Difference between revisions of "Installed Software"

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[[Category:Software]]
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#REDIRECT [[Applications]]
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==Cluster Software Upgrade (Update 09/07/12)==
 
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The transition from RHEL5/CentOS5 to RHEL6 is, for all practical purposes, complete.  The "rhel5" queue has been stopped and is no longer accepting jobs and will be removed once the few remaining jobs complete.  The interactive nodes test01, test04, and test05 will be upgraded by the end of the day on Friday, September 7 (today).
 
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A majority of applications have been recompiled or otherwise re-installed under RHEL6.  There are still a few lightly used applications remaining that we should be able to finish next week.  If the software you need is not available and you have not already submitted a support request to have it installed, you may do so at http://support.hpc.ufl.edu.
 
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-->
 
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==Note: Cluster Software Upgrade==
 
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One of our goals is to provide our users with a consistent, stable, and current software environment. The compute, login, and interactive nodes within the HPC Center have been running CentOS EL 5 (with updates) for over four years.      This is a long time in the open source software world. While our software was consistent and stable, it was no longer current. To remedy that shortcoming we upgraded all our systems to RedHat Enterprise Linux 6.3 (RHEL6). The migration was done without interruptions to user jobs as compute nodes were gradually migrated to RHEL6. The migration also afforded us an opportunity to remove software that was no longer used as we only installed software under RHEL6 on request. Therefore, if the software you need is no longer installed please open a [http://support.hpc.ufl.edu support ticket] requesting its installation as usual. If you run software you compiled it likely needs to be rebuilt. This is mandatory for all MPI software as we upgraded both MPI implementations and the Intel Compiler Suite on our systems. We also switched to the "[[Modules|Environment Modules]]" system for making software available. See [[Modules Basic Usage|the modules documentation]] for more information on how to use the modules system. If you attempt to run a program and it fails it means you have not loaded the appropriate module.
 
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==Installed Software List==
 
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Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''.
 
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'''Note:''' Click on the icons to the right of the column headings to sort the table.
 
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{|  border="1"  cellspacing="0" cellpadding="2" align="center"  class="wikitable sortable"
 
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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 software wiki pages and the output of "module spider software" for full version listing.</ref>
 
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! scope="col" | Website
 
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! scope="col" | Category
 
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|-
 
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<!-- | [[Abaqus]] || 6.6-1, 6.9-2 || [http://www.simulia.com/products/abaqus_standard.html] || Simulation
 
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|- -->
 
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| [[AbInit]] || 6.12.3 || [http://www.abinit.org/] || Ab Initio Quantum Chemistry, Density Functional Theory
 
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|-
 
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| [[Abyss]] || 1.3.3, 1.3.4, 1.3.4-mpi || [http://www.bcgsc.ca/platform/bioinfo/software/abyss] || Biology, NGS
 
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|-
 
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<!-- | [[ADMB]] || 9.1, 10.0, 10.1 || [http://admb-project.org/] || Modeling, math || X ||
 
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|- -->
 
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| [[ALLPATHS-LG]] || 42316 || [http://www.broadinstitute.org/software/allpaths-lg/blog/] || Biology, NGS
 
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|-
 
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| [[Amber]] || 11, 12 || [http://amber.scripps.edu/] || Simulation, chemistry
 
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|-
 
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<!-- | [[Amos]] || 3.0.0 || [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS] || Biology, Genomics || X ||
 
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|-
 
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| [[ANNOVAR]] || 20120308 || [http://www.openbioinformatics.org/annovar/] || Biology, Genomics || X ||
 
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|-
 
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| [[Ansys]] || 9.0, 10.0 || [http://www.ansys.com/] || Simulation, Engineering || X ||
 
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|-
 
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| [[antlr]] || 2.7.7, 3.1.3 || [http://www.antlr.org/] || Linguistics, Parser || X ||
 
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|-
 
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| [[arachne]] || 37618 || [http://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational] || Biology, Genomics || X ||
 
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|- -->
 
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| [[Amuse]] || 6.0 || [http://www.amusecode.org]|| Astrophysics
 
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|-
 
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| [[APT|Affymetrix Power Tools]] || 1.15.0 || [http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx] || Biology, Genomics, Microarray
 
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|-
 
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| [[Augustus]] || 2.6 || [http://augustus.gobics.de/]|| 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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<!-- | [[BayesPhylogenies]] || 2.0 || [http://www.evolution.reading.ac.uk/BayesPhy.html] || Biology, Phylogenetics || X ||
 
