Difference between revisions of "Installed Software"

From UFRC
Jump to navigation Jump to search
Line 12: Line 12:
 
! scope="col" | Category
 
! scope="col" | Category
 
|-
 
|-
−
<!-- | [[Abaqus]] || 6.6-1, 6.9-2 || [http://www.simulia.com/products/abaqus_standard.html] || Simulation
 
−
|- -->
 
 
| [[AbInit]] || 6.12.3 || [http://www.abinit.org/] || Ab Initio Quantum Chemistry, Density Functional Theory
 
| [[AbInit]] || 6.12.3 || [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
 
| [[Abyss]] || 1.3.4, '''1.3.7''' || [http://www.bcgsc.ca/platform/bioinfo/software/abyss] || Biology, NGS
 
|-
 
|-
−
<!-- | [[ADMB]] || 9.1, 10.0, 10.1 || [http://admb-project.org/] || Modeling, math || X ||
 
−
|- -->
 
 
| [[ALLPATHS-LG]] || 42316, 44837 || [http://www.broadinstitute.org/software/allpaths-lg/blog/] || Biology, NGS
 
| [[ALLPATHS-LG]] || 42316, 44837 || [http://www.broadinstitute.org/software/allpaths-lg/blog/] || Biology, NGS
 
|-
 
|-
Line 30: Line 26:
 
| [[ANNOVAR]] || 20120621,20121023,'''20130321''' || [http://www.openbioinformatics.org/annovar/] || Biology, Genomics
 
| [[ANNOVAR]] || 20120621,20121023,'''20130321''' || [http://www.openbioinformatics.org/annovar/] || Biology, Genomics
 
|-
 
|-
−
<!--
 
−
| [[Ansys]] || 9.0, 10.0 || [http://www.ansys.com/] || Simulation, Engineering || X ||
 
−
|-
 
−
| [[antlr]] || 2.7.7, 3.1.3 || [http://www.antlr.org/] || Linguistics, Parser || X ||
 
−
|-
 
−
| [[arachne]] || 37618 || [http://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational] || Biology, Genomics || X ||
 
−
|- -->
 
 
| [[Atlas]] || 3.10.1, 3.11.17 || [http://www.gnu.org/software/gsl] || Library, Math
 
| [[Atlas]] || 3.10.1, 3.11.17 || [http://www.gnu.org/software/gsl] || Library, Math
 
|-
 
|-
Line 57: Line 46:
 
| [[BamUtil]] || 1.0.2 || [http://genome.sph.umich.edu/wiki/BamUtil] || Biology, NGS
 
| [[BamUtil]] || 1.0.2 || [http://genome.sph.umich.edu/wiki/BamUtil] || Biology, NGS
 
|-
 
|-
−
<!-- | [[BayesPhylogenies]] || 2.0 || [http://www.evolution.reading.ac.uk/BayesPhy.html] || Biology, Phylogenetics || X ||
 
−
|- -->
 
 
| [[BayesRate]] || 1.3.43 || [http://sourceforge.net/projects/bayesrate/] || Biology, Phylogenetics
 
| [[BayesRate]] || 1.3.43 || [http://sourceforge.net/projects/bayesrate/] || Biology, Phylogenetics
 
|-
 
|-
Line 87: Line 74:
 
| [[BLASR]] || 20130815 || [https://github.com/PacificBiosciences/blasr] || Biology, NGS
 
| [[BLASR]] || 20130815 || [https://github.com/PacificBiosciences/blasr] || Biology, NGS
 
|-
 
|-
−
<!-- | [[bioscope]] || 1.2.1 || [http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/ngs-data-analysis-software/bioscope.html] || Biology, NGS || X ||
 
−
|- -->
 
 
| [[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
 
| [[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
 
|-
 
|-
Line 129: Line 114:
 
| [[Circos]] || 0.63-pre11 || [http://circos.ca/software/download/circos/] || Biology, Visualization
 
| [[Circos]] || 0.63-pre11 || [http://circos.ca/software/download/circos/] || Biology, Visualization
 
|-
 
|-
−
<!-- | [[Circuit]] || 3.5.1, 3.5.7 || [http://www.circuitscape.org/Circuitscape/Welcome.html] || GIS || X ||
 
−
|- -->
 
 
| [[CisGenome]] || 2.0 || [http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm] || Biology, Genomics, Peak Calling
 
| [[CisGenome]] || 2.0 || [http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm] || Biology, Genomics, Peak Calling
 
|-
 
|-
Line 143: Line 126:
 
| [[CMake]] || 2.8.8 || [http://www.cmake.org/] || Programming, Build System
 
| [[CMake]] || 2.8.8 || [http://www.cmake.org/] || Programming, Build System
 
|-
 
|-
−
| [[CNVSeq]] || 20110715 || [http://tiger.dbs.nus.edu.sg/cnv-seq/] || Biology, NGS ||
+
| [[CNVSeq]] || 20110715 || [http://tiger.dbs.nus.edu.sg/cnv-seq/] || Biology, NGS
−
|-
 
−
<!--
 
−
| [[CNVnator]] || 0.2.5 || [http://sv.gersteinlab.org/] || Biology, NGS || X ||
 
−
-->
 
 
|-
 
|-
 
| [[Coevol]] || 1.3c, 1.4b || [http://megasun.bch.umontreal.ca/People/lartillot/www/downloadcoevol.html] || Biology, Phylogenetics
 
| [[Coevol]] || 1.3c, 1.4b || [http://megasun.bch.umontreal.ca/People/lartillot/www/downloadcoevol.html] || Biology, Phylogenetics
Line 157: Line 136:
 
| [[Consed]] || 23.0 || [http://bozeman.mbt.washington.edu/consed/consed.html] || Biology, Genomics
 
| [[Consed]] || 23.0 || [http://bozeman.mbt.washington.edu/consed/consed.html] || Biology, Genomics
 
|-
 
|-
−
<!-- | [[CPMD]] || 3.11.1 || [http://www.cpmd.org/] || Simulation, Chemistry || X ||
 
