Difference between revisions of "Installed Software"

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#REDIRECT [[Applications]]
<!--
 
==Cluster Software Upgrade (Update 09/07/12)==
 
 
 
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).
 
 
 
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.
 
-->
 
==Note: Cluster Software Upgrade==
 
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 While our software was consistent and stable, it was no longer current.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.
 
 
 
==Installed Software List==
 
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''.
 
 
 
'''Note:''' Click on the icons to the right of the column headings to sort the table.
 
 
 
{|  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" | Website
 
! scope="col" | Category
 
|-
 
<!-- | [[Abaqus]] || 6.6-1, 6.9-2 || [http://www.simulia.com/products/abaqus_standard.html] || Simulation
 
|- -->
 
| [[Abyss]] || 1.3.3, 1.3.4, 1.3.4-mpi || [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 || [http://www.broadinstitute.org/software/allpaths-lg/blog/] || Biology, NGS
 
|-
 
| [[Amber]] || 11, 12 || [http://amber.scripps.edu/] || Simulation, chemistry
 
|-
 
<!-- | [[Amos]] || 3.0.0 || [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS] || Biology, Genomics || X ||
 
|-
 
| [[ANNOVAR]] || 20120308 || [http://www.openbioinformatics.org/annovar/] || Biology, Genomics || X ||
 
|-
 
| [[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 ||
 
|- -->
 
| [[Amuse]] || 6.0 || [http://www.amusecode.org]|| Astrophysics
 
|-
 
| [[Augustus]] || 2.6 || [http://augustus.gobics.de/]|| 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
 
|-
 
<!-- | [[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
 
|-
 
| [[Beast|BEAST]] || 1.7.2 || [http://beast.bio.ed.ac.uk/Main_Page]|| Biology, Phylogenetics
 
|-
 
| [[Bedtools|BEDTools]] || 2.16.2 || [http://code.google.com/p/bedtools/]|| Biology, NGS
 
|-
 
| [[BFAST]] || 0.7.0 || [http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page] || Biology, NGS
 
|-
 
| [[Bismark]] || 0.7.4 || [http://www.bioinformatics.babraham.ac.uk/projects/download.html#bismark] || Biology, Methylation, NGS
 
|-
 
| [[Bioconductor]] || Latest || [http://www.bioconductor.org/] || Biology, R, Statistics
 
|-
 
| [[Perl|BioPerl]] || 1.006901 || [http://bioperl.org/] || Biology, Perl
 
|-
 
| [[Python|BioPython]] || 1.59 || [http://biopython.org/] || Biology, Python
 
|-
 
<!-- | [[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]] || 2.2.26 (+ and legacy) || [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
 
|-
 
| [[Boost]] || 1.49.0 || [http://www.boost.org/] || C++, Library
 
|-
 
| [[Bwa]] || 0.6.1 || [http://bio-bwa.sourceforge.net/] || Biology, NGS
 
|-
 
| [[Bowtie]] || 0.12.8, 2.0.0b6 || [http://bowtie-bio.sourceforge.net/index.shtml] || Biology, NGS
 
|-
 
<!-- | [[BreakDancer]] || 1.1 || [http://breakdancer.sourceforge.net/index.html] || Biology, NGS, Genomics || X ||
 
|- -->
 
| [[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 || X ||
 
|- -->
 
| [[CD-HIT]] || 4.6 || [http://weizhong-lab.ucsd.edu/cd-hit/] || Biology, Genomics
 
|-
 
<!-- | [[CEGMA]] || 2.4.010312 || [http://korflab.ucdavis.edu/Datasets/cegma/] || Biology, Genomics, Annotation || X ||
 
|-
 
| [[CGATools]] || 1.5.0.31 || [http://cgatools.sourceforge.net/] || Biology, Genomics || X ||
 
|- -->
 
| [[Charmm]] || 36a3 || [http://www.charmm.org/] || Simulation, Chemistry
 
|-
 
<!-- | [[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
 
|-
 
| [[ClustalW]] || 2.1 || [http://www.clustal.org/clustal2/] || Biology, Genomics
 
|-
 
| [[CMake]] || 2.8.8 || [http://www.cmake.org/] || Programming
 
|-
 
<!-- | [[CNV-seq]] || 07.15.11 || [http://tiger.dbs.nus.edu.sg/cnv-seq/] || Biology, NGS || X ||
 
