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\bf package & \bf source & \bf description & BibTeX key \\ \hline
abacas & abacas & close gaps in genomic alignments from short reads & abacas\cite{abacas} \\
abinit & abinit & package for electronic structure calculations & abinit\cite{abinit} \\
abinit-data & abinit & package for electronic structure calculations (Data files) & abinit\cite{abinit} \\
abinit-doc & abinit & package for electronic structure calculations (Documentation) & abinit\cite{abinit} \\
abyss & abyss & de novo, parallel, sequence assembler for short reads & abyss\cite{abyss} \\
abyss & abyss & de novo, parallel, sequence assembler for short reads & abyss2009\cite{abyss2009} \\
acedb-other & acedb & retrieval of DNA or protein sequences & acedb1999\cite{acedb1999} \\
acedb-other-belvu & acedb & transitional package for belvu & acedb1999\cite{acedb1999} \\
acedb-other-dotter & acedb & transitional package for dotter & acedb\cite{acedb} \\
acedb-other-dotter & acedb & transitional package for dotter & acedb1999\cite{acedb1999} \\
aces3 & aces3 & Advanced Concepts in Electronic Structure III & aces3\cite{aces3} \\
aces3 & aces3 & Advanced Concepts in Electronic Structure III & aces32011\cite{aces32011} \\
aces3-data & aces3 & Advanced Concepts in Electronic Structure III & aces3\cite{aces3} \\
aces3-data & aces3 & Advanced Concepts in Electronic Structure III & aces32011\cite{aces32011} \\
adapterremoval & adapterremoval & rapid adapter trimming, identification, and read merging of gene sequences & adapterremoval\cite{adapterremoval} \\
adapterremoval-examples & adapterremoval & rapid adapter trimming, identification, and read merging (example data) & adapterremoval\cite{adapterremoval} \\
adun.app & adun.app & Molecular Simulator for GNUstep (GUI) & adun-app\cite{adun-app} \\
adun.app-dbg & adun.app & Molecular Simulator for GNUstep (debugging symbols) & adun-app\cite{adun-app} \\
adun-core & adun.app & Molecular Simulator & adun-app\cite{adun-app} \\
aegean & aegean & integrated genome analysis toolkit & aegean\cite{aegean} \\
aegean-dbg & aegean & integrated genome analysis toolkit, with debug symbols & aegean\cite{aegean} \\
aevol & aevol & digital genetics model to run Evolution Experiments in silico & aevol\cite{aevol} \\
aevol & aevol & digital genetics model to run Evolution Experiments in silico & aevol2007\cite{aevol2007} \\
aevol & aevol & digital genetics model to run Evolution Experiments in silico & aevol2010\cite{aevol2010} \\
aevol & aevol & digital genetics model to run Evolution Experiments in silico & aevol2010d\cite{aevol2010d} \\
aevol & aevol & digital genetics model to run Evolution Experiments in silico & aevol2012\cite{aevol2012} \\
aladin & aladin & Interactive sky atlas for astronomical images and datasets & aladin\cite{aladin} \\
alfa & alfa & Automated Line Fitting Algorithm & alfa\cite{alfa} \\
alien-hunter & alien-hunter & Interpolated Variable Order Motifs to identify horizontally acquired DNA & alien-hunter\cite{alien-hunter} \\
alter-sequence-alignment & alter-sequence-alignment & genomic sequences ALignment Transformation EnviRonment & alter-sequence-alignment\cite{alter-sequence-alignment} \\
altree & altree & program to perform phylogeny-based association and localization analysis & altree\cite{altree} \\
altree-examples & altree & example files for ALTree & altree\cite{altree} \\
amap-align & amap-align & Protein multiple alignment by sequence annealing & amap-align\cite{amap-align} \\
amide & amide & software for Medical Imaging & amide\cite{amide} \\
ampliconnoise & ampliconnoise & removal of noise from 454 sequenced PCR amplicons & ampliconnoise\cite{ampliconnoise} \\
andi & andi & Efficient Estimation of Evolutionary Distances & andi\cite{andi} \\
aoflagger & aoflagger & Find RFI in radio astronomical observations & aoflagger\cite{aoflagger} \\
aoflagger-dev & aoflagger & Find RFI in radio astronomical observations (development files) & aoflagger\cite{aoflagger} \\
apbs & apbs & Adaptive Poisson Boltzmann Solver & apbs\cite{apbs} \\
apbs & apbs & Adaptive Poisson Boltzmann Solver & apbs1993\cite{apbs1993} \\
apbs & apbs & Adaptive Poisson Boltzmann Solver & apbs1995\cite{apbs1995} \\
apbs & apbs & Adaptive Poisson Boltzmann Solver & apbs2001\cite{apbs2001} \\
apbs & apbs & Adaptive Poisson Boltzmann Solver & apbs2003\cite{apbs2003} \\
apbs-data & apbs & data files for APBS (Adaptive Poisson Boltzmann Solver) & apbs\cite{apbs} \\
apbs-data & apbs & data files for APBS (Adaptive Poisson Boltzmann Solver) & apbs1993\cite{apbs1993} \\
apbs-data & apbs & data files for APBS (Adaptive Poisson Boltzmann Solver) & apbs1995\cite{apbs1995} \\
apbs-data & apbs & data files for APBS (Adaptive Poisson Boltzmann Solver) & apbs2001\cite{apbs2001} \\
apbs-data & apbs & data files for APBS (Adaptive Poisson Boltzmann Solver) & apbs2003\cite{apbs2003} \\
aragorn & aragorn & tRNA and tmRNA detection in nucleotide sequences & aragorn\cite{aragorn} \\
arden & arden & specificity control for read alignments using an artificial reference & arden\cite{arden} \\
ariba & ariba & Antibiotic Resistance Identification By Assembly & ariba\cite{ariba} \\
artemis & artemis & genome browser and annotation tool & artemis\cite{artemis} \\
artemis & artemis & genome browser and annotation tool & artemis2000\cite{artemis2000} \\
artemis & artemis & genome browser and annotation tool & artemis2008\cite{artemis2008} \\
artfastqgenerator & artfastqgenerator & outputs artificial FASTQ files derived from a reference genome & artfastqgenerator\cite{artfastqgenerator} \\
artfastqgenerator-doc & artfastqgenerator & outputs artificial FASTQ files derived from a reference genome (doc) & artfastqgenerator\cite{artfastqgenerator} \\
artfastqgenerator-examples & artfastqgenerator & ou7puts artificial FASTQ files derived from a reference genome (examples) & artfastqgenerator\cite{artfastqgenerator} \\
art-nextgen-simulation-tools & art-nextgen-simulation-tools & simulation tools to generate synthetic next-generation sequencing reads & art-nextgen-simulation-tools\cite{art-nextgen-simulation-tools} \\
art-nextgen-simulation-tools-profiles & art-nextgen-simulation-tools & profiles for art simulation tools & art-nextgen-simulation-tools\cite{art-nextgen-simulation-tools} \\
asdftool & python-asdf & Command line tool to manipulate ASDF scientific data files & python-asdf\cite{python-asdf} \\
asl-doc & asl & documentation for ASL & asl\cite{asl} \\
asl-tools & asl & command-line tools for ASL & asl\cite{asl} \\
assemblytics & assemblytics & detect and analyze structural variants from a genome assembly & assemblytics\cite{assemblytics} \\
astrometry-data-tycho2 & tycho2 & Astrometry.net Tycho-2 index files & tycho2\cite{tycho2} \\
astrometry-data-tycho2-07 & tycho2 & Astrometry.net Tycho-2 index files (22'-30') & tycho2\cite{tycho2} \\
astrometry-data-tycho2-07-bigendian & tycho2 & Astrometry.net Tycho-2 big endian index files (22'-30') & tycho2\cite{tycho2} \\
astrometry-data-tycho2-07-littleendian & tycho2 & Astrometry.net Tycho-2 little endian index files (22'-30') & tycho2\cite{tycho2} \\
astrometry-data-tycho2-08 & tycho2 & Astrometry.net Tycho-2 index files (30'-44') & tycho2\cite{tycho2} \\
astrometry-data-tycho2-08-bigendian & tycho2 & Astrometry.net Tycho-2 big endian index files (30'-44') & tycho2\cite{tycho2} \\
astrometry-data-tycho2-08-littleendian & tycho2 & Astrometry.net Tycho-2 little endian index files (30'-44') & tycho2\cite{tycho2} \\
astrometry-data-tycho2-09 & tycho2 & Astrometry.net Tycho-2 index files (44'-60') & tycho2\cite{tycho2} \\
astrometry-data-tycho2-09-bigendian & tycho2 & Astrometry.net Tycho-2 big endian index files (44'-60') & tycho2\cite{tycho2} \\
astrometry-data-tycho2-09-littleendian & tycho2 & Astrometry.net Tycho-2 little endian index files (44'-60') & tycho2\cite{tycho2} \\
astrometry-data-tycho2-10-19 & tycho2 & Astrometry.net Tycho-2 index files (60'-2000') & tycho2\cite{tycho2} \\
astrometry-data-tycho2-10-19-bigendian & tycho2 & Astrometry.net Tycho-2 big endian index files (60'-2000') & tycho2\cite{tycho2} \\
astrometry-data-tycho2-10-19-littleendian & tycho2 & Astrometry.net Tycho-2 little endian index files (60'-2000') & tycho2\cite{tycho2} \\
astrometry.net & astrometry.net & Astrometry plate solver & astrometry-net\cite{astrometry-net} \\
astropy-utils & astropy & Command line tools from astropy & astropy\cite{astropy} \\
atac & kmer & genome assembly-to-assembly comparison & kmer\cite{kmer} \\
atac & kmer & genome assembly-to-assembly comparison & kmer2004\cite{kmer2004} \\
ataqv & ataqv & ATAC-seq QC and visualization & ataqv\cite{ataqv} \\
atropos & atropos & NGS read trimming tool that is specific, sensitive, and speedy & atropos\cite{atropos} \\
augustus & augustus & gene prediction in eukaryotic genomes & augustus\cite{augustus} \\
augustus & augustus & gene prediction in eukaryotic genomes & augustus2003\cite{augustus2003} \\
augustus & augustus & gene prediction in eukaryotic genomes & augustus2003f\cite{augustus2003f} \\
augustus & augustus & gene prediction in eukaryotic genomes & augustus2006\cite{augustus2006} \\
augustus & augustus & gene prediction in eukaryotic genomes & augustus2008\cite{augustus2008} \\
augustus & augustus & gene prediction in eukaryotic genomes & augustus2011\cite{augustus2011} \\
augustus-data & augustus & data files for AUGUSTUS & augustus\cite{augustus} \\
augustus-data & augustus & data files for AUGUSTUS & augustus2003\cite{augustus2003} \\
augustus-data & augustus & data files for AUGUSTUS & augustus2003f\cite{augustus2003f} \\
augustus-data & augustus & data files for AUGUSTUS & augustus2006\cite{augustus2006} \\
augustus-data & augustus & data files for AUGUSTUS & augustus2008\cite{augustus2008} \\
augustus-data & augustus & data files for AUGUSTUS & augustus2011\cite{augustus2011} \\
augustus-doc & augustus & documentation files for AUGUSTUS & augustus\cite{augustus} \\
augustus-doc & augustus & documentation files for AUGUSTUS & augustus2003\cite{augustus2003} \\
augustus-doc & augustus & documentation files for AUGUSTUS & augustus2003f\cite{augustus2003f} \\
augustus-doc & augustus & documentation files for AUGUSTUS & augustus2006\cite{augustus2006} \\
augustus-doc & augustus & documentation files for AUGUSTUS & augustus2008\cite{augustus2008} \\
augustus-doc & augustus & documentation files for AUGUSTUS & augustus2011\cite{augustus2011} \\
autodocktools & autodocktools & GUI to help set up, launch and analyze AutoDock dockings & autodocktools\cite{autodocktools} \\
autodocktools & autodocktools & GUI to help set up, launch and analyze AutoDock dockings & autodocktools2008\cite{autodocktools2008} \\
autodocktools & autodocktools & GUI to help set up, launch and analyze AutoDock dockings & autodocktools2016\cite{autodocktools2016} \\
autodock-vina & autodock-vina & docking of small molecules to proteins & autodock-vina\cite{autodock-vina} \\
avogadro & avogadro & Molecular Graphics and Modelling System & avogadro\cite{avogadro} \\
avogadro-data & avogadro & Molecular Graphics and Modelling System (Data Files) & avogadro\cite{avogadro} \\
avogadro-utils & avogadrolibs & Molecular Graphics and Modelling System (library) & avogadrolibs\cite{avogadrolibs} \\
bagel & bagel & Computational Chemistry Package & bagel\cite{bagel} \\
bagel-data & bagel & Computational Chemistry Package (data files) & bagel\cite{bagel} \\
baitfisher & baitfisher & software package for designing hybrid enrichment probes & baitfisher\cite{baitfisher} \\
bali-phy & bali-phy & Bayesian Inference of Alignment and Phylogeny & bali-phy\cite{bali-phy} \\
ballview & ball & free molecular modeling and molecular graphics tool & ball\cite{ball} \\
ballview & ball & free molecular modeling and molecular graphics tool & ball2010\cite{ball2010} \\
ballview-dbg & ball & debug symbols for BALL and VIEW libraries & ball\cite{ball} \\
ballview-dbg & ball & debug symbols for BALL and VIEW libraries & ball2010\cite{ball2010} \\
bamtools & bamtools & toolkit for manipulating BAM (genome alignment) files & bamtools\cite{bamtools} \\
bandage & bandage & Bioinformatics Application for Navigating De novo Assembly Graphs Easily & bandage\cite{bandage} \\
bcalm & bcalm & de Bruijn compaction in low memory & bcalm\cite{bcalm} \\
bcftools & bcftools & genomic variant calling and manipulation of VCF/BCF files & bcftools\cite{bcftools} \\
beads & beads & 2-DE electrophoresis gel image spot detection & beads\cite{beads} \\
beagle & beagle & Genotype calling, genotype phasing and imputation of ungenotyped markers & beagle\cite{beagle} \\
beagle & beagle & Genotype calling, genotype phasing and imputation of ungenotyped markers & beagle2013\cite{beagle2013} \\
beagle & beagle & Genotype calling, genotype phasing and imputation of ungenotyped markers & beagle2016\cite{beagle2016} \\
beagle & beagle & Genotype calling, genotype phasing and imputation of ungenotyped markers & beagle2018\cite{beagle2018} \\
beagle-doc & beagle & Documentation for Beagle & beagle\cite{beagle} \\
beagle-doc & beagle & Documentation for Beagle & beagle2013\cite{beagle2013} \\
beagle-doc & beagle & Documentation for Beagle & beagle2016\cite{beagle2016} \\
beagle-doc & beagle & Documentation for Beagle & beagle2018\cite{beagle2018} \\
beast2-mcmc & beast2-mcmc & Bayesian MCMC phylogenetic inference & beast2-mcmc\cite{beast2-mcmc} \\
beast2-mcmc-doc & beast2-mcmc & Bayesian MCMC phylogenetic inference - documentation & beast2-mcmc\cite{beast2-mcmc} \\
beast2-mcmc-examples & beast2-mcmc & Bayesian MCMC phylogenetic inference - example data & beast2-mcmc\cite{beast2-mcmc} \\
beast-mcmc & beast-mcmc & Bayesian MCMC phylogenetic inference & beast-mcmc\cite{beast-mcmc} \\
beast-mcmc-doc & beast-mcmc & Bayesian MCMC phylogenetic inference - documentation & beast-mcmc\cite{beast-mcmc} \\
beast-mcmc-examples & beast-mcmc & Bayesian MCMC phylogenetic inference - example data & beast-mcmc\cite{beast-mcmc} \\
bedops & bedops & high-performance genomic feature operations & bedops\cite{bedops} \\
bedops-doc & bedops & high-performance genomic feature operations (documentation) & bedops\cite{bedops} \\
bedtools & bedtools & suite of utilities for comparing genomic features & bedtools\cite{bedtools} \\
bedtools-test & bedtools & test data for the bedtools package & bedtools\cite{bedtools} \\
belvu & seqtools & multiple sequence alignment viewer and phylogenetic tool & seqtools\cite{seqtools} \\
belvu & seqtools & multiple sequence alignment viewer and phylogenetic tool & seqtools1994\cite{seqtools1994} \\
belvu & seqtools & multiple sequence alignment viewer and phylogenetic tool & seqtools2005\cite{seqtools2005} \\
berkeley-express & berkeley-express & Streaming quantification for high-throughput sequencing & berkeley-express\cite{berkeley-express} \\
berkeley-express & berkeley-express & Streaming quantification for high-throughput sequencing & berkeley-express2011\cite{berkeley-express2011} \\
berkeley-express & berkeley-express & Streaming quantification for high-throughput sequencing & berkeley-express2013\cite{berkeley-express2013} \\
berkeley-express-doc & berkeley-express & Documentation for RNA-Seq tool eXpress & berkeley-express\cite{berkeley-express} \\
berkeley-express-doc & berkeley-express & Documentation for RNA-Seq tool eXpress & berkeley-express2011\cite{berkeley-express2011} \\
berkeley-express-doc & berkeley-express & Documentation for RNA-Seq tool eXpress & berkeley-express2013\cite{berkeley-express2013} \\
biobambam2 & biobambam2 & tools for early stage alignment file processing & biobambam2\cite{biobambam2} \\
bio-eagle & bio-eagle & Haplotype phasing within a genotyped cohort or using a phased reference panel & bio-eagle\cite{bio-eagle} \\
bio-eagle & bio-eagle & Haplotype phasing within a genotyped cohort or using a phased reference panel & bio-eagle2016\cite{bio-eagle2016} \\
bio-eagle-examples & bio-eagle & Examples for bio-eagle & bio-eagle\cite{bio-eagle} \\
bio-eagle-examples & bio-eagle & Examples for bio-eagle & bio-eagle2016\cite{bio-eagle2016} \\
biomaj & biomaj & biological data-bank updater & biomaj\cite{biomaj} \\
biomaj-properties & biomaj & biological data-bank updater - example properties files & biomaj\cite{biomaj} \\
biom-format-tools & python-biom-format & command-line tools for BIOM format & python-biom-format\cite{python-biom-format} \\
bioperl & bioperl & Perl tools for computational molecular biology & bioperl\cite{bioperl} \\
bio-rainbow & bio-rainbow & clustering and assembling short reads for bioinformatics & bio-rainbow\cite{bio-rainbow} \\
biosig-tools & biosig4c++ & format conversion tools for biomedical data formats & biosig4c--\cite{biosig4c--} \\
biosyntax & biosyntax & Syntax Highlighting for Computational Biology (metapackage) & biosyntax\cite{biosyntax} \\
biosyntax-common & biosyntax & Syntax Highlighting for Computational Biology (common files) & biosyntax\cite{biosyntax} \\
biosyntax-example & biosyntax & Syntax Highlighting for Computational Biology (example) & biosyntax\cite{biosyntax} \\
biosyntax-gedit & biosyntax & Syntax Highlighting for Computational Biology (gedit) & biosyntax\cite{biosyntax} \\
biosyntax-less & biosyntax & Syntax Highlighting for Computational Biology (less) & biosyntax\cite{biosyntax} \\
biosyntax-vim & biosyntax & Syntax Highlighting for Computational Biology (vim) & biosyntax\cite{biosyntax} \\
bio-tradis & bio-tradis & analyse the output from TraDIS analyses of genomic sequences & bio-tradis\cite{bio-tradis} \\
bitseq & bitseq & Bayesian Inference of Transcripts from Sequencing Data & bitseq\cite{bitseq} \\
blasr & blasr & mapping single-molecule sequencing reads & blasr\cite{blasr} \\
blimps-examples & blimps & blocks database improved searcher (example data) & blimps\cite{blimps} \\
blimps-utils & blimps & blocks database improved searcher & blimps\cite{blimps} \\
blixem & seqtools & interactive browser of sequence alignments & seqtools\cite{seqtools} \\
blixem & seqtools & interactive browser of sequence alignments & seqtools1994\cite{seqtools1994} \\
blixem & seqtools & interactive browser of sequence alignments & seqtools2005\cite{seqtools2005} \\
bodr & bodr & Blue Obelisk Data Repository & bodr\cite{bodr} \\
bodr & bodr & Blue Obelisk Data Repository & bodr2006\cite{bodr2006} \\
bodr & bodr & Blue Obelisk Data Repository & bodr2008\cite{bodr2008} \\
bodr & bodr & Blue Obelisk Data Repository & bodr2011\cite{bodr2011} \\
bodr & bodr & Blue Obelisk Data Repository & bodr2011e\cite{bodr2011e} \\
bolt-lmm & bolt-lmm & Efficient large cohorts genome-wide Bayesian mixed-model association testing & bolt-lmm\cite{bolt-lmm} \\
bolt-lmm & bolt-lmm & Efficient large cohorts genome-wide Bayesian mixed-model association testing & bolt-lmm2015\cite{bolt-lmm2015} \\
bolt-lmm-example & bolt-lmm & Examples for bolt-lmm & bolt-lmm\cite{bolt-lmm} \\
bolt-lmm-example & bolt-lmm & Examples for bolt-lmm & bolt-lmm2015\cite{bolt-lmm2015} \\
bowtie & bowtie & Ultrafast memory-efficient short read aligner & bowtie\cite{bowtie} \\
bowtie2 & bowtie2 & ultrafast memory-efficient short read aligner & bowtie2\cite{bowtie2} \\
bowtie2-examples & bowtie2 & Examples for bowtie2 & bowtie2\cite{bowtie2} \\
bowtie-examples & bowtie & Examples for bowtie, the ultrafast memory-efficient short read aligner & bowtie\cite{bowtie} \\
brig & brig & BLAST Ring Image Generator & brig\cite{brig} \\
busco & busco & benchmarking sets of universal single-copy orthologs & busco\cite{busco} \\
bustools & bustools & program for manipulating BUS files for single cell RNA-Seq datasets & bustools\cite{bustools} \\
bwa & bwa & Burrows-Wheeler Aligner & bwa\cite{bwa} \\
caffe & caffe & Tools for fast, open framework for Deep Learning (CPU\_ONLY) & caffe\cite{caffe} \\
caffe-cpu & caffe & Fast, open framework for Deep Learning (Meta) & caffe\cite{caffe} \\
caffe-cuda & caffe-contrib & Fast, open framework for Deep Learning (Meta) & caffe-contrib\cite{caffe-contrib} \\
caffe-doc & caffe & Caffe's doxygen docs and examples & caffe\cite{caffe} \\
caffe-tools-cpu & caffe & Tools for fast, open framework for Deep Learning (CPU\_ONLY) & caffe\cite{caffe} \\
caffe-tools-cuda & caffe-contrib & Tools for fast, open framework for Deep Learning (CUDA) & caffe-contrib\cite{caffe-contrib} \\
caftools & caftools & maintenance of DNA sequence assemblies & caftools\cite{caftools} \\
cain & cain & simulations of chemical reactions & cain\cite{cain} \\
cain-examples & cain & examples for cain & cain\cite{cain} \\
cain-solvers & cain & solvers for cain & cain\cite{cain} \\
camitk-actionstatemachine & camitk & pipeline replay application for the CamiTK library & camitk\cite{camitk} \\
camitk-config & camitk & Computer Assisted Medical Intervention Tool Kit - config & camitk\cite{camitk} \\
camitk-imp & camitk & workbench application for the CamiTK library & camitk\cite{camitk} \\
canu & canu & single molecule sequence assembler for genomes & canu\cite{canu} \\
caret & caret & Computerized Anatomical Reconstruction and Editing Toolkit & caret\cite{caret} \\
cb2bib & cb2bib & extract bibliographic references from various sources & cb2bib\cite{cb2bib} \\
cclib & cclib & Parsers and algorithms for computational chemistry & cclib\cite{cclib} \\
cclib-data & cclib-data & Parsers and algorithms for computational chemistry (data files) & cclib-data\cite{cclib-data} \\
cct & cct & visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences & cct\cite{cct} \\
cct & cct & visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences & cct2017\cite{cct2017} \\
cct-examples & cct & example data for testing the package cct & cct\cite{cct} \\
cct-examples & cct & example data for testing the package cct & cct2017\cite{cct2017} \\
cd-hit & cd-hit & suite of programs designed to quickly group sequences & cd-hit\cite{cd-hit} \\
centrifuge & centrifuge & rapid and memory-efficient system for classification of DNA sequences & centrifuge\cite{centrifuge} \\
cgview & cgview & Circular Genome Viewer & cgview\cite{cgview} \\
changeo & changeo & Repertoire clonal assignment toolkit (Python 3) & changeo\cite{changeo} \\
chemps2 & chemps2 & Executable to call libchemps2-3 from the command line & chemps2\cite{chemps2} \\
chemps2 & chemps2 & Executable to call libchemps2-3 from the command line & chemps22014\cite{chemps22014} \\
chemps2 & chemps2 & Executable to call libchemps2-3 from the command line & chemps22014c\cite{chemps22014c} \\
chemps2 & chemps2 & Executable to call libchemps2-3 from the command line & chemps22014d\cite{chemps22014d} \\
chemps2 & chemps2 & Executable to call libchemps2-3 from the command line & chemps22016\cite{chemps22016} \\
chemps2-doc & chemps2 & Documentation of the libchemps2-3 package & chemps2\cite{chemps2} \\
chemps2-doc & chemps2 & Documentation of the libchemps2-3 package & chemps22014\cite{chemps22014} \\
chemps2-doc & chemps2 & Documentation of the libchemps2-3 package & chemps22014c\cite{chemps22014c} \\
chemps2-doc & chemps2 & Documentation of the libchemps2-3 package & chemps22014d\cite{chemps22014d} \\
chemps2-doc & chemps2 & Documentation of the libchemps2-3 package & chemps22016\cite{chemps22016} \\
chemtool & chemtool & chemical structures drawing program & chemtool\cite{chemtool} \\
chimeraslayer & microbiomeutil & detects likely chimeras in PCR amplified DNA & microbiomeutil\cite{microbiomeutil} \\
chip-seq & chip-seq & tools performing common ChIP-Seq data analysis tasks & chip-seq\cite{chip-seq} \\
chip-seq-data & chip-seq & tools performing common ChIP-Seq data analysis tasks (data) & chip-seq\cite{chip-seq} \\
chromhmm & chromhmm & Chromatin state discovery and characterization & chromhmm\cite{chromhmm} \\
chromhmm & chromhmm & Chromatin state discovery and characterization & chromhmm2017\cite{chromhmm2017} \\
chromhmm-example & chromhmm & Chromatin state discovery and characterization (example) & chromhmm\cite{chromhmm} \\
chromhmm-example & chromhmm & Chromatin state discovery and characterization (example) & chromhmm2017\cite{chromhmm2017} \\
chromimpute & chromimpute & Large-scale systematic epigenome imputation & chromimpute\cite{chromimpute} \\
circlator & circlator & circularize genome assemblies & circlator\cite{circlator} \\
circos & circos & plotter for visualizing data & circos\cite{circos} \\
clearcut & clearcut & extremely efficient phylogenetic tree reconstruction & clearcut\cite{clearcut} \\
clonalframe & clonalframe & inference of bacterial microevolution using multilocus sequence data & clonalframe\cite{clonalframe} \\
clonalframeml & clonalframeml & Efficient Inference of Recombination in Whole Bacterial Genomes & clonalframeml\cite{clonalframeml} \\
clonalorigin & clonalorigin & inference of homologous recombination in bacteria using whole genome sequences & clonalorigin\cite{clonalorigin} \\
clustalo & clustalo & General-purpose multiple sequence alignment program for proteins & clustalo\cite{clustalo} \\
clustalo & clustalo & General-purpose multiple sequence alignment program for proteins & clustalo2018\cite{clustalo2018} \\
clustalw & clustalw & global multiple nucleotide or peptide sequence alignment & clustalw\cite{clustalw} \\
clustalx & clustalx & Multiple alignment of nucleic acid and protein sequences (graphical interface) & clustalx\cite{clustalx} \\
cluster3 & cluster3 & Reimplementation of the Eisen-clustering software & cluster3\cite{cluster3} \\
cminpack-doc & cminpack & Nonlinear equations and nonlinear least squares problems (doc) & cminpack\cite{cminpack} \\
cmtk & cmtk & Computational Morphometry Toolkit & cmtk\cite{cmtk} \\
cnrun & cnrun & NeuroML-capable neuronal network simulator & cnrun\cite{cnrun} \\
cnrun-tools & cnrun & NeuroML-capable neuronal network simulator (tools) & cnrun\cite{cnrun} \\
cnvkit & cnvkit & Copy number variant detection from targeted DNA sequencing & cnvkit\cite{cnvkit} \\
codonw & codonw & Correspondence Analysis of Codon Usage & codonw\cite{codonw} \\
cod-tools & cod-tools & tools for manipulating CIF format files & cod-tools\cite{cod-tools} \\
cohomcalg & cohomcalg & sheaf cohomology of line bundles on toric varieties & cohomcalg\cite{cohomcalg} \\
cohomcalg-common & cohomcalg & sheaf cohomology of line bundles on toric varieties (common files) & cohomcalg\cite{cohomcalg} \\
coinor-csdp & coinor-csdp & A software package for semidefinite programming & coinor-csdp\cite{coinor-csdp} \\
coinor-csdp-dbg & coinor-csdp & A software package for semidefinite programming & coinor-csdp\cite{coinor-csdp} \\
coinor-csdp-doc & coinor-csdp & A software package for semidefinite programming & coinor-csdp\cite{coinor-csdp} \\
comet-ms & comet-ms & Tandem mass spectrometry (MS/MS) search engine & comet-ms\cite{comet-ms} \\
comet-ms-dbg & comet-ms & Tandem mass spectrometry (MS/MS) search engine - debug symbols & comet-ms\cite{comet-ms} \\
concavity & concavity & predictor of protein ligand binding sites from structure and conservation & concavity\cite{concavity} \\
concavity-dbg & concavity & predictor of protein ligand binding sites (debug) & concavity\cite{concavity} \\
condor & condor & transitional dummy package & condor\cite{condor} \\
condor-dbg & condor & transitional dummy package & condor\cite{condor} \\
condor-dev & condor & transitional dummy package & condor\cite{condor} \\
condor-doc & condor & transitional dummy package & condor\cite{condor} \\
connectagram & connectagram & word unscrambling game & connectagram\cite{connectagram} \\
connectagram-data & connectagram & word unscrambling game - data files & connectagram\cite{connectagram} \\
conservation-code & conservation-code & protein sequence conservation scoring tool & conservation-code\cite{conservation-code} \\
cp2k & cp2k & Ab Initio Molecular Dynamics & cp2k\cite{cp2k} \\
cp2k & cp2k & Ab Initio Molecular Dynamics & cp2k1997\cite{cp2k1997} \\
cp2k & cp2k & Ab Initio Molecular Dynamics & cp2k1999\cite{cp2k1999} \\
cp2k & cp2k & Ab Initio Molecular Dynamics & cp2k2000\cite{cp2k2000} \\
cp2k & cp2k & Ab Initio Molecular Dynamics & cp2k2005\cite{cp2k2005} \\
cp2k & cp2k & Ab Initio Molecular Dynamics & cp2k2007\cite{cp2k2007} \\
cp2k & cp2k & Ab Initio Molecular Dynamics & cp2k2008\cite{cp2k2008} \\
cp2k & cp2k & Ab Initio Molecular Dynamics & cp2k2013\cite{cp2k2013} \\
cp2k-data & cp2k & Ab Initio Molecular Dynamics (data files) & cp2k\cite{cp2k} \\
cp2k-data & cp2k & Ab Initio Molecular Dynamics (data files) & cp2k1997\cite{cp2k1997} \\
cp2k-data & cp2k & Ab Initio Molecular Dynamics (data files) & cp2k1999\cite{cp2k1999} \\
cp2k-data & cp2k & Ab Initio Molecular Dynamics (data files) & cp2k2000\cite{cp2k2000} \\
cp2k-data & cp2k & Ab Initio Molecular Dynamics (data files) & cp2k2005\cite{cp2k2005} \\
cp2k-data & cp2k & Ab Initio Molecular Dynamics (data files) & cp2k2007\cite{cp2k2007} \\
cp2k-data & cp2k & Ab Initio Molecular Dynamics (data files) & cp2k2008\cite{cp2k2008} \\
cp2k-data & cp2k & Ab Initio Molecular Dynamics (data files) & cp2k2013\cite{cp2k2013} \\
cpl-plugin-muse & cpl-plugin-muse & ESO data reduction pipeline for the MUSE instrument & cpl-plugin-muse\cite{cpl-plugin-muse} \\
cpl-plugin-muse-calib & cpl-plugin-muse & ESO data reduction pipeline calibration data downloader for MUSE & cpl-plugin-muse\cite{cpl-plugin-muse} \\
cpl-plugin-muse-doc & cpl-plugin-muse & ESO data reduction pipeline documentation for MUSE & cpl-plugin-muse\cite{cpl-plugin-muse} \\
cpl-plugin-sinfo & cpl-plugin-sinfo & ESO data reduction pipeline SINFONI & cpl-plugin-sinfo\cite{cpl-plugin-sinfo} \\
cpl-plugin-sinfo-calib & cpl-plugin-sinfo & ESO data reduction pipeline calibration data downloader for SINFONI & cpl-plugin-sinfo\cite{cpl-plugin-sinfo} \\
cpl-plugin-sinfo-doc & cpl-plugin-sinfo & ESO data reduction pipeline documentation for SINFONI & cpl-plugin-sinfo\cite{cpl-plugin-sinfo} \\
crac & crac & integrated RNA-Seq read analysis & crac\cite{crac} \\
crac & crac & integrated RNA-Seq read analysis & crac2013\cite{crac2013} \\
ctn & ctn & Central Test Node, a DICOM implementation for medical imaging & ctn\cite{ctn} \\
ctn-dev & ctn & Development files for Central Test Node, a DICOM implementation & ctn\cite{ctn} \\
cufflinks & cufflinks & Transcript assembly, differential expression and regulation for RNA-Seq & cufflinks\cite{cufflinks} \\
cufflinks & cufflinks & Transcript assembly, differential expression and regulation for RNA-Seq & cufflinks2012\cite{cufflinks2012} \\
cutadapt & python-cutadapt & Clean biological sequences from high-throughput sequencing reads & python-cutadapt\cite{python-cutadapt} \\
cutemaze & cutemaze & single player maze game & cutemaze\cite{cutemaze} \\
cwltool & cwltool & Common Workflow Language reference implementation & cwltool\cite{cwltool} \\
cython & cython & C-Extensions for Python & cython\cite{cython} \\
cython3 & cython & C-Extensions for Python 3 & cython\cite{cython} \\
cython3-dbg & cython & C-Extensions for Python 3 - debug build & cython\cite{cython} \\
cython-dbg & cython & C-Extensions for Python - debug build & cython\cite{cython} \\
cython-doc & cython & C-Extensions for Python - documentation & cython\cite{cython} \\
daligner & daligner & local alignment discovery between long nucleotide sequencing reads & daligner\cite{daligner} \\
dawg & dawg & simulate the evolution of recombinant DNA sequences & dawg\cite{dawg} \\
deepnano & deepnano & alternative basecaller for MinION reads of genomic sequences & deepnano\cite{deepnano} \\
deepnano-data & deepnano & alternative basecaller for MinION reads of genomic sequences (data) & deepnano\cite{deepnano} \\
delly & delly & Structural variant discovery by read analysis & delly\cite{delly} \\
dialign & dialign & Segment-based multiple sequence alignment & dialign\cite{dialign} \\
dialign-tx & dialign-t & Segment-based multiple sequence alignment & dialign-t\cite{dialign-t} \\
dialign-tx-data & dialign-t & Segment-based multiple sequence alignment (data files) & dialign-t\cite{dialign-t} \\
diamond-aligner & diamond-aligner & accelerated BLAST compatible local sequence aligner & diamond-aligner\cite{diamond-aligner} \\
dicompyler & dicompyler & radiation therapy research platform & dicompyler\cite{dicompyler} \\
dict-wn & wordnet & electronic lexical database of English language for dict & wordnet\cite{wordnet} \\
dict-wn & wordnet & electronic lexical database of English language for dict & wordnet1998\cite{wordnet1998} \\
dict-wn & wordnet & electronic lexical database of English language for dict & wordnet2005\cite{wordnet2005} \\
dindel & dindel & determines indel calls from short-read data & dindel\cite{dindel} \\
disulfinder & disulfinder & cysteines disulfide bonding state and connectivity predictor & disulfinder\cite{disulfinder} \\
disulfinder & disulfinder & cysteines disulfide bonding state and connectivity predictor & disulfinder2002\cite{disulfinder2002} \\
disulfinder & disulfinder & cysteines disulfide bonding state and connectivity predictor & disulfinder2003\cite{disulfinder2003} \\
disulfinder & disulfinder & cysteines disulfide bonding state and connectivity predictor & disulfinder2004\cite{disulfinder2004} \\
disulfinder-data & disulfinder & data files for predictor of disulfide bonds in proteins & disulfinder\cite{disulfinder} \\
