Package : "ACeDB"
Description	 "Object-oriented biological database engine"
Category	 "Database"
Documentation	 "$doc\/acedb\/acedb-man-0.pdf"
Documentation	 "http:\/\/www.acedb.org"
Documentation	 "$doc\/acedb\/howto\/howto.html"
Documentation	 "http:\/\/www.acedb.org\/Tutorial\/brief-tutorial.shtml"
Program	 "xace"
Program	 "tace"
Program	 "acedemo"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
Platform	 "solaris-amd64"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "Babraham Bioinformatics"
Documentation	 "http:\/\/www.bioinformatics.babraham.ac.uk\/"
Program	 "FastQC"
Program	 "trim_galore"

Package : "bioLegato"
Description	 "Programmable graphic user interface"
Category	 "Sequence"
Documentation	 "http:\/\/www.bioinformatics.org\/wiki\/Biolegato"
Documentation	 "$doc\/bioLegato\/bioLegato_man.txt"
Documentation	 "$doc\/bioLegato\/docs"
Program	 "BLExtractSubset.py"
Program	 "blrevcomp"
Program	 "bldna"
Program	 "blmarker"
Program	 "bltree"
Program	 "blprotein"
Program	 "birch"
Program	 "MakeCons"
Program	 "phylcnv.py"
Program	 "blgeneric"
Program	 "blnalign"
Program	 "blpalign"
Program	 "gstat.py"
Program	 "blnfetch"
Program	 "blpfetch"
Program	 "seqfetch.py"
Program	 "blast2gi.py"
Program	 "ncbiquery.py"
Program	 "blncbi"
Program	 "blsort.py"
Program	 "BLHelper.py"
Program	 "BIRCHSettings.py"
Program	 "chooseviewer.py"
Program	 "blastdbkit.py"
Program	 "bltable"
Program	 "DirChooser2"
Program	 "ConfirmBox2"
Program	 "OkayBox2"
Program	 "ErrorBox2"
Program	 "blreads"
Program	 "guesspairs.py"
Program	 "blblastout.py"
Program	 "Gblocks.py"
Program	 "bl_rename.py"
Platform	 "solaris-sparc"
Platform	 "solaris-amd64"
Platform	 "linux-x86_64"
Platform	 "linux-intel"
Platform	 "osx-x86_64"
BIRCH	

Package : "BIRCH"
Description	 "Biological Research Computing Hierarchy"
Program	 "customdoc.py"
Program	 "htmldoc.py"
Program	 "birchhome.py"
Program	 "UNINSTALL-birch.py"
Program	 "birchdb"
Program	 "lbirchdb"
Program	 "ruler"
Program	 "doc2ace.py"
Program	 "dat2ace.py"
Program	 "fil.py"
Program	 "browser.csh"
Program	 "birchstats"
Program	 "btail.py"
Program	 "csv2phyl.sh"
Program	 "l-gbirchdb"
Program	 "pyc.py"
Program	 "phylip.py"
Program	 "birchadmin"
Program	 "birch"
Program	 "birchlib.py"
Program	 "birchscript.py"
Program	 "birchenv.py"
Program	 "rmlauncher.py"
Program	 "BIRCHSettings.py"
Program	 "delgi.py"
Program	 "birchprops"
Program	 "makelinks.sh"
Program	 "uniqid.py"
Program	 "taxfetch.py"
Program	 "BIRCHUserSettings.py"
Program	 "adaptercheck.py"
Program	 "fixfq.py"
Program	 "fastalen.py"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
Platform	 "solaris-amd64"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "Castresana"
Description	 "Biodiversity and Evolution"
Documentation	 "http:\/\/molevol.cmima.csic.es\/castresana\/research.html"
Program	 "Gblocks"
BIRCH	