−
|- -->
 
 
| [[covNMR]] || 2014 || [http://spin.ccic.ohio-state.edu/index.php/welcome/index] || Biochemistry
 
| [[covNMR]] || 2014 || [http://spin.ccic.ohio-state.edu/index.php/welcome/index] || Biochemistry
 
|-
 
|-
Line 175: Line 152:
 
| [[DDT]] || 4.1.0, 4.2.1 || [http://www.allinea.com/products/ddt] || Software
 
| [[DDT]] || 4.1.0, 4.2.1 || [http://www.allinea.com/products/ddt] || Software
 
|-
 
|-
−
<!-- | [[dar]] || 2.3.9 || [http://sourceforge.net/projects/dar/] || Backup || X ||
 
−
|-
 
−
| [[DeFuse|deFuse]] || 0.4.3 || [http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page] || Biology, RNA-seq || X ||
 
−
|- -->
 
 
| [[Delft3D]] || 3621 || [http://oss.deltares.nl/web/delft3d] || Hydrodynamics, Physics
 
| [[Delft3D]] || 3621 || [http://oss.deltares.nl/web/delft3d] || Hydrodynamics, Physics
 
|-
 
|-
Line 206: Line 179:
 
|-
 
|-
 
| [[EA-Utils]] || 1.1.2.537 || [https://code.google.com/p/ea-utils/] || Biology, NGS
 
| [[EA-Utils]] || 1.1.2.537 || [https://code.google.com/p/ea-utils/] || Biology, NGS
−
|-
 
−
<!-- | [[emacs]] || 21.4.1, 23.4.1 || [http://www.gnu.org/software/emacs/] || The Emacs editor
 
−
|-
 
−
| [[EMAN2]] || 2.04 || [http://blake.bcm.tmc.edu/emanwiki/EMAN2] || Biology, image processing || X ||
 
−
|- -->
 
 
|-
 
|-
 
| [[ECTools]] || 20140311 || [https://github.com/jgurtowski/ectools] || Biology, Sequencing, Bioinformatics
 
| [[ECTools]] || 20140311 || [https://github.com/jgurtowski/ectools] || Biology, Sequencing, Bioinformatics
Line 274: Line 242:
 
| [[FSL]] || 5.0.2.2 || [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL] || Biology, Neurology, Imaging
 
| [[FSL]] || 5.0.2.2 || [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL] || Biology, Neurology, Imaging
 
|-
 
|-
−
<!-- | [[gadget]] || 2.0.4, 2.0.5 || [http://confluence.atlassian.com/display/GADGETS/Atlassian+Gadgets+2.0.5+Release+Notes] || Software Development || X ||
 
−
|-
 
−
| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/]|| Quantum Chemistry|| X ||
 
−
|- -->
 
 
| [[Garli]] || 2.0, '''2.01''' || [https://www.nescent.org/wg_garli/Main_Page]||Biology, Phylogenetics
 
| [[Garli]] || 2.0, '''2.01''' || [https://www.nescent.org/wg_garli/Main_Page]||Biology, Phylogenetics
 
|-
 
|-
Line 286: Line 250:
 
| [[GATK]] || 1.6.9, 2.7.4, '''3.1.1''' || [http://www.broadinstitute.org/gsa/wiki/index.php/GATK] || Biology, NGS
 
| [[GATK]] || 1.6.9, 2.7.4, '''3.1.1''' || [http://www.broadinstitute.org/gsa/wiki/index.php/GATK] || Biology, NGS
 
|-
 
|-
−
<!-- | [[gulp]] || 4.0.3 || [http://projects.ivec.org/gulp/] || Modeling/simulation, Chemistry || X ||
 
−
|- -->
 
 
| [[Gaussian]] || E01, G03, G09-A.02, G09-C.01 || [http://www.gaussian.com/]||Modeling, Computational Chemistry
 
| [[Gaussian]] || E01, G03, G09-A.02, G09-C.01 || [http://www.gaussian.com/]||Modeling, Computational Chemistry
−
|-
 
−
<!-- | [[Geneid]] || 1.4 || [http://genome.crg.es/software/geneid/]||Biology, Genomics, Annotation|| -->
 
 
|-
 
|-
 
| [[Geant4]] || 4.10 || [http://geant4.cern.ch/support/about.shtml] || Physics
 
| [[Geant4]] || 4.10 || [http://geant4.cern.ch/support/about.shtml] || Physics
Line 338: Line 298:
 
| [[HTSeq]] || 0.5.3p3, '''0.6.1p1''' || [http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html] || Biology, NGS
 
| [[HTSeq]] || 0.5.3p3, '''0.6.1p1''' || [http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html] || Biology, NGS
 
|-
 
|-
−
<!-- | [[HugeSeq]] || 1.0.1 || [http://hugeseq.hugolam.com/]|| Biology, NGS, Genomics || X ||
 
−
|- -->
 
 
| [[HyPhy]] || 2.1.2.28 || [http://www.datam0nk3y.org/hyphywiki/index.php/Main_Page] || Biology, Phylogenetics
 
| [[HyPhy]] || 2.1.2.28 || [http://www.datam0nk3y.org/hyphywiki/index.php/Main_Page] || Biology, Phylogenetics
 
|-
 
|-
Line 352: Line 310:
 
| [[ImageMagick]] || 6.8.8-9 || [http://imagemagick.org/] || Image manipulation
 
| [[ImageMagick]] || 6.8.8-9 || [http://imagemagick.org/] || Image manipulation
 
|-
 
|-
−
<!-- | [[Inelastica]] || 1.1 (python/2.7.2) || [http://sourceforge.net/projects/inelastica/]||Quantum Chemistry|| X ||
 
−
|- -->
 
 
| [[Intel Compilers]] || 11.1, 2012 || [http://software.intel.com/en-us/intel-composer-xe/] || Programming, Compilers
 
| [[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
 
| [[IOAPI]] || 3.1 || [http://www.baronams.com/products/ioapi/] || Meteorology
 
|-
 
|-
−
<!-- | [[IE3D]] || 15.1 || [http://www.mentor.com/electromagnetic-simulation/]||Simulation, Design|| X ||
 