disulfinder-data & disulfinder & data files for predictor of disulfide bonds in proteins & disulfinder2002\cite{disulfinder2002} \\
disulfinder-data & disulfinder & data files for predictor of disulfide bonds in proteins & disulfinder2003\cite{disulfinder2003} \\
disulfinder-data & disulfinder & data files for predictor of disulfide bonds in proteins & disulfinder2004\cite{disulfinder2004} \\
dnaclust & dnaclust & tool for clustering millions of short DNA sequences & dnaclust\cite{dnaclust} \\
dnapi & dnapi & adapter prediction for small RNA sequencing - utils & dnapi\cite{dnapi} \\
dotter & seqtools & detailed comparison of two genomic sequences & seqtools\cite{seqtools} \\
dotter & seqtools & detailed comparison of two genomic sequences & seqtools1994\cite{seqtools1994} \\
dotter & seqtools & detailed comparison of two genomic sequences & seqtools1995\cite{seqtools1995} \\
dotter & seqtools & detailed comparison of two genomic sequences & seqtools2005\cite{seqtools2005} \\
drawxtl & drawxtl & crystal structure viewer & drawxtl\cite{drawxtl} \\
dssp & dssp & protein secondary structure assignment based on 3D structure & dssp\cite{dssp} \\
dssp-dbg & dssp & debugging symbols for dssp & dssp\cite{dssp} \\
ea-utils & ea-utils & command-line tools for processing biological sequencing data & ea-utils\cite{ea-utils} \\
edfbrowser & edfbrowser & viewer for biosignal storage files such as bdf and edf & edfbrowser\cite{edfbrowser} \\
edtsurf & edtsurf & triangulated mesh surfaces for protein structures & edtsurf\cite{edtsurf} \\
eigensoft & eigensoft & reduction of population bias for genetic analyses & eigensoft\cite{eigensoft} \\
elastix & elastix & toolbox for rigid and nonrigid registration of images & elastix\cite{elastix} \\
elastix & elastix & toolbox for rigid and nonrigid registration of images & elastix2010\cite{elastix2010} \\
elastix-doc & elastix & toolbox for rigid and nonrigid registration of images - docs & elastix\cite{elastix} \\
elastix-doc & elastix & toolbox for rigid and nonrigid registration of images - docs & elastix2010\cite{elastix2010} \\
emboss & emboss & European molecular biology open software suite & emboss\cite{emboss} \\
emboss-data & emboss & data files for the EMBOSS package & emboss\cite{emboss} \\
emboss-doc & emboss & documentation for EMBOSS & emboss\cite{emboss} \\
emboss-lib & emboss & EMBOSS Libraries & emboss\cite{emboss} \\
emboss-test & emboss & test files for the EMBOSS package & emboss\cite{emboss} \\
e-mem & e-mem & Efficient computation of Maximal Exact Matches for very large genomes & e-mem\cite{e-mem} \\
emmax & emmax & genetic mapping considering population structure & emmax\cite{emmax} \\
epigrass & epigrass & scientific tool for simulations and scenario analysis in network epidemiology & epigrass\cite{epigrass} \\
epigrass-doc & epigrass & Documentation for EpiGrass, a network epidemiology tool & epigrass\cite{epigrass} \\
ergo & ergo & Quantum chemistry program for large-scale calculations & ergo\cite{ergo} \\
ergo-data & ergo & Quantum chemistry program for large-scale calculations - data package & ergo\cite{ergo} \\
eso-midas & eso-midas & European Southern Observatory Munich Image Data Analysis System & eso-midas\cite{eso-midas} \\
eso-midas-testdata & eso-midas & Test data files for ESO-MIDAS & eso-midas\cite{eso-midas} \\
estscan & estscan & ORF-independent detector of coding DNA sequences & estscan\cite{estscan} \\
estscan & estscan & ORF-independent detector of coding DNA sequences & estscan1999\cite{estscan1999} \\
examl & examl & Exascale Maximum Likelihood (ExaML) code for phylogenetic inference & examl\cite{examl} \\
exonerate & exonerate & generic tool for pairwise sequence comparison & exonerate\cite{exonerate} \\
falcon & falcon & diploid-aware genome assembly of single-molecule sequencing reads & falcon\cite{falcon} \\
fasta3 & fasta3 & tools for searching collections of biological sequences & fasta3\cite{fasta3} \\
fasta3 & fasta3 & tools for searching collections of biological sequences & fasta31996\cite{fasta31996} \\
fasta3-doc & fasta3 & user guide for FASTA tools & fasta3\cite{fasta3} \\
fasta3-doc & fasta3 & user guide for FASTA tools & fasta31996\cite{fasta31996} \\
fastdnaml & fastdnaml & Tool for construction of phylogenetic trees of DNA sequences & fastdnaml\cite{fastdnaml} \\
fastlink & fastlink & faster version of pedigree programs of Linkage & fastlink\cite{fastlink} \\
fastlink-doc & fastlink & Some papers about fastlink & fastlink\cite{fastlink} \\
fastml & fastml & maximum likelihood ancestral amino-acid sequence reconstruction & fastml\cite{fastml} \\
fastml & fastml & maximum likelihood ancestral amino-acid sequence reconstruction & fastml2000\cite{fastml2000} \\
fastml & fastml & maximum likelihood ancestral amino-acid sequence reconstruction & fastml2002\cite{fastml2002} \\
fastp & fastp & Ultra-fast all-in-one FASTQ preprocessor & fastp\cite{fastp} \\
fastqtl & fastqtl & Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes & fastqtl\cite{fastqtl} \\
fastqtl-doc & fastqtl & QTL mapper in cis for molecular phenotypes - documentation & fastqtl\cite{fastqtl} \\
fasttree & fasttree & phylogenetic trees from alignments of nucleotide or protein sequences & fasttree\cite{fasttree} \\
fflas-ffpack & fflas-ffpack & Finite field linear algebra subroutines/package & fflas-ffpack\cite{fflas-ffpack} \\
fflas-ffpack-common & fflas-ffpack & Finite field linear algebra subroutines/package - common files & fflas-ffpack\cite{fflas-ffpack} \\
fflas-ffpack-dev-doc & fflas-ffpack & FFLAS-FFPACK Developer Documentation & fflas-ffpack\cite{fflas-ffpack} \\
fflas-ffpack-user-doc & fflas-ffpack & FFLAS-FFPACK User Documentation & fflas-ffpack\cite{fflas-ffpack} \\
fitgcp & fitgcp & fitting genome coverage distributions with mixture models & fitgcp\cite{fitgcp} \\
fitscheck & pyfits & transitional package for pyfits-utils & pyfits\cite{pyfits} \\
fitsh & fitsh & Software package for astronomical image processing & fitsh\cite{fitsh} \\
fitspng & fitspng & FITS to PNG converter & fitspng\cite{fitspng} \\
fityk & fityk & general-purpose nonlinear curve fitting and data analysis & fityk\cite{fityk} \\
flexbar & flexbar & flexible barcode and adapter removal for sequencing platforms & flexbar\cite{flexbar} \\
fonts-circos-symbols & circos & plotter for visualizing data - standard fonts & circos\cite{circos} \\
freebayes & freebayes & Bayesian haplotype-based polymorphism discovery and genotyping & freebayes\cite{freebayes} \\
freecontact & freecontact & fast protein contact predictor & freecontact\cite{freecontact} \\
fsa & fsa & Fast Statistical Alignment of protein, RNA or DNA sequences & fsa\cite{fsa} \\
fsl & fsl & transitional dummy package & fsl\cite{fsl} \\
fsl & fsl & transitional dummy package & fsl2004\cite{fsl2004} \\
fsl & fsl & transitional dummy package & fsl2009\cite{fsl2009} \\
fsl-4.1 & fsl & analysis tools for FMRI, MRI and DTI brain imaging & fsl\cite{fsl} \\
fsl-4.1 & fsl & analysis tools for FMRI, MRI and DTI brain imaging & fsl2004\cite{fsl2004} \\
fsl-4.1 & fsl & analysis tools for FMRI, MRI and DTI brain imaging & fsl2009\cite{fsl2009} \\
fsl-5.0 & fsl & transitional dummy package & fsl\cite{fsl} \\
fsl-5.0 & fsl & transitional dummy package & fsl2004\cite{fsl2004} \\
fsl-5.0 & fsl & transitional dummy package & fsl2009\cite{fsl2009} \\
fsl-5.0-core & fsl & analysis tools for FMRI, MRI and DTI brain imaging & fsl\cite{fsl} \\
fsl-5.0-core & fsl & analysis tools for FMRI, MRI and DTI brain imaging & fsl2004\cite{fsl2004} \\
fsl-5.0-core & fsl & analysis tools for FMRI, MRI and DTI brain imaging & fsl2009\cite{fsl2009} \\
fsl-core & fsl & metapackage for the latest version of FSL & fsl\cite{fsl} \\
fsl-core & fsl & metapackage for the latest version of FSL & fsl2004\cite{fsl2004} \\
fsl-core & fsl & metapackage for the latest version of FSL & fsl2009\cite{fsl2009} \\
fsl-doc-4.1 & fsl & documentation for FSL & fsl\cite{fsl} \\
fsl-doc-4.1 & fsl & documentation for FSL & fsl2004\cite{fsl2004} \\
fsl-doc-4.1 & fsl & documentation for FSL & fsl2009\cite{fsl2009} \\
fslview & fslview & viewer for (f)MRI and DTI data & fslview\cite{fslview} \\
fslview-doc & fslview & Documentation for FSLView & fslview\cite{fslview} \\
ftools-fv & ftools-fv & Tool for viewing and editing FITS format files & ftools-fv\cite{ftools-fv} \\
ftools-pow & ftools-fv & Curve plotting and image display interface tool & ftools-fv\cite{ftools-fv} \\
funtools & funtools & Minimal buy-in FITS utility package & funtools\cite{funtools} \\
gabedit & gabedit & graphical user interface to Ab Initio packages & gabedit\cite{gabedit} \\
garlic & garlic & visualization program for biomolecules & garlic\cite{garlic} \\
garlic & garlic & visualization program for biomolecules & garlic2005\cite{garlic2005} \\
gasic & gasic & genome abundance similarity correction & gasic\cite{gasic} \\
gatb-core & gatb-core & Genome Analysis Toolbox with de-Bruijn graph & gatb-core\cite{gatb-core} \\
gatb-core-testdata & gatb-core & Genome Analysis Toolbox with de-Bruijn graph (test data) & gatb-core\cite{gatb-core} \\
gausssum & gausssum & parse and display Gaussian, GAMESS, and etc's output & gausssum\cite{gausssum} \\
gbrowse & gbrowse & GMOD Generic Genome Browser & gbrowse\cite{gbrowse} \\
gbrowse-calign & gbrowse & CAlign helper & gbrowse\cite{gbrowse} \\
gbrowse-data & gbrowse & Sample data to use GBrowse & gbrowse\cite{gbrowse} \\
gdcm-doc & gdcm & Grassroots DICOM documentation & gdcm\cite{gdcm} \\
gdf-tools & libgdf & IO library for the GDF -- helper tools & libgdf\cite{libgdf} \\
gdl-astrolib & idlastro & Low-level astronomy software for GDL & idlastro\cite{idlastro} \\
gdl-coyote & coyote & GDL library from D. Fannings IDL courses & coyote\cite{coyote} \\
gdl-mpfit & mpfit & Robust non-linear least squares curve fitting for GDL & mpfit\cite{mpfit} \\
gemma & gemma & Genome-wide Efficient Mixed Model Association & gemma\cite{gemma} \\
gemma & gemma & Genome-wide Efficient Mixed Model Association & gemma2013\cite{gemma2013} \\
gemma & gemma & Genome-wide Efficient Mixed Model Association & gemma2014\cite{gemma2014} \\
gemma & gemma & Genome-wide Efficient Mixed Model Association & gemma2017\cite{gemma2017} \\
gemma-doc & gemma & Example folder for GEMMA & gemma\cite{gemma} \\
gemma-doc & gemma & Example folder for GEMMA & gemma2013\cite{gemma2013} \\
gemma-doc & gemma & Example folder for GEMMA & gemma2014\cite{gemma2014} \\
gemma-doc & gemma & Example folder for GEMMA & gemma2017\cite{gemma2017} \\
genometester & genometester & toolkit for performing set operations on k-mer lists & genometester\cite{genometester} \\
genometester & genometester & toolkit for performing set operations on k-mer lists & genometester2007\cite{genometester2007} \\
genometester & genometester & toolkit for performing set operations on k-mer lists & genometester2017\cite{genometester2017} \\
genomethreader & genomethreader & software tool to compute gene structure predictions & genomethreader\cite{genomethreader} \\
genometools & genometools & versatile genome analysis toolkit & genometools\cite{genometools} \\
genometools-common & genometools & shared data files for GenomeTools & genometools\cite{genometools} \\
genometools-dbg & genometools & versatile genome analysis toolkit, with debug symbols & genometools\cite{genometools} \\
genometools-doc & genometools & documentation for GenomeTools & genometools\cite{genometools} \\
gentle & gentle & suite to plan genetic cloning & gentle\cite{gentle} \\
getdp & getdp & general environment for the treatment of discrete problems & getdp\cite{getdp} \\
getdp-sparskit & getdp & general environment for the treatment of discrete problems & getdp\cite{getdp} \\
gff2aplot & gff2aplot & pair-wise alignment-plots for genomic sequences in PostScript & gff2aplot\cite{gff2aplot} \\
gff2ps & gff2ps & produces PostScript graphical output from GFF-files & gff2ps\cite{gff2ps} \\
giira & giira & RNA-Seq driven gene finding incorporating ambiguous reads & giira\cite{giira} \\
glam2 & glam2 & gapped protein motifs from unaligned sequences & glam2\cite{glam2} \\
glam2 & glam2 & gapped protein motifs from unaligned sequences & glam22004\cite{glam22004} \\
glueviz & glueviz & Linked data visualization & glueviz\cite{glueviz} \\
gmap & gmap & spliced and SNP-tolerant alignment for mRNA and short reads & gmap\cite{gmap} \\
gmap & gmap & spliced and SNP-tolerant alignment for mRNA and short reads & gmap2005\cite{gmap2005} \\
gmsh & gmsh & Three-dimensional finite element mesh generator & gmsh\cite{gmsh} \\
gmsh-doc & gmsh & Three-dimensional finite element mesh generator documentation & gmsh\cite{gmsh} \\
gmt & gmt & Generic Mapping Tools & gmt\cite{gmt} \\
gmt & gmt & Generic Mapping Tools & gmt1991\cite{gmt1991} \\
gmt & gmt & Generic Mapping Tools & gmt1995\cite{gmt1995} \\
gmt & gmt & Generic Mapping Tools & gmt1998\cite{gmt1998} \\
gmt-common & gmt & Generic Mapping Tools - Architecture-independent files & gmt\cite{gmt} \\
gmt-common & gmt & Generic Mapping Tools - Architecture-independent files & gmt1991\cite{gmt1991} \\
gmt-common & gmt & Generic Mapping Tools - Architecture-independent files & gmt1995\cite{gmt1995} \\
gmt-common & gmt & Generic Mapping Tools - Architecture-independent files & gmt1998\cite{gmt1998} \\
gmt-dbg & gmt & Generic Mapping Tools Library - Debugging symbols & gmt\cite{gmt} \\
gmt-dbg & gmt & Generic Mapping Tools Library - Debugging symbols & gmt1991\cite{gmt1991} \\
gmt-dbg & gmt & Generic Mapping Tools Library - Debugging symbols & gmt1995\cite{gmt1995} \\
gmt-dbg & gmt & Generic Mapping Tools Library - Debugging symbols & gmt1998\cite{gmt1998} \\
gmt-doc & gmt & Documentation for GMT, the Generic Mapping Tools & gmt\cite{gmt} \\
gmt-doc & gmt & Documentation for GMT, the Generic Mapping Tools & gmt1991\cite{gmt1991} \\
gmt-doc & gmt & Documentation for GMT, the Generic Mapping Tools & gmt1995\cite{gmt1995} \\
gmt-doc & gmt & Documentation for GMT, the Generic Mapping Tools & gmt1998\cite{gmt1998} \\
gmt-doc-pdf & gmt & PDF docs for GMT, the Generic Mapping Tools & gmt\cite{gmt} \\
gmt-doc-pdf & gmt & PDF docs for GMT, the Generic Mapping Tools & gmt1991\cite{gmt1991} \\
gmt-doc-pdf & gmt & PDF docs for GMT, the Generic Mapping Tools & gmt1995\cite{gmt1995} \\
gmt-doc-pdf & gmt & PDF docs for GMT, the Generic Mapping Tools & gmt1998\cite{gmt1998} \\
gmt-examples & gmt & Example scripts illustrating the use of GMT & gmt\cite{gmt} \\
gmt-examples & gmt & Example scripts illustrating the use of GMT & gmt1991\cite{gmt1991} \\
gmt-examples & gmt & Example scripts illustrating the use of GMT & gmt1995\cite{gmt1995} \\
gmt-examples & gmt & Example scripts illustrating the use of GMT & gmt1998\cite{gmt1998} \\
gmt-gshhg & gmt-gshhg & Global Self-consistent Hierarchical High-resolution Geography (GSHHG) & gmt-gshhg\cite{gmt-gshhg} \\
gmt-gshhg-full & gmt-gshhg & Full resolution coastlines for the Generic Mapping Tools & gmt-gshhg\cite{gmt-gshhg} \\
gmt-gshhg-high & gmt-gshhg & High resolution coastlines for the Generic Mapping Tools & gmt-gshhg\cite{gmt-gshhg} \\
gmt-gshhg-low & gmt-gshhg & Low resolution coastlines for the Generic Mapping Tools & gmt-gshhg\cite{gmt-gshhg} \\
gmt-tutorial-pdf & gmt & Tutorial for GMT, the Generic Mapping Tools (PDF) & gmt\cite{gmt} \\
gmt-tutorial-pdf & gmt & Tutorial for GMT, the Generic Mapping Tools (PDF) & gmt1991\cite{gmt1991} \\
gmt-tutorial-pdf & gmt & Tutorial for GMT, the Generic Mapping Tools (PDF) & gmt1995\cite{gmt1995} \\
gmt-tutorial-pdf & gmt & Tutorial for GMT, the Generic Mapping Tools (PDF) & gmt1998\cite{gmt1998} \\
gnss-sdr & gnss-sdr & Global navigation satellite systems software defined receiver & gnss-sdr\cite{gnss-sdr} \\
gnuastro & gnuastro & GNU Astronomy Utilities programs & gnuastro\cite{gnuastro} \\
gnudatalanguage & gnudatalanguage & Free IDL compatible incremental compiler & gnudatalanguage\cite{gnudatalanguage} \\
goldendict-wordnet & wordnet & electronic lexical database of English language (goldendict) & wordnet\cite{wordnet} \\
goldendict-wordnet & wordnet & electronic lexical database of English language (goldendict) & wordnet1998\cite{wordnet1998} \\
goldendict-wordnet & wordnet & electronic lexical database of English language (goldendict) & wordnet2005\cite{wordnet2005} \\
gpaw & gpaw & DFT and beyond within the projector-augmented wave method & gpaw\cite{gpaw} \\
grinder & grinder & Versatile omics shotgun and amplicon sequencing read simulator & grinder\cite{grinder} \\
gringo & gringo & grounding tools for (disjunctive) logic programs & gringo\cite{gringo} \\
gringo & gringo & grounding tools for (disjunctive) logic programs & gringo2011\cite{gringo2011} \\
gringo & gringo & grounding tools for (disjunctive) logic programs & gringo2014\cite{gringo2014} \\
gromacs & gromacs & Molecular dynamics simulator, with building and analysis tools & gromacs\cite{gromacs} \\
gromacs & gromacs & Molecular dynamics simulator, with building and analysis tools & gromacs2001\cite{gromacs2001} \\
gromacs & gromacs & Molecular dynamics simulator, with building and analysis tools & gromacs2005\cite{gromacs2005} \\
gromacs-data & gromacs & GROMACS molecular dynamics sim, data and documentation & gromacs\cite{gromacs} \\
gromacs-data & gromacs & GROMACS molecular dynamics sim, data and documentation & gromacs2001\cite{gromacs2001} \\
gromacs-data & gromacs & GROMACS molecular dynamics sim, data and documentation & gromacs2005\cite{gromacs2005} \\
gromacs-dev & gromacs & Dummy package for libgromacs-dev & gromacs\cite{gromacs} \\
gromacs-dev & gromacs & Dummy package for libgromacs-dev & gromacs2001\cite{gromacs2001} \\
gromacs-dev & gromacs & Dummy package for libgromacs-dev & gromacs2005\cite{gromacs2005} \\
gromacs-lam & gromacs & Transition package to gromacs-openmpi & gromacs\cite{gromacs} \\
gromacs-lam & gromacs & Transition package to gromacs-openmpi & gromacs2001\cite{gromacs2001} \\
gromacs-lam & gromacs & Transition package to gromacs-openmpi & gromacs2005\cite{gromacs2005} \\
gromacs-mpich & gromacs & Molecular dynamics sim, binaries for MPICH parallelization & gromacs\cite{gromacs} \\
gromacs-mpich & gromacs & Molecular dynamics sim, binaries for MPICH parallelization & gromacs2001\cite{gromacs2001} \\
gromacs-mpich & gromacs & Molecular dynamics sim, binaries for MPICH parallelization & gromacs2005\cite{gromacs2005} \\
gromacs-openmpi & gromacs & Molecular dynamics sim, binaries for OpenMPI parallelization & gromacs\cite{gromacs} \\
gromacs-openmpi & gromacs & Molecular dynamics sim, binaries for OpenMPI parallelization & gromacs2001\cite{gromacs2001} \\
gromacs-openmpi & gromacs & Molecular dynamics sim, binaries for OpenMPI parallelization & gromacs2005\cite{gromacs2005} \\
gubbins & gubbins & phylogenetic analysis of genome sequences & gubbins\cite{gubbins} \\
gwama & gwama & Genome-Wide Association Meta Analysis & gwama\cite{gwama} \\
gwama & gwama & Genome-Wide Association Meta Analysis & gwama2010\cite{gwama2010} \\
gwyddion & gwyddion & Scanning Probe Microscopy visualization and analysis tool & gwyddion\cite{gwyddion} \\
gwyddion-common & gwyddion & architecture-independent files for Gwyddion SPM analysis tool & gwyddion\cite{gwyddion} \\
gwyddion-plugins & gwyddion & plugins for Gwyddion SPM analysis tool & gwyddion\cite{gwyddion} \\
gyoto & gyoto & General relativistic geodesic integration and ray-tracing & gyoto\cite{gyoto} \\
gyoto-bin & gyoto & General relativistic ray-tracing command-line interface & gyoto\cite{gyoto} \\
gyoto-dbg & gyoto & debugging symbols for the Gyoto framework & gyoto\cite{gyoto} \\
gyoto-doc & gyoto & documentation for the Gyoto library & gyoto\cite{gyoto} \\
harvest-tools & harvest-tools & archiving and postprocessing for reference-compressed genomic multi-alignments & harvest-tools\cite{harvest-tools} \\
hhsuite & hhsuite & sensitive protein sequence searching based on HMM-HMM alignment & hhsuite\cite{hhsuite} \\
hhsuite & hhsuite & sensitive protein sequence searching based on HMM-HMM alignment & hhsuite2005\cite{hhsuite2005} \\
hhsuite & hhsuite & sensitive protein sequence searching based on HMM-HMM alignment & hhsuite2019\cite{hhsuite2019} \\
hhsuite-data & hhsuite & sensitive protein sequence searching based on HMM-HMM alignment (data) & hhsuite\cite{hhsuite} \\
hhsuite-data & hhsuite & sensitive protein sequence searching based on HMM-HMM alignment (data) & hhsuite2005\cite{hhsuite2005} \\
hhsuite-data & hhsuite & sensitive protein sequence searching based on HMM-HMM alignment (data) & hhsuite2019\cite{hhsuite2019} \\
hhsuite-dbg & hhsuite & sensitive protein sequence searching based on HMM-HMM alignment (debug) & hhsuite\cite{hhsuite} \\
hhsuite-dbg & hhsuite & sensitive protein sequence searching based on HMM-HMM alignment (debug) & hhsuite2005\cite{hhsuite2005} \\
hhsuite-dbg & hhsuite & sensitive protein sequence searching based on HMM-HMM alignment (debug) & hhsuite2019\cite{hhsuite2019} \\
hhsuite-doc & hhsuite & documentation for HHsuite for HMM-HMM comparisons & hhsuite\cite{hhsuite} \\
hhsuite-doc & hhsuite & documentation for HHsuite for HMM-HMM comparisons & hhsuite2005\cite{hhsuite2005} \\
hhsuite-doc & hhsuite & documentation for HHsuite for HMM-HMM comparisons & hhsuite2019\cite{hhsuite2019} \\
hilive & hilive & realtime alignment of Illumina reads & hilive\cite{hilive} \\
hinge & hinge & long read genome assembler based on hinging & hinge\cite{hinge} \\
hisat2 & hisat2 & graph-based alignment of short nucleotide reads to many genomes & hisat2\cite{hisat2} \\
hmmer & hmmer & profile hidden Markov models for protein sequence analysis & hmmer\cite{hmmer} \\
hmmer & hmmer & profile hidden Markov models for protein sequence analysis & hmmer1995\cite{hmmer1995} \\
hmmer2 & hmmer2 & profile hidden Markov models for protein sequence analysis & hmmer2\cite{hmmer2} \\
hmmer2-doc & hmmer2 & profile hidden Markov models for protein sequence analysis (docs) & hmmer2\cite{hmmer2} \\
hmmer2-pvm & hmmer2 & HMMER programs with PVM (Parallel Virtual Machine) support & hmmer2\cite{hmmer2} \\
hmmer-doc & hmmer & profile hidden Markov models for protein sequence analysis (docs) & hmmer\cite{hmmer} \\
hmmer-doc & hmmer & profile hidden Markov models for protein sequence analysis (docs) & hmmer1995\cite{hmmer1995} \\
hmmer-examples & hmmer & profile hidden Markov models for protein sequence analysis (examples) & hmmer\cite{hmmer} \\
hmmer-examples & hmmer & profile hidden Markov models for protein sequence analysis (examples) & hmmer1995\cite{hmmer1995} \\
hmmer-pvm & hmmer & HMMER programs with PVM (Parallel Virtual Machine) support & hmmer\cite{hmmer} \\
hmmer-pvm & hmmer & HMMER programs with PVM (Parallel Virtual Machine) support & hmmer1995\cite{hmmer1995} \\
htcondor & condor & distributed workload management system & condor\cite{condor} \\
htcondor-dbg & condor & distributed workload management system - debugging symbols & condor\cite{condor} \\
htcondor-dev & condor & distributed workload management system - development files & condor\cite{condor} \\
htcondor-doc & condor & distributed workload management system - documentation & condor\cite{condor} \\
htslib-test & htslib & Test data for HTSlib & htslib\cite{htslib} \\
hyphy-common & hyphy & Hypothesis testing using Phylogenies (common files) & hyphy\cite{hyphy} \\
hyphygui & hyphy & Hypothesis testing using Phylogenies (GTK+ gui) & hyphy\cite{hyphy} \\
hyphy-mpi & hyphy & Hypothesis testing using Phylogenies (MPI version) & hyphy\cite{hyphy} \\
hyphy-pt & hyphy & Hypothesis testing using Phylogenies (pthreads version) & hyphy\cite{hyphy} \\
idba & idba & iterative De Bruijn Graph short read assemblers & idba\cite{idba} \\
idba & idba & iterative De Bruijn Graph short read assemblers & idba2013\cite{idba2013} \\
idba-extra & idba & iterative De Bruijn Graph short read assemblers (extra tools) & idba\cite{idba} \\
idba-extra & idba & iterative De Bruijn Graph short read assemblers (extra tools) & idba2013\cite{idba2013} \\
igdiscover & igdiscover & analyzes antibody repertoires to find new V genes & igdiscover\cite{igdiscover} \\
igdiscover-doc & igdiscover & analyzes antibody repertoires to find new V genes - doc & igdiscover\cite{igdiscover} \\
igor & igor & infers V(D)J recombination processes from sequencing data & igor\cite{igor} \\
igv & igv & Integrative Genomics Viewer & igv\cite{igv} \\
igv & igv & Integrative Genomics Viewer & igv2012\cite{igv2012} \\
imagej & imagej & Image processing program with a focus on microscopy images & imagej\cite{imagej} \\
imview & imview & Image viewing and analysis application & imview\cite{imview} \\
indelible & indelible & powerful and flexible simulator of biological evolution & indelible\cite{indelible} \\
infernal & infernal & inference of RNA secondary structural alignments & infernal\cite{infernal} \\
infernal-dbg & infernal & debug information for infernal & infernal\cite{infernal} \\
infernal-doc & infernal & inference of RNA secondary structural alignments – documentation & infernal\cite{infernal} \\
inhomog & inhomog & kinematical backreaction and average scale factor evolution & inhomog\cite{inhomog} \\
ipig & ipig & integrating PSMs into genome browser visualisations & ipig\cite{ipig} \\
iqtree & iqtree & efficient phylogenetic software by maximum likelihood & iqtree\cite{iqtree} \\
iraf & iraf & Image Reduction and Analysis Facility & iraf\cite{iraf} \\
iraf-dev & iraf & Image Reduction and Analysis Facility (development files) & iraf\cite{iraf} \\
iraf-fitsutil & iraf-fitsutil & FITS utilities for IRAF & iraf-fitsutil\cite{iraf-fitsutil} \\
iraf-mscred & iraf-mscred & CCD mosaic reduction package for IRAF & iraf-mscred\cite{iraf-mscred} \\
iraf-noao & iraf & IRAF NOAO data reduction package & iraf\cite{iraf} \\
iraf-noao-dev & iraf & IRAF NOAO data reduction package (development files) & iraf\cite{iraf} \\
iraf-rvsao & iraf-rvsao & IRAF package to obtain radial velocities from spectra & iraf-rvsao\cite{iraf-rvsao} \\
iraf-wcstools & wcstools & Handle the WCS of a FITS image (IRAF package) & wcstools\cite{wcstools} \\
itksnap & itksnap & semi-automatic segmentation of structures in 3D images & itksnap\cite{itksnap} \\
iva & iva & iterative virus sequence assembler & iva\cite{iva} \\
jalview & jalview & multiple alignment editor & jalview\cite{jalview} \\
jalview & jalview & multiple alignment editor & jalview2011\cite{jalview2011} \\
jellyfish & jellyfish & count k-mers in DNA sequences & jellyfish\cite{jellyfish} \\
jellyfish1 & jellyfish1 & count k-mers in DNA sequences & jellyfish1\cite{jellyfish1} \\
jellyfish-examples & jellyfish & count k-mers in DNA sequences (examples for testing) & jellyfish\cite{jellyfish} \\
jemboss & emboss & graphical user interface to EMBOSS & emboss\cite{emboss} \\
jmodeltest & jmodeltest & HPC selection of models of nucleotide substitution & jmodeltest\cite{jmodeltest} \\
jmol & jmol & Molecular Viewer & jmol\cite{jmol} \\
jmol-applet & jmol & Jmol Java applet & jmol\cite{jmol} \\
jython-stilts & starjava-ttools & Starlink Tables Infrastructure Library Tool Set (Jython package) & starjava-ttools\cite{starjava-ttools} \\
kalign & kalign & Global and progressive multiple sequence alignment & kalign\cite{kalign} \\
kalign & kalign & Global and progressive multiple sequence alignment & kalign2005\cite{kalign2005} \\
kalign & kalign & Global and progressive multiple sequence alignment & kalign2009\cite{kalign2009} \\
kallisto & kallisto & near-optimal RNA-Seq quantification & kallisto\cite{kallisto} \\
kallisto-examples & kallisto & near-optimal RNA-Seq quantification (example data) & kallisto\cite{kallisto} \\
kaptive & kaptive & obtain information about K and O types for Klebsiella genome assemblies & kaptive\cite{kaptive} \\
kaptive-data & kaptive & reference data for kaptive for Klebsiella genome assemblies & kaptive\cite{kaptive} \\
kaptive-example & kaptive & example data for kaptive for Klebsiella genome assemblies & kaptive\cite{kaptive} \\
khmer & khmer & in-memory DNA sequence kmer counting, filtering \& graph traversal & khmer\cite{khmer} \\
khmer & khmer & in-memory DNA sequence kmer counting, filtering \& graph traversal & khmer2008\cite{khmer2008} \\
khmer & khmer & in-memory DNA sequence kmer counting, filtering \& graph traversal & khmer2012\cite{khmer2012} \\
khmer & khmer & in-memory DNA sequence kmer counting, filtering \& graph traversal & khmer2012c\cite{khmer2012c} \\
khmer & khmer & in-memory DNA sequence kmer counting, filtering \& graph traversal & khmer2014\cite{khmer2014} \\
khmer & khmer & in-memory DNA sequence kmer counting, filtering \& graph traversal & khmer2015\cite{khmer2015} \\
khmer-common & khmer & common files for the khmer project tools & khmer\cite{khmer} \\
khmer-common & khmer & common files for the khmer project tools & khmer2008\cite{khmer2008} \\
khmer-common & khmer & common files for the khmer project tools & khmer2012\cite{khmer2012} \\
khmer-common & khmer & common files for the khmer project tools & khmer2012c\cite{khmer2012c} \\
khmer-common & khmer & common files for the khmer project tools & khmer2014\cite{khmer2014} \\
khmer-common & khmer & common files for the khmer project tools & khmer2015\cite{khmer2015} \\
king-probe & king-probe & Evaluate and visualize protein interatomic packing & king-probe\cite{king-probe} \\
kissplice & kissplice & Detection of various kinds of polymorphisms in RNA-seq data & kissplice\cite{kissplice} \\
kleborate & kleborate & tool to screen Klebsiella genome assemblies & kleborate\cite{kleborate} \\
kleborate & kleborate & tool to screen Klebsiella genome assemblies & kleborate2018\cite{kleborate2018} \\
kleborate-examples & kleborate & tool to screen Klebsiella genome assemblies (example data) & kleborate\cite{kleborate} \\
kleborate-examples & kleborate & tool to screen Klebsiella genome assemblies (example data) & kleborate2018\cite{kleborate2018} \\
kma & kma & mapping genomic sequences to raw reads directly against redundant databases & kma\cite{kma} \\
kmc & kmc & count kmers in genomic sequences & kmc\cite{kmc} \\
kmer & kmer & suite of tools for DNA sequence analysis & kmer\cite{kmer} \\
kmer & kmer & suite of tools for DNA sequence analysis & kmer2004\cite{kmer2004} \\
kmer-examples & kmer & sample data for kmer suite of tools for DNA sequence analysis & kmer\cite{kmer} \\
kmer-examples & kmer & sample data for kmer suite of tools for DNA sequence analysis & kmer2004\cite{kmer2004} \\
kmerresistance & kmerresistance & correlates mapped genes with the predicted species of WGS samples & kmerresistance\cite{kmerresistance} \\
kraken & kraken & assigning taxonomic labels to short DNA sequences & kraken\cite{kraken} \\
kraken2 & kraken2 & taxonomic classification system using exact k-mer matches & kraken2\cite{kraken2} \\
lagan & lagan & highly parametrizable pairwise global genome sequence aligner & lagan\cite{lagan} \\
lamarc & lamarc & Likelihood Analysis with Metropolis Algorithm using Random Coalescence & lamarc\cite{lamarc} \\
lambda-align & lambda-align & Local Aligner for Massive Biological DatA & lambda-align\cite{lambda-align} \\
lambda-align2 & lambda-align2 & Local Aligner for Massive Biological DatA - v2 & lambda-align2\cite{lambda-align2} \\
last-align & last-align & genome-scale comparison of biological sequences & last-align\cite{last-align} \\
last-align & last-align & genome-scale comparison of biological sequences & last-align2019\cite{last-align2019} \\
leaff & kmer & biological sequence library utilities and applications & kmer\cite{kmer} \\
leaff & kmer & biological sequence library utilities and applications & kmer2004\cite{kmer2004} \\
libace-perl & libace-perl & Object-Oriented Access to ACEDB Databases & libace-perl\cite{libace-perl} \\
libajax6 & emboss & EMBOSS library for commands & emboss\cite{emboss} \\
libajax6-dev & emboss & development files for libajax & emboss\cite{emboss} \\
libaoflagger0 & aoflagger & Find RFI in radio astronomical observations (shared lib) & aoflagger\cite{aoflagger} \\
libapbs1 & apbs & Adaptive Poisson Boltzmann Solver & apbs\cite{apbs} \\
libapbs1 & apbs & Adaptive Poisson Boltzmann Solver & apbs1993\cite{apbs1993} \\
libapbs1 & apbs & Adaptive Poisson Boltzmann Solver & apbs1995\cite{apbs1995} \\
libapbs1 & apbs & Adaptive Poisson Boltzmann Solver & apbs2001\cite{apbs2001} \\
libapbs1 & apbs & Adaptive Poisson Boltzmann Solver & apbs2003\cite{apbs2003} \\
libapbs-dev & apbs & Adaptive Poisson Boltzmann Solver & apbs\cite{apbs} \\
libapbs-dev & apbs & Adaptive Poisson Boltzmann Solver & apbs1993\cite{apbs1993} \\
libapbs-dev & apbs & Adaptive Poisson Boltzmann Solver & apbs1995\cite{apbs1995} \\
libapbs-dev & apbs & Adaptive Poisson Boltzmann Solver & apbs2001\cite{apbs2001} \\
libapbs-dev & apbs & Adaptive Poisson Boltzmann Solver & apbs2003\cite{apbs2003} \\
libarmci-mpi-dev & armci-mpi & ARMCI-MPI (Development version) & armci-mpi\cite{armci-mpi} \\
libarrayfire-cpu3 & arrayfire & High performance library for parallel computing (CPU backend) & arrayfire\cite{arrayfire} \\
libarrayfire-cpu-dev & arrayfire & Development files for ArrayFire (CPU backend) & arrayfire\cite{arrayfire} \\
libarrayfire-dev & arrayfire & Common development files for ArrayFire & arrayfire\cite{arrayfire} \\
