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[[Category:Software]]
#REDIRECT [[Applications]]
==Installed Software List==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''.
 
'''Note:''' Click on the icons to the right of the column headings to sort the table.
 
[[#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]]
 
{|  border="1"  cellspacing="0" cellpadding="2" align="center"  class="wikitable sortable"
|-
! scope="col" | Name
! scope="col" class="unsortable" | Version <ref name="version">Up to 3 most recent/important releases are listed. See the software wiki pages and the output of "module spider software" for full version listing.</ref>
! scope="col" class="unsortable" | Website
! scope="col" | Category
|-
| <span id="A"></span> [[AbInit]] || 6.12.3, '''7.10.2''' || [http://www.abinit.org/] || Ab Initio Quantum Chemistry, Density Functional Theory
|-
| [[Abyss]] || 1.3.4, '''1.3.7''' || [http://www.bcgsc.ca/platform/bioinfo/software/abyss] || Biology, NGS
|-
| [[AFNI]] || 2011_12_21_1014 || [http://afni.nimh.nih.gov/afni] || Biology, Statistics, Imaging, Neurology
|-
| [[Agalma]] || 0.2.1, 0.3.5, 0.5.0 || [https://bitbucket.org/caseywdunn/agalma] || Biology, Bioinformatics, Genomics, SNP
|-
| [[ALLPATHS-LG]] || 42316, 44837 || [http://www.broadinstitute.org/software/allpaths-lg/blog/] || Biology, NGS
|-
| [[Amber]] || 11, '''12''', 14 || [http://ambermd.org/] || Simulation, chemistry
|-
| [[AMOS]] || 3.1.0 || [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS] || Biology, Genomics, NGS
|-
| [[ANNOVAR]] || 20120621,20121023,'''20130321''' || [http://www.openbioinformatics.org/annovar/] || Biology, Genomics
|-
| [[Atlas]] || 3.10.1, 3.11.17 || [http://www.gnu.org/software/gsl] || Library, Math
|-
| [[Amuse]] || 6.0 || [http://www.amusecode.org]|| Astrophysics
|-
| [[APT|Affymetrix Power Tools]] || 1.15.0 || [http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx] || Biology, Genomics, Microarray
|-
| [[ARC]] || 20140312 || [https://github.com/ibest/ARC] || Biology, NGS
|-
| [[Astral]] || 4.4.4, 4.7.6 || [https://github.com/smirarab/ASTRAL] || Biology, Bioinformatics, NGS, Phylogenetics
|-
| [[AtomEye]] || 3 || [http://li.mit.edu/Archive/Graphics/A/]|| Material Science
|-
| [[ATRAM]] || 20140624 || [https://github.com/juliema/aTRAM] || Biology, NGS
|-
| [[Augustus]] || 2.6 || [http://augustus.gobics.de/]|| Biology, NGS
|-
| <span id="B"></span> [[BamBam]] || 1.0 || [http://udall-lab.byu.edu/Research/Software/BamBam.aspx] || Biology, NGS
|-
| [[Bamstats]] || 20140602 || [https://github.com/lindenb/jvarkit/wiki/BamStats04] || Biology, NGS
|-
| [[Bamtools]] || 2.1.1 || [https://github.com/pezmaster31/bamtools/wiki] || Biology, NGS
|-
| [[BamUtil]] || 1.0.2 || [http://genome.sph.umich.edu/wiki/BamUtil] || Biology, NGS
|-
| [[BayesRate]] || 1.3.43 || [http://sourceforge.net/projects/bayesrate/] || Biology, Phylogenetics
|-
| [[Bbcp]] || 12.08.17.00.0  || [http://www.slac.stanford.edu/~abh/bbcp/]|| Network file transfer
|-
| [[Bcftools]] || 20140618 || [http://samtools.github.io/bcftools/] || Biology, Genomics, NGS
|-
| [[Beagle|BEAGLE]] || 3.2.2 || [http://faculty.washington.edu/browning/beagle/beagle.html] || Biology, Genetics, Genotyping
|-
| [[Beast|BEAST]] || 1.7.5, '''1.8.1''', 2.1.3 || [http://www.beast2.org/wiki/index.php/Main_Page]|| Biology, Phylogenetics
|-
| [[Bedops]] || 2.4.2 || [http://www.uwencode.org/software]||  Biology, Bioinformatics, Sequence, NGS
|-
| [[Bedtools|BEDTools]] || 2.16.2, 2.17.0, 2.23.0 || [http://code.google.com/p/bedtools/]|| Biology, NGS
|-
| [[BEST]] || 2.3 || [http://www.stat.osu.edu/~dkp/BEST] || Biology, Phylogenetics
|-
| [[BETA]] || 1.0.5 || [http://cistrome.org/BETA/] || Biology, NGS
|-
