortPairList()
-+void sortPairList(void)
- {
-   struct pairListNode *a, *b;
- 
---- a/src/hybrid-plot.c
-+++ b/src/hybrid-plot.c
-@@ -70,13 +70,13 @@
- void displayCallbackInput(void);
- void keyboardCallbackInput(unsigned char, int, int);
- 
--void fixLength();
--void fixGrid();
--void fixLabels();
--void fixZoomGrid();
--void fixZoomLabels();
-+void fixLength(void);
-+void fixGrid(void);
-+void fixLabels(void);
-+void fixZoomGrid(void);
-+void fixZoomLabels(void);
- void readFiles(char*);
--void sortTemps();
-+void sortTemps(void);
- double* inputRecords(FILE*);
- int filter(int, int);
- 
-@@ -1157,7 +1157,7 @@
-     }
- }
- 
--void fixLength()
-+void fixLength(void)
- {
-   int m, n;
- 
-@@ -1177,7 +1177,7 @@
-     }
- }
- 
--void fixGrid()
-+void fixGrid(void)
- {
-   int m;
- 
-@@ -1193,7 +1193,7 @@
-     g_grid = pow(10, m + 1);
- }
- 
--void fixLabels()
-+void fixLabels(void)
- {
-   int longestNum;
- 
-@@ -1202,7 +1202,7 @@
-     g_labels += g_grid;
- }
- 
--void fixZoomGrid()
-+void fixZoomGrid(void)
- {
-   int m;
- 
-@@ -1221,7 +1221,7 @@
-     g_zoomGrid = pow(10, m + 1);
- }
- 
--void fixZoomLabels()
-+void fixZoomLabels(void)
- {
-   int longestNum;
- 
-@@ -1310,7 +1310,7 @@
-   return scores;
- }
- 
--void sortTemps()
-+void sortTemps(void)
- {
-   int i, j;
-   char* tempC;
---- a/src/hybrid-plot-ng.c
-+++ b/src/hybrid-plot-ng.c
-@@ -24,28 +24,28 @@
-  */
- 
- #if HAVE_GD
--void initPNG();
-+void initPNG(void);
- void titlePNG(char*);
--void borderPNG();
--void gridPNG();
-+void borderPNG(void);
-+void gridPNG(void);
- void plotDotPNG(int, int, double);
- void vertCenterPNG(char*, int);
- void horzCenterPNG(char*, int);
- void selectionPNG(char*, int);
- #endif
- 
--void initPS();
-+void initPS(void);
- void titlePS(char*);
--void borderPS();
--void gridPS();
-+void borderPS(void);
-+void gridPS(void);
- void plotDotPS(int, int, double);
- void vertCenterPS(char*, int);
- void horzCenterPS(char*, int);
- void selectionPS(char*, int);
- 
--void fixSize();
--void fixGrid();
--void fixLabels();
-+void fixSize(void);
-+void fixGrid(void);
-+void fixLabels(void);
- double* inputRecords(FILE*);
- int filter(int, int);
- int (*getColor)(double);
-@@ -114,10 +114,10 @@
-   char* plotFile;
- 
-   /* functions to call - either PS or PNG */
--  void (*init)();
-+  void (*init)(void);
-   void (*title)(char*);
--  void (*border)();
--  void (*grid)();
-+  void (*border)(void);
-+  void (*grid)(void);
-   void (*plotDot)(int, int, double);
-   void (*vertCenter)(char*, int);
-   void (*horzCenter)(char*, int);
-@@ -474,7 +474,7 @@
-   return 0;
- }
- 
--void initPS()
-+void initPS(void)
- {
-   int i;
- 
-@@ -517,7 +517,7 @@
-   fprintf(g_file, "(%s) showCenter\n", wordString);
- }
- 
--void borderPS()
-+void borderPS(void)
- {
-   fputs("92 126 moveto\n", g_file);
-   fputs("576 126 lineto\n", g_file);
-@@ -527,7 +527,7 @@
-   fputs("stroke\n", g_file);
- }
- 
--void gridPS()
-+void gridPS(void)
- {
-   double x1, y1;
-   int i, j;
-@@ -639,7 +639,7 @@
- 
- #if HAVE_GD
- 
--void initPNG()
-+void initPNG(void)
- {
-   int i;
- 
-@@ -671,12 +671,12 @@
-   gdImageString(g_image, gdFontMediumBold, 306 - 7 * strlen(wordString) / 2, 51, (unsigned char*) wordString, g_black);
- }
- 
--void borderPNG()
-+void borderPNG(void)
- {
-   gdImageRectangle(g_image, 92, 92, 576, 576, g_black);
- }
- 
--void gridPNG()
-+void gridPNG(void)
- {
-   int i, j;
-   char buffer[8];
-@@ -776,7 +776,7 @@
- 
- #endif
- 
--void fixSize()
-+void fixSize(void)
- {
-   int m, n;
- 
-@@ -796,7 +796,7 @@
-     }
- }
- 
--void fixGrid()
-+void fixGrid(void)
- {
-   int m;
- 
-@@ -812,7 +812,7 @@
-     g_grid = pow(10, m + 1);
- }
- 
--void fixLabels()
-+void fixLabels(void)
- {
-   int longestNum;
- 
---- a/src/hybrid-ss.c
-+++ b/src/hybrid-ss.c
-@@ -47,10 +47,10 @@
- #define ssOK(i, j) 1
- #endif
- 
--void initializeMatrices();
--void fillMatrices1();
