Difference between revisions of "Installed Software"

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[[Category:Software]]
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#REDIRECT [[Applications]]
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* Last updated on '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''.bes
 
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* Up to three latest versions are listed. The default is shown in '''bold''' if it's not the latest version.
 
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* See output of 'module spider '''module_name'''' for a full list of provided versions.
 
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<span id="top"></span>
 
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<!--[[#0|0-9]]-->[[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] <!--[[#Z|Z]]-->
 
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{|  border="1"  cellspacing="0" cellpadding="2" align="center"  class="wikitable sortable" style="border-collapse: collapse; margin: 1em 1em 1em 0; border-top: none; border-right:none; "
 
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|-
 
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! scope="col" | Name
 
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! scope="col" class="unsortable" | Version <ref name="version">Up to 3 most recent/important releases are listed. See the individual application pages and the output of "module spider software" for full version listing.</ref>
 
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! scope="col" class="unsortable" | Website
 
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! scope="col" | Category
 
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|-
 
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| <span id="#"></span> [[4P]] || 1.0 || [https://github.com/anbena/4p] || Biology, SNP
 
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|-
 
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| <span id="A"></span> [[AbInit]] || 6.12.3, 7.10.2, 7.10.4 || [http://www.abinit.org/] || Quantum Chemistry, DFT
 
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|-
 
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| [[Abyss]] || 1.5.2, 1.9.0, 2.0.0 || [http://www.bcgsc.ca/platform/bioinfo/software/abyss] || Biology, NGS
 
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|-
 
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| [[ADMB]] || 11.5 || [http://www.admb-project.org/] || Math, Modeling, Optimization
 
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|-
 
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| [[AdmixTools]] || 20150311, 20160513 || [http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html] || Biology, Bioinformatics, Genomics, NGS
 
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|-
 
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| [[ADMIXTURE]] || 1.23, 1.3.0 || [https://www.genetics.ucla.edu/software/admixture/index.html] || Biology, Bioinformatics, Genomics, NGS
 
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|-
 
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| [[AEGeAn]] || 0.14.0 || [http://aegean.readthedocs.org/en/v0.12.2/index.html] || Biology, Genomics
 
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|-
 
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| [[AFNI]] || 2013_11_24, 2016_0_19 || [http://afni.nimh.nih.gov/afni] || Biology, Statistics, Imaging, Neurology
 
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|-
 
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| [[Agalma]] || 0.2.1, 0.3.5, 0.5.0 || [https://bitbucket.org/caseywdunn/agalma] || Biology, Bioinformatics, Genomics, SNP
 
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|-
 
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| [[AGOUTI]] || 0.3.3 || [https://github.com/svm-zhang/AGOUTI] || Biology, Genomics
 
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|-
 
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| [[ALE]] || 20150507 || [http://sc932.github.io/ALE/] || Biology, Bioinformatics, Assembly
 
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|-
 
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| [[ALLPATHS-LG]] || 42316, 44837 || [http://www.broadinstitute.org/software/allpaths-lg/blog/] || Biology, NGS
 
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|-
 
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| [[Amber]] || 11, '''12''', 14, 16 || [http://ambermd.org/] || Simulation, chemistry
 
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|-
 
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| [[AMAS]] || 0.98 || [https://github.com/marekborowiec/AMAS/] || Biology, Sequence Alignment
 
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|-
 
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| [[AMOS]] || 3.1.0 || [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS] || Biology, Genomics, NGS
 
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|-
 
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| [[AMPHORA2]] || 20140305 || [https://github.com/martinwu/AMPHORA2] || Biology, Phylogenetics
 
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|-
 
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| [[AMPtk]] || 0.8.0, 0.8.5 || [https://github.com/nextgenusfs/amptk] || Biology, Bioinformatics, NGS
 
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|-
 
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| [[Anvio]] || 2.0.0, 2.0.2, 2.1.0 || [https://github.com/meren/anvio] || Biology, Microbial 'omics
 
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|-
 
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| [[ANNOVAR]] || 20120621, 20150322 || [http://www.openbioinformatics.org/annovar/] || Biology, Genomics
 
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|-
 
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| [[AStalavista]] || 3.2 || [http://sammeth.net/confluence/display/ASTA/Home] || Biology, NGS, RNA-Seq, Genomics
 
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|-
 
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| [[ASTRID]] || 20150807 || [https://github.com/pranjalv123/ASTRID] || Biology, Genomics
 
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|-
 
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| [[Atlas]] || 3.10.1, 3.11.17 || [http://www.gnu.org/software/gsl] || Library, Math
 
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|-
 
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| [[Amuse]] || 6.0, 10.0 || [http://www.amusecode.org] || Astrophysics
 
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|-
 
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| [[ANGSD]] || 20150306, 20150909 || [http://popgen.dk/wiki/index.php/ANGSD] || Biology, NGS
 
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|-
 
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| [[APT|Affymetrix Power Tools]] || 1.15.0, 1.18.0 || [http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx] || Biology, Genomics, Microarray
 
−
|-
 
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| [[ARC]] || 20140312 || [https://github.com/ibest/ARC] || Biology, NGS
 
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|-
 
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| [[ARCS]] || 1.0.0 || [https://github.com/bcgsc/arcs] || Biology, Genomics
 
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|-
 
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| [[Armadillo]] || 6.200.3 || [http://arma.sourceforge.net/] || Library, C++ , Math
 
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|-
 
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| [[Astral]] || 4.10.6, 4.10.7, 5.0.3 || [https://github.com/smirarab/ASTRAL] || Biology, Bioinformatics, NGS, Phylogenetics
 
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|-
 
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| [[AtomEye]] || 3 || [http://li.mit.edu/Archive/Graphics/A/] || Material Science
 
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|-
 
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| [[ATRAM]] || 20140624 || [https://github.com/juliema/aTRAM] || Biology, NGS
 
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|-
 
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| [[Augustus]] || 2.6, 3.2.1, 3.2.2 || [http://augustus.gobics.de/] || Biology, NGS
 
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|-
 
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| [[Auto3DEM]] || 4.05.1, 4.05.2 || [http://cryoem.ucsd.edu/wikis/software/start.php?id=auto3dem:download] || Image Reconstruction
 
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|-
 
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| <span id="B"></span> [[BamBam]] || 1.0 || [http://udall-lab.byu.edu/Research/Software/BamBam.aspx] || Biology, NGS
 
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|-
 
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| [[BALI-PHY]] || 2.3.8 || [http://www.bali-phy.org/] || Bioinformatics, Bayesian Estimation
 
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|-
 
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| [[BAMM]] || 2.5.0 || [http://bamm-project.org/] || Biology, Phylogenetics
 
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|-
 
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| [[Bam-readcount]] || 20150216 || [https://github.com/genome/bam-readcount] || Biology, NGS
 
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|-
 
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| [[Bamstats]] || 20140602 || [https://github.com/lindenb/jvarkit/wiki/BamStats04] || Biology, NGS
 
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|-
 
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| [[Bamtools]] || 2.1.1 || [https://github.com/pezmaster31/bamtools/wiki] || Biology, NGS
 
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|-
 
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| [[BamUtil]] || 1.0.2 || [http://genome.sph.umich.edu/wiki/BamUtil] || Biology, NGS
 
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|-
 
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| [[Bam-Readcount]] || 20150616 || [https://github.com/genome/bam-readcount]] || Biology, Genomics
 
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|-
 
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| [[BAPS]] || 6.0 || [http://www.helsinki.fi/bsg/software/BAPS/] || Biology, Populaton genetics
 
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|-
 
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| [[Barrnap]] || 0.7 || [http://www.vicbioinformatics.com/software.barrnap.shtml] || Biology, RNA-Seq
 
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|-
 
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| [[Basemount]] || 0.1.2.464 || [https://help.basespace.illumina.com/articles/descriptive/introduction-to-basemount/] || Biology, DNA Sequencing
 
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|-
 
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| [[BayArea]] || 1.0.2 || [https://code.google.com/archive/p/bayarea/] || Biology
 
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|-
 
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| [[BayeScan]] || 2.1 || [http://cmpg.unibe.ch/software/BayeScan/index.html] || Biology, SNP
 
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|-
 
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| [[BayeScEnv]] || 1.1 || [https://github.com/devillemereuil/bayescenv]] || Biology, SNP, Phylogenetics
 
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|-
 
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| [[BayesRate]] || 1.3.43 || [http://sourceforge.net/projects/bayesrate/] || Biology, Phylogenetics
 
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|-
 
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| [[Bbcp]] || 12.08.17.00.0  || [http://www.slac.stanford.edu/~abh/bbcp/] || Network file transfer
 
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|-
 
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| [[BBMap]] || 36.23 || [https://sourceforge.net/projects/bbmap/] || Biology, Alignment
 
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|-
 
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| [[Bcbio-nextgen]] || 0.8.7, 0.9.9 || [https://github.com/chapmanb/bcbio-nextgen] || Biology, NGS
 
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|-
 
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| [[Bcftools]] || 1.2, 1.3.1, 1.4 || [http://samtools.github.io/bcftools/] || Biology, Genomics, NGS
 
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|-
 
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| [[Bcl2fastq]] || 2.16 || [http://support.illumina.com/downloads/bcl2fastq_conversion_software.html] || Biology, NGS, Illumina
 
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|-
 
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| [[Beagle|BEAGLE]] || 3.2.2, 4.0 || [http://faculty.washington.edu/browning/beagle/beagle.html] || Biology, Genetics, Genotyping
 
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|-
 
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| [[Beast|BEAST]] || 1.7.5, '''1.8.1''', 2.3.2 || [http://www.beast2.org/wiki/index.php/Main_Page]|| Biology, Phylogenetics
 
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|-
 
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| [[Bedops]] || 2.4.2 || [http://www.uwencode.org/software]||  Biology, Bioinformatics, Sequence, NGS
 
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|-
 
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| [[Bedtools|BEDTools]] || 2.23.0, 2.24.0, 2.26.0 || [https://github.com/arq5x/bedtools2]|| Biology, NGS
 
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|-
 
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| [[BEST]] || 2.3.1 || [http://www.stat.osu.edu/~dkp/BEST] || Biology, Phylogenetics
 
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|-
 
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| [[BESST]] || 2.2.4 || [https://github.com/ksahlin/BESST] || Biology, Bioinformatics
 
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|-
 
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| [[BETA]] || 1.0.5 || [http://cistrome.org/BETA/] || Biology, NGS
 
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|-
 
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| [[BFAST]] || 0.7.0 || [http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page] || Biology, NGS
 
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|-
 
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| [[Bismark]] || 0.7.7, 0.13.0, 0.17.0 || [http://www.bioinformatics.babraham.ac.uk/projects/download.html#bismark] || Biology, NGS, Methylation
 
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|-
 
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| [[BinPacker]] || 1.0 || [https://sourceforge.net/projects/transcriptomeassembly/] || Biology, RNA-Seq, Sequence Assembly
 
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|-
 
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| [[BinSanity]] || 0.1.3 || [https://github.com/edgraham/BinSanity] || Biology, Genomics
 
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|-
 
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| [[Bioconductor]] || Latest || [http://www.bioconductor.org/] || Biology, R, Statistics
 
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|-
 
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| [[Perl|BioPerl]] || 1.006901 || [http://bioperl.org/] || Biology, Perl
 
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|-
 
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| [[Python|BioPython]] || 1.59 || [http://biopython.org/] || Biology, Python
 
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|-
 
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| [[BLASR]] || 20130815 || [https://github.com/PacificBiosciences/blasr] || Biology, NGS
 
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|-
 
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| [[Blast|NCBI BLAST]] || 2.2.27, 2.5.0, 2.6.0 || [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download ] || Biology, Sequence alignment
 
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|-
 
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| [[Blast2go]] || 2.5.0-20120705 || [http://www.blast2go.com/b2ghome] || Biology, Annotation
 
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|-
 
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| [[BLAT]] || 20120524, 20140318 || [http://genome.ucsc.edu/goldenPath/help/blatSpec.html] || Biology, Sequence alignment
 
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|-
 
−
| [[Blender]] || 2.63 || [http://www.blender.org/] || Graphics
 
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|-
 
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| [[BLESS]] || 1.02 || [https://sourceforge.net/projects/bless-ec/files/] || Biology, NGS
 
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|-
 
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| [[BLUPF90]] || 20160604 || [http://nce.ads.uga.edu/wiki/doku.php?id=start] || Biology, Phylogenetics
 
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|-
 
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| [[BoltzTraP]] || 1.2.5 || [http://www.icams.de/content/departments/cmat/boltztrap/] || Physics
 
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|-
 
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| [[Boost]] || '''1.49.0''', 1.53.0, 1.54.0 || [http://www.boost.org/] || C++, Library
 
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|-
 
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| [[Bowtie]] || 0.12.9, 1.1.1, 1.2.0 || [http://bowtie-bio.sourceforge.net/index.shtml] || Biology, NGS
 
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|-
 
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| [[Bowtie2]] || 2.2.8, 2.2.9, 2.3.0 || [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml] || Biology, NGS
 
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|-
 
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| [[BPP]] || 1.9.0, 2.2, 3.2 || [http://abacus.gene.ucl.ac.uk/software.html] || Biology, Phylogenetics
 
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|-
 
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| [[BRANCH]] || 1.8.1 || [http://manuals.bioinformatics.ucr.edu/home/branch] || Biology, NGS, Mapping
 
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|-
 
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| [[BRATNextGen]] || 20150505 || [http://www.helsinki.fi/bsg/software/BRAT-NextGen/] || Biology, Genomics
 
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|-
 
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| [[BRIG]] || 0.95 || [https://sourceforge.net/projects/brig/] || Biology, Genomics
 
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|-
 
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| [[Bsoft]] || 1.9.1 || [http://lsbr.niams.nih.gov/bsoft/] || Biology, Image Analysis
 
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|-
 
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| [[Bsmap]] || 2.74, 2.87 || [https://code.google.com/p/bsmap/] || Biology, NGS, Methylation
 
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|-
 
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| [[BUCKy]] || 1.4.4 || [http://www.stat.wisc.edu/~ane/bucky/index.html] || Biology, Genomics
 
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|-
 
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| [[BUSCO]] || 1.1b1, 1.22, 2.0b || [http://busco.ezlab.org/] || Biology, Genomics
 
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|-
 
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| [[Bwa]] || 0.6.1, 0.7.12, 0.7.15 || [http://bio-bwa.sourceforge.net/] || Biology, NGS
 
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|-
 
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| [[BXH_XCEDE_tools]] || 1.11.1 || [https://xwiki.nbirn.org:8443/xwiki/bin/view/Function-BIRN/AutomatedQA] || Biology, Bioinformatics
 
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|-
 
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| <span id="C"></span> [[Camino]] || 20140723 || [http://cmic.cs.ucl.ac.uk/camino] || Biology, Neuroscience, Imaging
 
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|-
 
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| [[Canu]] || 1.0, 1.1, 1.3 || [http://canu.readthedocs.org/en/latest/] || Biology, Sequencing
 
