gentoo resync : 25.11.2020

91 files changed, 2372 insertions, 2855 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 4c7f9b88e8d6..9603eb7f0869 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest
deleted file mode 100644
index 0749a737c777..000000000000
--- a/sci-biology/amos/Manifest
+++ /dev/null
@@ -1,8 +0,0 @@
-AUX amos-3.1.0-fix-build-system.patch 3132 BLAKE2B a7758991b5916cec6e9a2a39ee55beef73d14c19b7154ab2ced8e41eca411d1b6cacda5b7388e3ee48f330e489e4012660b3c08383c423a8553d283cd1cc4764 SHA512 b23c168c166f8a1dad89d1b25536a59be3e68a6478cef3db5664dc901cef0547213a8622a72ee1a2e1d5b8930c65d95e309573f903423e8fb80fb7312d89f863
-AUX amos-3.1.0-gcc-4.7.patch 400 BLAKE2B af160452d1bf52df204156dc9039645483c0ee349b96c2562eba4608695ac76b308c9cc2bc82a55401b3d56c33c4d2bae9e07a0a62ed4a3b15becb8f95ecda7f SHA512 3777885d5cd5edcb881abfbe1580092e073311797bd4776cd3ec9d27b634339718238be7f452f1ea1a0aea5fb9f6059d6b6f6a47bc2a0fb6d1811a2ec51a0835
-AUX amos-3.1.0-goBambus2.py-indent-and-cleanup.patch 1057 BLAKE2B fde1011da762750140f8880968c952b275d625f92b43ee8c35aaa23b687cc8d6cda441aa7b7cc883a67efe2a0d4a9cc13ee9f6b3663fef9f8274693350fe8e87 SHA512 5d2a0d4b222a23f30db560937b1c0e447f61dc786e097b259696fa41dca1e57a17a1e684bbd9fa9ddcee1334f7e6e3a91ccb7567d4fe079c3bdb3bb54034d11f
-AUX amos-3.1.0-qa-Wformat.patch 4511 BLAKE2B 64064175db625a098a528f0c8036196968c58dae445edd3c98fc5627e3a84d593abc438958573ef7a28193d0d2fc76db30fe16a180a383dec9bae5084305505d SHA512 de0382f9128b46fef8e87d14de75bbc9f0af3e8bcbb915edab26a883186109ab29ddbb31c5cf70fc8d37700abe36fb73a7bdca46c29672052d01ebebffd52abe
-DIST amos-3.1.0-fix-c++14.patch.bz2 8033 BLAKE2B 942248f64906253205392df71010bf41105d2985fc8112e7443975d776cc484a4e2b6cf34284d4c384145bf32601892c06f156a0b0ccf0f2ce721de242e02e9b SHA512 76e26ca48a009cbf637d9462878223633e9b21cbd12d58a19e9a561f2cf4805791becc0b5f7aaf81975ca1e02b263cdd9d5ff310c4594670922ea65885ad9634
-DIST amos-3.1.0.tar.gz 2094268 BLAKE2B b9fb80d4e7b7e9e7769081c2680a3cba26591f00a4d9fdb17ad602e581dea5e8e2add4b0d9d3821a7f8a4ec1a45dfd867037baf35ecd401584f030c86b2b0f83 SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491
-EBUILD amos-3.1.0-r4.ebuild 1110 BLAKE2B 4730d6a04ba727fd72ea825c6c57d65079ae9ddb29411f0a26aa94653309364ddec742104783044549adc2a60f06a7452f76e392145aa02db472042dde05e1d5 SHA512 7cb40d45dabc4e6cc188d3edf8347f34578d1f955b2d522273f3b551be6974023145e35a443f0e4495d70746aa40b6c451cedf999c102f1f8f7ffbab09748d61
-MISC metadata.xml 345 BLAKE2B 750928cf3e96c24e2af8e84d5889100c1954eb140596368dc00d479f63898c82e3bb0e07a9e970c6c12eb36ed3ae84c6bcc7913cf3ed56e2d71120185d24a4f0 SHA512 a31ba5660e524b70517f2644bb929d4bc0428d1ea682752ca2ddefd3b5a8a5c8aabf7a9877fa61e8fe12599da65e9f0a6c1e7db90d61729e26c33b76303ff497
diff --git a/sci-biology/amos/amos-3.1.0-r4.ebuild b/sci-biology/amos/amos-3.1.0-r4.ebuild
deleted file mode 100644
index 0dbcaffd81da..000000000000
--- a/sci-biology/amos/amos-3.1.0-r4.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools flag-o-matic python-single-r1
-
-DESCRIPTION="A Modular, Open-Source whole genome assembler"
-HOMEPAGE="http://amos.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${PN}-3.1.0-fix-c++14.patch.bz2"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	${PYTHON_DEPS}
-	dev-perl/DBI
-	dev-perl/Statistics-Descriptive
-	sci-biology/mummer"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-gcc-4.7.patch
-	"${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
-	"${WORKDIR}"/${P}-fix-c++14.patch
-	"${FILESDIR}"/${P}-qa-Wformat.patch
-	"${FILESDIR}"/${P}-fix-build-system.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-
-	# prevent GCC 6 log pollution due
-	# to hash_map deprecation in C++11
-	append-cxxflags -Wno-cpp
-}
-
-src_configure() {
-	econf --with-qmake-qt4=no
-}
-
-src_install() {
-	default
-	python_fix_shebang "${ED%/}"/usr/bin/goBambus2
-}
diff --git a/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch b/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch
deleted file mode 100644
index 9c824dd2f122..000000000000
--- a/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch
+++ /dev/null
@@ -1,116 +0,0 @@
-* Use proper AR and not just 'ar'
-* Fix build system to build in parallel
-
---- a/configure.ac
-+++ b/configure.ac
-@@ -34,6 +34,7 @@
- AC_PROG_INSTALL
- AC_PROG_LN_S
- AC_PROG_RANLIB
-+AM_PROG_AR
- AC_PROG_CPP
- AC_PATH_PROG(PERL, [perl], [:])
- AC_PATH_PROG(PYTHON, [python], [:])
---- a/src/Align/Makefile.am
-+++ b/src/Align/Makefile.am
-@@ -133,7 +133,7 @@
- 
- ##-- hash-overlap
- hash_overlap_LDADD = \
--	$(top_builddir)/src/Align/libAlign.a \
-+	libAlign.a \
- 	$(top_builddir)/src/CelMsg/libCelMsg.a \
- 	$(top_builddir)/src/Slice/libSlice.a \
- 	$(top_builddir)/src/Common/libCommon.a \
-@@ -172,7 +172,7 @@
- 
- ##-- make-consensus
- make_consensus_LDADD = \
--	$(top_builddir)/src/Align/libAlign.a \
-+	libAlign.a \
- 	$(top_builddir)/src/CelMsg/libCelMsg.a \
- 	$(top_builddir)/src/Slice/libSlice.a \
- 	$(top_builddir)/src/Common/libCommon.a \
-@@ -182,7 +182,7 @@
- 
- ##-- make-consensus_poly
- make_consensus_poly_LDADD = \
--	$(top_builddir)/src/Align/libAlign_poly.a \
-+	libAlign_poly.a \
- 	$(top_builddir)/src/CelMsg/libCelMsg.a \
- 	$(top_builddir)/src/Slice/libSlice.a \
- 	$(top_builddir)/src/Common/libCommon.a \
-@@ -192,7 +192,7 @@
- 
- ##-- maligntest
- maligntest_LDADD = \
--	$(top_builddir)/src/Align/libAlign.a \
-+	libAlign.a \
- 	$(top_builddir)/src/CelMsg/libCelMsg.a \
- 	$(top_builddir)/src/Slice/libSlice.a \
- 	$(top_builddir)/src/Common/libCommon.a \
-@@ -202,7 +202,7 @@
- 
- ##-- merge-contigs
- merge_contigs_LDADD = \
--	$(top_builddir)/src/Align/libAlign.a \
-+	libAlign.a \
- 	$(top_builddir)/src/CelMsg/libCelMsg.a \
- 	$(top_builddir)/src/Slice/libSlice.a \
- 	$(top_builddir)/src/Common/libCommon.a \
-@@ -235,7 +235,7 @@
- 
- ##-- show-ma-asm
- show_ma_asm_LDADD = \
--	$(top_builddir)/src/Align/libAlign.a \
-+	libAlign.a \
- 	$(top_builddir)/src/Common/libCommon.a \
- 	$(top_builddir)/src/AMOS/libAMOS.a
- show_ma_asm_SOURCES = \
-@@ -261,7 +261,7 @@
- 
- ##-- simple-overlap
- simple_overlap_LDADD = \
--	$(top_builddir)/src/Align/libAlign.a \
-+	libAlign.a \
- 	$(top_builddir)/src/CelMsg/libCelMsg.a \
- 	$(top_builddir)/src/Slice/libSlice.a \
- 	$(top_builddir)/src/Common/libCommon.a \
-@@ -272,7 +272,7 @@
- 
- ##-- test-align
- test_align_LDADD = \
--	$(top_builddir)/src/Align/libAlign.a \
-+	libAlign.a \
- 	$(top_builddir)/src/CelMsg/libCelMsg.a \
- 	$(top_builddir)/src/Slice/libSlice.a \
- 	$(top_builddir)/src/Common/libCommon.a \
---- a/src/Bambus/Bundler/Makefile.am
-+++ b/src/Bambus/Bundler/Makefile.am
-@@ -47,7 +47,7 @@
- 	clk.cc
- 
- MarkRepeats_LDADD = \
--	$(top_builddir)/src/Bambus/Bundler/libBundler.a \
-+	libBundler.a \
- 	$(top_builddir)/src/Common/libCommon.a \
- 	$(top_builddir)/src/AMOS/libAMOS.a \
- 	$(top_builddir)/src/GNU/libGNU.a
-@@ -55,7 +55,7 @@
- 	MarkRepeats.cc
- 
- OrientContigs_LDADD = \
--	$(top_builddir)/src/Bambus/Bundler/libBundler.a \
-+	libBundler.a \
- 	$(top_builddir)/src/Common/libCommon.a \
- 	$(top_builddir)/src/AMOS/libAMOS.a \
- 	$(top_builddir)/src/GNU/libGNU.a
-@@ -63,7 +63,7 @@
- 	OrientContigs.cc
- 
- FilterEdgesByCluster_LDADD = \
--	$(top_builddir)/src/Bambus/Bundler/libBundler.a \
-+	libBundler.a \
- 	$(top_builddir)/src/Common/libCommon.a \
- 	$(top_builddir)/src/AMOS/libAMOS.a \
- 	$(top_builddir)/src/GNU/libGNU.a
diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
deleted file mode 100644
index de2a41184c52..000000000000
--- a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- src/Align/find-tandem.cc |    1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc
-index ddf1cab..a29e21e 100644
---- a/src/Align/find-tandem.cc
-+++ b/src/Align/find-tandem.cc
-@@ -7,6 +7,7 @@
- #include <vector>
- #include <ctime>
- #include <sys/time.h>
-+#include <unistd.h>
- using namespace std;
- 
- const int OFFSET_TABLE_SIZE = 100;
diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
deleted file mode 100644
index 97a8f59d0208..000000000000
--- a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- amos-3.1.0/src/Pipeline/goBambus2.py.orig	2013-09-11 01:05:29.850090457 +0200
-+++ amos-3.1.0/src/Pipeline/goBambus2.py	2013-09-11 01:07:03.250090701 +0200
-@@ -1,7 +1,7 @@
- #pipeline script for assembly + Bambus 2
- #contributed by Todd J Treangen
- 
--import string, sys, os, subprocess#, spincursor
-+import sys, os, subprocess#, spincursor
- 
- RED =    "\033[0;31m"
- GREEN =  "\033[0;32m"
-@@ -360,7 +360,7 @@
-                 print "\t\t%s...failed%s"%(RED,NONE)
-                 sys.exit(1)
- 
--       p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
-+        p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
- 
-         if xopt_dict["verbose"] == 1:
-             print "10) running OutputResults"
-@@ -388,4 +388,3 @@
-             else:
-                 print "\t\t%s...failed%s"%(RED,NONE)
-                 sys.exit(1)
--)
diff --git a/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch b/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch
deleted file mode 100644
index 13f4eeb247a1..000000000000
--- a/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch
+++ /dev/null
@@ -1,136 +0,0 @@
-Fix QA warnings, due to using incorrect format specifiers in printf:
-* contig-cmp.cc:237:50: warning: format ‘%u’ expects argument of type ‘unsigned int’,
-* but argument 3 has type ‘std::vector<Contig_t>::size_type {aka long unsigned int}’ [-Wformat=]
-*     fprintf (stderr, "%u b contigs\n", b . size ());
-
---- a/src/Align/align.cc
-+++ b/src/Align/align.cc
-@@ -1936,7 +1936,7 @@
-    n = align . size ();
-    con = consensus . c_str ();
- 
--   fprintf (fp, "\nConsensus len = %d\n", consensus . length ());
-+   fprintf (fp, "\nConsensus len = %zu\n", consensus . length ());
- 
-    for  (i = 0;  i < n;  i ++)
-      {
-@@ -3936,7 +3936,7 @@
-         }
- 
-       // Array of sum of quality scores in the slice for A,C,G,T,- resp.
--      for (j = 0; j < 6; j ++)
-+      for (j = 0; j < 5; j ++)
-         qvsum [j] = 0;
- 
-       int nof_ambiguities = 0;
---- a/src/Align/align_poly.cc
-+++ b/src/Align/align_poly.cc
-@@ -1761,7 +1761,7 @@
-    n = align . size ();
-    con = consensus . c_str ();
- 
--   fprintf (fp, "\nConsensus len = %d\n", consensus . length ());
-+   fprintf (fp, "\nConsensus len = %zu\n", consensus . length ());
-    for  (i = 0;  i < n;  i ++)
-      {
-       fprintf (fp, "\nString #%d:\n", i);
---- a/src/Align/count-qmers.cc
-+++ b/src/Align/count-qmers.cc
-@@ -191,8 +191,8 @@
- 
-     PrintMers(mer_table, min_count);
- 
--    fprintf(stderr, "reporter:counter:asm,reads_total,%ld\n", COUNT);
--    fprintf(stderr, "reporter:counter:asm,reads_bp,%ld\n",    LEN);
-+    fprintf(stderr, "reporter:counter:asm,reads_total,%lld\n", COUNT);
-+    fprintf(stderr, "reporter:counter:asm,reads_bp,%lld\n",    LEN);
-   }
-   catch (Exception_t & e)
-   {
---- a/src/Align/kmer-cov.cc
-+++ b/src/Align/kmer-cov.cc
-@@ -485,7 +485,7 @@
-           Kmer_Len = s . length ();
-       else if  (Kmer_Len != int (s . length ()))
-           {
--           sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d",
-+           sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d",
-                 s . c_str (), s . length (), Kmer_Len);
-            Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__);
-           }
---- a/src/Align/kmer-cov-plot.cc
-+++ b/src/Align/kmer-cov-plot.cc
-@@ -316,7 +316,7 @@
-     }
-     else if  (Kmer_Len != int (s . length ()))
-     {
--      sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d",
-+      sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d",
-                s . c_str (), s . length (), Kmer_Len);
-       Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__);
-     }
---- a/src/Align/make-consensus.cc
-+++ b/src/Align/make-consensus.cc
-@@ -303,7 +303,7 @@
-             break;
-         }
- 
--        sprintf (sid, "%ld", ++layout_id);
-+        sprintf (sid, "%u", ++layout_id);
-         cid = string (sid);
-         ID_t lid = layout.getIID ();
-         if (lid == 0)
---- a/src/Align/make-consensus_poly.cc
-+++ b/src/Align/make-consensus_poly.cc
-@@ -279,7 +279,7 @@
- 		   break;
- 	       }
- 		 
--	       sprintf(sid, "%ld", ++layout_id);
-+	       sprintf(sid, "%u", ++layout_id);
- 	       cid = string(sid);
- 	       ID_t lid = layout.getIID();
- 	       if (lid == 0) {
---- a/src/Align/simple-overlap.cc
-+++ b/src/Align/simple-overlap.cc
-@@ -422,7 +422,7 @@
-            "Options:\n"
-            "  -a       Also show alignments of overlaps \n"
-            "  -E <x>   Maximum error rate for overlaps is <x>\n"
--           "           e.g., -E 0.06 for 6% error rate\n"
-+           "           e.g., -E 0.06 for 6%% error rate\n"
-            "  -F       Input is a fasta file\n"
-            "  -h       Print this usage message\n"
-            "  -o <n>   Set minimum overlap length to <n>\n"
---- a/src/Compare/contig-cmp.cc
-+++ b/src/Compare/contig-cmp.cc
-@@ -145,7 +145,7 @@
- 
-    fclose (fp);
- 
--   fprintf (stderr, "%u a contigs\n", a . size ());
-+   fprintf (stderr, "%zu a contigs\n", a . size ());
-    vector <Unitig_t>  a_contig (max_id + 1);
-    n = a . size ();
-    for  (i = 0;  i < n;  i ++)
-@@ -234,7 +234,7 @@
- 
-    fclose (fp);
- 
--   fprintf (stderr, "%u b contigs\n", b . size ());
-+   fprintf (stderr, "%zu b contigs\n", b . size ());
-    vector <Unitig_t>  b_contig (max_id + 1);
-    n = b . size ();
-    for  (i = 0;  i < n;  i ++)
---- a/src/Staden/progs/trace_convert.c
-+++ b/src/Staden/progs/trace_convert.c
-@@ -6,6 +6,9 @@
- #include "traceType.h"
- #include "seqIOABI.h"
- 
-+#include <fcntl.h>
-+#include <unistd.h>
-+
- static char fileIdentifier[] = "$Id$";
- 
- struct opts {
diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml
deleted file mode 100644
index 2668bce2ac8a..000000000000
--- a/sci-biology/amos/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://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">amos</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/clustalw-mpi/Manifest b/sci-biology/clustalw-mpi/Manifest
index 3088142ea209..23d86f7036f9 100644
--- a/sci-biology/clustalw-mpi/Manifest
+++ b/sci-biology/clustalw-mpi/Manifest
@@ -1,4 +1,5 @@
-AUX 0.13-gentoo.patch 596 BLAKE2B 3d302656dfd4a4ecae645753643a9bf93c9643818e61f8ebda910eeea668bf5c5458f670e84243cb044cdad1add35a26b365f3478eb6f7ef7f98b8bc6bbf6f55 SHA512 4b0350f9ca8ce0d6e098faae5749bdc120b853dec745a07899e81bb195623affe46560d28a3c79db7af57551c9c873d91e693ee30a5c185ac4d2adb26a9d27c8
+AUX clustalw-mpi-0.13-fno-common.patch 449 BLAKE2B e1d8e7cd34e5fea17fb883861e2cb32874c34340b37f6d2983688930706b41cf1a7653b73d3860b8b5adcdca353b7a9ec94d9bda5090048d040dc6eb2b1a3d6b SHA512 71ea0f57c7235bc99f3e0d364476c268a27d2eeaba8e9bbcc01eceb0c84b1aabd0d9ce66dd738e6b0e75919f6cc18890e4dde7be6097e0e3051a9907bee56b4f
+AUX clustalw-mpi-0.13-makefile.patch 596 BLAKE2B 3d302656dfd4a4ecae645753643a9bf93c9643818e61f8ebda910eeea668bf5c5458f670e84243cb044cdad1add35a26b365f3478eb6f7ef7f98b8bc6bbf6f55 SHA512 4b0350f9ca8ce0d6e098faae5749bdc120b853dec745a07899e81bb195623affe46560d28a3c79db7af57551c9c873d91e693ee30a5c185ac4d2adb26a9d27c8
 DIST clustalw-mpi-0.13.tar.gz 154911 BLAKE2B 705f62263340b0ac13895657c97e185f395910f25653bdcc20cf867732c270c65eebebe5b914367a534a5d058909d0baf307c0a3727a2095d4f21c313e83b94d SHA512 e0008accb6c07584dc5ad1b953e0c668fad43ca3a86d88dbcf50fbfa858870131e4db005cc87b46f5268cd0795e9a2ce01326d8318d66b694a92b85e6f9635df
-EBUILD clustalw-mpi-0.13-r2.ebuild 962 BLAKE2B bcc71a3c09ae2d9e3c4f41b6a4e0771dd778c3cbdcf650cb9319124834a02d40b129757675ea060b6d39c699d3b123b757129f08b8d98c65b619b74467d8bd4b SHA512 48cd3c0ff42cf9c5185e70d0fbdb1b21020a7ad75156adba06346b7cd6847dfbb2752164edd93238890ef55d38565cdcc196355094ca3e8e253f3d508b409ef3
-MISC metadata.xml 491 BLAKE2B b65663a63fa098ac80bc0226163188776cb7805688651ea22724ed457924a3d970e5e368210a994f536f9152b3af2766d07c1eefb8b620299c3e1efffda840c3 SHA512 d242bee2ea381f992deb30b406b89ec2da08e1d513da5d9a94016ea07247670744d25bac8175607291c39d80090d3d1746154d3c60ba95bdd720d57c0212b3d0
+EBUILD clustalw-mpi-0.13-r3.ebuild 1012 BLAKE2B e1ae0c2237433f8826bcc66b6c3b11e8313a41ddb8201a6ffbb1300b7f9bfbb45c568e9903f9296ca97f54a9aec98199c2c9e4f942b43e89cfaff4fe982d7472 SHA512 9b5af106fa5daed7ff7c6ab49037ca82b42ce781138fa076efaf43f70b09ebfdcd45dc5e63d53a95a9414ca273260ebe5971664559001499cba8eefb80e26694
+MISC metadata.xml 487 BLAKE2B 7ca9b9cccd9bf7468703e755d4090e077a975c6463d97c612be7508ec38497d391e10fa5a50d5e76fc1f94f735b4062a4ea894d588706092166339c2046410f3 SHA512 4b7038b53d689f5a2e0f6a0b121235efb6d5c6fa9b8586107071f7820b0c2d9274a3b8b533afc84709df408751addf2b2408850542ed0083f47c7220d4bc61f5
diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild
index 76d3b80cde32..334c34e78ce6 100644
--- a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild
+++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -12,28 +12,31 @@ 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"
+IUSE="mpi-njtree static-pairalign"
 