-+void initializeMatrices(void);
-+void fillMatrices1(void);
- void fillMatrices2(double*, double*);
--void fillMatrices1_noI();
-+void fillMatrices1_noI(void);
- void fillMatrices2_noI(double*, double*);
- void calculateProb(double*, double*, double*, double*, double*, double);
- void calculateProb_noI(double*, double*, double*, double*, double*);
-@@ -713,7 +713,7 @@
- 
- #include "hybrid-ss_init.h"
- 
--void fillMatrices1()
-+void fillMatrices1(void)
- {
-   int i, j, k;
-   FILE* file;
-@@ -783,7 +783,7 @@
-     }
- }
- 
--void fillMatrices1_noI()
-+void fillMatrices1_noI(void)
- {
-   int i, j, k;
-   FILE* file;
---- a/src/hybrid-ss_init.h
-+++ b/src/hybrid-ss_init.h
-@@ -14,7 +14,7 @@
-   return length;
- } */
- 
--void prefilter()
-+void prefilter(void)
- {
-   char** in;
-   int i, j, k, count;
-@@ -45,7 +45,7 @@
-   free(in);
- }
- 
--void initializeMatrices()
-+void initializeMatrices(void)
- {
-   int i, j, k;
-   struct constraintListNode *top, *newTop;
---- a/src/hybrid-ss-min.c
-+++ b/src/hybrid-ss-min.c
-@@ -57,10 +57,10 @@
-   struct pairListNode* next;
- } *pairList;
- 
--void initializeMatrices();
--void fillMatrices1();
--void fillMatrices2();
--void computeQ53();
-+void initializeMatrices(void);
-+void fillMatrices1(void);
-+void fillMatrices2(void);
-+void computeQ53(void);
- void traceback(int, int, int, int*, int*, int*);
- void traceback_noI(int, int, int, int*, int*, int*);
- void setStack(int, int, int*, int*);
-@@ -108,7 +108,7 @@
- int equal(ENERGY, ENERGY);
- void push(struct stackNode**, int, int, int);
- void pushPairList(int, int, int, ENERGY);
--void sortPairList();
-+void sortPairList(void);
- 
- int g_len;
- ENERGY *q, *qprime, *qm, *q5, *q3;
-@@ -887,7 +887,7 @@
-   return length;
- }
- 
--void prefilter()
-+void prefilter(void)
- {
-   char** in;
-   int i, j, k, count;
-@@ -918,7 +918,7 @@
-   free(in);
- }
- 
--void initializeMatrices()
-+void initializeMatrices(void)
- {
-   int i, j, k;
-   struct constraintListNode* top;
-@@ -1072,7 +1072,7 @@
-     }
- }
- 
--void fillMatrices1()
-+void fillMatrices1(void)
- {
-   int i, j, k;
-   FILE* file;
-@@ -1181,7 +1181,7 @@
-     }
- }
- 
--void fillMatrices2()
-+void fillMatrices2(void)
- {
-   int i, j, k;
-   FILE* file;
-@@ -1283,7 +1283,7 @@
-     }
- }
- 
--void computeQ53()
-+void computeQ53(void)
- {
-   int i, j;
- 
-@@ -3137,7 +3137,7 @@
-   pairList = node;
- }
- 
--void sortPairList()
-+void sortPairList(void)
- {
-   struct pairListNode *a, *b;
- 
---- a/src/hybrid-ss-noml.c
-+++ b/src/hybrid-ss-noml.c
-@@ -45,11 +45,11 @@
- #define ssOK(i, j) 1
- #endif
- 
--void initializeMatrices();
--void fillMatrices1();
--void fillMatrices2();
--void fillMatrices1_noI();
--void fillMatrices2_noI();
-+void initializeMatrices(void);
-+void fillMatrices1(void);
-+void fillMatrices2(void);
-+void fillMatrices1_noI(void);
-+void fillMatrices2_noI(void);
- void calculateProb(double*, double*, double*, double);
- void calculateProb_noI(double*, double*, double*, double);
- void traceback(int*, int*, int*);
-@@ -652,7 +652,7 @@
-   return length;
- } */
- 
--void prefilter()
-+void prefilter(void)
- {
-   char** in;
-   int i, j, k, count;
-@@ -683,7 +683,7 @@
-   free(in);
- }
- 
--void initializeMatrices()
-+void initializeMatrices(void)
- {
-   int i, j, k;
-   struct constraintListNode *top, *newTop;
-@@ -826,7 +826,7 @@
- 	}
- }
- 
--void fillMatrices1()
-+void fillMatrices1(void)
- {
-   int i, j, k;
-   FILE* file;
-@@ -885,7 +885,7 @@
-     }
- }
- 
--void fillMatrices1_noI()
-+void fillMatrices1_noI(void)
- {
-   int i, j, k;
-   FILE* file;
-@@ -944,7 +944,7 @@
-     }
- }
- 
--void fillMatrices2()
-+void fillMatrices2(void)
- {
-   int i, j;
-   FILE* file;
-@@ -986,7 +986,7 @@
-     }
- }
- 
--void fillMatrices2_noI()
-+void fillMatrices2_noI(void)
- {
-   int i, j;
-   FILE* file;
---- a/src/hybrid-ss-simple.c
-+++ b/src/hybrid-ss-simple.c