libarrayfire-doc & arrayfire & Common documentation and examples for ArrayFire & arrayfire\cite{arrayfire} \\
libarrayfire-opencl3 & arrayfire & High performance library for parallel computing (OpenCL backend) & arrayfire\cite{arrayfire} \\
libarrayfire-opencl-dev & arrayfire & Development files for ArrayFire (OpenCL backend) & arrayfire\cite{arrayfire} \\
libarrayfire-unified3 & arrayfire & High performance library for parallel computing (unified backend) & arrayfire\cite{arrayfire} \\
libarrayfire-unified-dev & arrayfire & Development files for ArrayFire (unified backend) & arrayfire\cite{arrayfire} \\
libasl0 & asl & multiphysics simulation software & asl\cite{asl} \\
libasl-dev & asl & development files for ASL & asl\cite{asl} \\
libastrometry0 & astrometry.net & Astrometry plate solver (shared lib) & astrometry-net\cite{astrometry-net} \\
libastrometry-dev & astrometry.net & Astrometry plate solver (development files) & astrometry-net\cite{astrometry-net} \\
libavogadro1 & avogadro & Molecular Graphics and Modelling System (library) & avogadro\cite{avogadro} \\
libavogadro2-1 & avogadrolibs & Molecular Graphics and Modelling System (library) & avogadrolibs\cite{avogadrolibs} \\
libavogadro-dev & avogadrolibs & Molecular Graphics and Modelling System (development files) & avogadrolibs\cite{avogadrolibs} \\
libavogadro-doc & avogadrolibs & Molecular Graphics and Modelling System (lib documentation) & avogadrolibs\cite{avogadrolibs} \\
libball1.3 & ball & Biochemical Algorithms Library & ball\cite{ball} \\
libball1.3 & ball & Biochemical Algorithms Library & ball2010\cite{ball2010} \\
libball1.3-dev & ball & Header files for the Biochemical Algorithms Library & ball\cite{ball} \\
libball1.3-dev & ball & Header files for the Biochemical Algorithms Library & ball2010\cite{ball2010} \\
libball1.3-doc & ball & Documentation for the BALL library & ball\cite{ball} \\
libball1.3-doc & ball & Documentation for the BALL library & ball2010\cite{ball2010} \\
libball1.4 & ball & Biochemical Algorithms Library & ball\cite{ball} \\
libball1.4 & ball & Biochemical Algorithms Library & ball2010\cite{ball2010} \\
libball1.4-data & ball & Biochemical Algorithms Library (data files) & ball\cite{ball} \\
libball1.4-data & ball & Biochemical Algorithms Library (data files) & ball2010\cite{ball2010} \\
libball1.4-dev & ball & Header files for the Biochemical Algorithms Library & ball\cite{ball} \\
libball1.4-dev & ball & Header files for the Biochemical Algorithms Library & ball2010\cite{ball2010} \\
libball1.4-doc & ball & documentation for the BALL library & ball\cite{ball} \\
libball1.4-doc & ball & documentation for the BALL library & ball2010\cite{ball2010} \\
libball1.5 & ball & Biochemical Algorithms Library & ball\cite{ball} \\
libball1.5 & ball & Biochemical Algorithms Library & ball2010\cite{ball2010} \\
libball1.5-data & ball & Biochemical Algorithms Library (data files) & ball\cite{ball} \\
libball1.5-data & ball & Biochemical Algorithms Library (data files) & ball2010\cite{ball2010} \\
libball1.5-dev & ball & Header files for the Biochemical Algorithms Library & ball\cite{ball} \\
libball1.5-dev & ball & Header files for the Biochemical Algorithms Library & ball2010\cite{ball2010} \\
libball1.5-doc & ball & documentation for the BALL library & ball\cite{ball} \\
libball1.5-doc & ball & documentation for the BALL library & ball2010\cite{ball2010} \\
libballview1.3 & ball & Biochemical Algorithms Library, VIEW framework & ball\cite{ball} \\
libballview1.3 & ball & Biochemical Algorithms Library, VIEW framework & ball2010\cite{ball2010} \\
libballview1.3-dev & ball & Header files for the VIEW part of the Biochemical Algorithms Library & ball\cite{ball} \\
libballview1.3-dev & ball & Header files for the VIEW part of the Biochemical Algorithms Library & ball2010\cite{ball2010} \\
libballview1.4 & ball & Biochemical Algorithms Library, VIEW framework & ball\cite{ball} \\
libballview1.4 & ball & Biochemical Algorithms Library, VIEW framework & ball2010\cite{ball2010} \\
libballview1.4-dev & ball & Header files for the VIEW part of the Biochemical Algorithms Library & ball\cite{ball} \\
libballview1.4-dev & ball & Header files for the VIEW part of the Biochemical Algorithms Library & ball2010\cite{ball2010} \\
libballview1.5 & ball & Biochemical Algorithms Library, VIEW framework & ball\cite{ball} \\
libballview1.5 & ball & Biochemical Algorithms Library, VIEW framework & ball2010\cite{ball2010} \\
libballview1.5-dev & ball & Header files for the VIEW part of the Biochemical Algorithms Library & ball\cite{ball} \\
libballview1.5-dev & ball & Header files for the VIEW part of the Biochemical Algorithms Library & ball2010\cite{ball2010} \\
libbamtools2.3.0 & bamtools & dynnamic library for manipulating BAM (genome alignment) files & bamtools\cite{bamtools} \\
libbamtools2.4.0 & bamtools & dynamic library for manipulating BAM (genome alignment) files & bamtools\cite{bamtools} \\
libbamtools2.5.1 & bamtools & dynamic library for manipulating BAM (genome alignment) files & bamtools\cite{bamtools} \\
libbamtools-dev & bamtools & C++ API for manipulating BAM (genome alignment) files & bamtools\cite{bamtools} \\
libbamtools-doc & bamtools & docs for dynamic library for manipulating BAM (genome alignment) files & bamtools\cite{bamtools} \\
libbiojava1.7-java & biojava-live & Java API to biological data and applications (version 1.7) & biojava-live\cite{biojava-live} \\
libbiojava-java & biojava-live & Java API to biological data and applications (default version) & biojava-live\cite{biojava-live} \\
libbiojava-java-demos & biojava-live & Example programs for BioJava & biojava-live\cite{biojava-live} \\
libbiojava-java-doc & biojava-live & [Biology] Documentation for BioJava & biojava-live\cite{biojava-live} \\
libbio-perl-perl & bioperl & BioPerl core perl modules & bioperl\cite{bioperl} \\
libbiosig1 & biosig4c++ & I/O library for biomedical data - dynamic library & biosig4c--\cite{biosig4c--} \\
libbiosig1-dbg & biosig4c++ & I/O library for biomedical data - debug symbols & biosig4c--\cite{biosig4c--} \\
libbiosig2 & biosig4c++ & I/O library for biomedical data - dynamic library & biosig4c--\cite{biosig4c--} \\
libbiosig-dev & biosig4c++ & I/O library for biomedical data - development files & biosig4c--\cite{biosig4c--} \\
libblimps3 & blimps & blocks database improved searcher library & blimps\cite{blimps} \\
libblimps3-dev & blimps & blocks database improved searcher library (development) & blimps\cite{blimps} \\
libblis2 & blis & BLAS-like Library Instantiation Software Framework - shared library & blis\cite{blis} \\
libblis2-openmp & blis & BLAS-like Library Instantiation Software Framework - shared library & blis\cite{blis} \\
libblis2-pthread & blis & BLAS-like Library Instantiation Software Framework - shared library & blis\cite{blis} \\
libblis2-serial & blis & BLAS-like Library Instantiation Software Framework - shared library & blis\cite{blis} \\
libblis3 & blis & BLAS-like Library Instantiation Software Framework (32bit,meta) & blis\cite{blis} \\
libblis3-openmp & blis & BLAS-like Library Instantiation Software Framework (32bit,openmp) & blis\cite{blis} \\
libblis3-pthread & blis & BLAS-like Library Instantiation Software Framework (32bit,pthread) & blis\cite{blis} \\
libblis3-serial & blis & BLAS-like Library Instantiation Software Framework (32bit,serial) & blis\cite{blis} \\
libblis64-2 & blis & BLAS-like Library Instantiation Software Framework - shared library & blis\cite{blis} \\
libblis64-2-openmp & blis & BLAS-like Library Instantiation Software Framework - shared library & blis\cite{blis} \\
libblis64-2-pthread & blis & BLAS-like Library Instantiation Software Framework - shared library & blis\cite{blis} \\
libblis64-2-serial & blis & BLAS-like Library Instantiation Software Framework - shared library & blis\cite{blis} \\
libblis64-3 & blis & BLAS-like Library Instantiation Software Framework (64bit,meta) & blis\cite{blis} \\
libblis64-3-openmp & blis & BLAS-like Library Instantiation Software Framework (64bit,openmp) & blis\cite{blis} \\
libblis64-3-pthread & blis & BLAS-like Library Instantiation Software Framework (64bit,pthread) & blis\cite{blis} \\
libblis64-3-serial & blis & BLAS-like Library Instantiation Software Framework (64bit,serial) & blis\cite{blis} \\
libblis64-dev & blis & BLAS-like Library Instantiation Software Framework (dev,64bit,meta) & blis\cite{blis} \\
libblis64-openmp-dev & blis & BLAS-like Library Instantiation Software Framework (dev,64bit,openmp) & blis\cite{blis} \\
libblis64-pthread-dev & blis & BLAS-like Library Instantiation Software Framework (dev,64bit,pthread) & blis\cite{blis} \\
libblis64-serial-dev & blis & BLAS-like Library Instantiation Software Framework (dev,64bit,serial) & blis\cite{blis} \\
libblis-dev & blis & BLAS-like Library Instantiation Software Framework (dev,32bit,meta) & blis\cite{blis} \\
libblis-openmp-dev & blis & BLAS-like Library Instantiation Software Framework (dev,32bit,openmp) & blis\cite{blis} \\
libblis-pthread-dev & blis & BLAS-like Library Instantiation Software Framework (dev,32bit,pthread) & blis\cite{blis} \\
libblis-serial-dev & blis & BLAS-like Library Instantiation Software Framework (dev,32bit,serial) & blis\cite{blis} \\
libbwa-dev & bwa & Burrows-Wheeler Aligner source files & bwa\cite{bwa} \\
libcaffe1 & caffe & library of Caffe, deep learning framework (CPU\_ONLY) & caffe\cite{caffe} \\
libcaffe-cpu1 & caffe & library of Caffe, deep learning framework (CPU\_ONLY) & caffe\cite{caffe} \\
libcaffe-cpu-dev & caffe & development files for Caffe (CPU\_ONLY) & caffe\cite{caffe} \\
libcaffe-cuda1 & caffe-contrib & library of Caffe, deep leanring framework (CUDA) & caffe-contrib\cite{caffe-contrib} \\
libcaffe-cuda-dev & caffe-contrib & development files for Caffe (CUDA) & caffe-contrib\cite{caffe-contrib} \\
libcaffe-dev & caffe & development files for Caffe (CPU\_ONLY) & caffe\cite{caffe} \\
libcamitk3 & camitk & Computer Assisted Medical Intervention Tool Kit - runtime & camitk\cite{camitk} \\
libcamitk3-data & camitk & Computer Assisted Medical Intervention Tool Kit - data & camitk\cite{camitk} \\
libcamitk3-dev & camitk & Computer Assisted Medical Intervention Tool Kit - development & camitk\cite{camitk} \\
libcamitk3-doc & camitk & Computer Assisted Medical Intervention Tool Kit - documentation & camitk\cite{camitk} \\
libcamitk4 & camitk & Computer Assisted Medical Intervention Tool Kit - runtime & camitk\cite{camitk} \\
libcamitk4-data & camitk & Computer Assisted Medical Intervention Tool Kit - data & camitk\cite{camitk} \\
libcamitk4-doc & camitk & Computer Assisted Medical Intervention Tool Kit - documentation & camitk\cite{camitk} \\
libcamitk-dev & camitk & Computer Assisted Medical Intervention Tool Kit - development & camitk\cite{camitk} \\
libcdk-java & cdk & Chemistry Development Kit (CDK) Java libraries & cdk\cite{cdk} \\
libcexceptions0 & cod-tools & C exception handling library & cod-tools\cite{cod-tools} \\
libcexceptions-dev & cod-tools & C exception handling library (development files) & cod-tools\cite{cod-tools} \\
libcext0 & cpl & Commonly used utility functions for C programs & cpl\cite{cpl} \\
libcext-dev & cpl & Commonly used utility functions for C programs (development files) & cpl\cite{cpl} \\
libcext-doc & cpl & API documentation for ESO's C utility library libcext & cpl\cite{cpl} \\
libchemps2-2 & chemps2 & Spin-adapted DMRG for ab initio quantum chemistry & chemps2\cite{chemps2} \\
libchemps2-2 & chemps2 & Spin-adapted DMRG for ab initio quantum chemistry & chemps22014\cite{chemps22014} \\
libchemps2-2 & chemps2 & Spin-adapted DMRG for ab initio quantum chemistry & chemps22014c\cite{chemps22014c} \\
libchemps2-2 & chemps2 & Spin-adapted DMRG for ab initio quantum chemistry & chemps22014d\cite{chemps22014d} \\
libchemps2-2 & chemps2 & Spin-adapted DMRG for ab initio quantum chemistry & chemps22016\cite{chemps22016} \\
libchemps2-3 & chemps2 & Spin-adapted DMRG for ab initio quantum chemistry & chemps2\cite{chemps2} \\
libchemps2-3 & chemps2 & Spin-adapted DMRG for ab initio quantum chemistry & chemps22014\cite{chemps22014} \\
libchemps2-3 & chemps2 & Spin-adapted DMRG for ab initio quantum chemistry & chemps22014c\cite{chemps22014c} \\
libchemps2-3 & chemps2 & Spin-adapted DMRG for ab initio quantum chemistry & chemps22014d\cite{chemps22014d} \\
libchemps2-3 & chemps2 & Spin-adapted DMRG for ab initio quantum chemistry & chemps22016\cite{chemps22016} \\
libchemps2-dev & chemps2 & C++ headers, static library, and symlink for libchemps2-3 & chemps2\cite{chemps2} \\
libchemps2-dev & chemps2 & C++ headers, static library, and symlink for libchemps2-3 & chemps22014\cite{chemps22014} \\
libchemps2-dev & chemps2 & C++ headers, static library, and symlink for libchemps2-3 & chemps22014c\cite{chemps22014c} \\
libchemps2-dev & chemps2 & C++ headers, static library, and symlink for libchemps2-3 & chemps22014d\cite{chemps22014d} \\
libchemps2-dev & chemps2 & C++ headers, static library, and symlink for libchemps2-3 & chemps22016\cite{chemps22016} \\
libclassad3 & condor & Condor classads expression language - runtime library & condor\cite{condor} \\
libclassad7 & condor & HTCondor classads expression language - runtime library & condor\cite{condor} \\
libclassad8 & condor & HTCondor classads expression language - runtime library & condor\cite{condor} \\
libclassad-dev & condor & HTCondor classads expression language - development library & condor\cite{condor} \\
libclustalo-dev & clustalo & Library to embed Clustal Omega & clustalo\cite{clustalo} \\
libclustalo-dev & clustalo & Library to embed Clustal Omega & clustalo2018\cite{clustalo2018} \\
libclustalo-doc & clustalo & API documentation for library to embed Clustal Omega & clustalo\cite{clustalo} \\
libclustalo-doc & clustalo & API documentation for library to embed Clustal Omega & clustalo2018\cite{clustalo2018} \\
libcminpack1 & cminpack & Nonlinear equations and nonlinear least squares problems - runtime & cminpack\cite{cminpack} \\
libcminpack1.0.90 & cminpack & Nonlinear equations and nonlinear least squares problems - runtime & cminpack\cite{cminpack} \\
libcminpack-dev & cminpack & Nonlinear equations and nonlinear least squares problems - development & cminpack\cite{cminpack} \\
libcnrun2 & cnrun & NeuroML-capable neuronal network simulator (shared lib) & cnrun\cite{cnrun} \\
libcnrun2-dev & cnrun & NeuroML-capable neuronal network simulator (development files) & cnrun\cite{cnrun} \\
libcodcif2 & cod-tools & error-correcting CIF parser - shared library & cod-tools\cite{cod-tools} \\
libcodcif-dev & cod-tools & error-correcting CIF parser - headers and static libraries & cod-tools\cite{cod-tools} \\
libcod-cif-parser-bison-perl & cod-tools & error-correcting CIF parser - Perl bindings & cod-tools\cite{cod-tools} \\
libcod-cif-parser-yapp-perl & cod-tools & error-correcting CIF parser - pure Perl implementation & cod-tools\cite{cod-tools} \\
libcod-precision-perl & cod-tools & COD precision handling module for Perl language & cod-tools\cite{cod-tools} \\
libcod-usermessage-perl & cod-tools & COD message formatting module for Perl language & cod-tools\cite{cod-tools} \\
libcplcore20 & cpl & Fundamental CPL data types and functions & cpl\cite{cpl} \\
libcplcore26 & cpl & Fundamental CPL data types and functions & cpl\cite{cpl} \\
libcpl-dev & cpl & ESO library for automated astronomical data-reduction & cpl\cite{cpl} \\
libcpldfs20 & cpl & CPL functions for Data Flow System compatibility & cpl\cite{cpl} \\
libcpldfs26 & cpl & CPL functions for Data Flow System compatibility & cpl\cite{cpl} \\
libcpl-doc & cpl & API documentation for the Common Pipeline Library & cpl\cite{cpl} \\
libcpldrs20 & cpl & CPL higher level data processing algorithms & cpl\cite{cpl} \\
libcpldrs26 & cpl & CPL higher level data processing algorithms & cpl\cite{cpl} \\
libcplgasgano20 & cpl & CPL Java Native Interface library & cpl\cite{cpl} \\
libcplgasgano26 & cpl & CPL Java Native Interface library & cpl\cite{cpl} \\
libcplui20 & cpl & CPL framework interface library & cpl\cite{cpl} \\
libcplui26 & cpl & CPL framework interface library & cpl\cite{cpl} \\
libcv2.1 & opencv & computer vision library & opencv\cite{opencv} \\
libcv2.3 & opencv & computer vision library - libcv* translation package & opencv\cite{opencv} \\
libcv2.4 & opencv & computer vision library - libcv* translation package & opencv\cite{opencv} \\
libcvaux2.1 & opencv & computer vision extension library & opencv\cite{opencv} \\
libcvaux2.3 & opencv & computer vision library - libcvaux translation package & opencv\cite{opencv} \\
libcvaux2.4 & opencv & computer vision library - libcvaux translation package & opencv\cite{opencv} \\
libcvaux-dev & opencv & Translation package for libcvaux-dev & opencv\cite{opencv} \\
libcv-dev & opencv & Translation package for libcv-dev & opencv\cite{opencv} \\
libelpa0 & elpa & Eigenvalue SoLvers for Petaflop-Applications & elpa\cite{elpa} \\
libelpa0 & elpa & Eigenvalue SoLvers for Petaflop-Applications & elpa2014\cite{elpa2014} \\
libelpa15 & elpa & Eigenvalue SoLvers for Petaflop-Applications & elpa\cite{elpa} \\
libelpa15 & elpa & Eigenvalue SoLvers for Petaflop-Applications & elpa2014\cite{elpa2014} \\
libelpa4 & elpa & Eigenvalue SoLvers for Petaflop-Applications & elpa\cite{elpa} \\
libelpa4 & elpa & Eigenvalue SoLvers for Petaflop-Applications & elpa2014\cite{elpa2014} \\
libelpa-dev & elpa & Eigenvalue SoLvers for Petaflop-Applications (Development version) & elpa\cite{elpa} \\
libelpa-dev & elpa & Eigenvalue SoLvers for Petaflop-Applications (Development version) & elpa2014\cite{elpa2014} \\
libfreecontact0 & freecontact & fast protein contact predictor library & freecontact\cite{freecontact} \\
libfreecontact0-dbg & freecontact & debugging symbols for libfreecontact & freecontact\cite{freecontact} \\
libfreecontact0-dev & freecontact & fast protein contact predictor library - development files & freecontact\cite{freecontact} \\
libfreecontact0v5 & freecontact & fast protein contact predictor library & freecontact\cite{freecontact} \\
libfreecontact-dev & freecontact & fast protein contact predictor library - development files & freecontact\cite{freecontact} \\
libfreecontact-doc & freecontact & documentation for libfreecontact & freecontact\cite{freecontact} \\
libfreecontact-perl & libfreecontact-perl & fast protein contact predictor - binding for Perl & libfreecontact-perl\cite{libfreecontact-perl} \\
libfuntools1 & funtools & Minimal buy-in FITS library & funtools\cite{funtools} \\
libfuntools-dev & funtools & Minimal buy-in FITS library (development files) & funtools\cite{funtools} \\
libgatbcore2 & gatb-core & dynamic library of the Genome Analysis Toolbox & gatb-core\cite{gatb-core} \\
libgatbcore3 & gatb-core & dynamic library of the Genome Analysis Toolbox & gatb-core\cite{gatb-core} \\
libgatbcore-dev & gatb-core & development library of the Genome Analysis Toolbox & gatb-core\cite{gatb-core} \\
libgbtools0 & seqtools & library for visualising sequence alignments & seqtools\cite{seqtools} \\
libgbtools0 & seqtools & library for visualising sequence alignments & seqtools1994\cite{seqtools1994} \\
libgbtools0 & seqtools & library for visualising sequence alignments & seqtools2005\cite{seqtools2005} \\
libgbtools-dev & seqtools & library for visualising sequence alignments (devel) & seqtools\cite{seqtools} \\
libgbtools-dev & seqtools & library for visualising sequence alignments (devel) & seqtools1994\cite{seqtools1994} \\
libgbtools-dev & seqtools & library for visualising sequence alignments (devel) & seqtools2005\cite{seqtools2005} \\
libgdcm2.0 & gdcm & Grassroots DICOM runtime libraries & gdcm\cite{gdcm} \\
libgdcm2.0-dbg & gdcm & Grassroots DICOM runtime libraries, debug version & gdcm\cite{gdcm} \\
libgdcm2.2 & gdcm & Grassroots DICOM runtime libraries & gdcm\cite{gdcm} \\
libgdcm2.2-dbg & gdcm & Grassroots DICOM runtime libraries, debug version & gdcm\cite{gdcm} \\
libgdcm2.4 & gdcm & Grassroots DICOM runtime libraries & gdcm\cite{gdcm} \\
libgdcm2.4-dbg & gdcm & Grassroots DICOM runtime libraries, debug version & gdcm\cite{gdcm} \\
libgdcm2.6 & gdcm & Grassroots DICOM runtime libraries & gdcm\cite{gdcm} \\
libgdcm2.6-dbg & gdcm & Grassroots DICOM runtime libraries, debug version & gdcm\cite{gdcm} \\
libgdcm2.8 & gdcm & Grassroots DICOM runtime libraries & gdcm\cite{gdcm} \\
libgdcm2-dev & gdcm & Grassroots DICOM development libraries and headers & gdcm\cite{gdcm} \\
libgdcm3.0 & gdcm & Grassroots DICOM runtime libraries & gdcm\cite{gdcm} \\
libgdcm-cil & gdcm & Grassroots DICOM CLI bindings & gdcm\cite{gdcm} \\
libgdcm-dev & gdcm & Grassroots DICOM development libraries and headers & gdcm\cite{gdcm} \\
libgdcm-java & gdcm & Grassroots DICOM Java bindings & gdcm\cite{gdcm} \\
libgdcm-tools & gdcm & Grassroots DICOM tools and utilities & gdcm\cite{gdcm} \\
libgdf0 & libgdf & IO library for the GDF (general dataformat for biosignals) & libgdf\cite{libgdf} \\
libgdf0-dbg & libgdf & IO library for the GDF -- debug symbols & libgdf\cite{libgdf} \\
libgdf-dev & libgdf & IO library for the GDF -- development library & libgdf\cite{libgdf} \\
libgenometools0 & genometools & versatile genome analysis library & genometools\cite{genometools} \\
libgenometools0-dev & genometools & development files for GenomeTools & genometools\cite{genometools} \\
libgetoptions0 & cod-tools & Command line argument processing library for C & cod-tools\cite{cod-tools} \\
libgetoptions-dev & cod-tools & Command line argument processing library for C (development files) & cod-tools\cite{cod-tools} \\
libgkarrays1 & libgkarrays & library to query large collection of NGS sequences & libgkarrays\cite{libgkarrays} \\
libgkarrays-dev & libgkarrays & library to query large collection of NGS sequences (development) & libgkarrays\cite{libgkarrays} \\
libglobalarrays-dev & ga & Distributed Shared-Memory Programming Environment (development) & ga\cite{ga} \\
libglobalarrays-dev & ga & Distributed Shared-Memory Programming Environment (development) & ga2012\cite{ga2012} \\
libgmsh2 & gmsh & Three-dimensional finite element mesh generator. Shared library & gmsh\cite{gmsh} \\
libgmsh2v5 & gmsh & Three-dimensional finite element mesh generator. Shared library & gmsh\cite{gmsh} \\
libgmsh4 & gmsh & Three-dimensional finite element mesh generator shared library & gmsh\cite{gmsh} \\
libgmsh4.1 & gmsh & Three-dimensional finite element mesh generator shared library & gmsh\cite{gmsh} \\
libgmsh-dev & gmsh & Three-dimensional finite element mesh generator development files & gmsh\cite{gmsh} \\
libgmt4 & gmt & Generic Mapping Tools Library & gmt\cite{gmt} \\
libgmt4 & gmt & Generic Mapping Tools Library & gmt1991\cite{gmt1991} \\
libgmt4 & gmt & Generic Mapping Tools Library & gmt1995\cite{gmt1995} \\
libgmt4 & gmt & Generic Mapping Tools Library & gmt1998\cite{gmt1998} \\
libgmt5 & gmt & Generic Mapping Tools Library & gmt\cite{gmt} \\
libgmt5 & gmt & Generic Mapping Tools Library & gmt1991\cite{gmt1991} \\
libgmt5 & gmt & Generic Mapping Tools Library & gmt1995\cite{gmt1995} \\
libgmt5 & gmt & Generic Mapping Tools Library & gmt1998\cite{gmt1998} \\
libgmt6 & gmt & Generic Mapping Tools Library & gmt\cite{gmt} \\
libgmt6 & gmt & Generic Mapping Tools Library & gmt1991\cite{gmt1991} \\
libgmt6 & gmt & Generic Mapping Tools Library & gmt1995\cite{gmt1995} \\
libgmt6 & gmt & Generic Mapping Tools Library & gmt1998\cite{gmt1998} \\
libgmt-dev & gmt & Generic Mapping Tools Library - Development files & gmt\cite{gmt} \\
libgmt-dev & gmt & Generic Mapping Tools Library - Development files & gmt1991\cite{gmt1991} \\
libgmt-dev & gmt & Generic Mapping Tools Library - Development files & gmt1995\cite{gmt1995} \\
libgmt-dev & gmt & Generic Mapping Tools Library - Development files & gmt1998\cite{gmt1998} \\
libgnuastro1 & gnuastro & GNU Astronomy Utilities shared libraries & gnuastro\cite{gnuastro} \\
libgnuastro10 & gnuastro & GNU Astronomy Utilities shared libraries & gnuastro\cite{gnuastro} \\
libgnuastro6 & gnuastro & GNU Astronomy Utilities shared libraries & gnuastro\cite{gnuastro} \\
libgnuastro9 & gnuastro & GNU Astronomy Utilities shared libraries & gnuastro\cite{gnuastro} \\
libgnuastro-dev & gnuastro & GNU Astronomy Utilities development files & gnuastro\cite{gnuastro} \\
libgnudatalanguage0 & gnudatalanguage & Free IDL compatible incremental compiler shared library & gnudatalanguage\cite{gnudatalanguage} \\
libgromacs2 & gromacs & GROMACS molecular dynamics sim, shared libraries & gromacs\cite{gromacs} \\
libgromacs2 & gromacs & GROMACS molecular dynamics sim, shared libraries & gromacs2001\cite{gromacs2001} \\
libgromacs2 & gromacs & GROMACS molecular dynamics sim, shared libraries & gromacs2005\cite{gromacs2005} \\
libgromacs4 & gromacs & GROMACS molecular dynamics sim, shared libraries & gromacs\cite{gromacs} \\
libgromacs4 & gromacs & GROMACS molecular dynamics sim, shared libraries & gromacs2001\cite{gromacs2001} \\
libgromacs4 & gromacs & GROMACS molecular dynamics sim, shared libraries & gromacs2005\cite{gromacs2005} \\
libgromacs5 & gromacs & GROMACS molecular dynamics sim, shared libraries & gromacs\cite{gromacs} \\
libgromacs5 & gromacs & GROMACS molecular dynamics sim, shared libraries & gromacs2001\cite{gromacs2001} \\
libgromacs5 & gromacs & GROMACS molecular dynamics sim, shared libraries & gromacs2005\cite{gromacs2005} \\
libgromacs-dev & gromacs & GROMACS molecular dynamics sim, development kit & gromacs\cite{gromacs} \\
libgromacs-dev & gromacs & GROMACS molecular dynamics sim, development kit & gromacs2001\cite{gromacs2001} \\
libgromacs-dev & gromacs & GROMACS molecular dynamics sim, development kit & gromacs2005\cite{gromacs2005} \\
libgwyddion2-0 & gwyddion & libraries for Gwyddion SPM analysis tool & gwyddion\cite{gwyddion} \\
libgwyddion20-dev & gwyddion & header files for Gwyddion SPM analysis tool & gwyddion\cite{gwyddion} \\
libgwyddion20-doc & gwyddion & HTML library API documentation for Gwyddion SPM analysis tool & gwyddion\cite{gwyddion} \\
libgyoto0 & gyoto & General relativistic geodesic integration and ray-tracing & gyoto\cite{gyoto} \\
libgyoto0-dev & gyoto & development files for libgyoto & gyoto\cite{gyoto} \\
libgyoto2 & gyoto & General relativistic geodesic integration and ray-tracing & gyoto\cite{gyoto} \\
libgyoto2-dev & gyoto & development files for libgyoto & gyoto\cite{gyoto} \\
libgyoto6 & gyoto & Gyoto framework main library an standard plug-in & gyoto\cite{gyoto} \\
libgyoto6-dev & gyoto & development files for libgyoto & gyoto\cite{gyoto} \\
libgyoto7 & gyoto & Gyoto framework main library an standard plug-in & gyoto\cite{gyoto} \\
libgyoto7-dev & gyoto & development files for libgyoto & gyoto\cite{gyoto} \\
libgyoto8 & gyoto & Gyoto framework main library an standard plug-in & gyoto\cite{gyoto} \\
libgyoto8-dev & gyoto & development files for libgyoto & gyoto\cite{gyoto} \\
libhat-trie0 & libhat-trie & HAT-trie, an extremely efficient (space and time) modern variant of tries & libhat-trie\cite{libhat-trie} \\
libhat-trie0 & libhat-trie & HAT-trie, an extremely efficient (space and time) modern variant of tries & libhat-trie2005\cite{libhat-trie2005} \\
libhat-trie-dev & libhat-trie & Development headers and static libraries for HAT-trie library & libhat-trie\cite{libhat-trie} \\
libhat-trie-dev & libhat-trie & Development headers and static libraries for HAT-trie library & libhat-trie2005\cite{libhat-trie2005} \\
libhighgui2.1 & opencv & computer vision GUI library & opencv\cite{opencv} \\
libhighgui2.3 & opencv & computer vision library - libhighgui translation package & opencv\cite{opencv} \\
libhighgui2.4 & opencv & computer vision library - libhighgui translation package & opencv\cite{opencv} \\
libhighgui-dev & opencv & Translation package for libhighgui-dev & opencv\cite{opencv} \\
libhmmer2-dev & hmmer2 & profile hidden Markov models for protein sequence analysis (devel) & hmmer2\cite{hmmer2} \\
libhmsbeagle1 & libhmsbeagle & High-performance lib for Bayesian and Maximum Likelihood phylogenetics & libhmsbeagle\cite{libhmsbeagle} \\
libhmsbeagle1v5 & libhmsbeagle & High-performance lib for Bayesian and Maximum Likelihood phylogenetics & libhmsbeagle\cite{libhmsbeagle} \\
libhmsbeagle-dev & libhmsbeagle & High-performance lib for Bayesian and Maximum Likelihood phylogenetics (devel) & libhmsbeagle\cite{libhmsbeagle} \\
libhmsbeagle-java & libhmsbeagle & High-performance lib for Bayesian and Maximum Likelihood phylogenetics (java) & libhmsbeagle\cite{libhmsbeagle} \\
libhts1 & htslib & C library for high-throughput sequencing data formats & htslib\cite{htslib} \\
libhts2 & htslib & C library for high-throughput sequencing data formats & htslib\cite{htslib} \\
libhts3 & htslib & C library for high-throughput sequencing data formats & htslib\cite{htslib} \\
libhts-dev & htslib & development files for the HTSlib & htslib\cite{htslib} \\
libhts-private-dev & htslib & private development files for the HTSlib (use with care) & htslib\cite{htslib} \\
libij-java & imagej & Java library for ImageJ & imagej\cite{imagej} \\
libij-java-doc & imagej & documentation of libij-java & imagej\cite{imagej} \\
libinhomog0 & inhomog & shared library for kin.backreaction/average scale factor & inhomog\cite{inhomog} \\
libinhomog-dev & inhomog & static library for kin.backreaction/average scale factor & inhomog\cite{inhomog} \\
libisospec++1 & isospec & Isotopic fine structure calculator (C++ runtime) & isospec\cite{isospec} \\
libisospec++2 & isospec & Isotopic fine structure calculator (C++ runtime) & isospec\cite{isospec} \\
libisospec++-dev & isospec & Isotopic fine structure calculator (C++ development files) & isospec\cite{isospec} \\
libisospec++-doc & isospec & Isotopic fine structure calculator (C++ API documentation) & isospec\cite{isospec} \\
libjava-gmsh2 & gmsh & Three-dimensional finite element mesh generator. Java wrapper & gmsh\cite{gmsh} \\
libjellyfish-2.0-2 & jellyfish & count k-mers in DNA sequences (dynamic library of jellyfish) & jellyfish\cite{jellyfish} \\
libjellyfish-2.0-dev & jellyfish & count k-mers in DNA sequences (development files of jellyfish) & jellyfish\cite{jellyfish} \\
libjellyfish-perl & jellyfish & count k-mers in DNA sequences (Perl bindings of jellyfish) & jellyfish\cite{jellyfish} \\
libjloda-java & libjloda-java & Java library of data structures and algorithms for bioinformatics & libjloda-java\cite{libjloda-java} \\
libjmol-java & jmol & Java library for molecular structures & jmol\cite{jmol} \\
libjmol-java-doc & jmol & API documentation for libjmol-java & jmol\cite{jmol} \\
libjs-jquery-datatables & datatables.js & jQuery plug-in that makes nice tables from different data sources & datatables-js\cite{datatables-js} \\
libjung-free-java & libjung-free-java & Java Universal Network/Graph Framework & libjung-free-java\cite{libjung-free-java} \\
libjung-free-java-doc & libjung-free-java & Java Universal Network/Graph Framework (documentation) & libjung-free-java\cite{libjung-free-java} \\
libkmc-dev & kmc & library to access KMC k-mer count files & kmc\cite{kmc} \\
libkmer-dev & kmer & suite of tools for DNA sequence analysis (development lib) & kmer\cite{kmer} \\
libkmer-dev & kmer & suite of tools for DNA sequence analysis (development lib) & kmer2004\cite{kmer2004} \\
libm4ri-0.0.20080521 & libm4ri & Method of the Four Russians Inversion library, shared library & libm4ri\cite{libm4ri} \\
libm4ri-0.0.20140914 & libm4ri & Method of the Four Russians Inversion library, shared library & libm4ri\cite{libm4ri} \\
libm4ri-0.0.20140914-dbg & libm4ri & debugging symbols for libm4ri-0.0.20140914 & libm4ri\cite{libm4ri} \\
libm4ri-0.0.20200125 & libm4ri & Method of the Four Russians Inversion library, shared library & libm4ri\cite{libm4ri} \\
libm4ri-dev & libm4ri & Method of the Four Russians Inversion library, development files & libm4ri\cite{libm4ri} \\
libm4rie-0.0.20140914 & libm4rie & extended Method of the Four Russians Inversion library, shared library & libm4rie\cite{libm4rie} \\
libm4rie-0.0.20140914-dbg & libm4rie & debugging symbols for libm4rie-0.0.20140914 & libm4rie\cite{libm4rie} \\
libm4rie-0.0.20150908 & libm4rie & extended Method of the Four Russians Inversion library, shared library & libm4rie\cite{libm4rie} \\
libm4rie-0.0.20200125 & libm4rie & extended Method of the Four Russians Inversion library, shared library & libm4rie\cite{libm4rie} \\
libm4rie-dev & libm4rie & extended Method of the Four Russians Inversion library, development files & libm4rie\cite{libm4rie} \\
libmash-dev & mash & development headers and static library for Mash & mash\cite{mash} \\
libmathicgb0 & mathicgb & Compute Groebner bases (runtime library) & mathicgb\cite{mathicgb} \\
libmathicgb-dev & mathicgb & Compute Groebner bases (developer tools) & mathicgb\cite{mathicgb} \\
libmaxflow0 & maxflow & This library provides the maxflow-mincut algorithm & maxflow\cite{maxflow} \\
libmaxflow0 & maxflow & This library provides the maxflow-mincut algorithm & maxflow2005\cite{maxflow2005} \\
libmaxflow0-dbg & maxflow & Debug information for the maxflow-mincut algorithm & maxflow\cite{maxflow} \\
libmaxflow0-dbg & maxflow & Debug information for the maxflow-mincut algorithm & maxflow2005\cite{maxflow2005} \\