−
|- -->
 
 
| [[Iprscan]] || 4.8 || [http://www.ebi.ac.uk/Tools/pfa/iprscan/] || Biology, Genomics
 
| [[Iprscan]] || 4.8 || [http://www.ebi.ac.uk/Tools/pfa/iprscan/] || Biology, Genomics
 
|-
 
|-
Line 372: Line 326:
 
| [[Kent]] || 20120524 || [http://genomewiki.cse.ucsc.edu/index.php/The_source_tree] || Biology, NGS
 
| [[Kent]] || 20120524 || [http://genomewiki.cse.ucsc.edu/index.php/The_source_tree] || Biology, NGS
 
|-
 
|-
−
<!-- | [[Khmer]] || 20120321 || [https://github.com/ctb/khmer] || Biology, NGS, Utilities
 
−
|- -->
 
 
| [[Kmer]] || 1934 || [http://sourceforge.net/apps/mediawiki/kmer/index.php?title=Main_Page] || Biology, NGS
 
| [[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
 
|-
 
|-
 
| [[LAMMPS]] || 28Oct12, 30Sep13 || [http://lammps.sandia.gov/] || Molecular Dynamics Simulation
 
| [[LAMMPS]] || 28Oct12, 30Sep13 || [http://lammps.sandia.gov/] || Molecular Dynamics Simulation
Line 382: Line 336:
 
| [[Lastz]] || 1.03.02, 1.02.00 || [http://www.bx.psu.edu/~rsharris/lastz/] || Biology, NGS
 
| [[Lastz]] || 1.03.02, 1.02.00 || [http://www.bx.psu.edu/~rsharris/lastz/] || Biology, NGS
 
|-
 
|-
−
<!-- | [[libxc]] || 1.1.0 || [http://www.tddft.org/programs/octopus/wiki/index.php/Libxc] || Math, funtionals || X ||
 
−
|- -->
 
 
| [[LIBSVM]] || 3.12 || [http://www.csie.ntu.edu.tw/~cjlin/libsvm/] || Machine Learning
 
| [[LIBSVM]] || 3.12 || [http://www.csie.ntu.edu.tw/~cjlin/libsvm/] || Machine Learning
 
|-
 
|-
Line 396: Line 348:
 
| [[MACS]] || 1.4.2 || [http://liulab.dfci.harvard.edu/MACS/]||Biology, ChIP-Seq
 
| [[MACS]] || 1.4.2 || [http://liulab.dfci.harvard.edu/MACS/]||Biology, ChIP-Seq
 
|-
 
|-
−
<!-- | [[madness]] || 1769 || [http://code.google.com/p/m-a-d-n-e-s-s/]||Math, DIff. Equation solving|| X ||
 
−
|- -->
 
 
| [[mafft]] || 7.037, 6.903 || [http://mafft.cbrc.jp/alignment/software/]||Biology, Multiple sequence alignment
 
| [[mafft]] || 7.037, 6.903 || [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
 
| [[Maker]] || 2.10, 2.25b || [http://www.yandell-lab.org/software/maker.html] || Biology, Annotation, Genomics
 
|-
 
|-
−
<!-- | [[MapSplice]] || 1.15.2 || [http://www.netlab.uky.edu/p/bioinfo/MapSplice]|| Biology, Genomics || X ||
 
−
|- -->
 
 
| [[Maq]] || 0.7.1 || [http://maq.sourceforge.net/] || Biology, NGS
 
| [[Maq]] || 0.7.1 || [http://maq.sourceforge.net/] || Biology, NGS
 
|-
 
|-
Line 428: Line 376:
 
| [[GeneMark|MetaGeneMark]] || 2012.04 || [http://topaz.gatech.edu/GeneMark/metagenome/] || Biology, Genomics
 
| [[GeneMark|MetaGeneMark]] || 2012.04 || [http://topaz.gatech.edu/GeneMark/metagenome/] || Biology, Genomics
 
|-
 
|-
−
<!--| [[MetaPhyler]] || 1.13 || [http://www.cbcb.umd.edu/~boliu/metaphyler/] || Biology, Metagenomics || X ||
 
−
|-
 
−
| [[metis]] || 4.0 || [http://glaros.dtc.umn.edu/gkhome/views/metis]||Math, Graph partitioning|| X ||
 
−
|- -->
 
 
| [[Mfold]] || 3.6 || [http://mfold.rna.albany.edu/?q=mfold/download-mfold] || Biology, Genomics
 
| [[Mfold]] || 3.6 || [http://mfold.rna.albany.edu/?q=mfold/download-mfold] || Biology, Genomics
 
|-
 
|-
Line 476: Line 420:
 
| [[NetCDF]] || 4.2 || [http://www.unidata.ucar.edu/software/netcdf/]|| Data exchange, Tools
 
| [[NetCDF]] || 4.2 || [http://www.unidata.ucar.edu/software/netcdf/]|| Data exchange, Tools
 
|-
 
|-
−
<!-- | [[NetLogo]] || 4.1.3 || [http://ccl.northwestern.edu/netlogo/] || Modeling || X ||
 
−
|- -->
 
 
| [[Newbler]] || 2.6, 2.7 || [http://my454.com/products/analysis-software/index.asp] || Biology, NGS
 
| [[Newbler]] || 2.6, 2.7 || [http://my454.com/products/analysis-software/index.asp] || Biology, NGS
−
|-
 
−
<!-- | [[NFFT]] || 3.1.3 || [http://www-user.tu-chemnitz.de/~potts/nfft/] || NDFT, library, math || X ||
 