-@@ -47,11 +47,11 @@
- #define ssOK(i, j) 1
- #endif
- 
--void initializeMatrices();
--void fillMatrices1();
--void fillMatrices2();
--void fillMatrices1_noI();
--void fillMatrices2_noI();
-+void initializeMatrices(void);
-+void fillMatrices1(void);
-+void fillMatrices2(void);
-+void fillMatrices1_noI(void);
-+void fillMatrices2_noI(void);
- void calculateProb(double*, double*, double*, double);
- void calculateProb_noI(double*, double*, double*);
- void traceback(int*, int*, int*);
-@@ -598,7 +598,7 @@
- 
- #include "hybrid-ss_init.h"
- 
--void fillMatrices1()
-+void fillMatrices1(void)
- {
-   int i, j, k;
-   FILE* file;
-@@ -658,7 +658,7 @@
-     }
- }
- 
--void fillMatrices1_noI()
-+void fillMatrices1_noI(void)
- {
-   int i, j, k;
-   FILE* file;
-@@ -718,7 +718,7 @@
-     }
- }
- 
--void fillMatrices2()
-+void fillMatrices2(void)
- {
-   int i, j, k;
-   FILE* file;
-@@ -789,7 +789,7 @@
-     }
- }
- 
--void fillMatrices2_noI()
-+void fillMatrices2_noI(void)
- {
-   int i, j, k;
-   FILE* file;
---- a/src/util.h
-+++ b/src/util.h
-@@ -24,18 +24,18 @@
- 
- /* #define NO_GU_BASEPAIRS */
- 
--int roundInt(double d)
-+static int roundInt(double d)
- {
-   return (int) (d + .5);
- }
- 
--void strcatc(char* str, char c)
-+static void strcatc(char* str, char c)
- {
-   str[strlen(str) + 1] = 0;
-   str[strlen(str)] = c;
- }
- 
--char* filename(char* file)
-+static char* filename(char* file)
- {
-   char* name;
- 
-@@ -46,7 +46,7 @@
-   return name;
- }
- 
--void checkArray(char** array, unsigned int* available, unsigned int used, unsigned int increment)
-+static void checkArray(char** array, unsigned int* available, unsigned int used, unsigned int increment)
- {
-   if (used == *available)
-     {
-@@ -55,7 +55,7 @@
-     }
- }
- 
--int input(FILE* file, char** name, char** sequence)
-+static int input(FILE* file, char** name, char** sequence)
- {
-   /* read string from file */
-   int current, last, state;
-@@ -120,7 +120,7 @@
-   return 1;
- }
- 
--unsigned char toNum(char c)
-+static unsigned char toNum(char c)
- {
-   c = toupper(c);
-   switch (c)
-@@ -137,7 +137,7 @@
-   return 4;
- }
- 
--int seqcmp(unsigned char* seq1, unsigned char* seq2, int length)
-+static int seqcmp(unsigned char* seq1, unsigned char* seq2, int length)
- {
-   int i;
- 
-@@ -149,7 +149,7 @@
-   return 0;
- }
- 
--void readSequence(char* file, char** name, char** string, unsigned char** seq, int* len)
-+static void readSequence(char* file, char** name, char** string, unsigned char** seq, int* len)
- {
-   int i;
-   FILE* f;
-@@ -171,14 +171,14 @@
- }
- 
- #ifdef NO_GU_BASEPAIRS
--const int BPI[6][6] = {{6, 6, 6, 0, 6, 6},
-+static const int BPI[6][6] = {{6, 6, 6, 0, 6, 6},
- 		       {6, 6, 1, 6, 6, 6},
- 		       {6, 2, 6, 6, 6, 6},
- 		       {3, 6, 6, 6, 6, 6},
- 		       {6, 6, 6, 6, 6, 6},
- 		       {6, 6, 6, 6, 6, 6}};
- #else
--const int BPI[6][6] = {{6, 6, 6, 0, 6, 6},
-+static const int BPI[6][6] = {{6, 6, 6, 0, 6, 6},
- 		       {6, 6, 1, 6, 6, 6},
- 		       {6, 2, 6, 4, 6, 6},
- 		       {3, 6, 5, 6, 6, 6},
-@@ -187,7 +187,7 @@
- #endif
- #define basePairIndex(a, b) BPI[a][b]
- 
--int min3(int a, int b, int c)
-+static int min3(int a, int b, int c)
- {
-   if (a <= b && a <= c)
-     return a;
-@@ -196,7 +196,7 @@
-   return c;
- }
- 
--int same(unsigned char* a, unsigned char* b, int len)
-+static int same(unsigned char* a, unsigned char* b, int len)
- {
-   int i;
- 
-@@ -206,7 +206,7 @@
-   return 1;
- }
- 
--void version(const char* prog)
-+static void version(const char* prog)
- {
-   printf("%s (%s) %s\n", prog, PACKAGE_NAME, PACKAGE_VERSION);
-   puts("By Nicholas R. Markham and Michael Zuker");
-@@ -216,7 +216,7 @@
-   exit(EXIT_SUCCESS);
- }
- 
--void readOrDie(unsigned int num, const char* name, FILE* file, const char* format, ...)
-+static void readOrDie(unsigned int num, const char* name, FILE* file, const char* format, ...)
- {