Package : "CCB"
Description	 "Johns Hopkins Center for Computational Biology"
Category	 "Sequence - Annotation and Gene Discovery"
Category	 "Sequence - DNA Sequencing and Assembly"
Category	 "Gene Expression"
Documentation	 "http:\/\/www.ccb.jhu.edu\/software.shtml"
Program	 "hisat2"
Program	 "hisat2-build"
Program	 "hisat2-inspect"
Program	 "cufflinks"
Program	 "cuffcompare"
Program	 "cuffdiff"
Program	 "cuffmerge"
Program	 "cuffquant"
Program	 "cuffnorm"
Program	 "gffread"
Program	 "gtf_2_sam"
Program	 "stringtie"
Program	 "gffcompare"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "cd-hit"
Description	 "cluster sequences and remove redundancy"
Documentation	 "https:\/\/github.com\/weizhongli\/cdhit\/wiki"
Program	 "cd-hit"
Program	 "cd-hit-est"
Program	 "cd-hit-2d"
Program	 "cd-hit-est-2d"
Program	 "cd-hit-454"
Program	 "cd-hit-lap"
Program	 "cd-hit-div"
Program	 "cd-hit-dup"
BIRCH	

Package : "CLUSTAL"
Description	 "Multiple sequence alignment"
Category	 "Sequence - Multiple Alignment"
Documentation	 "http:\/\/www.clustal.org\/omega\/"
Program	 "clustalo"
BIRCH	

Package : "cutadapt"
Description	 "finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads"
Category	 "Sequence - DNA Sequencing and Assembly"
Documentation	 "https:\/\/cutadapt.readthedocs.io\/en\/stable\/index.html"
Program	 "cutadapt"
local	

Package : "Cytoscape"
Description	 "Cytoscape"
Category	 "Pathway Analysis"
Documentation	 "$doc\/cytoscape\/manual.pdf"
Program	 "cytoscape"
Platform	 "linux-intel"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
Platform	 "solaris-amd64"
Platform	 "solaris-sparc"
Platform	 "win7-64"
Platform	 "winxp-32"
BIRCH	

Package : "Darling Lab"
Description	 "Computational Genomics"
Program	 "Mauve"
BIRCH	

Package : "DIALIGN"
Description	 "Multiple sequence alignment"
Category	 "Sequence - Multiple Alignment"
Documentation	 "http:\/\/dialign-tx.gobics.de\/"
Program	 "dialign-tx"
Platform	 "linux-intel"
Platform	 "linux-x86_64"
Platform	 "solaris-amd64"
Platform	 "solaris-sparc"
Platform	 "osx-x86_64"
BIRCH	

Package : "DTU_Health_Tech"
Program	 "maxalign"

Package : "Durand"
Program	 "BlastViewer"

Package : "EBI"
Description	 "Sequence chromatogram viewer"
Program	 "TraceView"

Package : "EdwardsLab"
Program	 "fastq_pair"

Package : "FASTA"
Description	 "Pairwise and global similarity searches"
Category	 "Sequence - Pairwise Similarity"
Category	 "Sequence - Database Similarity Search"
Documentation	 "$doc\/fasta\/format.txt"
Documentation	 "$doc\/fasta\/fasta_guide.pdf"
Documentation	 "$doc\/fasta\/fasta36.1.html"
Documentation	 "$doc\/fasta\/fasta20.pdf"
Documentation	 "https:\/\/github.com\/wrpearson\/fasta36"
Program	 "garnier"
Program	 "grease"
Program	 "align"
Program	 "fasta"
Program	 "lalign"
Program	 "relate"
Program	 "ssearch"
Program	 "fastx"
Program	 "fasty"
Program	 "randseq"
Program	 "tfastx"
Program	 "tfasty"
Program	 "fasts"
Program	 "fastm"
Program	 "tfasts"
Program	 "fastf"
Program	 "tfastf"
Program	 "ggsearch"
Program	 "glsearch"
Program	 "map_db"
Program	 "fromgb"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
Platform	 "solaris-amd64"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "forester"
Description	 "Programs and API for phylogeny"
Category	 "Phylogeny"
Documentation	 "https:\/\/sites.google.com\/view\/archaeopteryx"
Program	 "phyloXMLconverter"
Program	 "decorator"
Program	 "confadd"
Program	 "Archaeopteryx"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
Platform	 "solaris-amd64"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"