 DEPEND="virtual/mpi"
 RDEPEND="${DEPEND}"
 
-PATCHES=( "${FILESDIR}"/${PV}-gentoo.patch )
+PATCHES=(
+	"${FILESDIR}"/${P}-makefile.patch
+	"${FILESDIR}"/${P}-fno-common.patch
+)
 
 src_prepare() {
 	default
 
-	if use mpi_njtree; then
+	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
+	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 ${PN}
-	newdoc README.${PN} README
+	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
new file mode 100644
index 000000000000..da74f0ba172d
--- /dev/null
+++ b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch
@@ -0,0 +1,13 @@
+--- 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/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch
index 6e36061cbb39..6e36061cbb39 100644
--- a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch
+++ b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch
diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml
index 8ab4494152c8..ffe2c4efec87 100644
--- a/sci-biology/clustalw-mpi/metadata.xml
+++ b/sci-biology/clustalw-mpi/metadata.xml
@@ -1,14 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://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>
+	<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/dialign-tx/Manifest b/sci-biology/dialign-tx/Manifest
index 443791cbbb26..ec6b81e67ea3 100644
--- a/sci-biology/dialign-tx/Manifest
+++ b/sci-biology/dialign-tx/Manifest
@@ -1,7 +1,8 @@
 AUX dialign-tx-1.0.2-fix-build-system.patch 588 BLAKE2B 3d9757b2b66497a47bfc3412a1e014f85e0dd12c2247103c813f3406ae0b34e8ba8a68cf31481f9f184095c07e63840fa2643c04a34a3e3f2605b90b2e8bba50 SHA512 30a474f59fb18dcef572299aa6bb6a22d9d6188193a3341bd04c32d6c388358e890ea17bcb8fd31fe80cee58330be6cb004b5936bf98d204e6f5a1e40627bf4f
-AUX dialign-tx-1.0.2-gnu89-inline.patch 493 BLAKE2B d37822818faabfa55cfd0a32cf0c0f22548ff29eb7c55712b1ef8e4fe4652531cfe821236e206a7bdaec74c4cac22e5d519be41f282b717d2119d7a79e478e44 SHA512 ad63585d93a10b44b1ca810b4a1bbbd991cc5fb1e762b941931d28f50dcc6a2bb6fdedea7c5faedcf4b2452dc8b99374423752694c5aa0a481ce5e97d8f5d3dd
+AUX dialign-tx-1.0.2-fno-common.patch 556 BLAKE2B d77bf94e61f376548f66776bde79081d18798d0645ec75fd314ac1394059e3498e20f638553b484e5e077cf5c253138ff57842920ce8237b63c4e799e51951cf SHA512 03b028cf2f0bf1b8e67bbc24fbbefc652ce2bd2de89aece26b32c6e2c86b8639cdbcf24e8a6a77ad31b690b5586f262affe39111483677372b547879207eacc3
+AUX dialign-tx-1.0.2-gnu89-inline.patch 1406 BLAKE2B 6a97e3300a730a87db721572fe6f4729b9915746d68f4b911ebe0d8ee91adade8b5584da39f1fdc549d6cbb0cbb941fddb4e63f669197a8761ee680bd35d9bac SHA512 55125d6634704cc2bfa4b44f502998bfb6e051190d398c8f3d3e9d48256b3f7fb2c9e54500e8c6d01493f2f501caaf12d7f0954c1e6ab455201ac2b507f43069
 AUX dialign-tx-1.0.2-implicits.patch 780 BLAKE2B b6eb50c7eaecf6439a1d27a0173661efef100a10976abf521fe50a4687d7e89e0cb094693118a84e68daae3918708ee3323073299d3d28786031a1f41c39af75 SHA512 783afc4527e0a77f0aac66bd8aa00ce3e5ddd81dd652c7459e551c609755eb3b0bd5b02566d8d1636b8840ed8567bb5652866c41ecf038ac9fe5682e1edf3e64
 AUX dialign-tx-1.0.2-modernize.patch 6149 BLAKE2B f6f3044b38d4652c2bc3aa63714beb42220ac00d0ecfe68b692b7af0f6dc1d29a8d053962d324e33bf32df2b92bd0fad40b5ec352ae837f6eaba1920f73d8d90 SHA512 cf1c1200500eb3e5f159468fe52536e8ffff60de21e09bb81e585270224ac4ce93d59fe80bd5a8212a4154ad90b23ec415be11b42792440c7fd53f75762d047a
 DIST DIALIGN-TX_1.0.2.tar.gz 1765296 BLAKE2B 3cce811a58fcf210f42c4a783e8ebb56c66436912ff04bce270058193f0d7b21114d75e2d67829c7abfbb35814e5a16f7f952611729ab211d066403a411db94a SHA512 ff43f1f2900bdd12b7a8ba382a4d6ad68e6c2e6d7ceb1a65f0e571bb891cc2dc2661fb6ce698aaabf0e20c14565b5927ae0076a7170c8611679f936851a00c43
-EBUILD dialign-tx-1.0.2-r2.ebuild 950 BLAKE2B 127ba32952e662b90c43dd901f4fe8aa1f6bb99d57adfc39b3bc65dfc9b52ece3809386b3fa2bf4ee649c83b5cc93306930b995ced48f586edbbb85c551a55d2 SHA512 813f6a5337e0c390ef57eedbbb80b9553f0f9bc81fbdbed58d4572e7a3d8d830b15ed54aa9033fadfa49157fcee94ec43396b9cd1c03d9889079fb2d4267cf15
+EBUILD dialign-tx-1.0.2-r2.ebuild 999 BLAKE2B 4fe11a5ee9d9fbb624911096f9a326dd0431bcf9f5e314ec9b551dbd1772284527e5f6ea4344a3698e337c4fbd75f631c72fb8c248d451902f9cb68b0d7d55fd SHA512 d8df0ccec568af8b0671101af9a7a88b7f52bcbe7095700fbc4e32c238bb464a9d213c90ab162195685361fb60f035ac7f8fbdf580633a32315005fd7378ab4d
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
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
index 123977916f06..78681265a0b7 100644
--- a/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild
+++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -15,12 +15,13 @@ LICENSE="LGPL-2.1"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 
-S=${WORKDIR}/${MY_P}
+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() {
@@ -34,12 +35,12 @@ src_compile() {
 
 src_install() {
 	dobin source/dialign-tx
-	insinto /usr/$(get_libdir)/${PN}/conf
+	insinto /usr/$(get_libdir)/dialign-tx/conf
 	doins -r conf/.
 }
 
 pkg_postinst() {
 	einfo "The configuration directory is"
-	einfo "${EROOT%/}/usr/$(get_libdir)/${PN}/conf"
-	einfo "You will need to pass this to ${PN} on every run."
+	einfo "${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-fno-common.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch
new file mode 100644
index 000000000000..de3104fa0ebb
--- /dev/null
+++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fno-common.patch
@@ -0,0 +1,22 @@
+--- 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
index 21f576f07052..fc8d0284e6ab 100644
--- 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
@@ -1,5 +1,25 @@
+--- 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. 
diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest
index fd37224607b6..abf651b02922 100644
--- a/sci-biology/embassy-emnu/Manifest
+++ b/sci-biology/embassy-emnu/Manifest
@@ -1,4 +1,4 @@
-AUX embassy-emnu-1.05.650_fix-build-system.patch 4072 BLAKE2B d256a82e214b8900eaab252e6695c4120eabb8379a59cfffe6a8b70e5decaf681af42ed9de3f9f74215a1a7f21e11367763aa705d7495eca41ab3fea1483e056 SHA512 644c4f0930a157ae9121354b49ddeb756b25d823d25733405fcc500d2080067f013443ba43a1512c6940fc4fd19cfe38c336dd0c58237354bad580cf9ba68b2e
+AUX embassy-emnu-1.05.650_fix-build-system.patch 3844 BLAKE2B b77be3d3917db4cdfcfce201089595a80b970575f77dffbc366c77ae27010b9a78582b035728008b20ae11b0c7c18b7b20a5fdfcd59b840f85f54a1db2fc5496 SHA512 1836ba79762f62f9e27a770a35b89ae5f2821c4d23dc93b1ab3505404105280256f1c43287471385a5be71659fbe614f5f7f97d78a4743b3b1b90b303a25f674
 DIST embassy-emnu-1.05.660.tar.gz 425595 BLAKE2B ed6ab4a0572ac4b57cf0f0b75a3894b1f950f7f373a7c6797ea0c34ba1b0d0e044f2c6951aec7c084340c6b207aa4c8b386055e92ceb9fc83c920fc70e83e665 SHA512 0cb0dafd53c4fd410409430dc12353989d2c226191acace26e81b457602b6b6c60f8eb1d0d9b36ea90b2420010c1a3e887a2458e8487008a36775961e378d0dd
 EBUILD embassy-emnu-1.05.660.ebuild 470 BLAKE2B 4a5fb352f30c729ded48ba438d978ff7ba85ee419eb1dbe94df07f34dd2b6fa50527615678c166cd627090bb2b15bd88d6d8ffd3d66e16006714d9a175444dec SHA512 ec9df242ed5a421fdbc45b59c1a9a9a3cfe540bde2ea010a29ac56e758d26fa0f1a1c850de644e82486a574850b0702d7d87adebfd851cd40076e17596c88f05
 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e
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
index 4e14bac1704a..ecd7f928da3a 100644
--- 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
@@ -1,13 +1,6 @@
- configure.ac           | 67 +++++++++++---------------------------------------
- emboss_acd/Makefile.am |  2 +-
- src/Makefile.am        |  7 +++---
- 3 files changed, 18 insertions(+), 58 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index 7482ade..b815bdb 100644
 --- a/configure.ac
 +++ b/configure.ac
-@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+@@ -635,33 +635,6 @@
  
  
  
@@ -41,7 +34,7 @@ index 7482ade..b815bdb 100644
  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 @@ AX_LIB_POSTGRESQL
+@@ -737,21 +710,6 @@
  
  
  
@@ -63,7 +56,7 @@ index 7482ade..b815bdb 100644
  dnl Test if --enable-localforce given
  locallink="no"
  embprefix="/usr/local"
-@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs],
+@@ -874,6 +832,13 @@
  AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
  
  
@@ -77,23 +70,24 @@ index 7482ade..b815bdb 100644
  
  
  # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
-@@ -899,20 +864,16 @@ dnl fi
+@@ -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)])])
-+dnl Test if --enable-curses is given
-+AC_ARG_ENABLE([curses],
-+[AS_HELP_STRING([--enable-curses], [curses])])
- 
+-
 -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])
@@ -105,8 +99,6 @@ index 7482ade..b815bdb 100644
  
  
  
-diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
-index e1c1878..e253c95 100644
 --- a/emboss_acd/Makefile.am
 +++ b/emboss_acd/Makefile.am
 @@ -1,3 +1,3 @@
@@ -114,11 +106,9 @@ index e1c1878..e253c95 100644
 -pkgdata_DATA = *.acd
 +pkgdata_DATA = $(srcdir)/*.acd
  pkgdatadir=$(prefix)/share/EMBOSS/acd
-diff --git a/src/Makefile.am b/src/Makefile.am
-index b295079..330c76f 100644
 --- a/src/Makefile.am
 +++ b/src/Makefile.am
-@@ -17,9 +17,8 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
+@@ -17,9 +17,8 @@
  	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
  	-I../../../ajax/acd -I../../../plplot
  else
@@ -130,10 +120,21 @@ index b295079..330c76f 100644
  endif
  
  if ISSHARED
-@@ -57,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+@@ -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 \
+-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-meme/Manifest b/sci-biology/embassy-meme/Manifest
deleted file mode 100644
index b52ed7b5f840..000000000000
--- a/sci-biology/embassy-meme/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX embassy-meme-4.7.650_fix-build-system.patch 2860 BLAKE2B 4b6d608d6fde975acd09373b39c64449585cd5f76e323fdd07c9ee9f741cf0f679a143bdd8ef110a0d93b70451425cf021b763860ef376b03c13f8a9456f8e62 SHA512 c44b219c75e67d17fcfd56145ae3709053bda38b8690141d1e9b846e4e4a9cab135f0dc9c5399e4712cf030ad562dd075f45c393e78157a2c1b92d80903b3d1c
-DIST embassy-meme-4.7.660.tar.gz 622448 BLAKE2B 93bbbe3de085aa2cd843349f8397b2d1f547be62afdb7deb30eec90a891f7825c847b92754bd956388b1bfe0250cabcbc7ad68f7d0378748a7949001016d344c SHA512 0536531b198aac09a9fe6c17cf1c60c766789c94a7f83f743a90aaa65061c95534bf398c53611a34549b7ec1a4928fdc45fe0d2553f25f85eeda41f90c2e8c6f
-EBUILD embassy-meme-4.7.660.ebuild 381 BLAKE2B 05a00fd0ca6d8e16bf61fe932f1e9805bac024fbd5bbee7bb4a37e2b3aaa3e394f5d9b8a9d208c127833c25b3de749abf27d849fe2bf0ab22557d565e3ce923f SHA512 b31045a88106d64ddbdd91cb85d06328b99b57eb490aa9f74f9cbf2464e3ed6485ca5e54ebd8146df8aacf0d44ee8f6f1d68cbb7a9e9dd3f2f46d637e2a8404b
-MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e
diff --git a/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild b/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild
deleted file mode 100644
index 8752e78d8fc9..000000000000
--- a/sci-biology/embassy-meme/embassy-meme-4.7.660.ebuild
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-EBO_DESCRIPTION="MEME - Multiple Em for Motif Elicitation"
-
-EBO_EAUTORECONF=1
-
-inherit emboss-r2
-
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="sci-biology/meme"
-
-S="${WORKDIR}/MEME-4.7.650"
-PATCHES=( "${FILESDIR}"/${PN}-4.7.650_fix-build-system.patch )
diff --git a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
deleted file mode 100644
index 56f5814e1efa..000000000000
--- a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch
+++ /dev/null
@@ -1,100 +0,0 @@
- configure.ac    | 49 +++++++------------------------------------------
- src/Makefile.am |  6 ++----
- 2 files changed, 9 insertions(+), 46 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index 391989f..d921f25 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${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 @@ AX_LIB_POSTGRESQL
- 
- 
- 
--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 @@ AC_ARG_ENABLE([systemlibs],
- 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
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 1600399..9f28162 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \
- 	-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
-@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
- 	$(XLIB)
- else
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+        -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-meme/metadata.xml b/sci-biology/embassy-meme/metadata.xml
deleted file mode 100644
index d1b9a7602ec2..000000000000
--- a/sci-biology/embassy-meme/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://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
index 5fd9d2e68b89..cf5e861ca30d 100644
--- a/sci-biology/embassy-phylipnew/Manifest
+++ b/sci-biology/embassy-phylipnew/Manifest
@@ -1,4 +1,5 @@
-AUX embassy-phylipnew-3.69.650_fix-build-system.patch 3255 BLAKE2B 9dfa7b3fb97508e7807b5b3d3ddfa48b1bb78cff3b8e658a0ca786e3c472f997267252c39bde9bbea4311f7b2192c2a0553617a7991e43aca3aa66db289dec41 SHA512 a0d4dcb3e7d4ce9b5cbd68168ebe7c8d248aa1166a6a52a0a77031291af8d2d32af0243571b669b9318426f753251d983ebb9b96eb1da81b594f4f4d20d7c249
+AUX embassy-phylipnew-3.69.650-fno-common.patch 16289 BLAKE2B 346f5d704be918503a80ab224e1892953a2d1d6ef642e6ced95fcb1476954e09d983bd0eef1d6afe71d2c4e043a05a99dd92748151e337ac5d3646d91008c2e9 SHA512 0ea1f10865832a44647f0888eabef1df6e5baadace9fda782f171d52eef70fc7d8ef80317d46eaeb029896b8b0b4ca0d845561ae761daf406f7c26e18ebd1341
+AUX embassy-phylipnew-3.69.650_fix-build-system.patch 3019 BLAKE2B 39c2d7843ffac8c0a04c70d307d5651f2e53cc386c3a9b1f312d4fd53a9b9ba235a02931c4812a750da8711988e262b1c9a51a7152da20f61cd56c0d21607a89 SHA512 7d46280ffadcbc07e01d09a49a7896539a5c0c271979fcb3e1ffdf385051812adeaabec186c73e2105a710eee2fd340d89bbcbd4ecfa112879fb00cbc58c2dfe
 DIST embassy-phylipnew-3.69.660.tar.gz 1741298 BLAKE2B 58a2c66ffb9c447fa17462bf54d7b8e65702701d74c1f16ec6906a3acaf076ebcab30982befe6334101bc483901132069a71ffa0e2334aaee0da02a30276b7f2 SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5
-EBUILD embassy-phylipnew-3.69.660.ebuild 361 BLAKE2B 46ace0d20506300a83a423edd19d0305d4e7a072348a7355271dce004e896d92ebd04f2ff342060a5ee2c78f92bd9a6bbccb895eeef462891f78e08d49bcd553 SHA512 3836e21a22a375a4b58fc32b29bdf0481f7bd175b44a131069f6b68ee04d5b507732cc8cc8429afd47f4b26b853c54dd244cd1535a6209708b65989f11d7aa2e
+EBUILD embassy-phylipnew-3.69.660.ebuild 409 BLAKE2B 35bac3a33793b140470ef4c627b578317f22efdd7d9c71eeae947f0a6399d94829c5ceeb85d537616811f593b3b54eeda9c1f9bbf0710a20d3eba12891c0f07e SHA512 d088e1121fed9e50066767b58a4d2ea61e5ad5167293cc3780e9bec71f4613d144b985f96d235ab9665a94bff8703a005cdc86916d63cf593941a3e6aeac1165
 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e
diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild
index 3ac088ed6ef9..c5ba6a540bfc 100644
--- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild
+++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -14,4 +14,7 @@ LICENSE+=" free-noncomm"
 KEYWORDS="~amd64 ~x86 ~x86-linux"
 
 S="${WORKDIR}/PHYLIPNEW-3.69.650"
-PATCHES=( "${FILESDIR}"/${PN}-3.69.650_fix-build-system.patch )
+PATCHES=(
+	"${FILESDIR}"/${PN}-3.69.650_fix-build-system.patch
+	"${FILESDIR}"/${PN}-3.69.650-fno-common.patch
+)
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
new file mode 100644
index 000000000000..448000547471
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-fno-common.patch
@@ -0,0 +1,627 @@
+--- 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
index 1cba944094a2..95951e632188 100644
--- 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
@@ -1,13 +1,6 @@
- configure.ac           | 49 +++++++------------------------------------------
- emboss_acd/Makefile.am |  2 +-
- src/Makefile.am        |  7 ++-----
- 3 files changed, 10 insertions(+), 48 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index e5bfaf1..09ed517 100644
 --- a/configure.ac
 +++ b/configure.ac
-@@ -635,33 +635,6 @@ AS_CASE([${host_os}],
+@@ -635,33 +635,6 @@
  
  
  
@@ -41,7 +34,7 @@ index e5bfaf1..09ed517 100644
  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 @@ AX_LIB_POSTGRESQL
+@@ -781,21 +754,6 @@
  
  
  
@@ -63,7 +56,7 @@ index e5bfaf1..09ed517 100644
  dnl Test if --enable-localforce given
  locallink="no"
  embprefix="/usr/local"
-@@ -918,6 +876,13 @@ AC_ARG_ENABLE([systemlibs],
+@@ -918,6 +876,13 @@
  AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
  