libmaxflow-dev & maxflow & Development files for the maxflow-mincut algorithm & maxflow\cite{maxflow} \\
libmaxflow-dev & maxflow & Development files for the maxflow-mincut algorithm & maxflow2005\cite{maxflow2005} \\
libmeryl-dev & kmer & in- and out-of-core kmer counting and utilities (development lib) & kmer\cite{kmer} \\
libmeryl-dev & kmer & in- and out-of-core kmer counting and utilities (development lib) & kmer2004\cite{kmer2004} \\
libmia-2.2-0 & mia & library for 2D and 3D gray scale image processing & mia\cite{mia} \\
libmia-2.2-0-dbg & mia & Debug information for the MIA library & mia\cite{mia} \\
libmia-2.2-dev & mia & library for 2D and 3D gray scale image processing, development files & mia\cite{mia} \\
libmia-2.2-doc & mia & library for 2D and 3D gray scale image processing, documentation & mia\cite{mia} \\
libmia-2.4-0 & mia & library for 2D and 3D gray scale image processing & mia\cite{mia} \\
libmia-2.4-4 & mia & library for 2D and 3D gray scale image processing & mia\cite{mia} \\
libmia-2.4-dev & mia & library for 2D and 3D gray scale image processing, development files & mia\cite{mia} \\
libmia-2.4-doc & mia & library for 2D and 3D gray scale image processing, documentation & mia\cite{mia} \\
libmialm3 & libmialm & Landmark handling for the MIA tool chain & libmialm\cite{libmialm} \\
libmialm3-dbg & libmialm & Debug information  for the MIA landmark library & libmialm\cite{libmialm} \\
libmialm-dev & libmialm & Development files for the MIA landmark library & libmialm\cite{libmialm} \\
libmialm-doc & libmialm & Documentation for the MIA landmark library & libmialm\cite{libmialm} \\
libminimap0 & minimap & library for approximate mapping of long biosequences & minimap\cite{minimap} \\
libminimap2-dev & minimap2 & development headers for libminimap & minimap2\cite{minimap2} \\
libminimap-dev & minimap & development headers for libminimap & minimap\cite{minimap} \\
libmodhmm0 & libpsortb & library for constructing, training and scoring hidden Markov models & libpsortb\cite{libpsortb} \\
libmodhmm-dev & libpsortb & library for constructing, training and scoring hidden Markov models (dev) & libpsortb\cite{libpsortb} \\
libmsnumpress1 & libmsnumpress & Numeric data compression for mass spectrometry (runtime) & libmsnumpress\cite{libmsnumpress} \\
libmsnumpress-dev & libmsnumpress & Numeric data compression for mass spectrometry (devel files) & libmsnumpress\cite{libmsnumpress} \\
libncl1 & libncl & NEXUS Class Library & libncl\cite{libncl} \\
libncl2 & libncl & NEXUS Class Library & libncl\cite{libncl} \\
libncl-dev & libncl & NEXUS Class Library (static lib and header files) & libncl\cite{libncl} \\
libnfft3-1 & nfft & Library for computing Non-uniform Fast Fourier Transforms & nfft\cite{nfft} \\
libnfft3-2 & nfft & library for computing non-uniform Fourier transforms & nfft\cite{nfft} \\
libnfft3-dbg & nfft & Library for computing Non-uniform Fast Fourier Transforms - debug symbols & nfft\cite{nfft} \\
libnfft3-dev & nfft & development files for the NFFT library & nfft\cite{nfft} \\
libnfft3-doc & nfft & documentation for the NFFT library & nfft\cite{nfft} \\
libnfft3-double2 & nfft & library for computing non-uniform Fourier transforms (double precision) & nfft\cite{nfft} \\
libnfft3-long2 & nfft & library for computing non-uniform Fourier transforms (long-double precision) & nfft\cite{nfft} \\
libnfft3-single2 & nfft & library for computing non-uniform Fourier transforms (single precision) & nfft\cite{nfft} \\
libnucleotidelikelihoodcore0 & beast-mcmc & implementation of LikelihoodCore for nucleotides used by beast-mcmc & beast-mcmc\cite{beast-mcmc} \\
libnucleus6 & emboss & EMBOSS library for molecular sequence analysis & emboss\cite{emboss} \\
libnucleus6-dev & emboss & development files for libnucleus & emboss\cite{emboss} \\
liboakleaf0 & oakleaf & Robust statistical estimates library (run-time support) & oakleaf\cite{oakleaf} \\
liboakleaf-dev & oakleaf & Robust statistical estimates library (development) & oakleaf\cite{oakleaf} \\
liboakleaf-doc & oakleaf & Robust statistical estimates library (documentation) & oakleaf\cite{oakleaf} \\
liboctave1 & octave & Shared libraries of the GNU Octave language & octave\cite{octave} \\
liboctave2 & octave & Shared libraries of the GNU Octave language & octave\cite{octave} \\
liboctave3v5 & octave & Shared libraries of the GNU Octave language & octave\cite{octave} \\
liboctave6 & octave & shared libraries of the GNU Octave language & octave\cite{octave} \\
liboctave7 & octave & shared libraries of the GNU Octave language & octave\cite{octave} \\
liboctave-dev & octave & development files for the GNU Octave language & octave\cite{octave} \\
libopencv2.4-java & opencv & Java bindings for the computer vision library & opencv\cite{opencv} \\
libopencv2.4-jni & opencv & Java jni library for the computer vision library & opencv\cite{opencv} \\
libopencv3.2-java & opencv & Java bindings for the computer vision library & opencv\cite{opencv} \\
libopencv3.2-jni & opencv & Java jni library for the computer vision library & opencv\cite{opencv} \\
libopencv4.1-jni & opencv & Java jni library for the computer vision library & opencv\cite{opencv} \\
libopencv4.2-java & opencv & Java bindings for the computer vision library & opencv\cite{opencv} \\
libopencv4.2-jni & opencv & Java jni library for the computer vision library & opencv\cite{opencv} \\
libopencv-calib3d2.3 & opencv & computer vision Camera Calibration library & opencv\cite{opencv} \\
libopencv-calib3d2.4 & opencv & computer vision Camera Calibration library & opencv\cite{opencv} \\
libopencv-calib3d2.4v5 & opencv & computer vision Camera Calibration library & opencv\cite{opencv} \\
libopencv-calib3d3.2 & opencv & computer vision Camera Calibration library & opencv\cite{opencv} \\
libopencv-calib3d4.1 & opencv & computer vision Camera Calibration library & opencv\cite{opencv} \\
libopencv-calib3d4.2 & opencv & computer vision Camera Calibration library & opencv\cite{opencv} \\
libopencv-calib3d-dev & opencv & development files for libopencv-calib3d4.2 & opencv\cite{opencv} \\
libopencv-contrib2.3 & opencv & computer vision contrib library & opencv\cite{opencv} \\
libopencv-contrib2.4 & opencv & computer vision contrib library & opencv\cite{opencv} \\
libopencv-contrib2.4v5 & opencv & computer vision contrib library & opencv\cite{opencv} \\
libopencv-contrib3.2 & opencv & computer vision contrlib library & opencv\cite{opencv} \\
libopencv-contrib4.1 & opencv & computer vision contrlib library & opencv\cite{opencv} \\
libopencv-contrib4.2 & opencv & computer vision contrlib library & opencv\cite{opencv} \\
libopencv-contrib-dev & opencv & development files for libopencv-contrib4.2 & opencv\cite{opencv} \\
libopencv-core2.3 & opencv & computer vision core library & opencv\cite{opencv} \\
libopencv-core2.4 & opencv & computer vision core library & opencv\cite{opencv} \\
libopencv-core2.4v5 & opencv & computer vision core library & opencv\cite{opencv} \\
libopencv-core3.2 & opencv & computer vision core library & opencv\cite{opencv} \\
libopencv-core4.1 & opencv & computer vision core library & opencv\cite{opencv} \\
libopencv-core4.2 & opencv & computer vision core library & opencv\cite{opencv} \\
libopencv-core-dev & opencv & development files for libopencv-core4.2 & opencv\cite{opencv} \\
libopencv-dev & opencv & development files for opencv & opencv\cite{opencv} \\
libopencv-dnn4.1 & opencv & computer vision Deep neural network module & opencv\cite{opencv} \\
libopencv-dnn4.2 & opencv & computer vision Deep neural network module & opencv\cite{opencv} \\
libopencv-dnn-dev & opencv & development files for libopencv-dnn4.2 & opencv\cite{opencv} \\
libopencv-features2d2.3 & opencv & computer vision Feature Detection and Descriptor Extraction library & opencv\cite{opencv} \\
libopencv-features2d2.4 & opencv & computer vision Feature Detection and Descriptor Extraction library & opencv\cite{opencv} \\
libopencv-features2d2.4v5 & opencv & computer vision Feature Detection and Descriptor Extraction library & opencv\cite{opencv} \\
libopencv-features2d3.2 & opencv & computer vision Feature Detection and Descriptor Extraction library & opencv\cite{opencv} \\
libopencv-features2d4.1 & opencv & computer vision Feature Detection and Descriptor Extraction library & opencv\cite{opencv} \\
libopencv-features2d4.2 & opencv & computer vision Feature Detection and Descriptor Extraction library & opencv\cite{opencv} \\
libopencv-features2d-dev & opencv & development files for libopencv-features2d4.2 & opencv\cite{opencv} \\
libopencv-flann2.3 & opencv & computer vision Clustering and Search in Multi-Dimensional spaces library & opencv\cite{opencv} \\
libopencv-flann2.4 & opencv & computer vision Clustering and Search in Multi-Dimensional spaces library & opencv\cite{opencv} \\
libopencv-flann2.4v5 & opencv & computer vision Clustering and Search in Multi-Dimensional spaces library & opencv\cite{opencv} \\
libopencv-flann3.2 & opencv & computer vision Clustering and Search in Multi-Dimensional spaces library & opencv\cite{opencv} \\
libopencv-flann4.1 & opencv & computer vision Clustering and Search in Multi-Dimensional spaces library & opencv\cite{opencv} \\
libopencv-flann4.2 & opencv & computer vision Clustering and Search in Multi-Dimensional spaces library & opencv\cite{opencv} \\
libopencv-flann-dev & opencv & development files for libopencv-flann4.2 & opencv\cite{opencv} \\
libopencv-gpu2.3 & opencv & computer vision GPU Processing library & opencv\cite{opencv} \\
libopencv-gpu2.4 & opencv & computer vision GPU library & opencv\cite{opencv} \\
libopencv-gpu2.4v5 & opencv & computer vision GPU library & opencv\cite{opencv} \\
libopencv-gpu-dev & opencv & development files for libopencv-gpu2.4v5 & opencv\cite{opencv} \\
libopencv-highgui2.3 & opencv & computer vision High-level GUI and Media I/O library & opencv\cite{opencv} \\
libopencv-highgui2.4 & opencv & computer vision High-level GUI and Media I/O library & opencv\cite{opencv} \\
libopencv-highgui2.4-deb0 & opencv & computer vision High-level GUI and Media I/O library & opencv\cite{opencv} \\
libopencv-highgui3.2 & opencv & computer vision High-level GUI and Media I/O library & opencv\cite{opencv} \\
libopencv-highgui4.1 & opencv & computer vision High-level GUI and Media I/O library & opencv\cite{opencv} \\
libopencv-highgui4.2 & opencv & computer vision High-level GUI and Media I/O library & opencv\cite{opencv} \\
libopencv-highgui-dev & opencv & development files for libopencv-highgui4.2 & opencv\cite{opencv} \\
libopencv-imgcodecs3.2 & opencv & computer vision Image Codecs library & opencv\cite{opencv} \\
libopencv-imgcodecs4.1 & opencv & computer vision Image Codecs library & opencv\cite{opencv} \\
libopencv-imgcodecs4.2 & opencv & computer vision Image Codecs library & opencv\cite{opencv} \\
libopencv-imgcodecs-dev & opencv & development files for libopencv-imgcodecs4.2 & opencv\cite{opencv} \\
libopencv-imgproc2.3 & opencv & computer vision Image Processing library & opencv\cite{opencv} \\
libopencv-imgproc2.4 & opencv & computer vision Image Processing library & opencv\cite{opencv} \\
libopencv-imgproc2.4v5 & opencv & computer vision Image Processing library & opencv\cite{opencv} \\
libopencv-imgproc3.2 & opencv & computer vision Image Processing library & opencv\cite{opencv} \\
libopencv-imgproc4.1 & opencv & computer vision Image Processing library & opencv\cite{opencv} \\
libopencv-imgproc4.2 & opencv & computer vision Image Processing library & opencv\cite{opencv} \\
libopencv-imgproc-dev & opencv & development files for libopencv-imgproc4.2 & opencv\cite{opencv} \\
libopencv-legacy2.3 & opencv & computer vision legacy library & opencv\cite{opencv} \\
libopencv-legacy2.4 & opencv & computer vision legacy library & opencv\cite{opencv} \\
libopencv-legacy2.4v5 & opencv & computer vision legacy library & opencv\cite{opencv} \\
libopencv-legacy-dev & opencv & development files for libopencv-legacy & opencv\cite{opencv} \\
libopencv-ml2.3 & opencv & computer vision Machine Learning library & opencv\cite{opencv} \\
libopencv-ml2.4 & opencv & computer vision Machine Learning library & opencv\cite{opencv} \\
libopencv-ml2.4v5 & opencv & computer vision Machine Learning library & opencv\cite{opencv} \\
libopencv-ml3.2 & opencv & computer vision Machine Learning library & opencv\cite{opencv} \\
libopencv-ml4.1 & opencv & computer vision Machine Learning library & opencv\cite{opencv} \\
libopencv-ml4.2 & opencv & computer vision Machine Learning library & opencv\cite{opencv} \\
libopencv-ml-dev & opencv & development files for libopencv-ml4.2 & opencv\cite{opencv} \\
libopencv-objdetect2.3 & opencv & computer vision Object Detection library & opencv\cite{opencv} \\
libopencv-objdetect2.4 & opencv & computer vision Object Detection library & opencv\cite{opencv} \\
libopencv-objdetect2.4v5 & opencv & computer vision Object Detection library & opencv\cite{opencv} \\
libopencv-objdetect3.2 & opencv & computer vision Object Detection library & opencv\cite{opencv} \\
libopencv-objdetect4.1 & opencv & computer vision Object Detection library & opencv\cite{opencv} \\
libopencv-objdetect4.2 & opencv & computer vision Object Detection library & opencv\cite{opencv} \\
libopencv-objdetect-dev & opencv & development files for libopencv-objdetect4.2 & opencv\cite{opencv} \\
libopencv-ocl2.4 & opencv & computer vision OpenCL support library & opencv\cite{opencv} \\
libopencv-ocl2.4v5 & opencv & computer vision OpenCL support library & opencv\cite{opencv} \\
libopencv-ocl-dev & opencv & development files for libopencv-ocl2.4v5 & opencv\cite{opencv} \\
libopencv-photo2.4 & opencv & computer vision computational photography library & opencv\cite{opencv} \\
libopencv-photo2.4v5 & opencv & computer vision computational photography library & opencv\cite{opencv} \\
libopencv-photo3.2 & opencv & computer vision computational photography library & opencv\cite{opencv} \\
libopencv-photo4.1 & opencv & computer vision computational photography library & opencv\cite{opencv} \\
libopencv-photo4.2 & opencv & computer vision computational photography library & opencv\cite{opencv} \\
libopencv-photo-dev & opencv & development files for libopencv-photo4.2 & opencv\cite{opencv} \\
libopencv-shape3.2 & opencv & computer vision shape descriptors and matchers library & opencv\cite{opencv} \\
libopencv-shape4.1 & opencv & computer vision shape descriptors and matchers library & opencv\cite{opencv} \\
libopencv-shape4.2 & opencv & computer vision shape descriptors and matchers library & opencv\cite{opencv} \\
libopencv-shape-dev & opencv & development files for libopencv-shape4.2 & opencv\cite{opencv} \\
libopencv-stitching2.4 & opencv & computer vision image stitching library & opencv\cite{opencv} \\
libopencv-stitching2.4v5 & opencv & computer vision image stitching library & opencv\cite{opencv} \\
libopencv-stitching3.2 & opencv & computer vision image stitching library & opencv\cite{opencv} \\
libopencv-stitching4.1 & opencv & computer vision image stitching library & opencv\cite{opencv} \\
libopencv-stitching4.2 & opencv & computer vision image stitching library & opencv\cite{opencv} \\
libopencv-stitching-dev & opencv & development files for libopencv-stitching4.2 & opencv\cite{opencv} \\
libopencv-superres2.4 & opencv & computer vision Super Resolution library & opencv\cite{opencv} \\
libopencv-superres2.4v5 & opencv & computer vision Super Resolution library & opencv\cite{opencv} \\
libopencv-superres3.2 & opencv & computer vision Super Resolution library & opencv\cite{opencv} \\
libopencv-superres4.1 & opencv & computer vision Super Resolution library & opencv\cite{opencv} \\
libopencv-superres4.2 & opencv & computer vision Super Resolution library & opencv\cite{opencv} \\
libopencv-superres-dev & opencv & development files for libopencv-superres4.2 & opencv\cite{opencv} \\
libopencv-ts2.4 & opencv & computer vision ts library & opencv\cite{opencv} \\
libopencv-ts2.4v5 & opencv & computer vision ts library & opencv\cite{opencv} \\
libopencv-ts-dev & opencv & development files for TS library of OpenCV (Open Computer Vision) & opencv\cite{opencv} \\
libopencv-video2.3 & opencv & computer vision Video analysis library & opencv\cite{opencv} \\
libopencv-video2.4 & opencv & computer vision Video analysis library & opencv\cite{opencv} \\
libopencv-video2.4v5 & opencv & computer vision Video analysis library & opencv\cite{opencv} \\
libopencv-video3.2 & opencv & computer vision Video analysis library & opencv\cite{opencv} \\
libopencv-video4.1 & opencv & computer vision Video analysis library & opencv\cite{opencv} \\
libopencv-video4.2 & opencv & computer vision Video analysis library & opencv\cite{opencv} \\
libopencv-video-dev & opencv & development files for libopencv-video4.2 & opencv\cite{opencv} \\
libopencv-videoio3.2 & opencv & computer vision Video I/O library & opencv\cite{opencv} \\
libopencv-videoio4.1 & opencv & computer vision Video I/O library & opencv\cite{opencv} \\
libopencv-videoio4.2 & opencv & computer vision Video I/O library & opencv\cite{opencv} \\
libopencv-videoio-dev & opencv & development files for libopencv-videoio4.2 & opencv\cite{opencv} \\
libopencv-videostab2.4 & opencv & computer vision video stabilization library & opencv\cite{opencv} \\
libopencv-videostab2.4v5 & opencv & computer vision video stabilization library & opencv\cite{opencv} \\
libopencv-videostab3.2 & opencv & computer vision video stabilization library & opencv\cite{opencv} \\
libopencv-videostab4.1 & opencv & computer vision video stabilization library & opencv\cite{opencv} \\
libopencv-videostab4.2 & opencv & computer vision video stabilization library & opencv\cite{opencv} \\
libopencv-videostab-dev & opencv & development files for libopencv-videostab4.2 & opencv\cite{opencv} \\
libopencv-viz3.2 & opencv & computer vision 3D data visualization library & opencv\cite{opencv} \\
libopencv-viz4.1 & opencv & computer vision 3D data visualization library & opencv\cite{opencv} \\
libopencv-viz4.2 & opencv & computer vision 3D data visualization library & opencv\cite{opencv} \\
libopencv-viz-dev & opencv & development files for libopencv-viz4.2 & opencv\cite{opencv} \\
libopengm-bin & opengm & command line tools for OpenGM & opengm\cite{opengm} \\
libopengm-dev & opengm & C++ template library for discrete factor graph models & opengm\cite{opengm} \\
libopengm-doc & opengm & documentation and examples for OpenGM & opengm\cite{opengm} \\
libopenmeeg1 & openmeeg & library for solving EEG and MEG forward and inverse problems & openmeeg\cite{openmeeg} \\
libopenmeeg-dev & openmeeg & openmeeg library -- development files & openmeeg\cite{openmeeg} \\
libopenms1.11 & openms & library for LC/MS data management and analysis - runtime & openms\cite{openms} \\
libopenms2.4.0 & openms & library for LC/MS data management and analysis - runtime & openms\cite{openms} \\
libopenms-dev & openms & library for LC/MS data management and analysis - dev files & openms\cite{openms} \\
libopensurgsim & opensurgsim & Free platform for surgical simulation - runtime & opensurgsim\cite{opensurgsim} \\
libopensurgsim-dev & opensurgsim & Free platform for surgical simulation - development & opensurgsim\cite{opensurgsim} \\
liborthancclient0.8 & orthanc & Orthanc Client runtime library & orthanc\cite{orthanc} \\
liborthancclient-dev & orthanc & Orthanc Client development files & orthanc\cite{orthanc} \\
liborthancclient-doc & orthanc & Orthanc Client documentation & orthanc\cite{orthanc} \\
liboxli1 & khmer & in-memory DNA sequence analysis library from the khmer project & khmer\cite{khmer} \\
liboxli1 & khmer & in-memory DNA sequence analysis library from the khmer project & khmer2008\cite{khmer2008} \\
liboxli1 & khmer & in-memory DNA sequence analysis library from the khmer project & khmer2012\cite{khmer2012} \\
liboxli1 & khmer & in-memory DNA sequence analysis library from the khmer project & khmer2012c\cite{khmer2012c} \\
liboxli1 & khmer & in-memory DNA sequence analysis library from the khmer project & khmer2014\cite{khmer2014} \\
liboxli1 & khmer & in-memory DNA sequence analysis library from the khmer project & khmer2015\cite{khmer2015} \\
liboxli-dev & khmer & in-memory DNA sequence analysis dev library & khmer\cite{khmer} \\
liboxli-dev & khmer & in-memory DNA sequence analysis dev library & khmer2008\cite{khmer2008} \\
liboxli-dev & khmer & in-memory DNA sequence analysis dev library & khmer2012\cite{khmer2012} \\
liboxli-dev & khmer & in-memory DNA sequence analysis dev library & khmer2012c\cite{khmer2012c} \\
liboxli-dev & khmer & in-memory DNA sequence analysis dev library & khmer2014\cite{khmer2014} \\
liboxli-dev & khmer & in-memory DNA sequence analysis dev library & khmer2015\cite{khmer2015} \\
libpal-java & libpal-java & Phylogenetic Analysis Library & libpal-java\cite{libpal-java} \\
libpal-java-doc & libpal-java & Phylogenetic Analysis Library - documentation & libpal-java\cite{libpal-java} \\
libpapyrus3-dev & papyrus & DICOM compatible file format library & papyrus\cite{papyrus} \\
libpgsbox5 & wcslib & Draw and label curvilinear coordinate grids with pgplot & wcslib\cite{wcslib} \\
libpgsbox6 & wcslib & Draw and label curvilinear coordinate grids with pgplot & wcslib\cite{wcslib} \\
libpgsbox7 & wcslib & Draw and label curvilinear coordinate grids with pgplot & wcslib\cite{wcslib} \\
libpll0 & libpll & Phylogenetic Likelihood Library & libpll\cite{libpll} \\
libpll-dev & libpll & Phylogenetic Likelihood Library (development) & libpll\cite{libpll} \\
libpurify2.0 & purify & Routines for radio interferometric imaging (shared lib) & purify\cite{purify} \\
libpurify-dev & purify & Routines for radio interferometric imaging (development files) & purify\cite{purify} \\
libpwiz3 & libpwiz & library to perform proteomics data analyses (runtime) & libpwiz\cite{libpwiz} \\
libpwiz-dev & libpwiz & library to perform proteomics data analyses (devel files) & libpwiz\cite{libpwiz} \\
libpwiz-doc & libpwiz & set of programs to perform proteomics data analyses (doc) & libpwiz\cite{libpwiz} \\
libpwiz-tools & libpwiz & ProteoWizard command line tools & libpwiz\cite{libpwiz} \\
libqsopt-ex2 & qsopt-ex & Exact linear programming solver -- shared library & qsopt-ex\cite{qsopt-ex} \\
libqsopt-ex-dev & qsopt-ex & Exact linear programming solver -- development files & qsopt-ex\cite{qsopt-ex} \\
libqtpropertybrowser3 & camitk & Qt Property Browser Library - runtime & camitk\cite{camitk} \\
libqtpropertybrowser3-dev & camitk & Qt Property Browser Library - development & camitk\cite{camitk} \\
libqtpropertybrowser4 & camitk & Qt Property Browser Library - runtime & camitk\cite{camitk} \\
libqtpropertybrowser-dev & camitk & Qt Property Browser Library - development & camitk\cite{camitk} \\
librandom123-dev & librandom123 & parallel random numbers library & librandom123\cite{librandom123} \\
librandom123-doc & librandom123 & documentation and examples of parallel random numbers library & librandom123\cite{librandom123} \\
librelion-1.3-1 & relion & RELION dynnamic library (3D reconstructions in cryo-electron microscopy) & relion\cite{relion} \\
librelion-1.4-1 & relion & RELION dynnamic library (3D reconstructions in cryo-electron microscopy) & relion\cite{relion} \\
librelion-dev & relion & C++ API for RELION (3D reconstructions in cryo-electron microscopy) & relion\cite{relion} \\
librelion-dev-common & relion & C++ API for RELION (3D reconstructions in cryo-electron microscopy) & relion\cite{relion} \\
librelion+gui-1.3-1 & relion & RELION dynnamic library (3D reconstructions in cryo-electron microscopy) & relion\cite{relion} \\
librelion+gui-1.4-1 & relion & RELION dynnamic library (3D reconstructions in cryo-electron microscopy) & relion\cite{relion} \\
librelion+gui-dev & relion & C++ API for RELION (3D reconstructions in cryo-electron microscopy) & relion\cite{relion} \\
librelion+mpi-1.3-1 & relion & RELION dynnamic library (3D reconstructions in cryo-electron microscopy) & relion\cite{relion} \\
librelion+mpi-1.4-1 & relion & RELION dynnamic library (3D reconstructions in cryo-electron microscopy) & relion\cite{relion} \\
librelion+mpi-dev & relion & C++ API for RELION (3D reconstructions in cryo-electron microscopy) & relion\cite{relion} \\
librelion+mpi+gui-1.3-1 & relion & RELION dynnamic library (3D reconstructions in cryo-electron microscopy) & relion\cite{relion} \\
librelion+mpi+gui-1.4-1 & relion & RELION dynnamic library (3D reconstructions in cryo-electron microscopy) & relion\cite{relion} \\
librelion+mpi+gui-dev & relion & C++ API for RELION (3D reconstructions in cryo-electron microscopy) & relion\cite{relion} \\
librsb0 & librsb & recursive sparse blocks matrix computations library & librsb\cite{librsb} \\
librsb-dev & librsb & recursive sparse blocks matrix computations library (development) & librsb\cite{librsb} \\
librsb-doc & librsb & recursive sparse blocks matrix computations library (documentation) & librsb\cite{librsb} \\
libsbml5 & libsbml & System Biology Markup Language library & libsbml\cite{libsbml} \\
libsbml5-cil & libsbml & System Biology Markup Language library - CLI bindings & libsbml\cite{libsbml} \\
libsbml5-cil-doc & libsbml & System Biology Markup Language library -- CLI documentation & libsbml\cite{libsbml} \\
libsbml5-dbg & libsbml & System Biology Markup Language library - debug symbols & libsbml\cite{libsbml} \\
libsbml5-dev & libsbml & System Biology Markup Language library - development files & libsbml\cite{libsbml} \\
libsbml5-doc & libsbml & System Biology Markup Language library -- documentation & libsbml\cite{libsbml} \\
libsbml5-examples & libsbml & System Biology Markup Language library -- example files & libsbml\cite{libsbml} \\
libsbml5-java & libsbml & System Biology Markup Language library - Java bindings & libsbml\cite{libsbml} \\
libsbml5-java-doc & libsbml & System Biology Markup Language library -- Java documentation & libsbml\cite{libsbml} \\
libsbml5-octave & libsbml & System Biology Markup Language library - Octave bindings & libsbml\cite{libsbml} \\
libsbml5-perl & libsbml & System Biology Markup Language library - Perl bindings & libsbml\cite{libsbml} \\
libsbml5-perl-doc & libsbml & System Biology Markup Language library -- Perl documentation & libsbml\cite{libsbml} \\
libsbml5-python & libsbml & System Biology Markup Language library - Python bindings & libsbml\cite{libsbml} \\
libsbml5-python-doc & libsbml & System Biology Markup Language library -- Python documentation & libsbml\cite{libsbml} \\
libsc7 & mpqc & Scientific Computing Toolkit (library) & mpqc\cite{mpqc} \\
libsc7v5 & mpqc & Scientific Computing Toolkit (library) & mpqc\cite{mpqc} \\
libsc-data & mpqc & Scientific Computing Toolkit (basis set and atom data) & mpqc\cite{mpqc} \\
libsc-dev & mpqc & Scientific Computing Toolkit (development files) & mpqc\cite{mpqc} \\
libsc-doc & mpqc & Scientific Computing Toolkit (documentation) & mpqc\cite{mpqc} \\
libseqan2-dev & seqan2 & C++ library for the analysis of biological sequences (development) & seqan2\cite{seqan2} \\
libseqan3-dev & seqan3 & C++ library for the analysis of biological sequences v3 (development) & seqan3\cite{seqan3} \\
libseqlib1 & libseqlib & C++ htslib/bwa-mem/fermi interface for interrogating sequence data & libseqlib\cite{libseqlib} \\
libseqlib-dev & libseqlib & C++ htslib/bwa-mem/fermi interface for interrogating sequence data (dev) & libseqlib\cite{libseqlib} \\
libshark0 & shark & Shark machine learning library & shark\cite{shark} \\
libshark-dev & shark & development files for Shark & shark\cite{shark} \\
libsnp-sites1 & snp-sites & Shared libraries of the package snp-sites & snp-sites\cite{snp-sites} \\
libsnp-sites1-dev & snp-sites & Static libraries and header files for the package snp-sites & snp-sites\cite{snp-sites} \\
libsopt2.0 & sopt & Sparse OPTimisation shared library & sopt\cite{sopt} \\
libsopt3.0 & sopt & Sparse OPTimisation shared library & sopt\cite{sopt} \\
libsopt-dev & sopt & Development package for Sparse OPTimisation library & sopt\cite{sopt} \\
libssm1 & ssm & macromolecular superposition library - runtime & ssm\cite{ssm} \\
libssm1-dbg & ssm & macromolecular superposition library - debug symbols & ssm\cite{ssm} \\
libssm2 & ssm & macromolecular superposition library - runtime & ssm\cite{ssm} \\
libssm-bin & ssm & macromolecular superposition library - binaries & ssm\cite{ssm} \\
libssm-dev & ssm & macromolecular superposition library - development files & ssm\cite{ssm} \\
libssw0 & libssw & fast SIMD parallelized implementation of the Smith-Waterman algorithm & libssw\cite{libssw} \\
libssw-dev & libssw & Development headers and static libraries for libssw & libssw\cite{libssw} \\
libssw-java & libssw & Java bindings for libssw & libssw\cite{libssw} \\
libstarlink-ast0 & starlink-ast & Handle World Coordinate Systems in Astronomy (main shared lib) & starlink-ast\cite{starlink-ast} \\
libstarlink-ast9 & starlink-ast & Handle World Coordinate Systems in Astronomy (main shared lib) & starlink-ast\cite{starlink-ast} \\
libstarlink-ast-dev & starlink-ast & Handle World Coordinate Systems in Astronomy (development package) & starlink-ast\cite{starlink-ast} \\
libstarlink-ast-doc & starlink-ast & Handle World Coordinate Systems in Astronomy (documentation) & starlink-ast\cite{starlink-ast} \\
libstarlink-ast-err0 & starlink-ast & Handle World Coordinate Systems in Astronomy (error reporting) & starlink-ast\cite{starlink-ast} \\
libstarlink-ast-err9 & starlink-ast & Handle World Coordinate Systems in Astronomy (error reporting) & starlink-ast\cite{starlink-ast} \\
libstarlink-ast-grf3d0 & starlink-ast & Handle World Coordinate Systems in Astronomy (dummy 3d routines) & starlink-ast\cite{starlink-ast} \\
libstarlink-ast-grf3d9 & starlink-ast & Handle World Coordinate Systems in Astronomy (dummy 3d routines) & starlink-ast\cite{starlink-ast} \\
libstarlink-pal0 & starlink-pal & Positional Astronomy Library (shared library) & starlink-pal\cite{starlink-pal} \\
libstarlink-pal-dev & starlink-pal & Positional Astronomy Library (development files) & starlink-pal\cite{starlink-pal} \\
libstarlink-pal-doc & starlink-pal & Positional Astronomy Library (documentation) & starlink-pal\cite{starlink-pal} \\
libsvmloc0 & libpsortb & PSORTb adapted library for svm machine-learning library & libpsortb\cite{libpsortb} \\
libsvmloc-dev & libpsortb & PSORTb adapted library for svm machine-learning library (dev) & libpsortb\cite{libpsortb} \\
libtfbs-perl & libtfbs-perl & scanning DNA sequence with a position weight matrix & libtfbs-perl\cite{libtfbs-perl} \\
libtrilinos & trilinos & parallel solver libraries within an object-oriented software framework & trilinos\cite{trilinos} \\
libtrilinos-amesos12 & trilinos & direct sparse solver package - runtime files & trilinos\cite{trilinos} \\
libtrilinos-amesos2-12 & trilinos & next generation direct sparse solver package - runtime files & trilinos\cite{trilinos} \\
libtrilinos-amesos2-dev & trilinos & next generation direct sparse solver package - development files & trilinos\cite{trilinos} \\
libtrilinos-amesos-dev & trilinos & direct sparse solver package - development files & trilinos\cite{trilinos} \\
libtrilinos-anasazi12 & trilinos & large-scale eigenvalue algorithms - runtime files & trilinos\cite{trilinos} \\
libtrilinos-anasazi-dev & trilinos & large-scale eigenvalue algorithms - development files & trilinos\cite{trilinos} \\
libtrilinos-aztecoo12 & trilinos & object-oriented interface to the Aztec solver - runtime files & trilinos\cite{trilinos} \\
libtrilinos-aztecoo-dev & trilinos & object-oriented interface to the Aztec solver - development files & trilinos\cite{trilinos} \\
libtrilinos-belos12 & trilinos & iterative linear solvers - runtime files & trilinos\cite{trilinos} \\
libtrilinos-belos-dev & trilinos & iterative linear solvers - development files & trilinos\cite{trilinos} \\
libtrilinos-dbg & trilinos & parallel solver libraries within an object-oriented software framework & trilinos\cite{trilinos} \\
libtrilinos-dev & trilinos & parallel solver libraries within an object-oriented software framework & trilinos\cite{trilinos} \\
libtrilinos-doc & trilinos & parallel solver libraries within an object-oriented software framework & trilinos\cite{trilinos} \\
libtrilinos-epetra12 & trilinos & basis package for linear algebra - runtime files & trilinos\cite{trilinos} \\
libtrilinos-epetra-dev & trilinos & basis package for linear algebra - development files & trilinos\cite{trilinos} \\
libtrilinos-epetraext12 & trilinos & extensions to the Epetra toolkit - runtime files & trilinos\cite{trilinos} \\
libtrilinos-epetraext-dev & trilinos & extensions to the Epetra toolkit - development files & trilinos\cite{trilinos} \\
libtrilinos-galeri12 & trilinos & generation of distributed linear systems - runtime files & trilinos\cite{trilinos} \\
libtrilinos-galeri-dev & trilinos & generation of distributed linear systems - development files & trilinos\cite{trilinos} \\
libtrilinos-globipack12 & trilinos & 1D globalization capabilities - runtime files & trilinos\cite{trilinos} \\
libtrilinos-globipack-dev & trilinos & 1D globalization capabilities - development files & trilinos\cite{trilinos} \\