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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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| [[Beast|BEAST]] || 1.7.2 || [http://beast.bio.ed.ac.uk/Main_Page]|| Biology, Phylogenetics
 
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|-
 
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| [[Bedtools|BEDTools]] || 2.16.2 || [http://code.google.com/p/bedtools/]|| 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]] || 0.7.4, 0.7.7 || [http://www.bioinformatics.babraham.ac.uk/projects/download.html#bismark] || Biology, Methylation, NGS
 
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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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<!-- | [[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 ||
 
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|- -->
 
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| [[Blast|NCBI BLAST]] || 2.2.26 (+ and legacy) || [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 || [http://genome.ucsc.edu/goldenPath/help/blatSpec.html] || Biology, Sequence alignment
 
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|-
 
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| [[Boost]] || 1.49.0 || [http://www.boost.org/] || C++, Library
 
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|-
 
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| [[Bwa]] || 0.6.1 || [http://bio-bwa.sourceforge.net/] || Biology, NGS
 
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|-
 
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| [[Bowtie]] || 0.12.8, 2.0.0b6 || [http://bowtie-bio.sourceforge.net/index.shtml] || Biology, NGS
 
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|-
 
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<!-- | [[BreakDancer]] || 1.1 || [http://breakdancer.sourceforge.net/index.html] || Biology, NGS, Genomics || X ||
 
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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 || [http://weizhong-lab.ucsd.edu/cd-hit/] || Biology, Genomics
 
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|-
 
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<!-- | [[CEGMA]] || 2.4.010312 || [http://korflab.ucdavis.edu/Datasets/cegma/] || Biology, Genomics, Annotation || X ||
 
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|-
 
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| [[CGATools]] || 1.5.0.31 || [http://cgatools.sourceforge.net/] || Biology, Genomics || X ||
 
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|- -->
 
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| [[Charmm]] || 36a3 || [http://www.charmm.org/] || Simulation, Chemistry
 
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|-
 
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<!-- | [[Circuit]] || 3.5.1, 3.5.7 || [http://www.circuitscape.org/Circuitscape/Welcome.html] || GIS || X ||
 
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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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| [[ClustalW]] || 2.1 || [http://www.clustal.org/clustal2/] || Biology, Genomics
 
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|-
 
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| [[CMake]] || 2.8.8 || [http://www.cmake.org/] || Programming
 
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|-
 
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<!-- | [[CNV-seq]] || 07.15.11 || [http://tiger.dbs.nus.edu.sg/cnv-seq/] || Biology, NGS || X ||
 
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|-
 
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| [[CNVnator]] || 0.2.5 || [http://sv.gersteinlab.org/] || Biology, NGS || X ||
 
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|- -->
 
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| [[Consed]] || 23.0 || [http://bozeman.mbt.washington.edu/consed/consed.html] || Biology, Genomics
 
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|-
 
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<!-- | [[CPMD]] || 3.11.1 || [http://www.cpmd.org/] || Simulation, Chemistry || X ||
 
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|- -->
 
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| [[CUDA]] || 4.2 || [http://www.nvidia.com/object/cuda_home_new.html] || Programming, Graphics
 
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|-
 
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| [[Cufflinks|Cufflinks]] || 1.3.0, 2.0.0, 2.0.2 || [http://cufflinks.cbcb.umd.edu/] || Biology, NGS
 
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|-
 
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| [[Cutadapt]] || 1.1 || [http://code.google.com/p/cutadapt/] || Biology, NGS
 
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|-
 
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<!-- | [[dar]] || 2.3.9 || [http://sourceforge.net/projects/dar/] || Backup || X ||
 
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|-
 
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| [[DeFuse|deFuse]] || 0.4.3 || [http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page] || Biology, RNA-seq || X ||
 
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|- -->
 
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| [[Desmond]] || 3.0.3.1 || [http://www.deshawresearch.com/resources_desmond.html] || Simulation, Biology, Chemistry
 
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|-
 
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<!-- | [[Dindel]] || 1.01 || [http://www.sanger.ac.uk/resources/software/dindel/] || Biology, NGS, Genomics || X ||
 
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|- -->
 
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| [[DIYABC]] || many || [http://www1.montpellier.inra.fr/CBGP/diyabc/index.php] || Biology, Genomics
 
