Merge pull request #17 from BioArchLinux/mick

Mick

BioArchLinux/avogadro2/PKGBUILD

@@ -5,7 +5,7 @@ pkgname=avogadro2
 _pkgname=avogadroapp
 pkgver=1.95.1
 pkgrel=5
-pkgdesc="An advanced molecular editor"
+pkgdesc="An advanced molecular editor. https://doi.org/10.1186/1758-2946-4-17"
 arch=('x86_64')
 url="https://two.avogadro.cc"
 license=('BSD')

BioArchLinux/bali-phy/PKGBUILD

@@ -2,7 +2,7 @@
 pkgname=bali-phy
 pkgver=3.6.1
 pkgrel=4
-pkgdesc="Bayesian co-estimation of phylogenies and multiple alignments via MCMC"
+pkgdesc="Bayesian co-estimation of phylogenies and multiple alignments via MCMC. https://doi.org/10.1093/bioinformatics/btab129"
 arch=('x86_64')
 url="http://www.bali-phy.org/"
 license=('GPL')

BioArchLinux/beast/PKGBUILD

@@ -5,7 +5,7 @@ pkgname=beast
 pkgver=1.10.4
 pkgrel=8
 provides=("beast")
-pkgdesc="Bayesian Evolutionary Analysis Sampling Trees"
+pkgdesc="Bayesian Evolutionary Analysis Sampling Trees. https://doi.org/10.1186/1471-2148-7-214"
 arch=('x86_64')
 url="http://beast.community/"
 license=('LGPL-2.1 License')

BioArchLinux/beast2/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=beast2
 pkgver=2.6.6
 pkgrel=3
-pkgdesc="Bayesian Evolutionary Analysis by Sampling Trees"
+pkgdesc="Bayesian Evolutionary Analysis by Sampling Trees. https://doi.org/10.1371/journal.pcbi.1003537"
 arch=('x86_64')
 url="http://www.beast2.org/"
 license=('LGPL-2.1 License')

BioArchLinux/blast+/PKGBUILD

@@ -5,7 +5,7 @@
 pkgname=blast+
 pkgver=2.12.0
 pkgrel=4
-pkgdesc='BLAST tool suite from NCBI (blastn, blastp, blastx, psiblast, etc)'
+pkgdesc='BLAST tool suite from NCBI (blastn, blastp, blastx, psiblast, etc). https://doi.org/10.1186/1471-2105-10-421'
 arch=('x86_64')
 url='http://blast.ncbi.nlm.nih.gov'
 license=('custom')

BioArchLinux/bowtie/PKGBUILD

@@ -3,7 +3,7 @@
 pkgname=bowtie
 pkgver=1.3.1
 pkgrel=3
-pkgdesc="Bowtie is an alignment tool for short nucleotide sequences against long templates"
+pkgdesc="Bowtie is an alignment tool for short nucleotide sequences against long templates. https://doi.org/10.1186/gb-2009-10-3-r25"
 url="http://bowtie-bio.sf.net"
 arch=('x86_64' 'aarch64')
 license=('PerlArtistic')

BioArchLinux/bowtie2/PKGBUILD

@@ -3,7 +3,7 @@
 pkgname=bowtie2
 pkgver=2.4.4
 pkgrel=3
-pkgdesc="Tool for aligning sequencing reads to long reference sequences"
+pkgdesc="Tool for aligning sequencing reads to long reference sequences. https://doi.org/10.1038/nmeth.1923"
 arch=('x86_64' 'aarch64')
 url="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml"
 license=('GPL')

BioArchLinux/bwa/PKGBUILD

@@ -3,7 +3,7 @@
 pkgname=bwa
 pkgver=v0.7.17.r27.g3ddd7b8
 pkgrel=2
-pkgdesc="Burrows-Wheeler Aligner maps low-divergent sequences against a large reference genome"
+pkgdesc="Burrows-Wheeler Aligner maps low-divergent sequences against a large reference genome. https://doi.org/10.1093/bioinformatics/btp324"
 arch=('x86_64')
 url="http://bio-bwa.sourceforge.net/"
 license=('GPL3')

BioArchLinux/clustal-omega/PKGBUILD

@@ -3,7 +3,7 @@
 pkgname=clustal-omega
 pkgver=1.2.4
 pkgrel=5
-pkgdesc='A general purpose multiple sequence alignment program for protein and DNA/RNA'
+pkgdesc='A general purpose multiple sequence alignment program for protein and DNA/RNA. https://doi.org/10.1038/msb.2011.75'
 arch=('x86_64')
 url='http://www.clustal.org/omega'
 license=('GPL2')