| [[BFAST]] || 0.7.0 || [http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page] || Biology, NGS
|-
| [[Bismark]] || 0.7.4, 0.7.7, '''0.13.0''' || [http://www.bioinformatics.babraham.ac.uk/projects/download.html#bismark] || Biology, NGS, Methylation
|-
| [[Bioconductor]] || Latest || [http://www.bioconductor.org/] || Biology, R, Statistics
|-
| [[Perl|BioPerl]] || 1.006901 || [http://bioperl.org/] || Biology, Perl
|-
| [[PHYLDOG]] || 20130418 || [http://pbil.univ-lyon1.fr/software/phyldog] || Biology, Genomics, Phylogenetics
|-
| [[Phyluce]] || c561dd9 || [https://github.com/faircloth-lab/phyluce] || Biology, Phylogenetics
|-
| [[Python|BioPython]] || 1.59 || [http://biopython.org/] || Biology, Python
|-
| [[BLASR]] || 20130815 || [https://github.com/PacificBiosciences/blasr] || Biology, NGS
|-
| [[Blast|NCBI BLAST]] || 2.2.27, 2.2.28, '''2.2.29''' || [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download ] || Biology, Sequence alignment
|-
| [[Blast2go]] || 2.5.0-20120705 || [http://www.blast2go.com/b2ghome] || Biology, Annotation
|-
| [[BLAT]] || 20120524 || [http://genome.ucsc.edu/goldenPath/help/blatSpec.html] || Biology, Sequence alignment
|-
| [[Blender]] || 2.63 || [http://www.blender.org/] || Graphics
|-
| [[Boost]] || 1.49.0, 1.53.0, '''1.54.0''' || [http://www.boost.org/] || C++, Library
|-
| [[Bowtie]] || 0.12.9, '''1.0.0''' || [http://bowtie-bio.sourceforge.net/index.shtml] || Biology, NGS
|-
| [[Bowtie2]] || 2.1.0, 2.2.2, 2.2.3, '''2.2.4''' || [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml] || Biology, NGS
|-
| [[BPP]] || 2.2, 1.9.0 || [http://abacus.gene.ucl.ac.uk/software.html] || Biology, Phylogenetics
|-
| [[BRANCH]] || 1.8.1 || [http://manuals.bioinformatics.ucr.edu/home/branch] || Biology, NGS, Mapping
|-
| [[Bsmap]] || 2.74, '''2.87''' || [https://code.google.com/p/bsmap/] || Biology, NGS, Methylation
|-
| [[Bwa]] || 0.6.1, 0.7.9a, '''0.7.10''' || [http://bio-bwa.sourceforge.net/] || Biology, NGS
|-
| <span id="C"></span> [[Camino]] || 20140723 || [http://cmic.cs.ucl.ac.uk/camino] || Biology, Neuroscience, Imaging
|-
| [[CAP3]] || 20120705 || [http://seq.cs.iastate.edu/] || Biology, sequence assembly
|-
| [[CASAVA]] || 1.8.2 || [http://www.illumina.com/software/genome_analyzer_software.ilmn] || Biology, NGS
|-
| [[CD-HIT]] || 4.6 || [http://weizhong-lab.ucsd.edu/cd-hit/] || Biology, Genomics
|-
| [[CDO]] || 1.6.1 || [https://code.zmaw.de/projects/cdo] || Climate
|-
| [[CEAS]] || 1.0.2 || [http://liulab.dfci.harvard.edu/CEAS] || Biology, Genomics
|-
| [[CellProfiler]] || 2.0 || [http://cellprofiler.org] || Biology, Image Analysis
|-
| [[CGATools]] || 1.6.0.42 || [http://sourceforge.net/projects/cgatools/] || Biology, NGS
|-
| [[Charmm]] || 36a3 || [http://www.charmm.org/] || Simulation, Chemistry
|-
| [[Chartdirector]] || 5.1.0 || [http://www.advsofteng.com/] || Graphics
|-
| [[Chimera]] || 1.7 || [http://www.cgl.ucsf.edu/chimera/index.html] || Biology, Modeling
|-
| [[ChromEvol]] || 2.0 || [http://www.tau.ac.il/~itaymay/cp/chromEvol/index.html] || Biology, Phylogenetics
|-
| [[CIMS]] || 4.1.2 || [http://zhanglab.c2b2.columbia.edu/index.php/CIMS_Documentation] || Biology, Genomics
|-
| [[Circos]] || 0.63-pre11 || [http://circos.ca/software/download/circos/] || Biology, Visualization
|-
| [[CisGenome]] || 2.0 || [http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm] || Biology, Genomics, Peak Calling
|-
| [[Clann]] || 3.2.3 || [https://code.google.com/p/clann/] || Biology, Phylogenetics
|-
| [[CLHEP]] || 2.2.0.1 || [http://proj-clhep.web.cern.ch/proj-clhep/] || High Energy Physics
|-
| [[ClonalFrame]] || 1.1, 1.2 || [http://www.xavierdidelot.xtreemhost.com/clonalframe.htm] || Biology, Genomics, NGS
|-
| [[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