|-
 
| [[CNVnator]] || 0.2.5 || [http://sv.gersteinlab.org/] || Biology, NGS || X ||
 
|- -->
 
| [[Consed]] || 23.0 || [http://bozeman.mbt.washington.edu/consed/consed.html] || Biology, Genomics
 
|-
 
<!-- | [[CPMD]] || 3.11.1 || [http://www.cpmd.org/] || Simulation, Chemistry || X ||
 
|- -->
 
| [[CUDA]] || 4.2 || [http://www.nvidia.com/object/cuda_home_new.html] || Programming, Graphics
 
|-
 
| [[Cufflinks|Cufflinks]] || 1.3.0, 2.0.0, 2.0.2 || [http://cufflinks.cbcb.umd.edu/] || Biology, NGS
 
|-
 
| [[Cutadapt]] || 1.1 || [http://code.google.com/p/cutadapt/] || Biology, NGS
 
|-
 
<!-- | [[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 ||
 
|-
 
| [[Desmond]] || 2.4.2.1 || [http://www.deshawresearch.com/resources_desmond.html] || Simulation, Biology, Chemistry || X ||
 
|-
 
| [[Dindel]] || 1.01 || [http://www.sanger.ac.uk/resources/software/dindel/] || Biology, NGS, Genomics || X ||
 
|- -->
 
| [[DIYABC]] || many || [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
 
|-
 
| [[Dock]] || 6.5 || [http://dock.compbio.ucsf.edu/] || Chemistry, ligand binding prediction
 
|-
 
<!-- | [[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 ||
 
|- -->
 
| [[emboss]] || 6.5.7 || [http://emboss.sourceforge.net/] || Biology, multi-tool suite
 
|-
 
| [[Espresso]] || 5.0.1 || [http://www.quantum-espresso.org/] || Modeling, Physics
 
|-
 
| [[Exonerate]] || 2.2.0 || [http://www.ebi.ac.uk/~guy/exonerate/] || Biology, Genomics
 
|-
 
| [[FAR]] || 2.15 || [http://sourceforge.net/apps/mediawiki/theflexibleadap/index.php?title=Main_Page] || Biology, Genomics
 
|-
 
| [[FASTA]] || 34.26.5 || [http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml] || Biology, Genomics
 
|-
 
| [[FastQC]] || 0.9.6, 0.10.1 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/] || Biology, NGS
 
|-
 
| [[Fastx_toolkit]]|| 0.0.13.2 || [http://hannonlab.cshl.edu/fastx_toolkit/] || Biology, NGS
 
|-
 
<!-- | [[FFTW]] || 3.3.2 || [http://www.fftw.org/] || Math, Library, C++
 
|-
 
| [[fluent]] || 6.3.26 || [http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+FLUENT] || Simulation || X ||
 
|-
 
| [[FragGeneScan]] || 1.16 || [http://omics.informatics.indiana.edu/FragGeneScan/] || Biology, NGS || X ||
 
|- -->
 
| [[FreeBayes]] || 0.9.6 || [http://bioinformatics.bc.edu/marthlab/FreeBayes] || Biology
 
|-
 
<!-- | [[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 || [https://www.nescent.org/wg_garli/Main_Page]||Biology, Phylogenetics
 
|-
 
| [[GATK]] || 1.6.9 || [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
 
|-
 
<!-- | [[Geneid]] || 1.4 || [http://genome.crg.es/software/geneid/]||Biology, Genomics, Annotation|| X ||
 
|- -->
 
| [[GeneMark]] || 2012.04 || [http://exon.gatech.edu/] || Biology, Genomics, Metagenomics
 
|-
 
| [[Genewise]] || 2.2.0 || [http://www.ebi.ac.uk/Tools/Wise2]||Biology, Genomics, Annotation
 