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|-
 
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| [[CAP3]] || 20120705 || [http://seq.cs.iastate.edu/] || Biology, Sequence Assembly
 
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|-
 
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| [[CASAVA]] || 1.8.2 || [http://www.illumina.com/software/genome_analyzer_software.ilmn] || Biology, NGS
 
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|-
 
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| [[CD-HIT]] || 4.6, 4.6.4 || [http://weizhong-lab.ucsd.edu/cd-hit/] || Biology, Genomics
 
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|-
 
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| [[CDO]] || 1.6.1, 1.7.2rc5 || [https://code.zmaw.de/projects/cdo] || Climate
 
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|-
 
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| [[CEAS]] || 1.0.2 || [http://liulab.dfci.harvard.edu/CEAS] || Biology, Genomics
 
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|-
 
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| [[CellProfiler]] || 2.0 || [http://cellprofiler.org] || Biology, Image Analysis
 
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|-
 
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| [[CellRanger]] || 1.2.1, 1.3.0 || [https://support.10xgenomics.com/single-cell/software/pipelines/latest/what-is-cell-ranger] || Biology, Bioinformatics, NGS, RNA-Seq
 
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|-
 
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| [[CFITSIO]] || 3.370 || [http://heasarc.gsfc.nasa.gov/fitsio/] || Library, C
 
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|-
 
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| [[CGATools]] || 1.6.0.42 || [http://sourceforge.net/projects/cgatools/] || Biology, NGS
 
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|-
 
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| [[Charmm]] || 36a3 || [http://www.charmm.org/] || Simulation, Chemistry
 
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|-
 
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| [[Chartdirector]] || 5.1.0 || [http://www.advsofteng.com/] || Graphics
 
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|-
 
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| [[CheckM]] || 1.0.4 || [https://github.com/Ecogenomics/CheckM] || Biology, Genomics
 
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|-
 
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| [[Chimera]] || 1.7 || [http://www.cgl.ucsf.edu/chimera/index.html] || Biology, Modeling
 
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|-
 
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| [[ChromEvol]] || 2.0 || [http://www.tau.ac.il/~itaymay/cp/chromEvol/index.html] || Biology, Phylogenetics
 
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|-
 
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| [[CIMS]] || 4.1.2 || [http://zhanglab.c2b2.columbia.edu/index.php/CIMS_Documentation] || Biology, Genomics
 
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|-
 
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| [[Circos]] || 0.63-pre11, 0.69-2 || [http://circos.ca/software/download/circos/] || Biology, Visualization
 
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|-
 
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| [[CisGenome]] || 2.0 || [http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm] || Biology, Genomics, Peak Calling
 
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|-
 
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| [[Clann]] || 3.2.3 || [https://code.google.com/p/clann/] || Biology, Phylogenetics
 
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|-
 
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| [[CLARK]] || 1.2.2-b || [http://clark.cs.ucr.edu/] || Biology, Genomics
 
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|-
 
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| [[CLHEP]] || 2.2.0.1 || [http://proj-clhep.web.cern.ch/proj-clhep/] || High Energy Physics
 
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|-
 
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| [[CLIPper]] || 1.0 || [https://github.com/YeoLab/clipper/wiki/CLIPper-Home] || Biology, Sequencing
 
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|-
 
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| [[CLIPSeqTools]] || 0.1.7 || [http://mourelatos.med.upenn.edu/clipseqtools/] || Biology, Sequencing
 
−
|-
 
−
| [[ClonalFrame]] || 1.1, 1.2 || [http://www.xavierdidelot.xtreemhost.com/clonalframe.htm] || Biology, Genomics, NGS
 
−
|-
 
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| [[ClonalFrameML]] || 1.25 || [https://code.google.com/p/clonalframeml/] || Biology, Genomics, NGS
 
−
|-
 
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| [[ClustalW]] || 2.1 || [http://www.clustal.org/clustal2/] || Biology, Genomics
 
−
|-
 
−
| [[Cluster3]] || 1.52 || [http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm] || Biology, Genomics
 
−
|-
 
−
| [[Clview]] || 20130402 || [http://sourceforge.net/projects/clview/] || Biology, Genomics
 
−
|-
 
−
| [[ClustalO]] || 1.2.0 || [http://www.clustal.org/omega/] || Biology, Genomics
 
−
|-
 
−
| [[CLUMPP]] || 1.1.2 || [https://web.stanford.edu/group/rosenberglab/clumpp.html]] || Biology, Bioinformatics
 
−
|-
 
−
| [[ClusterFinder]] || 313 || [http://iroatech.com/page/The%20ClusterFinderTM%20Software] || Biology, Metabolomics
 
−
|-
 
−
| [[CMake]] || 2.8.8, 2.9.12.1, 3.1.0 || [http://www.cmake.org/] || Programming, Build System
 
−
|-
 
−
| [[CMWP]] || 140518 || [http://csendes.elte.hu/mwp/] || Biology, Genomics
 
−
|-
 
−
| [[CNVnator]] || 0.3.2 || [https://github.com/abyzovlab/CNVnator] || Biology, Genomics
 
−
|-
 
−
| [[CNVSeq]] || 20110715 || [http://tiger.dbs.nus.edu.sg/cnv-seq/] || Biology, NGS
 
−
|-
 
−
| [[Cobrapy]] || 0.3.2 || [https://cobrapy.readthedocs.org/en/latest/] || Biology, Metabolomics, Modeling
 
−
|-
 
−
| [[Coevol]] || 1.3c, 1.4b || [http://megasun.bch.umontreal.ca/People/lartillot/www/downloadcoevol.html] || Biology, Phylogenetics
 
−
|-
 
−
| [[CoMap]] || 1.4.1 || [http://home.gna.org/comap] || Biology, Genomics
 
−
|-
 
−
| [[CONSEL]] || 0.20 || [http://www.sigmath.es.osaka-u.ac.jp/shimo-lab/prog/consel/] || Biology, Phylogenetcs
 
−
|-
 
−
| [[CONCOCT]] || 0.3.1 || [https://github.com/BinPro/CONCOCT] || Biology, Genomics
 
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|-
 
−
| [[ContaVect]] || 0.2 || [https://github.com/a-slide/ContaVect] || Biology, Phylogenetics
 
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|-
 
−
| [[CoNIFER]] || 0.2.2 || [http://conifer.sourceforge.net/download.html] || Biology, Genomics
 
−
|-
 
−
| [[Consed]] || 23.0 || [http://bozeman.mbt.washington.edu/consed/consed.html] || Biology, Genomics
 
−
|-
 
−
| [[Coreutils]] || 8.23 || [https://www.gnu.org/software/coreutils/] || GNU Utilities, Computer Science
 
−
|-
 
−
| [[Corset]] || 1.06 || [https://github.com/Oshlack/Corset] || Biology, NGS
 
−
|-
 
−
| [[covNMR]] || 2014 || [http://spin.ccic.ohio-state.edu/index.php/welcome/index] || Biochemistry
 
−
|-
 
−
| [[CPLEX]] || 12.6.5 || [http://www-01.ibm.com/software/commerce/optimization/cplex-optimizer/] || Optimizer
 
−
|-
 
−
| [[CUDA]] || 4.2, 5.5 || [http://www.nvidia.com/object/cuda_home_new.html] || Programming, Graphics
 
−
|-
 
−
| [[CrossMap]] || 0.2.3 || [http://crossmap.sourceforge.net/] || Biology, Genomics
 
−
|-
 
−
| [[Crux]] || 1.40 || [http://cruxtoolkit.sourceforge.net/] || Biology, Mass-Spectrometry
 
−
|-
 
−
| [[Cufflinks|Cufflinks]] || 1.3.0, 2.0.2, 2.2.1 || [http://cufflinks.cbcb.umd.edu/] || Biology, NGS
 
−
|-
 
−
| [[Cutadapt]] || 1.7.1, 1.8.1, 1.10 || [http://code.google.com/p/cutadapt/] || Biology, NGS
 
−
|-
 
−
| [[CUTE]] || 20160116, 20161010 || [http://members.ift.uam-csic.es/dmonge/CUTE.html] || Cosmology
 
−
|-
 
−
| [[Cytoscape]] || 3.4.0 || [http://www.cytoscape.org/what_is_cytoscape.html]] || Biology, Bioinformatics
 
−
|-
 
−
| <span id="D"></span> [[DAKOTA]] || 5.4.0 || [http://dakota.sandia.gov/index.html] || Computational Science
 
−
|-
 
−
| [[DaPars]] || 0.9.0 || [https://code.google.com/p/dapars/] || Biology, NGS, RNA-Seq
 
−
|-
 
−
| [[DALIGNER]] || 1.0 || [https://github.com/thegenemyers/DALIGNER] || Biology, Sequencing
 
−
|-
 
−
| [[Datamash]] || 1.1.0 || [http://www.gnu.org/software/datamash/] || Math
 
−
|-
 
−
| [[DCMTK]] || 3.6.0 || [http://dicom.offis.de/dcmtk.php.en] || Biology, Neuroscience, Imaging
 
−
|-
 
−
| [[DSSAT]] || 4.5 || [http://dssat.net/about] || Biology
 
−
|-
 
−
| [[dDocent]] || 20160425 || [https://github.com/jpuritz/dDocent] || Biology
 
−
|-
 
−
| [[DDSCAT]] || 7.3.0 || [https://code.google.com/p/ddscat/] || Astrophysics
 
−
|-
 
−
| [[DDT]] || 4.1.0, 4.2.1 || [http://www.allinea.com/products/ddt] || Software
 
−
|-
 
−
| [[Dealii]] || 8.3.0 || [https://dealii.org/download.html] || Library
 
−
|-
 
−
| [[DeconSeq]] || 0.4.3 || [http://deconseq.sourceforge.net/] || Biology, Phylogenetics
 
−
|-
 
−
| [[Delft3D]] || 3621 || [http://oss.deltares.nl/web/delft3d] || Hydrodynamics, Physics
 
−
|-
 
−
| [[DeepPicker]] || 20161102 || [https://github.com/nejyeah/DeepPicker-python] || Deep Learning, Cross-Molecule Training
 
−
|-
 
−
| [[DeepTools]] || 2.4.3 || [https://github.com/fidelram/deepTools] || Biology, Bioinformatics, NGS
 
−
|-
 
−
| [[Desmond]] || 3.0.3.1 || [http://www.deshawresearch.com/resources_desmond.html] || Simulation, Biology, Chemistry
 
−
|-
 
−
| [[DETONATE]] || 1.9, 1.11 || [http://deweylab.biostat.wisc.edu/detonate/] || Biology, NGS
 
−
|-
 
−
| [[DEXTRACTOR]] || 1.0 || [https://github.com/thegenemyers/DEXTRACTOR] || Biology, Sequencing
 
−
|-
 
−
| [[Dalton]] || 2011 || [http://daltonprogram.org] || Quantum Chemistry
 
−
|-
 
−
| [[Diamond]] || 0.5.1, 0.8.5 || [http://ab.inf.uni-tuebingen.de/software/diamond/] ||  Computational Biology, Genomics
 
−
|-
 
−
| [[Dibig Tools]] || 1.0 || [http://compbio.ufl.edu/dibig-tools-available-on-hipergator/] ||  Bioinformatics, PBS, Torque, Jobs
 
−
|-
 
−
| [[DiffReps]] || 1.55.4 || [https://code.google.com/p/diffreps/] || Biology, NGS, ChIP-Seq
 
−
|-
 
−
| [[Dindel]] || 1.01 || [http://www.sanger.ac.uk/resources/software/dindel/] || Biology, NGS
 
−
|-
 
−
| [[DISCOVARdenovo]] || 52488 || [http://www.broadinstitute.org/software/discovar/blog/?page_id=14] || Biology, NGS
 
−
|-
 
−
| [[DIYABC]] || 1.0.4.43b, 2.0.3 || [http://www1.montpellier.inra.fr/CBGP/diyabc/index.php] || Biology, Genomics
 
−
|-
 
−
| [[Dlpoly]] || 4.03.4 || [http://www.cse.clrc.ac.uk/ccg/software/DL_POLY/index.shtml]  || Simulation, Biology, Chemistry
 
−
|-
 
−
| [[Dlpoly-Classic]] || 1.9 || [http://www.ccp5.ac.uk/DL_POLY_CLASSIC/]  || Simulation, Biology, Chemistry
 
−
|-
 
−
| [[DNA Clust]] || 3.0 || [http://sourceforge.net/projects/dnaclust/] || Biology, Genomics
 
−
|-
 
−
| [[Dock]] || 6.5, 6.6, 6.7 || [http://dock.compbio.ucsf.edu/] || Chemistry, ligand binding prediction
 
−
|-
 
−
| [[DOT]] || 2.0 || [http://www.sdsc.edu/CCMS/DOT/] || Biology, Bioinformatics, Docking
 
−
|-
 
−
| [[DosageConvertor]] || 1.0.3 || [http://genome.sph.umich.edu/wiki/DosageConvertor] || Biology, Converter
 
−
|-
 
−
| [[Doxygen]] || 1.8.3.1 || [http://www.sdsc.edu/CCMS/DOT/] || Programming, Documentation
 
−
|-
 
−
| [[DSSP]] || 2.2.1 || [http://swift.cmbi.ru.nl/gv/dssp/] || Biology, Molecular Dynamics
 
−
|-
 
−
| [[DTI-TK]] || 2.3.1 || [http://www.nitrc.org/projects/dtitk/] || Biology, Neurology, Imaging
 
−
|-
 
−
| <span id="E"></span> [[EA-Utils]] || 1.1.2.537 || [https://code.google.com/p/ea-utils/] || Biology, NGS
 
−
|-
 
−
| [[ECTools]] || 20140311, 20141201 || [https://github.com/jgurtowski/ectools] || Biology, Sequencing, Bioinformatics
 
−
|-
 
−
| [[ECE]] || 1.0 || [https://www.ece.ufl.edu/] || Ece
 
−
|-
 
−
| [[EEGLAB]] || 12.0.2.1b, 13.2.2b, 13.4.4b || [http://sccn.ucsd.edu/wiki/EEGLAB] || Biology, Matlab
 
−
|-
 
−
| [[ED2]] || 2.1 || [https://github.com/EDmodel/ED2] || Biology
 
−
|-
 
−
| [[eGene-MVN]] || 0.1 || [http://genetics.cs.ucla.edu/metatissue/index.html] || Biology, Genetics
 
−
|-
 
−
| [[eigenMT]] || 20160228 || [http://montgomerylab.stanford.edu/resources/eigenMT/eigenMT.html] || Biology, Genetics
 
−
|-
 
−
| [[EIGENSOFT]] || 4.2, 5.0.1, 6.0.1 || [http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html] || Biology, Population
 
−
|-
 
−
| [[emboss]] || 6.5.7 || [http://emboss.sourceforge.net/] || Biology, multi-tool suite
 
−
|-
 
−
| [[EMAN2]] || 2.11 || [http://ncmi.bcm.edu/ncmi/software/counter_222/software_130] || Biology
 