BioArchLinux/clustalw/PKGBUILD

@@ -3,7 +3,7 @@
 pkgname=clustalw
 pkgver=2.1
 pkgrel=5
-pkgdesc='Multiple alignment of nucleic acid and protein sequences (command line tool)'
+pkgdesc='Multiple alignment of nucleic acid and protein sequences (command line tool). https://doi.org/10.1093/bioinformatics/btm404'
 arch=('x86_64')
 url='http://www.clustal.org/clustal2'
 license=('LGPL3')

BioArchLinux/clustalx/PKGBUILD

@@ -5,7 +5,7 @@
 pkgname=clustalx
 pkgver=2.1
 pkgrel=5
-pkgdesc='Multiple alignment of nucleic acid and protein sequences (command line tool'
+pkgdesc='Multiple alignment of nucleic acid and protein sequences (command line tool). https://doi.org/10.1093/bioinformatics/btm404'
 arch=('x86_64')
 url='http://www.clustal.org/clustal2'
 license=('LGPL3')

BioArchLinux/easycodeml/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=easycodeml
 pkgver=1.21
 pkgrel=1
-pkgdesc="A visual tool for analysis of selection using CodeML"
+pkgdesc="A visual tool for analysis of selection using CodeML. https://doi.org/10.1002/ece3.5015"
 arch=('x86_64')
 url="https://github.com/BioEasy/EasyCodeML"
 license=('LGPL3')

BioArchLinux/emboss/PKGBUILD

@@ -5,7 +5,7 @@ pkgname=emboss
 _pkgname=EMBOSS
 pkgver=6.6.0
 pkgrel=6
-pkgdesc="A collection of molecular biology applications"
+pkgdesc="A collection of molecular biology applications. https://doi.org/10.1016/s0168-9525(00)02024-2"
 arch=('x86_64' 'i686')
 url="http://emboss.sourceforge.net/"
 depends=('gd' 'pcre' 'java-runtime')

BioArchLinux/fasttree/PKGBUILD

@@ -2,7 +2,7 @@
 pkgname=fasttree
 pkgver=2.1.9
 pkgrel=3
-pkgdesc="Approximately-Maximum-Likelihood Trees for Large Alignments"
+pkgdesc="Approximately-Maximum-Likelihood Trees for Large Alignments. https://doi.org/10.1371/journal.pone.0009490"
 arch=(i686 x86_64)
 url="http://www.microbesonline.org/fasttree/"
 license=('GPL')

BioArchLinux/fastx-toolkit/PKGBUILD

@@ -3,7 +3,7 @@
 pkgname=fastx-toolkit
 pkgver=0.0.14
 pkgrel=3
-pkgdesc="The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing."
+pkgdesc="The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing"
 arch=("any")
 url="https://github.com/agordon/fastx_toolkit"
 license=('AGPL3')

BioArchLinux/gblocks/PKGBUILD

@@ -8,7 +8,7 @@ provides=("gblocks")
 pkgver=0.91b
 pkgrel=4
 pkgdesc="A program written in ANSI C language that eliminates poorly aligned\
- positions and divergent regions of an alignment of DNA or protein sequences"
+ positions and divergent regions of an alignment of DNA or protein sequences. https://doi.org/10.1093/oxfordjournals.molbev.a026334"
 
 url='http://molevol.cmima.csic.es/castresana/Gblocks.html'
 arch=('x86_64')

BioArchLinux/gsalign/PKGBUILD

@@ -0,0 +1,29 @@
+# Maintainer:  Mick Elliot <m.g.elliot@rug.nl>
+# Contributor: Mick Elliot <m.g.elliot@rug.nl>
+
+pkgname=gsalign
+pkgnamecaps=GSAlign
+pkgver=1.0.22
+pkgrel=1
+pkgdesc='An ultra-fast sequence alignment algorithm for intra-species genome comparison. https://doi.org/10.1186/s12864-020-6569-1'
+arch=('x86_64')
+url="https://github.com/hsinnan75/${pkgnamecaps}"
+license=('MIT')
+depends=(gcc-libs zlib)
+provides=()
+source=("${pkgver}.tar.gz::${url}/archive/refs/tags/${pkgver}.tar.gz") 
+sha256sums=('832eb3f570756cf6c0165036994a184e8882b152f3163d50367caa9d0815f619')
+
+build() {
+  cd "${pkgnamecaps}-${pkgver}"
+  make
+}
+
+package() {
+  cd "${pkgnamecaps}-${pkgver}"
+  install -Dm644 LICENSE "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+  install -Dm644 bin/bwt_index "${pkgdir}/usr/bin/bwt_index"
+  install -Dm644 bin/${pkgnamecaps} "${pkgdir}/usr/bin/${pkgnamecaps}"
+  chmod +x "${pkgdir}/usr/bin/bwt_index"
+  chmod +x "${pkgdir}/usr/bin/${pkgnamecaps}"
+}