|-
| [[CMake]] || 2.8.8, 2.9.12.1, 3.1.0 || [http://www.cmake.org/] || Programming, Build System
|-
| [[CNVSeq]] || 20110715 || [http://tiger.dbs.nus.edu.sg/cnv-seq/] || Biology, NGS
|-
| [[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
|-
| [[CONCOCT]] || 0.3.1 || [https://github.com/BinPro/CONCOCT] || 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
|-
| [[covNMR]] || 2014 || [http://spin.ccic.ohio-state.edu/index.php/welcome/index] || Biochemistry
|-
| [[CUDA]] || 4.2, 5.5 || [http://www.nvidia.com/object/cuda_home_new.html] || Programming, Graphics
|-
| [[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]] || 1.1 || [http://code.google.com/p/cutadapt/] || Biology, NGS
|-
| <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
|-
| [[DCMTK]] || 3.6.0 || [http://dicom.offis.de/dcmtk.php.en] || Biology, Neuroscience, Imaging
|-
| [[DSSAT]] || 4.5 || [http://dssat.net/about] || 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
|-
| [[Delft3D]] || 3621 || [http://oss.deltares.nl/web/delft3d] || Hydrodynamics, Physics
|-
| [[Desmond]] || 3.0.3.1 || [http://www.deshawresearch.com/resources_desmond.html] || Simulation, Biology, Chemistry
|-
| [[Dalton]] || 2011 || [http://daltonprogram.org] || Quantum Chemistry
|-
| [[Diamond]] || 0.5.1|| [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
|-
| [[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
|-
| [[DNA Clust]] || 3.0 || [http://sourceforge.net/projects/dnaclust/] || Biology, Genomics
|-
| [[Dock]] || 6.5, 6.6 || [http://dock.compbio.ucsf.edu/] || Chemistry, ligand binding prediction
|-
| [[DOT]] || 2.0 || [http://www.sdsc.edu/CCMS/DOT/] || Biology, Bioinformatics, Docking
|-
| [[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
|-
| [[EEGLAB]] || 12.0.2.1b || [http://sccn.ucsd.edu/wiki/EEGLAB] || Biology, Matlab
|-
| [[EIGENSOFT]] || 4.2, '''5.0.1''' || [http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html] || Biology, Population
|-
| [[emboss]] || 6.5.7 || [http://emboss.sourceforge.net/] || Biology, multi-tool suite
|-
| [[EMIRGE]] || 20130727 || [https://github.com/csmiller/EMIRGE] || Biology, NGS
|-
| [[eQTLA]] || 1.1 || [http://research.lunenfeld.ca/silverberg/] || Biology, Genomics
|-
| [[Eqtlbma]] || 1.2.2 || [https://github.com/timflutre/eqtlbma] || Biology, Genotyping
|-
| [[Espresso]] || 5.0.1 || [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
|-
| [[Eval]] || 2.2.8 || [http://mblab.wustl.edu/software.html] || Biology, Genomics, GUI
|-
| [[ExaBayes]] || 1.2.1 || [http://sco.h-its.org/exelixis/web/software/exabayes/] || Biology, Phylogenetics
|-
| [[ExaML]] || 1.0.3, 1.0.5, 1.0.12 || [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> [[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
|-
| [[FastML]] || 3.0 || [http://fastml.tau.ac.il/overview.php] || Biology, Phylogenetics, ML
|-
| [[FastQC]] || 0.9.6, 0.10.1 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/] || Biology, NGS
|-
| [[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
|-
| [[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 || [http://www.ffmpeg.org/] || Multimedia, audio, video
|-
| [[FFTW]] || 3.3.2, 3.3.3 || [http://www.fftw.org/] || Math, Library, C++
|-
| [[FLASH]] || 1.2.10 || [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''' || [http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent/] || Simulation, Fluid Dynamics
|-
| [[FragGeneScan]] || 1.16 || [http://omics.informatics.indiana.edu/FragGeneScan/] || Biology, NGS, Genomics
|-
| [[FreeBayes]] || 0.9.6, 0.9.15 || [http://bioinformatics.bc.edu/marthlab/FreeBayes] || Biology, NGS, SNP Calling
|-
| [[Freesurfer]] || 5.2.0 || [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> [[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