−
|-
 
−
| [[EMMAX]] || 20100307, 20120210 || [http://genetics.cs.ucla.edu/emmax/] || Biology, NGS, Mapping
 
−
|-
 
−
| [[EMC]] || 9.3.9 || [http://montecarlo.sourceforge.net/emc/Welcome.html] || Monte Carlo Simulations
 
−
|-
 
−
| [[EMIRGE]] || 20130727 || [https://github.com/csmiller/EMIRGE] || Biology, NGS
 
−
|-
 
−
| [[Ensembl_Tools]] || 80 || [http://useast.ensembl.org/info/docs/tools/index.html] || Biology, Bioinformatics
 
−
|-
 
−
| [[EPACTS]] || 3.2.6 || [http://genome.sph.umich.edu/wiki/EPACTS#Installation_Details] || Biology, Bioinformatics, Genomics
 
−
|-
 
−
| [[EPOCH]] || 4.7.3 || [http://ccpforge.cse.rl.ac.uk/gf/project/epoch/] || Astronomy, CPPP
 
−
|-
 
−
| [[eQTLA]] || 1.1 || [http://research.lunenfeld.ca/silverberg/] || Biology, Genomics
 
−
|-
 
−
| [[Eqtlbma]] || 1.2.2 || [https://github.com/timflutre/eqtlbma] || Biology, Genotyping
 
−
|-
 
−
| [[Esmf]] || 6.3.0rp1 || [http://www.earthsystemmodeling.org/] || Climate
 
−
|-
 
−
| [[Espresso]] || 5.0.1, 5.2.0, 5.2.1, 5.3.0 || [http://www.quantum-espresso.org/] || Modeling, Physics
 
−
|-
 
−
| [[ESPRIT]] || 201211 || [http://www.acsu.buffalo.edu/~yijunsun/lab/ESPRIT.html] || Biology, NGS, Metagenomics
 
−
|-
 
−
| [[ETE2]] || 2.1 || [http://ete.cgenomics.org/] || Biology, Phylogenetics
 
−
|-
 
−
| [[ETE3]] || 3.0.0 || [http://etetoolkit.org/] || Biology, Phylogenetics
 
−
|-
 
−
| [[Eval]] || 2.2.8 || [http://mblab.wustl.edu/software.html] || Biology, Genomics, GUI
 
−
|-
 
−
| [[ExaBayes]] || 1.4.1, 1.5 || [http://sco.h-its.org/exelixis/web/software/exabayes/] || Biology, Phylogenetics
 
−
|-
 
−
| [[ExaML]] || 1.0.5, 1.0.12, 3.0.14, 3.0.17 || [https://github.com/stamatak/ExaML] || Biology, Phylogenetics
 
−
|-
 
−
| [[ExomeCNV]] || 1.4 || [https://secure.genome.ucla.edu/index.php/ExomeCNV_User_Guide] || Biology, NGS, Genomics
 
−
|-
 
−
| [[Exonerate]] || 2.2.0 || [http://www.ebi.ac.uk/~guy/exonerate/] || Biology, Genomics
 
−
|-
 
−
| [[eXpress]] || 1.3.1 || [http://bio.math.berkeley.edu/eXpress/] || Biology, NGS
 
−
|-
 
−
| <span id="F"></span>[[FALCON]] || 20160828, 20161222 || [https://github.com/PacificBiosciences/FALCON] || Biology, Bioinformatics, NGS, Sequencing
 
−
|-
 
−
| [[FALCON_unzip]] || 20160623, 20161222 || [https://github.com/PacificBiosciences/FALCON_unzip] || Biology, Bioinformatics
 
−
|-
 
−
|[[FAR]] || 2.15 || [http://sourceforge.net/apps/mediawiki/theflexibleadap/index.php?title=Main_Page] || Biology, Genomics
 
−
|-
 
−
| [[FASTA]] || 34.26.5, 36.3.6d || [http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml] || Biology, Genomics
 
−
|-
 
−
| [[FAST-iCLIP]] || 0.9.1 || [https://github.com/ChangLab/FAST-iCLIP] || Biology, Sequencing
 
−
|-
 
−
| [[FastML]] || 3.0 || [http://fastml.tau.ac.il/overview.php] || Biology, Phylogenetics, ML
 
−
|-
 
−
| [[FastQC]] || 0.10.1, 0.11.2, 0.11.4 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/] || Biology, NGS
 
−
|-
 
−
| [[Fastq-tools]] || 0.7, 0.8 || [http://homes.cs.washington.edu/~dcjones/fastq-tools/] || Biology, NGS
 
−
|-
 
−
| [[FastStructure]] || 20150112 || [http://rajanil.github.io/fastStructure/] || Biology, Genomics
 
−
|-
 
−
| [[FastTree]] || 2.1.7 || [http://meta.microbesonline.org/fasttree/] || Biology, Phylogenetics
 
−
|-
 
−
| [[Fastx_toolkit]]|| 0.0.13.2 || [http://hannonlab.cshl.edu/fastx_toolkit/] || Biology, NGS
 
−
|-
 
−
| [[Fathmm]] || 20150225 || [http://fathmm.biocompute.org.uk/] || Biology, Genomics
 
−
|-
 
−
| [[FcGENE|fcGENE]] || 1.0.7 || [http://sourceforge.net/projects/fcgene/] || Biology, Genomics, SNP
 
−
|-
 
−
| [[Ferret]]|| 6.82 || [http://ferret.wrc.noaa.gov/Ferret/] || Oceanography, Meteorology
 
−
|-
 
−
| [[FFmpeg]] || 2.1.3, 2.8.3 || [http://www.ffmpeg.org/] || Multimedia, audio, video
 
−
|-
 
−
| [[FFTW]] || 3.3.2, 3.3.3, 3.3.4 || [http://www.fftw.org/] || Math, Library, C++
 
−
|-
 
−
| [[FineSTRUCTURE]] || 2.0.7 || [http://www.paintmychromosomes.com/] || Biology, Populatiopn Genetics
 
−
|-
 
−
| [[FLASH]] || 1.2.10, 1.2.11 || [http://ccb.jhu.edu/software/FLASH/] || Biology, Genomics, NGS
 
−
|-
 
−
| [[Flexbar]] || 2.3 || [http://sourceforge.net/projects/flexbar] || Biology, Genomics, NGS
 
−
|-
 
−
| [[Fluent]] || 14.5.7, 15.0.7, 16.0, 17.2 || [http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent/] || Simulation, Fluid Dynamics
 
−
|-
 
−
| [[fqtools]] || 20160224 || [https://github.com/alastair-droop/fqtools] || Biology, Bioinformatics, NGS
 
−
|-
 
−
| [[FragGeneScan]] || 1.16 || [http://omics.informatics.indiana.edu/FragGeneScan/] || Biology, NGS, Genomics
 
−
|-
 
−
| [[FrameDP]] || 1.2.2 || [https://iant.toulouse.inra.fr/FrameDP] || Biology, Sequencing
 
−
|-
 
−
| [[Frealign]] || 9.11 || [http://grigoriefflab.janelia.org/frealign] || Image Reconsctruction
 
−
|-
 
−
| [[FreeBayes]] || 1.0.1, 1.0.2, 1.1.0 || [http://bioinformatics.bc.edu/marthlab/FreeBayes] || Biology, NGS, SNP Calling
 
−
|-
 
−
| [[FREEC]] || 9.6 || [https://github.com/BoevaLab/FREEC] || Biology, Sequencing
 
−
|-
 
−
| [[Freesurfer]] || 5.2.0, 5.3.0 || [http://surfer.nmr.mgh.harvard.edu/] || Biology, Neurology, Imaging
 
−
|-
 
−
| [[FSL]] || 5.0.2.2 || [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL] || Biology, Neurology, Imaging
 
−
|-
 
−
| <span id="G"></span>[[Galaxy]] || latest || [https://galaxyproject.org/] || Biology, Chemistry, Other
 
−
|-
 
−
| [[GapFiller]] || 1.11 || [http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/gapfiller/] || Biology, NGS
 
−
|-
 
−
| [[Garli]] || '''2.0''', 2.01 || [https://www.nescent.org/wg_garli/Main_Page] || Biology, Phylogenetics
 
−
|-
 
−
| [[GAML]] || 20150610 || [http://compbio.fmph.uniba.sk/gaml/] || Biology, NGS
 
−
|-
 
−
| [[GAMBIT]] || 15.1.0, 16.0.0 || [http://gambit-project.org/] || Game Theory
 
−
|-
 
−
| [[GARM]] || 0.7.4 || [http://garm-meta-assem.sourceforge.net/] || Biology, NGS
 
−
|-
 
−
| [[GASVPro]] || 201310 || [https://code.google.com/p/gasv/] || Biology, NGS, Genomics
 
−
|-
 
−
| [[GATE]] || 7.0 || [http://wiki.opengatecollaboration.org/index.php/Main_Page] || Data Analysis
 
−
|-
 
−
| [[GATK]] || 1.6.9, 3.4.46, 3.5.0 || [http://www.broadinstitute.org/gsa/wiki/index.php/GATK] || Biology, NGS
 
−
|-
 
−
| [[Gaussian]] || G03, G09-A.02, G09-C.01 || [http://www.gaussian.com/] || Modeling, Computational Chemistry
 
−
|-
 
−
| [[Gblocks]] || 0.91b || [http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_documentation.html] || Genomics, Alignment tool
 
−
|-
 
−
| [[GCTA]] || 1.24.7, 1.26.0 || [http://cnsgenomics.com/software/gcta/index.html] || Biology, Genomics, SNP
 
−
|-
 
−
| [[GDAL]] || 1.11.2 || [http://www.gdal.org]|| Geospatial Data Modeling, Geospatial Library
 
−
|-
 
−
| [[GDC-Client]] || 1.0.1 || [https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool] || Biology, Bioinformatics, Sequencing, NGS
 
−
|-
 
−
| [[Geant4]] || 4.10 || [http://geant4.cern.ch/support/about.shtml] || Physics
 
−
|-
 
−
| [[GEM]] || 20130406 || [http://sourceforge.net/projects/gma-bio/] || Biology, NGS
 
−
|-
 
−
| [[gem5]] || 2.0 || [http://www.gem5.org/]] || Computer Simulator
 
−
|-
 
−
| [[GEMINI]] || 4.6.6a, 0.13.1, 0.18.0 || [https://github.com/arq5x/gemini] || Biology, Genomics, Genetics
 
−
|-
 
−
| [[GenBank Tools]] || 20140130 || [http://www.ncbi.nlm.nih.gov/genbank] || Biology, Genomics
 
−
|-
 
−
| [[GeneMark]] || 2012.04 || [http://exon.gatech.edu/] || Biology, Genomics, Metagenomics
 
−
|-
 
−
| [[GeneSeqer]] || 20140226 || [http://brendelgroup.org/bioinformatics2go/GeneSeqer.php] || Biology, Genomics
 
−
|-
 
−
| [[Genewise]] || 2.2.0 || [http://www.ebi.ac.uk/Tools/Wise2] || Biology, Genomics, Annotation
 
−
|-
 
−
| [[Genome STRiP]] || 2.00.1602 || [http://www.broadinstitute.org/software/genomestrip/] || Biology, genomics, NGS
 
−
|-
 
−
| [[GenomicConsensus]] || 20160523 || [https://github.com/PacificBiosciences/GenomicConsensus] || Biology, Phylogenetics
 
−
|-
 
−
| [[GenomicTools]] || 2.7.0 || [http://code.google.com/p/ibm-cbc-genomic-tools/] || Biology, NGS
 
−
|-
 
−
| [[GenomeTools]] || 1.5.7 || [http://genometools.org/index.html] || Biology, Bioinformatics
 
−
|-
 
−
| [[GenSel]] || 4.90 || [http://www.oalib.com/references/11104881] || Biology, Genetics
 
−
|-
 
−
| [[GET_HOMOLOGUES]] || 20150529 || [http://omictools.com/get-homologues-s6106.html] || Biology, Genomics
 
−
|-
 
−
| [[GFOLD]] || 1.1.4 || [http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html] || Biology, RNA-seq
 
−
|-
 
−
| [[Gffread]] || 0.9.8c || [https://github.com/gpertea/gffread] || Biology, Bioinformatics
 
−
|-
 
−
| [[GKNO]] || 1.30.18 || [http://code.google.com/p/ibm-cbc-genomic-tools/] || Biology, NGS,
 
−
|-
 
−
| [[Git]] || 1.8.2.1, 1.9.0 || [https://code.google.com/p/git-core/] || Development, Revision Control
 
−
|-
 
−
| [[Glimmer]] || 3.02 || [https://ccb.jhu.edu/software/glimmer/index.shtml] || Biology, Microbial Annotation
 
−
|-
 
−
| [[Globus]] || 2.1.3 || [https://www.globus.org/] || Data Transfer
 
−
|-
 
−
| [[GLPK]] || 4.55 || [https://github.com/gkno/gkno_launcher/wiki/Documentation#installing] ||  Biology, Genomics
 
−
|-
 
−
| [[Gmap]] || 20150723, 20160501, 20160816 || [http://research-pub.gene.com/gmap/] || Biology, Genomics
 
−
|-
 
−
| [[GNU_Compiler_Collection|GNU Compilers]] || 5.2.0 || [http://www.gnu.org] || Compilers, Programming
 
−
|-
 
−
| [[GnuPlot]] || 4.6.0, 5.0.3 || [http://gnuplot.sourceforge.net/] || Graphics, Plotting, Programming
 
−
|-
 
−
| [[Grace]] || 5.1.22 || [http://plasma-gate.weizmann.ac.il/Grace/] || Graphics, plotting, 2D
 
−
|-
 
−
| [[GrADS]] || 2.0.1 || [http://www.iges.org/grads] || Earth Science
 
−
|-
 
−
| [[GramCluster]] || 1.3 || [http://bioinfo.unl.edu/gramcluster.php] || Biology, Sequencing
 
−
|-
 
−
| [[GRASS]] || 7.0 || [https://grass.osgeo.org/] || Geography
 
−
|-
 
−
| [[GraphViz]] || 2.38.0 || [http://www.graphviz.org/] || Graphics, plotting, visualization
 
−
|-
 
−
| [[GraphMap]] || 0.4.0 || [https://github.com/isovic/graphmap] || Biology, Sequencing
 
−
|-
 
−
| [[Gromacs]] || 4.5.5, 4.6.5, 5.1.2 || [http://www.gromacs.org/] || Chemistry, Modeling, Simulation
 
−
|-
 
−
| [[GSNP]] || 1.0 || [http://jil.genomics.org.cn/index.php/en/software/gsnp.html] || Biology, Bioinformatics, NGS
 
−
|-
 
−
| [[GSL]] || 1.15 || [http://www.gnu.org/software/gsl/] || Library, Math, C++, C
 
−
|-
 
−
| [[Gsutil]] || 4.15 || [https://cloud.google.com/storage/docs/gsutil_install?hl=en#install] || Cloud, Storage, Google
 
−
|-
 
−
| [[Gubbins]] || 20150519, 20160421 || [http://wiki.rc.ufl.edu/doc/Gubbins] || Biology, Phylogenetics, Genomics
 