BioArchLinux/gsalign/lilac.py

@@ -0,0 +1,12 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()
+
+

BioArchLinux/gsalign/lilac.yaml

@@ -0,0 +1,10 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: michaelgelliot
+    email: m.g.elliot@rug.nl
+update_on:
+  - source: github
+    github: hsinnan75/GSAlign
+    use_max_tag: true
+
+

BioArchLinux/hmmer/PKGBUILD

@@ -5,7 +5,7 @@
 pkgname=hmmer
 pkgver=3.3.2
 pkgrel=1
-pkgdesc="Profile hidden Markov models (HMMs) for database searching using consensus sequences"
+pkgdesc="Profile hidden Markov models (HMMs) for database searching using consensus sequences. https://doi.org/10.1093/bioinformatics/14.9.755"
 arch=('i686' 'x86_64')
 checkdepends=('perl-perl4-corelibs' 'python')
 license=('GPL')

BioArchLinux/htslib/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=htslib
 pkgver=1.14
 pkgrel=4
-pkgdesc='A C library for high-throughput sequencing data formats'
+pkgdesc='A C library for high-throughput sequencing data formats. https://doi.org/10.1093/gigascience/giab007'
 arch=('x86_64')
 url="https://github.com/samtools/${pkgname}"
 license=('MIT GPL')

BioArchLinux/insight-toolkit/PKGBUILD

@@ -7,7 +7,7 @@
 pkgname=insight-toolkit
 pkgver=5.2.1
 pkgrel=17
-pkgdesc='Cross-platform system that provides developers with an extensive suite of software tools for image analysis'
+pkgdesc='Cross-platform system that provides developers with an extensive suite of software tools for image analysis. https://doi.org/10.3389/fninf.2014.00044'
 arch=('i686' 'x86_64')
 url='http://www.itk.org/'
 license=('APACHE')

BioArchLinux/iqtree/PKGBUILD

@@ -9,7 +9,7 @@
 pkgname=iqtree
 pkgver=2.1.3
 pkgrel=3
-pkgdesc="Efficient phylogenomic software by maximum likelihood; multicore version (OMP)"
+pkgdesc="Efficient phylogenomic software by maximum likelihood; multicore version (OMP). https://doi.org/10.1093/molbev/msaa015"
 arch=(x86_64)
 url="http://www.iqtree.org/"
 license=('GPL2')

BioArchLinux/jane/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=jane
 pkgver=4.01
 pkgrel=2
-pkgdesc="software tool for the cophylogeny reconstruction problem"
+pkgdesc="software tool for the cophylogeny reconstruction problem. https://doi.org/10.1186/1748-7188-5-16"
 arch=('x86_64')
 url="https://www.cs.hmc.edu/~hadas/jane/"
 license=('Harvey Mudd College source code & Apache License')

BioArchLinux/jmodeltest/PKGBUILD

@@ -5,7 +5,7 @@ pkgname=jmodeltest
 pkgver=2.1.10r20160303
 _pkgver=2.1.10
 pkgrel=4
-pkgdesc="Phylogenetic Model Averaging, more models, new heuristics and high-performance computing"
+pkgdesc="Phylogenetic Model Averaging, more models, new heuristics and high-performance computing. https://doi.org/10.1093/molbev/msn083"
 arch=('x86_64')
 provides=("jmodeltest")
 url="https://github.com/ddarriba/jmodeltest2"

BioArchLinux/lra/PKGBUILD

@@ -0,0 +1,26 @@
+# Maintainer:  Mick Elliot <m.g.elliot@rug.nl>
+# Contributor: Mick Elliot <m.g.elliot@rug.nl>
+
+pkgname=lra
+pkgver=1.3.2
+pkgrel=1
+pkgdesc='A long read aligner for sequences and contigs. https://doi.org/10.1371/journal.pcbi.1009078'
+arch=('x86_64')
+url="https://github.com/ChaissonLab/${pkgname^^}"
+license=('USC-RL v1.0')
+depends=('zlib' 'htslib')
+provides=()
+source=("${pkgver}.tar.gz::${url}/archive/refs/tags/${pkgver}.tar.gz")
+sha256sums=('a0ec18d4bd2bc196eb4063ad45fcdb306f212feddca6a7aca8ef87122a0cca1f')
+
+build() {
+  cd "${pkgname^^}-${pkgver}"
+  make
+}
+
+package() {
+  cd "${pkgname^^}-${pkgver}"
+  install -Dm644 LICENSE.txt "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+  install -Dm644 lra "${pkgdir}/usr/bin/${pkgname}"
+  chmod +x "${pkgdir}/usr/bin/${pkgname}"
+}