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|-
 
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| [[Dlpoly]] || 4.03.4 || [http://www.cse.clrc.ac.uk/ccg/software/DL_POLY/index.shtml]  || Simulation, Biology, Chemistry
 
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|-
 
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| [[Dock]] || 6.5 || [http://dock.compbio.ucsf.edu/] || Chemistry, ligand binding prediction
 
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|-
 
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<!-- | [[emacs]] || 21.4.1, 23.4.1 || [http://www.gnu.org/software/emacs/] || The Emacs editor
 
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|-
 
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| [[EMAN2]] || 2.04 || [http://blake.bcm.tmc.edu/emanwiki/EMAN2] || Biology, image processing || X ||
 
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|- -->
 
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| [[emboss]] || 6.5.7 || [http://emboss.sourceforge.net/] || Biology, multi-tool suite
 
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|-
 
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| [[Espresso]] || 5.0.1 || [http://www.quantum-espresso.org/] || Modeling, Physics
 
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|-
 
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| [[ESPRIT]] || 201211 || [http://www.acsu.buffalo.edu/~yijunsun/lab/ESPRIT.html] || Biology, NGS, Metagenomics
 
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|-
 
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| [[ETE2]] || 2.1 || [http://ete.cgenomics.org/] || Biology, Phylogenetics
 
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|-
 
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| [[Exonerate]] || 2.2.0 || [http://www.ebi.ac.uk/~guy/exonerate/] || Biology, Genomics
 
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|-
 
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| [[FAR]] || 2.15 || [http://sourceforge.net/apps/mediawiki/theflexibleadap/index.php?title=Main_Page] || Biology, Genomics
 
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|-
 
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| [[FASTA]] || 34.26.5 || [http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml] || Biology, Genomics
 
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|-
 
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| [[FastQC]] || 0.9.6, 0.10.1 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/] || Biology, NGS
 
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|-
 
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| [[Fastx_toolkit]]|| 0.0.13.2 || [http://hannonlab.cshl.edu/fastx_toolkit/] || Biology, NGS
 
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|-
 
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| [[Ferret]]|| 6.82 || [http://ferret.wrc.noaa.gov/Ferret/] || Oceanography, Meteorology
 
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|-
 
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| [[FFTW]] || 3.3.2 || [http://www.fftw.org/] || Math, Library, C++
 
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|-
 
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<!-- |[[fluent]] || 6.3.26 || [http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+FLUENT] || Simulation || X ||
 
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|- -->
 
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| [[FragGeneScan]] || 1.16 || [http://omics.informatics.indiana.edu/FragGeneScan/] || Biology, NGS, Genomics
 
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|-
 
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| [[FreeBayes]] || 0.9.6 || [http://bioinformatics.bc.edu/marthlab/FreeBayes] || Biology
 
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|-
 
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<!-- | [[gadget]] || 2.0.4, 2.0.5 || [http://confluence.atlassian.com/display/GADGETS/Atlassian+Gadgets+2.0.5+Release+Notes] || Software Development || X ||
 
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|-
 
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| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/]|| Quantum Chemistry|| X ||
 
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|- -->
 
−
| [[Garli]] || 2.0 || [https://www.nescent.org/wg_garli/Main_Page]||Biology, Phylogenetics
 
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|-
 
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| [[GATK]] || 1.6.9 || [http://www.broadinstitute.org/gsa/wiki/index.php/GATK] || Biology, NGS
 
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|-
 
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<!-- | [[gulp]] || 4.0.3 || [http://projects.ivec.org/gulp/] || Modeling/simulation, Chemistry || X ||
 
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|- -->
 
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| [[Gaussian]] || E01, G03, G09-A.02, G09-C.01 || [http://www.gaussian.com/]||Modeling, Computational Chemistry
 
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|-
 
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<!-- | [[Geneid]] || 1.4 || [http://genome.crg.es/software/geneid/]||Biology, Genomics, Annotation|| X ||
 
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|- -->
 
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| [[GeneMark]] || 2012.04 || [http://exon.gatech.edu/] || Biology, Genomics, Metagenomics
 
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|-
 
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| [[Genewise]] || 2.2.0 || [http://www.ebi.ac.uk/Tools/Wise2]||Biology, Genomics, Annotation
 
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|-
 
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| [[GenomicTools]] || 2.7.0 || [http://code.google.com/p/ibm-cbc-genomic-tools/] || Biology, NGS
 
