2020-11-01 19:05:25 UTC

15 files changed, 63 insertions, 72 deletions

diff --git a/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r2 b/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r3
index 1a2b33695ede..e4b04ac529da 100644
--- a/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r2
+++ b/metadata/md5-cache/sci-biology/clustalw-mpi-0.13-r3
@@ -1,13 +1,13 @@
 DEFINED_PHASES=install prepare
 DEPEND=virtual/mpi
 DESCRIPTION=An MPI implemention of the ClustalW general purpose multiple alignment algorithm
-EAPI=6
+EAPI=7
 HOMEPAGE=http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php
-IUSE=mpi_njtree static_pairalign
+IUSE=mpi-njtree static-pairalign
 KEYWORDS=~amd64 ~x86
 LICENSE=public-domain
 RDEPEND=virtual/mpi
 SLOT=0
 SRC_URI=http://web.bii.a-star.edu.sg/~kuobin/clustalw-mpi/clustalw-mpi-0.13.tar.gz
 _eclasses_=multilib	98584e405e2b0264d37e8f728327fed1	toolchain-funcs	605c126bed8d87e4378d5ff1645330cb
-_md5_=9e376a1d2ae782d9495b0c6c318aa097
+_md5_=689841db0e3b7d6629b51049a2942165
diff --git a/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2 b/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2
index 2d5ce76ef3b1..182030e32736 100644
--- a/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2
+++ b/metadata/md5-cache/sci-biology/dialign-tx-1.0.2-r2
@@ -1,10 +1,10 @@
 DEFINED_PHASES=compile configure install postinst
 DESCRIPTION=Greedy and progressive approaches for segment-based multiple sequence alignment
-EAPI=6
+EAPI=7
 HOMEPAGE=http://dialign-tx.gobics.de/
 KEYWORDS=~amd64 ~x86
 LICENSE=LGPL-2.1
 SLOT=0
 SRC_URI=http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz
 _eclasses_=multilib	98584e405e2b0264d37e8f728327fed1	toolchain-funcs	605c126bed8d87e4378d5ff1645330cb
-_md5_=b04d9beffea802bb82f896df101ca660
+_md5_=b2a78c4cfa60eb348ae63d076ecb5fba
diff --git a/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660 b/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660
index 1d531d916493..0fc366f7cfd2 100644
--- a/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660
+++ b/metadata/md5-cache/sci-biology/embassy-phylipnew-3.69.660
@@ -10,4 +10,4 @@ RDEPEND=dev-libs/expat dev-libs/libpcre:3 sci-libs/plplot:= sys-libs/zlib mysql?
 SLOT=0
 SRC_URI=ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.660.tar.gz -> embassy-phylipnew-3.69.660.tar.gz
 _eclasses_=autotools	7d999b62b8749fad43fff00620cedf47	desktop	7fd20552ce4cc97e8acb132a499a7dd8	edos2unix	33e347e171066657f91f8b0c72ec8773	emboss-r2	8895be811ae4511c202bcf2ddb7dbfd8	epatch	ed88001f77c6dd0d5f09e45c1a5b480e	estack	686eaab303305a908fd57b2fd7617800	eutils	2d5b3f4b315094768576b6799e4f926e	flag-o-matic	09a8beb8e6a8e02dc1e1bd83ac353741	l10n	8cdd85e169b835d518bc2fd59f780d8e	libtool	f143db5a74ccd9ca28c1234deffede96	ltprune	db8b7ce9d0e663594bcb4a4e72131a79	multilib	98584e405e2b0264d37e8f728327fed1	preserve-libs	ef207dc62baddfddfd39a164d9797648	toolchain-funcs	605c126bed8d87e4378d5ff1645330cb	vcs-clean	2a0f74a496fa2b1552c4f3398258b7bf	wrapper	4251d4c84c25f59094fd557e0063a974
-_md5_=052915aa60b919df12c7c4274d5be551
+_md5_=5f78f83387f741c46031c218b1965467
diff --git a/metadata/md5-cache/sci-biology/gmap-2015.12.31.5 b/metadata/md5-cache/sci-biology/gmap-2015.12.31.5
deleted file mode 100644