-   va_list arg;
-   va_start(arg, format);
diff --git a/sci-biology/unafold/files/unafold-3.8-doc-version.patch b/sci-biology/unafold/files/unafold-3.8-doc-version.patch
deleted file mode 100644
index b15858fd69e6..000000000000
--- a/sci-biology/unafold/files/unafold-3.8-doc-version.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/tests/hybrid.tml
-+++ b/tests/hybrid.tml
-@@ -10,7 +10,7 @@
-   </test>
-   <test command="hybrid --version" return="0">
-     <stdin></stdin>
--    <stdout>hybrid (UNAFold) 3.7
-+    <stdout>hybrid (UNAFold) 3.8
- By Nicholas R. Markham and Michael Zuker
- Copyright (C) 2006
- Rensselaer Polytechnic Institute
diff --git a/sci-biology/unafold/metadata.xml b/sci-biology/unafold/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/unafold/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/unafold/unafold-3.8-r1.ebuild b/sci-biology/unafold/unafold-3.8-r1.ebuild
deleted file mode 100644
index 3ad5b77f4f20..000000000000
--- a/sci-biology/unafold/unafold-3.8-r1.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools
-
-DESCRIPTION="Unified Nucleic Acid Folding and hybridization package"
-HOMEPAGE="http://mfold.rna.albany.edu/"
-SRC_URI="http://dinamelt.bioinfo.rpi.edu/download/${P}.tar.bz2"
-
-LICENSE="unafold"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
-	media-libs/freeglut
-	media-libs/gd
-	virtual/opengl
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-build/autoconf-archive
-	dev-lang/perl
-	test? ( dev-perl/XML-Parser )
-"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-doc-version.patch
-	"${FILESDIR}"/${P}-autotools.patch
-	"${FILESDIR}"/${P}-clang16.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	econf --disable-coverage
-}
diff --git a/sci-biology/update-blastdb/Manifest b/sci-biology/update-blastdb/Manifest
deleted file mode 100644
index 8afbb996d842..000000000000
--- a/sci-biology/update-blastdb/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ncbi_cxx--12_0_0.tar.gz 37925914 BLAKE2B 45490961293d8b3ace24c21602f4039041003f9b45d9f1763957c97ba1e55d6d336c33b6116262b2e774cc26b9366cc3d61bead0c0c7fbd4c461cad2921d80d4 SHA512 1a79f2d95960efde6263289814102499460ec235dad36337dd398d668665e44015e06e40fd0e66a8fb16f526d326949adcaadcb667debeba5d8570b1a92e30ed
diff --git a/sci-biology/update-blastdb/metadata.xml b/sci-biology/update-blastdb/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/update-blastdb/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild b/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild
deleted file mode 100644
index b53a64bbadda..000000000000
--- a/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MY_PV="$(ver_rs 1- _)"
-
-DESCRIPTION="update_blastdb.pl for local blast db maintainance"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
-SRC_URI="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
-S="${WORKDIR}"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	dev-lang/perl
-	!sci-biology/ncbi-tools++"
-
-src_install() {
-	dobin ncbi_cxx--${MY_PV}/src/app/blast/update_blastdb.pl
-}
diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest
deleted file mode 100644
index 36aa8e465e22..000000000000
--- a/sci-biology/vcftools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST vcftools-0.1.16.tar.gz 480575 BLAKE2B 5c0bf67aef8ef4705f621485df4c556f6bace190311c308f0364f3e274cf4818f56f2186905fdfb7459dc4be9664a8b1ff631e2cecd03abd7aa82dcfc7e5aa64 SHA512 c4dd5ceb3ad0512e839154d8a05ef3e7a03cbe52c3099df48775b35460fce7ef10102819c2d1cefa33b98ad09e7bd1608e871978860ec9c0b0c2e781892b22e6
diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml
deleted file mode 100644
index b48544aee61e..000000000000
--- a/sci-biology/vcftools/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">vcftools</remote-id>
-    <remote-id type="github">vcftools/vcftools</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/vcftools/vcftools-0.1.16.ebuild b/sci-biology/vcftools/vcftools-0.1.16.ebuild