  
@@ -77,8 +70,6 @@ index e5bfaf1..09ed517 100644
  
  
  # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
-diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
-index e1c1878..e253c95 100644
 --- a/emboss_acd/Makefile.am
 +++ b/emboss_acd/Makefile.am
 @@ -1,3 +1,3 @@
@@ -86,11 +77,9 @@ index e1c1878..e253c95 100644
 -pkgdata_DATA = *.acd
 +pkgdata_DATA = $(srcdir)/*.acd
  pkgdatadir=$(prefix)/share/EMBOSS/acd
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 1883ce9..fb1787f 100644
 --- a/src/Makefile.am
 +++ b/src/Makefile.am
-@@ -16,10 +16,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \
+@@ -16,10 +16,7 @@
  	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
  	-I../../../ajax/acd -I../../../plplot
  else
@@ -102,10 +91,21 @@ index 1883ce9..fb1787f 100644
  endif
  
  if ISSHARED
-@@ -120,5 +117,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+@@ -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 \
+-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/gmap/Manifest b/sci-biology/gmap/Manifest
index 2221d6ef0191..389c55c2b131 100644
--- a/sci-biology/gmap/Manifest
+++ b/sci-biology/gmap/Manifest
@@ -1,3 +1,4 @@
-DIST gmap-gsnap-2015-12-31.v5.tar.gz 4169874 BLAKE2B bbbf53b72b5b7f97ba0eb05db7daa3d1f8a9330f32b96c2460a904a9f9f22078093f6fa585a12d4275e0943145ee78ef99348de4f19349dfa4e81d5f65572e1c SHA512 d42623c60c298d9d3009893432f3eef8cb764bf7cf26b42e6a95b27a468fffab20c8307597c4c8e1afdd61f35652246568c3162137ce59fc4850aaab1062bb48
-EBUILD gmap-2015.12.31.5.ebuild 573 BLAKE2B 0f419e1978d475ea2cc509667d0bf5c389761a42439c8778309217a8b3bcb47215344531784b576d5dba5f0c972cf51a6cafc624f0a0ea3a899387b7a507200b SHA512 8a07e7de0c5d57a2fdc4b7e9da261f469722482be4acdaebcdd76b67d26440ad04cf93ce51a98e908a19ccb6d98bc2725103f9cac7cfcf254812d6499ce8aa70
+AUX gmap-2020.10.27-fno-common.patch 483 BLAKE2B 61055eccbfddd694128288594056d880beaab5f8cf61774c7f745a948fff15ff7e5261c333a0f26152e6f23d8546958e497b7975c9d8150b5279076be05dd4b0 SHA512 ea3de0c56db2c4683cad8471e5f772670288d003e7be8404b8c7528af5d4624c40f390c77b35c3f435ce8459e629783b1d26e8a76f2a479aed3c22feaa78a1a0
+DIST gmap-gsnap-2020-10-27.tar.gz 4480720 BLAKE2B 9f8e8bfab19c079111d42ec466dd145385d35e3fde0a809e46776ed1b62b599664f12618803ea4475b6961a053423a8794d0b77eb0b308bdfa927b5bcaa7d49c SHA512 22e59adf404f5ef524b3cd472fb3124d03c8c55aa7946b9dc3901f5070339dc765f8f1ecc7e394b69a14bf80923f7a9db8d545e45328a346996b3288115a535b
+EBUILD gmap-2020.10.27.ebuild 479 BLAKE2B f3363283af3980dd1d95f33d66ea0bbe54780e9d4ff0a1b0c601d545592086a27d4af2c446b500a43a20887bb0df9632e6716fccb3e925e786b007b2ddbe5302 SHA512 7db5938e76273af4063b2c84c292ad657f50d40ccff35fe391217fefcc358882d86dbc5db1fee448b7e36b0ca5a3c6aae438691838df61274df6682d1c473671
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
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
new file mode 100644
index 000000000000..cc225a78c26e
--- /dev/null
+++ b/sci-biology/gmap/files/gmap-2020.10.27-fno-common.patch
@@ -0,0 +1,22 @@
+--- 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-2015.12.31.5.ebuild b/sci-biology/gmap/gmap-2020.10.27.ebuild
index 82ae6f3f2748..a90f0f631068 100644
--- a/sci-biology/gmap/gmap-2015.12.31.5.ebuild
+++ b/sci-biology/gmap/gmap-2020.10.27.ebuild
@@ -1,12 +1,9 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit versionator
-
-MY_BASE_PV="$(replace_all_version_separators '-' $(get_version_component_range 1-3))"
-MY_PV="${MY_BASE_PV}.v$(get_version_component_range 4)"
+MY_PV="$(ver_rs 1- '-')"
 
 DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences"
 HOMEPAGE="http://research-pub.gene.com/gmap/"
@@ -14,7 +11,7 @@ SRC_URI="http://research-pub.gene.com/gmap/src/gmap-gsnap-${MY_PV}.tar.gz"
 
 LICENSE="gmap"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
 
-S="${WORKDIR}/gmap-${MY_BASE_PV}"
+S="${WORKDIR}/gmap-${MY_PV}"
+PATCHES=( "${FILESDIR}"/${PN}-2020.10.27-fno-common.patch )
diff --git a/sci-biology/lagan/Manifest b/sci-biology/lagan/Manifest
index bb94011e3eae..6b6322158a4d 100644
--- a/sci-biology/lagan/Manifest
+++ b/sci-biology/lagan/Manifest
@@ -1,7 +1,11 @@
-AUX lagan-2.0-fix-c++14.patch 13525 BLAKE2B 79037fa65301393f3a007adb424f4a88f72f46ad0cf7c310a07f14b64437fb8fd3dc6da90df5c79e468b424a895797cf01e5b30413435a18ea933d912eb0428e SHA512 f62b523cf9692a1394276ac674ccf7ce9a0070c646c95d1f20b8e0ace61afffd04aae3a098511bb106ab62089e70bebfae6ba25aaffcccbbe7f8397a30c2900a
-AUX lagan-2.0-flags.patch 5848 BLAKE2B 41394e65d15be217dea753a9641ee72833ff87f5101fa19ba009f4ca4b97d8fe22594d041105ba03ddb53ad83f635fec79e9125f539eff3cd1cbcdc186d3023e SHA512 63917ed217c44cade1c87dd6498cb7f6180c30eaba3875fa77f7e73b894aadab1469aca87650d1017a44fcac548552c3bdfcaff29b24023d23c7424079ad91cf
-AUX lagan-2.0-gcc4.3.patch 821 BLAKE2B c25d5afef654a27a61fb658de4fc26afe713400133123b47202fab8861c95b6ed56a229b0f88a811b5dc36e94125d0c333c6b13a14e1f1ff944c68c2ee3acd1c SHA512 91b56b0cfc27f799fed164a8a32b4840ea2e7f7796d334b2bce8bd27bc2fb96b4cdb0912c737c874f767a16ffcdd4e4623a0f80a35082aa4289882d1502cc0df
-AUX lagan-2.0-qa-implicit-declarations.patch 2371 BLAKE2B e6ad9e67c322271fab92bf32094903d201f5cd81ce6cbf5f5f14708d53eac649024ca1c7e378a2a7ee26b0e4a7d99b275476f32ec32d1e20575d09dc9e2845c5 SHA512 eec54cec02a5c8c875a4d64238276f116baa8f3d780573ca5143621ca62a1e96ba4045ae37d45321fc040b78216607d787c2c6c909a8264f17f99a0e07295bf5
+AUX lagan-2.0-C99-static-inline.patch 7673 BLAKE2B 42b4ab27fa4a86786cdf02c8d7b16b1dc1439d2a6af15b6b9a7bfd46c97debf150140b5a9697d8d47d40d983388cd2f7f9167971b8166f385be83870ea095790 SHA512 db1798730a3dc093d56e6f778dd7380d8dab8f1919b74e3eb752cde353e85385755cdabf61c2692e666acf50b21f34d341c79a3c67ddefbc824d8c78d077345d
+AUX lagan-2.0-ambiguous-end.patch 1445 BLAKE2B 3d5e0467dfe60e2d5c25b8f90ba5d25e22bfcf63f8cf3b016cd02a837b51a1e653f8cb2ff5afb73ab7dbd38a22bc9d7fb7646080b6b02cde50fbe4beb55cce60 SHA512 85a9d3d1ce9efd00fdb98835e849fe4d22c059d5e4b8b3c11b7c227d5fd74ae522e3189c38c2ea62fb98c21228591dcaa8ea5a80c9d56c46420e716c30ce8a4d
+AUX lagan-2.0-conflicting-getline.patch 711 BLAKE2B 7ab19955c833e47dee06f214b52a79a55313ce7abf338cdeb4121a84b93027af601eb4379686bb2e4a5ebe215bf4321f8504ad4d91d8e7434575e0dead871d54 SHA512 867613347b50ab20e6640c7250609cd697d2217fe1c7731ee2688ccaff5e959fd1f0c96c80eabcb878d35bd679eb28931c75be808502fd4ad0fe184ddc2a6ea2
+AUX lagan-2.0-gcc-10.patch 506 BLAKE2B 0c35eb155a80e3c71f70d2013d47e77f38f1c6a6f7db8cace6f80a3839b9d6ea97429802a4c4081195c5fb3dd17680ee0d1f37a9ffd3cb2c47223812ef8245e3 SHA512 fe71d037d89a888e14c7c5d411ef2dd80f4cd3627fdc706c0d78d89a9befbec55cd06a5eb763d5d16d708156f067cad6f515c04235dbc5f9e842f663eb44b8e7
+AUX lagan-2.0-gcc-4.8.patch 649 BLAKE2B 4a4f76ce4709a3ae6210574604549aedc66ecbe27b6276d4470bb910765326028b94d2fdc1a28b5cfc63ff6b44005e2a33b42b42adb3f633af1649897e08b522 SHA512 504b9dbddbca07fd1bb3ebec8a8087af6548ac17c96acb8e76740ca2e63d40b695aed1e1e94cfbd24c6b2836c98e787dffddbb9884c338fd69a8b4e37046f7cb
+AUX lagan-2.0-gcc-9.patch 781 BLAKE2B 8280ebd4f445441d41a73e786568e4d1e17bbd2e73ac52f828651576bfb128986911efb8ce8b988bc540643f647d992bbf6793e0081adffe6aacace81174e0c7 SHA512 ecc007c8e266e5d859f9f5db99c9ea9d1048b7faba7dbad29ee9c04ee8cbd628e052615cec4123446d54f05f5c906a58e6e90cf6ac449e245c02d721750998ff
+AUX lagan-2.0-makefile.patch 6257 BLAKE2B 284dc6f21dd303f4b10f6e8cb30054c4ddd8df62c7c43c42a20351f4d81db4360c75feea8f55d32323c3349dc896c94213da7ab9074ee78f78e8ed82b0a0e211 SHA512 fc255585fc53c66b0a2f4e46788a59f8fdfae67b5f9ca4f4b0ac9224a7a915a387d991cb20315aa18a42df82ffa2b832270f0919f9939faf3b979d026e562c81
+AUX lagan-2.0-qa-implicit-declarations.patch 1396 BLAKE2B 556a43acf76e20a8484fd6ab5d0682b4b29206568b657b8daf09f79577890afd8a594b3897fc2322fffb5e2810a018638af0488c872e9d0794cb685a55b91e79 SHA512 4275aacf1dfa7d712a14ea5d8eafe11045c3b47a02c92915703d095af7b00f2206687eec568d14bfd00718f6b2430bd38cf70ac86cc5d550870d19f5fe6c6d97
 DIST lagan20.tar.gz 589115 BLAKE2B 8aaee40b767d7c1828760449e3bf2718210ad345447524ec2c391eb9f2856023f9258618d3d2625b15c42af814615870082bff6320ba0372dff79221798d2618 SHA512 f77217ab534df33834a725eb6e1b716f7bbffa98768a42c2294a6ab62404192e560bb05ffd41e4cdccb5b96ef9efceb8ecdc06472bbc6a301e1d11572ba29b98
-EBUILD lagan-2.0-r3.ebuild 1659 BLAKE2B 0ee31ba110a6238ac9218fc3d59347c9ee97fa11ce097c0a1f5e53c45fefa74ed83e35a1314e2f7fd57fbb3bdb64863109400af32f39f6dba13c273d722ded99 SHA512 b5efe429851ae0a3676a6e63017ebabdcae169667d091b2e69c0c2daa401f34e0ff3b789f8bacd78376befc466bb20de8f0d80bae63c332a6c412f01794f457b
+EBUILD lagan-2.0-r4.ebuild 1493 BLAKE2B 81a03c4ab005e5190a2275fa160b86fb16bfb3d8ef1dc794363df692cce7eb8389974af99acbaa5677903db2d75e02e63920cae712abcd7aa421fe7326b8afda SHA512 b9b8e5e12a9ea1276f38806f933cbe7e73b63782510f4e66336ab0a5e1ceeb634d46b81eecf953421d5eaf7e1ce42e130df40b66e6137f0aa8af68155e36363f
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
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
new file mode 100644
index 000000000000..2c9d88111aee
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch
@@ -0,0 +1,258 @@
+--- 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
new file mode 100644
index 000000000000..945120b1fc47
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch
@@ -0,0 +1,49 @@
+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
new file mode 100644
index 000000000000..075753a924c9
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch
@@ -0,0 +1,24 @@
+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-fix-c++14.patch b/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch
deleted file mode 100644
index 9865f2756c5a..000000000000
--- a/sci-biology/lagan/files/lagan-2.0-fix-c++14.patch
+++ /dev/null
@@ -1,473 +0,0 @@
-Fix building with C++14, which errors out due to namespace collisions with std::end
-in C++14 mode, due to crappy 'using namespace std' declared everywhere.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=594148
-
---- a/src/ancseq.cpp
-+++ b/src/ancseq.cpp
-@@ -30,7 +30,6 @@
- #include <stdlib.h>
- #include <stdio.h>
- 
--using namespace std;
- 
- #include "util.cpp"
- #include "faindex.cpp"
---- a/src/ancseqrest.cpp
-+++ b/src/ancseqrest.cpp
-@@ -31,7 +31,6 @@
- #include <stdlib.h>
- #include <stdio.h>
- 
--using namespace std;
- 
- #define fastaRowLength 50
- typedef char* pchar;
---- a/src/cutmfa.cpp
-+++ b/src/cutmfa.cpp
-@@ -45,7 +45,6 @@
- #include <stdlib.h>
- #include <stdio.h>
- 
--using namespace std;
- 
- // TODO refactor in classes and normal make project
- 
---- a/src/glocal/glocal.cpp
-+++ b/src/glocal/glocal.cpp
-@@ -7,9 +7,9 @@
- }
- 
- //vectors that would be needed globally
--vector<Fragment> fragments;
--vector<Point>startPoints;
--vector<Point>endPoints;
-+std::vector<Fragment> fragments;
-+std::vector<Point>startPoints;
-+std::vector<Point>endPoints;
- long long int numFragments;
- InterPoint inter;
- 
-@@ -19,7 +19,7 @@
- RI RI_regions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
- LI LI_regions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
- 
--vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
-+std::vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
- 
- Name allNames;
- 
---- a/src/glocal/io.cpp
-+++ b/src/glocal/io.cpp
-@@ -3,9 +3,9 @@
- #include<io.h>
- #include<algorithm>
- 
--extern vector <Fragment> fragments;
--extern vector <Point> startPoints;
--extern vector <Point> endPoints;
-+extern std::vector <Fragment> fragments;
-+extern std::vector <Point> startPoints;
-+extern std::vector <Point> endPoints;
- extern Name allNames;
- 
- bool PointCompare(const Point &f1, const Point &f2) {
-@@ -223,8 +223,8 @@
- 		startPoints.push_back(startPoint);
- 		endPoints.push_back(endPoint);
- 	}
--	sort(startPoints.begin(), startPoints.end(), PointCompare);
--	sort(endPoints.begin(), endPoints.end(), PointCompare);
-+	std::sort(startPoints.begin(), startPoints.end(), PointCompare);
-+	std::sort(endPoints.begin(), endPoints.end(), PointCompare);
- }
- 
- 
---- a/src/glocal/leftinfluence.cpp
-+++ b/src/glocal/leftinfluence.cpp
-@@ -154,8 +154,8 @@
- 
- 	if (second->score == -1) { return TRUE; }
- 
--	dummy.seq1Start = max(first->seq1End, second->seq1End) + 2;
--	dummy.seq2Start = max(first->getSeq2End(LeftInfluence->reflectFlag), second->getSeq2End(LeftInfluence->reflectFlag)) + 1;
-+	dummy.seq1Start = std::max(first->seq1End, second->seq1End) + 2;
-+	dummy.seq2Start = std::max(first->getSeq2End(LeftInfluence->reflectFlag), second->getSeq2End(LeftInfluence->reflectFlag)) + 1;
- 
- 	if (first->getSeq2End(LeftInfluence->reflectFlag) > second->getSeq2End(LeftInfluence->reflectFlag)) {
- 		dummy.nameIter = first->nameIter;
-@@ -444,7 +444,7 @@
- 	temp.seq1 = col - diag;
- 	temp.seq2 = col;
- 
--	pair<Point,LI*> pairp(temp, LeftInfluence);
-+	std::pair<Point,LI*> pairp(temp, LeftInfluence);
- 	tempinter = inter.insert(pairp);
- 
- 	colInter->second = tempinter;
---- a/src/glocal/leftinfluence.h
-+++ b/src/glocal/leftinfluence.h
-@@ -39,15 +39,15 @@
- 
- 
- 
--typedef list<Fragment*> Owner;
--typedef map <long long int ,Owner::iterator,longlongCompare2> CBound;
-+typedef std::list<Fragment*> Owner;
-+typedef std::map <long long int ,Owner::iterator,longlongCompare2> CBound;
- 
--typedef multimap <Point ,struct LI *,paircomp> InterPoint;
-+typedef std::multimap <Point ,struct LI *,paircomp> InterPoint;
- 
--typedef map <long long int ,InterPoint::iterator,longlongCompare2> CInter;
--typedef map <long long int,Owner::iterator,longlongCompare2> DBound;
-+typedef std::map <long long int ,InterPoint::iterator,longlongCompare2> CInter;
-+typedef std::map <long long int,Owner::iterator,longlongCompare2> DBound;
- 
--typedef map <long long int,InterPoint::iterator,longlongCompare2> DInter;
-+typedef std::map <long long int,InterPoint::iterator,longlongCompare2> DInter;
- 
- 
- 
---- a/src/glocal/rightinfluence.h
-+++ b/src/glocal/rightinfluence.h
-@@ -17,7 +17,7 @@
- };
- 
- 
--typedef  map<const long long int , Fragment*,longlongCompare> Active;
-+typedef  std::map<const long long int , Fragment*,longlongCompare> Active;
- 
- typedef struct RI {
-   //List of active regions
---- a/src/glocal/score.cpp
-+++ b/src/glocal/score.cpp
-@@ -4,7 +4,7 @@
- #include<rightinfluence.h>
- #include<fstream>
- 
--extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
-+extern std::vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
- 
- 
- float Score::getScore(Fragment *up, Fragment * down) {
-@@ -36,7 +36,7 @@
- 
- 
- void initScoreFunctionPointers(char * scoreFileName) {
--	ifstream SFP;
-+	std::ifstream SFP;
- 	char line[255];
- 
- 	SFP.open(scoreFileName);
---- a/src/glocal/structs.h
-+++ b/src/glocal/structs.h
-@@ -12,7 +12,6 @@
- #include <list>
- #include <string.h>
- 
--using namespace std;
- 
- #define RIGHT 0
- #define LEFT 1
-@@ -49,7 +48,7 @@
- };
- 
- 
--typedef map<const char*,long long int ,ltstr> Name;
-+typedef std::map<const char*,long long int ,ltstr> Name;
- 
- 
- typedef struct Fragment {
---- a/src/lagan2mfa.cpp
-+++ b/src/lagan2mfa.cpp
-@@ -6,7 +6,6 @@
- #include <stdlib.h>
- #include <stdio.h>
- 
--using namespace std;
- 
- // TODO refactor in classes and normal make project
- 
---- a/src/makecons.cpp
-+++ b/src/makecons.cpp
-@@ -18,7 +18,6 @@
- #include <ctype.h>
- #include <time.h>
- 
--using namespace std;
- 
- #define fastaRowLength 50
- #define bufSize 2000
---- a/src/utils/Glue.cpp
-+++ b/src/utils/Glue.cpp
-@@ -170,7 +170,7 @@
- }
- 
- void printCoordinates (int seq, int begin, int end){
--  cout << seqs[seq].getID() << ":" << getSeqCoord(seq, begin) << "-" << getSeqCoord(seq, end) << " ";
-+  std::cout << seqs[seq].getID() << ":" << getSeqCoord(seq, begin) << "-" << getSeqCoord(seq, end) << " ";
- }
- 
- int printRegion (int begin, int end){
-@@ -183,7 +183,7 @@
-       score += rescoreRegion (seqs[i], seqs[j], begin, end);
-     }
-   }
--  cout << score << endl;
-+  std::cout << score << std::endl;
-   return score;
- }
- 
-@@ -223,7 +223,7 @@
-     }    
-   }
- 
--  cout << "= score=" << score << endl;
-+  std::cout << "= score=" << score << std::endl;
- }
- 
- int countLets (SafeVector<char> &data){
-@@ -355,7 +355,7 @@
-   FILE* outfile;
-   
-   if (argc < 2 || argc > 3){
--    cerr << "Usage: Glue align.mfa \n" << endl;
-+    std::cerr << "Usage: Glue align.mfa \n" << std::endl;
-     exit (1);
-   }
-   
-@@ -375,7 +375,7 @@
-   SafeVector<int> merged1label, merged2label;
-   int begin1 = 1, end1 = 1;
- 
--  ifstream data (argv[1]);
-+  std::ifstream data (argv[1]);
-   int alignNum = 0;
-   strand.push_back ('?'); // nothing for alignNum 0
- 
-@@ -452,7 +452,7 @@
-   SafeVector<char> temp1 (begin1 - 1, 'N');
-   SafeVector<char> temp2 (begin1 - 1, '-');
- 
--  for (int i = 0; i < min ((int) temp2.size(), CNTG_BRK_N); i++)
-+  for (int i = 0; i < std::min ((int) temp2.size(), CNTG_BRK_N); i++)
-     temp2[i] = 'N';
- 
-   merged1 = merge (temp1, merged1);
-@@ -471,12 +471,12 @@
-       if (isalpha(merged2[j])) pos2++;
-       
-       if (merged1label[j] == i){
--	min1 = min (min1, pos1);
--	max1 = max (max1, pos1);
-+	min1 = std::min (min1, pos1);
-+	max1 = std::max (max1, pos1);
-       }
-       if (merged2label[j] == i){
--	min2 = min (min2, pos2);
--	max2 = max (max2, pos2);
-+	min2 = std::min (min2, pos2);
-+	max2 = std::max (max2, pos2);
-       }
-     }
- 
-@@ -489,6 +489,6 @@
-       fprintf (outfile, "%d %d %d 0 0 0 0 %c 0 %d %d\n", i, min1, max1, strand[i], min2, max2);
-   }
-   
--  printMFA (cout, merged1, string ("first"), 60);
--  printMFA (cout, merged2, string ("second"), 60);
-+  printMFA (std::cout, merged1, std::string ("first"), 60);
-+  printMFA (std::cout, merged2, std::string ("second"), 60);
- }
---- a/src/utils/MultiSequence.h
-+++ b/src/utils/MultiSequence.h
-@@ -12,7 +12,6 @@
- #include "Sequence.h"
- #include "SafeVector.h"
- 
--using namespace std;
- 
- class MultiSequence {
-  private:
-@@ -54,10 +53,10 @@
- 
-   // Read in all of the Sequences in an MFA file and append them to the
-   // existing MultiSequence object.
--  void addRawFromMFA (const string& filename){
-+  void addRawFromMFA (const std::string& filename){
-     
-     // open up file for reading
--    ifstream infile (filename.c_str());
-+    std::ifstream infile (filename.c_str());
-     
-     // check for error
-     assert (!infile.fail());
-@@ -75,7 +74,7 @@
- 
-   // Read in all of the Sequences in an MFA file and append them to the
-   // existing MultiSequence object.
--  void addRawFromMFA (ifstream &infile){
-+  void addRawFromMFA (std::ifstream &infile){
-     
-     // check for error
-     assert (!infile.fail());
-@@ -89,7 +88,7 @@
-   }
- 
-   // Writes sequences to outfile in XMFA format.
--  void writeToXMFA (ostream &outfile, int numColumns) const {
-+  void writeToXMFA (std::ostream &outfile, int numColumns) const {
-     for (int i = 0; i < (int) sequences.size(); ++i){
-       sequences[i].writeToXMFA (outfile, numColumns);
-     }
---- a/src/utils/Output.h
-+++ b/src/utils/Output.h
-@@ -2,18 +2,18 @@
- #define OUTPUT_H
- 
- // print reversed string in MFA format
--void printMFA (ostream &outfile, SafeVector<char> &data, string comment, int numColumns){
-+void printMFA (std::ostream &outfile, SafeVector<char> &data, std::string comment, int numColumns){
- 
-   int charsWritten = 0;
- 
--  outfile << ">" << comment << endl;
-+  outfile << ">" << comment << std::endl;
-   for (int i = 0; i < (int) data.size(); i++){
-     outfile << data[i];
-     charsWritten++;
--    if (charsWritten % numColumns == 0) outfile << endl;
-+    if (charsWritten % numColumns == 0) outfile << std::endl;
-   }
-   
--  if (charsWritten % numColumns != 0) outfile << endl;
-+  if (charsWritten % numColumns != 0) outfile << std::endl;
- }
- 
- 
---- a/src/utils/SafeVector.h
-+++ b/src/utils/SafeVector.h
-@@ -10,7 +10,6 @@
- #include <assert.h>
- #include <vector>
- 
--using namespace std;
- 
- // class derived from the STL std::vector
- template<class TYPE>
-@@ -19,9 +18,9 @@
- 
-   // miscellaneous constructors
-   SafeVector () {} 
--  SafeVector (size_t size) : vector<TYPE>(size) {} 
--  SafeVector (size_t size, const TYPE &value) : vector<TYPE>(size, value) {} 
--  SafeVector (const SafeVector &source) : vector<TYPE>(source) {}
-+  SafeVector (size_t size) : std::vector<TYPE>(size) {} 
-+  SafeVector (size_t size, const TYPE &value) : std::vector<TYPE>(size, value) {} 
-+  SafeVector (const SafeVector &source) : std::vector<TYPE>(source) {}
- 
- #ifdef ENABLE_CHECKS
- 
---- a/src/utils/Sequence.h
-+++ b/src/utils/Sequence.h
-@@ -8,15 +8,14 @@
- #include <string>
- #include "SafeVector.h"
- 
--using namespace std;
- 
- class Sequence {
- 
-  private:
- 
-   // Read header of MFA/XMFA file.
--  bool readHeader (ifstream &infile, bool &isXMFA){
--    string header;
-+  bool readHeader (std::ifstream &infile, bool &isXMFA){
-+    std::string header;
-     
-     while (true){
-       
-@@ -24,7 +23,7 @@
-       if (infile.fail() || infile.eof()) return false;
-       
-       // get new header line
--      getline (infile, header);
-+      std::getline (infile, header);
-       
-       // check that header line is not empty
-       if (header.length() != 0) break;
-@@ -64,7 +63,7 @@
-   int startCoord;            // sequence position of first character
-   int endCoord;              // sequence position of last character
-   char direction;            // + or -
--  string comment;            // comments                             
-+  std::string comment;            // comments                             
- 
-  public:
- 
-@@ -77,7 +76,7 @@
-   }
- 
-   // Constructor.  Reads in a sequence from the input file.
--  Sequence (ifstream &infile){
-+  Sequence (std::ifstream &infile){
- 
-     bool isXMFA = true;
-     
-@@ -147,7 +146,7 @@
-   }
- 
-   // Constructor.  Gets sequence from array data.
--  Sequence (SafeVector<char> data, string comment) : data(data), comment(comment) {
-+  Sequence (SafeVector<char> data, std::string comment) : data(data), comment(comment) {
-     length = data.size() - 1;
-     id = 0;
-     startCoord = 1;
-@@ -165,7 +164,7 @@
-     return temp;
-   }
- 
--  const string getComment () const {
-+  const std::string getComment () const {
-     return comment;
-   }
- 
-@@ -197,9 +196,9 @@
-   const int getEndCoord () const { assert (isValid); return endCoord; }
- 
-   // Print XMFA header only.
--  void writeXMFAHeader (ostream &outfile) const {
-+  void writeXMFAHeader (std::ostream &outfile) const {
-     assert (isValid);
--    outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << endl;
-+    outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << std::endl;
-   }
- 
-   // Return sequence ID.
-@@ -209,20 +208,20 @@
-   void setID (int id) { assert (isValid); this->id = id; }
- 
-   // Writes sequence to XMFA format.
--  void writeToXMFA (ostream &outfile, int numColumns) const {
-+  void writeToXMFA (std::ostream &outfile, int numColumns) const {
- 
-     assert (isValid);
-     
-     // print XMFA header
--    outfile << ">" << comment << endl;
-+    outfile << ">" << comment << std::endl;
-     //  outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << endl;
-     
-     // print character data
-     for (int i = 1; i <= length; ++i){
-       outfile << data[i];      
--      if (i % numColumns == 0) outfile << endl;
-+      if (i % numColumns == 0) outfile << std::endl;
-     }
--    if (length % numColumns != 0) outfile << endl;
-+    if (length % numColumns != 0) outfile << std::endl;
-   }
- };
- 
diff --git a/sci-biology/lagan/files/lagan-2.0-gcc-10.patch b/sci-biology/lagan/files/lagan-2.0-gcc-10.patch
new file mode 100644
index 000000000000..bd9824cf2ed0
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-gcc-10.patch
@@ -0,0 +1,27 @@
+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
new file mode 100644
index 000000000000..3d7ed780445f
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch
@@ -0,0 +1,25 @@
+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
new file mode 100644
index 000000000000..6ea30e57a854
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-gcc-9.patch
@@ -0,0 +1,25 @@
+# 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-gcc4.3.patch b/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch
deleted file mode 100644
index a4b1d6808e2f..000000000000
--- a/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-diff -durr lagan20-orig/src/glocal/score.cpp lagan20/src/glocal/score.cpp
---- lagan20-orig/src/glocal/score.cpp	2009-02-04 15:25:57.698333297 +0000
-+++ lagan20/src/glocal/score.cpp	2009-02-04 15:27:23.894092890 +0000
-@@ -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 -durr lagan20-orig/src/utils/Glue.cpp lagan20/src/utils/Glue.cpp
---- lagan20-orig/src/utils/Glue.cpp	2009-02-04 15:25:57.702333182 +0000
-+++ lagan20/src/utils/Glue.cpp	2009-02-04 15:27:04.190822654 +0000
-@@ -1,6 +1,7 @@
- #include "MultiSequence.h"
- #include "SafeVector.h"
- #include "Output.h"
-+#include <string.h>
- #include <math.h>
- #include <assert.h>
- #include <fstream>
diff --git a/sci-biology/lagan/files/lagan-2.0-flags.patch b/sci-biology/lagan/files/lagan-2.0-makefile.patch
index e324ef64c4c6..1bef6721ab9b 100644
--- a/sci-biology/lagan/files/lagan-2.0-flags.patch
+++ b/sci-biology/lagan/files/lagan-2.0-makefile.patch
@@ -1,107 +1,120 @@
-diff --git a/Makefile b/Makefile
-index fbbbe79..a1d449b 100644
 --- a/Makefile
 +++ b/Makefile
-@@ -1,5 +1,5 @@
+@@ -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)
-diff --git a/src/Makefile b/src/Makefile
-index 7f6b6fd..dd6309b 100644
+-	(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
-@@ -4,51 +4,51 @@ CFLAGS = -O3 # -Wall -W
+@@ -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))
-+	$(MAKE) -C glocal
++	(cd glocal && $(MAKE))
  clean: 
  	rm -f *.o *~ utils/*~ mlagan.purify core
- 	(cd glocal; $(MAKE) clean)
+-	(cd glocal; $(MAKE) clean)
++	(cd glocal && $(MAKE) clean)
  ../anchors: anchors.c skiplist.c
 -	$(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
-+	$(CC) $(CFLAGS) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -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) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
-diff --git a/src/glocal/Makefile b/src/glocal/Makefile
-index ce1421a..b82507f 100755
---- a/src/glocal/Makefile
-+++ b/src/glocal/Makefile
-@@ -10,10 +10,10 @@ TRGT = glocal
- OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o
- 
- .cpp.o:
--	$(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp
-+	$(CXX) $(CXXFLAGS) $(INCDIR) -c $*.cpp
- 
- $(TRGT): $(OBJECTS)
--	$(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
-+	$(CXX) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
- 
- clean :
- 	rm -f *.o ./*~ *~ core
++	$(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
index 4ba4ce49d770..29db043d5f34 100644
--- a/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch
+++ b/sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch
@@ -1,69 +1,34 @@
-Fix QA warnings due to implicit declarations:
-* filebuffer.c:123:34: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration]
-*      temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ?
-
---- a/src/filebuffer.c
-+++ b/src/filebuffer.c
-@@ -3,6 +3,7 @@
- #include <string.h>
- #include <stdio.h>
- #include <assert.h>
-+#include <ctype.h>
- 
- #ifdef CHAOS__FLAG
- char* alphabet = "ATCGNPCMHDEKRQSILVFYWX*";
 --- a/src/mlagan.c
 +++ b/src/mlagan.c
-@@ -934,6 +934,7 @@
-   return k;
+@@ -46,6 +46,7 @@
+     return 1;
  }
  