BioArchLinux/lra/lilac.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()
+

BioArchLinux/lra/lilac.yaml

@@ -0,0 +1,9 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: michaelgelliot
+    email: m.g.elliot@rug.nl
+update_on:
+  - source: github
+    github: ChaissonLab/LRA
+    use_max_tag: true
+

BioArchLinux/mafft/PKGBUILD

@@ -5,7 +5,7 @@
 pkgname=mafft
 pkgver=7.487
 pkgrel=1
-pkgdesc='Multiple alignment program for amino acid or nucleotide sequences'
+pkgdesc='Multiple alignment program for amino acid or nucleotide sequences. https://doi.org/10.1093/molbev/mst010'
 arch=('x86_64')
 url='https://mafft.cbrc.jp/alignment/software'
 license=('BSD')

BioArchLinux/mega/PKGBUILD

@@ -5,7 +5,7 @@ pkgname=mega
 _pkgname=mega
 pkgver=11.0.10
 pkgrel=2
-pkgdesc=" Molecular Evolutionary Genetics Analysis"
+pkgdesc="Molecular Evolutionary Genetics Analysis. https://doi.org/10.1093/molbev/msy096"
 arch=('x86_64')
 url="https://megasoftware.net"
 license=('custom')

BioArchLinux/minimap2/PKGBUILD

@@ -0,0 +1,25 @@
+# Maintainer:  Mick Elliot <m.g.elliot@rug.nl>
+# Contributor: Mick Elliot <m.g.elliot@rug.nl>
+
+pkgname=minimap2
+pkgver=2.24
+pkgrel=1
+pkgdesc='A versatile pairwise aligner for genomic and spliced nucleotide sequences. https://doi.org/10.1093/bioinformatics/bty191'
+arch=('x86_64')
+url="https://github.com/lh3/${pkgname}"
+license=('MIT')
+depends=(zlib)
+provides=()
+source=("${pkgver}.tar.gz::${url}/releases/download/v${pkgver}/${pkgname}-${pkgver}.tar.bz2")
+sha256sums=('9dd4c31ff082182948944bcdad6d328f64f09295d10547d72eba24189880a615')
+build() {
+  cd "${pkgname}-${pkgver}"
+  make
+}
+
+package() {
+  cd "${pkgname}-${pkgver}"
+  install -Dm644 LICENSE.txt "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+  install -Dm644 ${pkgname} "${pkgdir}/usr/bin/${pkgname}"
+  chmod +x "${pkgdir}/usr/bin/${pkgname}"
+}

BioArchLinux/minimap2/lilac.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()
+

BioArchLinux/minimap2/lilac.yaml

@@ -0,0 +1,10 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: michaelgelliot
+    email: m.g.elliot@rug.nl
+update_on:
+  - source: github
+    github: lh3/minimap2
+    use_max_tag: true
+
+

BioArchLinux/modeltest-ng/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=modeltest-ng
 pkgver=0.1.7
 pkgrel=4
-pkgdesc="A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models"
+pkgdesc="A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models. https://doi.org/10.1093/molbev/msz189"
 url='https://github.com/ddarriba/modeltest'
 arch=('x86_64')
 license=('GPL3')

BioArchLinux/morphoj/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=morphoj
 pkgver=1.07a
 pkgrel=3
-pkgdesc="MorphoJ is an integrated program package for doing geometric morphometrics"
+pkgdesc="MorphoJ is an integrated program package for doing geometric morphometrics. https://doi.org/10.1111/j.1755-0998.2010.02924.x"
 arch=('x86_64')
 depends=(
 	'java-runtime'

BioArchLinux/mrbayes-mpi/PKGBUILD

@@ -5,7 +5,7 @@
 pkgname=mrbayes-mpi
 pkgver=3.2.7
 pkgrel=5
-pkgdesc="MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models"
+pkgdesc="MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. https://doi.org/10.1093/sysbio/sys029"
 arch=('i686' 'x86_64')
 url="nbisweden.github.io/mrbayes/"
 license=('GPL3')

BioArchLinux/mrbayes/PKGBUILD

@@ -5,7 +5,7 @@ _up_pkgname=MrBayes
 pkgver=3.2.7
 pkgrel=4
 provides=("mrbayes")
-pkgdesc="A program for the Bayesian estimation of phylogeny"
+pkgdesc="A program for the Bayesian estimation of phylogeny. https://doi.org/10.1093/sysbio/sys029"
 arch=('i686' 'x86_64')
 license=('GPL')
 url="http://nbisweden.github.io/MrBayes/"