|-
| [[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, 2.7.4, '''3.1.1''' || [http://www.broadinstitute.org/gsa/wiki/index.php/GATK] || Biology, NGS
|-
| [[Gaussian]] || E01, 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
|-
| [[Geant4]] || 4.10 || [http://geant4.cern.ch/support/about.shtml] || Physics
|-
| [[GEM]] || 20130406 || [http://sourceforge.net/projects/gma-bio/] || Biology, NGS
|-
| [[GEMINI]] || 4.6.6a || [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
|-
| [[Genewise]] || 2.2.0 || [http://www.ebi.ac.uk/Tools/Wise2]||Biology, Genomics, Annotation
|-
| [[GenomicTools]] || 2.7.0 || [http://code.google.com/p/ibm-cbc-genomic-tools/] || Biology, NGS
|-
| [[GenSel]] || 4.90 || [http://www.oalib.com/references/11104881] || Biology, Genetics
|-
| [[GKNO]] || 1.30.18 || [http://code.google.com/p/ibm-cbc-genomic-tools/] || Biology, NGS
|-
| [[Git]] || 1.8.2.1 || [https://code.google.com/p/git-core/] || Development, Revision Control
|-
| [[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]] || 20130618, 20130720, '''20140530''' || [http://research-pub.gene.com/gmap/] || Biology, Genomics
|-
| [[GNU]] || 4.4.6, 4.7.2 || [http://www.gnu.org] || Compilers, Programming
|-
| [[GnuPlot]] || 4.6.0 || [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
|-
| [[GraphViz]] || 2.38.0 || [http://www.graphviz.org/] || Graphics, plotting, visualization
|-
| [[Gromacs]] || 4.5.5, 4.6.5 || [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
|-
| [[GULP]] || 4.0 || [http://projects.ivec.org/gulp/] || Material Science
|-
| <span id="H"></span> [[HaMStR]] || v8b || [http://www.deep-phylogeny.org/hamstr/] || Biology, Genomics
|-
| [[HapCompass]] || 0.7.7 || [http://www.brown.edu/Research/Istrail_Lab/hapcompass.php] || Biology, NGS, Genomics
|-
| [[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
|-
| [[HDF5]] || '''1.8.9''', 1.8.12|| [http://www.hdfgroup.org/HDF5/]||Library, Data
|-
| [[HMMER3]] || 3.0, 3.1b1 || [http://hmmer.janelia.org/]||Biology, Genomics
|-
| [[HMMSplicer]] || 0.9.5 || [http://derisilab.ucsf.edu/index.php?software=105] || Biology, Genomics
|-
| [[HOMER]] || 4.2 || [http://biowhat.ucsd.edu/homer/]||Biology, Genomics
|-
| [[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
|-
| [[HyPhy]] || 2.1.2.28 || [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> [[IDBA-UD]] || 1.0.9, 1.1.0 || [http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/] || Biology, NGS
|-
| [[iGTP]] || 1.1 || [http://genome.cs.iastate.edu/CBL/iGTP/] || Biology, Bioinformatics, Phylogenetics
|-
| [[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
|-
| [[Intel Compilers]] || 11.1, 2012 || [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
|-
| [[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]] || 1.6.0_31, 1.7.0_02 || [http://java.com] || Java Development Kit
|-
| [[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
|-
| <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 || [https://github.com/ged-lab/khmer] || Biology, NGS
|-
| [[KING]] || 1.4 || [http://people.virginia.edu/~wc9c/KING/index.html] || Biology, Genomics
|-
| [[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
|-
| <span id="L"></span> [[LAMMPS]] || 28Oct12, 30Sep13, 28Jun14 || [http://lammps.sandia.gov/] || Molecular Dynamics Simulation
|-
| [[Last]] || 193, 247 || [http://last.cbrc.jp/] || Biology, Sequence alignment
|-
| [[Lastz]] || 1.03.02, 1.02.00 || [http://www.bx.psu.edu/~rsharris/lastz/] || Biology, NGS
|-
| [[LIBSVM]] || 3.12 || [http://www.csie.ntu.edu.tw/~cjlin/libsvm/] || Machine Learning
|-
| [[LSC]] || 0.3, '''0.3.1''' || [http://www.stanford.edu/~kinfai/LSC/LSC.html] || Biology, NGS, Error correction
|-