 +int printXMFAAlign(FILE* outfile, align* myalign);
  
- int main(int argc, char** argv) {
-   FileBuffer seqfile;
+ void usage(void) {
+   printf("mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\n\n",
 --- a/src/order.c
 +++ b/src/order.c
-@@ -398,6 +398,9 @@
-   free(ends);
- }
+@@ -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);
-+
- void doAlign(dmat* mydm, seq* seq1, seq* seq2) {
-   align *a = (align*) makeAlign(mydm, seq1->lets, seq2->lets);
-   //  printf("into printing\n");
+ 
+ char* alpha = "ATCGN.";
+ 
 --- a/src/prolagan.c
 +++ b/src/prolagan.c
-@@ -949,6 +949,7 @@
-   return k;
+@@ -49,6 +49,7 @@
+     return 1;
  }
  
 +int printXMFAAlign(FILE* outfile, align* myalign);
  
- int main(int argc, char** argv) {
-   FileBuffer seqfile;
---- a/src/utils/contigorder.c
-+++ b/src/utils/contigorder.c
-@@ -12,7 +12,7 @@
-   int dummy, i;
-   
-   if (!(file = fopen (filename, "r"))){
--    fprintf (stderr, "contigorder: Error opening file: %s\n");
-+    fprintf (stderr, "contigorder: Error opening file: %s\n", filename);
-     exit (1);
-   }
-   
-@@ -49,7 +49,7 @@
-   }
- 
-   if (!(file = fopen (filename, "r"))){
--    fprintf (stderr, "contigorder: Error opening file: %s\n");
-+    fprintf (stderr, "contigorder: Error opening file: %s\n", filename);
-     exit (1);
-   }
-   
+ 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 @@
diff --git a/sci-biology/lagan/lagan-2.0-r3.ebuild b/sci-biology/lagan/lagan-2.0-r3.ebuild
deleted file mode 100644
index e326331e09fb..000000000000
--- a/sci-biology/lagan/lagan-2.0-r3.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-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/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-lang/perl"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-	"${FILESDIR}/${PN}-2.0-flags.patch"
-	"${FILESDIR}/${PN}-2.0-gcc4.3.patch"
-	"${FILESDIR}/${PN}-2.0-fix-c++14.patch"
-	"${FILESDIR}/${PN}-2.0-qa-implicit-declarations.patch"
-)
-
-src_prepare() {
-	sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/${PN}/lib\";" "${S}/supermap.pl" || die
-	# NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h
-	# where libc getline is erroneously used instead of own getline
-	sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die
-
-	default
-}
-
-src_compile() {
-	emake \
-		CC=$(tc-getCC) \
-		CXX=$(tc-getCXX) \
-		CXXFLAGS="${CXXFLAGS}" \
-		CFLAGS="${CFLAGS}"
-}
-
-src_install() {
-	newbin lagan.pl lagan
-	newbin slagan.pl slagan
-	dobin mlagan
-	rm -f lagan.pl slagan.pl utils/Utils.pm || die
-
-	insinto /usr/$(get_libdir)/${PN}/lib
-	doins Utils.pm
-
-	exeinto /usr/$(get_libdir)/${PN}/utils
-	doexe utils/*
-
-	exeinto /usr/$(get_libdir)/${PN}
-	doexe *.pl anchors chaos glocal order prolagan
-
-	insinto /usr/$(get_libdir)/${PN}
-	doins *.txt
-
-	dosym /usr/$(get_libdir)/${PN}/supermap.pl /usr/bin/supermap
-
-	echo "LAGAN_DIR=\"/usr/$(get_libdir)/${PN}\"" > 99${PN} || die
-	doenvd 99${PN}
-
-	dodoc Readmes/README.*
-}
diff --git a/sci-biology/lagan/lagan-2.0-r4.ebuild b/sci-biology/lagan/lagan-2.0-r4.ebuild
new file mode 100644
index 000000000000..4582d8f1078e
--- /dev/null
+++ b/sci-biology/lagan/lagan-2.0-r4.ebuild
@@ -0,0 +1,67 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+MY_P="lagan20"
+
+DESCRIPTION="The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA"
+HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
+SRC_URI="http://lagan.stanford.edu/lagan_web/${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/meme/Manifest b/sci-biology/meme/Manifest
deleted file mode 100644
index 773a56aca2d6..000000000000
--- a/sci-biology/meme/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-AUX meme-4.11.2_p2-fix-build-system.patch 10447 BLAKE2B 5ca1f4b43247f00b09012f503e0198306db39aa9992e56865d130d40f1530452784bf9edb508ad37d15fe4427fa2d19d4781db35e1f2b1b0257e8214e92734a4 SHA512 85181e114e825081ef52545fef7ab638c91029964eb8be2e1e4042d1d766d5376dbcabc9bd3902f19d162997dd63cb02fea66d231df6bafc0e74981373ea9724
-AUX meme-4.11.2_p2-patch1.patch 13820 BLAKE2B 3d5815bfe966e1d77cdf4491f34f3b3bd8ea674a5510a63d3cec0d0710c29d6d8cb6b1c284f2c8e9259687975644d39afabaf7c3708a3023d3939be4bf3174c1 SHA512 5a5989b5c626dee6aeaa435ce6c444caed6711d62216743d97215abddef95eb92c66544576866fc43c8efb090410aaed425231642dfcd9634b3f3025d5f1981f
-AUX meme-4.11.2_p2-patch2.patch 1684 BLAKE2B 7e5e22f90aa8424d26239a44e56c91ffe6709667a57bd73e058f1b9b012e3873ea6c226bfceefd4ab57989c3059f1fd2bf057bbc253620110fe26bb6370f6e7c SHA512 9c9b01196f76e3b02fa40c7a4d20bc77622cc3ac188584a53774be4ad72a889a72a7a57b38dda81fc7f1bb23db20eec50b0778b71caade4ddf65e49407f3ef8a
-DIST meme_4.11.2.tar.gz 18004930 BLAKE2B accacc7d2422ff6ea3411ff43ea664c94f5d6ba320e1cfec642a88cb6ea5303b2fe8c99a6c35d865c377560118402ab11f869930fd108f02eeaa06321db21655 SHA512 c97c3815e71e2fb5491548152f00688cdfbf4365f6027657e0ffc68e5d96cdd10a4708e0882ab7a5a61d78d93113c925cf5bb300fbe93fa4b2961becef497894
-EBUILD meme-4.11.2_p2.ebuild 2352 BLAKE2B d5946ace6bebec5fe7714b6db3d13185b7fb1cd07e4f24d1a6c7474556c8ed6a16e95f3ae2a3ace62c5e75ad1e8cf5f2832b6dafc2a3276d47e7a1c43c329b5d SHA512 fa4bd73f96f5f0f05dbbd12d316abe49d0414978cbcdc25bb625c288feb346d979c955316298489d951430faf60354f380ead663d04e5e711789e67d6be52e63
-MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch b/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch
deleted file mode 100644
index b548de5a39a5..000000000000
--- a/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch
+++ /dev/null
@@ -1,346 +0,0 @@
-Fix and modernise build system
-* Remove all *FLAGS setting, just append to the user-supplied ones
-* Add --enable-doc and --enable-examples configure flags
-* Install documentation and examples in correct directories
-* Discover libxml2 and libxslt dependencies using PKG_CHECK_MODULES
-* Install python and perl modules correctly
-
---- a/configure.ac
-+++ b/configure.ac
-@@ -76,61 +76,10 @@
- AM_CONDITIONAL(WANT_STRLCPY, test ["$have_strlcpy" = no])
- 
- # Check for compiler-specific settings
--LARGE_FILE_SUPPORT=`getconf LFS_CFLAGS`
--if test "${GCC}" = "yes"; then
--  ac_cc_opt="-O3"
--  ac_cc_debug_opt="-O0"
--  ac_cc_warn="-Wall -Wno-unused"
--  ac_cc_debug="-ggdb"
--  # Check for OS X llvm (clang) compiler
--  if `gcc --version |grep llvm >/dev/null`; then
--    ac_cc_debug="-g"
--  fi
--  CFLAGS="-std="gnu89" $ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT"
--else
--  ac_cc_opt="-O"
--  ac_cc_debug_opt=""
--  ac_cc_warn=""
--  ac_cc_debug="-g"
--  CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT"
--fi
--
--# Set up default libxml2 settings
--# check for installed copy of libxml2
--build_libxml2="yes"
--if test -n "$XML2_CONFIG"; then
--  # Require at least version 2.6
--  required_libxml2_version="2006000"
--  LIBXML2_VERSION="`$XML2_CONFIG --version | \
--    awk 'BEGIN { FS = "."; } { printf "%d", ($1 * 1000 + $2) * 1000 + $3;}'`"
--  if test -n "$LIBXML2_VERSION" && \
--     test "$LIBXML2_VERSION"  -ge "$required_libxml2_version"; then 
--    build_libxml2="no"
--    LIBXML2_LIBS="`$XML2_CONFIG --libs`"
--    LIBXML2_CFLAGS="`$XML2_CONFIG --cflags`"
--  fi
--fi
--if test -z "$LIBXML2_LIBS"; then
--  AC_MSG_WARN([libxml2 library not found])
--  LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"
--  LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include"
--fi
--
--# Set up default libxslt settings
--# check for installed copy of libxslt
--build_libxslt="yes"
--if test -n "$XSLT_CONFIG"; then
--  build_libxslt="no"
--  LIBXSLT_LIBS="`$XSLT_CONFIG --libs` -lexslt"
--  LIBXSLT_CFLAGS="`$XSLT_CONFIG --cflags`"
--fi
--if test -z "$LIBXSLT_LIBS"; then
--  AC_MSG_WARN([libxslt library not found])
--  LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"
--  LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"
--  LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"
--  LIBXSLT_CFLAGS="-I\${top_srcdir}/src/"
--fi
-+AC_PROG_MKDIR_P
-+AC_SYS_LARGEFILE
-+CFLAGS="-std=gnu89 -Wall -Wno-unused ${CFLAGS}"
-+CPPFLAGS="-DUNIX -D__USE_FIXED_PROTOTYPES__ ${CPPFLAGS}"
- 
- # who is installing 
- USER=`whoami`
-@@ -279,6 +227,16 @@
- AM_CONDITIONAL(PARALLEL, test ["$parallel" != no])
- AM_CONDITIONAL(PARALLEL_IS_LAM, test -n ["$lammpi"]) 
- 
-+dnl Documentation
-+AC_ARG_ENABLE([doc],
-+	AS_HELP_STRING([--enable-doc], [Enable installation of documentation]))
-+AM_CONDITIONAL([ENABLE_DOC], [test "x$enable_doc" = "xyes"])
-+
-+dnl Examples
-+AC_ARG_ENABLE([examples],
-+	AS_HELP_STRING([--enable-examples], [Enable installation of examples]))
-+AM_CONDITIONAL([ENABLE_EXAMPLES], [test "x$enable_examples" = "xyes"])
-+
- AC_ARG_ENABLE(
-     webservice,
-     [  --enable-webservice=deploy_dir       Deploy the MEME service on an existing Opal 2.5+ installation],
-@@ -309,24 +267,35 @@
- AM_CONDITIONAL(WEBEITHER, test ["x$OPAL_DEPLOY" != "x" -o "x$OPAL_URL" != "xno"])
- 
- # enable building of included libxml2
--AC_ARG_ENABLE(
--    build_libxml2,
--    [  --enable-build-libxml2     Build included version of libxml2. Default is to use pre-existing locally installed copy.],
--    build_libxml2=$enableval; \
--    LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"; \
--    LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" , )
--AM_CONDITIONAL(BUILD_LIBXML2, test ["$build_libxml2" = yes])
-+AC_ARG_ENABLE([build-libxml2],
-+	AS_HELP_STRING([--enable-build-libxml2], [Build included version of libxml2. Default is to use pre-existing locally installed copy.]))
-+AS_IF([test "x$enable_build_libxml2" = "xyes"], [
-+	dnl Enable building of bundled libs
-+	LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include"
-+	LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"
-+	],[
-+	dnl Use system libraries
-+	PKG_CHECK_MODULES([LIBXML2], [libxml-2.0 >= 2.6])
-+])
-+AM_CONDITIONAL([BUILD_LIBXML2], [test "x$enable_build_libxml2" = "xyes"])
-+
- 
- # enable building of included libxslt
--AC_ARG_ENABLE(
--    build_libxslt,
--    [  --enable-build-libxslt     Build included version of libxslt. Default is to use pre-existing locally installed copy.],
--    build_libxslt=$enableval; \
--    LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"; \
--    LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"; \
--    LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"; \
--    LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" , )
--AM_CONDITIONAL(BUILD_LIBXSLT, test ["$build_libxslt" = yes])
-+AC_ARG_ENABLE([build-libxslt],
-+	AS_HELP_STRING([--enable-build-libxslt], [Build included version of libxslt. Default is to use pre-existing locally installed copy.]))
-+AS_IF([test "x$enable_build_libxslt" = "xyes"], [
-+	dnl Enable building of bundled libs
-+	LIBXSLT_CFLAGS="-I\${top_srcdir}/src/"
-+	LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"
-+
-+	LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"
-+	LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"
-+	],[
-+	dnl Use system libraries
-+	PKG_CHECK_MODULES([LIBXSLT], [libxslt])
-+	PKG_CHECK_MODULES([LIBEXSLT], [libexslt])
-+])
-+AM_CONDITIONAL([BUILD_LIBXSLT], [test "x$enable_build_libxslt" = "xyes"])
- 
- # set website url
- AC_ARG_WITH(
-@@ -427,13 +396,13 @@
-     [AC_PATH_PROG(PERL, perl)])
- AC_DEFINE_UNQUOTED(PERL, "$PERL", [Path to Perl] )
- 
-+AC_ARG_WITH([perl-dir],
-+	AS_HELP_STRING([--with-perl-dir], [Perl modules directory]), [perlmoddir="$with_perl_dir"], [perlmoddir="lib/perl"])
-+AC_SUBST([perlmoddir])
-+
-+
- # set path to Python
--AC_ARG_WITH(
--    python,
--    [  --with-python=NAME     Set path to Python. Default is to take from user's PATH.],
--    [PYTHON=$withval],
--    [AC_PATH_PROG(PYTHON, python)])
--AC_DEFINE_UNQUOTED(PYTHON, "$PYTHON", [Path to Python] )
-+AM_PATH_PYTHON
- 
- # set path to convert utility
- AC_ARG_WITH(
-@@ -586,13 +555,15 @@
-         Configuration parameters
-         ========================
- 
--  Install path:               ${prefix}
-+  Install path (prefix):      ${prefix}
-   Install UID:                ${MEME_USER}
-   Version:                    ${VERSION}
--  C compiler:                 ${CC}
--  C compiler flags:           ${CFLAGS}
--  Linker:                     ${LD}
--  Special Libs:               ${LIBS}
-+  C compiler (CC):            ${CC}
-+  C compiler flags (CFLAGS):  ${CFLAGS}
-+  C preproc flags (CPPFLAGS): ${CPPFLAGS}
-+  Linker (LD):                ${LD}
-+  Linker flags (LDFLAGS):     ${LDFLAGS}
-+  Special Libs (LIBS):        ${LIBS}
-   MPICC                       ${MPICC}
-   MPIRUN                      ${MPIRUN}
-   MPI_CMD                     ${MPI_CMD}
---- a/doc/css/Makefile.am
-+++ b/doc/css/Makefile.am
-@@ -5,7 +5,7 @@
- 
- EXTRA_DIST = $(NORMAL_FILES)
- 
--if ! WEBSITE
--doccssdir = $(prefix)/doc/css
-+if ENABLE_DOC
-+doccssdir = $(htmldir)/css
- doccss_DATA =  $(NORMAL_FILES)
- endif
---- a/doc/examples/compute_prior_dist_example_output_files/Makefile.am
-+++ b/doc/examples/compute_prior_dist_example_output_files/Makefile.am
-@@ -7,8 +7,8 @@
- EXAMPLES = \
-   prior.dist.txt
- 
--if ! WEBSITE
--exdir = $(prefix)/doc/examples/compute_prior_dist_example_output_files
-+if ENABLE_EXAMPLES
-+exdir = $(docdir)/examples/compute_prior_dist_example_output_files
- ex_DATA = $(EXAMPLES)
- endif
- 
---- a/doc/examples/Makefile.am
-+++ b/doc/examples/Makefile.am
-@@ -22,8 +22,8 @@
- # load the EXAMPLE_OUTPUT_FILES variable
- include examples.mk
- 
--if ! WEBSITE
--exdir = $(prefix)/doc/examples
-+if ENABLE_EXAMPLES
-+exdir = $(docdir)/examples
- nobase_dist_ex_DATA = $(EXAMPLES) $(EXAMPLE_OUTPUT_FILES)
- endif
- 
---- a/doc/examples/sample_opal_scripts/Makefile.am
-+++ b/doc/examples/sample_opal_scripts/Makefile.am
-@@ -15,8 +15,8 @@
-   MemeClient.pl \
-   MemeClient.py
- 
--if ! WEBSITE
--exdir = $(prefix)/doc/examples/sample_opal_scripts
-+if ENABLE_EXAMPLES
-+exdir = $(docdir)/examples/sample_opal_scripts
- ex_DATA = $(EXAMPLES)
- endif
- 
---- a/doc/images/Makefile.am
-+++ b/doc/images/Makefile.am
-@@ -30,8 +30,8 @@
- 
- MEME_IMAGES = $(PROGRAM_ICONS) $(OTHER_IMAGES)
- 
--if ! WEBSITE
--memeimgdir = $(prefix)/doc/images
-+if ENABLE_DOC
-+memeimgdir = $(htmldir)/images
- memeimg_DATA = $(MEME_IMAGES)
- endif
- 
---- a/doc/js/Makefile.am
-+++ b/doc/js/Makefile.am
-@@ -41,8 +41,8 @@
- 
- BUILT_SOURCES = $(BUILT_FILES)
- 
--if ! WEBSITE
--docjsdir = $(prefix)/doc/js
-+if ENABLE_DOC
-+docjsdir = $(htmldir)/js
- docjs_DATA =  $(NORMAL_FILES) $(BUILT_FILES) $(SYMLINK_FILES)
- endif
- 
---- a/doc/Makefile.am
-+++ b/doc/Makefile.am
-@@ -129,8 +129,8 @@
-   update-sequence-db.html \
-   ismb94.pdf
- 
--if ! WEBSITE
--memedocdir = $(prefix)/doc
-+if ENABLE_DOC
-+memedocdir = $(htmldir)
- memedoc_DATA =  $(NORMAL_FILES)
- endif
- 
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -52,7 +52,7 @@
- endif
- 
- dbdir:
--	mkdir -p $(MEME_DB)
-+	$(MKDIR_P) $(DESTDIR)/$(MEME_DB)
- 
- all-local:
- if WEBSITE
-@@ -64,8 +64,8 @@
- endif
- 
- install-data-local:
--	mkdir -p $(MEME_LOGS)
--	chmod a+w $(MEME_LOGS)
-+	$(MKDIR_P) $(DESTDIR)/$(MEME_LOGS)
-+	chmod a+w $(DESTDIR)/$(MEME_LOGS)
- 
- distdir = $(PACKAGE)_$(VERSION)
- 
---- a/scripts/Makefile.am
-+++ b/scripts/Makefile.am
-@@ -22,8 +22,8 @@
-   -e 's%@WHICHJAVA@%$(JAVA)%' \
-   -e 's%@WHICHCONVERT@%$(CONVERT)%' \
-   -e 's%@WHICHGHOSTSCRIPT@%$(GHOSTSCRIPT)%' \
--  -e 's%@PERLLIBDIR@%$(libdir)/perl%' \
--  -e 's%@PYTHONLIBDIR@%$(libdir)/python%' \
-+  -e 's%@PERLLIBDIR@%$(perlmoddir)%' \
-+  -e 's%@PYTHONLIBDIR@%$(pythondir)%' \
-   -e 's%@JAVALIBDIR@%$(libdir)/java%' \
-   -e 's%@LAM_BIN@%$(LAMBIN)%' \
-   -e 's%@APPCONFIGDIR@%$(sysconfdir)%' \
-@@ -62,7 +62,7 @@
-   DiffXML.pm \
-   HypergeometricDynProg.pm
- 
--perlmoddir=$(libdir)/perl
-+perlmoddir = $(exec_prefix)/@perlmoddir@
- perlmod_SCRIPTS = \
-   $(BUILT_PERL_MOD) \
-   $(NORMAL_PERL_MOD)
-@@ -76,8 +76,7 @@
-   hypergeometric.py \
-   sequence.py
- 
--pythonlibdir=$(libdir)/python
--pythonlib_SCRIPTS = \
-+python_PYTHON = \
-   $(BUILT_PYTHON_LIB) \
-   $(NORMAL_PYTHON_LIB)
- 
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -19,7 +19,13 @@
- ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION)
- ARCHIVE_DATE = $(shell cat ../ARCHIVE_DATE)
- 
--SUBDIRS = filters libxml2 libxslt libexslt . parallel
-+SUBDIRS = filters . parallel
-+if BUILD_LIBXML2
-+SUBDIRS += libxml2
-+endif
-+if BUILD_LIBXSLT
-+SUBDIRS += libxslt libexslt
-+endif
- 
- BUILT_SOURCES = dir.h projrel.h
- 
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch
deleted file mode 100644
index 30a182f8f43a..000000000000
--- a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch
+++ /dev/null
@@ -1,383 +0,0 @@
---- a/doc/alphabet-format.html
-+++ b/doc/alphabet-format.html
-@@ -233,7 +233,7 @@
-           providing a reference on the meaning of the symbols used. If present, the
-           symbol name must be the second field.</p>
-           <p>The &quot;<span class="pdat">name</span>&quot; follows the rules of
--          <a href="qstr">quoted text</a>.</p>
-+          <a href="#qstr">quoted text</a>.</p>
-         </div>
-         <h5>color</h5>
-         <div class="indent">
---- a/doc/release-notes.html
-+++ b/doc/release-notes.html
-@@ -14,8 +14,26 @@
-       <h2>Motif-based sequence analysis tools</h2>
-     </div>
-     <h2>MEME Suite Release Notes</h2>
-+    <hr>
-+      <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b>
-+      <ul>
-+        <li>
-+            <b>Bug fixes</b>
-+            <ul>
-+              <li>
-+              Fixed bug in MCAST 4.11.2 that caused it to prematurely truncate
-+              reading the sequence file.
-+              </li>
-+              <li>
-+              Modified MEME to fall back to a simple Dirichlet prior when
-+              using DNA or a custom alphabet with a prior that requires
-+              a prior library, but no prior libray is specified.
-+              </li>
-+            </ul
-+        </li>
-+      </ul>
-+      <p>
-       <hr>
--      <p>
-         <b>MEME version 4.11.2 -- May 5 2016</b>
-       </p>
-       <ul>
---- a/src/fasta-io.c
-+++ b/src/fasta-io.c
-@@ -14,6 +14,7 @@
- #include "alphabet.h"
- #include "fasta-io.h"
- #include "io.h"
-+#include "seq-reader-from-fasta.h"
- #include "prior-reader-from-psp.h"
- #include "seq.h"
- 
-@@ -159,61 +160,6 @@
- }
- 
- /****************************************************************************
-- * Read raw sequence until a new sequence is encountered or too many letters
-- * are read.  The new sequence is appended to the end of the given
-- * sequence.
-- *
-- * Return: Was the sequence read completely?
-- ****************************************************************************/
--static BOOLEAN_T read_raw_sequence_from_reader(
--   DATA_BLOCK_READER_T *fasta_reader, // Sequence source
--   char* name, // Sequence ID (used in error messages).
--   ALPH_T* alph, // Alphabet in use
--   unsigned int offset, // Current position in raw_sequence.
--   unsigned int max_chars, // Maximum chars in raw_sequence.
--   char* raw_sequence // Pre-allocated sequence.
--) {
--  // tlb; change a_char to integer so it will compile on SGI