−
|-
 
−
| [[GULP]] || 4.0 || [http://projects.ivec.org/gulp/] || Material Science
 
−
|-
 
−
| <span id="H"></span> [[HaMStR]] || 13.2.2, 13.2.3, 13.2.4 || [http://www.deep-phylogeny.org/hamstr/] || Biology, Genomics
 
−
|-
 
−
| [[HapCompass]] || 0.7.7 || [http://www.brown.edu/Research/Istrail_Lab/hapcompass.php] || Biology, NGS, Genomics
 
−
|-
 
−
| [[HAPCUT]] || 0.7 || [https://github.com/vibansal/hapcut] || Biology, Assembly
 
−
|-
 
−
| [[Hapsembler]] || 2.21 || [http://compbio.cs.toronto.edu/hapsembler/hapsembler.html] || Biology, Genomics, NGS
 
−
|-
 
−
| [[HapTree]] || 1.0 || [http://groups.csail.mit.edu/cb/haptree/] || Biology, Genomics, NGS
 
−
|-
 
−
| [[hapQTL]] || 1.00 || [http://www.haplotype.org/hapQTL.html] || Biology, Genomics
 
−
|-
 
−
| [[HDF4]] || 4.2.11|| [http://www.hdfgroup.org/HDF4/] || Library, Data
 
−
|-
 
−
| [[HDF5]] || '''1.8.9''', 1.8.12, 1.8.15 || [http://www.hdfgroup.org/HDF5/] || Library, Data
 
−
|-
 
−
| [[HGTFinder]] || 20160720 || [http://cys.bios.niu.edu/HGTFinder/] || Biology, Genomics
 
−
|-
 
−
| [[HISAT2]] || 2.0.0b, 2.0.1b, 2.0.3b || [https://ccb.jhu.edu/software/hisat2/index.shtml] || Biology, Sequence Alignment, NGS
 
−
|-
 
−
| [[HMMER3]] || 3.0, 3.1b1, 3.1b2 || [http://hmmer.janelia.org/] || Biology, Genomics
 
−
|-
 
−
| [[HMMSplicer]] || 0.9.5 || [http://derisilab.ucsf.edu/index.php?software=105] || Biology, Genomics
 
−
|-
 
−
| [[HOMER]] || 4.2, 4.7, 4.8 || [http://biowhat.ucsd.edu/homer/] || Biology, Genomics
 
−
|-
 
−
| [[HOOMD]] || 1.3.3 || [https://codeblue.umich.edu/hoomd-blue/] || Chemistry
 
−
|-
 
−
| [[HTMLDoc]] || 1.2.82 || [http://www.msweet.org/projects.php?Z1] || Documentation, PDF, HTML
 
−
|-
 
−
| [[HTSeq]] || 0.5.3p3, 0.6.1p1 || [http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html] || Biology, NGS
 
−
|-
 
−
| [[Hyb]] || 20141126 || [https://github.com/gkudla/hyb] || Biology, NGS, RNA-Seq
 
−
|-
 
−
| [[HyPhy]] || 2.1.2.28, 2.2.6.1 || [http://www.datam0nk3y.org/hyphywiki/index.php/Main_Page] || Biology, Phylogenetics
 
−
|-
 
−
| [[Hypre]] || 1.10.0b, 2.8.0b || [http://www.llnl.gov/casc/hypre/software.html] || Library, Math, Physics
 
−
|-
 
−
| <span id="I"></span>[[iAssembler]] || 1.32 || [http://bioinfo.bti.cornell.edu/tool/iAssembler/] || Biology, Assembly
 
−
|-
 
−
| [[IBDNe]] || 20150815 || [http://faculty.washington.edu/browning/ibdne.html] || Biology, NGS
 
−
|-
 
−
| [[ICommands|iCommands]] || 3.3.1 || [https://pods.iplantcollaborative.org/wiki/display/DS/Using+iCommands] || Biology, iPlant, Data Tansfer
 
−
|-
 
−
| [[ICORN2]] || 0.95 || [http://icorn.sourceforge.net/] || Biology, Sequencing
 
−
|-
 
−
| [[IDBA-UD]] || 1.0.9, 1.1.0, 1.1.1 || [http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/] || Biology, NGS
 
−
|-
 
−
| [[IDBA-MT]] || 1.0 || [http://i.cs.hku.hk/~alse/hkubrg/projects/idba_mt/index.html] || Biology, NGS
 
−
|-
 
−
| [[IEP]] || 3.6 || [http://www.iep-project.org/] || Programming, Python, Editor
 
−
|-
 
−
| [[IGB]] || 8.4.1 || [http://bioviz.org/igb/index.html] || Biology, Genomics, NGS
 
−
|-
 
−
| [[IGV]] || 2.3.91 || [http://software.broadinstitute.org/software/igv] || Biology, Bioinformatics, NGS
 
−
|-
 
−
| [[iGTP]] || 1.1 || [http://genome.cs.iastate.edu/CBL/iGTP/] || Biology, Bioinformatics, Phylogenetics
 
−
|-
 
−
| [[illumiprocessor]] || 20150803 || [https://github.com/faircloth-lab/illumiprocessor/] || Biology, Sequencing
 
−
|-
 
−
| [[Ima|IM and IMa]] || 20091217 || [http://genfaculty.rutgers.edu/hey/software]||Biology, Population
 
−
|-
 
−
| [[Ima2|IMa2]] || 20120827 || [http://genfaculty.rutgers.edu/hey/software#IMa2]||Biology, Population
 
−
|-
 
−
| [[ImageJ]] || 1.48 || [http://rsbweb.nih.gov/ij] || Image manipulation
 
−
|-
 
−
| [[ImageMagick]] || 6.8.8-9 || [http://imagemagick.org/] || Image manipulation
 
−
|-
 
−
| [[IMOD]] || 4.7.15 || [http://bio3d.colorado.edu/imod/] || 3D modeling, Image Reconstruction
 
−
|-
 
−
| [[Intel Compilers]] || 2016.0.109 || [http://software.intel.com/en-us/intel-composer-xe/] || Programming, Compilers
 
−
|-
 
−
| [[IOAPI]] || 3.1 || [http://www.baronams.com/products/ioapi/] || Meteorology
 
−
|-
 
−
| [[Iprscan]] || 4.8 || [http://www.ebi.ac.uk/Tools/pfa/iprscan/] || Biology, Genomics
 
−
|-
 
−
| [[ipyrad]] || 0.4.4 || [https://github.com/dereneaton/ipyrad] || Biology, bioinformatics, NGS
 
−
|-
 
−
| [[IQ-TREE]] || 1.4.0, 1.4.2, 1.5.3 || [http://www.cibiv.at/software/iqtree/] || Biology, Phylogenetics
 
−
|-
 
−
| [[IRAP]] || 0.8.1p7 || [https://nunofonseca.github.io/irap/] || Biology, NGS, RNA-seq
 
−
|-
 
−
| [[iRep]] || 20161015 || [https://github.com/christophertbrown/iRep] || Biology,
 
−
|-
 
−
| [[ITK]] || 4.3.1 || [http://www.itk.org] || Biology, Genomics
 
−
|-
 
−
| [[ITK-SNAP]] || 3.0.0 || [http://www.itksnap.org/pmwiki/pmwiki.php?n=Main.HomePage] || Biology, Neuroscience, Imaging
 
−
|-
 
−
| <span id="J"></span> [[JAGS]] || 3.3.0 || [http://mcmc-jags.sourceforge.net] || Statistics
 
−
|-
 
−
| [[Java]] || 1.7.0_79, 1.8.0_31 || [http://java.com] || Java Development Kit
 
−
|-
 
−
| [[Je]] || 1.0. || [https://git.embl.de/grp-gbcs/Je] || Biology, NGS
 
−
|-
 
−
| [[Jellyfish]] || 2.1.1 || [http://www.genome.umd.edu/jellyfish.html] || Biology, NGS
 
−
|-
 
−
| [[JModelTest]] || 2.1.1 || [http://code.google.com/p/jmodeltest2/] || Biology, Phylogenetics, Genomics
 
−
|-
 
−
| [[Julia]] || 0.3.11, 0.4.6 || [http://julialang.org/] || Programming, Languages
 
−
|-
 
−
| <span id="K"></span> [[KaKs]] || 1.2 || [https://code.google.com/p/kaks-calculator/] || Biology, Phylogenetics
 
−
|-
 
−
| [[Kent]] || 20120524 || [http://genomewiki.cse.ucsc.edu/index.php/The_source_tree] || Biology, NGS
 
−
|-
 
−
| [[Khmer]] || 1.1, 2.0 || [https://github.com/ged-lab/khmer] || Biology, NGS
 
−
|-
 
−
| [[KIM]] || 1.7.2 || [https://openkim.org/kim-api/] || Library
 
−
|-
 
−
| [[KING]] || 1.4, 1.9 || [http://people.virginia.edu/~wc9c/KING/index.html] || Biology, Genomics
 
−
|-
 
−
| [[KisSplice]] || 2.4.0-p1 || [http://kissplice.prabi.fr/] || Biology, NGS
 
−
|-
 
−
| [[Kallisto]] || 0.42.3, 0.42.4 || [http://pachterlab.github.io/kallisto/starting.html] || Biology, NGS, RNA-Seq
 
−
|-
 
−
| [[KERAS]] || 1.0.8 || [https://keras.io/] || Deep Learning
 
−
|-
 
−
| [[Kmer]] || 1934 || [http://sourceforge.net/apps/mediawiki/kmer/index.php?title=Main_Page] || Biology, NGS
 
−
|-
 
−
| [[KmerGenie]] || 1.6741 || [http://kmergenie.bx.psu.edu/] || Biology, NGS, Utilities
 
−
|-
 
−
| [[Kraken]] || 0.10.4b || [http://ccb.jhu.edu/software/kraken/] || Biology, Genomics, Phylogenetics
 
−
|-
 
−
| [[Krona]] || 20161019 || [https://github.com/marbl/Krona/tree/master/KronaTools] || Biology, Bioinformatics
 
−
|-
 
−
| <span id="L"></span> [[Lace]] || 0.99 || [https://github.com/Oshlack/Lace] || Biology, NGS
 
−
|-
 
−
| [[LAMMPS]] || 28Oct12, 30Sep13, 28Jun14 || [http://lammps.sandia.gov/] || Molecular Dynamics Simulation
 
−
|-
 
−
| [[LAMP]] || 2.5 || [http://lamp.icsi.berkeley.edu/lamp/] || Biology, Genomics
 
−
|-
 
−
| [[Last]] || 247, 531, 801 || [http://last.cbrc.jp/] || Biology, Sequence alignment
 
−
|-
 
−
| [[Lastz]] || 1.03.02, 1.02.00 || [http://www.bx.psu.edu/~rsharris/lastz/] || Biology, NGS
 
−
|-
 
−
| [[LDhat]] || 2.2a || [https://github.com/auton1/LDhat] || Biology, Genomics
 
−
|-
 
−
| [[LIBSVM]] || 3.12 || [http://www.csie.ntu.edu.tw/~cjlin/libsvm/] || Machine Learning
 
−
|-
 
−
| [[LIGR]] || 2.05 || [http://sourceforge.net/projects/ligr-assembler/] || Biology, Assembly
 
−
|-
 
−
| [[LINKS]] || 1.8.5 || [https://github.com/warrenlr/LINKS/] || Biology, Genomics
 
−
|-
 
−
| [[LFMM]] || 1.4 || [http://membres-timc.imag.fr/Olivier.Francois/lfmm/index.htm] || Biology, Genomics
 
−
|-
 
−
| [[LSC]] || 0.3, 0.3.1 || [http://www.stanford.edu/~kinfai/LSC/LSC.html] || Biology, NGS, Error correction
 
−
|-
 
−
| [[lobSTR]] || 4.0.6 || [http://lobstr.teamerlich.org/index.html] || Biology, Phylogenetics
 
−
|-
 
−
| [[Loci]] || 3.3 || [http://www.tetraresearch.com/locichem/about-locichem/] || Fluid Dynamics
 
−
|-
 
−
| [[LoRMA]] || 0.3 || [https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/] || Biology, NGS
 
−
|-
 
−
| [[LS-DYNA]] || 700, 711, 800 || [http://www.lstc.com/products/ls-dyna] || Physics
 
−
|-
 
−
| [[Lumpy]] || 0.2.1 || [https://github.com/timflutre/eqtlbma] || Biology, SNP
 
−
|-
 
−
| [[LZO]] || 2.09 || [http://www.oberhumer.com/opensource/lzo/] || Library, Data Compression
 
−
|-
 
−
| <span id="M"></span> [[MACH]] || 1.0.18 || [http://www.sph.umich.edu/csg/abecasis/MACH] || Biology, Genomics
 
−
|-
 
−
| [[Mach2VCF]] || 20150515 || [https://github.com/Santy-8128/Mach2VCF] || Biology
 
−
|-
 
−
| [[M5nr|M5tools]] || 20121126 || [http://blog.metagenomics.anl.gov/howto/m5nr-%E2%80%94-the-m5-non-redundant-protein-database/] || Biology, Bioinformatics, Genomics
 
−
|-
 
−
| [[MACS]] || 1.4.2, 2.1.1 || [http://liulab.dfci.harvard.edu/MACS/]||Biology, ChIP-Seq
 
−
|-
 
−
| [[mafft]] || 7.215, 7.245, 7.294 || [http://mafft.cbrc.jp/alignment/software/] || Biology, Multiple sequence alignment
 
−
|-
 
−
| [[Mash]] || 1.1 || [http://mash.readthedocs.io/en/latest/] || Biology, Genomics
 
−
|-
 
−
| [[Maker]] || 2.25b, 2.31.6, 2.31.8 || [http://www.yandell-lab.org/software/maker.html] || Biology, Annotation, Genomics
 
−
|-
 
−
| [[MapSplice]] || 2.1.7 || [http://www.netlab.uky.edu/p/bioinfo/MapSpliceDownload] || Biology, NGS, RNA-Seq
 
−
|-
 
−
| [[MAPminer]] || 1.1 || [http://loco.biosci.arizona.edu/cranston/] || Biology, Phylogenetics
 
−
|-
 
−
| [[MassMine]] || 0.9.5, 0.10.0, 0.11.0 || [http://massmine.org/] || Data Mining
 
−
|-
 
−
| [[Maq]] || 0.7.1 || [http://maq.sourceforge.net/] || Biology, NGS
 
−
|-
 
−
| [[MARK]] || 2.0.1 || [http://www.phidot.org/software/mark/index.html] || Statistics
 
−
|-
 
−
| [[MarkerMiner]] || 20150429, 20150511 || [https://bitbucket.org/srikarchamala/markerminer] || Biology, Genomics
 
−
|-
 
−
| [[MaSuRCA]] || 2.3.2, 3.2.1 || [http://www.genome.umd.edu/masurca.html] || Biology, NGS
 
−
|-
 
−
| [[Matlab]] || 2012a, 2013a, 2014a || [http://www.mathworks.com]||Math, Simulation, Programming
 