| [[Loci]] || 3.3 || [http://www.tetraresearch.com/locichem/about-locichem/] || Fluid Dynamics
|-
| [[LS-DYNA]] || 700, '''711''' || [http://www.lstc.com/products/ls-dyna] || Physics
|-
| [[Lumpy]] || 0.2.1 || [https://github.com/timflutre/eqtlbma] || Biology, SNP
|-
| <span id="M"></span> [[MACH]] || 1.0.18 || [http://www.sph.umich.edu/csg/abecasis/MACH] || Biology, Genomics
|-
| [[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 || [http://liulab.dfci.harvard.edu/MACS/]||Biology, ChIP-Seq
|-
| [[mafft]] || 7.037, 6.903, 7.215 || [http://mafft.cbrc.jp/alignment/software/]||Biology, Multiple sequence alignment
|-
| [[Maker]] || 2.10, 2.25b || [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
|-
| [[Maq]] || 0.7.1 || [http://maq.sourceforge.net/] || Biology, NGS
|-
| [[MARK]] || 2.0.1 || [http://www.phidot.org/software/mark/index.html] || Statistics
|-
| [[MaSuRCA]] || 2.3.2 || [http://www.genome.umd.edu/masurca.html] || Biology, NGS
|-
| [[Matlab]] || 2012a, 2013a, 2014a || [http://www.mathworks.com]||Math, Simulation, Programming
|-
| [[MATS]] || 2.1.0, 3.0.6b, '''3.0.8''' || [http://rnaseq-mats.sourceforge.net/index.html]||BIology, NGS
|-
| [[Mauve]] || 2.3.1 || [http://gel.ahabs.wisc.edu/mauve/] || Biology, NGS
|-
| [[MCarts]] || 1.0.2 || [http://sourceforge.net/projects/mcarts/]||Biology, Genomics, Markov models
|-
| [[MCNP]] || 5, 6b2 || [http://mcnp-green.lanl.gov/about_mcnp5.html/] || Physics
|-
| [[MCNPX]] || 2.7.0, 2.7.0-i8 || [http://mcnpx.lanl.gov/] || Physics
|-
| [[Melting]] || 4.3.1 || [http://sourceforge.net/projects/melting/] || Biology, Genome, RNA, Folding
|-
| [[Meme]] || 4.8.1 || [http://meme.nbcr.net/meme/intro.html]||Biology, Motifs, Sequence analysis
|-
| [[Mercurial]] || 2.7 || [http://meme.nbcr.net/meme/intro.html]||Development, Revision Control
|-
| [[Metabin]] || 1.0 || [http://metabin.riken.jp/index] || Biology, Metagenomics
|-
| [[MetaCluster]] || 5.0beta || [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
|-
| [[MetaVelvet]] || 1.2.01 || [http://metavelvet.dna.bio.keio.ac.jp/] || 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
|-
| [[MIA]] || 20130301 || [https://github.com/udo-stenzel/mapping-iterative-assembler] || Biology, NGS
|-
| [[Midnight_Commander|Midnight Commander]] || 4.6.1 || [http://www.gnu.org/software/mc/] || Tools, Utilities
|-
| [[Migrate-n]] || 3.3.0 || [http://popgen.sc.fsu.edu/Migrate/Migrate-n.html] || Biology, Population
|-
| [[mira]] || 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, '''4.0.rc1''' || [http://mira-assembler.sourceforge.net/]||Biology, NGS
|-
| [[MISO]] || 0.4.4, '''0.4.9''' || [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 || [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 || [http://code.google.com/p/mosaik-aligner/] || Biology,NGS
|-
| [[Mothur]] || 1.31.2 || [http://www.mothur.org/wiki/Main_Page/] || Biology, Microbial Ecology
|-
| [[MOTU]] || 1.1 || [http://www.bork.embl.de/software/mOTU/] || Biology, Bioinformatics, Genomics
|-
| [[MP-EST]] || 1.4 || [https://code.google.com/p/mp-est/] || Biology, Phylogenetics
|-
| [[mpiP]] || 3.4.1 || [http://mpip.sourceforge.net] || Parallel Computing
|-
| [[MrBayes]] || 3.2.1 || [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
|-
| [[MZMine]] || 2.10 || [http://mzmine.sourceforge.net/] || Biology, Spectroscopy
|-
| <span id="N"></span> [[NAMD]] || 2.9 || [http://www.ks.uiuc.edu/Research/namd/] || Simulation, Chemistry, 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 || [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
|-
| [[NetCDF]] || 3.4.2, 4.2, 4.3 || [http://www.unidata.ucar.edu/software/netcdf/]|| Data exchange, Tools
|-
| [[Newbler]] || 2.6, 2.7 || [http://my454.com/products/analysis-software/index.asp] || Biology, NGS