index 9af4c172fcc5..000000000000
--- a/metadata/md5-cache/sci-biology/gmap-2015.12.31.5
+++ /dev/null
@@ -1,10 +0,0 @@
-DEFINED_PHASES=-
-DESCRIPTION=A Genomic Mapping and Alignment Program for mRNA and EST Sequences
-EAPI=6
-HOMEPAGE=http://research-pub.gene.com/gmap/
-KEYWORDS=~amd64 ~x86
-LICENSE=gmap
-SLOT=0
-SRC_URI=http://research-pub.gene.com/gmap/src/gmap-gsnap-2015-12-31.v5.tar.gz
-_eclasses_=estack	686eaab303305a908fd57b2fd7617800	versionator	2352c3fc97241f6a02042773c8287748
-_md5_=398e7f0670f5bd07e45f2780d7fe03cf
diff --git a/metadata/md5-cache/sci-biology/gmap-2020.10.27 b/metadata/md5-cache/sci-biology/gmap-2020.10.27
new file mode 100644
index 000000000000..487916a59aeb
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/gmap-2020.10.27
@@ -0,0 +1,9 @@
+DEFINED_PHASES=-
+DESCRIPTION=A Genomic Mapping and Alignment Program for mRNA and EST Sequences
+EAPI=7
+HOMEPAGE=http://research-pub.gene.com/gmap/
+KEYWORDS=~amd64 ~x86
+LICENSE=gmap
+SLOT=0
+SRC_URI=http://research-pub.gene.com/gmap/src/gmap-gsnap-2020-10-27.tar.gz
+_md5_=9c28013ebc925bd0d07b8a1b1f1dbc4d
diff --git a/metadata/md5-cache/sci-biology/lagan-2.0-r3 b/metadata/md5-cache/sci-biology/lagan-2.0-r4
index 3ea597b76b2d..3aabb8feb279 100644
--- a/metadata/md5-cache/sci-biology/lagan-2.0-r3
+++ b/metadata/md5-cache/sci-biology/lagan-2.0-r4
@@ -1,6 +1,6 @@
-DEFINED_PHASES=compile install prepare
+DEFINED_PHASES=configure install prepare
 DESCRIPTION=The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA
-EAPI=6
+EAPI=7
 HOMEPAGE=http://lagan.stanford.edu/lagan_web/index.shtml
 KEYWORDS=~amd64 ~x86
 LICENSE=GPL-2
@@ -8,4 +8,4 @@ RDEPEND=dev-lang/perl
 SLOT=0
 SRC_URI=http://lagan.stanford.edu/lagan_web/lagan20.tar.gz
 _eclasses_=multilib	98584e405e2b0264d37e8f728327fed1	toolchain-funcs	605c126bed8d87e4378d5ff1645330cb
-_md5_=c9dbddd6a22f2e20ff25d0aa1e6f4280
+_md5_=c4b4e347541c85d423cac28e03a104d4
diff --git a/metadata/md5-cache/sci-biology/newick-utils-1.6 b/metadata/md5-cache/sci-biology/newick-utils-1.6
deleted file mode 100644
index f9cdb1fd46cd..000000000000
--- a/metadata/md5-cache/sci-biology/newick-utils-1.6
+++ /dev/null
@@ -1,10 +0,0 @@
-DEFINED_PHASES=test
-DESCRIPTION=Tools for processing phylogenetic trees
-EAPI=6
-HOMEPAGE=http://cegg.unige.ch/newick_utils
-KEYWORDS=~amd64 ~x86
-LICENSE=BSD
-RDEPEND=!dev-games/libnw
-SLOT=0
-SRC_URI=http://cegg.unige.ch/pub/newick-utils-1.6.tar.gz
-_md5_=f70356a582d317400bf4cd17b73beb16
diff --git a/metadata/md5-cache/sci-biology/newick-utils-1.6-r1 b/metadata/md5-cache/sci-biology/newick-utils-1.6-r1
new file mode 100644
index 000000000000..c864843b760f
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/newick-utils-1.6-r1
@@ -0,0 +1,14 @@
+BDEPEND=>=app-portage/elt-patches-20170815 || ( >=sys-devel/automake-1.16.1:1.16 >=sys-devel/automake-1.15.1:1.15 ) >=sys-devel/autoconf-2.69 >=sys-devel/libtool-2.4
+DEFINED_PHASES=configure install prepare
+DEPEND=xml? ( dev-libs/libxml2 )
+DESCRIPTION=Tools for processing phylogenetic trees
+EAPI=7
+HOMEPAGE=http://cegg.unige.ch/newick_utils
+IUSE=xml
+KEYWORDS=~amd64 ~x86
+LICENSE=BSD
+RDEPEND=xml? ( dev-libs/libxml2 ) !dev-games/libnw
+SLOT=0
+SRC_URI=http://cegg.unige.ch/pub/newick-utils-1.6.tar.gz