Package : "FSAP"
Description	 "Sequence analysis tools"
Category	 "Sequence"
Program	 "numseq"
Program	 "bachrest"
Program	 "multidigest"
Program	 "gel"
Program	 "p1hom"
Program	 "p2hom"
Program	 "d3hom"
Program	 "d4hom"
Program	 "testcode"
Program	 "funnel"
Platform	 "linux-intel"
Platform	 "solaris-sparc"
Platform	 "solaris-amd64"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
Platform	 "macos-arm64"
BIRCH	

Package : "genographer"
Description	 "Score markers from gel images"
Category	 "Molecular Markers"
Program	 "genographer"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
Platform	 "solaris-amd64"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "GSC"
Description	 "UBC Michael Smith Genome Sciences Centre"
Category	 "Sequence - DNA Sequencing and Assembly"
Documentation	 "http:\/\/www.bcgsc.ca\/platform\/bioinfo\/software"
Program	 "ABySS"
Platform	 "linux-x86_64"
BIRCH	

Package : "HTSLIB"
Description	 "Libraries for High Throughput Sequencing reads"
Category	 "Sequence - DNA Sequencing and Assembly"
Documentation	 "http:\/\/www.htslib.org\/"
Program	 "samtools"
BIRCH	

Package : "jellyfish"
Description	 "Fast, Parallel k-mer Counting for DNA"
Documentation	 "http:\/\/www.genome.umd.edu\/jellyfish.html"
Program	 "jellyfish"
BIRCH	

Package : "LAST"
Description	 "Genome-Scale Sequence Comparison"
Category	 "Comparative Genomics"
Category	 "Sequence - Pairwise Similarity"
Documentation	 "https:\/\/gitlab.com\/mcfrith\/last"
Documentation	 "$doc\/last\/last-evalues.rst"
Documentation	 "$doc\/last\/last-tuning.rst"
Documentation	 "$doc\/last\/last-matrices.rst"
Documentation	 "$doc\/last\/FAQ.rst"
Documentation	 "$doc\/last\/last-repeats.rst"
Documentation	 "$doc\/last\/last-seeds.rst"
Documentation	 "$doc\/last\/last-cookbook.rst"
Program	 "last-bisulfite-paired.sh"
Program	 "last-bisulfite.sh"
Program	 "fastq-interleave"
Program	 "lastal"
Program	 "lastdb"
Program	 "last-dotplot"
Program	 "last-map-probs"
Program	 "last-merge-batches"
Program	 "last-pair-probs"
Program	 "last-postmask"
Program	 "last-split"
Program	 "last-train"
Program	 "maf-convert"
Program	 "maf-join"
Program	 "maf-sort"
Program	 "maf-swap"
Program	 "multiMito.sh"
Program	 "parallel-fasta"
Program	 "parallel-fastq"
Program	 "fasta-nr"
BIRCH	

Package : "MAFFT"
Description	 "Multiple sequence alignment by fast Fourier Transformation"
Category	 "Sequence - Multiple Alignment"
Documentation	 "http:\/\/mafft.cbrc.jp\/alignment\/software\/"
Program	 "mafft"
Platform	 "linux-intel"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "Mapmaker"
Description	 "Mapping with molecular and phenotypic markers"
Category	 "Genetics"
Category	 "Molecular Markers"
Documentation	 "$doc\/mapmaker\/DataPreparationGuide.txt"
Program	 "Mapmaker"
Program	 "MapmakerQTL"
Platform	 "solaris-sparc"

Package : "MCLAMP"
Description	 "Multiple alignment viewer"
Program	 "Jalview"
Platform	 "solaris-amd64"
Platform	 "linux-intel"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
Platform	 "solaris-sparc"