--  int a_char;
--  int start_update;
--  BOOLEAN_T return_value = TRUE;
--
--  // Start at the end of the given sequence.
--  assert(offset < max_chars);
--
--  DATA_BLOCK_T *seq_block = new_sequence_block(max_chars - offset);
--  return_value = !fasta_reader->get_next_block(fasta_reader, seq_block);
--
--  char *seq_buffer = get_sequence_from_data_block(seq_block);
--  size_t seq_buffer_size = get_num_read_into_data_block(seq_block);
--  int i;
--  for (i = 0; i < seq_buffer_size; ++i) {
--    a_char = seq_buffer[i];
--    // Skip non-alphabetic characters.
--    if (!isalnum(a_char) && a_char != '-' && a_char != '*' && a_char != '.') {
--      if ((a_char != ' ') && (a_char != '\t') && (a_char != '\n') && (a_char != '\r')) {
--        fprintf(stderr, "Warning: Skipping character %c in sequence %s.\n",
--                a_char, name);
--      }
--    } else {
--      // skip check if unknown alph
--      if (alph != NULL && !alph_is_known(alph, a_char)) {
--        fprintf(stderr, "Warning: Converting illegal character %c to %c ",
--                a_char, alph_wildcard(alph));
--        fprintf(stderr, "in sequence %s.\n", name);
--        a_char = alph_wildcard(alph);
--      }
--      raw_sequence[offset] = (char) a_char;
--      ++offset;
--    }
--  }
--
--  raw_sequence[offset] = '\0';
--  free_data_block(seq_block);
--  return(return_value);
--}
--
--/****************************************************************************
-  * Read one sequence from a file in Fasta format.
-  *
-  * Return: Was a sequence successfully read?
-@@ -320,44 +266,6 @@
- }
- 
- /****************************************************************************
-- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
-- * and copy them in to the raw sequence in the SEQ_T object starting at the
-- * given buffer offset. 
-- ****************************************************************************/
--void read_one_fasta_segment_from_reader(
--   DATA_BLOCK_READER_T *fasta_reader,
--   size_t max_size,
--   size_t buffer_offset,
--   SEQ_T *sequence
--) {
--
--  assert(sequence != NULL);
--  assert(get_seq_length(sequence) <= max_size);
--
--  // Get the raw sequence buffer from the SEQ_T
--  char *raw_sequence = get_raw_sequence(sequence);
--  if (raw_sequence == NULL) {
--    // Allocate space for raw sequence if not done yet.
--    raw_sequence = mm_malloc(sizeof(char) * max_size + 1);
--    raw_sequence[0] = 0;
--  }
--
--  // Read a block of sequence charaters into the
--  // raw sequence buffer for the SEQ_T.
--  char *name = get_seq_name(sequence);
--  BOOLEAN_T is_complete = read_raw_sequence_from_reader(
--    fasta_reader,
--    name,
--    NULL, //FIXME this is dodgy, need a proper way of getting the alphabet. The fasta_reader has it but it is not accessable!
--    buffer_offset,
--    max_size,
--    raw_sequence
--  );
--  set_raw_sequence(raw_sequence, is_complete, sequence);
--
--}
--
--/****************************************************************************
-  * Read all the sequences from a FASTA file at once.
-    Multiple files can be appended by calling this more than once.
-  ****************************************************************************/
---- a/src/fasta-io.h
-+++ b/src/fasta-io.h
-@@ -43,19 +43,6 @@
- );
- 
- /****************************************************************************
-- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
-- * and copy them in to the raw sequence in the SEQ_T object starting at the
-- * given buffer offset. 
-- ****************************************************************************/
--void read_one_fasta_segment_from_reader(
--  DATA_BLOCK_READER_T *fasta_reader,
--  size_t max_size,
--  size_t buffer_offset,
--  SEQ_T* sequence
--);
--
--
--/****************************************************************************
-  * Read all the sequences from a file in Fasta format.
-  ****************************************************************************/
- void read_many_fastas
---- a/src/init.c
-+++ b/src/init.c
-@@ -767,10 +767,16 @@
-       if (alph_is_builtin_protein(alph)) { // default mixture prior for proteins
-         plib_name = make_path_to_file(get_meme_etc_dir(), PROTEIN_PLIB);
-       } else {
--        fprintf(stderr, "The prior library must be specified for DNA or custom "
--            "alphabets when specifiying a prior type of 'dmix', 'mega' "
--            "or 'megap'.");
--        exit(1);
-+        fprintf(
-+          stderr, 
-+          "WARNING: When using DNA or a custom alphabet, "
-+          "and specifiying a prior type of\n"
-+          "'dmix', 'mega' or 'megap', a prior library must be provided.\n"
-+          "No prior library was provided, so a simple Dirichlet prior will be used.\n"
-+        );
-+        prior = "dirichlet";
-+        ptype = Dirichlet;
-+        if (beta <= 0) beta = 0.01; // default b = 0.01 for simple Dirichlet
-       }
-     }
-   }
---- a/src/seq-reader-from-fasta.c
-+++ b/src/seq-reader-from-fasta.c
-@@ -639,11 +639,140 @@
-   return fasta_reader->current_position;
- }
- 
-+
-+/****************************************************************************
-+ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
-+ * and copy them in to the raw sequence in the SEQ_T object starting at the
-+ * given buffer offset. 
-+ ****************************************************************************/
-+void read_one_fasta_segment_from_reader(
-+   DATA_BLOCK_READER_T *fasta_reader,
-+   size_t max_size,
-+   size_t offset,
-+   SEQ_T *sequence
-+) {
-+
-+
-+  assert(sequence != NULL);
-+  assert(offset < max_size);
-+
-+  // Get the raw sequence buffer from the SEQ_T
-+  char *raw_sequence = get_raw_sequence(sequence);
-+  if (raw_sequence == NULL) {
-+    // Allocate space for raw sequence if not done yet.
-+    raw_sequence = mm_malloc(sizeof(char) * max_size + 1);
-+    raw_sequence[0] = 0;
-+  }
-+
-+  // Read a block of sequence charaters into the
-+  // raw sequence buffer for the SEQ_T, starting at offset.
-+  BOOLEAN_T is_complete = read_raw_sequence_from_reader(
-+    fasta_reader,
-+    max_size - offset,
-+    raw_sequence + offset
-+  );
-+  set_raw_sequence(raw_sequence, is_complete, sequence);
-+}
-+
-+/****************************************************************************
-+ * Read raw sequence until a new sequence is encountered or too many letters
-+ * are read.
-+ *
-+ * Return: Was the sequence read completely?
-+ ****************************************************************************/
-+BOOLEAN_T read_raw_sequence_from_reader(
-+   DATA_BLOCK_READER_T *reader, // Sequence source
-+   unsigned int max_chars, // Maximum chars in raw_sequence.
-+   char* raw_sequence // Pre-allocated sequence buffer.
-+) {
-+
-+  SEQ_READER_FROM_FASTA_T *fasta_reader 
-+    = (SEQ_READER_FROM_FASTA_T *) get_data_block_reader_data(reader);
-+
-+  // Read sequence into temp. buffer from the sequence file.
-+  char buffer[max_chars];
-+  long start_file_pos = ftell(fasta_reader->fasta_file);
-+  size_t seq_index = 0;
-+  size_t total_read = 0;
-+  while (seq_index < max_chars) {
-+
-+    size_t num_char_read = fread(
-+      buffer,
-+      sizeof(char), 
-+      max_chars - seq_index,
-+      fasta_reader->fasta_file
-+    );
-+    fasta_reader->current_position += num_char_read;
-+    total_read += num_char_read;
-+
-+    if (feof(fasta_reader->fasta_file)) {
-+       fasta_reader->at_end_of_file = TRUE;
-+    }
-+    else if (num_char_read < (max_chars - seq_index)) {
-+      die(
-+        "Error while reading sequence from file:%s.\nError message: %s\n", 
-+        fasta_reader->filename,
-+        strerror(ferror(fasta_reader->fasta_file))
-+      );
-+    }
-+
-+    size_t i;
-+    for(i = 0; i < num_char_read; ++i) {
-+      char c = buffer[i];
-+      assert(c != 0);
-+      if (isspace(c)) {
-+        // Skip over white space
-+        fasta_reader->at_start_of_line = (c == '\n');
-+      }
-+      else if (c == '>' && fasta_reader->at_start_of_line == TRUE) {
-+        // We found the start of a new sequence while trying
-+        // to fill the buffer. Leave the buffer incomplete.
-+        // and wind back the file
-+        fseek(fasta_reader->fasta_file, start_file_pos + i - 1, SEEK_SET);
-+        fasta_reader->current_position = start_file_pos + i - 1;
-+        fasta_reader->at_end_of_seq = TRUE;
-+        fasta_reader->at_start_of_line = FALSE;
-+        fasta_reader->at_end_of_file = FALSE;
-+        break;
-+      }
-+      else {
-+        fasta_reader->at_start_of_line = FALSE;
-+        // Check that character is legal in alphabet. 
-+        // If not, replace with wild card character.
-+        if (alph_is_known(fasta_reader->alphabet, c)) {
-+          raw_sequence[seq_index] = c;
-+        }
-+        else {
-+          raw_sequence[seq_index] = alph_wildcard(fasta_reader->alphabet);
-+          fprintf(
-+            stderr, 
-+            "Warning: %c is not a valid character in %s alphabet.\n"
-+            "         Converting %c to %c.\n",
-+            c,
-+            alph_name(fasta_reader->alphabet),
-+            c,
-+            raw_sequence[i]
-+          );
-+        }
-+        ++seq_index;
-+      }
-+    }
-+    if (fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file) {
-+      break;
-+    }
-+  }
-+
-+  raw_sequence[seq_index] = '\0';
-+  return(fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file);
-+}
-+
- /******************************************************************************
-- * Fills in the next data block for the sequence. 
-- * During the first call for the sequence it fills in the full data block.
-- * On successive calls, shifts the sequence in the block down one position
-- * and reads one more character.
-+ * Populates the data block for the with the next block of sequence. 
-+ *
-+ * During the first call for the sequence it fills in a buffer from a file,
-+ * The sequence pointer in the data block is set to point at the start of the buffer.
-+ * On successive calls, the sequence pointer in the block is shifted down one position
-+ * in the buffer. When the end of the buffer is reached, it is filled again from the file.
-  * 
-  * Returns TRUE if it was able to completely fill the block, FALSE if 
-  * the next sequence or EOF was reached before the block was filled.
---- a/src/seq-reader-from-fasta.h
-+++ b/src/seq-reader-from-fasta.h
-@@ -37,5 +37,30 @@
-   int * end_ptr           // end position of sequence (chr:\d+-(\d+))
- );
- 
-+/****************************************************************************
-+ * Read raw sequence until a new sequence is encountered or too many letters
-+ * are read.
-+ *
-+ * Return: Was the sequence read completely?
-+ ****************************************************************************/
-+BOOLEAN_T read_raw_sequence_from_reader(
-+   DATA_BLOCK_READER_T *fasta_reader, // Sequence source
-+   unsigned int max_chars, // Maximum chars in raw_sequence.
-+   char* raw_sequence // Pre-allocated sequence.
-+);
-+
-+/****************************************************************************
-+ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
-+ * and copy them in to the raw sequence in the SEQ_T object starting at the
-+ * given buffer offset. 
-+ ****************************************************************************/
-+void read_one_fasta_segment_from_reader(
-+   DATA_BLOCK_READER_T *reader,
-+   size_t max_size,
-+   size_t offset,
-+   SEQ_T *sequence
-+);
-+
-+
- size_t get_current_pos_from_seq_reader_from_fasta(DATA_BLOCK_READER_T *reader);
- #endif
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch
deleted file mode 100644
index 498d1df7b664..000000000000
--- a/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch
+++ /dev/null
@@ -1,54 +0,0 @@
---- a/doc/release-notes.html
-+++ b/doc/release-notes.html
-@@ -15,6 +15,21 @@
-     </div>
-     <h2>MEME Suite Release Notes</h2>
-     <hr>
-+      <b>MEME version 4.11.2 patch 2 -- October 24, 2016</b>
-+      <ul>
-+        <li>
-+            <b>Bug fixes</b>
-+            <ul>
-+              <li>
-+              Fixed bug in handling of RNA-like custom alphabets.
-+              </li>
-+              <li>
-+              Fixed bug in MAST -comp option.
-+              </li>
-+            </ul
-+        </li>
-+      </ul>
-+      <hr>
-       <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b>
-       <ul>
-         <li>
---- a/src/alph-in.c
-+++ b/src/alph-in.c
-@@ -1044,7 +1044,7 @@
-           lookup[0] = sym->complement;
-           comp2 = (ALPH_SYM_T*)rbtree_get(reader->merged, lookup);
-         }
--        if (comp1 != comp2) {
-+        if (comp1 && (comp1 != comp2)) {
-           add_msg(reader, parmsg_create(SEVERITY_ERROR, -1, -1, -1, 
-                 "not like %s alphabet as %c complement rules are incorrect",
-                 ext_name, req_syms[i]));
---- a/src/mast-util.c
-+++ b/src/mast-util.c
-@@ -740,14 +740,14 @@
- 
-   // create the frequency array  
-   alph = xlate ? xlate_dest_alph(xlate) : alph;
--  freq = allocate_array(alph_size_core(alph));
-+  freq = allocate_array(alph_size_full(alph));
-   init_array(0, freq);
- 
-   // count the number of letters of each type 
-   if (xlate) {
-     for (n=0; sequence[n]; n++) {
-       i = xlate_index(xlate, false, sequence+n);
--      if (i > 0 && i < alph_size_core(alph)) incr_array_item(i, 1, freq);
-+      if (i > 0 && i < alph_size_full(alph)) incr_array_item(i, 1, freq);
-     }
-   } else {
-     for (n=0; sequence[n]; n++) {
diff --git a/sci-biology/meme/meme-4.11.2_p2.ebuild b/sci-biology/meme/meme-4.11.2_p2.ebuild
deleted file mode 100644
index 0f7d25b43368..000000000000
--- a/sci-biology/meme/meme-4.11.2_p2.ebuild
+++ /dev/null
@@ -1,109 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools perl-functions python-single-r1 versionator
-
-MY_PV=$(get_version_component_range 1-3)
-MY_P=${PN}_${MY_PV}
-
-DESCRIPTION="The MEME/MAST system - Motif discovery and search"
-HOMEPAGE="http://meme-suite.org/tools/meme"
-SRC_URI="http://meme-suite.org/meme-software/${MY_PV}/${MY_P}.tar.gz"
-
-LICENSE="meme"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug doc examples mpi"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	app-shells/tcsh
-	dev-libs/libxml2:2
-	dev-libs/libxslt
-	sys-libs/zlib
-	app-text/ghostscript-gpl
-	media-gfx/imagemagick
-	dev-lang/perl:=
-	dev-perl/HTML-Parser
-	dev-perl/HTML-Template
-	dev-perl/Log-Log4perl
-	dev-perl/Math-CDF
-	dev-perl/XML-Compile-SOAP
-	dev-perl/XML-Compile-WSDL11
-	dev-perl/XML-Parser
-	dev-perl/XML-Simple
-	virtual/perl-Data-Dumper
-	virtual/perl-Exporter
-	virtual/perl-File-Path
-	virtual/perl-File-Spec
-	virtual/perl-File-Temp
-	virtual/perl-Getopt-Long
-	virtual/perl-Scalar-List-Utils
-	virtual/perl-Time-HiRes
-	mpi? ( virtual/mpi )"
-DEPEND="${RDEPEND}"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-S="${WORKDIR}/${MY_P}"
-PATCHES=(
-	"${FILESDIR}"/${PN}-4.11.2_p2-patch1.patch
-	"${FILESDIR}"/${PN}-4.11.2_p2-patch2.patch
-	"${FILESDIR}"/${PN}-4.11.2_p2-fix-build-system.patch
-)
-
-pkg_setup() {
-	python-single-r1_pkg_setup
-	perl_set_version
-}
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--sysconfdir="${EPREFIX}"/etc/${PN} \
-		--with-logs="${EPREFIX}"/var/log/${PN} \
-		--with-perl=perl \
-		--with-convert=convert \
-		--with-gs=gs \
-		--disable-build-libxml2 \
-		--disable-build-libxslt \
-		$(use_enable debug) \
-		$(use_enable doc) \
-		$(use_enable examples) \
-		$(use_enable !mpi serial) \
-		--with-perl-dir="${VENDOR_LIB#${EPREFIX}/usr}" \
-		PYTHON="${EPYTHON}"
-
-	# delete bundled libs, just to be sure. These need
-	# to be removed after econf, else AC_OUTPUT will fail
-	rm -r src/{libxml2,lib{,e}xslt} || die
-}
-
-src_test() {
-	# bug #297070
-	emake -j1 test
-}
-
-src_install() {
-	default
-	docompress -x /usr/share/doc/${PF}/examples
-
-	# prefix all binaries with 'meme-', in order
-	# to prevent collisions, bug 455010
-	cd "${ED%/}"/usr/bin/ || die
-	local i
-	for i in *; do
-		if [[ $i != meme-* ]]; then
-			mv {,meme-}"${i}" || die
-		fi
-	done
-
-	keepdir /var/log/meme
-}
diff --git a/sci-biology/meme/metadata.xml b/sci-biology/meme/metadata.xml
deleted file mode 100644
index 959160fe46b1..000000000000
--- a/sci-biology/meme/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://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/muscle/Manifest b/sci-biology/muscle/Manifest
index 9e311756e1fc..d4178fd5bb6a 100644
--- a/sci-biology/muscle/Manifest
+++ b/sci-biology/muscle/Manifest
@@ -1,4 +1,4 @@
-AUX 3.8.31-make.patch 989 BLAKE2B 1cbbee37b5c88a34705fd2adb78d4c5c1533a18f1896f3e4d909e17d15dbf5ccd5308137dd3a94f17ede40b637c9309e0694353e8f8e6c6c55cc966ebd4b52ef SHA512 e528b032d4e60d2ca22de1129da56125b8915ed288ee25965b2bc5b1d6118d1d589fa632dac9829011a405c3189b8b6b6c056eedde9dd30a9b6a6f572a5e2d2c
+AUX 3.8.31-make.patch 922 BLAKE2B 57f112a4538b1b0a791f9e151e0e27ba8c6af2beefb6ce95f064edd183315e17a09d92a9cd0a368907e2b4a1571463669e5ef83e96758603fa4807780ea98bc0 SHA512 c948991ab4f7b7d6e05ab63df00ea6ac576587e63f808c377cc86f4e3863c7cee207569d7f0a8572a8fcf81f2e23d9dd6b1270447a0028910301d74554ab1fac
 DIST muscle3.8.31_src.tar.gz 515267 BLAKE2B 79a8517f7a14d8ee907104e9035e1284fcabec556544508fd9b712789759448969ce39ecbefcedac62c435dc91e109b3b5b7027120691310ffebda80ca80dd9e SHA512 2baf2aae354ae1e3f529e627be2ace86e89dd15567e1f642a625b63f08ebe3d4bd7315080c7d786d95e3eda8703545ec74af9fe83ad1523d55d00137fb7274ce
-EBUILD muscle-3.8.31.ebuild 602 BLAKE2B fb70469bb54d0002cc73e364334355ffc3888248cf51ee59ec466cff5145380de0285601cdb20a91af068368fb2c3414d91bcb82a93dee9fb84d5b3bb6f565f1 SHA512 4167a3402188bc2b17baa5419fae65e1a10c5884d8419de929434e3d44d985889a5131d34dae3854bc58e25450ccbc055d38839255a8153eb2e4d19ae3b84253
+EBUILD muscle-3.8.31.ebuild 580 BLAKE2B d9ccdea4e8e87b89c107d019c7b1ac87ecadf16a92c093e488e7121f6438de4cf003ffe0114402b3b7c90b08e484216908bb01e950f49f014ac748af259dcf58 SHA512 2295bd95b0388e43d2209d37bc48f69a3937bb1a568003f00a66709bea980bc5598f632bf301852149bba24d1d782e86ffca5cc066367f0a3791cd51a6aef3e5
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/muscle/files/3.8.31-make.patch b/sci-biology/muscle/files/3.8.31-make.patch
index 7c0e7308df54..fa3f5c3a014b 100644
--- a/sci-biology/muscle/files/3.8.31-make.patch
+++ b/sci-biology/muscle/files/3.8.31-make.patch
@@ -1,7 +1,5 @@
-diff --git a/src/mk b/src/mk
-index 475d25a..d4b7e83 100755
---- a/src/mk
-+++ b/src/mk
+--- a/mk
++++ b/mk
 @@ -5,17 +5,14 @@ ObjNames='aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln
  rm -f *.o muscle.make.stdout.txt muscle.make.stderr.txt
  for CPPName in $CPPNames
diff --git a/sci-biology/muscle/muscle-3.8.31.ebuild b/sci-biology/muscle/muscle-3.8.31.ebuild
index 1e62a9d28eee..72c9a2c7e178 100644
--- a/sci-biology/muscle/muscle-3.8.31.ebuild
+++ b/sci-biology/muscle/muscle-3.8.31.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 MY_P="${PN}${PV}_src"
 