−
|- -->
 
 
|-
 
|-
 
| [[NEXUS_NCL|Nexus NCL]] || 2.1.18 || [http://ncl.sourceforge.net/] || Biology, Phylogenetics, Library
 
| [[NEXUS_NCL|Nexus NCL]] || 2.1.18 || [http://ncl.sourceforge.net/] || Biology, Phylogenetics, Library
Line 489: Line 428:
 
| [[Novoalign]] || 2.08.02, 3.00.02 || [http://www.novocraft.com/main/page.php?s=novoalign] || Biology, NGS
 
| [[Novoalign]] || 2.08.02, 3.00.02 || [http://www.novocraft.com/main/page.php?s=novoalign] || Biology, NGS
 
|-
 
|-
−
<!-- | [[NWChem]] || 6.0 || [http://www.nwchem-sw.org/index.php/Main_Page]||Simulation, Chemistry
 
−
|- -->
 
 
| [[Oases]] || 0.2.08 || [http://www.ebi.ac.uk/~zerbino/oases/] || Biology, NGS
 
| [[Oases]] || 0.2.08 || [http://www.ebi.ac.uk/~zerbino/oases/] || Biology, NGS
 
|-
 
|-
Line 504: Line 441:
 
|-
 
|-
 
| [[OrthoMCL]] || 2.0.2, 2.0.3, '''2.0.7''' || [http://orthomcl.org/]|| Biology, Genomics
 
| [[OrthoMCL]] || 2.0.2, 2.0.3, '''2.0.7''' || [http://orthomcl.org/]|| Biology, Genomics
−
<!--
 
−
|-
 
−
| [[PAL2NAL]] || 14 || [http://www.bork.embl.de/pal2nal/]|| Biology, Genomics
 
−
-->
 
 
|-
 
|-
 
| [[PAML]] || 4.7 || [http://abacus.gene.ucl.ac.uk/software/paml.html]||Biology, Phylogenetics
 
| [[PAML]] || 4.7 || [http://abacus.gene.ucl.ac.uk/software/paml.html]||Biology, Phylogenetics
Line 532: Line 465:
 
|-
 
|-
 
| [[PHITS]] || 2.52 || [http://www.oecd-nea.org/tools/abstract/detail/nea-1857/] || Physics
 
| [[PHITS]] || 2.52 || [http://www.oecd-nea.org/tools/abstract/detail/nea-1857/] || Physics
−
|-
 
−
<!-- | [[Phred]] || 020425 || [http://www.phrap.com/]|| Biology, Genomics, Sequencing || X ||
 
−
-->
 
 
|-
 
|-
 
| [[PhyloBayes]] || 3.3f, 1.4f MPI || [http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm] || Biology, Phylogenetics
 
| [[PhyloBayes]] || 3.3f, 1.4f MPI || [http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm] || Biology, Phylogenetics
Line 541: Line 471:
 
|-
 
|-
 
| [[Picard]] || 1.69, 1.72, 1.80 || [http://picard.sourceforge.net/] || Biology, NGS
 
| [[Picard]] || 1.69, 1.72, 1.80 || [http://picard.sourceforge.net/] || Biology, NGS
−
|-
 
−
<!-- | [[Pindel]] || 0.2.8 || [https://trac.nbic.nl/pindel/] || Biology, NGS || X ||
 
−
|-
 
−
| [[PQS]] || 3.3-19 ||[http://www.pqs-chem.com/software.php]||Modeling, Chemistry|| X ||
 
−
-->
 
 
|-
 
|-
 
| [[Preseq]] || 0.0.4 || [http://smithlab.usc.edu/plone/software/librarycomplexity] || Biology, NGS
 
| [[Preseq]] || 0.0.4 || [http://smithlab.usc.edu/plone/software/librarycomplexity] || Biology, NGS
−
<!--
 
−
|-
 
−
| [[Prinseq]] || 0.17 || [http://prinseq.sourceforge.net/index.html] || Biology, NGS || X ||
 
−
-->
 
 
|-
 
|-
 
| [[ProBABEL]] || 0.4.2 || [http://www.genabel.org/packages/probabel] || Biology, Genomics, GWAS  
 
| [[ProBABEL]] || 0.4.2 || [http://www.genabel.org/packages/probabel] || Biology, Genomics, GWAS  
Line 559: Line 480:
 
| [[Proteinortho]] || 4.26 || [http://www.bioinf.uni-leipzig.de/Software/proteinortho/index.html] || Biology, Genomics
 
| [[Proteinortho]] || 4.26 || [http://www.bioinf.uni-leipzig.de/Software/proteinortho/index.html] || Biology, Genomics
 
|-
 
|-
−
<!-- | [[PyOpenCL]] || 2012.04 || [http://mathema.tician.de/software/pyopencl]||python, parallel programming|| X ||
 
−
|- -->
 
 
| [[python]] || 2.6.8, 2.7.3 || [http://python.org] || Programming, scripting, language
 
| [[python]] || 2.6.8, 2.7.3 || [http://python.org] || Programming, scripting, language
 
|-
 
|-
Line 577: Line 496:
 
| [[RAxML]] || 7.9.1, 8.0.0, 8.0.25 || [http://sco.h-its.org/exelixis/software.html] || Biology, Phylogenetics
 
| [[RAxML]] || 7.9.1, 8.0.0, 8.0.25 || [http://sco.h-its.org/exelixis/software.html] || Biology, Phylogenetics
 
|-
 
|-
−
<!-- | [[RAxML-Light]]|| 1.0.5 ||[http://sco.h-its.org/exelixis/software.html]||Biology, Phylogenetics|| X ||
 
−
|- -->
 
 
| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/] || Biology, Genomics
 
| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/] || Biology, Genomics
 
|-
 
|-
Line 591: Line 508:
 
| [[RSEG]] || 0.4.8 || [http://smithlab.usc.edu/histone/rseg/] || Biology, NGS
 
| [[RSEG]] || 0.4.8 || [http://smithlab.usc.edu/histone/rseg/] || Biology, NGS
 
|-
 
|-
−
<!-- | [[Rosetta]] || 2.1.1, 2.1.2 || [https://www.rosettacommons.org/]||Biology, Structural, Modeling|| X ||
 