Package : "Mesquite"
Description	 "A modular system for evolutionary analysis"
Category	 "Phylogeny"
Category	 "Molecular Markers"
Documentation	 "http:\/\/www.mesquiteproject.org\/"
Program	 "mesquite"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
Platform	 "solaris-amd64"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "mourisl"
Documentation	 "https:\/\/github.com\/mourisl"
Program	 "Rcorrector"
BIRCH	

Package : "MrBayes"
Description	 "Bayesian inference of phylogeny"
Category	 "Phylogeny"
Documentation	 "http:\/\/mrbayes.csit.fsu.edu\/"
Program	 "mrbayes"
Platform	 "linux-intel"
Platform	 "solaris-amd64"
Platform	 "solaris-sparc"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "MWC"
Description	 "Oligonucleotide Molecular Weight Calculator"
Program	 "MWCalculator"
Platform	 "solaris-amd64"
Platform	 "linux-intel"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
Platform	 "solaris-sparc"

Package : "NCBI"
Description	 "Database tools - Natl. Ctr. for Biotech. Information"
Program	 "sequin"
Program	 "Cn3D"
Program	 "blastp"
Program	 "blastx"
Program	 "blastn"
Program	 "tblastn"
Program	 "tblastx"
Program	 "blast_formatter"
Program	 "makeblastdb"
Program	 "blastdbcmd"
Program	 "tbl2asn"
Program	 "magicblast"
Platform	 "solaris-amd64"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "NCBI-edirect"
Description	 "Entrez Direct: E-utilities on the command line"
Category	 "Database"
Documentation	 "$doc\/NCBI\/edirect\/chapter6.pdf"
Documentation	 "http:\/\/ncbi.nlm.nih.gov\/books\/NBK179288\/"
Documentation	 "http:\/\/www.ncbi.nlm.nih.gov\/books\/NBK25499\/"
Program	 "xtract"
Platform	 "linux-intel"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
Platform	 "solaris-amd64"
Platform	 "solaris-sparc"
BIRCH	

Package : "pal2nal"
Category	 "Sequence - Multiple Alignment"
Documentation	 "http:\/\/www.bork.embl.de\/pal2nal\/#Ref"
Program	 "pal2nal.pl"
BIRCH	

Package : "PHYLIP"
Description	 "Package for Inferring Phylogenies"
Category	 "Phylogeny"
Category	 "Sequence - Phylogeny"
Documentation	 "$doc\/Phylip\/main.html"
Documentation	 "$doc\/Phylip\/contchar.html"
Documentation	 "$doc\/Phylip\/discrete.html"
Documentation	 "$doc\/Phylip\/distance.html"
Documentation	 "$doc\/Phylip\/draw.html"
Documentation	 "$doc\/Phylip\/sequence.html"
Documentation	 "https:\/\/phylipweb.github.io\/phylip\/"
Documentation	 "https:\/\/github.com\/felsenst\/phylip"
Program	 "protpars"
Program	 "dnapars"
Program	 "dnamove"
Program	 "dnapenny"
Program	 "dnacomp"
Program	 "dnainvar"
Program	 "dnaml"
Program	 "dnamlk"
Program	 "dnadist"
Program	 "protdist"
Program	 "seqboot"
Program	 "fitch"
Program	 "kitsch"
Program	 "neighbor"
Program	 "contml"
Program	 "contrast"
Program	 "gendist"
Program	 "restml"
Program	 "restdist"
Program	 "mix"
Program	 "move"
Program	 "penny"
Program	 "dollop"
Program	 "dolmove"
Program	 "dolpenny"
Program	 "clique"
Program	 "factor"
Program	 "drawgram"
Program	 "drawtree"
Program	 "consense"
Program	 "pars"
Program	 "treedist"
Program	 "proml"
Program	 "promlk"
Program	 "retree"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
Platform	 "solaris-amd64"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "pigz"
Program	 "pigz"

Package : "pollux"
Description	 "DNA sequence read correction for all sequencing platforms"
Category	 "Sequence - DNA Sequencing"
Category	 "Sequence - DNA Sequencing and Assembly"
Documentation	 "https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-014-0435-6"
Program	 "pollux"
Platform	 "linux-x86_64"
BIRCH	