+_eclasses_=autotools	7d999b62b8749fad43fff00620cedf47	libtool	f143db5a74ccd9ca28c1234deffede96	multilib	98584e405e2b0264d37e8f728327fed1	toolchain-funcs	605c126bed8d87e4378d5ff1645330cb
+_md5_=fac40fe86b457a75883a5eb465ce18d8
diff --git a/metadata/md5-cache/sci-biology/paml-4.4c-r1 b/metadata/md5-cache/sci-biology/paml-4.4c-r1
deleted file mode 100644
index d2f6604ce281..000000000000
--- a/metadata/md5-cache/sci-biology/paml-4.4c-r1
+++ /dev/null
@@ -1,10 +0,0 @@
-DEFINED_PHASES=compile install prepare
-DESCRIPTION=Phylogenetic Analysis by Maximum Likelihood
-EAPI=5
-HOMEPAGE=http://abacus.gene.ucl.ac.uk/software/paml.html
-KEYWORDS=amd64 x86
-LICENSE=free-noncomm
-SLOT=0
-SRC_URI=http://abacus.gene.ucl.ac.uk/software/paml4.4c.tar.gz
-_eclasses_=estack	686eaab303305a908fd57b2fd7617800	multilib	98584e405e2b0264d37e8f728327fed1	toolchain-funcs	605c126bed8d87e4378d5ff1645330cb	versionator	2352c3fc97241f6a02042773c8287748
-_md5_=c46d709378282d4ccbb567aaa00ee01a
diff --git a/metadata/md5-cache/sci-biology/paml-4.9j b/metadata/md5-cache/sci-biology/paml-4.9j
new file mode 100644
index 000000000000..7c76b7ce86d5
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/paml-4.9j
@@ -0,0 +1,10 @@
+DEFINED_PHASES=compile configure install
+DESCRIPTION=Phylogenetic Analysis by Maximum Likelihood
+EAPI=7
+HOMEPAGE=http://abacus.gene.ucl.ac.uk/software/paml.html
+KEYWORDS=~amd64 ~x86
+LICENSE=free-noncomm
+SLOT=0
+SRC_URI=http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz
+_eclasses_=multilib	98584e405e2b0264d37e8f728327fed1	toolchain-funcs	605c126bed8d87e4378d5ff1645330cb
+_md5_=236ce838eff8e04f8059e18110b3ff38
diff --git a/metadata/md5-cache/sci-biology/seaview-4.5.4 b/metadata/md5-cache/sci-biology/seaview-4.5.4
deleted file mode 100644
index 40ee9d0794a3..000000000000
--- a/metadata/md5-cache/sci-biology/seaview-4.5.4
+++ /dev/null
@@ -1,13 +0,0 @@
-DEFINED_PHASES=install prepare
-DEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) virtual/pkgconfig
-DESCRIPTION=A graphical multiple sequence alignment editor
-EAPI=5
-HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html
-IUSE=+xft
-KEYWORDS=amd64 x86
-LICENSE=public-domain
-RDEPEND=sys-libs/zlib x11-libs/fltk:1 x11-libs/libX11 xft? ( x11-libs/libXft x11-libs/fltk:1[xft] ) sci-biology/clustalw || ( sci-libs/libmuscle sci-biology/muscle ) sci-biology/phyml
-SLOT=0
-SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.5.4.tar.gz
-_eclasses_=desktop	7fd20552ce4cc97e8acb132a499a7dd8	edos2unix	33e347e171066657f91f8b0c72ec8773	epatch	ed88001f77c6dd0d5f09e45c1a5b480e	estack	686eaab303305a908fd57b2fd7617800	eutils	2d5b3f4b315094768576b6799e4f926e	l10n	8cdd85e169b835d518bc2fd59f780d8e	ltprune	db8b7ce9d0e663594bcb4a4e72131a79	multilib	98584e405e2b0264d37e8f728327fed1	preserve-libs	ef207dc62baddfddfd39a164d9797648	toolchain-funcs	605c126bed8d87e4378d5ff1645330cb	vcs-clean	2a0f74a496fa2b1552c4f3398258b7bf	wrapper	4251d4c84c25f59094fd557e0063a974
-_md5_=38cc02682d853c813df2b6e81cbb51c5
diff --git a/metadata/md5-cache/sci-biology/seaview-4.6 b/metadata/md5-cache/sci-biology/seaview-4.6
deleted file mode 100644
index 1d6129786e67..000000000000
--- a/metadata/md5-cache/sci-biology/seaview-4.6
+++ /dev/null
@@ -1,13 +0,0 @@
-DEFINED_PHASES=install prepare