−
|-
 
−
| [[MATS]] || 2.1.0, 3.0.8, 3.0.9 || [http://rnaseq-mats.sourceforge.net/index.html]||BIology, NGS
 
−
|-
 
−
| [[Mauve]] || 2.3.1 || [http://gel.ahabs.wisc.edu/mauve/] || Biology, NGS
 
−
|-
 
−
| [[MaxBin]] || 2.1.1 || [http://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html] || Biology, NGS
 
−
|-
 
−
| [[MCarts]] || 1.0.2 || [http://sourceforge.net/projects/mcarts/]||Biology, Genomics, Markov models
 
−
|-
 
−
| [[MCNP]] || 5, 6b2, 6, 6.1 || [http://mcnp-green.lanl.gov/about_mcnp5.html/] || Physics
 
−
|-
 
−
| [[MCNPX]] || 2.7.0, 2.7.0-i8 || [http://mcnpx.lanl.gov/] || Physics
 
−
|-
 
−
| [[MEGAN]] || 5.10.3, 6.4.15 || [http://ab.inf.uni-tuebingen.de/software/megan5/] || Biology, NGS
 
−
|-
 
−
| [[Megraft]] || 1.0.2 || [http://microbiology.se/software/megraft/] || Biology, Sequencing
 
−
|-
 
−
| [[Melting]] || 4.3.1 || [http://sourceforge.net/projects/melting/] || Biology, Genome, RNA, Folding
 
−
|-
 
−
| [[Meme]] || 4.11.1, 4.11.2 || [http://meme.nbcr.net/meme/intro.html] || Biology, Motifs, Sequence analysis
 
−
|-
 
−
| [[Meraculous]] || 2.0.5 || [http://jgi.doe.gov/data-and-tools/meraculous/] || Biology, NGS
 
−
|-
 
−
| [[Mercurial]] || 4.0.2 || [http://meme.nbcr.net/meme/intro.html] || Development, Revision Control
 
−
|-
 
−
| [[Merlin]] || 1.1.2 || [http://csg.sph.umich.edu/abecasis/Merlin/index.html] || Biogolgy, SNP
 
−
|-
 
−
| [[Meta-Tissue]] || 0.4 || [http://genetics.cs.ucla.edu/metatissue/index.html] || Biology, Genetics
 
−
|-
 
−
| [[Metabin]] || 1.0 || [http://metabin.riken.jp/index] || Biology, Metagenomics
 
−
|-
 
−
| [[MetaCluster]] || 5.0b || [http://i.cs.hku.hk/~alse/MetaCluster/index.html] || Biology, Metagenomics
 
−
|-
 
−
| [[MetaCV]] || 2.3.0 || [http://metacv.sourceforge.net/] || Biology, NGS
 
−
|-
 
−
| [[METAL]] || 20110325 || [http://www.sph.umich.edu/csg/abecasis/metal/index.html] || Biology, Genomics
 
−
|-
 
−
| [[MetAMOS]] || 1.5.0rc4-20140827 || [https://github.com/treangen/metAMOS] || Biology, Bioinformatics, Genomics, Assembly
 
−
|-
 
−
| [[Metassembler]] || 1.5 || [http://sourceforge.net/projects/metassembler/] || Biology, Genomics
 
−
|-
 
−
| [[MetaVelvet]] || 1.2.01 || [http://metavelvet.dna.bio.keio.ac.jp/] || Biology, NGS
 
−
|-
 
−
| [[Metaxa2]] || 2.0.2, 2.1.1 || [http://microbiology.se/software/metaxa2/] || Biology, NGS
 
−
|-
 
−
| [[GeneMark|MetaGeneMark]] || 2012.04 || [http://topaz.gatech.edu/GeneMark/metagenome/] || Biology, Genomics
 
−
|-
 
−
| [[Mfold]] || 3.6 || [http://mfold.rna.albany.edu/?q=mfold/download-mfold] || Biology, Genomics
 
−
|-
 
−
| [[MGEScan]] || 1.1 || [https://github.com/MGEScan/mgescan] || Biology, Genomics
 
−
|-
 
−
| [[MHAP]] || 1.6 || [https://github.com/marbl/MHAP] || Biology, Sequencing
 
−
|-
 
−
| [[MIA]] || 20130301 || [https://github.com/udo-stenzel/mapping-iterative-assembler] || Biology, NGS
 
−
|-
 
−
| [[MicrobeCensus]] || 1.0.7 || [https://github.com/snayfach/MicrobeCensus] || Biology, NGS
 
−
|-
 
−
| [[MIDAS]] || 20160830 || [https://github.com/snayfach/MIDAS] || Biology, Phylogenetics
 
−
|-
 
−
| [[Midnight_Commander|Midnight Commander]] || 4.6.1 || [http://www.gnu.org/software/mc/] || Tools, Utilities
 
−
|-
 
−
| [[Migrate-n]] || 3.3.0, 3.6.6, 3.6.11 || [http://popgen.sc.fsu.edu/Migrate/Migrate-n.html] || Biology, Population
 
−
|-
 
−
| [[Minced]] || 0.2.0 || [https://github.com/ctSkennerton/minced/tree/master] || Biology, Genomics
 
−
|-
 
−
| [[Minimac]] || 2-20140915, 3-20151015 || [http://genome.sph.umich.edu/wiki/Minimac3] || Biology, Genomics
 
−
|-
 
−
| [[mira]] || 3.9.18, '''4.0.rc1''', 4.0.2|| [http://mira-assembler.sourceforge.net/]||Biology, NGS
 
−
|-
 
−
| [[MISO]] || 0.4.9, 0.5.2, 0.5.3 || [http://genes.mit.edu/burgelab/miso/] || Biology, NGS
 
−
|-
 
−
| [[MMSEQ]] || 1.0.8 || [https://github.com/eturro/mmseq] || Biology, NGS
 
−
|-
 
−
| [[MSMBuilder]] || 2.5.1 || [https://simtk.org/home/msmbuilder] || Molecular Dynamics
 
−
|-
 
−
| [[MOABS]] || 1.2.9, 1.3.2, 1.3.4 || [https://code.google.com/p/moabs/] || Biology, NGS, Genomics
 
−
|-
 
−
| [[Modeller]] || 9.11, 9.13, 9.14 || [http://salilab.org/modeller] || Biology, Modeling
 
−
|-
 
−
| [[Molden]] || 5.0 || [http://www.cmbi.ru.nl/molden/] || Molecular, electronic structure
 
−
|-
 
−
| [[MolPro]] || 2012.1p22 || [http://www.molpro.net/] || Quantum Chemistry, Ab Initio
 
−
|-
 
−
| [[mosaik]] || 2.1.33, 2.2.3 || [http://code.google.com/p/mosaik-aligner/] || Biology,NGS
 
−
|-
 
−
| [[Mothur]] || 1.36.1, 1.37.0, 1.38.1 || [http://www.mothur.org/wiki/Main_Page/] || Biology, Microbial Ecology
 
−
|-
 
−
| [[MotionCorr]] || 2.1 || [http://cryoem.ucsf.edu/software/driftcorr.html] || Motion Correction
 
−
|-
 
−
| [[MotionCor2]] || 01302017 || [http://msg.ucsf.edu/em/software/index.html] || Motion Correction
 
−
|-
 
−
| [[MOTU]] || 1.1 || [http://www.bork.embl.de/software/mOTU/] || Biology, Bioinformatics, Genomics
 
−
|-
 
−
| [[MPE2]] || 2.4.9b || [http://www.mcs.anl.gov/research/projects/perfvis/download/] || MPI
 
−
|-
 
−
| [[MP-EST]] || 1.4, 1.5 || [https://code.google.com/p/mp-est/] || Biology, Phylogenetics
 
−
|-
 
−
| [[mpiP]] || 3.4.1 || [http://mpip.sourceforge.net] || Parallel Computing
 
−
|-
 
−
| [[MrBayes]] || 3.2.1, 3.2.4, 3.2.5 || [http://mrbayes.scs.fsu.edu/] || Biology, Phylogenetics
 
−
|-
 
−
| [[MRIcron]] || 201306 || [http://www.mccauslandcenter.sc.edu/mricro/mricron/] || Biology, MRI, Imaging
 
−
|-
 
−
| [[MUMmer]] || 3.23 || [http://mummer.sourceforge.net/] || Biology, Genomics
 
−
|-
 
−
| [[MUSCLE]] || 3.8.31 || [http://www.drive5.com/muscle/] || Biology, Genomics
 
−
|-
 
−
| [[MuTect]] || 1.1.4, 1.1.7 || [http://www.broadinstitute.org/cancer/cga/mutect] || Biology, Genomics
 
−
|-
 
−
| [[MutSig]] || 1.4, 1.41|| [http://www.broadinstitute.org/cancer/cga/mutsig_download] || Biology, Genomics
 
−
|-
 
−
| [[MZMine]] || 2.19, 2.20, 2.21 || [http://mzmine.sourceforge.net/] || Biology, Spectroscopy
 
−
|-
 
−
| [[NAMD]] || 2.9, 2.11, 2.12 || [http://www.ks.uiuc.edu/Research/namd/] || Molecular Dynamics, Chemistry
 
−
|-
 
−
| [[Nanocorrect]] || 20150727 || [https://github.com/jts/nanocorrect/] || Biology, NGS
 
−
|-
 
−
| [[Nanopolish]] || 20150904 || [https://github.com/jts/nanopolish] || Biology
 
−
|-
 
−
| [[Nbody]] || 6 || [http://www.ast.cam.ac.uk/~sverre/web/pages/nbody.htm] || Astronomy
 
−
|-
 
−
| [[NCBI_CPP_Toolkit|NCBI C++ Toolkit]] || 12.0.0 || [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/] || Biology, C++, Development
 
−
|-
 
−
| [[NCL]] || 6.1.2, 6.3.0 || [http://www.ncl.ucar.edu] || Atmosphere Science
 
−
|-
 
−
| [[NCO]] || '''4.2.1''', 4.4.3 || [http://nco.sourceforge.net/] || Data exchange tools
 
−
|-
 
−
| [[Ncview]] || 2.1.2 || [http://meteora.ucsd.edu/~pierce/ncview_home_page.html] || Data visualization
 
−
|-
 
−
| [[NeEstimator]] || 2.01 || [http://www.molecularfisherieslaboratory.com.au/neestimator-software/] || Biology, Bioinformatics
 
−
|-
 
−
| [[NetCDF]] || 3.4.2, 4.2, 4.3 || [http://www.unidata.ucar.edu/software/netcdf/]|| Data exchange, Tools
 
−
|-
 
−
| [[NEURON]] || 7.4 || [http://www.neuron.yale.edu/neuron/] || Biology, Neuroscience
 
−
|-
 
−
| [[Newbler]] || 2.7, 2.8, 2.9 || [http://my454.com/products/analysis-software/index.asp] || Biology, NGS
 
−
|-
 
−
| [[Newick-utils|Newick utils]] || 1.6 || [http://cegg.unige.ch/newick_utils] || Biology, Phylogenetics
 
−
|-
 
−
| [[Nextallele]] || 20140718 || [https://code.google.com/p/nextallele/] || Biology, Genomics
 
−
|-
 
−
| [[NextGenMap]] || 0.5.3 || [https://github.com/Cibiv/NextGenMap] || Biology, Bioinformatics, NGS
 
−
|-
 
−
| [[NEXUS_NCL|Nexus NCL]] || 2.1.18 || [http://ncl.sourceforge.net/] || Biology, Phylogenetics, Library
 
−
|-
 
−
| [[NGS-bits]] || 0.1 || [https://github.com/imgag/ngs-bits] || Biology, Sequencing
 
−
|-
 
−
| [[ngsCAT]] || 0.1 || [http://www.bioinfomgp.org/ngscat] || Biology, Bioinformatics, NGS
 
−
|-
 
−
| [[ngsTools]] || 20150816 || [https://github.com/mfumagalli/ngsTools] || Biology, NGS
 
−
|-
 
−
| [[NGSUtils]] || 20130722, 20150206 || [http://ngsutils.org/] || Biology, NGS
 
−
|-
 
−
| [[Nipype]] || 0.10.0, 0.12.1 || [http://nipy.org/nipype/about.html] || Biology, Bioinformatics, Neuroscience, Imaging
 
−
|-
 
−
| [[NMRPipe]] || 7.9 || [http://spin.niddk.nih.gov/NMRPipe/] || Biology, Biochemistry
 
−
|-
 
−
| [[Novoalign]] || 2.08.02, 3.00.02 || [http://www.novocraft.com/main/page.php?s=novoalign] || Biology, NGS
 
−
|-
 
−
| [[NWChem]] || 6.5, 6.6 || [http://www.nwchem-sw.org/index.php/Main_Page] || Chemistry
 
−
|-
 
−
| [[NxTrim]] || 0.4.1 || [https://github.com/sequencing/NxTrim] || Biology, Bioinformatics, NGS
 
−
|-
 
−
| <span id="O"></span> [[Oases]] || 0.2.08 || [http://www.ebi.ac.uk/~zerbino/oases/] || Biology, NGS
 
−
|-
 
−
| [[Olego]] || 1.1.2, 1.1.5, 1.1.6 || [http://zhanglab.c2b2.columbia.edu/index.php/OLego_Documentation] || Biology, NGS, RNA-Seq
 
−
|-
 
−
| [[OCaml]] || 4.02.3 || [https://ocaml.org/] || Programming Languages, Scripting, Development
 
−
|-
 
−
| [[Octave]] || 3.6.4 || [http://www.gnu.org/software/octave/] || Numerical Computation
 
−
|-
 
−
| [[Oncotator]] || 1.5.2.0, 1.5.3.0, 1.8.0.0 || [https://github.com/broadinstitute/oncotator] || Biology, Genomics
 
−
|-
 
−
| [[OpenBabel]] || 2.3.2 || [http://openbabel.org/wiki/Main_Page]|| Biology, Chemistry
 
−
|-
 
−
| [[OpenCL]] || 1.1 || [http://www.khronos.org/opencl/] || Programming, Library
 
−
|-
 
−
| [[OpenCV]] || 2.4.8 || [http://opencv.org] || Computervision
 
−
|-
 
−
| [[OpenFOAM]] || 2.1.1, 3.0.1, 4.0 || [http://www.openfoam.org/] || Fluid Dynamics
 
−
|-
 
−
| [[OpenMM]] || 6.2.0 || [https://simtk.org/home/openmm] || Quantum Chemistry
 
−
|-
 
−
| [[Orange3]] || 3.3.6 || [https://github.com/biolab/orange3] || Data Mining, Visualization
 
−
|-
 
−
| [[OrthoFinder]] || 0.2.5, 0.6.0, 1.0.2 || [http://www.stevekellylab.com/software/orthofinder] || Biology, Genomics
 
−
|-
 
−
| [[OrthoMCL]] || 2.0.2, 2.0.3, 2.0.7 || [http://orthomcl.org/] || Biology, Genomics
 