deleted file mode 100644
index bfb38608417f..000000000000
--- a/sci-biology/vcftools/vcftools-0.1.16.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools flag-o-matic perl-functions toolchain-funcs
-
-DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
-HOMEPAGE="http://vcftools.sourceforge.net/"
-SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="lapack"
-
-RDEPEND="virtual/zlib:=
-	dev-lang/perl:=
-	lapack? ( virtual/lapack )"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	perl_set_version
-
-	append-flags $($(tc-getPKG_CONFIG) --cflags lapack)
-	append-libs $($(tc-getPKG_CONFIG) --libs lapack)
-
-	econf \
-		$(use_enable lapack pca) \
-		--with-pmdir="${VENDOR_LIB#"${EPREFIX}"/usr}"
-}
diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest
deleted file mode 100644
index e76561d597de..000000000000
--- a/sci-biology/velvet/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST velvet_1.2.10.tgz 18818559 BLAKE2B 5723c9c040e570cd88b774e5b0044dd04def88778fe2b137ec7c007ab83fc98e5423ad1d9d0499780cf6d3152347ca1a4e4e6b6c1900ce4adfc4930f1f6d3c34 SHA512 a6f3e35cebceb22cc10e83088b8cd9758492da78866237cae63d8826d6f5cfb44d82dd8bfcb1185d37cd434d4c7a0f2ac7135bb80a51db86e754afd6156ea874
diff --git a/sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch b/sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch
deleted file mode 100644
index 22cd48ee814f..000000000000
--- a/sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-https://bugs.gentoo.org/919223
---- a/src/readSet.c
-+++ b/src/readSet.c
-@@ -638,7 +638,8 @@ static void readFastXFile(int fileType, SequencesWriter *seqWriteInfo, char *fil
- 	FileGZOrAuto file;
- 	IDnum counter = 0;
- 
--        file.gzFile = file.autoFile = NULL;
-+        file.autoFile = NULL;
-+        file.gzFile = NULL;
-         if (fileType == AUTO) {
-         	file.autoFile = openFileAuto(filename);
-                 if (!file.autoFile)
-@@ -677,8 +678,10 @@ static void readFastXPair(int fileType, SequencesWriter *seqWriteInfo, char *fil
- 	if (cat==REFERENCE)
- 		exitErrorf(EXIT_FAILURE, false, "Cannot read reference sequence in 'separate' read mode");
- 
--        file1.gzFile = file1.autoFile = NULL;
--        file2.gzFile = file2.autoFile = NULL;
-+        file1.autoFile = NULL;
-+        file2.autoFile = NULL;
-+        file1.autoFile = NULL;
-+        file2.autoFile = NULL;
-         if (fileType == AUTO) {
-         	file1.autoFile = openFileAuto(filename1);
-                 if (!file1.autoFile)
diff --git a/sci-biology/velvet/metadata.xml b/sci-biology/velvet/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/velvet/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild
deleted file mode 100644
index 672f56781db5..000000000000
--- a/sci-biology/velvet/velvet-1.2.10.ebuild
+++ /dev/null
@@ -1,91 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit flag-o-matic toolchain-funcs
-
-MY_P="${PN}_${PV}"
-DESCRIPTION="A sequence assembler for very short reads"
-HOMEPAGE="https://www.ebi.ac.uk/~zerbino/velvet/"
-SRC_URI="https://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
-S="${WORKDIR}"/${MY_P}
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc openmp"
-
-BDEPEND="
-	doc? ( virtual/latex-base )
-	openmp? (
-		|| (
-			sys-devel/gcc[openmp]
-			llvm-runtimes/clang-runtime[openmp]
-		)
-	)
-"
-
-PATCHES=( "${FILESDIR}/${P}-incompatible-pointers.patch" )
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-src_prepare() {
-	default
-	if ! use doc; then
-		sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
-	fi
-	elog "Upstream recommends using -O3 in CFLAGS"
-	echo
-	elog "To adjust the MAXKMERLENGTH, CATEGORIES, BIGASSEMBLY, LONGSEQUENCES parameters"
-	elog "as described in the PDF manual, please set the variables by prepending VELVET_ in"
-	elog "front of it. For example VELVET_MAXKMERLENGTH, VELVET_CATEGORIES, ..."