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|-
 
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| [[Gmap]] || 20070928, 20120712 || [http://research-pub.gene.com/gmap/] || Biology, Genomics
 
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|-
 
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| [[GnuPlot]] || 4.6.0 || [http://gnuplot.sourceforge.net/] || Graphics, Plotting, Programming
 
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|-
 
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| [[Grace]] || 5.1.22 || [http://plasma-gate.weizmann.ac.il/Grace/] || Graphics, plotting, 2D
 
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|-
 
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| [[GrADS]] || 2.0.1 || [http://www.iges.org/grads] || Earth Science
 
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|-
 
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| [[Gromacs]] || 4.5.5 || [http://www.gromacs.org/] || Chemistry, Modeling, Simulation
 
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|-
 
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| [[GSL]] || 1.15 || [http://www.gnu.org/software/gsl/] || Library, Math, C++, C
 
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|-
 
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| [[HaMStR]] || v8b || [http://www.deep-phylogeny.org/hamstr/] || Biology, Genomics
 
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|-
 
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| [[HDF5]] || 1.8.9 || [http://www.hdfgroup.org/HDF5/]||Library, Data
 
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|-
 
−
| [[HMMER3]] || 3.0 || [http://hmmer.janelia.org/]||Biology, Genomics
 
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|-
 
−
| [[HTSeq]] || 0.5.3p3 || [http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html] || Biology, NGS
 
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|-
 
−
<!-- | [[HugeSeq]] || 1.0.1 || [http://hugeseq.hugolam.com/]|| Biology, NGS, Genomics || X ||
 
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|- -->
 
−
| [[HyPhy]] || 2.1.2.28 || [http://www.datam0nk3y.org/hyphywiki/index.php/Main_Page] || Biology, Phylogenetics
 
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|-
 
−
| [[Hypre]] || 2.8.0b || [http://www.llnl.gov/casc/hypre/software.html]||Library, Math, Physics
 
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|-
 
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| [[Ima|IM and IMa]] || 20091217 || [http://genfaculty.rutgers.edu/hey/software]||Biology, Population
 
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|-
 
−
| [[Ima2|IMa2]] || 20120827 || [http://genfaculty.rutgers.edu/hey/software#IMa2]||Biology, Population
 
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|-
 
−
<!-- | [[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
 
−
|-
 
−
<!-- | [[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
 
−
|-
 
−
| [[JDK]] || 1.6.0_31, 1.7.0_02 || [http://java.com] || Java Development Kit
 
−
|-
 
−
| [[Kent]] || 20120524 || [http://genomewiki.cse.ucsc.edu/index.php/The_source_tree] || Biology, NGS
 
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|-
 
−
<!-- | [[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
 
−
|-
 
−
| [[LAMMPS]] || 28Oct12 || [http://lammps.sandia.gov/] || Molecular Dynamics Simulation
 
−
|-
 
−
| [[Last]] || 193, 247 || [http://last.cbrc.jp/] || Biology, Sequence alignment
 
−
|-
 
−
| [[Lastz]] || 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
 
−
|-
 
−
| [[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]] || 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
 
−
|-
 
−
<!-- | [[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
 
−
|-
 
−
| [[Matlab]] || 2012a || [http://www.mathworks.com]||Math, Simulation, Programming
 
−
|-
 
−
| [[MATS]] || 2.1.0, 3.0.4, 3.0.6 || [http://rnaseq-mats.sourceforge.net/index.html]||BIology, NGS
 
−
|-
 
−
<!-- | [[Mauve]] || 2.3.1 || [http://gel.ahabs.wisc.edu/mauve/]||Biology, Multiple genome alignments || X ||
 
−
|-
 
−
| [[MCL]] || 11-335 || [http://www.micans.org/mcl/] || Biology, Genomics, Clustering|| X ||
 
−
|- -->
 
−
| [[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
 
−
|-
 
−
| [[Meme]] || 4.8.1 || [http://meme.nbcr.net/meme/intro.html]||Biology, Motifs, Sequence analysis
 
−
|-
 
−
| [[MetaCluster]] || 5.0beta || [http://i.cs.hku.hk/~alse/MetaCluster/index.html] || Biology
 
−
|-
 
−
| [[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
 
−
|-
 
−
<!--| [[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 ||
 
−
|- -->
 
−
| [[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 || [http://mira-assembler.sourceforge.net/]||Biology, NGS|| X ||
 