@@ -14,19 +14,18 @@ SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz"
 LICENSE="public-domain"
 SLOT="0"
 KEYWORDS="amd64 ppc x86"
-IUSE=""
 
 RDEPEND="!sci-libs/libmuscle"
-DEPEND=""
 
 S="${WORKDIR}"/${PN}${PV}/src
 
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-make.patch
+PATCHES=( "${FILESDIR}"/${PV}-make.patch )
+
+src_configure() {
 	tc-export CXX
 }
 
 src_install() {
-	dobin "${PN}"
+	dobin muscle
 	dodoc *.txt
 }
diff --git a/sci-biology/newick-utils/Manifest b/sci-biology/newick-utils/Manifest
index d20aa9ef0fb6..53dda9d90de9 100644
--- a/sci-biology/newick-utils/Manifest
+++ b/sci-biology/newick-utils/Manifest
@@ -1,3 +1,5 @@
+AUX newick-utils-1.6-deduplicate-libnw.patch 5843 BLAKE2B ce36e9b1160ccd2d41a29c28626086fc713d1bd24ce5d93b9def21780bac7275bcde87e3c39a51cfb8bc5db6f99094ab9412b25fcedbab6bac7ab14720c89eac SHA512 e189a53f97fc2a31305c1d8c52d088fe0a80031d3328fafbebdc8371d6ff030b1aa71ae008981c591519888457c345281986d0130653b60e492a19d063a957ba
+AUX newick-utils-1.6-fno-common.patch 1359 BLAKE2B ccc59ad91d69ac2268d26e6704eeafc15c65e883bf8292ddfa6f1f5e75ef368238cbb38dea7f18fdafbb390d4e916fae1184ff89d8746ae98dfd5d759be69154 SHA512 9f6e53485e5d6872393bbf6404a112a105cde6d2e8993bb0c28b73be0458ce64a438eb574b451eefad28076a63ef82b0d204e3e78e301543d320f0e7b34b7799
 DIST newick-utils-1.6.tar.gz 7518535 BLAKE2B 6b5456be6fec4311e40b19972736194a3f2eb51e8efc4a97cdcf027838459a8f22f41d10e49e7ac3e6461aa290aeed1813baeffcb5706749ebf1bf4333e28047 SHA512 1e327f9a32b5b0df097bcb63f933f9073a85f0499a2a48be122f4affca52ae1541e1a6e0cca7420447aa8fe8d10d6e76e8d89933b2f84e023d6c87b50808d96c
-EBUILD newick-utils-1.6.ebuild 399 BLAKE2B d7e3abeeb7c9abd0677733ec78edfbca2d036766a733d7fb5c89bc12280f0a48c24a841e09b31185c100f750c36a55252f51c287287de5baa3b01a1cc14a54fa SHA512 f359ffd190bf1631108c84ea5230e629b7aa3aa8426d9f3e49b5df4c7d22a75e29bb74215144ab7dfa506dbbec704164c80c58b57c87305314e320c62d764c8d
-MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
+EBUILD newick-utils-1.6-r1.ebuild 733 BLAKE2B 60cf97660294c13efba331d06d299ed21761446981e62832bf5d9fdb713196fa10f2713f0cd33e89c1dd31e5829decca3ce919806fbf92a5652e30cee4e10c6f SHA512 b6f9daeecf7035a145e53feeb9b70676154412dea04861f1093862fb0f943a2d3f26cb791506918f1f12596abe31680ce0a13081e88494270d295d5d5d70cf74
+MISC metadata.xml 355 BLAKE2B cabdb6f1dd0f44f079f81789daa15b311048672fc5b4a3e50f408a4f0a22abc30f9d20c24c34d8fdf5308ff6c18942438eca19b78540828999b506ac9f710430 SHA512 a9f72bde780552c341f039ac78d91c4958148b135a7944c232e5755edb54c064e8bb5107f54e39be798bedf0601ffaa60a0ff137709bc6b5c3a2fb65e4fe49bc
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
new file mode 100644
index 000000000000..ca997830aced
--- /dev/null
+++ b/sci-biology/newick-utils/files/newick-utils-1.6-deduplicate-libnw.patch
@@ -0,0 +1,153 @@
+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
new file mode 100644
index 000000000000..15847a52c480
--- /dev/null
+++ b/sci-biology/newick-utils/files/newick-utils-1.6-fno-common.patch
@@ -0,0 +1,41 @@
+--- 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
index 959160fe46b1..d9bc91509874 100644
--- a/sci-biology/newick-utils/metadata.xml
+++ b/sci-biology/newick-utils/metadata.xml
@@ -1,8 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
+	<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>
 </pkgmetadata>
diff --git a/sci-biology/newick-utils/newick-utils-1.6-r1.ebuild b/sci-biology/newick-utils/newick-utils-1.6-r1.ebuild
new file mode 100644
index 000000000000..3dcb438832a2
--- /dev/null
+++ b/sci-biology/newick-utils/newick-utils-1.6-r1.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools
+
+DESCRIPTION="Tools for processing phylogenetic trees"
+HOMEPAGE="http://cegg.unige.ch/newick_utils"
+SRC_URI="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() {
+	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/newick-utils/newick-utils-1.6.ebuild b/sci-biology/newick-utils/newick-utils-1.6.ebuild
deleted file mode 100644
index 845bc0116205..000000000000
--- a/sci-biology/newick-utils/newick-utils-1.6.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Tools for processing phylogenetic trees"
-HOMEPAGE="http://cegg.unige.ch/newick_utils"
-SRC_URI="http://cegg.unige.ch/pub/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=""
-RDEPEND="!dev-games/libnw"
-
-src_test() {
-	emake -C tests check-TESTS
-}
diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest
index 02b763e3dba9..e0f9ddd35a94 100644
--- a/sci-biology/paml/Manifest
+++ b/sci-biology/paml/Manifest
@@ -1,3 +1,5 @@
-DIST paml4.4c.tar.gz 2891715 BLAKE2B 04449b80e4fec080eabb69108d399a32278fcc79221e3c0d087ad1d978517ae2655bce8c300260dfb99d4d60700369ec338fa71c1d48f41a82017dbd3cae2397 SHA512 6a5f6d5baa91afa924ea392b76e59db6691fa9d6ee13a248dfe6e46d3fc83178ce41c2991de1c4cdb21952ee53771298aa0c62060f47d0dd84eaa76eb533498a
-EBUILD paml-4.4c-r1.ebuild 983 BLAKE2B 4c4da7c1bdfdb0f479b65b27c39463d3797384e69e11929e446e867a741a8d49102842aad00a3187abd119885fa23879f4c13128577d64de23b6011455271352 SHA512 a7d590056e148c08607c6c15e872f6fc4ea87166336f19eeef497efb4852481b782b83f8e40b6f50005dffaa45b1fb6d028cd101fd54efa643e3678e60836b04
+AUX paml-4.9j-fno-common.patch 521 BLAKE2B 93dda51495e65cde9b3e92379e43756c5efe77953b114ceb88c8dc9ae6453d5b2742e250cf9a2d6feec3e86ff430417a4ecd8fd06b199a899b14d0aeac5199e2 SHA512 c24431264c7a69077f9ea9f511e93d45ac8adc4a5cc41446ca96de4e270b918543fb1a424b9119bc1723b2a9574434321a55a5af88712e0f3d51ef5c964575fb
+AUX paml-4.9j-makefile.patch 1540 BLAKE2B 9ffa0f8fab089d26e325688596975944a10e9e62ba1554b532b3f31c7f508b5b1001f5481ad9b8ae7fa97ffd8bcdffda3c285935c8efa3442175f4686e0a44ad SHA512 51b05e865ff68d58cf0f8cc2bc23e8e90e5d12ac8daceb96ac9cc64fdf75c704b5b16b6b8248a0e3cd03c1b18e5bbb61727c281ad46b4988a197f695b464c80d
+DIST paml4.9j.tgz 6380272 BLAKE2B 58fc40904aff6ae539613e772fc0525b557c1e72c1a7a1d95176987bafed8771624ae6c53803bc71c5821a52de8212a49ad99c02c408870ec929c15b6bf217e0 SHA512 c5f3c42409bbaf5ac67c816a245f1d3175ee449dcf10232d9de539130341f80f85ae53518cbca549b1f42ddf64a6e8140a22b9da091d458b425512f11f8c1758
+EBUILD paml-4.9j.ebuild 843 BLAKE2B 8f92ab034a78571de1bccecc21d04fc9eef7414d98c5a3f4a6d4a96f59ddcd32e0c0c1c82928ed3949f7c64a493fbf5c3962016425ab8bcef6b3718cf50e49ba SHA512 74100d6e6a0913c0c1a56039468b5a78c86fc13fab054a0dc6fe307ba975f84865c999f5472c1e18a5bf28c7f0fe37359f3c557965b251968eba692bec49e607
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/paml/files/paml-4.9j-fno-common.patch b/sci-biology/paml/files/paml-4.9j-fno-common.patch
new file mode 100644
index 000000000000..66eeb8a56b86
--- /dev/null
+++ b/sci-biology/paml/files/paml-4.9j-fno-common.patch
@@ -0,0 +1,14 @@
+--- a/src/paml.h
++++ b/src/paml.h
+@@ -372,9 +372,9 @@
+ void printSptree(void);
+ 
+ 
+-enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes;
++typedef enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes;
+ 
+-enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions;
++typedef enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions;
+ 
+ 
+ /* use mean (0; default) for discrete gamma instead of median (1) */
diff --git a/sci-biology/paml/files/paml-4.9j-makefile.patch b/sci-biology/paml/files/paml-4.9j-makefile.patch
new file mode 100644
index 000000000000..611b80444c89
--- /dev/null
+++ b/sci-biology/paml/files/paml-4.9j-makefile.patch
@@ -0,0 +1,42 @@
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,27 +1,18 @@
+-PRGS =  baseml codeml basemlg mcmctree pamp evolver yn00 chi2 