libtrilinos-ifpack12 & trilinos & algebraic preconditioners - runtime files & trilinos\cite{trilinos} \\
libtrilinos-ifpack2-12 & trilinos & next generation algebraic preconditioners - runtime files & trilinos\cite{trilinos} \\
libtrilinos-ifpack2-dev & trilinos & next generation algebraic preconditioners - development files & trilinos\cite{trilinos} \\
libtrilinos-ifpack-dev & trilinos & algebraic preconditioners - development files & trilinos\cite{trilinos} \\
libtrilinos-intrepid12 & trilinos & compatible discretizations of PDEs - runtime files & trilinos\cite{trilinos} \\
libtrilinos-intrepid2-12 & trilinos & next generation compatible discretizations of PDEs - runtime files & trilinos\cite{trilinos} \\
libtrilinos-intrepid2-dev & trilinos & next generation compatible discretizations of PDEs - development files & trilinos\cite{trilinos} \\
libtrilinos-intrepid-dev & trilinos & compatible discretizations of PDEs - development files & trilinos\cite{trilinos} \\
libtrilinos-isorropia12 & trilinos & partitioning, load balancing, coloring of sparse matrices - runtime files & trilinos\cite{trilinos} \\
libtrilinos-isorropia-dev & trilinos & partitioning, load balancing, coloring of sparse matrices - development files & trilinos\cite{trilinos} \\
libtrilinos-kokkos12 & trilinos & Trilinos Kokkos programming model - runtime files & trilinos\cite{trilinos} \\
libtrilinos-kokkos-dev & trilinos & Trilinos Kokkos programming model - development files & trilinos\cite{trilinos} \\
libtrilinos-kokkos-kernels12 & trilinos & Kokkos local computational kernels - runtime files & trilinos\cite{trilinos} \\
libtrilinos-kokkos-kernels-dev & trilinos & Kokkos local computational kernels - development files & trilinos\cite{trilinos} \\
libtrilinos-komplex12 & trilinos & complex linear solver package - runtime files & trilinos\cite{trilinos} \\
libtrilinos-komplex-dev & trilinos & complex linear solver package - development files & trilinos\cite{trilinos} \\
libtrilinos-ml12 & trilinos & multigrid preconditioning - runtime files & trilinos\cite{trilinos} \\
libtrilinos-ml-dev & trilinos & multigrid preconditioning - development files & trilinos\cite{trilinos} \\
libtrilinos-moertel12 & trilinos & mortar methods package - runtime files & trilinos\cite{trilinos} \\
libtrilinos-moertel-dev & trilinos & mortar methods package - development files & trilinos\cite{trilinos} \\
libtrilinos-muelu12 & trilinos & next generation multilevel preconditioner capabilities - runtime files & trilinos\cite{trilinos} \\
libtrilinos-muelu-dev & trilinos & next generation multilevel preconditioner capabilities - development files & trilinos\cite{trilinos} \\
libtrilinos-nox12 & trilinos & robust solution of nonlinear equations - runtime files & trilinos\cite{trilinos} \\
libtrilinos-nox-dev & trilinos & robust solution of nonlinear equations - development files & trilinos\cite{trilinos} \\
libtrilinos-optipack12 & trilinos & Trilinos optimization algorithms - runtime files & trilinos\cite{trilinos} \\
libtrilinos-optipack-dev & trilinos & Trilinos optimization algorithms - development files & trilinos\cite{trilinos} \\
libtrilinos-pamgen12 & trilinos & hexahedral and quadrilateral mesh generator - runtime files & trilinos\cite{trilinos} \\
libtrilinos-pamgen-dev & trilinos & hexahedral and quadrilateral mesh generator - development files & trilinos\cite{trilinos} \\
libtrilinos-phalanx12 & trilinos & local field evaluation kernel - runtime files & trilinos\cite{trilinos} \\
libtrilinos-phalanx-dev & trilinos & local field evaluation kernel - development files & trilinos\cite{trilinos} \\
libtrilinos-pike12 & trilinos & physics integration kernels - runtime files & trilinos\cite{trilinos} \\
libtrilinos-pike-dev & trilinos & physics integration kernels - development files & trilinos\cite{trilinos} \\
libtrilinos-piro12 & trilinos & embedded nonlinear analysis package - runtime files & trilinos\cite{trilinos} \\
libtrilinos-piro-dev & trilinos & embedded nonlinear analysis package - development files & trilinos\cite{trilinos} \\
libtrilinos-pliris12 & trilinos & Trilinos dense solvers package - runtime files & trilinos\cite{trilinos} \\
libtrilinos-pliris-dev & trilinos & Trilinos dense solvers package - development files & trilinos\cite{trilinos} \\
libtrilinos-rol12 & trilinos & rapid optimization library - runtime files & trilinos\cite{trilinos} \\
libtrilinos-rol-dev & trilinos & rapid optimization library - development files & trilinos\cite{trilinos} \\
libtrilinos-rtop12 & trilinos & reductions/transformation operators - runtime files & trilinos\cite{trilinos} \\
libtrilinos-rtop-dev & trilinos & reductions/transformation operators - development files & trilinos\cite{trilinos} \\
libtrilinos-rythmos12 & trilinos & Trilinos transient integrator - runtime files & trilinos\cite{trilinos} \\
libtrilinos-rythmos-dev & trilinos & Trilinos transient integrator - development files & trilinos\cite{trilinos} \\
libtrilinos-sacado12 & trilinos & automatic differentiation for C++ applications - runtime files & trilinos\cite{trilinos} \\
libtrilinos-sacado-dev & trilinos & automatic differentiation for C++ applications - development files & trilinos\cite{trilinos} \\
libtrilinos-shards12 & trilinos & interoperability tools for PDE solving - runtime files & trilinos\cite{trilinos} \\
libtrilinos-shards-dev & trilinos & interoperability tools for PDE solving - development files & trilinos\cite{trilinos} \\
libtrilinos-shylu12 & trilinos & solving sparse linear systems - runtime files & trilinos\cite{trilinos} \\
libtrilinos-shylu-dev & trilinos & solving sparse linear systems - development files & trilinos\cite{trilinos} \\
libtrilinos-stokhos12 & trilinos & Trilinos uncertainty quantification package - runtime files & trilinos\cite{trilinos} \\
libtrilinos-stokhos-dev & trilinos & Trilinos uncertainty quantification package - development files & trilinos\cite{trilinos} \\
libtrilinos-stratimikos12 & trilinos & wrappers for linear solvers and preconditioners - runtime files & trilinos\cite{trilinos} \\
libtrilinos-stratimikos-dev & trilinos & wrappers for linear solvers and preconditioners - development files & trilinos\cite{trilinos} \\
libtrilinos-teko12 & trilinos & block preconditioners - runtime files & trilinos\cite{trilinos} \\
libtrilinos-teko-dev & trilinos & block preconditioners - development files & trilinos\cite{trilinos} \\
libtrilinos-teuchos12 & trilinos & common tools for Trilinos - runtime files & trilinos\cite{trilinos} \\
libtrilinos-teuchos-dev & trilinos & common tools for Trilinos - development files & trilinos\cite{trilinos} \\
libtrilinos-thyra12 & trilinos & interoperability layer for numerical software - runtime files & trilinos\cite{trilinos} \\
libtrilinos-thyra-dev & trilinos & interoperability layer for numerical software - development files & trilinos\cite{trilinos} \\
libtrilinos-tpetra12 & trilinos & templated numerical linear algebra package - runtime files & trilinos\cite{trilinos} \\
libtrilinos-tpetra-dev & trilinos & templated numerical linear algebra package - development files & trilinos\cite{trilinos} \\
libtrilinos-trilinoscouplings12 & trilinos & combining Trilinos packages - runtime files & trilinos\cite{trilinos} \\
libtrilinos-trilinoscouplings-dev & trilinos & combining Trilinos packages - development files & trilinos\cite{trilinos} \\
libtrilinos-trilinosss12 & trilinos & suitesparse with adaptations for Amesos - runtime files & trilinos\cite{trilinos} \\
libtrilinos-trilinosss-dev & trilinos & suitesparse with adaptations for Amesos - development files & trilinos\cite{trilinos} \\
libtrilinos-triutils12 & trilinos & utilities for Trilinos - runtime files & trilinos\cite{trilinos} \\
libtrilinos-triutils-dev & trilinos & utilities for Trilinos - development files & trilinos\cite{trilinos} \\
libtrilinos-xpetra12 & trilinos & conversion between Epetra and Teuchos objects - runtime files & trilinos\cite{trilinos} \\
libtrilinos-xpetra-dev & trilinos & conversion between Epetra and Teuchos objects - development files & trilinos\cite{trilinos} \\
libtrilinos-zoltan12 & trilinos & parallel dynamic load balancing - runtime files & trilinos\cite{trilinos} \\
libtrilinos-zoltan2-12 & trilinos & Trilinos next generation load balancing package - runtime files & trilinos\cite{trilinos} \\
libtrilinos-zoltan2-dev & trilinos & Trilinos next generation load balancing package - development files & trilinos\cite{trilinos} \\
libtrilinos-zoltan-dev & trilinos & parallel dynamic load balancing - development files & trilinos\cite{trilinos} \\
libvdjtools-java & vdjtools & Java library of vdjtools & vdjtools\cite{vdjtools} \\
libvisp2.9 & visp & visual servoing library & visp\cite{visp} \\
libvisp2.9 & visp & visual servoing library & visp2018\cite{visp2018} \\
libvisp2.9-dbg & visp & visual servoing library - debugging symbols & visp\cite{visp} \\
libvisp2.9-dbg & visp & visual servoing library - debugging symbols & visp2018\cite{visp2018} \\
libvisp-ar3.1 & visp & visual servoing platform ar library & visp\cite{visp} \\
libvisp-ar3.1 & visp & visual servoing platform ar library & visp2018\cite{visp2018} \\
libvisp-ar3.1-dbg & visp & Debugging symbol for libvisp-ar3.1 & visp\cite{visp} \\
libvisp-ar3.1-dbg & visp & Debugging symbol for libvisp-ar3.1 & visp2018\cite{visp2018} \\
libvisp-ar3.3 & visp & visual servoing platform ar library & visp\cite{visp} \\
libvisp-ar3.3 & visp & visual servoing platform ar library & visp2018\cite{visp2018} \\
libvisp-ar-dev & visp & development files for libvisp-ar & visp\cite{visp} \\
libvisp-ar-dev & visp & development files for libvisp-ar & visp2018\cite{visp2018} \\
libvisp-blob3.1 & visp & visual servoing platform blob tracking library & visp\cite{visp} \\
libvisp-blob3.1 & visp & visual servoing platform blob tracking library & visp2018\cite{visp2018} \\
libvisp-blob3.1-dbg & visp & Debugging symbol for libvisp-blob3.1 & visp\cite{visp} \\
libvisp-blob3.1-dbg & visp & Debugging symbol for libvisp-blob3.1 & visp2018\cite{visp2018} \\
libvisp-blob3.3 & visp & visual servoing platform blob tracking library & visp\cite{visp} \\
libvisp-blob3.3 & visp & visual servoing platform blob tracking library & visp2018\cite{visp2018} \\
libvisp-blob-dev & visp & development files for libvisp-blob & visp\cite{visp} \\
libvisp-blob-dev & visp & development files for libvisp-blob & visp2018\cite{visp2018} \\
libvisp-core3.1 & visp & visual servoing platform core library & visp\cite{visp} \\
libvisp-core3.1 & visp & visual servoing platform core library & visp2018\cite{visp2018} \\
libvisp-core3.1-dbg & visp & Debugging symbol for libvisp-core3.1 & visp\cite{visp} \\
libvisp-core3.1-dbg & visp & Debugging symbol for libvisp-core3.1 & visp2018\cite{visp2018} \\
libvisp-core3.3 & visp & visual servoing platform core library & visp\cite{visp} \\
libvisp-core3.3 & visp & visual servoing platform core library & visp2018\cite{visp2018} \\
libvisp-core-dev & visp & development files for libvisp-core & visp\cite{visp} \\
libvisp-core-dev & visp & development files for libvisp-core & visp2018\cite{visp2018} \\
libvisp-detection3.1 & visp & visual servoing platform detection library & visp\cite{visp} \\
libvisp-detection3.1 & visp & visual servoing platform detection library & visp2018\cite{visp2018} \\
libvisp-detection3.1-dbg & visp & Debugging symbol for libvisp-detection3.1 & visp\cite{visp} \\
libvisp-detection3.1-dbg & visp & Debugging symbol for libvisp-detection3.1 & visp2018\cite{visp2018} \\
libvisp-detection3.3 & visp & visual servoing platform detection library & visp\cite{visp} \\
libvisp-detection3.3 & visp & visual servoing platform detection library & visp2018\cite{visp2018} \\
libvisp-detection-dev & visp & development files for libvisp-detection & visp\cite{visp} \\
libvisp-detection-dev & visp & development files for libvisp-detection & visp2018\cite{visp2018} \\
libvisp-dev & visp & development files for ViSP & visp\cite{visp} \\
libvisp-dev & visp & development files for ViSP & visp2018\cite{visp2018} \\
libvisp-doc & visp & visual servoing library - documentation & visp\cite{visp} \\
libvisp-doc & visp & visual servoing library - documentation & visp2018\cite{visp2018} \\
libvisp-gui3.1 & visp & visual servoing platform gui library & visp\cite{visp} \\
libvisp-gui3.1 & visp & visual servoing platform gui library & visp2018\cite{visp2018} \\
libvisp-gui3.1-dbg & visp & Debugging symbol for libvisp-gui3.1 & visp\cite{visp} \\
libvisp-gui3.1-dbg & visp & Debugging symbol for libvisp-gui3.1 & visp2018\cite{visp2018} \\
libvisp-gui3.3 & visp & visual servoing platform gui library & visp\cite{visp} \\
libvisp-gui3.3 & visp & visual servoing platform gui library & visp2018\cite{visp2018} \\
libvisp-gui-dev & visp & development files for libvisp-gui & visp\cite{visp} \\
libvisp-gui-dev & visp & development files for libvisp-gui & visp2018\cite{visp2018} \\
libvisp-imgproc3.1 & visp & visual servoing platform imgproc library & visp\cite{visp} \\
libvisp-imgproc3.1 & visp & visual servoing platform imgproc library & visp2018\cite{visp2018} \\
libvisp-imgproc3.1-dbg & visp & Debugging symbol for libvisp-imgproc3.1 & visp\cite{visp} \\
libvisp-imgproc3.1-dbg & visp & Debugging symbol for libvisp-imgproc3.1 & visp2018\cite{visp2018} \\
libvisp-imgproc3.3 & visp & visual servoing platform imgproc library & visp\cite{visp} \\
libvisp-imgproc3.3 & visp & visual servoing platform imgproc library & visp2018\cite{visp2018} \\
libvisp-imgproc-dev & visp & development files for libvisp-imgproc & visp\cite{visp} \\
libvisp-imgproc-dev & visp & development files for libvisp-imgproc & visp2018\cite{visp2018} \\
libvisp-io3.1 & visp & visual servoing platform io library & visp\cite{visp} \\
libvisp-io3.1 & visp & visual servoing platform io library & visp2018\cite{visp2018} \\
libvisp-io3.1-dbg & visp & Debugging symbol for libvisp-io3.1 & visp\cite{visp} \\
libvisp-io3.1-dbg & visp & Debugging symbol for libvisp-io3.1 & visp2018\cite{visp2018} \\
libvisp-io3.3 & visp & visual servoing platform io library & visp\cite{visp} \\
libvisp-io3.3 & visp & visual servoing platform io library & visp2018\cite{visp2018} \\
libvisp-io-dev & visp & development files for libvisp-io & visp\cite{visp} \\
libvisp-io-dev & visp & development files for libvisp-io & visp2018\cite{visp2018} \\
libvisp-klt3.1 & visp & visual servoing platform klt tracking library & visp\cite{visp} \\
libvisp-klt3.1 & visp & visual servoing platform klt tracking library & visp2018\cite{visp2018} \\
libvisp-klt3.1-dbg & visp & Debugging symbol for libvisp-klt3.1 & visp\cite{visp} \\
libvisp-klt3.1-dbg & visp & Debugging symbol for libvisp-klt3.1 & visp2018\cite{visp2018} \\
libvisp-klt3.3 & visp & visual servoing platform klt tracking library & visp\cite{visp} \\
libvisp-klt3.3 & visp & visual servoing platform klt tracking library & visp2018\cite{visp2018} \\
libvisp-klt-dev & visp & development files for libvisp-klt & visp\cite{visp} \\
libvisp-klt-dev & visp & development files for libvisp-klt & visp2018\cite{visp2018} \\
libvisp-mbt3.1 & visp & visual servoing platform mbt library & visp\cite{visp} \\
libvisp-mbt3.1 & visp & visual servoing platform mbt library & visp2018\cite{visp2018} \\
libvisp-mbt3.1-dbg & visp & Debugging symbol for libvisp-mbt3.1 & visp\cite{visp} \\
libvisp-mbt3.1-dbg & visp & Debugging symbol for libvisp-mbt3.1 & visp2018\cite{visp2018} \\
libvisp-mbt3.3 & visp & visual servoing platform mbt library & visp\cite{visp} \\
libvisp-mbt3.3 & visp & visual servoing platform mbt library & visp2018\cite{visp2018} \\
libvisp-mbt-dev & visp & development files for libvisp-mbt & visp\cite{visp} \\
libvisp-mbt-dev & visp & development files for libvisp-mbt & visp2018\cite{visp2018} \\
libvisp-me3.1 & visp & visual servoing platform me tracking library & visp\cite{visp} \\
libvisp-me3.1 & visp & visual servoing platform me tracking library & visp2018\cite{visp2018} \\
libvisp-me3.1-dbg & visp & Debugging symbol for libvisp-me3.1 & visp\cite{visp} \\
libvisp-me3.1-dbg & visp & Debugging symbol for libvisp-me3.1 & visp2018\cite{visp2018} \\
libvisp-me3.3 & visp & visual servoing platform me tracking library & visp\cite{visp} \\
libvisp-me3.3 & visp & visual servoing platform me tracking library & visp2018\cite{visp2018} \\
libvisp-me-dev & visp & development files for libvisp-me & visp\cite{visp} \\
libvisp-me-dev & visp & development files for libvisp-me & visp2018\cite{visp2018} \\
libvisp-robot3.1 & visp & visual servoing platform robot library & visp\cite{visp} \\
libvisp-robot3.1 & visp & visual servoing platform robot library & visp2018\cite{visp2018} \\
libvisp-robot3.1-dbg & visp & Debugging symbol for libvisp-robot3.1 & visp\cite{visp} \\
libvisp-robot3.1-dbg & visp & Debugging symbol for libvisp-robot3.1 & visp2018\cite{visp2018} \\
libvisp-robot3.3 & visp & visual servoing platform robot library & visp\cite{visp} \\
libvisp-robot3.3 & visp & visual servoing platform robot library & visp2018\cite{visp2018} \\
libvisp-robot-dev & visp & development files for libvisp-robot & visp\cite{visp} \\
libvisp-robot-dev & visp & development files for libvisp-robot & visp2018\cite{visp2018} \\
libvisp-sensor3.1 & visp & visual servoing platform sensor library & visp\cite{visp} \\
libvisp-sensor3.1 & visp & visual servoing platform sensor library & visp2018\cite{visp2018} \\
libvisp-sensor3.1-dbg & visp & Debugging symbol for libvisp-sensor3.1 & visp\cite{visp} \\
libvisp-sensor3.1-dbg & visp & Debugging symbol for libvisp-sensor3.1 & visp2018\cite{visp2018} \\
libvisp-sensor3.3 & visp & visual servoing platform sensor library & visp\cite{visp} \\
libvisp-sensor3.3 & visp & visual servoing platform sensor library & visp2018\cite{visp2018} \\
libvisp-sensor-dev & visp & development files for libvisp-sensor & visp\cite{visp} \\
libvisp-sensor-dev & visp & development files for libvisp-sensor & visp2018\cite{visp2018} \\
libvisp-tt3.1 & visp & visual servoing platform tt library & visp\cite{visp} \\
libvisp-tt3.1 & visp & visual servoing platform tt library & visp2018\cite{visp2018} \\
libvisp-tt3.1-dbg & visp & Debugging symbol for libvisp-tt3.1 & visp\cite{visp} \\
libvisp-tt3.1-dbg & visp & Debugging symbol for libvisp-tt3.1 & visp2018\cite{visp2018} \\
libvisp-tt3.3 & visp & visual servoing platform tt library & visp\cite{visp} \\
libvisp-tt3.3 & visp & visual servoing platform tt library & visp2018\cite{visp2018} \\
libvisp-tt-dev & visp & development files for libvisp-tt & visp\cite{visp} \\
libvisp-tt-dev & visp & development files for libvisp-tt & visp2018\cite{visp2018} \\
libvisp-tt-mi3.1 & visp & visual servoing platform tt-mi library & visp\cite{visp} \\
libvisp-tt-mi3.1 & visp & visual servoing platform tt-mi library & visp2018\cite{visp2018} \\
libvisp-tt-mi3.1-dbg & visp & Debugging symbol for libvisp-tt-mi3.1 & visp\cite{visp} \\
libvisp-tt-mi3.1-dbg & visp & Debugging symbol for libvisp-tt-mi3.1 & visp2018\cite{visp2018} \\
libvisp-tt-mi3.3 & visp & visual servoing platform tt-mi library & visp\cite{visp} \\
libvisp-tt-mi3.3 & visp & visual servoing platform tt-mi library & visp2018\cite{visp2018} \\
libvisp-tt-mi-dev & visp & development files for libvisp-tt-mi & visp\cite{visp} \\
libvisp-tt-mi-dev & visp & development files for libvisp-tt-mi & visp2018\cite{visp2018} \\
libvisp-vision3.1 & visp & visual servoing platform vision library & visp\cite{visp} \\
libvisp-vision3.1 & visp & visual servoing platform vision library & visp2018\cite{visp2018} \\
libvisp-vision3.1-dbg & visp & Debugging symbol for libvisp-vision3.1 & visp\cite{visp} \\
libvisp-vision3.1-dbg & visp & Debugging symbol for libvisp-vision3.1 & visp2018\cite{visp2018} \\
libvisp-vision3.3 & visp & visual servoing platform vision library & visp\cite{visp} \\
libvisp-vision3.3 & visp & visual servoing platform vision library & visp2018\cite{visp2018} \\
libvisp-vision-dev & visp & development files for libvisp-vision & visp\cite{visp} \\
libvisp-vision-dev & visp & development files for libvisp-vision & visp2018\cite{visp2018} \\
libvisp-visual-features3.1 & visp & visual servoing platform visual-features library & visp\cite{visp} \\
libvisp-visual-features3.1 & visp & visual servoing platform visual-features library & visp2018\cite{visp2018} \\
libvisp-visual-features3.1-dbg & visp & Debugging symbol for libvisp-visual-features3.1 & visp\cite{visp} \\
libvisp-visual-features3.1-dbg & visp & Debugging symbol for libvisp-visual-features3.1 & visp2018\cite{visp2018} \\
libvisp-visual-features3.3 & visp & visual servoing platform visual-features library & visp\cite{visp} \\
libvisp-visual-features3.3 & visp & visual servoing platform visual-features library & visp2018\cite{visp2018} \\
libvisp-visual-features-dev & visp & development files for libvisp-visual-features & visp\cite{visp} \\
libvisp-visual-features-dev & visp & development files for libvisp-visual-features & visp2018\cite{visp2018} \\
libvisp-vs3.1 & visp & visual servoing platform vs library & visp\cite{visp} \\
libvisp-vs3.1 & visp & visual servoing platform vs library & visp2018\cite{visp2018} \\
libvisp-vs3.1-dbg & visp & Debugging symbol for libvisp-vs3.1 & visp\cite{visp} \\
libvisp-vs3.1-dbg & visp & Debugging symbol for libvisp-vs3.1 & visp2018\cite{visp2018} \\
libvisp-vs3.3 & visp & visual servoing platform vs library & visp\cite{visp} \\
libvisp-vs3.3 & visp & visual servoing platform vs library & visp2018\cite{visp2018} \\
libvisp-vs-dev & visp & development files for libvisp-vs & visp\cite{visp} \\
libvisp-vs-dev & visp & development files for libvisp-vs & visp2018\cite{visp2018} \\
libvmtk1.0 & vmtk & runtime libraries for vmtk & vmtk\cite{vmtk} \\
libvmtk1.3 & vmtk & runtime libraries for vmtk & vmtk\cite{vmtk} \\
libvmtk-dev & vmtk & shared links and header files for vmtk & vmtk\cite{vmtk} \\
libvoro++1 & voro++ & library for the computation of the Voronoi diagram (shared library) & voro--\cite{voro--} \\
libvotca-csg2 & votca-csg & VOTCA's coarse-graining library & votca-csg\cite{votca-csg} \\
libvotca-csg2-dev & votca-csg & VOTCA's coarse-graining library, development kit & votca-csg\cite{votca-csg} \\
libvotca-csg3 & votca-csg & VOTCA's coarse-graining library & votca-csg\cite{votca-csg} \\
libvotca-csg5 & votca-csg & VOTCA's coarse-graining library & votca-csg\cite{votca-csg} \\
libvotca-csg6 & votca-csg & VOTCA's coarse-graining library & votca-csg\cite{votca-csg} \\
libvotca-csg-dev & votca-csg & VOTCA's coarse-graining library, development kit & votca-csg\cite{votca-csg} \\
libvotca-tools2 & votca-tools & VOTCA's tools library & votca-tools\cite{votca-tools} \\
libvotca-tools3 & votca-tools & VOTCA's tools library & votca-tools\cite{votca-tools} \\
libvotca-tools5 & votca-tools & VOTCA's tools library & votca-tools\cite{votca-tools} \\
libvotca-tools6 & votca-tools & VOTCA's tools library & votca-tools\cite{votca-tools} \\
libvotca-tools-dev & votca-tools & VOTCA's tools library, development kit & votca-tools\cite{votca-tools} \\
libvtkgdcm2.0 & gdcm & Grassroots DICOM VTK runtime libraries & gdcm\cite{gdcm} \\
libvtkgdcm2.2 & gdcm & Grassroots DICOM VTK runtime libraries & gdcm\cite{gdcm} \\
libvtkgdcm2.4 & gdcm & Grassroots DICOM VTK runtime libraries & gdcm\cite{gdcm} \\
libvtkgdcm2.6 & gdcm & Grassroots DICOM VTK runtime libraries & gdcm\cite{gdcm} \\
libvtkgdcm2.8a & gdcm & Grassroots DICOM VTK runtime libraries & gdcm\cite{gdcm} \\
libvtkgdcm2-dev & gdcm & Grassroots DICOM VTK development libraries and headers & gdcm\cite{gdcm} \\
libvtkgdcm3.0 & gdcm & Grassroots DICOM VTK runtime libraries & gdcm\cite{gdcm} \\
libvtkgdcm-cil & gdcm & Grassroots DICOM VTK CLI bindings & gdcm\cite{gdcm} \\
libvtkgdcm-dev & gdcm & Grassroots DICOM VTK development libraries and headers & gdcm\cite{gdcm} \\
libvtkgdcm-java & gdcm & Grassroots DICOM VTK Java bindings & gdcm\cite{gdcm} \\
libvtkgdcm-tools & gdcm & Grassroots DICOM VTK tools and utilities & gdcm\cite{gdcm} \\
libwcs4 & wcslib & Implementation of the FITS WCS standard & wcslib\cite{wcslib} \\
libwcs5 & wcslib & Implementation of the FITS WCS standard & wcslib\cite{wcslib} \\
libwcs6 & wcslib & Implementation of the FITS WCS standard & wcslib\cite{wcslib} \\
libwcs7 & wcslib & Implementation of the FITS WCS standard & wcslib\cite{wcslib} \\
libwcstools0 & wcstools & Handle the WCS of a FITS image (shared library) & wcstools\cite{wcstools} \\
libwcstools1 & wcstools & Handle the WCS of a FITS image (shared library) & wcstools\cite{wcstools} \\
libwcstools-dev & wcstools & Handle the WCS of a FITS image (development files) & wcstools\cite{wcstools} \\
libwsclean0 & wsclean & Fast generic widefield interferometric imager (shared library) & wsclean\cite{wsclean} \\
libwsclean2 & wsclean & Fast generic widefield interferometric imager (shared library) & wsclean\cite{wsclean} \\
libxc1 & libxc & Library of Exchange-Correlation Functionals & libxc\cite{libxc} \\
libxc4 & libxc & Library of Exchange-Correlation Functionals & libxc\cite{libxc} \\
libxc5 & libxc & Library of Exchange-Correlation Functionals & libxc\cite{libxc} \\
libxc-dev & libxc & Library of Exchange-Correlation Functionals (development files) & libxc\cite{libxc} \\
libxpa1 & xpa & Seamless communication between Unix programs (shared library) & xpa\cite{xpa} \\
libxpa-dev & xpa & Seamless communication between Unix programs (development files) & xpa\cite{xpa} \\
libyade & yade & Platform for discrete element modeling. Libraries & yade\cite{yade} \\
libzerg0 & libzerg & C library for lexically scanning the output of NCBI BLAST programs & libzerg\cite{libzerg} \\
libzerg0-dbg & libzerg & debugging symbols for libzerg & libzerg\cite{libzerg} \\
libzerg0-dev & libzerg & development libraries and header files for libzerg & libzerg\cite{libzerg} \\
libzerg-perl & libzerg-perl & fast perl module for parsing the output of NCBI BLAST programs & libzerg-perl\cite{libzerg-perl} \\
lipsia & lipsia & analysis suite for MRI and fMRI data & lipsia\cite{lipsia} \\
lipsia-doc & lipsia & documentation for LIPSIA & lipsia\cite{lipsia} \\
loki & loki & MCMC linkage analysis on general pedigrees & loki\cite{loki} \\
loki & loki & MCMC linkage analysis on general pedigrees & loki2005\cite{loki2005} \\
loki-doc & loki & MCMC linkage analysis on general pedigrees (PS manual) & loki\cite{loki} \\
loki-doc & loki & MCMC linkage analysis on general pedigrees (PS manual) & loki2005\cite{loki2005} \\
ltrsift & ltrsift & postprocessing and classification of LTR retrotransposons & ltrsift\cite{ltrsift} \\
ltrsift-dbg & ltrsift & postprocessing and classification of LTR retrotransposons, with debug symbols & ltrsift\cite{ltrsift} \\
ltrsift-examples & ltrsift & example data for LTRsift & ltrsift\cite{ltrsift} \\
lua-cnrun & cnrun & NeuroML-capable neuronal network simulator (Lua package) & cnrun\cite{cnrun} \\
macs & macs & Model-based Analysis of ChIP-Seq on short reads sequencers & macs\cite{macs} \\
macsyfinder & macsyfinder & detection of macromolecular systems in protein datasets & macsyfinder\cite{macsyfinder} \\
maffilter & maffilter & process genome alignment in the Multiple Alignment Format & maffilter\cite{maffilter} \\
maffilter-examples & maffilter & process genome alignment in the Multiple Alignment Format (example data) & maffilter\cite{maffilter} \\
mafft & mafft & Multiple alignment program for amino acid or nucleotide sequences & mafft\cite{mafft} \\
mafft & mafft & Multiple alignment program for amino acid or nucleotide sequences & mafft2009\cite{mafft2009} \\
mapdamage & mapdamage & tracking and quantifying damage patterns in ancient DNA sequences & mapdamage\cite{mapdamage} \\
mapsembler2 & mapsembler2 & bioinformatics targeted assembly software & mapsembler2\cite{mapsembler2} \\
maq & maq & maps short fixed-length polymorphic DNA sequence reads to reference sequences & maq\cite{maq} \\
maqview & maqview & graphical read alignment viewer for short gene sequences & maqview\cite{maqview} \\
mash & mash & fast genome and metagenome distance estimation using MinHash & mash\cite{mash} \\
mash-doc & mash & documentation for Mash & mash\cite{mash} \\
massxpert & massxpert & linear polymer mass spectrometry software & massxpert\cite{massxpert} \\
massxpert-data & massxpert & linear polymer mass spectrometry software - arch-indep data & massxpert\cite{massxpert} \\
massxpert-dbg & massxpert & linear polymer mass spectrometry software - debugging symbols & massxpert\cite{massxpert} \\
massxpert-doc & massxpert & Linear polymer mass spectrometry software - manual & massxpert\cite{massxpert} \\
mathicgb & mathicgb & Compute Groebner bases (command line tool) & mathicgb\cite{mathicgb} \\
matlab-gdf & libgdf & IO library for the GDF -- Matlab interface & libgdf\cite{libgdf} \\
maude & maude & high-performance logical framework & maude\cite{maude} \\
mauve-aligner & mauve-aligner & multiple genome alignment & mauve-aligner\cite{mauve-aligner} \\
mcl & mcl & Markov Cluster algorithm & mcl\cite{mcl} \\
mcl-doc & mcl & documentation for mcl & mcl\cite{mcl} \\
melting & melting & compute the melting temperature of nucleic acid duplex & melting\cite{melting} \\
melting-gui & melting & graphical interface to compute the melting temperature of nucleic acid duplex & melting\cite{melting} \\
meryl & kmer & in- and out-of-core kmer counting and utilities & kmer\cite{kmer} \\
meryl & kmer & in- and out-of-core kmer counting and utilities & kmer2004\cite{kmer2004} \\
meshlab & meshlab & System for processing and editing triangular meshes & meshlab\cite{meshlab} \\
metaphlan2 & metaphlan2 & Metagenomic Phylogenetic Analysis & metaphlan2\cite{metaphlan2} \\
metastudent & metastudent & predictor of Gene Ontology terms from protein sequence & metastudent\cite{metastudent} \\
metastudent-data & metastudent-data & predictor of Gene Ontology terms from protein sequence - data files & metastudent-data\cite{metastudent-data} \\
metastudent-data-2 & metastudent-data-2 & predictor of Gene Ontology terms from protein sequence - data \#2 & metastudent-data-2\cite{metastudent-data-2} \\
mgltools-pmv & mgltools-pmv & Python-based Molecular Viewer & mgltools-pmv\cite{mgltools-pmv} \\
mgltools-pmv-test & mgltools-pmv & Python-based Molecular Viewer (functionality tests) & mgltools-pmv\cite{mgltools-pmv} \\
mhap & mhap & locality-sensitive hashing to detect long-read overlaps & mhap\cite{mhap} \\
mia-doctools & mia & Helper scripts for run-time document creation & mia\cite{mia} \\
mialmpick & mialmpick & Tools for landmark picking in 3D volume data sets & mialmpick\cite{mialmpick} \\
mialmpick-dbg & mialmpick & Debug information landmark picking tool mialmpick & mialmpick\cite{mialmpick} \\
mia-tools & mia & Command line tools for gray scale image processing & mia\cite{mia} \\
mia-tools-dbg & mia & Debugging information for the MIA command line tools & mia\cite{mia} \\
mia-tools-doc & mia & Cross-referenced documentation of the MIA command line tools & mia\cite{mia} \\
microbegps & microbegps & explorative taxonomic profiling tool for metagenomic data & microbegps\cite{microbegps} \\
microbiomeutil & microbiomeutil & Microbiome Analysis Utilities & microbiomeutil\cite{microbiomeutil} \\
microbiomeutil-data & microbiomeutil & Reference 16S sequences and NAST-alignments used by microbiomeutil tools & microbiomeutil\cite{microbiomeutil} \\
minia & minia & short-read biological sequence assembler & minia\cite{minia} \\
miniasm & miniasm & ultrafast de novo assembler for long noisy DNA sequencing reads & miniasm\cite{miniasm} \\
minimac4 & minimac4 & Fast Imputation Based on State Space Reduction HMM & minimac4\cite{minimac4} \\
minimac4 & minimac4 & Fast Imputation Based on State Space Reduction HMM & minimac42012\cite{minimac42012} \\
minimac4 & minimac4 & Fast Imputation Based on State Space Reduction HMM & minimac42014\cite{minimac42014} \\
minimap & minimap & tool for approximate mapping of long biosequences such as DNA reads & minimap\cite{minimap} \\
minimap2 & minimap2 & versatile pairwise aligner for genomic and spliced nucleotide sequences & minimap2\cite{minimap2} \\
mipe & mipe & Tools to store PCR-derived data & mipe\cite{mipe} \\
mira-assembler & mira & Whole Genome Shotgun and EST Sequence Assembler & mira\cite{mira} \\
mira-doc & mira & documentation for the mira assembler & mira\cite{mira} \\
mira-examples & mira & files to experiment with the mira assembler & mira\cite{mira} \\
mira-rfam-12s-rrna & mira & extract of RFAM 12 rRNA database & mira\cite{mira} \\
mirtop & mirtop & annotate miRNAs with a standard mirna/isomir naming & mirtop\cite{mirtop} \\
mirtop & mirtop & annotate miRNAs with a standard mirna/isomir naming & mirtop2019\cite{mirtop2019} \\
missfits & missfits & Basic maintenance and packaging tasks on FITS files & missfits\cite{missfits} \\
mlv-smile & mlv-smile & Find statistically significant patterns in sequences & mlv-smile\cite{mlv-smile} \\
mlv-smile & mlv-smile & Find statistically significant patterns in sequences & mlv-smile1999\cite{mlv-smile1999} \\
mlv-smile & mlv-smile & Find statistically significant patterns in sequences & mlv-smile1999d\cite{mlv-smile1999d} \\
mlv-smile & mlv-smile & Find statistically significant patterns in sequences & mlv-smile2000\cite{mlv-smile2000} \\