BioArchLinux/mummer4/PKGBUILD

@@ -0,0 +1,35 @@
+# Maintainer:  Mick Elliot <m.g.elliot@rug.nl>
+# Contributor: Mick Elliot <m.g.elliot@rug.nl>
+
+pkgname=mummer4
+pkgver=4.0.0rc1
+pkgrel=1
+pkgdesc="A fast and versatile genome alignment system. https://doi.org/10.1371/journal.pcbi.1005944"
+arch=('x86_64')
+url="https://mummer4.github.io/"
+license=('PerlArtistic')
+depends=(gcc-libs)
+makedepends=(sh perl)
+provides=()
+source=("https://github.com/${pkgname}/mummer/releases/download/v${pkgver}/mummer-${pkgver}.tar.gz")
+sha256sums=('85006adb2d6539c2f738c3e3bb14b58bb6f62cd6c6ca5ede884a87ae76e07d1d')
+
+build() {
+  cd "mummer-${pkgver}"
+  ./configure --prefix=/usr
+  make
+}
+
+# check seems to fail due to an apparent bug in test_md5
+# see also https://github.com/mummer4/mummer/issues/147
+
+# check() {
+#   cd "mummer-${pkgver}"
+#   make check
+# }
+
+package() {
+  cd "mummer-${pkgver}"
+  make DESTDIR="$pkgdir/" install
+}
+

BioArchLinux/mummer4/lilac.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()
+

BioArchLinux/mummer4/lilac.yaml

@@ -0,0 +1,10 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: michaelgelliot
+    email: m.g.elliot@rug.nl
+update_on:
+  - source: regex
+    regex: v(\d+.\d+.\w+)
+    url: https://github.com/mummer4/mummer/releases
+
+

BioArchLinux/muscle/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=muscle
 pkgver=5.0.1428
 pkgrel=5
-pkgdesc="multiple sequence comparison by log-expectation"
+pkgdesc="Multiple sequence alignment software enabling improved estimates of phylogenetic tree confidence by ensemble bootstrapping. https://doi.org/10.1101/2021.06.20.449169"
 arch=('i686' 'x86_64')
 url="http://www.drive5.com/muscle/"
 license=('GPL3')

BioArchLinux/paml/PKGBUILD

@@ -2,7 +2,7 @@
 pkgname=paml
 pkgver=4.10.1
 pkgrel=2
-pkgdesc="Phylogenetic analysis by maximum likelihood"
+pkgdesc="Phylogenetic analysis by maximum likelihood. https://doi.org/10.1093/molbev/msm088"
 arch=('x86_64')
 url="http://abacus.gene.ucl.ac.uk/software/"
 license=('GPL3')

BioArchLinux/paup/PKGBUILD

@@ -4,7 +4,7 @@ pkgname=paup
 pkgver=4a168
 _execname=paup${pkgver//.0/}_ubuntu64
 pkgrel=4
-pkgdesc="Phylogenetic Analysis Using PAUP"
+pkgdesc="Phylogenetic Analysis Using PAUP. https://doi.org/10.1002/0471250953.bi0604s00"
 arch=('i686' 'x86_64')
 url="http://phylosolutions.com/paup-test/"
 license=('custom')

BioArchLinux/phylip/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=phylip
 pkgver=3.698
 pkgrel=4
-pkgdesc="A collection of programmes for evolutive genetics and inferring phylogenies"
+pkgdesc="A collection of programmes for evolutive genetics and inferring phylogenies. https://doi.org/10.1111/j.1096-0031.1989.tb00562.x"
 arch=('i686' 'x86_64')
 url="http://evolution.genetics.washington.edu/phylip.html"
 source=(http://evolution.gs.washington.edu/phylip/download/phylip-$pkgver.zip

BioArchLinux/phylobayes-mpi/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=phylobayes
 pkgname=$_pkgname-mpi
 pkgver=1.8c
 pkgrel=4
-pkgdesc="phylogenetic reconstruction using infinite mixtures"
+pkgdesc="phylogenetic reconstruction using infinite mixtures. https://doi.org/10.1093/molbev/msh112"
 arch=('i686' 'x86_64')
 url="https://github.com/bayesiancook/pbmpi"
 license=('GPL2')

BioArchLinux/phylobayes/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=phylobayes
 pkgver=4.1c
 pkgrel=3
-pkgdesc="phylogenetic reconstruction using infinite mixtures"
+pkgdesc="phylogenetic reconstruction using infinite mixtures. https://doi.org/10.1093/molbev/msh112"
 arch=('i686' 'x86_64')
 url="https://github.com/bayesiancook/phylobayes"
 license=('unknow')