|-
| [[Nextallele]] || 20140718 || [https://code.google.com/p/nextallele/] || Biology, Genomics
|-
| [[NEXUS_NCL|Nexus NCL]] || 2.1.18 || [http://ncl.sourceforge.net/] || Biology, Phylogenetics, Library
|-
| [[ngsCAT]] || 0.1 || [http://www.bioinfomgp.org/ngscat] || Biology, Bioinformatics, NGS
|-
| [[NGSUtils]] || 20130722 || [http://ngsutils.org/] || Biology, NGS
|-
| [[Nipype]] || 0.10.0 || [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
|-
| <span id="O"></span> [[Oases]] || 0.2.08 || [http://www.ebi.ac.uk/~zerbino/oases/] || Biology, NGS
|-
| [[Olego]] || 1.1.2, '''1.1.5''' || [http://zhanglab.c2b2.columbia.edu/index.php/OLego_Documentation] || Biology, NGS, RNA-Seq
|-
| [[Octave]] || 3.6.4 || [http://www.gnu.org/software/octave/]|| Numerical Computation
|-
| [[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 || [http://www.openfoam.org/]||Fluid Dynamics
|-
| [[OpenMM]] || 6.2.0 || [https://simtk.org/home/openmm]||Quantum Chemistry
|-
| [[OrthoMCL]] || 2.0.2, 2.0.3, '''2.0.7''' || [http://orthomcl.org/]|| Biology, Genomics
|-
| [[p4vasp]] || 0.3.29 || [http://www.p4vasp.at/] || Molecular, Electronic Structure
|-
| [[Pacbio]] || 2.2.0.133377 || [http://www.pacb.com/devnet/] || Biology, Bioinformatics, NGS
|-
| <span id="P"></span> [[PALES]] || 122 || [http://spin.niddk.nih.gov/bax/software/PALES/index.html] || Physics
|-
| [[PAML]] || 4.7, 4.8a || [http://abacus.gene.ucl.ac.uk/software/paml.html]||Biology, Phylogenetics
|-
| [[Pandaseq]] || 20140808 || [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 || [http://www.paraview.org]||Data Analysis
|-
| [[PartitionFinder]] || 1.0.1, 1.1.1 || [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-r20130605p1, '''2.0-r20130907''' || [http://http://pasa.sourceforge.net/]|| Biology, Genomics
|-
| [[PAUP]] || 4.0b10 || [http://paup.csit.fsu.edu/] || Biology, Phylogenetics
|-
| [[PBJelly]] || 14.7.14 || [http://sourceforge.net/projects/pb-jelly/] || Biology, Bioinformatics
|-
| [[DRMAA|pbsdrmaa]] || 1.0.17 || [http://apps.man.poznan.pl/trac/pbs-drmaa/wiki] || Libraries, Torque
|-
| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html]|| Biology, Chip-Seq
|-
| [[PEAR]] || 0.9.2 || [http://www.exelixis-lab.org/web/software/pear] || Biology, NGS
|-
| [[PDT]] || 3.18 || [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
|-
| [[Phenix]] || 1.8.1069 || [http://www.phenix-online.org/] || Crystallography
|-
| [[PfamScan]] || 1.3 || [http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/] || Biology, Genomics
|-
| [[PHITS]] || 2.52 || [http://www.oecd-nea.org/tools/abstract/detail/nea-1857/] || Physics
|-
| [[Phonopy]] || 1.9.2 || [http://phonopy.sourceforge.net/] || Chemistry
|-
| [[PhyloBayes]] || 3.3f, 1.4f MPI || [http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm] || Biology, Phylogenetics
|-
| [[Phylosift]] || 1.1 || [https://github.com/gjospin/PhyloSift] ||  Biology, Genomics, Phylogenetics, Taxonomy
|-
| [[PhyML]] || 3.0, 20121109 || [http://code.google.com/p/phyml/] || Biology, Phylogenetics
|-
| [[Picard]] || 1.69, 1.72, 1.80 || [http://picard.sourceforge.net/] || Biology, NGS
|-
| [[PLAST]] || 1.0 || [ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/] || Biology, Bioinformatics
|-
| [[Plink]] || 1.07 || [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
|-
| [[Preseq]] || 0.0.4 || [http://smithlab.usc.edu/plone/software/librarycomplexity] || Biology, NGS
|-
| [[Primer3]] || 2.3.4 || [http://sourceforge.net/projects/primer3/] || Biology, Genomics
|-
| [[Prokka]] || 1.10 || [http://www.vicbioinformatics.com/software.prokka.shtml] || Biology, Genomics, Bioinformatics, Assembly
|-