-	elog "Set them either in your environment or in /etc/portage/make.conf, then re-emerge"
-	elog "the package. For example:"
-	elog "  VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
-
-	if [[ $(tc-getCC) =~ gcc ]]; then
-		local eopenmp=-fopenmp
-	elif [[ $(tc-getCC) =~ icc ]]; then
-		local eopenmp=-openmp
-	else
-		elog "Cannot detect compiler type so not setting openmp support"
-	fi
-	append-flags -fPIC ${eopenmp}
-	append-ldflags ${eopenmp}
-
-	tc-export CC
-
-	MAKE_XOPTS=(
-		CC="$(tc-getCC)"
-		CFLAGS="${CFLAGS}"
-		OPT="${CFLAGS}"
-	)
-	use openmp && MAKE_XOPTS+=( OPENMP=1 )
-	[[ ! -z "${VELVET_MAXKMERLENGTH}" ]] && MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} )
-	[[ ! -z "${VELVET_CATEGORIES}" ]] && MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} )
-	[[ ! -z "${VELVET_BIGASSEMBLY}" ]] && MAKE_XOPTS+=( BIGASSEMBLY=${VELVET_BIGASSEMBLY} )
-	[[ ! -z "${VELVET_LONGSEQUENCES}" ]] && MAKE_XOPTS+=( LONGSEQUENCES=${VELVET_LONGSEQUENCES} )
-}
-
-src_compile() {
-	emake "${MAKE_XOPTS[@]}" -j1
-	emake "${MAKE_XOPTS[@]}" -j1 color
-}
-
-src_test() {
-	emake "${MAKE_XOPTS[@]}" -j1 test
-}
-
-src_install() {
-	dobin velvet{g,h,g_de,h_de}
-	insinto /usr/share/${PN}
-	doins -r contrib
-	dodoc Manual.pdf CREDITS.txt ChangeLog
-}
diff --git a/sci-biology/yass/Manifest b/sci-biology/yass/Manifest
deleted file mode 100644
index b03d8af279ca..000000000000
--- a/sci-biology/yass/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST yass-1.14.tar.gz 235530 BLAKE2B 55b7e8e7834f3a76a09e5e509884b391053fe97a7d5aeb3132009c8050014fb6dae92f7b246c85646a872fd5bde7a4b8c3bd0124fb38c7d0f648b85c63d99ad7 SHA512 fdfac6f391848d0bd35829a966721a242697b0832803092bd7ea2116149332642ddf3bf5f095fe707f6edbbb9454efe068852fe6d5cdfe937445d9d32a521fa2
diff --git a/sci-biology/yass/files/1.14-as-needed.patch b/sci-biology/yass/files/1.14-as-needed.patch
deleted file mode 100644
index e57503801c7a..000000000000
--- a/sci-biology/yass/files/1.14-as-needed.patch
+++ /dev/null
@@ -1,207 +0,0 @@
-diff --git a/configure.ac b/configure.ac
-index 68453ef..3ecfd21 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -28,13 +28,11 @@ AC_CHECK_FUNCS([floor memset clock pow sqrt strchr strdup strtol strtoul])
- dnl 1) threads options
- 
- dnl abc) : with-threads option
--AC_ARG_WITH(
--	threads,
--	[  --with-threads          compile with all threads],
--	[threads="yes"],
--	[threads="no"])
-+AC_ARG_ENABLE(
-+	[threads],
-+	AS_HELP_STRING([--enable-threads], [compile with all threads]))
- 
--if test "$threads" = "yes"; then
-+AS_IF([test "x$enable_threads" = "xyes"], [
-   AC_MSG_RESULT(detected cpu parameter: threads);
-  
-   dnl pthread library here ? (UNIX system)
-@@ -46,167 +44,25 @@ if test "$threads" = "yes"; then
-     AC_MSG_RESULT(yes)
-     AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
-        CFLAGS=" $CFLAGS -DTHREAD_ASSEMBLE_ALIGN -DTHREAD_FORWARD_REVERSE -DTHREAD_QUERY_CHUNK "
--       LDFLAGS="$LDFLAGS -lpthread"
-+       LIBS="$LIBS -lpthread"
-   else
-     AC_MSG_RESULT(no : disabling \"--with-threads\" parameter)
-   fi
--
--else
--   if test -s /proc/cpuinfo; then
--      AC_MSG_CHECKING(for multi-processor)
--      dnl Multithread advice
--      if test `grep -c '^processor' /proc/cpuinfo` -gt 2; then
--         AC_MSG_RESULT(yes) 
--         AC_MSG_RESULT(- try \"configure --with-threads\")
--      else
--         AC_MSG_RESULT(no)