−
|-
 
−
| [[OTB]] || 5.6.1 || [https://www.orfeo-toolbox.org/] || Geospacial Imaging
 
−
|-
 
−
| [[p4vasp]] || 0.3.29 || [http://www.p4vasp.at/] || Molecular, Electronic Structure
 
−
|-
 
−
| [[p53MH]] || 20020901 || [http://www.jurgott.org/linkage/p53MH.htm] || Biology, Sequencing
 
−
|-
 
−
| [[Pacbio]] || 2.2.0, 2.3.0p5 || [http://www.pacb.com/devnet/] || Biology, Bioinformatics, NGS
 
−
|-
 
−
| [[Package-GFE]] || 20150701 || [https://github.com/Takahiro-Maruki/Package-GFE] || Biology, Genomics
 
−
|-
 
−
| <span id="P"></span> [[PALES]] || 122 || [http://spin.niddk.nih.gov/bax/software/PALES/index.html] || Physics
 
−
|-
 
−
| [[PALADIN]] || 1.3.1 || [https://github.com/twestbrookunh/paladin] || Biology, Phylogenetics
 
−
|-
 
−
| [[PAML]] || 4.7, 4.8a, 4.9a || [http://abacus.gene.ucl.ac.uk/software/paml.html]||Biology, Phylogenetics
 
−
|-
 
−
| [[Pandaseq]] || 20140808, 20150627 || [https://github.com/neufeld/pandaseq]||Biology, Bioinformatics, NGS, Sequencing
 
−
|-
 
−
| [[PAPI]] || 5.1.0.2 || [http://icl.cs.utk.edu/papi/software/]|| Software, Computing
 
−
|-
 
−
| [[Parallel]] || 20150122 || [http://www.gnu.org/software/parallel/] || Programming, Languages
 
−
|-
 
−
| [[ParaView]] || 4.1.0, 4.2.0, 4.3.0 || [http://www.paraview.org] || Data Analysis
 
−
|-
 
−
| [[Parsimonator]] || 1.0.2 || [http://sco.h-its.org/exelixis/web/software/parsimonator/index.html] || Biology, Bioinformatics
 
−
|-
 
−
| [[PartitionFinder]] || 20161114, 20161205|| [http://www.robertlanfear.com/partitionfinder/] || Biology, Phylogenetics, Evolution
 
−
|-
 
−
| [[Parflow]] || v615 || [https://computation.llnl.gov/casc/parflow/parflow_home.html] || Ecology, Modeling
 
−
|-
 
−
| [[PASA]] || 1.5, 2.0-r20150209 || [http://http://pasa.sourceforge.net/]|| Biology, Genomics
 
−
|-
 
−
| [[PASTA]] || 20160616 || [https://github.com/smirarab/pasta] || Biology, Sequence alignment,
 
−
|-
 
−
| [[PAUP]] || 4.0b10, 4.1a147 || [http://paup.csit.fsu.edu/] || Biology, Phylogenetics
 
−
|-
 
−
| [[PAUDA]] || 1.0.1 || [http://ab.inf.uni-tuebingen.de/software/pauda/] || Biology, Bioinformatics, Sequence alignment
 
−
|-
 
−
| [[PBalign]] || 20160921 || [https://github.com/PacificBiosciences/pbalign] || Biology, Bioinformatics
 
−
|-
 
−
| [[PBCore]] || 20151201 || [https://github.com/PacificBiosciences/pbcore] || Biology, Bioinformatics
 
−
|-
 
−
| [[PBCommand]] || 20151203 || [https://github.com/PacificBiosciences/pbcommand] || Biology, Library
 
−
|-
 
−
| [[PBJelly]] || 14.7.14, 15.2.20, 15.8.24 || [http://sourceforge.net/projects/pb-jelly/] || Biology, Bioinformatics
 
−
|-
 
−
| [[DRMAA|pbsdrmaa]] || 1.0.17 || [http://apps.man.poznan.pl/trac/pbs-drmaa/wiki] || Libraries, Torque
 
−
|-
 
−
| [[p4est]] || 1.1 || [http://www.p4est.org/] || Library
 
−
|-
 
−
| [[pbsmrtpipe]] || 20151202 || [http://pbsmrtpipe.readthedocs.org/en/master/index.html] || Biology
 
−
|-
 
−
| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html]|| Biology, Chip-Seq
 
−
|-
 
−
| [[PEAR]] || 0.9.2, 0.9.6 || [http://www.exelixis-lab.org/web/software/pear] || Biology, NGS
 
−
|-
 
−
| [[PDT]] || 3.18, 3.20, 3.22 || [http://www.cs.uoregon.edu/Research/pdt/home.php]|| Programming, Profiler
 
−
|-
 
−
| [[Perl]] || 5.16.0 || [http://www.perl.org/]||Programming, Language
 
−
|-
 
−
| [[PerM]] || 0.4.0 || [http://code.google.com/p/perm/] || Biology, NGS
 
−
|-
 
−
| [[PETSc]] || 2.3, 3.3 || [http://www.mcs.anl.gov/petsc/index.html] || Math, Numerical solvers
 
−
|-
 
−
| [[PGDSpider]] || 2.0.9.0 || [http://www.cmpg.unibe.ch/software/PGDSpider/] || Biology, NGS
 
−
|-
 
−
| [[Phenix]] || 1.8.1069, 1.10.2155 || [http://www.phenix-online.org/] || Crystallography
 
−
|-
 
−
| [[PHYLDOG]] || 20130418 || [http://pbil.univ-lyon1.fr/software/phyldog] || Biology, Genomics, Phylogenetics
 
−
|-
 
−
| [[Phyluce]] || 20140427, 20151103, 20160715 || [https://github.com/faircloth-lab/phyluce] || Biology, Phylogenetics
 
−
|-
 
−
| [[Phyutility]] || 2.7.1 || [https://github.com/blackrim/phyutility] || Biology, Bioinformatics
 
−
|-
 
−
| [[PfamScan]] || 1.3 || [http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/] || Biology, Genomics
 
−
|-
 
−
| [[PHITS]] || 2.52, 2.76. 2.82 || [http://www.oecd-nea.org/tools/abstract/detail/nea-1857/] || Physics
 
−
|-
 
−
| [[PIPE-CLIP]] || 1.1.0 || [https://github.com/QBRC/PIPE-CLIP] || Biology, NGS
 
−
|-
 
−
| [[Pipits]] || 1.3.6 || [https://github.com/hsgweon/pipits] || Biology, Sequencing
 
−
|-
 
−
| [[piPipes]] || 1.5.0 || [https://github.com/bowhan/piPipes] || Biology, Phylogenetics
 
−
|-
 
−
| [[Phonopy]] || 1.9.2 || [http://phonopy.sourceforge.net/] || Chemistry
 
−
|-
 
−
| [[PHYLIP]] || 3.696 || [http://evolution.genetics.washington.edu/phylip.html] || Biology, Phylogenetics
 
−
|-
 
−
| [[PhyloBayes]] || 3.3f, 1.4f MPI || [http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm] || Biology, Phylogenetics
 
−
|-
 
−
| [[PhyloNet]] || 3.5.7 || [http://bioinfo.cs.rice.edu/phylonet] || Biology, Phylogenetics
 
−
|-
 
−
| [[Phylosift]] || 1.1 || [https://github.com/gjospin/PhyloSift] ||  Biology, Genomics, Phylogenetics, Taxonomy
 
−
|-
 
−
| [[PhyML]] || 3.0, 3.1 || [http://code.google.com/p/phyml/] || Biology, Phylogenetics
 
−
|-
 
−
| [[Picard]] || 1.72, 1.80, 2.0.1 || [http://picard.sourceforge.net/] || Biology, NGS
 
−
|-
 
−
| [[PICRUSt]] || 1.0.0, 1.1.0 || [https://picrust.github.io/picrust/install.html] || Biology, Phylogenetics
 
−
|-
 
−
| [[Piranha]] || 1.2.1 || [http://smithlabresearch.org/software/piranha/] || Biology, Phylogenetics
 
−
|-
 
−
| [[PLAST]] || 1.0 || [ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/] || Biology, Bioinformatics
 
−
|-
 
−
| [[Platypus]] || 0.8.1 || [http://www.well.ox.ac.uk/platypus] || Biology, NGS
 
−
|-
 
−
| [[Plink]] || 1.07, 1.90b3, 1.90b3.39 || [http://pngu.mgh.harvard.edu/~purcell/plink/] || Biology, GWAS
 
−
|-
 
−
| [[PLINKSEQ]] || 0.10 || [https://atgu.mgh.harvard.edu/plinkseq/index.shtml] || Biology, Genomics
 
−
|-
 
−
| [[PluMiST]] || 1.1 || [http://www.cibiv.at/software/plumist/] || Biology, Phylogenetics, Genomics
 
−
|-
 
−
| [[PolyPhen]] || 2.2.2.r405b || [http://genetics.bwh.harvard.edu/pph2/dokuwiki/start] || Biology, Genomics
 
−
|-
 
−
| [[PonyTools]] || 0.1 || [https://github.com/schae234/PonyTools] || Biology, Genomics
 
−
|-
 
−
| [[Poretools]] || 0.5.0 || [https://github.com/arq5x/poretools] || Biology, Sequencing
 
−
|-
 
−
| [[POV-Ray]] || 3.7 || [http://www.povray.org/] || 3D, Graphics
 
−
|-
 
−
| [[Prank]] || 20150803 || [https://sourceforge.net/projects/bbmap/] || Biology, Bioinformatics, Alignment
 
−
|-
 
−
| [[Preseq]] || 0.0.4 || [http://smithlab.usc.edu/plone/software/librarycomplexity] || Biology, NGS
 
−
|-
 
−
| [[PRICE]] || 1.2 || [http://derisilab.ucsf.edu/software/price/] || Biology, NGS
 
−
|-
 
−
| [[Primer3]] || 2.3.4 || [http://sourceforge.net/projects/primer3/] || Biology, Genomics
 
−
|-
 
−
| [[PRIMUS]] || 1.8.0 || [https://primus.gs.washington.edu/primusweb/index.html] || Biology, Phylogenetics
 
−
|-
 
−
| [[PRINSEQ]] || 0.20.4 || [https://sourceforge.net/projects/prinseq/?source=navbar] || Biology, Sequencing
 
−
|-
 
−
| [[Prodigal]] || 2.6.3 || [https://github.com/hyattpd/Prodigal] || Biology, Genomics
 
−
|-
 
−
| [[ProfessAtQE]] || 2014 || [http://www.qtp.ufl.edu/ofdft/research/computation.shtml]|| Material Science, Molecular Dynamics
 
−
|-
 
−
| [[Prokka]] || 1.10, 1.11 || [http://www.vicbioinformatics.com/software.prokka.shtml] || Biology, Genomics, Bioinformatics, Assembly
 
−
|-
 
−
| [[ProBABEL]] || 0.4.2, 0.4.3, 0.4.5 || [http://www.genabel.org/packages/probabel] || Biology, Genomics, GWAS
 
−
|-
 
−
| [[Probalign]] || 1.4 || [http://probalign.njit.edu/standalone.html] || Biology, Genomics
 
−
|-
 
−
| [[Proovread]] || 1.03rcl || [http://proovread.bioapps.biozentrum.uni-wuerzburg.de/] || Biology, Genomics, NGS
 
−
|-
 
−
| [[Proteinortho]] || 4.26, 5.11 || [http://www.bioinf.uni-leipzig.de/Software/proteinortho/index.html] || Biology, Genomics
 
−
|-
 
−
| [[PROVEAN]] || 1.1.5 || [http://provean.jcvi.org/] || Biology, Genomics
 
−
|-
 
−
| [[PyAni]] || 0.2.1 || [https://github.com/widdowquinn/pyani] || Bilogy, Genomics
 
−
|-
 
−
| [[PyHDF]] || 0.9.0 || [http://hdfeos.org/software/pyhdf.php] || Library, HDF4
 
−
|-
 
−
| [[Python]] || '''2.7.6''', 3.5.0 || [http://python.org] || Biology, Genomics, NGS
 
−
|-
 
−
| [[Pyfasta]] || 0.5.2 || [https://pypi.python.org/pypi/pyfasta/] || Biology, Phylogenetics
 
−
|-
 
−
| [[Pyrad]] || 3.0.63 || [http://dereneaton.com/software/pyrad/] || Biology, Sequencing Alignment, Assembly
 
−
|-
 
−
| [[QDD]] || 3.1.2 || [http://net.imbe.fr/~emeglecz/qdd.html] || Programming, scripting, language
 
−
|-
 
−
| [[QGIS]] || 2.18.0 || [http://www.qgis.org/en/site/about/index.html] || Geography
 
−
|-
 
−
| <span id="Q"></span> [[QIIME]] || 1.9.0, 1.9.1 || [http://qiime.org/index.html] || Biology, Ecology
 
−
|-
 
−
| [[QIIME2]] || 2.0.6 || [https://docs.qiime2.org/] || Biology, Ecology
 
−
|-
 
−
| [[QT]] || 4.8.3 || [http://qt-project.org]|| Computer Science
 
−
|-
 
−
| [[QUAST]] || 2.3, 4.4 || [http://sourceforge.net/projects/quast] || Biology, NGS
 
−
|-
 
−
| [[Quake]] || 0.3 || [http://www.cbcb.umd.edu/software/quake/] || Biology, Sequencing
 
−
|-
 
−
| [[Quantas]] || 1.0.4, 1.0.8 || [http://zhanglab.c2b2.columbia.edu/index.php/Quantas_Documentation] || Biology, Bioinformatics, NGS
 
−
|-
 
−
| [[QualiMap]] || 2.1.1 || [http://qualimap.bioinfo.cipf.es/] || Biology, Sequence alignment
 
−
|-
 
−
| [[Quickquartet]] || 1.0.0 || [https://code.google.com/p/quickquartet/] || Biology, Phylogenetics
 
−
|-
 
−
| <span id="R"></span> [[R]] || Rmpi/3.3.1, 3.2.0, 3.3.0 || [http://www.r-project.org/] || Statistics, Programming
 
−
|-
 
−
| [[R2R]] || 1.0.4 || [http://breaker.research.yale.edu/R2R/] || Biology, RNA
 
−
|-
 
−
| [[R8S]] || 1.71, 1.8 || [http://loco.biosci.arizona.edu/r8s/] || Biology, Evolution
 
−
|-
 
−
| [[Racon]] || 20161013 || [https://github.com/isovic/racon] || Biology, Sequencing
 
−
|-
 
−
| [[RADICAL]] || 0.2 || [http://desalle.amnh.org/software.html] || Biology, Phylogenetics, Genomics
 
−
|-
 
−
| [[Randfold]] || 2.0.1 || [http://bioinformatics.psb.ugent.be/software/details/Randfold] || Biology, RNA
 
−
|-
 
−
| [[Rascaf]] || 1.0.2 || [https://github.com/mourisl/Rascaf] || Biology, RNA-Seq
 
−
|-
 
−
| [[RAxML]] || 8.1.23, 8.2.2, 8.2.3 || [http://sco.h-its.org/exelixis/software.html] || Biology, Phylogenetics
 