mmass & mmass & Mass spectrometry tool for proteomics & mmass\cite{mmass} \\
mmass-doc & mmass & Mass spectrometry tool for proteomics - documentation & mmass\cite{mmass} \\
mmass-modules & mmass & Mass spectrometry tool for proteomics - extension modules & mmass\cite{mmass} \\
mmseqs2 & mmseqs2 & ultra fast and sensitive protein search and clustering & mmseqs2\cite{mmseqs2} \\
mmseqs2-examples & mmseqs2 & optional resources for the mmseqs2 package & mmseqs2\cite{mmseqs2} \\
mobyle & mobyle & Web portal that provides web forms for command-line software & mobyle\cite{mobyle} \\
mobyle-utils & mobyle & binary tools used by Mobyle & mobyle\cite{mobyle} \\
mocassin & mocassin & MOnte CArlo SimulationS of Ionised Nebulae & mocassin\cite{mocassin} \\
mocassin-benchmarks & mocassin & benchmarks for the photoionisation code MOCASSIN & mocassin\cite{mocassin} \\
mocassin-data & mocassin & atomic and optical data for the photoionisation code MOCASSIN & mocassin\cite{mocassin} \\
mocassin-examples & mocassin & Examples for the photoionisation code MOCASSIN & mocassin\cite{mocassin} \\
montage & montage & Toolkit for assembling FITS images into mosaics & montage\cite{montage} \\
montage-gridtools & montage & Create files to run montage on the grid & montage\cite{montage} \\
mothur & mothur & sequence analysis suite for research on microbiota & mothur\cite{mothur} \\
mothur-mpi & mothur & mpi-enabled binary for mothur & mothur\cite{mothur} \\
mpgrafic & mpgrafic & MPI version of N-body initial conditions grafic package & mpgrafic\cite{mpgrafic} \\
mpqc & mpqc & Massively Parallel Quantum Chemistry Program & mpqc\cite{mpqc} \\
mpqc-openmpi & mpqc & Massively Parallel Quantum Chemistry Program (OpenMPI transitional package) & mpqc\cite{mpqc} \\
mpqc-support & mpqc & Massively Parallel Quantum Chemistry Program (support tools) & mpqc\cite{mpqc} \\
mptp & mptp & single-locus species delimitation & mptp\cite{mptp} \\
mrbayes & mrbayes & Bayesian Inference of Phylogeny & mrbayes\cite{mrbayes} \\
mrbayes & mrbayes & Bayesian Inference of Phylogeny & mrbayes2001\cite{mrbayes2001} \\
mrbayes & mrbayes & Bayesian Inference of Phylogeny & mrbayes2003\cite{mrbayes2003} \\
mrbayes-dbg & mrbayes & Bayesian Inference of Phylogeny - debug symbols & mrbayes\cite{mrbayes} \\
mrbayes-dbg & mrbayes & Bayesian Inference of Phylogeny - debug symbols & mrbayes2001\cite{mrbayes2001} \\
mrbayes-dbg & mrbayes & Bayesian Inference of Phylogeny - debug symbols & mrbayes2003\cite{mrbayes2003} \\
mrbayes-doc & mrbayes & Bayesian Inference of Phylogeny - manual & mrbayes\cite{mrbayes} \\
mrbayes-doc & mrbayes & Bayesian Inference of Phylogeny - manual & mrbayes2001\cite{mrbayes2001} \\
mrbayes-doc & mrbayes & Bayesian Inference of Phylogeny - manual & mrbayes2003\cite{mrbayes2003} \\
mrbayes-mpi & mrbayes & Bayesian Inference of Phylogeny - mpi version & mrbayes\cite{mrbayes} \\
mrbayes-mpi & mrbayes & Bayesian Inference of Phylogeny - mpi version & mrbayes2001\cite{mrbayes2001} \\
mrbayes-mpi & mrbayes & Bayesian Inference of Phylogeny - mpi version & mrbayes2003\cite{mrbayes2003} \\
mrs & mrs & Information Retrieval System for Biomedical databanks & mrs\cite{mrs} \\
mrtrix & mrtrix & diffusion-weighted MRI white matter tractography & mrtrix\cite{mrtrix} \\
mrtrix3 & mrtrix3 & diffusion-weighted MRI white matter tractography & mrtrix3\cite{mrtrix3} \\
mrtrix3-doc & mrtrix3 & documentation for mrtrix3 & mrtrix3\cite{mrtrix3} \\
mrtrix-doc & mrtrix & documentation for mrtrix & mrtrix\cite{mrtrix} \\
mssstest & mssstest & Normalisation of disease scores for patients with Multiple Sclerosis & mssstest\cite{mssstest} \\
msxpertsuite & msxpertsuite & mass spectrometry software suite - metapackage & msxpertsuite\cite{msxpertsuite} \\
msxpertsuite-massxpert & msxpertsuite & mass spectrometry software suite - massXpert & msxpertsuite\cite{msxpertsuite} \\
msxpertsuite-massxpert-data-doc & msxpertsuite & mass spectrometry software suite - massXpert - data and doc & msxpertsuite\cite{msxpertsuite} \\
msxpertsuite-minexpert & msxpertsuite & mass spectrometry software suite - mineXpert & msxpertsuite\cite{msxpertsuite} \\
msxpertsuite-minexpert-data-doc & msxpertsuite & mass spectrometry software suite - mineXpert - data and doc & msxpertsuite\cite{msxpertsuite} \\
multiqc & multiqc & output integration for RNA sequencing across tools and samples & multiqc\cite{multiqc} \\
mummer & mummer & Efficient sequence alignment of full genomes & mummer\cite{mummer} \\
mummer-doc & mummer & Documentation for MUMmer & mummer\cite{mummer} \\
munipack & munipack & Astronomical photometry software package & munipack\cite{munipack} \\
munipack-cli & munipack & Command line interface of Munipack & munipack\cite{munipack} \\
munipack-core & munipack & Core routines of Munipack & munipack\cite{munipack} \\
munipack-doc & munipack & Documentation of Munipack & munipack\cite{munipack} \\
munipack-gui & munipack & Graphical user interface of Munipack & munipack\cite{munipack} \\
murasaki & murasaki & homology detection tool across multiple large genomes & murasaki\cite{murasaki} \\
murasaki-common & murasaki & homology detection tool across multiple large genomes (common files) & murasaki\cite{murasaki} \\
murasaki-mpi & murasaki & homology detection tool across multiple large genomes (MPI-version) & murasaki\cite{murasaki} \\
muscle & muscle & Multiple alignment program of protein sequences & muscle\cite{muscle} \\
muscle & muscle & Multiple alignment program of protein sequences & muscle2004\cite{muscle2004} \\
mustang & mustang & multiple structural alignment of proteins & mustang\cite{mustang} \\
mustang-testdata & mustang & multiple structural alignment of proteins, test data & mustang\cite{mustang} \\
nanook & nanook & pre- and post-alignment analysis of nanopore sequencing data & nanook\cite{nanook} \\
nast-ier & microbiomeutil & NAST-based DNA alignment tool & microbiomeutil\cite{microbiomeutil} \\
ncbi-cn3d & ncbi-tools6 & 3-dimensional viewer for biological molecules & ncbi-tools6\cite{ncbi-tools6} \\
ncbi-epcr & epcr & Tool to test a DNA sequence for the presence of sequence tagged sites & epcr\cite{epcr} \\
ncbi-epcr & epcr & Tool to test a DNA sequence for the presence of sequence tagged sites & epcr2004\cite{epcr2004} \\
ncbi-seg & ncbi-seg & tool to mask segments of low compositional complexity in amino acid sequences & ncbi-seg\cite{ncbi-seg} \\
ncbi-seg-dbg & ncbi-seg & debug symbols for ncbi-seg & ncbi-seg\cite{ncbi-seg} \\
ncl-tools & libncl & tools to deal with NEXUS files & libncl\cite{libncl} \\
nco & nco & Command-line operators to analyze netCDF files & nco\cite{nco} \\
ncoils & coils & coiled coil secondary structure prediction & coils\cite{coils} \\
neat & neat & Nebular Empirical Analysis Tool & neat\cite{neat} \\
neobio & neobio & computes alignments of amino acid and nucleotide sequences & neobio\cite{neobio} \\
njplot & njplot & phylogenetic tree drawing program & njplot\cite{njplot} \\
norsnet & norsnet & tool to identify unstructured loops in proteins & norsnet\cite{norsnet} \\
norsp & norsp & predictor of non-regular secondary structure & norsp\cite{norsp} \\
nwchem & nwchem & High-performance computational chemistry software & nwchem\cite{nwchem} \\
nwchem-data & nwchem & High-performance computational chemistry software (data files) & nwchem\cite{nwchem} \\
obitools & obitools & programs to analyze NGS data in a DNA metabarcoding context & obitools\cite{obitools} \\
octave & octave & GNU Octave language for numerical computations & octave\cite{octave} \\
octave-biosig & biosig4c++ & Octave bindings for BioSig library & biosig4c--\cite{biosig4c--} \\
octave-common & octave & architecture-independent files for octave & octave\cite{octave} \\
octave-dbg & octave & Debug symbols for octave & octave\cite{octave} \\
octave-divand & octave-divand & n-dimensional interpolation for Octave & octave-divand\cite{octave-divand} \\
octave-doc & octave & documentation of the GNU Octave language & octave\cite{octave} \\
octave-fuzzy-logic-toolkit & octave-fuzzy-logic-toolkit & fuzzy logic toolkit for Octave & octave-fuzzy-logic-toolkit\cite{octave-fuzzy-logic-toolkit} \\
octave-gdf & libgdf & IO library for the GDF -- Octave interface & libgdf\cite{libgdf} \\
octave-gmt & gmt & Support of GMT grid files for Octave & gmt\cite{gmt} \\
octave-gmt & gmt & Support of GMT grid files for Octave & gmt1991\cite{gmt1991} \\
octave-gmt & gmt & Support of GMT grid files for Octave & gmt1995\cite{gmt1995} \\
octave-gmt & gmt & Support of GMT grid files for Octave & gmt1998\cite{gmt1998} \\
octave-htmldoc & octave & transitional package for Octave HTML documentation & octave\cite{octave} \\
octave-info & octave & transitional package for Octave info documentation & octave\cite{octave} \\
octave-interval & octave-interval & real-valued interval arithmetic for Octave & octave-interval\cite{octave-interval} \\
octave-interval-doc & octave-interval & real-valued interval arithmetic for Octave (arch-indep files) & octave-interval\cite{octave-interval} \\
octave-level-set & octave-level-set & level-set toolbox for Octave & octave-level-set\cite{octave-level-set} \\
octave-lssa & octave-lssa & least squares spectral analysis for Octave & octave-lssa\cite{octave-lssa} \\
octave-ltfat & octave-ltfat & Large Time/Frequency Analysis Toolbox & octave-ltfat\cite{octave-ltfat} \\
octave-ltfat-common & octave-ltfat & Large Time/Frequency Analysis Toolbox (arch-indep files) & octave-ltfat\cite{octave-ltfat} \\
octave-nurbs & octave-nurbs & non-uniform rational B-splines for Octave & octave-nurbs\cite{octave-nurbs} \\
octave-nurbs & octave-nurbs & non-uniform rational B-splines for Octave & octave-nurbs2011\cite{octave-nurbs2011} \\
octave-queueing & octave-queueing & Queueing Networks and Markov chains analysis for Octave & octave-queueing\cite{octave-queueing} \\
octave-splines & octave-splines & cubic spline functions for Octave & octave-splines\cite{octave-splines} \\
octave-stk & octave-stk & (not so) Small Toolbox for Kriging & octave-stk\cite{octave-stk} \\
octave-tisean & octave-tisean & nonlinear time series analysis for Octave & octave-tisean\cite{octave-tisean} \\
octave-tisean & octave-tisean & nonlinear time series analysis for Octave & octave-tisean2000,\cite{octave-tisean2000,} \\
octave-tisean & octave-tisean & nonlinear time series analysis for Octave & octave-tisean2004\cite{octave-tisean2004} \\
openbabel & openbabel & Chemical toolbox utilities (cli) & openbabel\cite{openbabel} \\
opencfu & opencfu & count cell colonies (CFUs) on agar plates by processing digital pictures & opencfu\cite{opencfu} \\
opencv-data & opencv & development data for opencv & opencv\cite{opencv} \\
opencv-doc & opencv & OpenCV documentation and examples & opencv\cite{opencv} \\
openmeeg-tools & openmeeg & openmeeg library -- command line tools & openmeeg\cite{openmeeg} \\
openmolcas & openmolcas & Quantum chemistry software package & openmolcas\cite{openmolcas} \\
openmolcas-data & openmolcas & Quantum chemistry software package (data files) & openmolcas\cite{openmolcas} \\
openms & openms & package for LC/MS data management and analysis & openms\cite{openms} \\
openms-common & openms & package for LC/MS data management and analysis - shared data & openms\cite{openms} \\
openms-doc & openms & package for LC/MS data management and analysis - documentation & openms\cite{openms} \\
opensurgsim-doc & opensurgsim & Free platform for surgical simulation - documentation & opensurgsim\cite{opensurgsim} \\
optimir & optimir & Integrating genetic variations in miRNA alignment & optimir\cite{optimir} \\
orthanc & orthanc & Lightweight, RESTful DICOM server for medical imaging & orthanc\cite{orthanc} \\
orthanc-dev & orthanc & Orthanc development files & orthanc\cite{orthanc} \\
orthanc-dicomweb & orthanc-dicomweb & Plugin to extend Orthanc with support of WADO and DICOMweb & orthanc-dicomweb\cite{orthanc-dicomweb} \\
orthanc-doc & orthanc & Documentation of Orthanc & orthanc\cite{orthanc} \\
orthanc-imagej & orthanc-imagej & ImageJ plugin to import images from Orthanc & orthanc-imagej\cite{orthanc-imagej} \\
orthanc-mysql & orthanc-mysql & Plugins to use MySQL or MariaDB as a database back-end to Orthanc & orthanc-mysql\cite{orthanc-mysql} \\
orthanc-postgresql & orthanc-postgresql & Plugins to use PostgreSQL as a database back-end to Orthanc & orthanc-postgresql\cite{orthanc-postgresql} \\
orthanc-python & orthanc-python & Develop plugins for Orthanc using the Python programming language & orthanc-python\cite{orthanc-python} \\
orthanc-webviewer & orthanc-webviewer & Web viewer of medical images for Orthanc & orthanc-webviewer\cite{orthanc-webviewer} \\
orthanc-wsi & orthanc-wsi & Whole-slide imaging support for Orthanc (digital pathology) & orthanc-wsi\cite{orthanc-wsi} \\
otf-symbols-circos & circos & transitional dummy package & circos\cite{circos} \\
pal2nal & pal2nal & converts proteins to genomic DNA alignment & pal2nal\cite{pal2nal} \\
paleomix & paleomix & pipelines and tools for the processing of ancient and modern HTS data & paleomix\cite{paleomix} \\
palp & palp & Package for Analyzing Lattice Polytopes & palp\cite{palp} \\
paml & paml & Phylogenetic Analysis by Maximum Likelihood (PAML) & paml\cite{paml} \\
paml-doc & paml & Documentation for PAML & paml\cite{paml} \\
paraclu & paraclu & Parametric clustering of genomic and transcriptomic features & paraclu\cite{paraclu} \\
parsnp & parsnp & rapid core genome multi-alignment & parsnp\cite{parsnp} \\
patman & patman & rapid alignment of short sequences to large databases & patman\cite{patman} \\
pbhoney & pbsuite & genomic structural variation discovery & pbsuite\cite{pbsuite} \\
pbjelly & pbsuite & genome assembly upgrading tool & pbsuite2012\cite{pbsuite2012} \\
pbsim & pbsim & simulator for PacBio sequencing reads & pbsim\cite{pbsim} \\
pdb2pqr & pdb2pqr & Preparation of protein structures for electrostatics calculations & pdb2pqr\cite{pdb2pqr} \\
pdb2pqr & pdb2pqr & Preparation of protein structures for electrostatics calculations & pdb2pqr2004\cite{pdb2pqr2004} \\
pdb2pqr-doc & pdb2pqr & example files accompanying pdb2pqr & pdb2pqr\cite{pdb2pqr} \\
pdb2pqr-doc & pdb2pqr & example files accompanying pdb2pqr & pdb2pqr2004\cite{pdb2pqr2004} \\
perlprimer & perlprimer & Graphical design of primers for PCR & perlprimer\cite{perlprimer} \\
perlprimer & perlprimer & Graphical design of primers for PCR & perlprimer2007\cite{perlprimer2007} \\
perlprimer-doc & perlprimer & Tutorial to perlprimer & perlprimer\cite{perlprimer} \\
perlprimer-doc & perlprimer & Tutorial to perlprimer & perlprimer2007\cite{perlprimer2007} \\
perm & perm & efficient mapping of short reads with periodic spaced seeds & perm\cite{perm} \\
pftools & pftools & build and search protein and DNA generalized profiles & pftools\cite{pftools} \\
phast & phast & phylogenetic analysis with space/time models & phast\cite{phast} \\
phipack & phipack & PHI test and other tests of recombination & phipack\cite{phipack} \\
php5-gdcm & gdcm & Grassroots DICOM PHP5 bindings & gdcm\cite{gdcm} \\
php5-vtkgdcm & gdcm & Grassroots DICOM VTK PHP bindings & gdcm\cite{gdcm} \\
phybin & phybin & binning/clustering newick trees by topology & phybin\cite{phybin} \\
phyml & phyml & Phylogenetic estimation using Maximum Likelihood & phyml\cite{phyml} \\
phyml & phyml & Phylogenetic estimation using Maximum Likelihood & phyml2003\cite{phyml2003} \\
physamp & physamp & sample sequence alignment corresponding to phylogeny & physamp\cite{physamp} \\
phyutility & phyutility & simple analyses or modifications on both phylogenetic trees and data matrices & phyutility\cite{phyutility} \\
piler & piler & genomic repeat analysis & piler\cite{piler} \\
pilercr & pilercr & software for finding CRISPR repeats & pilercr\cite{pilercr} \\
pilon & pilon & automated genome assembly improvement and variant detection tool & pilon\cite{pilon} \\
pirs & pirs & Profile based Illumina pair-end Reads Simulator & pirs\cite{pirs} \\
pirs-examples & pirs & profile basd Illumina pair-end Reads Simulator (example data) & pirs\cite{pirs} \\
pirs-profiles & pirs & profile basd Illumina pair-end Reads Simulator (profile data) & pirs\cite{pirs} \\
placnet & placnet & Plasmid Constellation Network project & placnet\cite{placnet} \\
plasmidseeker & plasmidseeker & identification of known plasmids from whole-genome sequencing reads & plasmidseeker\cite{plasmidseeker} \\
plast & plast & Parallel Local Sequence Alignment Search Tool & plast\cite{plast} \\
plast-example & plast & Parallel Local Sequence Alignment Search Tool (example data) & plast\cite{plast} \\
plink & plink & whole-genome association analysis toolset & plink\cite{plink} \\
plink1.9 & plink1.9 & whole-genome association analysis toolset & plink1-9\cite{plink1-9} \\
plink2 & plink2 & whole-genome association analysis toolset & plink2\cite{plink2} \\
plip & plip & fully automated protein-ligand interaction profiler & plip\cite{plip} \\
poa & poa & Partial Order Alignment for multiple sequence alignment & poa\cite{poa} \\
poretools & poretools & toolkit for nanopore nucleotide sequencing data & poretools\cite{poretools} \\
poretools-data & poretools & toolkit for nanopore nucleotide sequencing data -- sample datasets & poretools\cite{poretools} \\
pprepair & pprepair & planar partition repair tool & pprepair\cite{pprepair} \\
praat & praat & program for speech analysis and synthesis & praat\cite{praat} \\
prank & prank & Probabilistic Alignment Kit for DNA, codon and amino-acid sequences & prank\cite{prank} \\
predictnls & predictnls & prediction and analysis of protein nuclear localization signals & predictnls\cite{predictnls} \\
predictprotein & predictprotein & suite of protein sequence analysis tools & predictprotein\cite{predictprotein} \\
prepair & prepair & polygon repair tool & prepair\cite{prepair} \\
prepair & prepair & polygon repair tool & prepair2012\cite{prepair2012} \\
prepair-data & prepair & polygon repair tool -- example data & prepair\cite{prepair} \\
prepair-data & prepair & polygon repair tool -- example data & prepair2012\cite{prepair2012} \\
prime-phylo & prime-phylo & bayesian estimation of gene trees taking the species tree into account & prime-phylo\cite{prime-phylo} \\
primer3 & primer3 & tool to design flanking oligo nucleotides for DNA amplification & primer3\cite{primer3} \\
primer3-examples & primer3 & tool to design flanking oligo nucleotides for DNA amplification (examples) & primer3\cite{primer3} \\
prinseq-lite & prinseq-lite & PReprocessing and INformation of SEQuence data (lite version) & prinseq-lite\cite{prinseq-lite} \\
prinseq-lite-examples & prinseq-lite & PReprocessing and INformation of SEQuence data (example data) & prinseq-lite\cite{prinseq-lite} \\
proalign & proalign & Probabilistic multiple alignment program & proalign\cite{proalign} \\
probabel & probabel & Toolset for Genome-Wide Association Analysis & probabel\cite{probabel} \\
probabel-examples & probabel & Example files for ProbABEL & probabel\cite{probabel} \\
probalign & probalign & multiple sequence alignment using partition function posterior probabilities & probalign\cite{probalign} \\
probcons & probcons & PROBabilistic CONSistency-based multiple sequence alignment & probcons\cite{probcons} \\
probcons-extra & probcons & Extra programs from the probcons package & probcons\cite{probcons} \\
proda & proda & multiple alignment of protein sequences & proda\cite{proda} \\
prodigal & prodigal & Microbial (bacterial and archaeal) gene finding program & prodigal\cite{prodigal} \\
profbval & profbval & predictor of flexible/rigid protein residues from sequence & profbval\cite{profbval} \\
profbval & profbval & predictor of flexible/rigid protein residues from sequence & profbval2005\cite{profbval2005} \\
profisis & profisis & prediction of protein-protein interaction sites from sequence & profisis\cite{profisis} \\
profnet-bval & profnet & neural network architecture for profbval & profnet\cite{profnet} \\
profnet-chop & profnet & neural network architecture for profchop & profnet\cite{profnet} \\
profnet-con & profnet & neural network architecture for profcon & profnet\cite{profnet} \\
profnet-dbg & profnet & debug files for profnet packages & profnet\cite{profnet} \\
profnet-isis & profnet & neural network architecture for profisis & profnet\cite{profnet} \\
profnet-md & profnet & neural network architecture for metadisorder & profnet\cite{profnet} \\
profnet-norsnet & profnet & neural network architecture for norsnet & profnet\cite{profnet} \\
profnet-prof & profnet & neural network architecture for profacc & profnet\cite{profnet} \\
profnet-snapfun & profnet & neural network architecture for snapfun & profnet\cite{profnet} \\
profphd & profphd & secondary structure and solvent accessibility predictor & profphd\cite{profphd} \\
profphd & profphd & secondary structure and solvent accessibility predictor & profphd1994\cite{profphd1994} \\
profphd & profphd & secondary structure and solvent accessibility predictor & profphd1995\cite{profphd1995} \\
profphd-net & profnet & neural network architecture for profphd & profnet\cite{profnet} \\
proftmb & proftmb & per-residue prediction of bacterial transmembrane beta barrels & proftmb\cite{proftmb} \\
proftmb-dbg & proftmb & debugging symbols for proftmb & proftmb\cite{proftmb} \\
progressivemauve & progressivemauve & multiple genome alignment algorithms & progressivemauve\cite{progressivemauve} \\
prokka & prokka & rapid annotation of prokaryotic genomes & prokka\cite{prokka} \\
proteinortho & proteinortho & Detection of (Co-)orthologs in large-scale protein analysis & proteinortho\cite{proteinortho} \\
prottest & prottest & selection of best-fit models of protein evolution & prottest\cite{prottest} \\
pscan-chip & pscan-chip & ChIP-based identifcation of TF binding sites & pscan-chip\cite{pscan-chip} \\
pscan-chip-data & pscan-chip & auxiliary data for PScan-ChIP & pscan-chip\cite{pscan-chip} \\
pscan-tfbs & pscan-tfbs & search for transcription factor binding sites & pscan-tfbs\cite{pscan-tfbs} \\
psfex & psfex & Point Spread Function model extractor & psfex\cite{psfex} \\
psi4 & psi4 & Quantum Chemical Program Suite & psi4\cite{psi4} \\
psi4-data & psi4 & Quantum Chemical Program Suite (data files) & psi4\cite{psi4} \\
psortb & psortb & bacterial localization prediction tool & psortb\cite{psortb} \\
psychopy & psychopy & environment for creating psychology stimuli in Python & psychopy\cite{psychopy} \\
purify & purify & Collection of routines for radio interferometric imaging & purify\cite{purify} \\
pybedtools-bin & python-pybedtools & Scripts produced for pybedtools & python-pybedtools\cite{python-pybedtools} \\
pycorrfit & pycorrfit & tool for fitting correlation curves on a logarithmic plot & pycorrfit\cite{pycorrfit} \\
pyfits-utils & pyfits & transitional package for astropy-utils & pyfits\cite{pyfits} \\
pyfr & pyfr & flux reconstruction in Python & pyfr\cite{pyfr} \\
pyfr-doc & pyfr & documentation for PyFR & pyfr\cite{pyfr} \\
pynast & pynast & alignment of short DNA sequences & pynast\cite{pynast} \\
python3-apbslib & apbs & Adaptive Poisson Boltzmann Solver & apbs\cite{apbs} \\
python3-apbslib & apbs & Adaptive Poisson Boltzmann Solver & apbs1993\cite{apbs1993} \\
python3-apbslib & apbs & Adaptive Poisson Boltzmann Solver & apbs1995\cite{apbs1995} \\
python3-apbslib & apbs & Adaptive Poisson Boltzmann Solver & apbs2001\cite{apbs2001} \\
python3-apbslib & apbs & Adaptive Poisson Boltzmann Solver & apbs2003\cite{apbs2003} \\
python3-asdf & python-asdf & Python 3 library for the Advanced Scientific Data Format & python-asdf\cite{python-asdf} \\
python3-astrometry & astrometry.net & Astrometry plate solver (Python package) & astrometry-net\cite{astrometry-net} \\
python3-astroml & astroml & Python 3 Machine Learning library for astronomy & astroml\cite{astroml} \\
python3-astropy & astropy & Core functionality for performing astrophysics with Python & astropy\cite{astropy} \\
python3-astroscrappy & astroscrappy & Optimized Cosmic Ray Annihilation in Python & astroscrappy\cite{astroscrappy} \\
python3-avogadro & avogadrolibs & Molecular Graphics and Modelling System (Python 3 module) & avogadrolibs\cite{avogadrolibs} \\
python3-ball & ball & Python bindings for the Biochemical Algorithms Library & ball\cite{ball} \\
python3-ball & ball & Python bindings for the Biochemical Algorithms Library & ball2010\cite{ball2010} \\
python3-biom-format & python-biom-format & Biological Observation Matrix (BIOM) format (Python 3) & python-biom-format\cite{python-biom-format} \\
python3-biopython & python-biopython & Python3 library for bioinformatics & python-biopython\cite{python-biopython} \\
python3-biopython-sql & python-biopython & Biopython support for the BioSQL database schema (Python 3) & python-biopython\cite{python-biopython} \\
python3-biosig & biosig4c++ & Python3 bindings for BioSig library & biosig4c--\cite{biosig4c--} \\
python3-biotools & python-biotools & Python3 bioinformatics utilities for high-throughput genomic sequencing & python-biotools\cite{python-biotools} \\
python3-brian & brian & simulator for spiking neural networks & brian\cite{brian} \\
python3-brian & brian & simulator for spiking neural networks & brian2009\cite{brian2009} \\
python3-brian-lib & brian & simulator for spiking neural networks -- extensions & brian\cite{brian} \\
python3-brian-lib & brian & simulator for spiking neural networks -- extensions & brian2009\cite{brian2009} \\
python3-caffe & caffe & Python3 interface of Caffe (CPU\_ONLY) & caffe\cite{caffe} \\
python3-caffe-cpu & caffe & Python3 interface of Caffe (CPU\_ONLY) & caffe\cite{caffe} \\
python3-caffe-cuda & caffe-contrib & Python3 interface of Caffe (CUDA) & caffe-contrib\cite{caffe-contrib} \\
python3-cclib & cclib & Parsers and algorithms for computational chemistry (Python3 module) & cclib\cite{cclib} \\
python3-chemps2 & chemps2 & Python 3 interface for libchemps2-3 & chemps2\cite{chemps2} \\
python3-chemps2 & chemps2 & Python 3 interface for libchemps2-3 & chemps22014\cite{chemps22014} \\
python3-chemps2 & chemps2 & Python 3 interface for libchemps2-3 & chemps22014c\cite{chemps22014c} \\
python3-chemps2 & chemps2 & Python 3 interface for libchemps2-3 & chemps22014d\cite{chemps22014d} \\
python3-chemps2 & chemps2 & Python 3 interface for libchemps2-3 & chemps22016\cite{chemps22016} \\
python3-cobra & python-cobra & constraint-based modeling of biological networks with Python 3 & python-cobra\cite{python-cobra} \\
python3-cogent3 & python-cogent & framework for genomic biology & python-cogent\cite{python-cogent} \\
python3-cpl & python-cpl & Control pipeline recipes from the ESO (Python3) & python-cpl\cite{python-cpl} \\
python3-cutadapt & python-cutadapt & Clean biological sequences from high-throughput sequencing reads (Python 3) & python-cutadapt\cite{python-cutadapt} \\
python3-cyvcf2 & cyvcf2 & VCF parser based on htslib (Python 3) & cyvcf2\cite{cyvcf2} \\
python3-deeptools & python-deeptools & platform for exploring biological deep-sequencing data & python-deeptools\cite{python-deeptools} \\
python3-deeptools & python-deeptools & platform for exploring biological deep-sequencing data & python-deeptools2014\cite{python-deeptools2014} \\
python3-dendropy & python-dendropy & DendroPy Phylogenetic Computing Library (Python 3) & python-dendropy\cite{python-dendropy} \\
python3-deprecation & python-deprecation & Library to handle automated deprecations & python-deprecation\cite{python-deprecation} \\
python3-dna-jellyfish & jellyfish & count k-mers in DNA sequences (Python bindings of jellyfish) & jellyfish\cite{jellyfish} \\
python3-dnapilib & dnapi & adapter prediction for small RNA sequencing - library & dnapi\cite{dnapi} \\
python3-drizzle & python-drizzle & Dithered image combination for Python & python-drizzle\cite{python-drizzle} \\
python3-drizzle-dbg & python-drizzle & Python3 binding to libdrizzle - debug symbols & python-drizzle\cite{python-drizzle} \\
python3-emcee & emcee & Affine-invariant ensemble MCMC sampling for Python 3 & emcee\cite{emcee} \\
python3-fastcluster & r-cran-fastcluster & Fast hierarchical clustering routines for Python 3 & r-cran-fastcluster\cite{r-cran-fastcluster} \\
python3-freecontact & python-freecontact & fast protein contact predictor - binding for Python3 & python-freecontact\cite{python-freecontact} \\
python3-gammapy & gammapy & Python package for gamma-ray astronomy & gammapy\cite{gammapy} \\
python3-gdcm & gdcm & Grassroots DICOM Python bindings & gdcm\cite{gdcm} \\
python3-gdl & gnudatalanguage & Python interface for the GNU Data Language & gnudatalanguage\cite{gnudatalanguage} \\
python3-genometools & genometools & Python3 bindings for genometools & genometools\cite{genometools} \\
python3-gfapy & gfapy & flexible and extensible software library for handling sequence graphs & gfapy\cite{gfapy} \\
python3-glue & glueviz & Python 3 library for data interaction & glueviz\cite{glueviz} \\
python3-gmsh & gmsh & Three-dimensional finite element mesh generator Python 3 wrapper & gmsh\cite{gmsh} \\
python3-gyoto & gyoto & General relativistic geodesic integration for the Python 3 language & gyoto\cite{gyoto} \\
python3-hisat2 & hisat2 & Python scripts accompanying hisat2 & hisat2\cite{hisat2} \\
python3-htseq & htseq & Python3 high-throughput genome sequencing read analysis utilities & htseq\cite{htseq} \\
python3-isospec & isospec & Isotopic fine structure calculator for Python 3 & isospec\cite{isospec} \\
python3-mia & pymia & Python-3 bindings for the MIA image processing library & pymia\cite{pymia} \\
python3-mia-dbg & pymia & Debug information for Python-3 bindings for MIA & pymia\cite{pymia} \\
python3-mirtop & mirtop & annotate miRNAs with a standard mirna/isomir naming (Python 3) & mirtop\cite{mirtop} \\
python3-mirtop & mirtop & annotate miRNAs with a standard mirna/isomir naming (Python 3) & mirtop2019\cite{mirtop2019} \\
python3-mofapy & r-bioc-mofa & Multi-Omics Factor Analysis (MOFA) - Python module & r-bioc-mofa\cite{r-bioc-mofa} \\
python3-montagepy & montage & Python toolkit for assembling FITS images into mosaics & montage\cite{montage} \\
python3-nipy & nipy & Analysis of structural and functional neuroimaging data & nipy\cite{nipy} \\
python3-nipy-lib & nipy & Analysis of structural and functional neuroimaging data (compiled modules) & nipy\cite{nipy} \\
python3-nipy-lib-dbg & nipy & Analysis of structural and functional neuroimaging data (debug symbols) & nipy\cite{nipy} \\
python3-nltk & nltk & Python3 libraries for natural language processing & nltk\cite{nltk} \\
python3-opencv & opencv & Python 3 bindings for the computer vision library & opencv\cite{opencv} \\
python3-pandas & pandas & data structures for "relational" or "labeled" data & pandas\cite{pandas} \\
python3-pandas-lib & pandas & low-level implementations and bindings for pandas & pandas\cite{pandas} \\
python3-presto & presto & toolkit for processing B and T cell sequences & presto\cite{presto} \\
python3-pyani & python-pyani & Python3 module for average nucleotide identity analyses & python-pyani\cite{python-pyani} \\
python3-pybedtools & python-pybedtools & Python 3 wrapper around BEDTools for bioinformatics work & python-pybedtools\cite{python-pybedtools} \\
python3-pybel & pybel & Biological Expression Language & pybel\cite{pybel} \\
python3-pycodcif & cod-tools & error-correcting CIF parser - Python3 bindings & cod-tools\cite{cod-tools} \\
python3-pyfaidx & python-pyfaidx & efficient random access to fasta subsequences for Python 3 & python-pyfaidx\cite{python-pyfaidx} \\
python3-pyfits & pyfits & Python3 module for reading, writing, and manipulating FITS files & pyfits\cite{pyfits} \\
python3-pymzml & python-pymzml & mzML mass spectrometric data parsing (Python 3.x) & python-pymzml\cite{python-pymzml} \\
python3-pysynphot & pysynphot & Python Synthetic Photometry Utilities & pysynphot\cite{pysynphot} \\
python3-pywps & pywps & Implementation of OGC's Web Processing Service - Python module & pywps\cite{pywps} \\
python3-pywps & pywps & Implementation of OGC's Web Processing Service - Python module & pywps2007\cite{pywps2007} \\
python3-qcelemental & qcelemental & Periodic table, physical constants, and molecule parsing for quantum chemistry & qcelemental\cite{qcelemental} \\
python3-qcelemental & qcelemental & Periodic table, physical constants, and molecule parsing for quantum chemistry & qcelemental2014\cite{qcelemental2014} \\
python3-qcelemental & qcelemental & Periodic table, physical constants, and molecule parsing for quantum chemistry & qcelemental2014c\cite{qcelemental2014c} \\
python3-qcelemental & qcelemental & Periodic table, physical constants, and molecule parsing for quantum chemistry & qcelemental2014d\cite{qcelemental2014d} \\
python3-qcelemental & qcelemental & Periodic table, physical constants, and molecule parsing for quantum chemistry & qcelemental2016\cite{qcelemental2016} \\
python3-requirements-detector & python-requirements-detector & finds and lists the requirements of a Python project & python-requirements-detector\cite{python-requirements-detector} \\