+-CC = cc # cc, gcc, cl

++PRGS =  baseml basemlg codeml evolver pamp mcmctree infinitesites yn00 chi2

+ 

+-CFLAGS = -O3

++CFLAGS += -Wno-unused-result

+ #CFLAGS = -fast

+ 

+-LIBS = -lm # -lM

++LDLIBS = -lm

+ 

+ all : $(PRGS)

+ 

+-baseml : baseml.c tools.c treesub.c treespace.c paml.h 

+-	$(CC) $(CFLAGS) -o $@ baseml.c tools.c $(LIBS)

+-basemlg : basemlg.c  tools.c treesub.c treespace.c paml.h 

+-	$(CC) $(CFLAGS) -o $@ basemlg.c tools.c $(LIBS)

+-codeml : codeml.c  tools.c treesub.c treespace.c paml.h 

+-	$(CC) $(CFLAGS) -o $@ codeml.c tools.c $(LIBS)

+-evolver : evolver.c  tools.c treesub.c treespace.c paml.h 

+-	$(CC) $(CFLAGS) -o $@ evolver.c tools.c $(LIBS)

+-pamp : pamp.c  tools.c treesub.c treespace.c paml.h 

+-	$(CC) $(CFLAGS) -o $@ pamp.c tools.c $(LIBS)

+-mcmctree : mcmctree.c  tools.c treesub.c treespace.c paml.h 

+-	$(CC) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS)

+-	$(CC) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.c $(LIBS)

+-yn00: yn00.c tools.c paml.h

+-	$(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)

+-chi2 : chi2.c

+-	$(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)

++baseml: tools.o paml.h 

++basemlg: tools.o paml.h 

++codeml: tools.o paml.h 

++evolver: tools.o paml.h 

++pamp: tools.o paml.h 

++mcmctree: tools.o paml.h 

++infinitesites: tools.o paml.h 

++	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -DINFINITESITES mcmctree.c -o infinitesites tools.o $(LDLIBS)

++yn00: tools.o paml.h

diff --git a/sci-biology/paml/paml-4.4c-r1.ebuild b/sci-biology/paml/paml-4.4c-r1.ebuild
deleted file mode 100644
index 27fe5ed4c769..000000000000
--- a/sci-biology/paml/paml-4.4c-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs versionator
-
-MY_P=$(version_format_string '${PN}$1$2')
-
-DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
-HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
-SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz"
-
-LICENSE="free-noncomm"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE=""
-
-S=${WORKDIR}/${MY_P}
-
-src_prepare() {
-	# Notice send by mail to prof. Ziheng Yang
-	sed -i "s/\$(CC)/& \$(LDFLAGS)/" src/Makefile || die #335608
-}
-
-src_compile() {
-	emake -C src \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS} -Wno-unused-result" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dodoc README.txt doc/*
-
-	insinto /usr/share/${PN}/control
-	doins *.ctl
-
-	insinto /usr/share/${PN}/dat
-	doins stewart* *.dat dat/*
-
-	insinto /usr/share/${PN}
-	doins -r examples/
-
-	cd src || die
-	dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2
-}
diff --git a/sci-biology/paml/paml-4.9j.ebuild b/sci-biology/paml/paml-4.9j.ebuild
new file mode 100644
index 000000000000..e8a5d07ee40c
--- /dev/null
+++ b/sci-biology/paml/paml-4.9j.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
+HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
+SRC_URI="http://abacus.gene.ucl.ac.uk/software/${P/-/}.tgz"
+
+LICENSE="free-noncomm"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/${P/-/}"
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.9j-makefile.patch
+	"${FILESDIR}"/${PN}-4.9j-fno-common.patch
+)
+
+src_configure() {
+	tc-export CC
+}
+
+src_compile() {
+	emake -C src
+}
+
+src_install() {
+	dobin src/{baseml,basemlg,codeml,evolver,pamp,mcmctree,infinitesites,yn00,chi2}
+
+	dodoc -r README.txt doc/.
+
+	insinto /usr/share/${PN}/control
+	doins *.ctl
+
+	insinto /usr/share/${PN}/dat
+	doins -r stewart* *.dat dat/.
+
+	insinto /usr/share/${PN}
+	doins -r examples
+}
diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest
index 4a74a1a8a1f8..c88142631f51 100644
--- a/sci-biology/phylip/Manifest
+++ b/sci-biology/phylip/Manifest
@@ -1,7 +1,6 @@
 AUX README.Gentoo 643 BLAKE2B 95193d4c9c8fc8fb5796bb0a8ca470f440ac66eb1da9b9ed4784494a6a4c9bb12a451223c0ff81ae3ba80da81f4d8d3a00a21cad557f575a81325a180a819c0e SHA512 63ec15ce2788171e5351977bae21e11a7c8609eeed4893849fabc909f0c6713033e253768ea3f485245456a9083ad4aa613e2503ebb4eb71f7b670f1af593f2a
-DIST phylip-3.69.tar.gz 1511935 BLAKE2B 76aa5a79d2553c6f269c011f633d1101ee4d85ac398a36dd463e5605d90833ecb1e5f6c21edba3e142e2d4ab5ef034fa739e52e0ab3f941a7987915ae352be0b SHA512 e36d12bfe597896b4298c1d0e3b0b7bd783573dc03e861b9472d8284391b2339cb3fb58eb6580298724bbd516127b68925815455514f939da9272fcfed7e229d
-DIST phylip-3.696.tar.gz 3955721 BLAKE2B dc75fc442eb63e44bc2e68e5dc97b3ff8f741bfa53740ed57ca114b53dcb71db9baeb9a96c3e693f7fae92afbaa71c7b5acfb39e7770bacb6aafa8c33b355be6 SHA512 711a9a34be72b0f63c746733cd1384f091b7cc597dbd9a40c130e074efbf0a0ecc30e5a6b3452bb73dc69cddbdae2fc07d1c0a68f0be207471eab73ab876c6be
-EBUILD phylip-3.69-r1.ebuild 1146 BLAKE2B 690bd802cb7ed4dce34de3c272357df93c528881efe5b40c8b4e3f6c281791eb6809559a5f1680da55d5c9466cac666d290722a513eb3364245bf5f6bcd9204e SHA512 7e7eada3c9c1b6ae479360749d40943ec977505986871ffe8f5972604e2834aaddfd015f49b9e60f3f3292f8e98f410fdeecd240f34a47b86046972f067111c5
-EBUILD phylip-3.696-r1.ebuild 1130 BLAKE2B 94c4b4213d24b46fe60f3d180a1d8a742f9c173f5482e18e1521b0f3e61ac2738038c5a558fdbdeaece2f9887e08796d6981bc3ff54bec2e60dfb0ebffa7d156 SHA512 02e33c7a34910a006fb0e63d9cac40b9e71446b5b64185b968d46fdcb78217c4f2bdfe02b96ae2eefe10839e892c2c533581e9d149cfc63f1d64b2b87b1416a9
-EBUILD phylip-3.696-r2.ebuild 1204 BLAKE2B d6fcbe08f0528d657bc30da9c61c67571ee403c7f15caec8a86d2ed9a75958e471f8b2582d39c86f1ddb675636bf9d211665d398593651c968b9d87b9fac4a2a SHA512 2827584e9293a5bc95087c0d3f19b4d0ac1a7ecac6b5b81738abb16ee007d65ab91e14baf0885578afc4c369841456583d88ee51bf0738b3d04d4924eb086e5c
+AUX phylip-3.698-fno-common.patch 1934 BLAKE2B 613149dd930aa3efc921d5844e97c76475bffaedfe701d46ae980a4fabd0896d6d81fde4722599217508689d41ec70e110cbf0638abad13b2c0dbbf1c6c2f159 SHA512 4e89f330338da601ac7311995a341cab235288d82b9a63ba632b830eb99052191a920f51f43236c1a71f07ce3e427dd58ff5bc0004d1ed4ebbea8bf223390aa1
+AUX phylip-3.698-makefile.patch 9481 BLAKE2B fc8b863c05953333588f174251e40a86138a5cf2b08206861bef594ebea1d7d63b53895517bb6916e1c06c700b379cd93e76a673af4ec225502ac886dbe702d5 SHA512 6713644543f676dd6b21408675ac65c38f6a2fed4bd04619c19de881e5269e4c0bb89e440cf59dd0f1f13ad72cbbf420baccdaeb6a0c7a2a807895f87376d76f
+DIST phylip-3.698.zip 9675991 BLAKE2B 8d020cf17b3245b9827af4bdd1d17167c3e1a41ae805766c4b72f09de107775314a2a296c00f84f928487403cc02741fd46ae73585d0dba143f4b926777e9add SHA512 7f822dabd1ffdb6a689e0c308f5a3ae129bd86e305086a18c0c755ac3c6ca28a4337d52ced76b280706926370e23f19f304851ef82e32833d1945ed277f7d70d
+EBUILD phylip-3.698.ebuild 1193 BLAKE2B c196d7cdfe79a17691c2fe5567a30c0b937015ef3f8f1ce11a317dd1c86913487e6ac9a80f6ec21b80be804e7fcc1193522d3c4879d32e7510e7a9b89f1ce3b3 SHA512 da567382dfd57d40fca30845346f6ae8a5ce1bf16475bb1bdd5a220eb47d629b9904d4e0e76797971fcb2cfa795cc69a1480292a262350eb891b407e44f00509
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/phylip/files/phylip-3.698-fno-common.patch b/sci-biology/phylip/files/phylip-3.698-fno-common.patch
new file mode 100644
index 000000000000..986b1d9650ab
--- /dev/null
+++ b/sci-biology/phylip/files/phylip-3.698-fno-common.patch
@@ -0,0 +1,70 @@
+--- 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
new file mode 100644
index 000000000000..f55ab98dd9cb
--- /dev/null
+++ b/sci-biology/phylip/files/phylip-3.698-makefile.patch
@@ -0,0 +1,266 @@
+--- 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 $(LIBS) -o treedist
+ 
+ 
+ # ----------------------------------------------------------------------------
diff --git a/sci-biology/phylip/phylip-3.69-r1.ebuild b/sci-biology/phylip/phylip-3.69-r1.ebuild
deleted file mode 100644
index e54c75d9b356..000000000000
--- a/sci-biology/phylip/phylip-3.69-r1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION=" The PHYLogeny Inference Package"
-HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
-SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="free-noncomm"
-IUSE=""
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos"
-
-RDEPEND="x11-libs/libXaw"
-DEPEND="${RDEPEND}
-	x11-base/xorg-proto"
-
-S="${WORKDIR}/${P}/src"
-
-src_prepare() {
-	sed \
-		-e "s/CFLAGS  = -O3 -fomit-frame-pointer/CFLAGS = ${CFLAGS}/" \
-		-e "s/CC        = cc/CC        = $(tc-getCC)/" \
-		-e "s/DC        = cc/DC        = $(tc-getCC)/" \
-		-e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
-		-i Makefile || die "Patching Makefile failed."
-	mkdir ../fonts || die
-}
-
-src_compile() {
-	emake -j1 all put
-}
-
-src_install() {
-	cd "${WORKDIR}/${P}" || die
-
-	mv exe/font* fonts || die "Font move failed."
-	mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
-
-	dobin exe/*
-
-	dodoc "${FILESDIR}"/README.Gentoo
-
-	dohtml -r phylip.html doc
-
-	insinto /usr/share/${PN}/
-	doins -r fonts
-}
diff --git a/sci-biology/phylip/phylip-3.696-r1.ebuild b/sci-biology/phylip/phylip-3.696-r1.ebuild
deleted file mode 100644
index 85150acaf9cb..000000000000
--- a/sci-biology/phylip/phylip-3.696-r1.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit 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}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD-2"
-IUSE=""
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
-
-RDEPEND="x11-libs/libXaw"
-DEPEND="${RDEPEND}
-	x11-base/xorg-proto"
-
-S="${WORKDIR}/${P}/src"
-
-src_prepare() {
-	mv Makefile.unx Makefile || die
-	sed \
-		-e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
-		-i Makefile || die "Patching Makefile failed."
-	mkdir ../fonts || die
-}
-
-src_compile() {
-	emake -j1 \
-		CC="$(tc-getCC)" \
-		DC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS} -Wno-unused-result" \
-		all put
-}
-
-src_install() {
-	cd "${WORKDIR}/${P}" || die
-
-	mv exe/font* fonts || die "Font move failed."
-	mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
-
-	dolib.so exe/*so && rm exe/*so
-	dobin exe/*
-
-	dodoc "${FILESDIR}"/README.Gentoo
-
-	dohtml -r phylip.html doc
-
-	insinto /usr/share/${PN}/
-	doins -r fonts
-}
diff --git a/sci-biology/phylip/phylip-3.696-r2.ebuild b/sci-biology/phylip/phylip-3.696-r2.ebuild
deleted file mode 100644
index 66391e0e662d..000000000000
--- a/sci-biology/phylip/phylip-3.696-r2.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION=" The PHYLogeny Inference Package"
-HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
-SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD-2"
-IUSE=""
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
-# 'mix' tool collides with dev-lang/elixir, bug #537514
-RDEPEND="x11-libs/libXaw
-	!!dev-lang/elixir"
-DEPEND="${RDEPEND}
-	x11-base/xorg-proto"
-
-S="${WORKDIR}/${P}/src"
-
-src_prepare() {
-	mv Makefile.unx Makefile || die
-	sed \
-		-e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
-		-i Makefile || die "Patching Makefile failed."
-	mkdir ../fonts || die
-}
-
-src_compile() {
-	emake -j1 \
-		CC="$(tc-getCC)" \
-		DC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS} -Wno-unused-result" \
-		all put
-}
-
-src_install() {
-	cd "${WORKDIR}/${P}" || die
-
-	mv exe/font* fonts || die "Font move failed."
-	mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
-
-	dolib.so exe/*so && rm exe/*so
-	dobin exe/*
-
-	dodoc "${FILESDIR}"/README.Gentoo
-
-	dohtml -r phylip.html doc
-
-	insinto /usr/share/${PN}/
-	doins -r fonts
-}
diff --git a/sci-biology/phylip/phylip-3.698.ebuild b/sci-biology/phylip/phylip-3.698.ebuild
new file mode 100644
index 000000000000..0a8ef8f815ec
--- /dev/null
+++ b/sci-biology/phylip/phylip-3.698.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION=" The PHYLogeny Inference Package"
+HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
+SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.zip"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+# 'mix' tool collides with dev-lang/elixir, bug #537514
+RDEPEND="
+	x11-libs/libXaw
+	!dev-lang/elixir"
+DEPEND="${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/profphd/Manifest b/sci-biology/profphd/Manifest
index 7085f0176e19..e4fd19dff774 100644
--- a/sci-biology/profphd/Manifest
+++ b/sci-biology/profphd/Manifest
@@ -1,6 +1,5 @@
 AUX profphd-1.0.39-perl.patch 376 BLAKE2B 16911d2f6952f9740f3cd16121bf6dab5e5571ce1f7e5ac671dde719146e55f2735f2951629220fe56a93c1243e792ddd820978163023b44613d8d08d037cd6a SHA512 e4004dbb835560b3a2aa140aea0ed57812ee9dc11dc18fb7b1dbdeee73bacfef3fecfd686f15fa87cde5597ddb322057d67fa61708ba3077c5449f93a0284b8e
-DIST profphd-1.0.39.tar.xz 4406776 BLAKE2B 9ac4bccd1fedf04f9556ff6953452879fc8cf9deb92853214b2c8b5c0b1c4daf3e5e0044d10ded9540e9dd3f40a6fee3a25ae808fd1e94b90e0db23f3af7b6df SHA512 0ea6a34a8dad8fcd0d8b23e7a7d476e211587bf580389e9f43ed857bab7853cbe5ce698d2a610e9344e9bc95661cf074355310ea02c1a03e6378058ba169b15b
+AUX profphd-1.0.40-symlink.patch 793 BLAKE2B 98e5f001570522bb1643d3aad1f2497bd84035c932d19b1b9c90d2933b08eb7d2b6c1871b356205494494c8225fac3d6d697aaac6229885876c439679455f092 SHA512 7985c4743ade3b73a7fdd0c697c84c3b5fdcba3c33c66d1d6aab7d4493ca4d1197c4c438ef79f44667ed2c86e6ee9c789c36928430605aac6438d9e734e8c56a
 DIST profphd-1.0.40.tar.xz 4491592 BLAKE2B 2aa1e091c0674fa5318a075148a63b15354ecb6d8d6f7ac41d1d05f8bea17c47b6f37be707cc1c738e22342c26ae9be59cabf919610e5bffd5028fc587b2995b SHA512 287f1a548030e7978119788dffdf2529e0018cd772bc820e116f79ed10cefd440645424b56415333362098a1ed32f4841d3fd4069adede2a95968f81c63956e3
-EBUILD profphd-1.0.39.ebuild 833 BLAKE2B c173db3f129f9aecf3c0d8da461ef24c07b8de59e1c7adae3e9c39f227951b889fbcb71b78deb6fe45a7850f41cfddf87004fad251fdbd0425b5a7d6f96d60e5 SHA512 a2e15d1bd08ffa70e966001cc1a9787e2ad4c736e4275dee7ea8695ff6b36869c6acc60b6ae3e1fc607f86adff8bd5ae518dac2004f6c3b9657c5a53a732a123
-EBUILD profphd-1.0.40.ebuild 841 BLAKE2B c9b34a5bd892bab4dcc868ea1c3a5404c99d6a10f82ac217ea315a2203d4f0a7c65372cf5714eb480003729931362afdeba13e21e80c4590e392cd14d0bffed4 SHA512 c08773dfc516365b2d75cd0f7869f8c1178a17921ebd65e5ea1b78c236449ea818ce3086e63fd43eeb0ed9b4919b48e7f9f9d1e5a148de5a8e63342bf45d2d9d
+EBUILD profphd-1.0.40.ebuild 787 BLAKE2B 382eef046bb2eddcbd7e8dd8a798096f4719c4df589f8022c51cf07bc7e920c161b9c9dc8dde7ee92eca9d998cc98ddc3aecdcbaa3de533a42556ff2e382931d SHA512 c583b877a4c912e473231d74ec84bb25bcc9f6d90d466fce7b73b1701e205a2c2ab57039e12ad755b7f3a296e7d8b95f752bb308337d012084ec3ea3738a69d2
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/profphd/files/profphd-1.0.40-symlink.patch b/sci-biology/profphd/files/profphd-1.0.40-symlink.patch
new file mode 100644
index 000000000000..7733d55af4a6
--- /dev/null
+++ b/sci-biology/profphd/files/profphd-1.0.40-symlink.patch
@@ -0,0 +1,11 @@
+--- 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/profphd-1.0.39.ebuild b/sci-biology/profphd/profphd-1.0.39.ebuild
deleted file mode 100644
index cacbc13cbdf2..000000000000
--- a/sci-biology/profphd/profphd-1.0.39.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-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/${P}.tar.xz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="dev-lang/perl"
-RDEPEND="${DEPEND}
-	dev-perl/librg-utils-perl
-	sci-libs/profnet
-	sci-libs/profphd-utils
-"
-
-src_prepare() {
-	sed \
-		-e '/ln -s/s:prof$:profphd:g' \
-		-i src/prof/Makefile || die
-	epatch "${FILESDIR}"/${P}-perl.patch
-}
-
-src_compile() {
-	emake prefix="${EPREFIX}/usr"
-}
-
-src_install() {
-	emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install
-}
diff --git a/sci-biology/profphd/profphd-1.0.40.ebuild b/sci-biology/profphd/profphd-1.0.40.ebuild
index 8e24cebeb5f3..4f9a16a9fe9d 100644
--- a/sci-biology/profphd/profphd-1.0.40.ebuild
+++ b/sci-biology/profphd/profphd-1.0.40.ebuild
@@ -1,37 +1,33 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-inherit eutils
+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"
 
-SLOT="0"
 LICENSE="GPL-2"
+SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
 
 DEPEND="dev-lang/perl"
-RDEPEND="${DEPEND}
+RDEPEND="
+	${DEPEND}
 	dev-perl/librg-utils-perl
 	sci-libs/profnet
-	sci-libs/profphd-utils
-"
+	sci-libs/profphd-utils"
 