BioArchLinux/phylonet-hmm/PKGBUILD

@@ -9,7 +9,7 @@ depends=(
 	'java-runtime'
 )
 makedepends=('ant')
-pkgdesc="An HMM-based comparative genomic framework for detecting introgression in eukaryotes"
+pkgdesc="An HMM-based comparative genomic framework for detecting introgression in eukaryotes. https://doi.org/10.1371/journal.pcbi.1003649"
 arch=('x86_64')
 url="https://bioinfocs.rice.edu/node/108"
 license=('GPL')

BioArchLinux/phylonet/PKGBUILD

@@ -8,7 +8,7 @@ pkgrel=4
 depends=(
 	'java-runtime'
 )
-pkgdesc="TA suite of software tools for reconstructing/analyzing phylogenetic networks in the presence of reticulate evolutionary events"
+pkgdesc="TA suite of software tools for reconstructing/analyzing phylogenetic networks in the presence of reticulate evolutionary events. https://doi.org/10.1093/sysbio/syy015"
 arch=('x86_64')
 url="https://bioinfocs.rice.edu/PhyloNet"
 license=('GPL2')

BioArchLinux/phylonium/PKGBUILD

@@ -2,7 +2,7 @@
 pkgname=phylonium
 pkgver=1.6
 pkgrel=1
-pkgdesc="Fast and Accurate Estimation of Evolutionary Distances"
+pkgdesc="Fast and Accurate Estimation of Evolutionary Distances. https://doi.org/10.1093/bioinformatics/btz903"
 url="https://github.com/evolbioinf/phylonium/"
 license=("GPL3") # "custom:ISC"
 depends=("libdivsufsort")

BioArchLinux/phylosuite/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=phylosuite
 pkgver=1.2.2
 pkgrel=4
-pkgdesc="an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies"
+pkgdesc="an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. https://doi.org/10.1111/1755-0998.13096"
 arch=('x86_64')
 url="https://github.com/dongzhang0725/PhyloSuite"
 license=('GPL3')

BioArchLinux/phyml/PKGBUILD

@@ -4,7 +4,7 @@ pkgname=phyml
 pkgver=3.3.20211231
 pkgrel=1
 epoch=1
-pkgdesc="Builds phylogenies from DNA or protein sequences using a maximum likelihood approach"
+pkgdesc="Builds phylogenies from DNA or protein sequences using a maximum likelihood approach. https://doi.org/10.1093/sysbio/syq010"
 arch=('i686' 'x86_64')
 url="https://github.com/stephaneguindon/phyml"
 license=('GPL2')

BioArchLinux/pibuss/PKGBUILD

@@ -8,7 +8,7 @@ pkgrel=4
 depends=(
 	'java-runtime'
 )
-pkgdesc="a BEAST/BEAGLE utility for sequence simulation, which provides an easy to use interface that allows flexible and extensible phylogenetic data fabrication"
+pkgdesc="a BEAST/BEAGLE utility for sequence simulation, which provides an easy to use interface that allows flexible and extensible phylogenetic data fabrication. https://doi.org/10.1186/1471-2105-15-133"
 arch=('x86_64')
 url="https://rega.kuleuven.be/cev/ecv/software/pibuss"
 license=('custom')

BioArchLinux/popart/PKGBUILD

@@ -3,7 +3,7 @@
 pkgname=popart
 pkgver=20190715.150937
 pkgrel=3
-pkgdesc="free population genetics software"
+pkgdesc="Full-feature software for haplotype network reconstruction. https://doi.org/10.1111/2041-210X.12410"
 arch=('x86_64')
 url="http://popart.otago.ac.nz/index.shtml"
 license=('LGPLv2')

BioArchLinux/primer3/PKGBUILD

@@ -3,7 +3,7 @@
 pkgname=primer3
 pkgver=2.5.0
 pkgrel=4
-pkgdesc="Tool to design flanking oligo nucleotides for DNA amplification"
+pkgdesc="Tool to design flanking oligo nucleotides for DNA amplification. https://doi.org/10.1093/nar/gks596"
 arch=('i686' 'x86_64')
 license=('GPL2')
 depends=('gcc-libs')

BioArchLinux/rasp/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=rasp
 pkgver=20211014
 pkgrel=4
-pkgdesc="Reconstruct Ancestral State in Phylogenies is a tool for inferring ancestral state"
+pkgdesc="Ancestral state reconstruction tool for multiple genes and characters. https://doi.org/10.1093/molbev/msz257"
 arch=('x86_64')
 url="http://mnh.scu.edu.cn/soft/blog/rasp/"
 license=('GPL3')

BioArchLinux/raxml-mpi/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=raxml-mpi
 pkgver=8.2.12
 pkgrel=4
-pkgdesc="Randomized Axelerated Maximum Likelihood"
+pkgdesc="Randomized Axelerated Maximum Likelihood. https://doi.org/10.1093/bioinformatics/btu033"
 arch=('x86_64')
 url="http://sco.h-its.org/exelixis/web/software/raxml/"
 license=('GPL3')