-DEPEND=sys-libs/zlib x11-libs/fltk:1 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 virtual/pkgconfig
-DESCRIPTION=A graphical multiple sequence alignment editor
-EAPI=6
-HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html
-IUSE=+xft
-KEYWORDS=~amd64 ~x86
-LICENSE=public-domain
-RDEPEND=sys-libs/zlib x11-libs/fltk:1 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
-SLOT=0
-SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.6.tar.gz
-_eclasses_=desktop	7fd20552ce4cc97e8acb132a499a7dd8	edos2unix	33e347e171066657f91f8b0c72ec8773	epatch	ed88001f77c6dd0d5f09e45c1a5b480e	estack	686eaab303305a908fd57b2fd7617800	eutils	2d5b3f4b315094768576b6799e4f926e	l10n	8cdd85e169b835d518bc2fd59f780d8e	ltprune	db8b7ce9d0e663594bcb4a4e72131a79	multilib	98584e405e2b0264d37e8f728327fed1	preserve-libs	ef207dc62baddfddfd39a164d9797648	toolchain-funcs	605c126bed8d87e4378d5ff1645330cb	vcs-clean	2a0f74a496fa2b1552c4f3398258b7bf	wrapper	4251d4c84c25f59094fd557e0063a974
-_md5_=1a6723f1ab0e67cc0d63dd54a902900f
diff --git a/metadata/md5-cache/sci-biology/seaview-4.6-r1 b/metadata/md5-cache/sci-biology/seaview-4.6-r1
new file mode 100644
index 000000000000..3e67065268c3
--- /dev/null
+++ b/metadata/md5-cache/sci-biology/seaview-4.6-r1
@@ -0,0 +1,14 @@
+BDEPEND=virtual/pkgconfig
+DEFINED_PHASES=install prepare
+DEPEND=sci-biology/clustalw:2 sci-biology/phyml || ( sci-libs/libmuscle sci-biology/muscle ) sys-libs/zlib x11-libs/fltk:1[xft?] x11-libs/libX11 xft? ( x11-libs/libXft )
+DESCRIPTION=A graphical multiple sequence alignment editor
+EAPI=7
+HOMEPAGE=http://pbil.univ-lyon1.fr/software/seaview.html
+IUSE=+xft
+KEYWORDS=~amd64 ~x86
+LICENSE=public-domain
+RDEPEND=sci-biology/clustalw:2 sci-biology/phyml || ( sci-libs/libmuscle sci-biology/muscle ) sys-libs/zlib x11-libs/fltk:1[xft?] x11-libs/libX11 xft? ( x11-libs/libXft )
+SLOT=0
+SRC_URI=ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.6.tar.gz
+_eclasses_=desktop	7fd20552ce4cc97e8acb132a499a7dd8	multilib	98584e405e2b0264d37e8f728327fed1	toolchain-funcs	605c126bed8d87e4378d5ff1645330cb
+_md5_=a742711d8523a4e49524662c12d647c2
diff --git a/metadata/pkg_desc_index b/metadata/pkg_desc_index
index f364c7b8e5c5..1e0bd95a7134 100644
--- a/metadata/pkg_desc_index
+++ b/metadata/pkg_desc_index
@@ -15707,7 +15707,7 @@ sci-biology/bwa 0.7.17: Burrows-Wheeler Alignment Tool, a fast short genomic seq
 sci-biology/cd-hit 4.6.6: Clustering Database at High Identity with Tolerance
 sci-biology/clustal-omega 1.2.4: Scalable multiple alignment of protein sequences
 sci-biology/clustalw 1.83-r4 2.1-r1: General purpose multiple alignment program for DNA and proteins
-sci-biology/clustalw-mpi 0.13-r2: An MPI implemention of the ClustalW general purpose multiple alignment algorithm
+sci-biology/clustalw-mpi 0.13-r3: An MPI implemention of the ClustalW general purpose multiple alignment algorithm
 sci-biology/clustalx 2.1-r3: Graphical interface for the ClustalW multiple alignment program
 sci-biology/consed 29: A genome sequence finishing program
 sci-biology/cutg 160-r1: Codon usage tables calculated from GenBank
@@ -15744,14 +15744,14 @@ sci-biology/gatk 2.4: The Genome Analysis Toolkit
 sci-biology/gibbs 3.1: Identify motifs, conserved regions, in DNA or protein sequences