−
|-
 
−
| [[Ray]] || 2.3.1 || [http://denovoassembler.sourceforge.net/index.html] || Biology, Genomics, NGS
 
−
|-
 
−
| [[REAGO]] || 1.1 || [https://github.com/chengyuan/reago-1.1] || Biology, Assembly
 
−
|-
 
−
| [[REAPR]] || 1.0.18 || [http://www.sanger.ac.uk/resources/software/reapr/#t_2] || Biology, Bioinformatics, Assembly
 
−
|-
 
−
| [[Recycler]] || 0.62 || [https://github.com/Shamir-Lab/Recycler] || Biology, Bioinformatics
 
−
|-
 
−
| [[RELION]] || 1.4 || [http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page] || Biology, Bioinformatics
 
−
|-
 
−
| [[REPdenovo]] || 20170222 || [https://github.com/Reedwarbler/REPdenovo] || Biology, Phylogenetics
 
−
|-
 
−
| [[RepeatExplorer]] || 20150506 || [http://www.repeatexplorer.org/] || Biology, Genomics
 
−
|-
 
−
| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/] || Biology, Genomics
 
−
|-
 
−
| [[RepeatModeler]] || 1.0.8 || [http://www.repeatmasker.org/RepeatModeler.html] || Biology, Bioinformatics
 
−
|-
 
−
| [[Reptile]] || 1.1 || [http://aluru-sun.ece.iastate.edu/doku.php?id=reptile] || Biology, NGS, error correction
 
−
|-
 
−
| [[RevBayes]] || 1.0.0, 1.0.3 || [http://revbayes.github.io/about.html] || Biology, Phylogenetics
 
−
|-
 
−
| [[riboPicker]] || 0.4.3 || [http://ribopicker.sourceforge.net/] || Biology, Sequence
 
−
|-
 
−
| [[RNAhybrid]] || 2.1.1 || [http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/] || Biology, Genomics
 
−
|-
 
−
| [[rRNASelector]] || 1.0.0 || [http://www.ezbiocloud.net/sw/rrnaselector] || Biology, Sequencing
 
−
|-
 
−
| [[rnaseqlib]] || 20150721 || [https://github.com/yarden/rnaseqlib] || Biology, Phylogenetics, RNA-Seq
 
−
|-
 
−
| [[rnaQUAST]] || 1.2.0 || [http://bioinf.spbau.ru/en/rnaquast] || Biology, NGS, Sequencing
 
−
|-
 
−
| [[ROOT]] || 6.0 || [http://root.cern.ch/drupal/] || Data Analysis
 
−
|-
 
−
| [[Roary]] || 3.4.1 || [http://sanger-pathogens.github.io/Roary/] || Biology, Genomics
 
−
|-
 
−
| [[Rosetta]] || 2014wk4 || [https://www.rosettacommons.org/about] || Biology, Structure, Modelling
 
−
|-
 
−
| [[RSEG]] || 0.4.8 || [http://smithlab.usc.edu/histone/rseg/] || Biology, NGS
 
−
|-
 
−
| [[RSEM]] || 1.2.19, 1.2.28, 1.2.29 || [http://deweylab.biostat.wisc.edu/rsem] || Biology, NGS, RNA-Seq
 
−
|-
 
−
| [[RSeQC]] || 2.3.7, 2.6.2 || [http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/] || Biology, NGS, RNA-Seq
 
−
|-
 
−
| [[RStudio]] || 0.99.902, 0.99.903 || [https://www.rstudio.com/] || R, Statistics, Programming
 
−
|-
 
−
| [[RTGTools]] || 3.7.1 || [http://realtimegenomics.com/products/rtg-tools/] || Biology, NGS
 
−
|-
 
−
| [[Ruby]] || 1.9.3-p0 || [http://www.ruby-lang.org/en/] || Programming, Scripting, Language
 
−
|-
 
−
| <span id="S"></span> [[Sailfish]] || 0.6.3 || [http://www.cs.cmu.edu/~ckingsf/software/sailfish/] || Biology, NGS, RNA-Seq
 
−
|-
 
−
| [[Salmon]] || 0.6.0, 0.7.2 || [https://github.com/COMBINE-lab/salmon] || Biology, RNA-seq
 
−
|-
 
−
| [[SMC++]] || 1.7.0 || [https://github.com/popgenmethods/smcpp] || Biology, NGS
 
−
|-
 
−
| [[Sambamba]] || 0.5.0-dev, 0.5.10, 0.6.3 || [http://lomereiter.github.io/sambamba/index.html] || Biology, NGS
 
−
|-
 
−
| [[Samstat]] || 1.08 || [http://samstat.sourceforge.net/] || Biology, NGS, Bioinformatics, Sequencing
 
−
|-
 
−
| [[Samblaster]] || 0.1.14 || [https://github.com/GregoryFaust/samblaster] || Biology, NGS
 
−
|-
 
−
| [[samtools]] || 1.1, 1.2, 1.3.1 || [http://samtools.sourceforge.net/] || Biology, NGS
 
−
|-
 
−
| [[SAS]] || 9.3 || [http://www.sas.com] || Statistics, Graphing
 
−
|-
 
−
| [[SATe]] || 2.2.7 || [http://phylo.bio.ku.edu/software/sate/sate2.html] ||Biology, Phylogenetics
 
−
|-
 
−
| [[Scala]] || 2.11.5 || [http://www.scala-lang.org/] || Programming, Language
 
−
|-
 
−
| [[Scalablast]] || 2.4.53 || [http://omics.pnl.gov/software/ScalaBLAST.php] || Biology, Genomics
 
−
|-
 
−
| [[Scalpel]] || 0.1.1 || [http://sourceforge.net/projects/scalpel/] || Biology, NGS
 
−
|-
 
−
| [[SCRIPTURE]] || 20101211 || [http://software.broadinstitute.org/software/scripture/] || Biology, Bioinformatics, Genomics
 
−
|-
 
−
| [[Shannon]] || 20160211 || [http://sreeramkannan.github.io/Shannon/] || Biology, RNA-Seq
 
−
|-
 
−
| [[SHAPEIT]] || 2.5.5 || [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html] || Biology, SNP
 
−
|-
 
−
| [[SHAPE-MaP]] || 1.2 || [http://www.chem.unc.edu/rna/software.html] || Biology, Phylogenetics
 
−
|-
 
−
| [[Sharcgs]] || 1.2.11 || [http://sharcgs.molgen.mpg.de/index.shtml] || Biology, NGS, Assembly
 
−
|-
 
−
| [[SHEsisPlus]] || 1.0 || [https://github.com/celaoforever/SHEsisPlus] || Biology, Phylogenetics
 
−
|-
 
−
| [[shustring]] || 2.6 || [http://guanine.evolbio.mpg.de/homePage/node4.html] || Biology, Sequencing
 
−
|-
 
−
| [[SCons]] || 2.3.0 || [http://sourceforge.net/projects/scons/] || Programming
 
−
|-
 
−
| [[Scoary]] || 1.6.10 || [https://github.com/AdmiralenOla/Scoary] || Biology, Bioinformatics, Genomics
 
−
|-
 
−
| [[SCRATCH1D]] || 1.0 || [http://download.igb.uci.edu/] || Biology, Genomics
 
−
|-
 
−
| [[Scythe]] || 0.991 || [https://github.com/vsbuffalo/scythe] || Biology, NGS
 
−
|-
 
−
| [[SDT]] || 1.2 || [http://web.cbio.uct.ac.za/~brejnev/] || Biology, Sequencing
 
−
|-
 
−
| [[Segemehl]] || 0.1.9 || [http://www.bioinf.uni-leipzig.de/Software/segemehl/] || Biology, NGS, Mapper
 
−
|-
 
−
| [[SEPP]] || 1.0, 3.0 || [https://github.com/smirarab/sepp] || Biology, Phylogenetics, HMM
 
−
|-
 
−
| [[SGA]] || 0.10.14 || [https://github.com/jts/sga] || Biology, Assembly
 
−
|-
 
−
| [[Seq-Gen]] || 1.3.3 || [http://tree.bio.ed.ac.uk/software/seqgen/] || Biology, Phylogenetics
 
−
|-
 
−
| [[SeqPrep]] || 0.5 || [https://github.com/jstjohn/SeqPrep] || Biology, NGS
 
−
|-
 
−
| [[Seqmagick]] || 20150923 || [http://fhcrc.github.io/seqmagick/#seqmagick] || Biology, Phylogenetics
 
−
|-
 
−
| [[SeqMap]] || 1.0.13 || [http://www-personal.umich.edu/~jianghui/seqmap/] || Biology, NGS
 
−
|-
 
−
| [[Seqtk]] || 20140729 || [https://github.com/lh3/seqtk] || Biology, NGS
 
−
|-
 
−
| [[SEQuel]] || 1.0.1 || [http://bix.ucsd.edu/SEQuel/index.html] || Biology, NGS
 
−
|-
 
−
| [[SeqyClean]] || 1.8.10 || [https://bitbucket.org/izhbannikov/seqyclean] || Biology, NGS, Bioinformatics
 
−
|-
 
−
| [[ShoRAH]] || 20131204 || [https://github.com/ozagordi/shorah] || Biology, NGS, quality filter
 
−
|-
 
−
| [[SHRiMP]] || 2.2.3 || [http://proovread.bioapps.biozentrum.uni-wuerzburg.de/] || Biology, NGS
 
−
|-
 
−
| [[SICER]] || 1.1 || [http://home.gwu.edu/~wpeng/Software.htm] || Biology, ChIP-Seq
 
−
|-
 
−
| [[Sickle]] || 1.200, 1.33 || [https://github.com/najoshi/sickle] || Biology, NGS, quality filter
 
−
|-
 
−
| [[Siesta]] || 2.0.2,3.1 || [http://icmab.cat/leem/siesta/] || Simulation, Physics, Ab Initio
 
−
|-
 
−
| [[SIFT]] || 4.0.3b || [http://sift.jcvi.org/] || Biology, Genomics
 
−
|-
 
−
| [[SignalP]] || 4.1c || [http://www.cbs.dtu.dk/services/SignalP/] || Biology, NGS
 
−
|-
 
−
| [[Silo]] || 4.7 || [https://wci.llnl.gov/codes/silo/index.html] || Library, Data
 
−
|-
 
−
| [[SIPeS]] || 2.0 || [http://gmdd.shgmo.org/Computational-Biology/ChIP-Seq/download/SIPeS] || Biology, Bioinformatics, ChIP-Seq
 
−
|-
 
−
| [[Slicer]] || 4.3.1 || [http://www.slicer.org/] || Biology, Imaging
 
−
|-
 
−
| [[SMALT]] || 0.7.6 || [https://www.sanger.ac.uk/resources/software/smalt/] || Biology, NGS
 
−
|-
 
−
| [[Snap]] || 20100728, 0.15.4 || [http://homepage.mac.com/iankorf] || Biology, Genomics
 
−
|-
 
−
| [[SNAPE-pooled]] || 20130407 || [https://code.google.com/p/snape-pooled/] || Biology, SNP
 
−
|-
 
−
| [[SNeP]] || 1.1 || [http://sourceforge.net/projects/snepnetrends/files/?source=navbar] || Biology, Phylogenics
 
−
|-
 
−
| [[SnpEff]] || 4.1i, 4.2, 4.3 || [http://snpeff.sourceforge.net/] || Biology, NGS, Genomics
 
−
|-
 
−
| [[SNPhylo]] || 20140701 || [http://chibba.pgml.uga.edu/snphylo/] || Bilogy, Phylogenetics
 
−
|-
 
−
| [[SNP-sites]] || 2.0.3 || [https://github.com/sanger-pathogens/snp-sites] || Biology, SNP
 
−
|-
 
−
| [[Snippy]] || 20160419 || [https://github.com/tseemann/snippy] || Biology, Phylogenetics
 
−
|-
 
−
| [[SOAPdenovo]] || 1.05 || [http://soap.genomics.org.cn/soapdenovo.html] || Biology, NGS
 
−
|-
 
−
| [[SOAPdenovo-Trans]] || 1.01, 1.03 || [http://soap.genomics.org.cn/SOAPdenovo-Trans.html] || Biology, NGS
 
−
|-
 
−
| [[SOAPec]] || 2.03 || [https://sourceforge.net/projects/soapdenovo2/files/ErrorCorrection/] || Biology, Phylogenetics
 
−
|-
 
−
| [[SOAPsplice]] || 1.10 || [http://soap.genomics.org.cn/soapsplice.html] || Biology, NGS
 
−
|-
 
−
| [[SortMeRNA]] || 2.1 || [http://bioinfo.lifl.fr/RNA/sortmerna/] || Biology, Sequencing, NGS
 
−
|-
 
−
| [[SparCC]] || 201402 || [https://bitbucket.org/yonatanf/sparcc/overview] || Microbial Ecology
 
−
|-
 
−
| [[Spades]] || 3.8.0, 3.9.0, 3.10.0 || [http://bioinf.spbau.ru/en/spades] || Biology, NGS
 
−
|-
 
−
| [[Spanki]] || 0.4.1, 0.4.3, 0.5.0 || [http://www.cbcb.umd.edu/software/spanki/] || Biology, NGS, RNA-Seq
 
−
|-
 
−
| [[SPARTA+]] || 2.60 || [http://spin.niddk.nih.gov/bax/software/SPARTA+/]||Chemistry
 
−
|-
 
−
| [[Spidey]] || 20150922 || [http://www.ncbi.nlm.nih.gov/spidey/] || Biology, Genomics
 
−
|-
 
−
| [[SPIMAP]] || 1.1 || [http://compbio.mit.edu/spimap/] || Biology, Phylogenetics
 
−
|-
 
−
| [[SpliceTrap]] || 0.90.5 || [http://rulai.cshl.edu/splicetrap/] || Biology, NGS, RNA-Seq
 
−
|-
 
−
| [[SPM]] || 8 || [http://www.fil.ion.ucl.ac.uk/spm/] || Biology, Statistics, Neurology, Imaging
 
−
|-
 
−
| [[Sputnik]] || 1.0 || [http://espressosoftware.com/sputnik/] || Biology, Genomics
 
−
|-
 
−
| [[SQLite]] || 3.8.8.2 || [http://www.sqlite.org/] || Database
 
−
|-
 
−
| [[SQL_Developer]] || 4.1.2 || [http://www.oracle.com/technetwork/developer-tools/sql-developer/overview/index.html] || Programming, Oracle, Sql
 
−
|-
 
−
| [[SRA]] || 2.1.10 || [http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software] || biology, NGS
 
−
|-
 
−
| [[SSPACE]] || 2.0, 3.0 || [http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/] || Biology, NGS
 
−
|-
 
−
| [[SST-Core]] || 6.0.0 || [http://sst-simulator.org/SSTPages/SSTBuildAndInstall6dot0dot0SeriesQuickStart/] || MPI
 
−
|-
 
−
| [[SSR_pipeline]] || 0.951 || [http://pubs.usgs.gov/ds/778/] || Bilogy, DNA Sequencing
 