-src_prepare() {
-	sed \
-		-e '/ln -s/s:prof$:profphd:g' \
-		-i src/prof/Makefile || die
-	epatch "${FILESDIR}"/${PN}-1.0.39-perl.patch
-}
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.0.39-perl.patch
+	"${FILESDIR}"/${PN}-1.0.40-symlink.patch
+)
 
 src_compile() {
-	emake prefix="${EPREFIX}/usr"
+	emake prefix="${EPREFIX}"/usr
 }
 
 src_install() {
-	emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install
+	emake prefix="${EPREFIX}"/usr DESTDIR="${D}" install
+	einstalldocs
 }
diff --git a/sci-biology/seaview/Manifest b/sci-biology/seaview/Manifest
index 370ccb30d448..dd7a8e73e258 100644
--- a/sci-biology/seaview/Manifest
+++ b/sci-biology/seaview/Manifest
@@ -1,5 +1,5 @@
-DIST seaview_4.5.4.tar.gz 420608 BLAKE2B 14b044706440da88987cd6b546595497f2de61e8d03615bfce4634104914a56544a464b0abedc83e6c96329697dccb2087c2b1af5a1fdbf0d9bdc26418a49a75 SHA512 a8a2e49a13f87ae4279311068147169b1e17874e9ce5787003b854c7271efc7a128db6916bb883a9b7b0b90f855fe40d83c77e9fd9f5751464e04346b9923301
+AUX seaview-4.6-Wreserved-user-defined-literal.patch 3271 BLAKE2B 695411acffed448ecc792753a9c8f969e4e88fea711b163a9b45f7b5878e44f5504d162991924958d8910c5eb7241b893ae27ea328a5efb754ba13ed0ddf7422 SHA512 fe9837a85e68e486fcc1a1903af027a71916aa70bf54d8616f5be6b13c52ca4ca7f5d2901724e3ec2e3e754c2772c59d3db78fb6e75432ef7f67e99692571bfe
+AUX seaview-4.6-fno-common.patch 3171 BLAKE2B a3dfdb8d90279cdc16489d5e304eb81d3893f63d55ec5363d86fce5d90aa87c003fb2f41dafb09f46002aa1b45871161ff5b0de6e22bd24d77c98727880818d5 SHA512 89b1d46956232b6c7a3979c804339e2bc4e9f99224c7c06091a2526c92ddd55415762a39d183e0249ae7251afada28bfb6f863bd91167ea647d76d4c548c1f6a
 DIST seaview_4.6.tar.gz 424258 BLAKE2B e958ff4b1f6bb283a2122d65917a352914f33e5c9593c34c449800fbcac74b0dd4fa98bb1f47c45e11f24e07dfebb3ced54fbd8440b2bcd2b1df32dc398d5892 SHA512 e005d9dcc9e03c5636404e94f0059f7d4a9289fe77ecdab765e3ca2b59d826b8711a344f3824d079383a7ede0fe17b3b06694dfb7b709bb6a0a1e38cef6ee1d6
-EBUILD seaview-4.5.4.ebuild 2013 BLAKE2B 91c192d7cb22411f7af4366088c1e47c657fc75855cab2a289d4a1d7cec206302b2670612117334d6c6b79d25c578daf3da5cbd053dc98602ead9033c3b90f35 SHA512 41eeabeb570a22219f7ad649a4eb127b94a253f914ea6637fcce518da3607e3fb42b528d3aa436f6b86e54b695d31900b29558ec0696c1e4bf3264c42cdfc945
-EBUILD seaview-4.6.ebuild 1997 BLAKE2B 1c7c01e0a52f943b9506954d84519c8ff09b15d307476aa659f7bb49af9de1ea02076bb74bcebaac49a571d18624455879c321faa7458f8ac2660773eb4b8706 SHA512 5768df52c205ccfaa4d2d52ec753125dd77eb91a7b0be959dbc67aca00c0a66dc3f13b125d073450a81a06eea29880503981942042c77a0c6e1bb8f19f070cb8
+EBUILD seaview-4.6-r1.ebuild 2106 BLAKE2B 6a7d4e6295285cd072db997acc3f9467fb46a813a8da640372ec55228792d85f43fce137b2c5f90d60c6e77918280192967001ad7ac6a2a80a69c390cf6ed218 SHA512 76b24794f87383ec39638569e7c61c5f500ea84a89cabb04d1bbcf101bffecc97e99729a4e29f3d4252a980c8a40889d1e4161ebea272a09946a78ecd4b75f4c
 MISC metadata.xml 621 BLAKE2B 9c56cc2099ed696942e2958926ee8c9f24be26fd273e74a7f789d368c3a222f084363ec3a4eada5e1197c4a81f533074f4b05c43d1e9c951e66261d55bc4d9e8 SHA512 7c49694ef56359e58b76b0dd7715d28615a541655c6ccaa2d7d64041c7340082bd5026fa2baa5a15e51e3aa27309d5a72ab836a5ee554366eb324406a50a09c4
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
new file mode 100644
index 000000000000..c9595748e901
--- /dev/null
+++ b/sci-biology/seaview/files/seaview-4.6-Wreserved-user-defined-literal.patch
@@ -0,0 +1,76 @@
+--- 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
new file mode 100644
index 000000000000..24cc28dfb3b7
--- /dev/null
+++ b/sci-biology/seaview/files/seaview-4.6-fno-common.patch
@@ -0,0 +1,110 @@
+--- 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/seaview-4.5.4.ebuild b/sci-biology/seaview/seaview-4.5.4.ebuild
deleted file mode 100644
index 33ee6f65ccbd..000000000000
--- a/sci-biology/seaview/seaview-4.5.4.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils multilib 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"
-
-CDEPEND="
-	sys-libs/zlib
-	x11-libs/fltk:1
-	x11-libs/libX11
-	xft? (
-		x11-libs/libXft
-		x11-libs/fltk:1[xft] )"
-RDEPEND="${CDEPEND}
-	sci-biology/clustalw
-	|| ( sci-libs/libmuscle sci-biology/muscle )
-	sci-biology/phyml"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	# 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/seaview/seaview-4.6.ebuild b/sci-biology/seaview/seaview-4.6-r1.ebuild
index 4ad8ad61b72b..469f88728120 100644
--- a/sci-biology/seaview/seaview-4.6.ebuild
+++ b/sci-biology/seaview/seaview-4.6-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit desktop toolchain-funcs
 
 DESCRIPTION="A graphical multiple sequence alignment editor"
 HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html"
@@ -15,19 +15,24 @@ KEYWORDS="~amd64 ~x86"
 IUSE="+xft"
 
 RDEPEND="
+	sci-biology/clustalw:2
+	sci-biology/phyml
+	|| (
+		sci-libs/libmuscle
+		sci-biology/muscle
+	)
 	sys-libs/zlib
-	x11-libs/fltk:1
+	x11-libs/fltk:1[xft?]
 	x11-libs/libX11
-	xft? (
-		x11-libs/libXft
-		x11-libs/fltk:1[xft] )
-	sci-biology/clustalw:2
-	|| ( sci-libs/libmuscle sci-biology/muscle )
-	sci-biology/phyml"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
+	xft? ( x11-libs/libXft )"
+DEPEND="${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
diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest
deleted file mode 100644
index 6a5d38227ddb..000000000000
--- a/sci-biology/shrimp/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST SHRiMP_2_2_3.src.tar.gz 4596867 BLAKE2B 64e485b8e2524062c11c581bbcac426800c9f42f61da467378dbfd3add63f721a9da9c04df61bde3704e654a20395e799e89fc5e47129b1d3f5bc93f960470fa SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5
-EBUILD shrimp-2.2.3.ebuild 1818 BLAKE2B 4878f0ce5782f0bc5fb5d4b14d5d713f21268b612cb18a2f14e19e3cca1c2270940b1f74220da0788fea9e142c803bcc77b9b2c04479a9432f06b9b29f3f7705 SHA512 2bfdb6f1cf7678dc9fafd66c25c07f55671f39600a44c606bac33652806105ff448d231202fb405307a0a49716557aa7cc63d371163821af2d919422ff9e2e6f
-MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/shrimp/metadata.xml b/sci-biology/shrimp/metadata.xml
deleted file mode 100644
index 959160fe46b1..000000000000
--- a/sci-biology/shrimp/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://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/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild
deleted file mode 100644
index 2b57b032a1b2..000000000000
--- a/sci-biology/shrimp/shrimp-2.2.3.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit flag-o-matic python-single-r1 toolchain-funcs
-
-MY_PV=${PV//./_}
-
-DESCRIPTION="SHort Read Mapping Package"
-HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"
-SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
-
-LICENSE="shrimp"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="custom-cflags +cpu_flags_x86_sse2"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# file collision on /usr/bin/utils #453044
-DEPEND="!sci-mathematics/cado-nfs"
-RDEPEND="${DEPEND}
-	${PYTHON_DEPS}"
-
-S=${WORKDIR}/SHRiMP_${MY_PV}
-
-pkg_pretend() {
-	use cpu_flags_x86_sse2 || die "This package needs sse2 support in your CPU"
-}
-
-pkg_setup() {
-	if [[ ${CC} == *gcc* ]] &&	! tc-has-openmp; then
-		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
-		die "C compiler lacks OPENMP support"
-	fi
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	sed \
-		-e '1 a #include <stdint.h>' \
-		-i common/dag_glue.cpp || die
-	# respect LDFLAGS wrt 331823
-	sed \
-		-e "s/LDFLAGS/LIBS/" \
-		-e "s/\$(LD)/& \$(LDFLAGS)/" \
-		-e 's/-static//' \
-		-i Makefile || die
-
-	append-flags -fopenmp
-	if ! use custom-cflags; then
-		append-flags -O3
-		replace-flags -O* -O3
-	fi
-	tc-export CXX
-
-	cd utils || die
-	sed -e '/^#!/d' -i *py || die
-	sed -e '1i#!/usr/bin/python' -i *py || die
-}
-
-src_compile() {
-	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	local i
-	newdoc bin/README README.bin && rm bin/README
-	dobin bin/* utils/split-contigs utils/temp-sink
-	dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES
-
-	pushd utils > /dev/null
-
-	python_doscript *py
-
-	rm *.py *.o *.c split-contigs temp-sink || die
-	insinto /usr/share/${PN}
-	doins -r *
-}
diff --git a/sci-biology/unafold/Manifest b/sci-biology/unafold/Manifest
index 5c5b222e5a61..818622d6ba58 100644
--- a/sci-biology/unafold/Manifest
+++ b/sci-biology/unafold/Manifest
@@ -1,3 +1,4 @@
+AUX unafold-3.8-doc-version.patch 308 BLAKE2B 6fba108c6338f9b974fc20e328f9af7d4ffc735889a32b74e36573ed68453af11922c15c626c48b997784378ad9cec79fe928ef184a224bcca570c7d59158851 SHA512 53a7ad53704830ac50fa463fb340cd8823e57af83b97ee40a969a338af62bce11934bc54b37a43b4f5bdd4faea919b2e3b4d8532926a8c185f53dcb5ce3c5afd
 DIST unafold-3.8.tar.bz2 282418 BLAKE2B 0dddff9dc440362ce3b24d18f42aa47d2dc817de93eba900de76dc73393feabb09ac57cb77af6c8db0ab8c0958f0fd459911fd813fa004b616fedffe9aebd069 SHA512 4c83cf0122e4d4ec2b713833adb11eb608b0f880f5b68114aefd8c7fa980c8d02f9a6cfc0c88cd640b4457e65954b05189118e8ac5ed207b2f9910738ca71a6c
-EBUILD unafold-3.8-r1.ebuild 589 BLAKE2B 345d178e5bdec00c1a6420b6b4d6598ffcb49474bd756b8a6dd50406fb1718969debeeeb27a2a804c53b6c518583e12499a0ca99d136b2bb47ffa559a87bd7e9 SHA512 4b025f8e4b52ef5e833d299973d44e5846000c45b7f36f200dc14414cb1367188f228e8fba23782f19475a38eb6f6d1cf8ca053b5d70f8b573aee69da7fc71b9
+EBUILD unafold-3.8-r1.ebuild 609 BLAKE2B 4f6e5867e63d272781eb88b6cfef00e41a067b7e97a8c61ee0e5c380369e155452afa6c35f153a3b3c39ea54cd02c2ed039ea793fb0f52b7afc91bf45e2c8ca4 SHA512 3ffe39a79f0162a645237cc5c4763abd0b41775f09546d2cf792ed9dcfe30219ba9540feac3ae8758616c5f0f48de3b7643b17d6682cf426a8f9f799e509b9e1
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/unafold/files/unafold-3.8-doc-version.patch b/sci-biology/unafold/files/unafold-3.8-doc-version.patch
new file mode 100644
index 000000000000..b15858fd69e6
--- /dev/null
+++ b/sci-biology/unafold/files/unafold-3.8-doc-version.patch
@@ -0,0 +1,11 @@
+--- 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/unafold-3.8-r1.ebuild b/sci-biology/unafold/unafold-3.8-r1.ebuild
index e4fff4e8cabd..6aec75f0336d 100644
--- a/sci-biology/unafold/unafold-3.8-r1.ebuild
+++ b/sci-biology/unafold/unafold-3.8-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit flag-o-matic
 
@@ -14,14 +14,17 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="custom-cflags"
 
-DEPEND=""
-RDEPEND="${DEPEND}"
+RDEPEND="
+	media-libs/freeglut
+	media-libs/gd
+	virtual/opengl"
+DEPEND="${RDEPEND}"
 
-src_prepare() {
+PATCHES=( "${FILESDIR}"/${P}-doc-version.patch )
+
+src_configure() {
 	# recommended in README
 	use custom-cflags || append-flags -O3
 
-	sed \
-		-e 's:hybrid (UNAFold) 3.7:hybrid (UNAFold) 3.8:g' \
-		-i tests/hybrid.tml || die
+	default
 }
diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
deleted file mode 100644
index 0de0a4ebedfe..000000000000
--- a/sci-biology/vienna-rna/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-AUX vienna-rna-2.1.1-impl-decl.patch 354 BLAKE2B d9d7a4e749a2c8681dc619961291f5e082681f15729a72ee1423bc4af71e8f745a558506e7147846c84df8fb7e5d316d1bc253f8125487a4ea6aab3c05b19bd8 SHA512 7c288b4889f11b5cc4e6db5b5db6dfcd70843aa135181e8d819ae86c90faed4a43e08f99b47f418caa23643642e68bf5e153f4d279f7566433af1c9093ec6e8b
-AUX vienna-rna-2.1.1-prll.patch 885 BLAKE2B 168d4b1a4c5ff0eb92379fe5762e7f0d6b7676c774c659422923c894bfcdb9efbbe20979ed87129c688b6ced9ad19cc51716164a0056b19fbc80fc27bbd32d57 SHA512 1b80636b43e1ce9ca54431358b45f2503ef3f49b8cd049b5ef501058e1771bda3628c88e63cc1bea9a32aff5a004ccef663b47dae385a5df6071793f292dff94
-AUX vienna-rna-2.1.8-bindir.patch 367 BLAKE2B 9bf3df6c604d5ac0661188d4f662ee12387f8bb30c2e3ecbd4a7bfd0a73ff5419f7a10b2fe70efd53e4b634bfdd3c1039ec000b26e7f5edbbcc4242a4edf5914 SHA512 aee16e7ff546aff38dd4a29d43502f4eb50778e6377a7d57f6a010dacc6a5f02162418fde27df03d1ba27f02361835d63dcefd866b8ac22f17a926c28fa4e9bf
-DIST ViennaRNA-2.1.8.tar.gz 5464683 BLAKE2B ed2086461b37c90de11638852680507c823495abacec1e797c589c22d07dc48b4833d8d6916e5c95083bb9b970c659bbfb14ca45e155486333a915593c4caf01 SHA512 84f9db1247ff7a77aa6550b6285d9bed31fa6ce179aab26eef798c65a07f5cbd89f944630dfa5d29a43401b12a439324b57ee69047a3985e3a4f1e88dffca60e
-EBUILD vienna-rna-2.1.8.ebuild 2588 BLAKE2B 5a1692be0a587cc85dcf0a60c609ff0c4eade92e5da98ce05bf2d90a195e606d9ca9262774c2c6875b1d9d53451b5043d7c4ae8a3446d4ebf3607effe039cd92 SHA512 4474f2bf042a31e02fd7b9882f6b5ec17fef4ba9f23eab29a39e9c09ea29414e836c029e568a905a2c315370c763384f9d84547a56a8806216dc825d51c3d378
-MISC metadata.xml 1324 BLAKE2B ba9d5e1f5893344fd1899e3723e1b86bac75546cde97b311fe7ef9dc2068f1a063cd5a5d2ac65d1195f532441194e8943ad2ec44db9a5c614ed0c8d894a900bb SHA512 8198db695aea5244b62fab23fd0a53a0657f8d37cc741f60869a39374e97c725b564086d852e37216c584083168881eba246f59b840d6a41bfe9246d3bd88d4b
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch
deleted file mode 100644
index de457f318e8e..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- Readseq/readseq.c | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/Readseq/readseq.c b/Readseq/readseq.c
-index 8af7b39..56a25ae 100644
---- a/Readseq/readseq.c
-+++ b/Readseq/readseq.c
-@@ -171,6 +171,7 @@ link -w -o readseq -t MPST -c 'MPS ' 
- #include <stdio.h>
- #include <string.h>
- #include <ctype.h>
-+#include <stdlib.h>
- 
- #include "ureadseq.h"
- 
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch
deleted file mode 100644
index ee4aef5c3308..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- Readseq/Makefile | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/Readseq/Makefile b/Readseq/Makefile
-index f073aaa..05f2edd 100644
---- a/Readseq/Makefile
-+++ b/Readseq/Makefile
-@@ -6,11 +6,11 @@
- #
- 
- # pick an ANSI C compiler (the default Sun CC is not ANSI)
--CC=gcc  # Gnu C Compiler
-+CC?=gcc  # Gnu C Compiler
- #CC=cc  # SGI Irix
- #CC=vcc # some DEC Ultrix
- 
--CFLAGS=
-+CFLAGS?=
- #CFLAGS= -DSMALLCHECKSUM  # if you prefer to use a GCG-standard 13 bit checksum
- #    instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
- 
-@@ -40,7 +40,7 @@ all: build test
- 
- build: $(SOURCES)
- 	@echo "Compiling readseq..."
--	$(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ureadasn.c
- 
- # if using NCBI, uncomment these lines in place of build: above
- #build: $(SOURCES)
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch
deleted file mode 100644
index e54dff95b485..000000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch
+++ /dev/null
@@ -1,10 +0,0 @@
-diff --git a/Utils/Makefile.am b/Utils/Makefile.am
-index f42ebf4..d84a0f1 100644
---- a/Utils/Makefile.am
-+++ b/Utils/Makefile.am
-@@ -1,4 +1,4 @@
--pkgbindir = $(pkgdatadir)/bin
-+pkgbindir = $(prefix)/bin
- pkgbin_PROGRAMS = b2ct popt ct2db
- 
- pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl
diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml
deleted file mode 100644
index bbc3d41fb4a6..000000000000
--- a/sci-biology/vienna-rna/metadata.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		The Vienna RNA Package consists of a C code library and several
-		stand-alone programs for the prediction and comparison of RNA secondary
-		structures. RNA secondary structure prediction through energy
-		minimization is the most used function in the package. We provide three
-		kinds of dynamic programming algorithms for structure prediction: the
-		minimum free energy algorithm of (Zuker and Stiegler 1981) which yields a
-		single optimal structure, the partition function algorithm of
-		(McCaskill 1990) which calculates base pair probabilities in the
-		thermodynamic ensemble, and the suboptimal folding algorithm of
-		(Wuchty et.al 1999) which generates all suboptimal structures within a
-		given energy range of the optimal energy. For secondary structure
-		comparison, the package contains several measures of distance
-		(dissimilarities) using either string alignment or tree-editing
-		(Shapiro and Zhang 1990). Finally, we provide an algorithm to design
-		sequences with a predefined structure (inverse folding).
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild
deleted file mode 100644
index 7664f6d3dc6e..000000000000
--- a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild
+++ /dev/null
@@ -1,112 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-DISTUTILS_OPTIONAL=true
-AUTOTOOLS_AUTORECONF=true
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs
-
-DESCRIPTION="RNA secondary structure prediction and comparison"
-HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
-SRC_URI="http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="vienna-rna"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE="doc openmp python static-libs"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	dev-lang/perl
-	media-libs/gd
-	doc? ( dev-texlive/texlive-latex )
-	python? ( ${PYTHON_DEPS} )"
-DEPEND="${RDEPEND}
-	python? ( dev-lang/swig:0 )"
-
-S="${WORKDIR}/ViennaRNA-${PV}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-bindir.patch
-	"${FILESDIR}"/${PN}-2.1.1-prll.patch
-	"${FILESDIR}"/${PN}-2.1.1-impl-decl.patch
-)
-
-src_prepare() {
-	sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
-	sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' interfaces/Perl/Makefile.am || die
-
-	autotools-utils_src_prepare
-
-	if use python; then
-		cd interfaces/Python || die
-		local PATCHES=()
-		distutils-r1_src_prepare
-	fi
-}
-
-src_configure() {
-	local myeconfargs=(
-		--with-cluster
-		$(use_enable openmp)
-	)
-
-	use doc || \
-		myeconfargs+=(
-			--without-doc-pdf
-			--without-doc-html
-			--without-doc
-			)
-	autotools-utils_src_configure
-	sed \
-		-e "s:CC=gcc:CC=$(tc-getCC):" \
-		-e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \
-		-i Readseq/Makefile || die
-	if use python; then
-		cd interfaces/Python || die
-		distutils-r1_src_configure
-	fi
-}
-
-src_compile() {
-	autotools-utils_src_compile
-	autotools-utils_src_compile -C Readseq build CC=$(tc-getCC)
-
-	# TODO: Add (optional?) support for the NCBI toolkit.
-	if use python; then
-		cd interfaces/Python || die
-		emake RNA_wrap.c
-		distutils-r1_src_compile
-	fi
-}
-
-src_test() {
-	autotools-utils_src_compile -C interfaces/Perl check
-	use python && autotools-utils_src_compile -C interfaces/Python check
-	autotools-utils_src_compile -C Readseq test
-}
-
-src_install() {
-	autotools-utils_src_install
-
-	if ! use static-libs; then
-		rm -f "${ED}"/usr/$(get_libdir)/*.a || die
-	fi
-
-	newbin Readseq/readseq readseq-vienna
-	dodoc Readseq/Readseq.help
-	newdoc Readseq/Readme README.readseq
-	newdoc Readseq/Formats Formats.readseq
-
-	# remove perlocal.pod to avoid file collisions (see #240358)
-	perl_delete_localpod || die "Failed to remove perlocal.pod"
-	if use python; then
-		cd interfaces/Python || die
-		distutils-r1_src_install
-	fi
-}