−
|-
 
−
| [[Ruby]] || 1.9.3 || [http://www.ruby-lang.org/en]||Programming, Language, Scripting|| X ||
 
−
|-
 
−
| [[RSMToolkit]] || 2961 || [http://www.adoptech.com/software/RSMToolkit.htm]||Math, Modeling, Geometry|| X ||
 
−
|- -->
 
 
| [[Sailfish]] || 0.6.3 || [http://www.cs.cmu.edu/~ckingsf/software/sailfish/] || Biology, NGS, RNA-Seq
 
| [[Sailfish]] || 0.6.3 || [http://www.cs.cmu.edu/~ckingsf/software/sailfish/] || Biology, NGS, RNA-Seq
 
|-
 
|-
Line 605: Line 516:
 
| [[SATe]] || 2.2.7 || [http://phylo.bio.ku.edu/software/sate/sate2.html] ||Biology, Phylogenetics
 
| [[SATe]] || 2.2.7 || [http://phylo.bio.ku.edu/software/sate/sate2.html] ||Biology, Phylogenetics
 
|-
 
|-
−
<!--
 
−
| [[Scala]] || 2.9.1 || [http://www.scala-lang.org/]|| Programming, language, java || X ||
 
−
|- -->
 
 
| [[Sharcgs]] || 1.2.11 || [http://sharcgs.molgen.mpg.de/index.shtml] || Biology, NGS, de novo assembly
 
| [[Sharcgs]] || 1.2.11 || [http://sharcgs.molgen.mpg.de/index.shtml] || Biology, NGS, de novo assembly
 
|-
 
|-
 
| [[Schrodinger]] || 2012, 2013 || [http://www.schrodinger.com/] || Simulation, chemistry
 
| [[Schrodinger]] || 2012, 2013 || [http://www.schrodinger.com/] || Simulation, chemistry
 
|-
 
|-
−
<!-- | [[Segminator]] || 0.0.2 || [http://www.bioinf.manchester.ac.uk/segminator/index.html]|| Biology, NGS || X ||
 
−
|- -->
 
−
| [[SCons]] || 2.3.0 || [http://sourceforge.net/projects/scons/] || Programming, Build System
 
−
|- -->
 
 
| [[SeqPrep]] || 0.5 || [https://github.com/jstjohn/SeqPrep] || Biology, NGS
 
| [[SeqPrep]] || 0.5 || [https://github.com/jstjohn/SeqPrep] || Biology, NGS
 
|-
 
|-
Line 660: Line 564:
 
| [[SRA]] || 2.1.10 || [http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software]] || biology, NGS
 
| [[SRA]] || 2.1.10 || [http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software]] || biology, NGS
 
|-
 
|-
−
<!-- | [[SRNAPredict]] || 3.0 || [http://www.tufts.edu/sackler/waldorlab/sRNAPredict.html]|| Biology, Genomics || X ||
 
−
|-
 
−
| [[SRNAScanner]] || 200903 || [http://cluster.physics.iisc.ernet.in/sRNAscanner/]|| Biology, Genomics || X ||
 
−
|- -->
 
 
| [[SSPACE]] || 2.0 || [http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/] || Biology, NGS
 
| [[SSPACE]] || 2.0 || [http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/] || Biology, NGS
 
|-
 
|-
Line 694: Line 594:
 
| [[tgicl]] || 2.1 || [http://compbio.dfci.harvard.edu/tgi/software/] || Biology, sequencing, clustering
 
| [[tgicl]] || 2.1 || [http://compbio.dfci.harvard.edu/tgi/software/] || Biology, sequencing, clustering
 
|-
 
|-
−
<!-- | [[Trimal]] || 1.2 || [http://trimal.cgenomics.org/] || Biology, NGS || X ||
 
−
|- -->
 
 
| [[Tophat]] || 1.4.1, 2.0.1, '''2.0.8b''' || [http://tophat.cbcb.umd.edu/] || Biology, NGS
 
| [[Tophat]] || 1.4.1, 2.0.1, '''2.0.8b''' || [http://tophat.cbcb.umd.edu/] || Biology, NGS
 
|-
 
|-
Line 730: Line 628:
 
| [[WebLogo]] || 3.3 || [http://code.google.com/p/weblogo/] || Biology, Genomics
 
| [[WebLogo]] || 3.3 || [http://code.google.com/p/weblogo/] || Biology, Genomics
 
|-
 
|-
−
<!-- | [[weka]] || 3.6.2 ||[http://www.cs.waikato.ac.nz/ml/weka/]||Data mining algorithms|| X ||
 
−
|- -->
 
 
| [[WDSSII]] || 1 || [http://www.wdssii.org] || Meteorology
 
| [[WDSSII]] || 1 || [http://www.wdssii.org] || Meteorology
 
|-
 
|-

Revision as of 16:24, 9 August 2014

Installed Software List

Last updated 2014-08-09.

Note: Click on the icons to the right of the column headings to sort the table.