|-
 
| [[Gmap]] || 20070928, 20120712 || [http://research-pub.gene.com/gmap/] || Biology, Genomics
 
|-
 
| [[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
 
|-
 
| [[Gromacs]] || 4.5.5 || [http://www.gromacs.org/] || Chemistry, Modeling, Simulation
 
|-
 
| [[GSL]] || 1.15 || [http://www.gnu.org/software/gsl/] || Library, Math, C++, C
 
|-
 
| [[HaMStR]] || v8b || [http://www.deep-phylogeny.org/hamstr/] || Biology, Genomics
 
|-
 
| [[HDF5]] || 1.8.9 || [http://www.hdfgroup.org/HDF5/]||Library, Data
 
|-
 
| [[HMMER3]] || 3.0 || [http://hmmer.janelia.org/]||Biology, Genomics
 
|-
 
| [[HTSeq]] || 0.5.3p3 || [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
 
|-
 
| [[Hypre]] || 2.8.0b || [http://www.llnl.gov/casc/hypre/software.html]||Library, Math, Physics
 
|-
 
<!-- | [[IM and IMa]] || 2009.12.17 || [http://genfaculty.rutgers.edu/hey/software]||Biology, Population|| X ||
 
|-
 
| [[IMa2]] || 8.26.11 || [http://genfaculty.rutgers.edu/hey/software#IMa2]||Biology, Population|| X ||
 
|-
 
| [[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_12, 1.7.0 || [http://java.com] || Java Development Kit || X ||
 
|- -->
 
| [[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
 
|-
 
| [[Lammps]] || 25Jul12 || [http://lammps.sandia.gov/] || 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 ||
 
|- -->
 
| [[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 || [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
 
|-
 
| [[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]] || 4.0.9 || [http://nco.sourceforge.net/]|| Data exchange tools ||  X ||
 
|- -->
 
| [[NETCDF]] || in process || [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|| X ||
 
|-
 
| [[Oases]] || 0.2.04 || [http://www.ebi.ac.uk/~zerbino/oases/] || Biology, NGS || X ||
 
|-
 
| [[OpenFOAM]] || 1.7.1 || [http://www.openfoam.com/]||Molecular Dynamics|| X ||
 
|-
 
| [[OrthoMCL]] || 2.0 || [http://orthomcl.org/]|| Biology, Genomics || X ||
 
|-
 
| [[PAL2NAL]] || 14 || [http://www.bork.embl.de/pal2nal/]|| Biology, Genomics|| X ||
 
|-
 
| [[PAML]] || 4.4e || [http://abacus.gene.ucl.ac.uk/software/paml.html]||Biology, Phylogenetics|| X ||
 
|-
 
| [[TAU|PAPI]] || 4.1.2.1 || [http://icl.cs.utk.edu/papi/software/index.html]||CPU API|| X ||
 
|- -->
 
| [[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
 
|-
 
<!-- | [[TAU|PDT]] || 3.16 || [http://www.cs.uoregon.edu/Research/tau/home.php]||Programming, Profiler|| X ||
 
|- -->
 
| [[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-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 || [http://code.google.com/p/phyml/] || Biology, Phylogenetics
 
|-
 
| [[Picard]] || 1.69, 1.72 || [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, 2.15.0-mpi, Rmpi/2.15.1 || [http://www.r-project.org/] || Statistics, Programming
 
|-
 
| [[R8S]] || 1.71 || [http://loco.biosci.arizona.edu/r8s/] || Biology, Evolution
 
|-
 
| [[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]] || 3.0b || [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|| X ||
 
|- -->
 
|-
 
| [[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]] || 2.20.1 ||[http://www.cs.uoregon.edu/Research/tau/home.php]||Profiling, Tracing, Programming|| X ||
 
|- -->
 
| [[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]] || r20120518, r20120608, r20120905 || [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 || [http://cms.mpi.univie.ac.at/vasp/] || Quantum Chemistry, Ab Initio
 
|-
 
| [[VCFtools]] || 0.1.9 || [http://vcftools.sourceforge.net/] || Biology, SNPs
 
|-
 
| [[velvet]] || 1.2.06 || [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]] ||  || [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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