| [[ProBABEL]] || 0.4.2, 0.4.3 || [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 || [http://www.bioinf.uni-leipzig.de/Software/proteinortho/index.html] || Biology, Genomics
|-
| [[python]] || 2.6.8, 2.7.3, 2.7.5, '''2.7.6''', 2.7.8 || [http://python.org] || Biology, Genomics, NGS
|-
| [[QDD]] || 3.1.2 || [http://net.imbe.fr/~emeglecz/qdd.html] || Programming, scripting, language
|-
| <span id="Q"></span> [[QIIME]] || 1.5.0 || [http://qiime.org/index.html]|| Biology, Ecology
|-
| [[QT]] || 4.8.3 || [http://qt-project.org]|| Computer Science
|-
| [[QUAST]] || 2.3 || [http://sourceforge.net/projects/quast] || Biology, NGS
|-
| [[Quickquartet]] || 1.0.0 || [https://code.google.com/p/quickquartet/] || Biology, Phylogenetics
|-
| <span id="R"></span> [[R]] || 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0, 3.0.1, 3.0.2 || [http://www.r-project.org/] || Statistics, Programming
|-
| [[R8S]] || 1.71 || [http://loco.biosci.arizona.edu/r8s/] || Biology, Evolution
|-
| [[RADICAL]] || 0.2 || [http://desalle.amnh.org/software.html] || Biology, Phylogenetics, Genomics
|-
| [[RAxML]] || 7.9.1, 8.0.25, '''8.1.12''' || [http://sco.h-its.org/exelixis/software.html] || Biology, Phylogenetics
|-
| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/] || Biology, Genomics
|-
| [[Reptile]] || 1.1 || [http://aluru-sun.ece.iastate.edu/doku.php?id=reptile] || Biology, NGS, error correction
|-
| [[riboPicker]] || 0.4.3 || [http://ribopicker.sourceforge.net/] || Biology, Sequence
|-
| [[RNAhybrid]] || 2.1.1 || [http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/] || Biology, Genomics
|-
| [[ROOT]] || 6.0 || [http://root.cern.ch/drupal/] || Data Analysis
|-
| [[Rosetta]] || 2014wk4 || [https://www.rosettacommons.org/about] || Biology, Structure, Modelling
|-
| [[RSEG]] || 0.4.8 || [http://smithlab.usc.edu/histone/rseg/] || Biology, NGS
|-
| [[RSEM]] || 1.1.17, 1.2.7, 1.2.19 || [http://deweylab.biostat.wisc.edu/rsem] || Biology, NGS, RNA-Seq
|-
| [[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
|-
| [[Sambamba]] || 0.5.0-dev, 0.5.1 || [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]] || 0.1.16, 0.1.18, '''0.1.19''', 1.0, 1.1, 1.2 || [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
|-
| [[Scalablast]] || 2.4.53, 2.11.5 || [http://omics.pnl.gov/software/ScalaBLAST.php] || Biology, Genomics
|-
| [[Scalpel]] || 0.1.1 || [http://sourceforge.net/projects/scalpel/] || Biology, NGS
|-
| [[Sharcgs]] || 1.2.11 || [http://sharcgs.molgen.mpg.de/index.shtml] || Biology, NGS, Assembly
|-
| [[Schrodinger]] || 2012, 2013 || [http://www.schrodinger.com/] || Simulation, chemistry
|-
| [[SCons]] || 2.3.0 || [http://sourceforge.net/projects/scons/] || Programming
|-
| [[Scythe]] || 0.991 || [https://github.com/vsbuffalo/scythe] || Biology, NGS
|-
| [[Segemehl]] || 0.1.9 || [http://www.bioinf.uni-leipzig.de/Software/segemehl/] || Biology, NGS, Mapper
|-
| [[SeqPrep]] || 0.5 || [https://github.com/jstjohn/SeqPrep] || Biology, NGS
|-
| [[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
|-
| [[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
|-
| [[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 || [http://homepage.mac.com/iankorf] || Biology, Genomics
|-
| [[SnpEff]] || 3.3h, 4.0e || [http://snpeff.sourceforge.net/] || Biology, NGS, Genomics
|-
| [[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
|-
| [[SOAPsplice]] || 1.10 || [http://soap.genomics.org.cn/soapsplice.html] || Biology, NGS
|-
| [[SparCC]] || 201402 || [https://bitbucket.org/yonatanf/sparcc/overview] || Microbial Ecology
|-
| [[Spades]] || 2.5.0, 2.5.1, 3.0.0, 3.1.0, '''3.5.0''' || [http://bioinf.spbau.ru/en/spades] || Biology, NGS
|-
| [[Spanki]] || 0.4.1, '''0.4.3''' || [http://www.cbcb.umd.edu/software/spanki/] || Biology, NGS, RNA-Seq
|-