Name Version [1] Website Category
AbInit 6.12.3 [1] Ab Initio Quantum Chemistry, Density Functional Theory
Abyss 1.3.4, 1.3.7 [2] Biology, NGS
ALLPATHS-LG 42316, 44837 [3] Biology, NGS
AFNI 2011_12_21_1014 [4] Biology, Statistics, Imaging, Neurology
Amber 11, 12, 14 [5] Simulation, chemistry
AMOS 3.1.0 [6] Biology, Genomics, NGS
ANNOVAR 20120621,20121023,20130321 [7] Biology, Genomics
Atlas 3.10.1, 3.11.17 [8] Library, Math
Amuse 6.0 [9] Astrophysics
Affymetrix Power Tools 1.15.0 [10] Biology, Genomics, Microarray
AtomEye 3 [11] Material Science
ATRAM 20140624 [12] Biology, NGS
Augustus 2.6 [13] Biology, NGS
BamBam 1.0 [14] Biology, NGS
Bamstats 20140602 [15] Biology, NGS
Bamtools 2.1.1 [16] Biology, NGS
BamUtil 1.0.2 [17] Biology, NGS
BayesRate 1.3.43 [18] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [19] Network file transfer
Bcftools 20140618 [20]] Biology, Genomics, NGS
BEAGLE 3.2.2 [21] Biology, Genetics, Genotyping
BEAST 1.7.5, 2.0.1, 2.0.2.pre [22] Biology, Phylogenetics
BEDTools 2.16.2, 2.17.0 [23] Biology, NGS
BEST 2.3 [24] Biology, Phylogenetics
BETA 1.0.5 [25] Biology, NGS
BFAST 0.7.0 [26] Biology, NGS
Bismark 0.7.4, 0.7.7 [27] Biology, Methylation, NGS
Bioconductor Latest [28] Biology, R, Statistics
BioPerl 1.006901 [29] Biology, Perl
BioPython 1.59 [30] Biology, Python
BLASR 20130815 [31] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [32] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [33] Biology, Annotation
BLAT 20120524 [34] Biology, Sequence alignment
Blender 2.63 [35] Graphics
Boost 1.49.0, 1.53.0, 1.54.0 [36] C++, Library
Bowtie 0.12.8, 0.12.9, 1.0.0 [37] Biology, NGS
Bowtie2 2.1.0, 2.2.2, 2.2.3 [38] Biology, NGS
BRANCH 1.8.1 [39] Biology, NGS, Mapping
Bwa 0.6.1, 0.7.9a, 0.7.10 [40] Biology, NGS
Camino 20140723 [41] Biology, Neuroscience, Imaging
CAP3 20120705 [42] Biology, sequence assembly
CASAVA 1.8.2 [43] Biology, NGS
CD-HIT 4.6 [44] Biology, Genomics
CDO 1.6.1 [45] Climate
CEAS 1.0.2 [46] Biology, Genomics
CellProfiler 2.0 [47] Biology, Image Analysis
Charmm 36a3 [48] Simulation, Chemistry
Chartdirector 5.1.0 [49] Graphics
CIMS 4.1.2 [50] Biology, Genomics
Circos 0.63-pre11 [51] Biology, Visualization
CisGenome 2.0 [52] Biology, Genomics, Peak Calling
CLHEP 2.2.0.1 [53] High Energy Physics
ClonalFrame 1.1, 1.2 [54] Biology, Genomics, NGS
ClustalW 2.1 [55] Biology, Genomics
Clview 20130402 [56] Biology, Genomics
CMake 2.8.8 [57] Programming, Build System
CNVSeq 20110715 [58] Biology, NGS
Coevol 1.3c, 1.4b [59] Biology, Phylogenetics
CoMap 1.4.1 [60] Biology, Genomics
CONCOCT 0.3.1 [61] Biology, Genomics
Consed 23.0 [62] Biology, Genomics
covNMR 2014 [63] Biochemistry
CUDA 4.2, 5.5 [64] Programming, Graphics
Cufflinks 1.3.0, 2.0.2, 2.2.1 [65] Biology, NGS
Cutadapt 1.1 [66] Biology, NGS
DAKOTA 5.4.0 [67] Computational Science
DCMTK 3.6.0 [68] Biology, Neuroscience, Imaging
DDSCAT 7.3.0 [69] Astrophysics
DDT 4.1.0, 4.2.1 [70] Software
Delft3D 3621 [71] Hydrodynamics, Physics
Desmond 3.0.3.1 [72] Simulation, Biology, Chemistry
Dalton 2011 [73] Quantum Chemistry
DiffReps 1.55.4 [74] Biology, NGS, ChIP-Seq
Dindel 1.01 [75] Biology, NGS
DIYABC many [76] Biology, Genomics
Dlpoly 4.03.4 [77] Simulation, Biology, Chemistry
DNA Clust 3.0 [78] Biology, Genomics
Dock 6.5, 6.6 [79] Chemistry, ligand binding prediction
DOT 2.0 [80] Biology, Bioinformatics, Docking
Doxygen 1.8.3.1 [81] Programming, Documentation
DSSP 2.2.1 [82] Biology, Molecular Dynamics
DTI-TK 2.3.1 [83] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [84] Biology, NGS
ECTools 20140311 [85] Biology, Sequencing, Bioinformatics
EEGLAB 12.0.2.1b [86] Biology, Matlab
EIGENSOFT 4.2, 5.0.1 [87] Biology, Population
emboss 6.5.7 [88] Biology, multi-tool suite
EMIRGE 20130727 [89] Biology, NGS
eQTLA 1.1 [90] Biology, Genomics
Eqtlbma 1.2.2 [91] Biology, Genotyping
Espresso 5.0.1 [92] Modeling, Physics
ESPRIT 201211 [93] Biology, NGS, Metagenomics
ETE2 2.1 [94] Biology, Phylogenetics
Eval 2.2.8 [95] Biology, Genomics, GUI
ExaML 1.0.3, 1.0.5, 1.0.12 [96] Biology, Phylogenetics
Exonerate 2.2.0 [97] Biology, Genomics
eXpress 1.3.1 [98] Biology, NGS
FAR 2.15 [99] Biology, Genomics
FASTA 34.26.5, 36.3.6d [100] Biology, Genomics
FastML 3.0 [101] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [102] Biology, NGS
FastTree 2.1.7 [103] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [104] Biology, NGS
fcGENE 1.0.7 [105] Biology, Genomics, SNP
Ferret 6.82 [106] Oceanography, Meteorology
FFmpeg 2.1.3 [107] Multimedia, audio, video
FFTW 3.3.2, 3.3.3 [108] Math, Library, C++
FLASH 1.2.10 [109] Biology, Genomics, NGS