BioArchLinux/raxml-ng-mpi/PKGBUILD

@@ -6,7 +6,7 @@ pkgname=raxml-ng-mpi
 pkgver=1.1.0
 _commit=411611611793e53c992717d869ca64370f2e4789
 pkgrel=17
-pkgdesc="A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion"
+pkgdesc="A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. https://doi.org/10.1093/bioinformatics/btz305"
 url='https://github.com/amkozlov/raxml-ng'
 arch=('x86_64')
 license=('AGPL3')

BioArchLinux/raxml-ng/PKGBUILD

@@ -5,7 +5,7 @@ pkgname=raxml-ng
 pkgver=1.1.0
 _commit=411611611793e53c992717d869ca64370f2e4789
 pkgrel=16
-pkgdesc="A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion"
+pkgdesc="A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. https://doi.org/10.1093/bioinformatics/btz305"
 url='https://github.com/amkozlov/raxml-ng'
 arch=('x86_64')
 license=('AGPL3')

BioArchLinux/raxml/PKGBUILD

@@ -3,7 +3,7 @@
 pkgname=raxml
 pkgver=8.2.12
 pkgrel=4
-pkgdesc="Randomized Axelerated Maximum Likelihood"
+pkgdesc="Randomized Axelerated Maximum Likelihood. https://doi.org/10.1093/bioinformatics/btu033"
 arch=('x86_64')
 url="http://sco.h-its.org/exelixis/web/software/raxml/"
 license=('GPL3')

BioArchLinux/raxmlgui/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=raxmlgui
 pkgver=2.0.6
 pkgrel=2
-pkgdesc="A new user-friendly program integrating RAxML-NG and ModelTest-NG for cutting-edge phylogenetic analysis"
+pkgdesc="A new user-friendly program integrating RAxML-NG and ModelTest-NG for cutting-edge phylogenetic analysis. https://doi.org/10.1111/2041-210X.13512"
 arch=('x86_64')
 url="https://antonellilab.github.io/raxmlGUI"
 provides=("raxmlgui")

BioArchLinux/samtools/PKGBUILD

@@ -7,7 +7,7 @@
 pkgname=samtools
 pkgver=1.14
 pkgrel=4
-pkgdesc="tools for manipulating next-generation sequencing data"
+pkgdesc="tools for manipulating next-generation sequencing data. https://doi.org/10.1093/bioinformatics/btp352"
 arch=('i686' 'x86_64')
 url="http://www.htslib.org/"
 license=('custom')

BioArchLinux/seaview/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=seaview
 pkgver=5.0.5
 pkgrel=3
-pkgdesc="GUI for multiple sequence alignment and molecular phylogeny"
+pkgdesc="GUI for multiple sequence alignment and molecular phylogeny. https://doi.org/10.1093/molbev/msp259"
 arch=('x86_64')
 url="http://doua.prabi.fr/software/seaview"
 license=('GPL3')

BioArchLinux/seqan/PKGBUILD

@@ -1,7 +1,7 @@
 pkgname=seqan
 pkgver=2.4.0
 pkgrel=4
-pkgdesc="SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data"
+pkgdesc="SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. https://doi.org/10.1186/1471-2105-9-11"
 arch=("any")
 url="http://www.seqan.de"
 license=('custom')

BioArchLinux/seqan3/PKGBUILD

@@ -1,7 +1,7 @@
 pkgname=seqan3
 pkgver=3.1.0
 pkgrel=4
-pkgdesc="The modern C++ library for sequence analysis. Contains version 3 of the library and API docs."
+pkgdesc="The modern C++ library for sequence analysis. Contains version 3 of the library and API docs. https://doi.org/10.1016/j.jbiotec.2017.07.017"
 arch=("any")
 url="http://www.seqan.de"
 license=('custom')

BioArchLinux/spread/PKGBUILD

@@ -8,7 +8,7 @@ pkgrel=4
 depends=(
 	'java-runtime'
 )
-pkgdesc="a user-friendly application to analyze and visualize phylogeographic reconstructions resulting from Bayesian inference of spatio-temporal diffusion"
+pkgdesc="a user-friendly application to analyze and visualize phylogeographic reconstructions resulting from Bayesian inference of spatio-temporal diffusion. https://doi.org/10.1093/bioinformatics/btr481"
 arch=('x86_64')
 url="https://rega.kuleuven.be/cev/ecv/software/${pkgname}"
 license=('custom')