--      fi;
--   fi;
--fi
--
--
--
--
--
--dnl a) : with-thread-fr option
--AC_ARG_WITH(
--	thread-fr,
--	[  --with-thread-fr        compile with two separate threads for Forward and Reverse sequence],
--	[thread_forward_reverse="yes"],
--	[thread_forward_reverse="no"])
--
--if test "$thread_forward_reverse" = "yes"; then
--  AC_MSG_RESULT(detected cpu parameter: thread-fr);
-- 
--  dnl pthread library here ? (UNIX system)
--  AC_MSG_CHECKING(for pthread lib)
--  AC_CHECK_LIB(pthread, pthread_create,
--	[have_pthread="yes"],
--	[have_pthread="no"])
--  if test "$have_pthread" = "yes"; then
--    AC_MSG_RESULT(yes)
--    AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
--       CFLAGS=" $CFLAGS -DTHREAD_FORWARD_REVERSE "
--       LDFLAGS="$LDFLAGS -lpthread"  
--  else
--    AC_MSG_RESULT(no : disabling \"--with-thread-fr\" parameter)
--  fi
--
--else
--   if test -s /proc/cpuinfo; then
--      AC_MSG_CHECKING(for multi-processor)
--      dnl Multithread advice
--      if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then
--         AC_MSG_RESULT(yes) 
--         AC_MSG_RESULT(- try \"configure --with-thread-fr\")
--      else
--         AC_MSG_RESULT(no)
--      fi;
--   fi;
--fi
--
--
--
--
--
--dnl b) : with-thread-aa option
--AC_ARG_WITH(
--	thread-aa,
--	[  --with-thread-aa        compile with two separate threads for Assemble and Align steps],
--	[thread_assemble_align="yes"],
--	[thread_assemble_align="no"])
--
--if test "$thread_assemble_align" = "yes"; then
--  AC_MSG_RESULT(detected cpu parameter: thread-aa);
-- 
--  dnl pthread library here ? (UNIX system)
--  AC_MSG_CHECKING(for pthread lib)
--  AC_CHECK_LIB(pthread, pthread_create,
--	[have_pthread="yes"],
--	[have_pthread="no"])
--  if test "$have_pthread" = "yes"; then
--    AC_MSG_RESULT(yes)
--    AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
--       CFLAGS=" $CFLAGS -DTHREAD_ASSEMBLE_ALIGN "
--       LDFLAGS="$LDFLAGS -lpthread"  
--  else
--    AC_MSG_RESULT(no : disabling \"--with-thread-aa\" parameter)
--  fi
--
--else
--   if test -s /proc/cpuinfo; then
--      AC_MSG_CHECKING(for multi-processor)
--      dnl Multithread advice
--      if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then
--         AC_MSG_RESULT(yes) 
--         AC_MSG_RESULT(- try \"configure --with-thread-aa\")
--      else
--         AC_MSG_RESULT(no)
--      fi;
--   fi;
--fi
--
--
--dnl c) : with-thread-qc option
--AC_ARG_WITH(
--	thread-qc,
--	[  --with-thread-qc        compile with threads for the query chunks],
--	[thread_query_chunk="yes"],
--	[thread_query_chunk="no"])
--
--if test "$thread_query_chunk" = "yes"; then
--  AC_MSG_RESULT(detected cpu parameter: thread-qc);
-- 
--  dnl pthread library here ? (UNIX system)
--  AC_MSG_CHECKING(for pthread lib)
--  AC_CHECK_LIB(pthread, pthread_create,
--	[have_pthread="yes"],
--	[have_pthread="no"])
--  if test "$have_pthread" = "yes"; then
--    AC_MSG_RESULT(yes)
--    AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer])
--       CFLAGS=" $CFLAGS -DTHREAD_QUERY_CHUNK "
--       LDFLAGS="$LDFLAGS -lpthread"  
--  else
--    AC_MSG_RESULT(no : disabling \"--with-thread-qc\" parameter)
--  fi
--
--else
--   if test -s /proc/cpuinfo; then
--      AC_MSG_CHECKING(for multi-processor)
--      dnl Multithread advice
--      if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then
--         AC_MSG_RESULT(yes) 