−
|- -->
 
−
| [[MISO]] || 0.4.4 || [http://genes.mit.edu/burgelab/miso/] || Biology, NGS
 
−
|-
 
−
| [[MSMBuilder]] || 2.5.1 || [https://simtk.org/home/msmbuilder] || Molecular Dynamics
 
−
|-
 
−
| [[Molden]] || 5.0 || [http://www.cmbi.ru.nl/molden/] || Molecular, electronic structure
 
−
|-
 
−
| [[mosaik]] || 2.1.33 || [http://code.google.com/p/mosaik-aligner/] || Biology,NGS
 
−
|-
 
−
<!-- | [[MPIBlast]] || 1.6.0 || [http://www.mpiblast.org/]||Biology, Sequence alignment|| X ||
 
−
|- -->
 
−
| [[MrBayes]] || 3.2.1 || [http://mrbayes.scs.fsu.edu/] || Biology, Phylogenetics
 
−
|-
 
−
| [[MUMmer]] || 3.23 || [http://mummer.sourceforge.net/] || Biology, Genomics
 
−
|-
 
−
| [[MUSCLE]] || 3.8.31 || [http://www.drive5.com/muscle/] || Biology, Genomics
 
−
|-
 
−
| [[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
 
−
|-
 
−
| [[NCO]] || 4.2.1 || [http://nco.sourceforge.net/] || 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
 
−
|-
 
−
<!-- | [[NFFT]] || 3.1.3 || [http://www-user.tu-chemnitz.de/~potts/nfft/] || NDFT, library, math || X ||
 
−
|- -->
 
−
| [[Novoalign]] || 2.08.02 || [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
 
−
|-
 
−
| [[OpenFOAM]] || 2.1.1 || [http://www.openfoam.org/]||Fluid Dynamics
 
−
|-
 
−
<!--
 
−
| [[OrthoMCL]] || 2.0 || [http://orthomcl.org/]|| Biology, Genomics
 
−
|-
 
−
| [[PAL2NAL]] || 14 || [http://www.bork.embl.de/pal2nal/]|| Biology, Genomics
 
−
|-
 
−
| [[PAML]] || 4.4e || [http://abacus.gene.ucl.ac.uk/software/paml.html]||Biology, Phylogenetics
 
−
-->
 
−
|-
 
−
| [[PartitionFinder]] || 1.0.1 || [http://www.robertlanfear.com/partitionfinder/] || Biology, Phylogenetics, Evolution
 
−
|-
 
−
| [[Parflow]] || v615 || [https://computation.llnl.gov/casc/parflow/parflow_home.html] || Ecology, Modeling
 
−
|-
 
−
| [[PASA]] || 1.5, r20120625 || [http://http://pasa.sourceforge.net/]|| Biology, Genomics
 
−
|-
 
−
| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html]||Biology, Chip-Seq
 
−
|-
 
−
| [[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
 
−
|-
 
−
| [[Phenix]] || 1.8.1069 || [http://www.phenix-online.org/] || Crystallography
 
−
|-
 
−
<!-- | [[PETSc]] || 2.3.3-p8, 3.0.0-p12 || [http://www.mcs.anl.gov/petsc/petsc-as/]||MPI toolkit|| X ||
 
−
|-
 
−
| [[Phred]] || 020425 || [http://www.phrap.com/]|| Biology, Genomics, Sequencing || X ||
 
−
|-
 
−
| [[PhyloBayes]] || 3.3b || [http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm] || Biology, Phylogenetics || X ||
 
−
|- -->
 
−
| [[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
 
−
|-
 
−
<!-- | [[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 ||
 
−
|-
 
−
| [[Prinseq]] || 0.17 || [http://prinseq.sourceforge.net/index.html] || Biology, NGS || X ||
 
−
|- -->
 
−
| [[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
 
−
|-
 
−
| [[QIIME]] || 1.5.0 || [http://qiime.org/index.html]|| Biology, Ecology
 
−
|-
 
−
| [[R]] || 2.15.0, 2.15.1, 2.15.0-mpi, Rmpi/2.15.1 || [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]] || 7.3.2.0705 || [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
 
−
|-
 
−
| [[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
 
−
|-
 
−
<!-- | [[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 ||
 
−
|- -->
 
−
| [[samtools]] || 0.1.16, 0.1.18 || [http://samtools.sourceforge.net/] || Biology, NGS
 