BioArchLinux/spread3/PKGBUILD

@@ -8,7 +8,7 @@ pkgrel=4
 depends=(
 	'java-runtime'
 )
-pkgdesc="a user-friendly application to analyze and visualize pathogen phylodynamic reconstructions resulting from Bayesian inference of sequence and trait evolutionary processes"
+pkgdesc="a user-friendly application to analyze and visualize pathogen phylodynamic reconstructions resulting from Bayesian inference of sequence and trait evolutionary processes. https://doi.org/10.1093/molbev/msw082"
 arch=('x86_64')
 url="https://rega.kuleuven.be/cev/ecv/software/SpreaD3"
 license=('custom')

BioArchLinux/tempest/PKGBUILD

@@ -7,7 +7,7 @@ pkgrel=4
 depends=(
 	'java-runtime'
 )
-pkgdesc="a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies"
+pkgdesc="a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies. https://doi.org/10.1093/ve/vew007"
 arch=('x86_64')
 url="http://tree.bio.ed.ac.uk/software/tempest/"
 license=('GPL2')

BioArchLinux/tiger/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=tiger
 pkgver=1.02
 pkgrel=4
-pkgdesc="Identifying rapidly-evolving characters in evolutionary data"
+pkgdesc="Identifying rapidly-evolving characters in evolutionary data. https://doi.org/10.1093/sysbio/syr064"
 arch=('x86_64')
 url="http://mcinerneylab.com/software/tiger/",""
 license=('GPL3')

BioArchLinux/tnt-gui/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=tnt-gui
 pkgver=2021.12.27
 pkgrel=1
-pkgdesc="Tree analysis using New Technology"
+pkgdesc="Tree analysis using New Technology. https://doi.org/10.1111/cla.12160"
 arch=('x86_64')
 url="http://www.lillo.org.ar/phylogeny/tnt/"
 license=('custom')

BioArchLinux/tnt-mpi/PKGBUILD

@@ -5,7 +5,7 @@ pkgname=tnt-mpi
 _pkgname=mpitnt
 pkgver=2021.12.27
 pkgrel=1
-pkgdesc="Tree analysis using New Technology"
+pkgdesc="Tree analysis using New Technology. https://doi.org/10.1111/cla.12160"
 arch=('x86_64')
 url="http://www.lillo.org.ar/phylogeny/tnt/"
 provides=('tnt')

BioArchLinux/tnt/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=tnt
 pkgver=2021.12.27
 pkgrel=1
-pkgdesc="Tree analysis using New Technology"
+pkgdesc="Tree analysis using New Technology. https://doi.org/10.1111/cla.12160"
 arch=('x86_64')
 url="http://www.lillo.org.ar/phylogeny/tnt/"
 provides=('tnt')

BioArchLinux/tracer/PKGBUILD

@@ -5,7 +5,7 @@ pkgname=tracer
 _pkgname=Tracer
 pkgver=1.7.2
 pkgrel=3
-pkgdesc="Posterior summarisation in Bayesian phylogenetics"
+pkgdesc="Posterior summarisation in Bayesian phylogenetics. https://doi.org/10.1093/sysbio/syy032"
 arch=('x86_64')
 url="https://github.com/beast-dev/tracer"
 license=('unknown')

BioArchLinux/tracy/PKGBUILD

@@ -3,7 +3,7 @@
 pkgname=tracy
 pkgver=0.6.1
 pkgrel=4
-pkgdesc="Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files"
+pkgdesc="Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files. https://doi.org/10.1186/s12864-020-6635-8"
 arch=('x86_64')
 url="https://github.com/gear-genomics/tracy"
 license=('BSDv3')

BioArchLinux/trimal/PKGBUILD

@@ -2,7 +2,7 @@
 pkgname=trimal
 pkgver=1.4.1
 pkgrel=6
-pkgdesc="A tool for automated alignment trimming in large-scale phylogenetic analyses"
+pkgdesc="A tool for automated alignment trimming in large-scale phylogenetic analyses. https://doi.org/10.1093/bioinformatics/btp348"
 arch=('x86_64')
 url="trimal.cgenomics.org"
 license=('GPL')

BioArchLinux/ugene/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=ugene
 pkgver=41.0
 pkgrel=3
-pkgdesc="A free cross-platform genome analysis suite"
+pkgdesc="A free cross-platform genome analysis suite. https://doi.org/10.1093/bioinformatics/bts091"
 arch=('x86_64')
 url="http://ugene.net"
 license=('GPL')

BioArchLinux/vcftools/PKGBUILD

@@ -4,7 +4,7 @@
 pkgname=vcftools
 pkgver=0.1.16
 pkgrel=4
-pkgdesc="A set of tools written in Perl and C++ for working with VCF files"
+pkgdesc="A set of tools written in Perl and C++ for working with VCF files. https://doi.org/10.1093/bioinformatics/btr330"
 arch=('x86_64')
 url="https://vcftools.github.io/"
 license=('LGPL3')