−
|-
 
−
| [[Stacks]] || 1.21, 1.24, 1.35 || [http://creskolab.uoregon.edu/stacks/] || Biology, Genomics, NGS
 
−
|-
 
−
| [[Staden]] || 1.14.6 || [http://staden.sourceforge.net/staden_home.html] || Biology, Sequencing
 
−
|-
 
−
| [[Stampy]] || 1.0.31 || [http://www.well.ox.ac.uk/stampy] || Biology, Bioinformatics, Sequencing
 
−
|-
 
−
| [[STAR]] || 2.4.0j, 2.5.1b || [https://code.google.com/p/rna-star/] || Biology, NGS, Alignment
 
−
|-
 
−
| [[STAR-CCM+]] || 8.06 || [http://wiki.hpc.ufl.edu/doc/STAR-CCM+]||Mechanical Engineering
 
−
|-
 
−
| [[Stata]] || 10.1, 13 || [http://www.stata.com/]||Statistics, Data analysis
 
−
|-
 
−
| [[Stringtie]] || 1.0.0, 1.1.2, 1.2.1 || [http://ccb.jhu.edu/software/stringtie/] || Biology, NGS, Alignment
 
−
|-
 
−
| [[Structure]] || 2.3.3, 2.3.4 || [http://pritch.bsd.uchicago.edu/structure_software/release_versions/v2.3.3/html/structure.html]|| Biology, Population
 
−
|-
 
−
| [[Subread]] || 1.5.0-p1, 1.5.1 || [http://bioinf.wehi.edu.au/subread-package/] || Biology, Sequencing, SNP
 
−
|-
 
−
| [[SUNDIALS]] || 2.3.0, 2.5.0 || [https://computation.llnl.gov/casc/sundials/main.html] || Numerical Solver
 
−
|-
 
−
| [[SVDetect]] || 0.8b || [http://svdetect.sourceforge.net/Site/Home.html] || Biology, NGS, SNP
 
−
|-
 
−
| [[swak4Foam]] || 2.x || [http://openfoamwiki.net/index.php/Contrib/swak4Foam]|| Fluid Dynamics
 
−
|-
 
−
| [[swarm]] || 1.2.11 || [https://github.com/torognes/swarm]|| Data Analysis
 
−
|-
 
−
| [[SWEEP]] || 20160722 || [https://github.com/jclev-uga/SWEEP/] || Biology, SNP
 
−
|-
 
−
| [[Swig]] || 2.0.9 || [http://www.swig.org/]|| Programming, C, C++, Python
 
−
|-
 
−
| [[SwitchSeq]] || 20140907 || [https://github.com/mgonzalezporta/SwitchSeq] || Biology, NGS
 
−
|-
 
−
| [[Syzygy]] || 1.2.7 || [http://www.broadinstitute.org/software/syzygy/] || Biology, Genomics
 
−
|-
 
−
| <span id="T"></span> [[TetGen]] || 1.5.0 || [http://wias-berlin.de/software/tetgen/] || Tetrahedral Meshes 3D
 
−
|-
 
−
| [[tapir]] || 20160825 || [https://github.com/faircloth-lab/tapir] || Biology, Phylogenetics
 
−
|-
 
−
| [[TAPIS]] || 1.2.1 || [https://bitbucket.org/comp_bio/tapis] || Biology, Sequencing
 
−
|-
 
−
| [[TASSEL]] || 5.0, 5.2.29 || [http://www.maizegenetics.net/index.php?option=com_content&task=view&id=89&Itemid=119] || Biology, Genomics
 
−
|-
 
−
| [[TAU]] || 2.21.4, 2.23, 2.24, 2.52 ||[http://www.cs.uoregon.edu/Research/tau/home.php]||Profiling, Tracing, Programming
 
−
|-
 
−
| [[taxMap]] || 0.1 || [https://github.com/nygenome/taxmaps] || Biology, Phylogenetics, Taxonomy
 
−
|-
 
−
| [[T-Coffee]] || 9.03.r1318 || [http://www.tcoffee.org/Projects/tcoffee/] || Biology, Genomics, Multiple Alignment
 
−
|-
 
−
| [[TensorFlow]] || 0.10.0, 1.0.0 || [https://github.com/tensorflow/tensorflow] || Library, Math
 
−
|-
 
−
| [[TESS]] || 2.3.1 || [http://membres-timc.imag.fr/Olivier.Francois/tess.html] || Biology, Genomics, Markov
 
−
|-
 
−
| [[tgicl]] || 2.1 || [http://compbio.dfci.harvard.edu/tgi/software/] || Biology, sequencing, clustering
 
−
|-
 
−
| [[Tmux]] || 2.0 || [https://github.com/tmux/tmux] || GNU, Terminal Multiplexer
 
−
|-
 
−
| [[TomoPy]] || 0.0.3 || [https://github.com/tomopy/tomopy] || Biology, Neuroimaging
 
−
|-
 
−
| [[Tophat]] || 1.4.1, 2.0.13, 2.1.0 || [http://tophat.cbcb.umd.edu/] || Biology, NGS
 
−
|-
 
−
| [[Torch]] || 20160704, 20171102 || [http://torch.ch/] || Lua
 
−
|-
 
−
| [[Totalview]] || 8.12.0 || [http://www.roguewave.com/products/totalview.aspx] || Computer Science
 
−
|-
 
−
| [[TPP]] || 4.7.0 || [http://sourceforge.net/projects/sashimi/] || Bioinformatics, MassSpec
 
−
|-
 
−
| [[TrackTools]] || 2011 || [http://marecilab.mbi.ufl.edu/software/TrackTools/TrackTools.zip] || Bioinformatics
 
−
|-
 
−
| [[TrackVis]] || 0.5.2.2 || [http://trackvis.org] || Biology, Spectroscopy
 
−
|-
 
−
| [[Tracula]] || 5.3.2014_05_26 || [http://ftp.nmr.mgh.harvard.edu/fswiki/Tracula] || Biology, Bioinformatics, Neuroscience, Imaging
 
−
|-
 
−
| [[TraitRate]] || 1.1 || [http://www.tau.ac.il/~itaymay/cp/traitRate/index.html] || Biology, Evolution
 
−
|-
 
−
| [[Trans-ABySS]] || 1.5.4 || [https://github.com/bcgsc/transabyss] || Biology, Phylogenetics
 
−
|-
 
−
| [[TransDecoder]] || 20140704, 2.0.1, 3.0.0 || [http://transdecoder.github.io/] || Biology, NGS
 
−
|-
 
−
| [[Transrate]] || 1.0.1 || [http://hibberdlab.com/transrate/index.html] || Biology, Assembly
 
−
|-
 
−
| [[TraCeR]] || 20160519 || [https://github.com/Teichlab/tracer] || Biology, Bioinformatics
 
−
|-
 
−
| [[TreeCorr]] || 3.2.3 || [https://github.com/rmjarvis/TreeCorr] || Physics
 
−
|-
 
−
| [[TreeFix]] || 1.1.7, 1.1.10 || [http://compbio.mit.edu/treefix/] || Biology, Phylogenetics
 
−
|-
 
−
| [[TreeMix]] || 1.12 || [https://bitbucket.org/nygcresearch/treemix/wiki/Home] || Biology, Phylogenetics
 
−
|-
 
−
| [[TreePL]] || 20150305 || [https://github.com/blackrim/treePL/wiki] || Biology, Phylogenetics
 
−
|-
 
−
| [[TriMetAss]] || 1.1 || [http://microbiology.se/software/trimetass/] || Biology, Bioinformatics, NGS
 
−
|-
 
−
| [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html] || Biology, Genomics
 
−
|-
 
−
| [[Trilinos]] || 11.4.1, 11.8.1 || [http://trilinos.sandia.gov] || Math Algorithm
 
−
|-
 
−
| [[trimAl]] || 1.2 || [http://trimal.cgenomics.org/introduction] || Biology, Genomics, Sequence Alignment
 
−
|-
 
−
| [[Trim Galore]] || 0.2.8, 0.4.1 || [http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/] || Biology, NGS
 
−
|-
 
−
| [[Trimmomatic]] || 0.32, 0.33, 0.36 || [http://www.usadellab.org/cms/index.php?page=trimmomatic] || Biology, NGS
 
−
|-
 
−
| [[Trinity]] || r20160329-2.2.0, r20161120-2.3.2 || [http://trinityrnaseq.sourceforge.net/] || Biology, NGS, RNA-Seq
 
−
|-
 
−
| [[Trinotate]] || 2.0.1, 3.0.1 || [http://trinotate.github.io/] || Biology
 
−
|-
 
−
| [[TRNAscan-SE]] || 1.23 || [http://selab.janelia.org/tRNAscan-SE/] || Biology, NGS, Bioinformatics
 
−
|-
 
−
| [[Twinscan]] || 4.1.2 || [http://mblab.wustl.edu/software.html#twinscanLink] || Biology, Genomics
 
−
|-
 
−
| <span id="U"></span> [[usearch]] || 7.0.1001-64, 8.0.1517, 9.2.64 || [http://www.drive5.com/usearch/] || Biology, Sequence analysis
 
−
|-
 
−
| [[UDUNITS]] || 2.2.17 || [http://www.unidata.ucar.edu/software/udunits/] || Library, Units, Programming
 
−
|-
 
−
| [[UFITS]] || 0.7.2 || [https://github.com/nextgenusfs/ufits] || Biology, NGS
 
−
|-
 
−
| [[UNAFold]] || 3.8 || [http://dinamelt.rit.albany.edu/unafold/] || Biology, Genome, RNA, Folding
 
−
|-
 
−
| [[UProC]] || 1.2.0 || [http://uproc.gobics.de/] || Biology, Genomics
 
−
|-
 
−
| <span id="V"></span> [[Valgrind]] || 3.9.0 || [http://valgrind.org] || Computer Science
 
−
|-
 
−
| [[VarDictJava]] || 20160521 || [https://github.com/AstraZeneca-NGS/VarDictJava] || Biology, NGS
 
−
|-
 
−
| [[VarScan]] || 2.3.6 || [http://varscan.sourceforge.net/] || Biology, NGS, Genomics
 
−
|-
 
−
| [[VASP]] || 5.3.2, 5.3.3, 5.3.5, 5.4.1 || [http://cms.mpi.univie.ac.at/vasp/] || Quantum Chemistry, Ab Initio
 
−
|-
 
−
| [[VAST-TOOLS]] || 20150506 || [https://github.com/vastgroup/vast-tools] || Biology, NGS, RNA-Seq
 
−
|-
 
−
| [[VCFLib]] || 20141119, 20150313 || [https://github.com/ekg/vcflib] || Biology, NGS, Genomics
 
−
|-
 
−
| [[VCFtools]] || 0.1.12a, 0.1.12b, 0.1.14 || [http://vcftools.sourceforge.net/] || Biology, SNPs
 
−
|-
 
−
| [[velvet]] || 1.2.06, 1.2.07, 1.2.10 || [http://www.ebi.ac.uk/~zerbino/velvet/] || Biology, Genomics, NGS
 
−
|-
 
−
| [[VEP]] || 74, 83 || [http://useast.ensembl.org/info/docs/tools/vep/script/index.html] || Biology, NGS
 
−
|-
 
−
| [[VICUNA]] || 1.3 || [http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna] || Biology, Assembly
 
−
|-
 
−
| [[ViennaRNA]] || 2.2.6 || [https://www.tbi.univie.ac.at/RNA/] || Biology, RNA-seq
 
−
|-
 
−
| [[Vim]] || 7.4.5 || [http://www.vim.org] || Programming, Scripting, Language
 
−
|-
 
−
| [[vmd]] || 1.9.1 || [http://ftp.ks.uiuc.edu/Research/vmd/] || Biology, Visualization
 
−
|-
 
−
| [[VSearch]] || 20151022, 20161209-2.3.4 || [https://github.com/torognes/vsearch] || Biology, NGS
 
−
|-
 
−
| [[VT]] || 20140903, 20160129 || [https://github.com/atks/vt] || Biology, Genomics
 
−
|-
 
−
| [[VTK]] ||  6.1.0 || [http://www.vtk.org/] || Visualization, Graphics
 
−
|-
 
−
| [[V-Phaser2]] || 02112013 || [http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/v-phaser-2] || Biology, Phylogenetics
 
−
|-
 
−
| [[Virsorter]] || 1.0.3 || [https://github.com/simroux/VirSorter] || Biology, Phylogenetics
 
−
|-
 
−
| <span id="W"></span>[[w2rap-contiger]] || 20161124 || [https://github.com/bioinfologics/w2rap-contigger] || Biology, Genomics
 
−
|-
 
−
| [[Wannier90]] || 1.2, 2.0.0 ||[http://www.wannier.org/index.html]||Computational Physics
 
−
|-
 
−
| [[WebLogo]] || 3.3 || [http://code.google.com/p/weblogo/] || Biology, Genomics
 
−
|-
 
−
| [[WEVOTE]] || 1.5.0, 1.8.0 || [https://github.com/aametwally/WEVOTE] || Biology, Genomics
 
−
|-
 
−
| [[WDSSII]] || 1 || [http://www.wdssii.org] || Meteorology
 
−
|-
 
−
| [[WIEN2k]] || 12.1 || [http://www.wien2k.at] || Material Science, Chemistry
 
−
|-
 
−
| [[Wgs]] or [[Celera]] || 8.2, 8.3rc1, 8.3rc1.r4638  || [http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page] || Biology, NGS
 
−
|-
 
−
| [[wublast]] || 2.0 || [http://blast.wustl.edu/] || Biology, Sequence Alignment
 
−
|-
 
−
| <span id="Y"></span> [[YAHA]] || 0.1.82 || [http://faculty.virginia.edu/irahall/yaha/] || Biology NGS
 
−
|-
 
−
| [[Xander]] || 20151222 || [https://github.com/rdpstaff/Xander_assembler] || Biology, Phylogenetics
 
−
|-
 
−
| <span id="X"></span> [[XCrySDen]] || 1.5.60 || [http://www.xcrysden.org] || Computational Material Science
 
−
|-
 
−
| [[Yambo]] || 3.3.0 || [http://www.yambo-code.org] || Physics
 
−
|-
 
−
| [[YASM]] || 1.3.0 || [http://yasm.tortall.net] || Computer Science
 
−
|-
 
−
| [[Yasra]] || 2.32 || [http://www.bx.psu.edu/miller_lab/] || Biology, NGS
 
−
|-
 
−
| [[Zagros]] || 1.0.0 || [http://smithlabresearch.org/software/zagros/] || Biology, NGS
 
−
|-
 
−
| [[Zeo++]] || 0.2.2 || [http://www.maciejharanczyk.info/Zeopp/about.html] || Chemistry
 
−
|-
 
−
| [[Zorro]] || 2.2 || [http://loco.biosci.arizona.edu/zorro/] || Biology, Sequencing
 
−
|}
 
−
 
 
−
<references />
 
−
=Add New App=
 
−
To add a documentation page for a new piece of software installed into /apps please go to [[Add New App Page]].
 

Latest revision as of 17:41, 28 September 2017

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