−
|-
 
−
| [[SAS]] || 9.3 || [http://www.sas.com] || Statistics, Graphing
 
−
|-
 
−
<!-- | [[SATe]] || 2.1.0 || [http://phylo.bio.ku.edu/software/sate/sate2.html] ||Biology, Phylogenetics|| X ||
 
−
|-
 
−
| [[Scala]] || 2.9.1 || [http://www.scala-lang.org/]|| Programming, language, java || X ||
 
−
|- -->
 
−
| [[Schrodinger]] || 2012 || [http://www.schrodinger.com/] || Simulation, chemistry
 
−
|-
 
−
<!-- | [[Segminator]] || 0.0.2 || [http://www.bioinf.manchester.ac.uk/segminator/index.html]|| Biology, NGS || X ||
 
−
|- -->
 
−
| [[SeqPrep]] || 0.5 || [https://github.com/jstjohn/SeqPrep] || Biology, NGS
 
−
|-
 
−
| [[SEQuel]] || 1.0.1 || [http://bix.ucsd.edu/SEQuel/index.html] || Biology, NGS
 
−
|-
 
−
| [[Sickle]] || 1.200 || [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
 
−
|-
 
−
| [[Snap]] || 20100728 || [http://homepage.mac.com/iankorf] || Biology, Genomics
 
−
|-
 
−
| [[SOAPdenovo]] || 1.05 || [http://soap.genomics.org.cn/soapdenovo.html] || Biology, NGS
 
−
|-
 
−
| [[SOAPdenovo-Trans]] || 1.01 || [http://soap.genomics.org.cn/SOAPdenovo-Trans.html] || Biology, NGS
 
−
|-
 
−
| [[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
 
−
|-
 
−
| [[Sputnik]] || 1.0 || [http://espressosoftware.com/sputnik/] || Biology, Genomics
 
−
|-
 
−
| [[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 ||
 
−
|- -->
 
−
| [[Stacks]] || 0.9995 || [http://creskolab.uoregon.edu/stacks/] || Biology, Genomics, NGS
 
−
|-
 
−
<!-- | [[Staden]] || 2.0.0b9 || [http://staden.sourceforge.net/]|| Biology, Genomics, Sequencing || X || X
 
−
|-
 
−
| [[Stata]] || 10 || [http://www.stata.com/]||Statistics, Data analysis|| X ||
 
−
|- -->
 
−
| [[Structure]] || 2.3.3 || [http://pritch.bsd.uchicago.edu/structure_software/release_versions/v2.3.3/html/structure.html]|| Biology, Population
 
−
|-
 
−
| [[TAU]] || 2.21.4 ||[http://www.cs.uoregon.edu/Research/tau/home.php]||Profiling, Tracing, Programming
 
−
|-
 
−
| [[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 || [http://tophat.cbcb.umd.edu/] || Biology, NGS
 
−
|-
 
−
| [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html] || Biology, Genomics
 
−
|-
 
−
| [[Trinity]] || r20120608, r20120905, r20121005 || [http://trinityrnaseq.sourceforge.net/] || Biology, RNA-Seq
 
−
|-
 
−
| [[Twinscan]] || 4.1.2 || [http://mblab.wustl.edu/software.html#twinscanLink] || Biology, Genomics
 
−
|-
 
−
| [[usearch]] || 5.2.32|| [http://www.drive5.com/usearch/] || Biology, Sequence analysis
 
−
|-
 
−
| [[VASP]] || 4.6.34, 5.2.12, 5.3.2 || [http://cms.mpi.univie.ac.at/vasp/] || Quantum Chemistry, Ab Initio
 
−
|-
 
−
| [[VCFtools]] || 0.1.9, 0.1.10 || [http://vcftools.sourceforge.net/] || Biology, SNPs
 
−
|-
 
−
| [[velvet]] || 1.2.06, 1.2.07 || [http://www.ebi.ac.uk/~zerbino/velvet/] || Biology, NGS
 
−
|-
 
−
| [[vmd]] || 1.9.1 ||[http://ftp.ks.uiuc.edu/Research/vmd/]||Biology, Visualization
 
−
|-
 
−
| [[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
 
−
|-
 
−
| [[wgs]] || 7.0.1.22 || [http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page] || Biology, NGS
 
−
|-
 
−
| [[wublast]] || 2.0 || [http://blast.wustl.edu/] || Biology, Sequence Alignment
 
−
|}
 
−
 
 
−
<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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