Flexbar 2.3 [110] Biology, Genomics, NGS
Fluent 14.5.7, 15.0 [111] Simulation, Fluid Dynamics
FragGeneScan 1.16 [112] Biology, NGS, Genomics
FreeBayes 0.9.6 [113] Biology, NGS, SNP Calling
Freesurfer 5.2.0 [114] Biology, Neurology, Imaging
FSL 5.0.2.2 [115] Biology, Neurology, Imaging
Garli 2.0, 2.01 [116] Biology, Phylogenetics
GASVPro 201310 [117] Biology, NGS, Genomics
GATE 7.0 [118] Data Analysis
GATK 1.6.9, 2.7.4, 3.1.1 [119] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [120] Modeling, Computational Chemistry
Geant4 4.10 [121] Physics
GEM 20130406 [122] Biology, NGS
GEMINI 4.6.6a [123] Biology, Genomics, Genetics
GenBank Tools 20140130 [124] BIology< Genomics
GeneMark 2012.04 [125] Biology, Genomics, Metagenomics
Genewise 2.2.0 [126] Biology, Genomics, Annotation
GenomicTools 2.7.0 [127] Biology, NGS
Git 1.8.2.1 [128] Development, Revision Control
Gmap 20130618, 20130720, 20140530 [129] Biology, Genomics
GnuPlot 4.6.0 [130] Graphics, Plotting, Programming
Grace 5.1.22 [131] Graphics, plotting, 2D
GrADS 2.0.1 [132] Earth Science
GraphViz 2.38.0 [133] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5 [134] Chemistry, Modeling, Simulation
GSL 1.15 [135] Library, Math, C++, C
GULP 4.0 [136] Material Science
HaMStR v8b [137] Biology, Genomics
Hapsembler 2.21 [138] Biology, Genomics, NGS
HDF5 1.8.9, 1.8.12 [139] Library, Data
HMMER3 3.0 [140] Biology, Genomics
HMMSplicer 0.9.5 [141] Biology, Genomics
HOMER 4.2 [142] Biology, Genomics
HTSeq 0.5.3p3, 0.6.1p1 [143] Biology, NGS
HyPhy 2.1.2.28 [144] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [145] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [146] Biology, NGS
IM and IMa 20091217 [147] Biology, Population
IMa2 20120827 [148] Biology, Population
ImageMagick 6.8.8-9 [149] Image manipulation
Intel Compilers 11.1, 2012 [150] Programming, Compilers
IOAPI 3.1 [151] Meteorology
Iprscan 4.8 [152] Biology, Genomics
ITK 4.3.1 [153] Biology, Genomics
ITK-SNAP 3.0.0 [154] Biology, Neuroscience, Imaging
JAGS 3.3.0 [155] Statistics
Java 1.6.0_31, 1.7.0_02 [156] Java Development Kit
Kent 20120524 [157] Biology, NGS
Kmer 1934 [158] Biology, NGS
KmerGenie 1.6741 [159] Biology, NGS, Utilities
LAMMPS 28Oct12, 30Sep13 [160] Molecular Dynamics Simulation
Last 193, 247 [161] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [162] Biology, NGS
LIBSVM 3.12 [163] Machine Learning
LSC 0.3, 0.3.1 [164] Biology, NGS, Error correction
Loci 3.3 [165] Fluid Dynamics
LS-DYNA 700, 711 [166] Physics
MACH 1.0.18 [167] Biology, Genomics
MACS 1.4.2 [168] Biology, ChIP-Seq
mafft 7.037, 6.903 [169] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [170] Biology, Annotation, Genomics
Maq 0.7.1 [171] Biology, NGS
Matlab 2012a, 2013a, 2014a [172] Math, Simulation, Programming
MATS 2.1.0, 3.0.6b, 3.0.8 [173] BIology, NGS
MCarts 1.0.2 [174] Biology, Genomics, Markov models
MCNP 5, 6b2 [175] Physics
MCNPX 2.7.0, 2.7.0-i8 [176] Physics
Meme 4.8.1 [177] Biology, Motifs, Sequence analysis
Mercurial 2.7 [178] Development, Revision Control
Metabin 1.0 [179] Biology, Metagenomics
MetaCluster 5.0beta [180] Biology, Metagenomics
MetaVelvet 1.2.01 [181] Biology, NGS
MetaGeneMark 2012.04 [182] Biology, Genomics
Mfold 3.6 [183] Biology, Genomics
Midnight Commander 4.6.1 [184] Tools, Utilities
Migrate-n 3.3.0 [185] Biology, Population
mira 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 [186] Biology, NGS
MISO 0.4.4, 0.4.9 [187] Biology, NGS
MSMBuilder 2.5.1 [188] Molecular Dynamics
Modeller 9.11, 9.13, 9.14 [189] Biology, Modeling
Molden 5.0 [190] Molecular, electronic structure
mosaik 2.1.33 [191] Biology,NGS
Mothur 1.31.2 [192] Biology, Microbial Ecology
MP-EST 1.4 [193] Biology, Phylogenetics
mpiP 3.4.1 [194] Parallel Computing
MrBayes 3.2.1 [195] Biology, Phylogenetics
MRIcron 201306 [196] Biology, MRI, Imaging
MUMmer 3.23 [197] Biology, Genomics
MUSCLE 3.8.31 [198] Biology, Genomics
NAMD 2.9 [199] Simulation, Chemistry, Biology
Nbody 6 [200] Astronomy
NCBI C++ Toolkit 12.0.0 [201] Biology, C++, Development
NCL 6.1.2 [202] Atmosphere Science
NCO 4.2.1, 4.4.3 [203] Data exchange tools
NetCDF 4.2 [204] Data exchange, Tools
Newbler 2.6, 2.7 [205] Biology, NGS
Nexus NCL 2.1.18 [206] Biology, Phylogenetics, Library
NMRPipe 7.9 [207] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [208] Biology, NGS
Oases 0.2.08 [209] Biology, NGS
Olego 1.1.2, 1.1.5 [210] Biology, NGS, RNA-Seq
Octave 3.6.4 [211] Numerical Computation
OpenBabel 2.3.2 [212] Biology, Chemistry
OpenCV 2.4.8 [213] Computervision
OpenFOAM 2.1.1 [214] Fluid Dynamics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [215] Biology, Genomics