python3-ruffus & python-ruffus & Python3 computation pipeline library widely used in bioinformatics & python-ruffus\cite{python-ruffus} \\
python3-sbml5 & libsbml & System Biology Markup Language library - Python3 bindings & libsbml\cite{libsbml} \\
python3-sbml5-doc & libsbml & System Biology Markup Language library - Python3 documentation & libsbml\cite{libsbml} \\
python3-shapely & python-shapely & geometric objects, predicates, and operations (Python 3) & python-shapely\cite{python-shapely} \\
python3-spectral-cube & spectral-cube & Manipulate astronomical data cubes with Python & spectral-cube\cite{spectral-cube} \\
python3-statsmodels & statsmodels & Python3 module for the estimation of statistical models & statsmodels\cite{statsmodels} \\
python3-statsmodels-lib & statsmodels & Python3 low-level implementations and bindings for statsmodels & statsmodels\cite{statsmodels} \\
python3-sunpy & sunpy & Software library for solar physics based on Python & sunpy\cite{sunpy} \\
python3-theano & theano & CPU/GPU math expression compiler for Python 3 & theano\cite{theano} \\
python3-vispy & python-vispy & interactive visualization in Python 3 & python-vispy\cite{python-vispy} \\
python3-vtkgdcm & gdcm & Grassroots DICOM VTK/Python bindings & gdcm\cite{gdcm} \\
python3-yade & yade & Platform for discrete element modeling. Python bindings & yade\cite{yade} \\
python3-yt & yt & Framework for analyzing and visualizing simulation data (Python 3) & yt\cite{yt} \\
python-asdf & python-asdf & Python library for the Advanced Scientific Data Format & python-asdf\cite{python-asdf} \\
python-asdf-doc & python-asdf & Python library for the Advanced Scientific Data Format (documentation) & python-asdf\cite{python-asdf} \\
python-astrometry & astrometry.net & Astrometry plate solver (Python package) & astrometry-net\cite{astrometry-net} \\
python-astroml & astroml & Python Machine Learning library for astronomy & astroml\cite{astroml} \\
python-astropy & python-astropy & Core functionality for performing astrophysics with Python & python-astropy\cite{python-astropy} \\
python-astropy-doc & astropy & Core functionality for performing astrophysics with Python (doc) & astropy\cite{astropy} \\
python-astroscrappy & astroscrappy & Optimized Cosmic Ray Annihilation in Python 2 & astroscrappy\cite{astroscrappy} \\
python-avogadro & avogadro & Molecular Graphics and Modelling System (Python module) & avogadro\cite{avogadro} \\
python-ball & ball & Python bindings for the Biochemical Algorithms Library & ball\cite{ball} \\
python-ball & ball & Python bindings for the Biochemical Algorithms Library & ball2010\cite{ball2010} \\
python-ballview & ball & Python bindings for VIEW-parts of the Biochemical Algorithms Library & ball\cite{ball} \\
python-ballview & ball & Python bindings for VIEW-parts of the Biochemical Algorithms Library & ball2010\cite{ball2010} \\
python-biom-format & python-biom-format & Biological Observation Matrix (BIOM) format (Python 2) & python-biom-format\cite{python-biom-format} \\
python-biom-format-doc & python-biom-format & documentation for BIOM format & python-biom-format\cite{python-biom-format} \\
python-biopython & python-biopython & Python library for bioinformatics (implemented in Python 2) & python-biopython\cite{python-biopython} \\
python-biopython-doc & python-biopython & Documentation for the Biopython library & python-biopython\cite{python-biopython} \\
python-biopython-sql & python-biopython & Biopython support for the BioSQL database schema (Python 2) & python-biopython\cite{python-biopython} \\
python-biosig & biosig4c++ & Python bindings for BioSig library & biosig4c--\cite{biosig4c--} \\
python-biotools & python-biotools & Python bioinformatics utilities for high-throughput genomic sequencing & python-biotools\cite{python-biotools} \\
python-brian & brian & simulator for spiking neural networks & brian\cite{brian} \\
python-brian & brian & simulator for spiking neural networks & brian2009\cite{brian2009} \\
python-brian-doc & brian & simulator for spiking neural networks - documentation & brian\cite{brian} \\
python-brian-doc & brian & simulator for spiking neural networks - documentation & brian2009\cite{brian2009} \\
python-brian-lib & brian & simulator for spiking neural networks -- extensions & brian\cite{brian} \\
python-brian-lib & brian & simulator for spiking neural networks -- extensions & brian2009\cite{brian2009} \\
python-casmoothing & python-casmoothing & Context-aware mesh smoothing for biomedical applications & python-casmoothing\cite{python-casmoothing} \\
python-cclib & cclib & Parsers and algorithms for computational chemistry (Python module) & cclib\cite{cclib} \\
python-chemps2 & chemps2 & Python 2 interface for libchemps2-2 & chemps2\cite{chemps2} \\
python-chemps2 & chemps2 & Python 2 interface for libchemps2-2 & chemps22014\cite{chemps22014} \\
python-chemps2 & chemps2 & Python 2 interface for libchemps2-2 & chemps22014c\cite{chemps22014c} \\
python-chemps2 & chemps2 & Python 2 interface for libchemps2-2 & chemps22014d\cite{chemps22014d} \\
python-chemps2 & chemps2 & Python 2 interface for libchemps2-2 & chemps22016\cite{chemps22016} \\
python-cinfony & cinfony & Python abstraction layer to cheminformatics toolkits & cinfony\cite{cinfony} \\
python-cobra & python-cobra & constraint-based modeling of biological networks (Python 2) & python-cobra\cite{python-cobra} \\
python-cobra-data & python-cobra & constraint-based modeling of biological networks (data) & python-cobra\cite{python-cobra} \\
python-cogent & python-cogent & framework for genomic biology & python-cogent\cite{python-cogent} \\
python-cogent-dbg & python-cogent & debug information for pycogent & python-cogent\cite{python-cogent} \\
python-cogent-doc & python-cogent & docs for python3-cogent3 & python-cogent\cite{python-cogent} \\
python-cpl & python-cpl & Control pipeline recipes from the European Southern Observatory & python-cpl\cite{python-cpl} \\
python-cutadapt & python-cutadapt & Clean biological sequences from high-throughput sequencing reads (Python 2) & python-cutadapt\cite{python-cutadapt} \\
python-cyvcf2 & cyvcf2 & VCF parser based on htslib (Python 2) & cyvcf2\cite{cyvcf2} \\
python-dendropy & python-dendropy & DendroPy Phylogenetic Computing Library (Python 2) & python-dendropy\cite{python-dendropy} \\
python-deprecation & python-deprecation & Library to handle automated deprecations - Python 2.x & python-deprecation\cite{python-deprecation} \\
python-dipy & dipy & Python library for the analysis of diffusion MRI datasets & dipy\cite{dipy} \\
python-dipy-doc & dipy & Python library for the analysis of diffusion MRI datasets -- documentation & dipy\cite{dipy} \\
python-dipy-lib & dipy & Python library for the analysis of diffusion MRI datasets -- extensions & dipy\cite{dipy} \\
python-drizzle & python-drizzle & Dithered image combination for Python 2 & python-drizzle\cite{python-drizzle} \\
python-drizzle-dbg & python-drizzle & Python binding to libdrizzle - debug symbols & python-drizzle\cite{python-drizzle} \\
python-drizzle-doc & python-drizzle & Dithered image combination for Python (API documentation) & python-drizzle\cite{python-drizzle} \\
python-drizzle-testdata & python-drizzle & Dithered image combination for Python (Test data) & python-drizzle\cite{python-drizzle} \\
python-emcee & emcee & Affine-invariant ensemble MCMC sampling for Python & emcee\cite{emcee} \\
python-expyriment & python-expyriment & Python library for cognitive and neuroscientific experiments & python-expyriment\cite{python-expyriment} \\
python-fastcluster & r-cran-fastcluster & Fast hierarchical clustering routines for Python & r-cran-fastcluster\cite{r-cran-fastcluster} \\
python-freecontact & python-freecontact & fast protein contact predictor - binding for Python & python-freecontact\cite{python-freecontact} \\
python-gdcm & gdcm & Grassroots DICOM Python bindings & gdcm\cite{gdcm} \\
python-gdl & gnudatalanguage & Python interface for the GNU Data Language & gnudatalanguage\cite{gnudatalanguage} \\
python-genometools & genometools & Python bindings for genometools & genometools\cite{genometools} \\
python-glue & glueviz & Python 2 library for data interaction & glueviz\cite{glueviz} \\
python-gmsh & gmsh & Three-dimensional finite element mesh generator. Python wrapper & gmsh\cite{gmsh} \\
python-gyoto & gyoto & General relativistic geodesic integration for the Python 2 language & gyoto\cite{gyoto} \\
python-htseq & htseq & Python high-throughput genome sequencing read analysis utilities & htseq\cite{htseq} \\
python-htseq-doc & htseq & documetation for HTSeq (high-throughput genome sequencing) & htseq\cite{htseq} \\
python-mia & pymia & Python-2 bindings for the MIA image processing library & pymia\cite{pymia} \\
python-mia-dbg & pymia & Debug information for Python-2 bindings for MIA & pymia\cite{pymia} \\
python-nipy & nipy & Analysis of structural and functional neuroimaging data & nipy\cite{nipy} \\
python-nipy-doc & nipy & documentation and examples for NiPy & nipy\cite{nipy} \\
python-nipy-lib & nipy & Analysis of structural and functional neuroimaging data & nipy\cite{nipy} \\
python-nipy-lib-dbg & nipy & Analysis of structural and functional neuroimaging data & nipy\cite{nipy} \\
python-nipype & nipype & Neuroimaging data analysis pipelines in Python & nipype\cite{nipype} \\
python-nipype-doc & nipype & Neuroimaging data analysis pipelines in Python -- documentation & nipype\cite{nipype} \\
python-nltk & nltk & Python libraries for natural language processing & nltk\cite{nltk} \\
python-openbabel & openbabel & Chemical toolbox library (python bindings) & openbabel2008\cite{openbabel2008} \\
python-opencv & opencv & Python bindings for the computer vision library & opencv\cite{opencv} \\
python-opengm & opengm & Python interface to OpenGM & opengm\cite{opengm} \\
python-opengm-doc & opengm & documentation for the Python interface to OpenGM & opengm\cite{opengm} \\
python-openmeeg & openmeeg & openmeeg library -- Python bindings & openmeeg\cite{openmeeg} \\
python-pandas & pandas & data structures for "relational" or "labeled" data & pandas\cite{pandas} \\
python-pandas-doc & pandas & data structures for "relational" or "labeled" data - documentation & pandas\cite{pandas} \\
python-pandas-lib & pandas & low-level implementations and bindings for pandas & pandas\cite{pandas} \\
python-pybedtools-doc & python-pybedtools & Documentation for pybedtools library & python-pybedtools\cite{python-pybedtools} \\
python-pycodcif & cod-tools & error-correcting CIF parser - Python bindings & cod-tools\cite{cod-tools} \\
python-pyfaidx & python-pyfaidx & efficient random access to fasta subsequences for Python & python-pyfaidx\cite{python-pyfaidx} \\
python-pyfaidx-examples & python-pyfaidx & example data for efficient random access to fasta subsequences for Python & python-pyfaidx\cite{python-pyfaidx} \\
python-pyfits & pyfits & Python module for reading, writing, and manipulating FITS files & pyfits\cite{pyfits} \\
python-pymzml & python-pymzml & mzML mass spectrometric data parsing (Python 2.x) & python-pymzml\cite{python-pymzml} \\
python-pymzml-doc & python-pymzml & mzML mass spectrometric data parsing - documentation & python-pymzml\cite{python-pymzml} \\
python-pysynphot & pysynphot & Python Synthetic Photometry Utilities & pysynphot\cite{pysynphot} \\
python-pytrilinos & trilinos & parallel solver libraries within an object-oriented software framework & trilinos\cite{trilinos} \\
python-pywps & pywps & Implementation of OGC's Web Processing Service - Python 2 module & pywps\cite{pywps} \\
python-pywps & pywps & Implementation of OGC's Web Processing Service - Python 2 module & pywps2007\cite{pywps2007} \\
python-requirements-detector & python-requirements-detector & finds and lists the requirements of a Python project (Python 2) & python-requirements-detector\cite{python-requirements-detector} \\
python-ruffus & python-ruffus & Python computation pipeline library widely used in bioinformatics & python-ruffus\cite{python-ruffus} \\
python-ruffus-doc & python-ruffus & documentation for python-ruffus computation pipeline library & python-ruffus\cite{python-ruffus} \\
python-scikits.statsmodels & statsmodels & transitional compatibility package for statsmodels migration & statsmodels\cite{statsmodels} \\
python-shapely & python-shapely & geometric objects, predicates, and operations (Python 2) & python-shapely\cite{python-shapely} \\
python-shapely-doc & python-shapely & geometric objects, predicates, and operations (documentation) & python-shapely\cite{python-shapely} \\
python-spectral-cube & spectral-cube & Manipulate astronomical data cubes with Python 2 & spectral-cube\cite{spectral-cube} \\
python-statsmodels & statsmodels & Python module for the estimation of statistical models & statsmodels\cite{statsmodels} \\
python-statsmodels-doc & statsmodels & documentation and examples for statsmodels & statsmodels\cite{statsmodels} \\
python-statsmodels-lib & statsmodels & low-level implementations and bindings for statsmodels & statsmodels\cite{statsmodels} \\
python-sunpy & sunpy & Software library for solar physics based on Python & sunpy\cite{sunpy} \\
python-theano & theano & CPU/GPU math expression compiler for Python & theano\cite{theano} \\
python-visionegg & visionegg & Python library for 2D/3D visual stimulus generation & visionegg\cite{visionegg} \\
python-vispy & python-vispy & interactive visualization in Python 2 & python-vispy\cite{python-vispy} \\
python-vispy-doc & python-vispy & interactive visualization in Python [documentation] & python-vispy\cite{python-vispy} \\
python-vmtk & vmtk & Python interface for vmtk & vmtk\cite{vmtk} \\
python-vtkgdcm & gdcm & Grassroots DICOM VTK/Python bindings & gdcm\cite{gdcm} \\
python-yade & yade & Platform for discrete element modeling. Python bindings & yade\cite{yade} \\
python-yt & yt & Framework for analyzing and visualizing simulation data (Python 2) & yt\cite{yt} \\
pywps & pywps & Implementation of OGC's Web Processing Service & pywps\cite{pywps} \\
pywps & pywps & Implementation of OGC's Web Processing Service & pywps2007\cite{pywps2007} \\
pywps-doc & pywps & Implementation of OGC's Web Processing Service - Documentation & pywps\cite{pywps} \\
pywps-doc & pywps & Implementation of OGC's Web Processing Service - Documentation & pywps2007\cite{pywps2007} \\
pywps-wsgi & pywps & Implementation of OGC's Web Processing Service - WSGI example & pywps\cite{pywps} \\
pywps-wsgi & pywps & Implementation of OGC's Web Processing Service - WSGI example & pywps2007\cite{pywps2007} \\
q2cli & q2cli & Click-based command line interface for QIIME 2 & q2cli\cite{q2cli} \\
q2-cutadapt & q2-cutadapt & QIIME 2 plugin to work with adapters in sequence data & q2-cutadapt\cite{q2-cutadapt} \\
q2-demux & q2-demux & QIIME 2 plugin for demultiplexing of sequence reads & q2-demux\cite{q2-demux} \\
q2-feature-classifier & q2-feature-classifier & QIIME 2 plugin supporting taxonomic classification & q2-feature-classifier\cite{q2-feature-classifier} \\
q2-feature-table & q2-feature-table & QIIME 2 plugin supporting operations on feature tables & q2-feature-table\cite{q2-feature-table} \\
q2-metadata & q2-metadata & QIIME 2 plugin for working with and visualizing Metadata & q2-metadata\cite{q2-metadata} \\
q2-quality-filter & q2-quality-filter & QIIME2 plugin for PHRED-based filtering and trimming & q2-quality-filter\cite{q2-quality-filter} \\
q2templates & q2templates & Design template package for QIIME 2 Plugins & q2templates\cite{q2templates} \\
q2-types & q2-types & QIIME 2 plugin defining types for microbiome analysis & q2-types\cite{q2-types} \\
qiime & qiime & Quantitative Insights Into Microbial Ecology & qiime\cite{qiime} \\
qiime-data & qiime & Quantitative Insights Into Microbial Ecology (supporting data) & qiime\cite{qiime} \\
qiime-doc & qiime & Quantitative Insights Into Microbial Ecology (tutorial) & qiime\cite{qiime} \\
qrisk2 & qrisk2 & cardiovascular disease risk calculator & qrisk2\cite{qrisk2} \\
qsopt-ex & qsopt-ex & Exact linear programming solver & qsopt-ex\cite{qsopt-ex} \\
qtltools & qtltools & Tool set for molecular QTL discovery and analysis & qtltools\cite{qtltools} \\
qtltools & qtltools & Tool set for molecular QTL discovery and analysis & qtltools2017\cite{qtltools2017} \\
qtltools-example & qtltools & Tool set for molecular QTL discovery and analysis - example & qtltools\cite{qtltools} \\
qtltools-example & qtltools & Tool set for molecular QTL discovery and analysis - example & qtltools2017\cite{qtltools2017} \\
quantum-espresso & espresso & Electronic-Structure and Ab-Initio Molecular Dynamics Suite & espresso\cite{espresso} \\
quantum-espresso-data & espresso & Electronic-Structure and Ab-Initio Molecular Dynamics Suite (Documentation) & espresso\cite{espresso} \\
quorum & quorum & QUality Optimized Reads of genomic sequences & quorum\cite{quorum} \\
qutemol & qutemol & interactive visualization of macromolecules & qutemol\cite{qutemol} \\
raccoon & raccoon & preparation of in silico drug screening projects & raccoon\cite{raccoon} \\
racon & racon & consensus module for raw de novo DNA assembly of long uncorrected reads & racon\cite{racon} \\
radiant & radiant & explore hierarchical metagenomic data with zoomable pie charts & radiant\cite{radiant} \\
ragout & ragout & Reference-Assisted Genome Ordering UTility & ragout\cite{ragout} \\
ragout & ragout & Reference-Assisted Genome Ordering UTility & ragout2014\cite{ragout2014} \\
ragout-examples & ragout & Reference-Assisted Genome Ordering UTility (example data) & ragout\cite{ragout} \\
ragout-examples & ragout & Reference-Assisted Genome Ordering UTility (example data) & ragout2014\cite{ragout2014} \\
rambo-k & rambo-k & Read Assignment Method Based On K-mers & rambo-k\cite{rambo-k} \\
rapmap & rapmap & rapid sensitive and accurate DNA read mapping via quasi-mapping & rapmap\cite{rapmap} \\
rapmap & rapmap & rapid sensitive and accurate DNA read mapping via quasi-mapping & rapmap2016\cite{rapmap2016} \\
rapmap-dev & rapmap & rapmap - rapid sensitive and accurate DNA read mapping (some headers) & rapmap\cite{rapmap} \\
rapmap-dev & rapmap & rapmap - rapid sensitive and accurate DNA read mapping (some headers) & rapmap2016\cite{rapmap2016} \\
rapmap-example-data & rapmap & example data for rapmap - rapid sensitive and accurate DNA read mapping & rapmap\cite{rapmap} \\
rapmap-example-data & rapmap & example data for rapmap - rapid sensitive and accurate DNA read mapping & rapmap2016\cite{rapmap2016} \\
rasmol & rasmol & visualization of biological macromolecules & rasmol\cite{rasmol} \\
rasmol-doc & rasmol & documentation for rasmol & rasmol\cite{rasmol} \\
raster3d & raster3d & tools for generating images of proteins or other molecules & raster3d\cite{raster3d} \\
raster3d & raster3d & tools for generating images of proteins or other molecules & raster3d1988\cite{raster3d1988} \\
raster3d & raster3d & tools for generating images of proteins or other molecules & raster3d1991\cite{raster3d1991} \\
raster3d & raster3d & tools for generating images of proteins or other molecules & raster3d1994\cite{raster3d1994} \\
raster3d-doc & raster3d & documents and example files for Raster3D & raster3d\cite{raster3d} \\
raster3d-doc & raster3d & documents and example files for Raster3D & raster3d1988\cite{raster3d1988} \\
raster3d-doc & raster3d & documents and example files for Raster3D & raster3d1991\cite{raster3d1991} \\
raster3d-doc & raster3d & documents and example files for Raster3D & raster3d1994\cite{raster3d1994} \\
rate4site & rate4site & detector of conserved amino-acid sites & rate4site\cite{rate4site} \\
rate4site-dbg & rate4site & debugging symbols for rate4site-dbg & rate4site\cite{rate4site} \\
rawtran & rawtran & RAW photo to FITS converter & rawtran\cite{rawtran} \\
rawtran-doc & rawtran & Documentation of Rawtran & rawtran\cite{rawtran} \\
raxml & raxml & Randomized Axelerated Maximum Likelihood of phylogenetic trees & raxml\cite{raxml} \\
raxml & raxml & Randomized Axelerated Maximum Likelihood of phylogenetic trees & raxml2006\cite{raxml2006} \\
ray & ray & de novo genome assemblies of next-gen sequencing data & ray\cite{ray} \\
ray & ray & de novo genome assemblies of next-gen sequencing data & ray2012\cite{ray2012} \\
ray-doc & ray & documentation for ray parallel de novo genome assembler & ray\cite{ray} \\
ray-doc & ray & documentation for ray parallel de novo genome assembler & ray2012\cite{ray2012} \\
ray-extra & ray & Scripts and XSL sheets for post-processing for ray & ray\cite{ray} \\
ray-extra & ray & Scripts and XSL sheets for post-processing for ray & ray2012\cite{ray2012} \\
r-bioc-affy & r-bioc-affy & BioConductor methods for Affymetrix Oligonucleotide Arrays & r-bioc-affy\cite{r-bioc-affy} \\
r-bioc-altcdfenvs & r-bioc-altcdfenvs & BioConductor alternative CDF environments & r-bioc-altcdfenvs\cite{r-bioc-altcdfenvs} \\
r-bioc-aroma.light & r-bioc-aroma.light & BioConductor methods normalization and visualization of microarray data & r-bioc-aroma-light\cite{r-bioc-aroma-light} \\
r-bioc-biobase & r-bioc-biobase & base functions for Bioconductor & r-bioc-biobase\cite{r-bioc-biobase} \\
r-bioc-biocgenerics & r-bioc-biocgenerics & generic functions for Bioconductor & r-bioc-biocgenerics\cite{r-bioc-biocgenerics} \\
r-bioc-biomart & r-bioc-biomart & GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene) & r-bioc-biomart\cite{r-bioc-biomart} \\
r-bioc-biomart & r-bioc-biomart & GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene) & r-bioc-biomart2005\cite{r-bioc-biomart2005} \\
r-bioc-bitseq & r-bioc-bitseq & transcript expression inference and analysis for RNA-seq data & r-bioc-bitseq\cite{r-bioc-bitseq} \\
r-bioc-cummerbund & r-bioc-cummerbund & tool for analysis of Cufflinks RNA-Seq output & r-bioc-cummerbund\cite{r-bioc-cummerbund} \\
r-bioc-dada2 & r-bioc-dada2 & sample inference from amplicon sequencing data & r-bioc-dada2\cite{r-bioc-dada2} \\
r-bioc-deseq2 & r-bioc-deseq2 & R package for RNA-Seq Differential Expression Analysis & r-bioc-deseq2\cite{r-bioc-deseq2} \\
r-bioc-dirichletmultinomial & r-bioc-dirichletmultinomial & Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data & r-bioc-dirichletmultinomial\cite{r-bioc-dirichletmultinomial} \\
r-bioc-ebseq & r-bioc-ebseq & R package for RNA-Seq Differential Expression Analysis & r-bioc-ebseq\cite{r-bioc-ebseq} \\
r-bioc-edger & r-bioc-edger & Empirical analysis of digital gene expression data in R & r-bioc-edger\cite{r-bioc-edger} \\
r-bioc-edger & r-bioc-edger & Empirical analysis of digital gene expression data in R & r-bioc-edger2007\cite{r-bioc-edger2007} \\
r-bioc-genomicalignments & r-bioc-genomicalignments & BioConductor representation and manipulation of short genomic alignments & r-bioc-genomicalignments\cite{r-bioc-genomicalignments} \\
r-bioc-genomicfeatures & r-bioc-genomicfeatures & GNU R tools for making and manipulating transcript centric annotations & r-bioc-genomicfeatures\cite{r-bioc-genomicfeatures} \\
r-bioc-geoquery & r-bioc-geoquery & Get data from NCBI Gene Expression Omnibus (GEO) & r-bioc-geoquery\cite{r-bioc-geoquery} \\
r-bioc-gviz & r-bioc-gviz & Plotting data and annotation information along genomic coordinates & r-bioc-gviz\cite{r-bioc-gviz} \\
r-bioc-hilbertvis & r-bioc-hilbertvis & GNU R package to visualise long vector data & r-bioc-hilbertvis\cite{r-bioc-hilbertvis} \\
r-bioc-limma & r-bioc-limma & linear models for microarray data & r-bioc-limma\cite{r-bioc-limma} \\
r-bioc-mergeomics & r-bioc-mergeomics & Integrative network analysis of omics data & r-bioc-mergeomics\cite{r-bioc-mergeomics} \\
r-bioc-mofa & r-bioc-mofa & Multi-Omics Factor Analysis (MOFA) & r-bioc-mofa\cite{r-bioc-mofa} \\
r-bioc-multtest & r-bioc-multtest & Bioconductor resampling-based multiple hypothesis testing & r-bioc-multtest\cite{r-bioc-multtest} \\
r-bioc-pcamethods & r-bioc-pcamethods & BioConductor collection of PCA methods & r-bioc-pcamethods\cite{r-bioc-pcamethods} \\
r-bioc-phyloseq & r-bioc-phyloseq & GNU R handling and analysis of high-throughput microbiome census data & r-bioc-phyloseq\cite{r-bioc-phyloseq} \\
r-bioc-qusage & r-bioc-qusage & qusage: Quantitative Set Analysis for Gene Expression & r-bioc-qusage\cite{r-bioc-qusage} \\
r-bioc-qvalue & r-bioc-qvalue & GNU R package for Q-value estimation for FDR control & r-bioc-qvalue\cite{r-bioc-qvalue} \\
r-bioc-rtracklayer & r-bioc-rtracklayer & GNU R interface to genome browsers and their annotation tracks & r-bioc-rtracklayer\cite{r-bioc-rtracklayer} \\
r-bioc-shortread & r-bioc-shortread & GNU R classes and methods for high-throughput short-read sequencing data & r-bioc-shortread\cite{r-bioc-shortread} \\
r-bioc-tfbstools & r-bioc-tfbstools & GNU R Transcription Factor Binding Site (TFBS) Analysis & r-bioc-tfbstools\cite{r-bioc-tfbstools} \\
r-bioc-tximport & r-bioc-tximport & transcript-level estimates for biological sequencing & r-bioc-tximport\cite{r-bioc-tximport} \\
r-bioc-variantannotation & r-bioc-variantannotation & BioConductor annotation of genetic variants & r-bioc-variantannotation\cite{r-bioc-variantannotation} \\
r-cran-ade4 & r-cran-ade4 & GNU R analysis of ecological data & r-cran-ade4\cite{r-cran-ade4} \\
r-cran-adegenet & r-cran-adegenet & GNU R exploratory analysis of genetic and genomic data & r-cran-adegenet\cite{r-cran-adegenet} \\
r-cran-adephylo & r-cran-adephylo & GNU R exploratory analyses for the phylogenetic comparative method & r-cran-adephylo\cite{r-cran-adephylo} \\
r-cran-alakazam & r-cran-alakazam & Immunoglobulin Clonal Lineage and Diversity Analysis & r-cran-alakazam\cite{r-cran-alakazam} \\
r-cran-alakazam & r-cran-alakazam & Immunoglobulin Clonal Lineage and Diversity Analysis & r-cran-alakazam2014\cite{r-cran-alakazam2014} \\
r-cran-apcluster & r-cran-apcluster & Affinity Propagation Clustering & r-cran-apcluster\cite{r-cran-apcluster} \\
r-cran-ape & r-cran-ape & GNU R package for Analyses of Phylogenetics and Evolution & r-cran-ape\cite{r-cran-ape} \\
r-cran-ape & r-cran-ape & GNU R package for Analyses of Phylogenetics and Evolution & r-cran-ape1950\cite{r-cran-ape1950} \\
r-cran-ape & r-cran-ape & GNU R package for Analyses of Phylogenetics and Evolution & r-cran-ape1973\cite{r-cran-ape1973} \\
r-cran-ape & r-cran-ape & GNU R package for Analyses of Phylogenetics and Evolution & r-cran-ape1981\cite{r-cran-ape1981} \\
r-cran-ape & r-cran-ape & GNU R package for Analyses of Phylogenetics and Evolution & r-cran-ape1985\cite{r-cran-ape1985} \\
r-cran-ape & r-cran-ape & GNU R package for Analyses of Phylogenetics and Evolution & r-cran-ape1990\cite{r-cran-ape1990} \\
r-cran-ape & r-cran-ape & GNU R package for Analyses of Phylogenetics and Evolution & r-cran-ape2004\cite{r-cran-ape2004} \\
r-cran-ape & r-cran-ape & GNU R package for Analyses of Phylogenetics and Evolution & r-cran-ape2006\cite{r-cran-ape2006} \\
r-cran-ape & r-cran-ape & GNU R package for Analyses of Phylogenetics and Evolution & r-cran-ape2012\cite{r-cran-ape2012} \\
r-cran-bigmemory & r-cran-bigmemory & Manage Massive Matrices with Shared Memory and Memory-Mapped Files & r-cran-bigmemory\cite{r-cran-bigmemory} \\
r-cran-bio3d & r-cran-bio3d & GNU R package for biological structure analysis & r-cran-bio3d\cite{r-cran-bio3d} \\
r-cran-blockmodeling & r-cran-blockmodeling & Generalized and classical blockmodeling of valued networks & r-cran-blockmodeling\cite{r-cran-blockmodeling} \\
r-cran-blockmodeling & r-cran-blockmodeling & Generalized and classical blockmodeling of valued networks & r-cran-blockmodeling2007\cite{r-cran-blockmodeling2007} \\
r-cran-blockmodeling & r-cran-blockmodeling & Generalized and classical blockmodeling of valued networks & r-cran-blockmodeling2008\cite{r-cran-blockmodeling2008} \\
r-cran-bms & r-cran-bms & GNU R package for Bayesian model averaging for linear models & r-cran-bms\cite{r-cran-bms} \\
r-cran-boolnet & r-cran-boolnet & assembling, analyzing and visualizing Boolean networks & r-cran-boolnet\cite{r-cran-boolnet} \\
r-cran-calibrate & r-cran-calibrate & Calibration of Scatterplot and Biplot Axes & r-cran-calibrate\cite{r-cran-calibrate} \\
r-cran-cmprsk & r-cran-cmprsk & GNU R subdistribution analysis of competing risks & r-cran-cmprsk\cite{r-cran-cmprsk} \\
r-cran-colorspace & r-cran-colorspace & GNU R Color Space Manipulation & r-cran-colorspace\cite{r-cran-colorspace} \\
r-cran-dosefinding & r-cran-dosefinding & Planning and Analyzing Dose Finding experiments & r-cran-dosefinding\cite{r-cran-dosefinding} \\
r-cran-ellipse & r-cran-ellipse & GNU R functions for drawing ellipses and ellipse-like confidence regions & r-cran-ellipse\cite{r-cran-ellipse} \\
r-cran-epi & r-cran-epi & GNU R epidemiological analysis & r-cran-epi\cite{r-cran-epi} \\
r-cran-evd & r-cran-evd & GNU R Functions for extreme value distributions & r-cran-evd\cite{r-cran-evd} \\
r-cran-expm & r-cran-expm & GNU R Computation of the matrix exponential and related quantities & r-cran-expm\cite{r-cran-expm} \\
r-cran-factominer & r-cran-factominer & Multivariate Exploratory Data Analysis and Data Mining & r-cran-factominer\cite{r-cran-factominer} \\
r-cran-factominer & r-cran-factominer & Multivariate Exploratory Data Analysis and Data Mining & r-cran-factominer2013\cite{r-cran-factominer2013} \\
r-cran-factominer & r-cran-factominer & Multivariate Exploratory Data Analysis and Data Mining & r-cran-factominer2015\cite{r-cran-factominer2015} \\
r-cran-factominer & r-cran-factominer & Multivariate Exploratory Data Analysis and Data Mining & r-cran-factominer2016\cite{r-cran-factominer2016} \\
r-cran-fastcluster & r-cran-fastcluster & Fast hierarchical clustering routines for GNU R & r-cran-fastcluster\cite{r-cran-fastcluster} \\
r-cran-fitdistrplus & r-cran-fitdistrplus & support fit of parametric distribution & r-cran-fitdistrplus\cite{r-cran-fitdistrplus} \\
r-cran-flashclust & r-cran-flashclust & Implementation of optimal hierarchical clustering & r-cran-flashclust\cite{r-cran-flashclust} \\
r-cran-genabel & r-cran-genabel & GNU R package for genome-wide SNP association analysis & r-cran-genabel\cite{r-cran-genabel} \\
r-cran-ggplot2 & r-cran-ggplot2 & implementation of the Grammar of Graphics & r-cran-ggplot2\cite{r-cran-ggplot2} \\
r-cran-gprofiler & r-cran-gprofiler & Interface to the 'g:Profiler' Toolkit & r-cran-gprofiler\cite{r-cran-gprofiler} \\
r-cran-isospec & isospec & Isotopic fine structure calculator for GNU R & isospec\cite{isospec} \\
r-cran-kaos & r-cran-kaos & Encoding of Sequences Based on Frequency Matrix Chaos & r-cran-kaos\cite{r-cran-kaos} \\
r-cran-knitr & r-cran-knitr & GNU R package for dynamic report generation using Literate Programming & r-cran-knitr\cite{r-cran-knitr} \\
r-cran-lexrankr & r-cran-lexrankr & extractive summarization of text with the LexRank algorithm & r-cran-lexrankr\cite{r-cran-lexrankr} \\
r-cran-maldiquant & r-cran-maldiquant & GNU R package for quantitative analysis of mass spectrometry data & r-cran-maldiquant\cite{r-cran-maldiquant} \\
r-cran-maxlik & r-cran-maxlik & GNU R maximum likelihood estimation & r-cran-maxlik\cite{r-cran-maxlik} \\
r-cran-metamix & r-cran-metamix & GNU R bayesian mixture analysis for metagenomic community profiling & r-cran-metamix\cite{r-cran-metamix} \\
r-cran-mixtools & r-cran-mixtools & GNU R tools for analyzing finite mixture models & r-cran-mixtools\cite{r-cran-mixtools} \\
r-cran-msm & r-cran-msm & GNU R Multi-state Markov and hidden Markov models in continuous time & r-cran-msm\cite{r-cran-msm} \\
r-cran-nmf & r-cran-nmf & GNU R framework to perform non-negative matrix factorization & r-cran-nmf\cite{r-cran-nmf} \\
r-cran-pcapp & r-cran-pcapp & Robust PCA by Projection Pursuit & r-cran-pcapp\cite{r-cran-pcapp} \\
r-cran-phangorn & r-cran-phangorn & GNU R package for phylogenetic analysis & r-cran-phangorn\cite{r-cran-phangorn} \\
r-cran-phytools & r-cran-phytools & GNU R phylogenetic tools for comparative biology & r-cran-phytools\cite{r-cran-phytools} \\
r-cran-plotrix & r-cran-plotrix & GNU R package providing various plotting functions & r-cran-plotrix\cite{r-cran-plotrix} \\
r-cran-propclust & r-cran-propclust & Propensity Clustering and Decomposition & r-cran-propclust\cite{r-cran-propclust} \\
r-cran-propclust & r-cran-propclust & Propensity Clustering and Decomposition & r-cran-propclustb\cite{r-cran-propclustb} \\
r-cran-propclust & r-cran-propclust & Propensity Clustering and Decomposition & r-cran-propclustc\cite{r-cran-propclustc} \\
r-cran-pscbs & r-cran-pscbs & R package: Analysis of Parent-Specific DNA Copy Numbers & r-cran-pscbs\cite{r-cran-pscbs} \\
r-cran-pvclust & r-cran-pvclust & Hierarchical Clustering with P-Values via Multiscale Bootstrap & r-cran-pvclust\cite{r-cran-pvclust} \\
r-cran-qqman & r-cran-qqman & R package for visualizing GWAS results using Q-Q and manhattan plots & r-cran-qqman\cite{r-cran-qqman} \\
r-cran-qtl & r-cran-qtl & GNU R package for genetic marker linkage analysis & r-cran-qtl\cite{r-cran-qtl} \\
r-cran-ranger & r-cran-ranger & Fast Implementation of Random Forests & r-cran-ranger\cite{r-cran-ranger} \\
r-cran-relsurv & r-cran-relsurv & GNU R relative survival & r-cran-relsurv\cite{r-cran-relsurv} \\
r-cran-reshape & r-cran-reshape & Flexibly reshape data & r-cran-reshape\cite{r-cran-reshape} \\