 sci-biology/glimmer 3.02-r3 3.02b: An HMM-based microbial gene finding system from TIGR
 sci-biology/glimmerhmm 3.0.1-r1: A eukaryotic gene finding system from TIGR
-sci-biology/gmap 2015.12.31.5: A Genomic Mapping and Alignment Program for mRNA and EST Sequences
+sci-biology/gmap 2020.10.27: A Genomic Mapping and Alignment Program for mRNA and EST Sequences
 sci-biology/hmmer 2.3.2-r4 3.1_beta2: Sequence analysis using profile hidden Markov models
 sci-biology/iedera 1.05-r1: A subset seed design tool for DNA sequence alignment
 sci-biology/infernal 1.0.2-r1: Inference of RNA alignments
 sci-biology/iqpnni 3.3.2-r1: Important Quartet Puzzling and NNI Operation
 sci-biology/kalign 2.03-r2: Global and progressive multiple sequence alignment
 sci-biology/kallisto 0.43.1 9999: Near-optimal RNA-Seq quantification
-sci-biology/lagan 2.0-r3: The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA
+sci-biology/lagan 2.0-r4: The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA
 sci-biology/libgtextutils 0.6.1: Gordon Text utils Library
 sci-biology/mafft 7.305: Multiple sequence alignments using a variety of algorithms
 sci-biology/maq 0.7.1-r2: Mapping and Assembly with Qualities, mapping NGS reads to reference genomes
@@ -15764,10 +15764,10 @@ sci-biology/mrbayes 3.1.2-r2: Bayesian Inference of Phylogeny
 sci-biology/mummer 3.23: A rapid whole genome aligner
 sci-biology/muscle 3.8.31: Multiple sequence comparison by log-expectation
 sci-biology/ncbi-tools 2.2.26-r2: Development toolkit and applications for computational biology, including BLAST
-sci-biology/newick-utils 1.6: Tools for processing phylogenetic trees
+sci-biology/newick-utils 1.6-r1: Tools for processing phylogenetic trees
 sci-biology/njplot 2.3-r2: A phylogenetic tree drawing program which supports tree rooting
 sci-biology/pals 1.0-r1: Pairwise Aligner for Long Sequences
-sci-biology/paml 4.4c-r1: Phylogenetic Analysis by Maximum Likelihood
+sci-biology/paml 4.9j: Phylogenetic Analysis by Maximum Likelihood
 sci-biology/phrap 1.080812-r2: Shotgun assembly and alignment utilities
 sci-biology/phred 071220-r1: A base caller for Sanger DNA sequencing
 sci-biology/phylip 3.698: The PHYLogeny Inference Package
@@ -15795,7 +15795,7 @@ sci-biology/repeatmasker-libraries 20120418: A special version of RepBase used b
 sci-biology/rmblast 1.2-r1: RepeatMasker compatible version of NCBI BLAST+
 sci-biology/rnaview 20040713-r4: Generates 2D displays of RNA/DNA secondary structures with tertiary interactions
 sci-biology/samtools 0.1.20-r4 1.10: Utilities for analysing and manipulating the SAM/BAM alignment formats
-sci-biology/seaview 4.5.4 4.6: A graphical multiple sequence alignment editor
+sci-biology/seaview 4.6-r1: A graphical multiple sequence alignment editor
 sci-biology/seqan 2.4.0 9999: C++ Sequence Analysis Library
 sci-biology/sibsim4 0.20: A rewrite and improvement upon sim4, a DNA-mRNA aligner
 sci-biology/sim4 20030921-r2: A program to align cDNA and genomic DNA
diff --git a/metadata/timestamp.chk b/metadata/timestamp.chk
index 33aa9b01f641..ba5f7461d4e2 100644
--- a/metadata/timestamp.chk
+++ b/metadata/timestamp.chk
@@ -1 +1 @@
-Sun, 01 Nov 2020 18:35:15 +0000
+Sun, 01 Nov 2020 19:05:26 +0000