| [[SPARTA+]] || 2.60 || [http://spin.niddk.nih.gov/bax/software/SPARTA+/]||Chemistry
|-
| [[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
|-
| [[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 || [http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/] || Biology, NGS
|-
| [[Stacks]] || 0.9995 || [http://creskolab.uoregon.edu/stacks/] || Biology, Genomics, NGS
|-
| [[STAR]] || 2.3.0e || [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]] || 0.97 || [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
|-
| [[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
|-
| [[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> [[TASSEL]] || 5.0 || [http://www.maizegenetics.net/index.php?option=com_content&task=view&id=89&Itemid=119] || Biology, Genomics
|-
| [[TAU]] || 2.21.4, 2.23 ||[http://www.cs.uoregon.edu/Research/tau/home.php]||Profiling, Tracing, Programming
|-
| [[T-Coffee]] || 9.03.r1318 || [http://www.tcoffee.org/Projects/tcoffee/] || Biology, Genomics, Multiple Alignment
|-
| [[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
|-
| [[TomoPy]] || 0.0.3 || [https://github.com/tomopy/tomopy] || Biology, Neuroimaging
|-
| [[Tophat]] || 1.4.1, '''2.0.13''' || [http://tophat.cbcb.umd.edu/] || Biology, NGS
|-
| [[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
|-
| [[TransDecoder]] || 20140704 || [http://transdecoder.github.io/] || Biology, NGS
|-
| [[TreeFix]] || 1.1.7 || [http://compbio.mit.edu/treefix/] || Biology, Phylogenetics
|-
| [[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
|-
| [[Trim Galore]] || 0.2.8 || [http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/] || Biology, NGS
|-
| [[Trimmomatic]] || 0.22, 0.32 || [http://www.usadellab.org/cms/index.php?page=trimmomatic] || Biology, NGS
|-
| [[Trinity]] || r20131110, r20140413, r20150215-2.0.4 || [http://trinityrnaseq.sourceforge.net/] || Biology, NGS, RNA-Seq
|-
| [[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 || [http://www.drive5.com/usearch/] || Biology, Sequence analysis
|-
| [[UDUNITS]] || 2.2.17 || [http://www.unidata.ucar.edu/software/udunits/] || Library, Units, Programming
|-
| [[UNAFold]] || 3.8 || [http://dinamelt.rit.albany.edu/unafold/] || Biology, Genome, RNA, Folding
|-
| <span id="V"></span> [[Valgrind]] || 3.9.0 || [http://valgrind.org] || Computer Science
|-
| [[VASP]] || 4.6.34, 5.2.12, 5.3.2, 5.3.3, '''5.3.5''' || [http://cms.mpi.univie.ac.at/vasp/] || Quantum Chemistry, Ab Initio
|-
| [[VarScan]] || 2.3.6 || [http://varscan.sourceforge.net/] || Biology, NGS, Genomics
|-
| [[VCFLib]] || 20121207 || [https://github.com/ekg/vcflib] || Biology, NGS, Genomics
|-
| [[VCFtools]] || 0.1.9, 0.1.10 || [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 || [http://useast.ensembl.org/info/docs/tools/vep/script/index.html] || Biology, NGS
|-
| [[Vim]] || 7.4.5-minimal, 7.4.5-py2, 7.4.5 || [http://www.vim.org] || Programming, Scripting, Language
|-
| [[vmd]] || 1.9.1 ||[http://ftp.ks.uiuc.edu/Research/vmd/]||Biology, Visualization
|-
| [[VTK]] ||  6.1.0 || [http://www.vtk.org/] || Visualization, Graphics
|-
| <span id="W"></span> [[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
|-
| [[WDSSII]] || 1 || [http://www.wdssii.org] || Meteorology
|-
| [[WIEN2k]] || 12.1 || [http://www.wien2k.at] || Material Science, Chemistry
|-
| [[Wgs]] or [[Celera]] || 8.1, 8.2, 8.3rc1 || [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
|-
| [[XCrySDen]] || 1.5.60 || [http://www.xcrysden.org] || Computational Material Science
|-
| [[Yambo]] || 3.3.0 || [http://www.yambo-code.org] || Physics
|-
| [[Yasra]] || 2.32 || [http://www.bx.psu.edu/miller_lab/] || Biology, NGS
|}
 
<references />
 
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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