r-cran-rniftilib & r-cran-rniftilib & GNU/R interface to NIFTICLIB & r-cran-rniftilib\cite{r-cran-rniftilib} \\
r-cran-rocr & r-cran-rocr & GNU R package to prepare and display ROC curves & r-cran-rocr\cite{r-cran-rocr} \\
r-cran-r.oo & r-cran-r.oo & GNU R object-oriented programming with or without references & r-cran-r-oo\cite{r-cran-r-oo} \\
r-cran-rsvd & r-cran-rsvd & Randomized Singular Value Decomposition & r-cran-rsvd\cite{r-cran-rsvd} \\
r-cran-scatterplot3d & r-cran-scatterplot3d & GNU R package for Visualizing Multivariate Data & r-cran-scatterplot3d\cite{r-cran-scatterplot3d} \\
r-cran-segmented & r-cran-segmented & GNU R segmented relationships in regression models & r-cran-segmented\cite{r-cran-segmented} \\
r-cran-seqinr & r-cran-seqinr & GNU R biological sequences retrieval and analysis & r-cran-seqinr\cite{r-cran-seqinr} \\
r-cran-seroincidence & r-cran-seroincidence & GNU R seroincidence calculator tool & r-cran-seroincidence\cite{r-cran-seroincidence} \\
r-cran-seroincidence & r-cran-seroincidence & GNU R seroincidence calculator tool & r-cran-seroincidence2009\cite{r-cran-seroincidence2009} \\
r-cran-seurat & r-cran-seurat & Tools for Single Cell Genomics & r-cran-seurat\cite{r-cran-seurat} \\
r-cran-seurat & r-cran-seurat & Tools for Single Cell Genomics & r-cran-seurat2015\cite{r-cran-seurat2015} \\
r-cran-shazam & r-cran-shazam & Immunoglobulin Somatic Hypermutation Analysis & r-cran-shazam\cite{r-cran-shazam} \\
r-cran-shazam & r-cran-shazam & Immunoglobulin Somatic Hypermutation Analysis & r-cran-shazam2016\cite{r-cran-shazam2016} \\
r-cran-spam & r-cran-spam & GNU R functions for sparse matrix algebra & r-cran-spam\cite{r-cran-spam} \\
r-cran-spatstat & r-cran-spatstat & GNU R Spatial Point Pattern analysis, model-fitting, simulation, tests & r-cran-spatstat\cite{r-cran-spatstat} \\
r-cran-spp & r-cran-spp & GNU R ChIP-seq processing pipeline & r-cran-spp\cite{r-cran-spp} \\
r-cran-stringi & r-cran-stringi & GNU R character string processing facilities & r-cran-stringi\cite{r-cran-stringi} \\
r-cran-surveillance & r-cran-surveillance & GNU R package for the Modeling and Monitoring of Epidemic Phenomena & r-cran-surveillance\cite{r-cran-surveillance} \\
r-cran-tcr & r-cran-tcr & Advanced Data Analysis of Immune Receptor Repertoires & r-cran-tcr\cite{r-cran-tcr} \\
r-cran-tfmpvalue & r-cran-tfmpvalue & GNU R P-Value Computation for Position Weight Matrices & r-cran-tfmpvalue\cite{r-cran-tfmpvalue} \\
r-cran-tidyverse & r-cran-tidyverse & Easily Install and Load the 'Tidyverse' & r-cran-tidyverse\cite{r-cran-tidyverse} \\
r-cran-tigger & r-cran-tigger & Infers new Immunoglobulin alleles from Rep-Seq Data & r-cran-tigger\cite{r-cran-tigger} \\
r-cran-vcd & r-cran-vcd & GNU R Visualizing Categorical Data & r-cran-vcd\cite{r-cran-vcd} \\
r-cran-wgcna & r-cran-wgcna & Weighted Correlation Network Analysis & r-cran-wgcna\cite{r-cran-wgcna} \\
rdp-alignment & rdp-alignment & Ribosomal Database Project (RDP) alignment tools package & rdp-alignment\cite{rdp-alignment} \\
rdp-classifier & rdp-classifier & extensible sequence classifier for fungal lsu, bacterial and archaeal 16s & rdp-classifier\cite{rdp-classifier} \\
rdp-classifier-doc & rdp-classifier & documentation and examples for rdp-classifier & rdp-classifier\cite{rdp-classifier} \\
readseq & readseq & Conversion between sequence formats & readseq\cite{readseq} \\
reapr & reapr & universal tool for genome assembly evaluation & reapr\cite{reapr} \\
relion-bin & relion & toolkit for 3D reconstructions in cryo-electron microscopy & relion\cite{relion} \\
relion-bin+gui & relion & parallel toolkit for 3D reconstructions in cryo-electron microscopy & relion\cite{relion} \\
relion-bin+mpi & relion & parallel toolkit for 3D reconstructions in cryo-electron microscopy & relion\cite{relion} \\
relion-bin+mpi+gui & relion & parallel toolkit for 3D reconstructions in cryo-electron microscopy & relion\cite{relion} \\
repeatmasker-recon & repeatmasker-recon & finds repeat families from biological sequences & repeatmasker-recon\cite{repeatmasker-recon} \\
resfinder & resfinder & identify acquired antimicrobial resistance genes & resfinder\cite{resfinder} \\
resfinder-db & resfinder-db & ResFinder database is a curated database of acquired resistance genes & resfinder-db\cite{resfinder-db} \\
resfinder-example & resfinder & identify acquired antimicrobial resistance genes (example data) & resfinder\cite{resfinder} \\
rnahybrid & rnahybrid & Fast and effective prediction of microRNA/target duplexes & rnahybrid\cite{rnahybrid} \\
rna-star & rna-star & ultrafast universal RNA-seq aligner & rna-star\cite{rna-star} \\
roary & roary & high speed stand alone pan genome pipeline & roary\cite{roary} \\
roguenarok & roguenarok & versatile and scalable algorithm for rogue taxon identification & roguenarok\cite{roguenarok} \\
r-other-curvefdp & r-other-curvefdp & estimation of confidence levels for peptide identifications & r-other-curvefdp\cite{r-other-curvefdp} \\
r-other-mott-happy & r-other-mott-happy & GNU R package for fine-mapping complex diseases & r-other-mott-happy\cite{r-other-mott-happy} \\
r-other-mott-happy.hbrem & r-other-mott-happy & GNU R package for fine-mapping complex diseases & r-other-mott-happy\cite{r-other-mott-happy} \\
r-other-mott-happy.hbrem-dbg & r-other-mott-happy & Debug information for Happy R package native library & r-other-mott-happy\cite{r-other-mott-happy} \\
r-other-nitpick & r-other-nitpick & peak identification for mass spectrometry data & r-other-nitpick\cite{r-other-nitpick} \\
rsem & rsem & RNA-Seq by Expectation-Maximization & rsem\cite{rsem} \\
rtax & rtax & Classification of sequence reads of 16S ribosomal RNA gene & rtax\cite{rtax} \\
saint & saint & Significance Analysis of INTeractome & saint\cite{saint} \\
saint & saint & Significance Analysis of INTeractome & saint2010\cite{saint2010} \\
salmon & salmon & wicked-fast transcript quantification from RNA-seq data & salmon\cite{salmon} \\
salmon & salmon & wicked-fast transcript quantification from RNA-seq data & salmon2019\cite{salmon2019} \\
sambamba & sambamba & tools for working with SAM/BAM data & sambamba\cite{sambamba} \\
samblaster & samblaster & marks duplicates, extracts discordant/split reads & samblaster\cite{samblaster} \\
samtools & samtools & processing sequence alignments in SAM, BAM and CRAM formats & samtools\cite{samtools} \\
samtools-test & samtools & test files for the samtools package & samtools\cite{samtools} \\
saods9 & saods9 & Image display tool for astronomy & saods9\cite{saods9} \\
saods9-blt & saods9 & BLT subpackage for saods9 & saods9\cite{saods9} \\
saods9-data & saods9 & Image display tool for astronomy (shared data) & saods9\cite{saods9} \\
saods9-doc & saods9 & Image display tool for astronomy (help files/documentation) & saods9\cite{saods9} \\
saods9-tclpackages & saods9 & Tcl/Tk packages provided with DS9 & saods9\cite{saods9} \\
sbmltoolbox & sbmltoolbox & libsbml toolbox for octave and matlab & sbmltoolbox\cite{sbmltoolbox} \\
scamp & scamp & Compute astrometric and photometric solutions & scamp\cite{scamp} \\
scoary & scoary & pangenome-wide association studies & scoary\cite{scoary} \\
scrm & scrm & simulator of evolution of genetic sequences & scrm\cite{scrm} \\
seaview & seaview & Multiplatform interface for sequence alignment and phylogeny & seaview\cite{seaview} \\
seaview & seaview & Multiplatform interface for sequence alignment and phylogeny & seaview1996\cite{seaview1996} \\
seer & seer & genomic sequence element (kmer) enrichment analysis & seer\cite{seer} \\
segemehl & segemehl & short read mapping with gaps & segemehl\cite{segemehl} \\
segemehl & segemehl & short read mapping with gaps & segemehl2012\cite{segemehl2012} \\
segemehl & segemehl & short read mapping with gaps & segemehl2014\cite{segemehl2014} \\
seqan3-doc & seqan3 & C++ library for the analysis of biological sequences v3 (documentation) & seqan3\cite{seqan3} \\
seqan-apps & seqan2 & C++ library for the analysis of biological sequences & seqan2\cite{seqan2} \\
seqan-dev & seqan & C++ library for the analysis of biological sequences (development) & seqan\cite{seqan} \\
seq-gen & seq-gen & simulate the evolution of nucleotide or amino acid sequences & seq-gen\cite{seq-gen} \\
seqsero & seqsero & Salmonella serotyping from genome sequencing data & seqsero\cite{seqsero} \\
sextractor & source-extractor & Dummy transitional package for name change & source-extractor\cite{source-extractor} \\
sga & sga & de novo genome assembler that uses string graphs & sga\cite{sga} \\
shapeit4 & shapeit4 & fast and accurate method for estimation of haplotypes (phasing) & shapeit4\cite{shapeit4} \\
shapeit4-example & shapeit4 & fast and accurate method for estimation of haplotypes (phasing) - example & shapeit4\cite{shapeit4} \\
shark-doc & shark & documentation for Shark & shark\cite{shark} \\
shelxle & shelxle & graphical user interface for SHELXL & shelxle\cite{shelxle} \\
sibelia & sibelia & comparative genomics tool & sibelia\cite{sibelia} \\
sibelia-examples & sibelia & comparative genomics tool (example data) & sibelia\cite{sibelia} \\
sift & sift & predicts if a substitution in a protein has a phenotypic effect & sift\cite{sift} \\
sift & sift & predicts if a substitution in a protein has a phenotypic effect & sift2001\cite{sift2001} \\
sift & sift & predicts if a substitution in a protein has a phenotypic effect & sift2002\cite{sift2002} \\
sift & sift & predicts if a substitution in a protein has a phenotypic effect & sift2003\cite{sift2003} \\
sift & sift & predicts if a substitution in a protein has a phenotypic effect & sift2006\cite{sift2006} \\
sigma-align & sigma-align & Simple greedy multiple alignment of non-coding DNA sequences & sigma-align\cite{sigma-align} \\
sim4 & sim4 & tool for aligning cDNA and genomic DNA & sim4\cite{sim4} \\
sim4db & kmer & batch spliced alignment of cDNA sequences to a target genome & kmer\cite{kmer} \\
sim4db & kmer & batch spliced alignment of cDNA sequences to a target genome & kmer2004\cite{kmer2004} \\
simka & simka & comparative metagenomics method dedicated to NGS datasets & simka\cite{simka} \\
simkamin & simka & approximate comparative metagenomics method dedicated to NGS datasets & simka\cite{simka} \\
skesa & skesa & strategic Kmer extension for scrupulous assemblies & skesa\cite{skesa} \\
skewer & skewer & post-processing of high-throughput DNA sequence reads & skewer\cite{skewer} \\
skycat & skycat & Image visualization and access to catalogs and data for astronomy & skycat\cite{skycat} \\
skyview & skyview & Image generation from a range of remote databases & skyview\cite{skyview} \\
skyview-java & skyview & Image generation from a range of remote databases (Java package) & skyview\cite{skyview} \\
skyview-java-doc & skyview & Image generation from a range of remote databases (API doc) & skyview\cite{skyview} \\
smalr & smalr & interrogation of the methylation status of nucleotide sequencing reads & smalr\cite{smalr} \\
snakemake & snakemake & pythonic workflow management system & snakemake\cite{snakemake} \\
snap & snap & location of genes from DNA sequence with hidden markov model & snap\cite{snap} \\
snap-aligner & snap-aligner & Scalable Nucleotide Alignment Program & snap-aligner\cite{snap-aligner} \\
sniffles & sniffles & structural variation caller using third-generation sequencing & sniffles\cite{sniffles} \\
snpomatic & snpomatic & fast, stringent short-read mapping software & snpomatic\cite{snpomatic} \\
snp-sites & snp-sites & Binary code for the package snp-sites & snp-sites\cite{snp-sites} \\
soapaligner & soapaligner & aligner of short reads of next generation sequencers & soapaligner\cite{soapaligner} \\
soapdenovo & soapdenovo & short-read assembly method to build de novo draft assembly & soapdenovo\cite{soapdenovo} \\
soapdenovo2 & soapdenovo2 & short-read assembly method to build de novo draft assembly & soapdenovo2\cite{soapdenovo2} \\
soapsnp & soapsnp & resequencing utility that can assemble consensus sequence of genomes & soapsnp\cite{soapsnp} \\
sortmerna & sortmerna & tool for filtering, mapping and OTU-picking NGS reads & sortmerna\cite{sortmerna} \\
source-extractor & source-extractor & Source extractor for astronomical images & source-extractor\cite{source-extractor} \\
spaced & spaced & alignment-free sequence comparison using spaced words & spaced\cite{spaced} \\
spades & spades & genome assembler for single-cell and isolates data sets & spades\cite{spades} \\
spades & spades & genome assembler for single-cell and isolates data sets & spades2013\cite{spades2013} \\
spades & spades & genome assembler for single-cell and isolates data sets & spades2014\cite{spades2014} \\
spades & spades & genome assembler for single-cell and isolates data sets & spades2015\cite{spades2015} \\
spades & spades & genome assembler for single-cell and isolates data sets & spades2016\cite{spades2016} \\
spades & spades & genome assembler for single-cell and isolates data sets & spades2017\cite{spades2017} \\
spades & spades & genome assembler for single-cell and isolates data sets & spades2019\cite{spades2019} \\
spades & spades & genome assembler for single-cell and isolates data sets & spades2019h\cite{spades2019h} \\
splash & splash & Visualisation tool for Smoothed Particle Hydrodynamics simulation & splash\cite{splash} \\
spread-phy & spread-phy & analyze and visualize phylogeographic reconstructions & spread-phy\cite{spread-phy} \\
sra-toolkit & sra-sdk & utilities for the NCBI Sequence Read Archive & sra-sdk\cite{sra-sdk} \\
sra-toolkit-libs0 & sra-sdk & Libraries for the SRA Toolkit & sra-sdk\cite{sra-sdk} \\
sra-toolkit-libs-dev & sra-sdk & Development files for the NCBI SRA Toolkit's libraries & sra-sdk\cite{sra-sdk} \\
srst2 & srst2 & Short Read Sequence Typing for Bacterial Pathogens & srst2\cite{srst2} \\
ssake & ssake & genomics application for assembling millions of very short DNA sequences & ssake\cite{ssake} \\
ssake-examples & ssake & example data for SSAKE, a genomic assembler of short reads & ssake\cite{ssake} \\
sspace & sspace & scaffolding pre-assembled contigs after extension & sspace\cite{sspace} \\
ssw-align & libssw & Smith-Waterman aligner based on libssw & libssw\cite{libssw} \\
stacks & stacks & pipeline for building loci from short-read DNA sequences & stacks\cite{stacks} \\
stacks-web & stacks & web interface for displaying loci from short-read sequences & stacks\cite{stacks} \\
staden & staden & DNA sequence assembly (Gap4/Gap5), editing and analysis tools & staden\cite{staden} \\
staden-common & staden & Architecture independent files for Staden & staden\cite{staden} \\
starlink-table-java & starjava-table & Starlink Tables Infrastructure Library & starjava-table\cite{starjava-table} \\
starlink-table-java-doc & starjava-table & Starlink Tables Infrastructure Library (documentation) & starjava-table\cite{starjava-table} \\
starlink-topcat-java & starjava-topcat & Tool for OPerations on Catalogues And Tables (Java library) & starjava-topcat\cite{starjava-topcat} \\
starlink-topcat-java-doc & starjava-topcat & Tool for OPerations on Catalogues And Tables (JavaDoc) & starjava-topcat\cite{starjava-topcat} \\
starlink-ttools-java & starjava-ttools & Starlink Tables Infrastructure Library Tool Set (Java library) & starjava-ttools\cite{starjava-ttools} \\
starlink-ttools-java-doc & starjava-ttools & Starlink Tables Infrastructure Library Tool Set (Javadoc) & starjava-ttools\cite{starjava-ttools} \\
stiff & stiff & convert scientific FITS images to the TIFF format & stiff\cite{stiff} \\
stilts & starjava-ttools & Starlink Tables Infrastructure Library Tool Set & starjava-ttools\cite{starjava-ttools} \\
stilts-doc & starjava-ttools & Starlink Tables Infrastructure Library Tool Set (documentation) & starjava-ttools\cite{starjava-ttools} \\
stringtie & stringtie & assemble short RNAseq reads to transcripts & stringtie\cite{stringtie} \\
stringtie & stringtie & assemble short RNAseq reads to transcripts & stringtie2016\cite{stringtie2016} \\
suitename & suitename & categorize each suite in an RNA backbone & suitename\cite{suitename} \\
sumo & sumo & Simulation of Urban MObility (SUMO) & sumo\cite{sumo} \\
sumo-doc & sumo & Simulation of Urban MObility (SUMO), documentation and examples & sumo\cite{sumo} \\
sumo-tools & sumo & Simulation of Urban MObility (SUMO), tools and scripts & sumo\cite{sumo} \\
sumtrees & python-dendropy & Phylogenetic Tree Summarization and Annotation & python-dendropy\cite{python-dendropy} \\
surankco & surankco & Supervised Ranking of Contigs in de novo Assemblies & surankco\cite{surankco} \\
swarm & swarm-cluster & robust and fast clustering method for amplicon-based studies & swarm-cluster\cite{swarm-cluster} \\
swarm & swarm-cluster & robust and fast clustering method for amplicon-based studies & swarm-cluster2014\cite{swarm-cluster2014} \\
swarp & swarp & Resample and co-add together FITS images & swarp\cite{swarp} \\
sweed & sweed & assessment of SNPs for their evolutionary advantage & sweed\cite{sweed} \\
synphot-data & pysynphot & Optional data files for pysynphot & pysynphot\cite{pysynphot} \\
tabix & htslib & generic indexer for TAB-delimited genome position files & htslib\cite{htslib} \\
tandem-mass & tandem-mass & mass spectrometry software for protein identification & tandem-mass\cite{tandem-mass} \\
tandem-mass-dbg & tandem-mass & mass spectrometry software for protein identification - debug symbols & tandem-mass\cite{tandem-mass} \\
tanglet & tanglet & single player word finding game based on Boggle & tanglet\cite{tanglet} \\
tanglet-data & tanglet & single player word finding game based on Boggle - data files & tanglet\cite{tanglet} \\
tantan & tantan & low complexity and tandem repeat masker for biosequences & tantan\cite{tantan} \\
tcl-funtools & funtools & Minimal buy-in FITS library (Tcl interface) & funtools\cite{funtools} \\
tcliis & saods9 & Tcl IIS protocol package & saods9\cite{saods9} \\
tcl-xpa & xpa & Seamless communication between Unix programs (Tcl interface) & xpa\cite{xpa} \\
t-coffee & t-coffee & Multiple Sequence Alignment & t-coffee\cite{t-coffee} \\
t-coffee-doc & t-coffee & PDF and HTML accompaning documents to T-Coffee & t-coffee\cite{t-coffee} \\
t-coffee-examples & t-coffee & annotated examples for the use of T-Coffee & t-coffee\cite{t-coffee} \\
theano-doc & theano & CPU/GPU math expression compiler for Python (docs) & theano\cite{theano} \\
theseus & theseus & superimpose macromolecules using maximum likelihood & theseus\cite{theseus} \\
theseus & theseus & superimpose macromolecules using maximum likelihood & theseus2006\cite{theseus2006} \\
theseus & theseus & superimpose macromolecules using maximum likelihood & theseus2008\cite{theseus2008} \\
theseus-examples & theseus & superimpose macromolecules using maximum likelihood (examples) & theseus\cite{theseus} \\
theseus-examples & theseus & superimpose macromolecules using maximum likelihood (examples) & theseus2006\cite{theseus2006} \\
theseus-examples & theseus & superimpose macromolecules using maximum likelihood (examples) & theseus2008\cite{theseus2008} \\
thesias & thesias & Testing Haplotype Effects In Association Studies & thesias\cite{thesias} \\
thesias & thesias & Testing Haplotype Effects In Association Studies & thesias2002\cite{thesias2002} \\
thesias & thesias & Testing Haplotype Effects In Association Studies & thesias2004\cite{thesias2004} \\
tigr-glimmer & tigr-glimmer & Gene detection in archea and bacteria & tigr-glimmer\cite{tigr-glimmer} \\
tigr-glimmer & tigr-glimmer & Gene detection in archea and bacteria & tigr-glimmer2007\cite{tigr-glimmer2007} \\
tigr-glimmer & tigr-glimmer & Gene detection in archea and bacteria & tigr-glimmer2012\cite{tigr-glimmer2012} \\
tksao & saods9 & Tk widgets for astronomical imaging and data visualization & saods9\cite{saods9} \\
tm-align & tm-align & structural alignment of proteins & tm-align\cite{tm-align} \\
tnseq-transit & tnseq-transit & statistical calculations of essentiality of genes or genomic regions & tnseq-transit\cite{tnseq-transit} \\
toil & toil & cross-platform workflow engine & toil\cite{toil} \\
topcat & starjava-topcat & Tool for OPerations on Catalogues And Tables & starjava-topcat\cite{starjava-topcat} \\
topcat-doc & starjava-topcat & Tool for OPerations on Catalogues And Tables (documentation) & starjava-topcat\cite{starjava-topcat} \\
tophat & tophat & fast splice junction mapper for RNA-Seq reads & tophat\cite{tophat} \\
tophat-recondition & tophat-recondition & post-processor for TopHat unmapped reads & tophat-recondition\cite{tophat-recondition} \\
topp & openms & set of programs implementing The OpenMS Proteomic Pipeline & openms\cite{openms} \\
toppred & toppred & transmembrane topology prediction & toppred\cite{toppred} \\
trace2dbest & trace2dbest & bulk submission of chromatogram data to dbEST & trace2dbest\cite{trace2dbest} \\
trace2dbest & trace2dbest & bulk submission of chromatogram data to dbEST & trace2dbest2009\cite{trace2dbest2009} \\
trace2dbest-doc & trace2dbest & Documentation and sample files for trace2dbest & trace2dbest\cite{trace2dbest} \\
trace2dbest-doc & trace2dbest & Documentation and sample files for trace2dbest & trace2dbest2009\cite{trace2dbest2009} \\
tracetuner & tracetuner & interpretation of DNA Sanger sequencing data & tracetuner\cite{tracetuner} \\
transrate-tools & transrate-tools & helper for transrate & transrate-tools\cite{transrate-tools} \\
transtermhp & transtermhp & find rho-independent transcription terminators in bacterial genomes & transtermhp\cite{transtermhp} \\
travis & travis & trajectory analyzer and visualizer & travis\cite{travis} \\
travis & travis & trajectory analyzer and visualizer & travis2013\cite{travis2013} \\
tree-ppuzzle & tree-puzzle & Parallelized reconstruction of phylogenetic trees by maximum likelihood & tree-puzzle\cite{tree-puzzle} \\
tree-ppuzzle & tree-puzzle & Parallelized reconstruction of phylogenetic trees by maximum likelihood & tree-puzzle1996\cite{tree-puzzle1996} \\
tree-ppuzzle & tree-puzzle & Parallelized reconstruction of phylogenetic trees by maximum likelihood & tree-puzzle1997\cite{tree-puzzle1997} \\
tree-ppuzzle & tree-puzzle & Parallelized reconstruction of phylogenetic trees by maximum likelihood & tree-puzzle1997d\cite{tree-puzzle1997d} \\
tree-ppuzzle & tree-puzzle & Parallelized reconstruction of phylogenetic trees by maximum likelihood & tree-puzzle2002\cite{tree-puzzle2002} \\
tree-ppuzzle & tree-puzzle & Parallelized reconstruction of phylogenetic trees by maximum likelihood & tree-puzzle2003\cite{tree-puzzle2003} \\
tree-puzzle & tree-puzzle & Reconstruction of phylogenetic trees by maximum likelihood & tree-puzzle\cite{tree-puzzle} \\
tree-puzzle & tree-puzzle & Reconstruction of phylogenetic trees by maximum likelihood & tree-puzzle1996\cite{tree-puzzle1996} \\
tree-puzzle & tree-puzzle & Reconstruction of phylogenetic trees by maximum likelihood & tree-puzzle1997\cite{tree-puzzle1997} \\
tree-puzzle & tree-puzzle & Reconstruction of phylogenetic trees by maximum likelihood & tree-puzzle1997d\cite{tree-puzzle1997d} \\
tree-puzzle-doc & tree-puzzle & Reconstruction of phylogenetic trees by maximum likelihood (doc) & tree-puzzle\cite{tree-puzzle} \\
tree-puzzle-doc & tree-puzzle & Reconstruction of phylogenetic trees by maximum likelihood (doc) & tree-puzzle1996\cite{tree-puzzle1996} \\
tree-puzzle-doc & tree-puzzle & Reconstruction of phylogenetic trees by maximum likelihood (doc) & tree-puzzle1997\cite{tree-puzzle1997} \\
tree-puzzle-doc & tree-puzzle & Reconstruction of phylogenetic trees by maximum likelihood (doc) & tree-puzzle1997d\cite{tree-puzzle1997d} \\
treeview & treeview & Java re-implementation of Michael Eisen's TreeView & treeview\cite{treeview} \\
treeviewx & treeviewx & Displays and prints phylogenetic trees & treeviewx\cite{treeviewx} \\
trilinos-all-dev & trilinos & object-oriented framework for large-scale problems - development files (ALL) & trilinos\cite{trilinos} \\
trilinos-dev & trilinos & object-oriented framework for large-scale problems - development files & trilinos\cite{trilinos} \\
trilinos-doc & trilinos & object-oriented framework for large-scale problems - documentation & trilinos\cite{trilinos} \\
trimmomatic & trimmomatic & flexible read trimming tool for Illumina NGS data & trimmomatic\cite{trimmomatic} \\
trinculo & trinculo & toolkit to carry out genetic association for multi-category phenotypes & trinculo\cite{trinculo} \\
trinityrnaseq & trinityrnaseq & RNA-Seq De novo Assembly & trinityrnaseq\cite{trinityrnaseq} \\
trinityrnaseq-examples & trinityrnaseq & RNA-Seq De novo Assembly common example and testing files & trinityrnaseq\cite{trinityrnaseq} \\
trnascan-se & trnascan-se & detection of transfer RNA genes in genomic sequence & trnascan-se\cite{trnascan-se} \\
trnascan-se-common & trnascan-se & detection of transfer RNA genes in genomic sequence (common files) & trnascan-se\cite{trnascan-se} \\
uc-echo & uc-echo & error correction algorithm designed for short-reads from NGS & uc-echo\cite{uc-echo} \\
ugene & ugene & integrated bioinformatics toolkit & ugene\cite{ugene} \\
ugene & ugene & integrated bioinformatics toolkit & ugene2014\cite{ugene2014} \\
ugene & ugene & integrated bioinformatics toolkit & ugene2018\cite{ugene2018} \\
ugene-data & ugene & required data for UGENE - integrated bioinformatics toolkit & ugene\cite{ugene} \\
ugene-data & ugene & required data for UGENE - integrated bioinformatics toolkit & ugene2014\cite{ugene2014} \\
ugene-data & ugene & required data for UGENE - integrated bioinformatics toolkit & ugene2018\cite{ugene2018} \\
umis & umis & tools for processing UMI RNA-tag data & umis\cite{umis} \\
umis-examples & umis & tools for processing UMI RNA-tag data (examples) & umis\cite{umis} \\
unicycler & unicycler & hybrid assembly pipeline for bacterial genomes & unicycler\cite{unicycler} \\
unicycler & unicycler & hybrid assembly pipeline for bacterial genomes & unicycler2017\cite{unicycler2017} \\
unicycler-data & unicycler & hybrid assembly pipeline for bacterial genomes (data package) & unicycler\cite{unicycler} \\
unicycler-data & unicycler & hybrid assembly pipeline for bacterial genomes (data package) & unicycler2017\cite{unicycler2017} \\
varna & varna & Visualization Applet for RNA & varna\cite{varna} \\
varscan & varscan & variant detection in next-generation sequencing data & varscan\cite{varscan} \\
vcftools & vcftools & Collection of tools to work with VCF files & vcftools\cite{vcftools} \\
vdjtools & vdjtools & framework for post-analysis of B/T cell repertoires & vdjtools\cite{vdjtools} \\
velvet & velvet & Nucleic acid sequence assembler for very short reads & velvet\cite{velvet} \\
velvet-example & velvet & Example data for the Velvet sequence assembler & velvet\cite{velvet} \\
velvet-long & velvet & Nucleic acid sequence assembler for very short reads, long version & velvet\cite{velvet} \\
velvet-tests & velvet & Test data for the Velvet sequence assembler & velvet\cite{velvet} \\
vg & vg & tools for working with genome variation graphs & vg\cite{vg} \\
vg-docs & vg & tools for working with genome variation graphs -- docs & vg\cite{vg} \\
virulencefinder & virulencefinder & identify virulence genes in total or partial sequenced isolates of bacteria & virulencefinder\cite{virulencefinder} \\
virulencefinder-examples & virulencefinder & example data for virulencefinder & virulencefinder\cite{virulencefinder} \\
visp-images-data & visp-images & visual servoing library - dataset reference files & visp-images\cite{visp-images} \\
visp-images-data & visp-images & visual servoing library - dataset reference files & visp-images2018\cite{visp-images2018} \\
vmtk & vmtk & the Vascular Modeling Toolkit & vmtk\cite{vmtk} \\
voro++ & voro++ & library for the computation of the Voronoi diagram & voro--\cite{voro--} \\
voro++-dev & voro++ & library for the computation of the Voronoi diagram (dev files) & voro--\cite{voro--} \\
voro++-examples & voro++ & library for the computation of the Voronoi diagram (examples) & voro--\cite{voro--} \\
voronota & voronota & Voronoi diagram-based tool to find atom contacts & voronota\cite{voronota} \\
votca-csg & votca-csg & VOTCA's coarse-graining engine & votca-csg\cite{votca-csg} \\
votca-csg-scripts & votca-csg & VOTCA's coarse-graining scripts & votca-csg\cite{votca-csg} \\
votca-csg-tutorials & votca-csg & VOTCA's coarse-graining tutorials & votca-csg\cite{votca-csg} \\
votca-tools & votca-tools & VOTCA's tools library, helper binaries & votca-tools\cite{votca-tools} \\
vsearch & vsearch & tool for processing metagenomic sequences & vsearch\cite{vsearch} \\
wannier90 & wannier90 & Maximally Localized Wannier Functions - executables & wannier90\cite{wannier90} \\
wannier90-data & wannier90 & Maximally Localized Wannier Functions - documentation and examples & wannier90\cite{wannier90} \\
wcslib-dev & wcslib & Header files and static library for wcslib and pgsbox & wcslib\cite{wcslib} \\
wcslib-doc & wcslib & API documentation for wcslib & wcslib\cite{wcslib} \\
wcslib-tools & wcslib & Command line tools utilizing wcslib & wcslib\cite{wcslib} \\
wcstools & wcstools & Handle the WCS of a FITS image & wcstools\cite{wcstools} \\
weightwatcher & weightwatcher & Combine maps and polygon data for astronomical image processing & weightwatcher\cite{weightwatcher} \\
wham-align & wham-align & Wisconsin's High-Throughput Alignment Method & wham-align\cite{wham-align} \\
wigeon & microbiomeutil & reimplementation of the Pintail 16S DNA anomaly detection utility & microbiomeutil\cite{microbiomeutil} \\
wise & wise & comparison of biopolymers, like DNA and protein sequences & wise\cite{wise} \\
wise-data & wise & data files for the wise package & wise\cite{wise} \\
wise-doc & wise & documentation for the wise package & wise\cite{wise} \\
wordnet & wordnet & electronic lexical database of English language & wordnet\cite{wordnet} \\
wordnet & wordnet & electronic lexical database of English language & wordnet1998\cite{wordnet1998} \\
wordnet & wordnet & electronic lexical database of English language & wordnet2005\cite{wordnet2005} \\
wordnet-base & wordnet & electronic lexical database of English language (base data) & wordnet\cite{wordnet} \\
wordnet-base & wordnet & electronic lexical database of English language (base data) & wordnet1998\cite{wordnet1998} \\
wordnet-base & wordnet & electronic lexical database of English language (base data) & wordnet2005\cite{wordnet2005} \\
wordnet-dev & wordnet & electronic lexical database of English language (devel) & wordnet\cite{wordnet} \\
wordnet-dev & wordnet & electronic lexical database of English language (devel) & wordnet1998\cite{wordnet1998} \\
wordnet-dev & wordnet & electronic lexical database of English language (devel) & wordnet2005\cite{wordnet2005} \\
wordnet-grind & wordnet & WordNet lexicographer files processor & wordnet\cite{wordnet} \\
wordnet-grind & wordnet & WordNet lexicographer files processor & wordnet1998\cite{wordnet1998} \\
wordnet-grind & wordnet & WordNet lexicographer files processor & wordnet2005\cite{wordnet2005} \\
wordnet-gui & wordnet & electronic lexical database of English language (GUI) & wordnet\cite{wordnet} \\
wordnet-gui & wordnet & electronic lexical database of English language (GUI) & wordnet1998\cite{wordnet1998} \\
wordnet-gui & wordnet & electronic lexical database of English language (GUI) & wordnet2005\cite{wordnet2005} \\
wordnet-sense-index & wordnet & electronic lexical database of English language (index) & wordnet\cite{wordnet} \\
wordnet-sense-index & wordnet & electronic lexical database of English language (index) & wordnet1998\cite{wordnet1998} \\
wordnet-sense-index & wordnet & electronic lexical database of English language (index) & wordnet2005\cite{wordnet2005} \\
wsclean & wsclean & Fast generic widefield interferometric imager & wsclean\cite{wsclean} \\
wsclean-dev & wsclean & Fast generic widefield interferometric imager (development files) & wsclean\cite{wsclean} \\
wtdbg2 & wtdbg2 & de novo sequence assembler for long noisy reads & wtdbg2\cite{wtdbg2} \\
xcrysden & xcrysden & Crystalline and Molecular Structure Visualizer & xcrysden\cite{xcrysden} \\
xcrysden-data & xcrysden & Crystalline and Molecular Structure Visualizer (Data Files) & xcrysden\cite{xcrysden} \\
xmds2 & xmds2 & eXtensible Multi-Dimensional Simulator & xmds2\cite{xmds2} \\
xmds2-doc & xmds2 & documentation for the eXtensible Multi-Dimensional Simulator & xmds2\cite{xmds2} \\
xpa-tools & xpa & Tools for seamless communication between Unix programs & xpa\cite{xpa} \\
yade & yade & Platform for discrete element modeling & yade\cite{yade} \\
yade-doc & yade & Platform for discrete element modeling. Documentation & yade\cite{yade} \\
yaha & yaha & find split-read mappings on single-end queries & yaha\cite{yaha} \\
yorick-gyoto & gyoto & General relativistic geodesic integration for the Yorick language & gyoto\cite{gyoto} \\
zalign & zalign & parallel local alignment of biological sequences & zalign\cite{zalign} \\
\end{longtable}

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