--         AC_MSG_RESULT(- try \"configure --with-thread-qc\")
--      else
--         AC_MSG_RESULT(no)
--      fi;
--   fi;
--fi
--
--
--
-+])
- 
- dnl 2) : low-memory option
--AC_ARG_WITH(
--	low-memory,
--	[  --with-low-memory       use less memory, but can miss some repeats],
--	[low_memory="yes"],
--	[low_memory="no"])
-+AC_ARG_ENABLE(
-+	[lowmemory],
-+	AS_HELP_STRING([--enable-lowmemory], [use less memory, but can miss some repeats]))
- 
--if test "$low_memory" = "yes"; then
-+AS_IF([test "x$enable_lowmemory" = "xyes"], [
-    AC_MSG_RESULT(detected memory parameter: low memory);
-    CFLAGS=" $CFLAGS -DLOW_MEMORY "
--else
--   AC_MSG_RESULT(detected memory parameter : plain memory) 
--fi
--
--
--CFLAGS="$CFLAGS -O3 -Wall -ansi -pedantic -funroll-loops -pipe -fomit-frame-pointer "
--LDFLAGS="$LDFLAGS -lm"
-+])
- 
- AC_SUBST(CFLAGS)
- AC_SUBST(LDFLAGS)
-+
- AM_WITH_DMALLOC
- AM_INIT_AUTOMAKE
- AC_CONFIG_FILES([Makefile
-diff --git a/src/Makefile.am b/src/Makefile.am
-index e456f94..8d90ca9 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -6,3 +6,4 @@
- bin_PROGRAMS = yass
- yass_SOURCES = align.c assemble.c avl.c display.c global_var.c hash.c kword.c list.c main.c prdyn.c proba.c red_black.c regroup.c threads.c tuple.c util.c \
-                align.h assemble.h avl.h display.h global_var.h hash.h kword.h list.h        prdyn.h proba.h red_black.h regroup.h threads.h tuple.h util.h
-+yass_LDADD = -lm
diff --git a/sci-biology/yass/files/yass-1.14-lowmem-define.patch b/sci-biology/yass/files/yass-1.14-lowmem-define.patch
deleted file mode 100644
index 64f2e216a05b..000000000000
--- a/sci-biology/yass/files/yass-1.14-lowmem-define.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Add missing function definition to hash.c
-Whole hash.c is used only if USE=lowmem is enabled.
-https://bugs.gentoo.org/919215
---- a/src/hash.h
-+++ b/src/hash.h
-@@ -57,6 +57,7 @@
-   
- }Table_hash;
- 
-+long int hashVerifie (Table_hash *table, char *mess,long int diag);
- 
- /*
-  *
diff --git a/sci-biology/yass/metadata.xml b/sci-biology/yass/metadata.xml
deleted file mode 100644
index 4688bfdad406..000000000000
--- a/sci-biology/yass/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <use>
-    <flag name="lowmem">Build for environments with low amounts of memory</flag>
-  </use>
-</pkgmetadata>
diff --git a/sci-biology/yass/yass-1.14-r4.ebuild b/sci-biology/yass/yass-1.14-r4.ebuild
deleted file mode 100644
index a484aca4269f..000000000000
--- a/sci-biology/yass/yass-1.14-r4.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools
-
-DESCRIPTION="Genomic similarity search with multiple transition constrained spaced seeds"
-HOMEPAGE="http://bioinfo.lifl.fr/yass/"
-SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="lowmem threads"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-as-needed.patch
-	"${FILESDIR}"/${P}-lowmem-define.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		$(use_enable threads) \
-		$(use_enable lowmem lowmemory) \
-		--without-dmalloc
-}
author	root <root@alpha.trunkmasters.com>	2026-06-04 16:24:49 -0500
committer	root <root@alpha.trunkmasters.com>	2026-06-04 16:24:49 -0500
commit	a3ceca1b4c0d9bdb550dc23f06ffbb5a8e033bc7 (patch)
tree	0c52bbae1c242fbc296bd650fcd1167685f81492 /sci-biology
parent	bfd9c39e4712ebdb442d4ca0673061faed1e70e1 (diff)
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