Package : "PRIMER3"
Description	 "Oligonucleotide design"
Category	 "Sequence - Oligonucleotides"
Documentation	 "http:\/\/primer3.sourceforge.net\/"
Program	 "primer3_core"
BIRCH	

Package : "READSEQ"
Description	 "Sequence format translator"
Program	 "readseq"
Platform	 "solaris-amd64"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "Saint Petersberg Algorithmic Biology Lab"
Documentation	 "http:\/\/bioinf.spbau.ru\/en"
Program	 "spades"
Program	 "dipspades"
Program	 "truspades"
Program	 "rnaspades"
Program	 "quast"

Package : "Salmon"
Documentation	 "https:\/\/salmon.readthedocs.io\/en\/latest\/index.html"
Program	 "salmon"
BIRCH	

Package : "SangerSeqTools"
Description	 "Package for visualizing sequence alignments"
Category	 "Sequence - Pairwise Similarity"
Category	 "Sequence - Multiple Alignment"
Documentation	 "http:\/\/www.sanger.ac.uk\/science\/tools\/seqtools"
Program	 "dotter"
Platform	 "linux-x86_64"
BIRCH	

Package : "SeqKit"
Program	 "seqkit"

Package : "SOAP"
Program	 "SOAPdenovo-Trans"
Program	 "SOAPdenovo2"

Package : "TIGR-TM4"
Description	 "TIGR Microarray programs"
Category	 "Gene Expression"
Documentation	 "http:\/\/www.tm4.org"
Program	 "ExpressConverter"
Program	 "midas"
Program	 "tmev"
Platform	 "solaris-sparc"
Platform	 "solaris-amd64"
Platform	 "linux-intel"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "transrate"
Description	 "de-novo transcriptome assembly quality analysis"
Category	 "Gene Expression"
Documentation	 "http:\/\/hibberdlab.com\/transrate"
Program	 "transrate"
BIRCH	

Package : "Trimmomatic"
Program	 "Trimmomatic"

Package : "Trinity"
Description	 "RNA-Seq De novo Assembly"
Category	 "Gene Expression"
Documentation	 "http:\/\/github.com\/trinityrnaseq\/trinityrnaseq\/wiki"
Program	 "Trinity"
Platform	 "linux-x86_64"
BIRCH	

Package : "WebLogo"
Description	 "Create sequence logos"
Category	 "Sequence - Pattern Discovery and Matching"
Program	 "WebLogo"
Data	 "http:\/\/weblogo.threeplusone.com"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "weighbor"
Description	 "weighted neighbor-joining"
Category	 "Phylogeny"
Documentation	 "http:\/\/www.t10.lanl.gov\/billb\/weighbor"
Program	 "weighbor"
Platform	 "solaris-sparc"
Platform	 "solaris-amd64"
Platform	 "linux-intel"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "Wellcome_Trust_Sanger_Institute"
Description	 "Genomics Applications"
Documentation	 "https:\/\/www.sanger.ac.uk\/science\/tools"
Program	 "artemis"
Platform	 "solaris-amd64"
Platform	 "solaris-sparc"
Platform	 "linux-intel"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"
BIRCH	

Package : "XYLEM"
Description	 "Create and manipulate database subsets"
Category	 "Database"
Program	 "getob"
Program	 "ribosome"
Program	 "prot2nuc"
Program	 "clu2ig"
Program	 "reform"
Program	 "fetch"
Program	 "features"
Program	 "splitdb"
Program	 "getloc"
Program	 "xylem_shuffle"
Platform	 "linux-intel"
Platform	 "solaris-sparc"
Platform	 "solaris-amd64"
Platform	 "linux-x86_64"
Platform	 "osx-x86_64"

Package : "Zmasek"
Description	 "Programs of Christian Zmasek"
Program	 "Archaeopteryx"
BIRCH