PAML 4.7 [216] Biology, Phylogenetics
ParaView 4.1.0 [217] Data Analysis
PartitionFinder 1.0.1, 1.1.1 [218] Biology, Phylogenetics, Evolution
Parflow v615 [219] Ecology, Modeling
PASA 1.5, 2.0-r20130605p1, 2.0-r20130907 [220] Biology, Genomics
PeakSplitter 1.0 [221] Biology, Chip-Seq
PDT 3.18 [222] Programming, Profiler
Perl 5.16.0 [223] Programming, Language
PerM 0.4.0 [224] Biology, NGS
PETSc 2.3, 3.3 [225] Math, Numerical solvers
Phenix 1.8.1069 [226] Crystallography
PHITS 2.52 [227] Physics
PhyloBayes 3.3f, 1.4f MPI [228] Biology, Phylogenetics
PhyML 3.0, 20121109 [229] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [230] Biology, NGS
Preseq 0.0.4 [231] Biology, NGS
ProBABEL 0.4.2 [232] Biology, Genomics, GWAS
Proovread 1.03rcl [233] Biology, Genomics, NGS
Proteinortho 4.26 [234] Biology, Genomics
python 2.6.8, 2.7.3 [235] Programming, scripting, language
QIIME 1.5.0 [236] Biology, Ecology
QT 4.8.3 [237] Computer Science
Quickquartet 1.0.0 [238] Biology, Phylogenetics
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 [239] Statistics, Programming
R8S 1.71 [240] Biology, Evolution
RADICAL 0.2 [241] Biology, Phylogenetics, Genomics
RAxML 7.9.1, 8.0.0, 8.0.25 [242] Biology, Phylogenetics
RepeatMasker 3.3.0 [243] Biology, Genomics
Reptile 1.1 [244] Biology, NGS, error correction
riboPicker 0.4.3 [245] Biology, Sequence
RNAhybrid 2.1.1 [246] Biology, Genomics
ROOT 6.0 [247] Data Analysis
RSEG 0.4.8 [248] Biology, NGS
Sailfish 0.6.3 [249] Biology, NGS, RNA-Seq
samtools 0.1.16, 0.1.18, 0.1.19 [250] Biology, NGS
SAS 9.3 [251] Statistics, Graphing
SATe 2.2.7 [252] Biology, Phylogenetics
Sharcgs 1.2.11 [253] Biology, NGS, de novo assembly
Schrodinger 2012, 2013 [254] Simulation, chemistry
SeqPrep 0.5 [255] Biology, NGS
SEQuel 1.0.1 [256] Biology, NGS
Seqtk 20140729 [257] Biology, NGS
SeqyClean 1.8.10 [258] Biology, NGS, quality filter
Sickle 1.200 [259] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [260] Simulation, Physics, Ab Initio
SIFT 4.0.3b [261] Biology, Genomics
Silo 4.7 [262] Library, Data
Slicer 4.3.1 [263] Biology, Imaging
SMALT 0.7.6 [264] Biology, NGS
Snap 20100728 [265] Biology, Genomics
SOAPdenovo 1.05 [266] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [267] Biology, NGS
SparCC 201402 [268] Microbial Ecology
Spades 2.5.0, 2.5.1, 3.0.0 [269] Biology, NGS
Spanki 0.4.1, 0.4.3 [270] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [271] Chemistry
SPIMAP 1.1 [272] Biology, Phylogenetics
SpliceTrap 0.90.5 [273] Biology, NGS, RNA-Seq
SPM 8 [274] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [275] Biology, Genomics
SRA 2.1.10 [276]] biology, NGS
SSPACE 2.0 [277] Biology, NGS
Stacks 0.9995 [278] Biology, Genomics, NGS
STAR 2.3.0e [279] Biology, NGS, Alignment
STAR-CCM+ 8.06 [280] Mechanical Engineering
Stata 10.1, 13 [281] Statistics, Data analysis
Stringtie 0.97 [282] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [283] Biology, Population
SUNDIALS 2.3.0, 2.5.0 [284] Numerical Solver
swak4Foam 2.x [285] Fluid Dynamics
Swig 2.0.9 [286] Programming, C, C++, Python
Syzygy 1.2.7 [287] Biology, Genomics
TAU 2.21.4, 2.23 [288] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [289] Biology, Genomics, Multiple Alignment
TESS 2.3.1 [290] Biology, Genomics, Markov
tgicl 2.1 [291] Biology, sequencing, clustering
Tophat 1.4.1, 2.0.1, 2.0.8b [292] Biology, NGS
Totalview 8.12.0 [293] Computer Science
TPP 4.7.0 [294] Bioinformatics, MassSpec
TreeFix 1.1.7 [295] Biology, Phylogenetics
TRF 4.04 [296] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [297] Math Algorithm
Trimmomatic 0.22, 0.32 [298] Biology, NGS
Trinity r20131110, r20140413 [299] Biology, NGS, RNA-Seq
Twinscan 4.1.2 [300] Biology, Genomics
usearch 5.2.32, 7.0.959, 7.0.1001-64 (licensed 64-bit) [301] Biology, Sequence analysis
Valgrind 3.9.0 [302] Computer Science
VASP 4.6.34, 5.2.12, 5.3.2, 5.3.3 [303] Quantum Chemistry, Ab Initio
VCFtools 0.1.9, 0.1.10 [304] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [305] Biology, NGS
vmd 1.9.1 [306] Biology, Visualization
Wannier90 1.2, 2.0.0 [307] Computational Physics
WebLogo 3.3 [308] Biology, Genomics
WDSSII 1 [309] Meteorology
WIEN2k 12.1 [310] Material Science, Chemistry
wgs 7.0.1.22 [311] Biology, NGS
wublast 2.0 [312] Biology, Sequence Alignment
Yambo 3.3.0 [313] Physics
Yasra 2.32 [314] Biology, NGS
  1. ↑ 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.

To add a documentation page for a new piece of software installed into /apps please go to Add New App Page.

Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=Installed_Software&oldid=12611"