Difference between revisions of "Installed Software"

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[[Category:Software]]
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#REDIRECT [[Applications]]
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The following is a list of the installed software at the UF HPC Center.
 
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List updated '''22 March 2012'''.
 
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==Software==
 
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{|  border="1"  cellspacing="0" cellpadding="2"
 
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! Software !! Version !! Home Website !! Category !! Notes
 
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|-
 
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| [[Abaqus]] || 6.6-1, 6.9-2 || [http://www.simulia.com/products/abaqus_standard.html Abaqus] || Simulation ||
 
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|-
 
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| [[Abyss]] || 1.3.1 || [http://www.bcgsc.ca/platform/bioinfo/software/abyss Abyss] || Biology, NGS ||
 
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|-
 
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| [[ADMB]] || 9.1, 10.0 || [http://admb-project.org/ ADMB] || Modeling, math ||
 
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|-
 
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| [[ALLPATHS-LG]] || 39099 || [http://www.broadinstitute.org/software/allpaths-lg/blog/ ALLPATHS-LG] || Biology, NGS ||
 
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|-
 
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| [[Amber]] || 10,11.old, 11 || [http://amber.scripps.edu/ Amber] || Simulation, chemistry ||
 
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|-
 
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| [[Amos]] || 3.0.0 || [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS AMOS] || Biology, Genomics ||
 
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|-
 
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| [[Ansys]] || 10.0 || [http://www.ansys.com/ Ansys] || Simulation, Engineering ||
 
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|-
 
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| [[antlr]] || 2.7.7, 3.1.3 || [http://www.antlr.org/ Antlr] || Linguistics, Parser ||
 
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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- Arachne] || Biology, Genomics ||
 
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|-
 
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| [[Bamtools]] || 2.1.0 || [https://github.com/pezmaster31/bamtools/wiki Bamtools] || Biology, NGS ||
 
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|-
 
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| [[beast]] || 1.6.2 || [http://beast.bio.ed.ac.uk/Main_Page BEAST] || Biology, Phylogenetics ||
 
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|-
 
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| [[BFAST]] || 0.7.0 || [http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page BFAST] || Biology, NGS ||
 
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|-
 
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| [[Bioconductor]] || 2011-11-16 || [http://www.bioconductor.org/ Bioconductor] || Biology, R, Statistics ||
 
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|-
 
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| [[Perl|BioPerl]] || || [http://bioperl.org/ BioPerl] || Biology, Perl ||
 
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|-
 
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| [[Python|Biopython]] || || [http://biopython.org/ BioPython] || Biology, Python ||
 
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|-
 
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| [[bioscope]] || 1.0.1, 1.2.1 || [http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/ngs-data-analysis-software/bioscope.html ABI BioScope] || Biology, NGS ||
 
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|-
 
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| [[Blast]] || 2.2.24, 2.2.25 || [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download  NCBI] || Biology, Sequence alignment ||
 
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|-
 
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| [[Blast2go]] || 2.5.0 || [http://www.blast2go.com/b2ghome Blast2go] || Biology, Annotation ||
 
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|-
 
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| [[BLAT]] || 34 || [http://genome.ucsc.edu/goldenPath/help/blatSpec.html BLAT] || Biology, Sequence alignment ||
 
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|-
 
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| [[Boost]] || 1.37.0, 1.46.1 || [http://www.boost.org/ Boost] || C++, Library ||
 
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|-
 
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| [[bwa]] || 0.5.9, 0.5.10, 0.6.0 (default) || [http://bio-bwa.sourceforge.net/ BWA] || Biology, NGS ||
 
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|-
 
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| [[Bowtie]] || 0.12.7 (default), 2.0.0-beta3 || [http://bowtie-bio.sourceforge.net/index.shtml Bowtie] || Biology, NGS ||
 
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|-
 
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| [[CAP3]] || 20071015 || [http://seq.cs.iastate.edu/ CAP3] || Biology, sequence assembly ||
 
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|-
 
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| [[CASAVA]] || 1.8.2 || [http://www.illumina.com/software/genome_analyzer_software.ilmn CASAVA] || Biology, NGS ||
 
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|-
 
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| [[CD-HIT]] || 4.5.7 || [http://weizhong-lab.ucsd.edu/cd-hit/ CD-HIT] || Biology, Genomics ||
 
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|-
 
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| [[CEGMA]] || 2.3 || [http://korflab.ucdavis.edu/Datasets/cegma/ CEGMA] || Biology, Genomics, Annotation ||
 
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|-
 
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| [[Charmm]] || 35b2 || [http://www.charmm.org/ Charmm] || Simulation, Chemistry ||
 
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|-
 
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| [[Circuit]] ||   || [http://www.circuitscape.org/Circuitscape/Welcome.html Circuitscape] || GIS ||
 
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|-
 
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| [[CisGenome]] || 2.0 || [http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm CisGenome] || Biology, Genomics, Peak Calling ||
 
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|-
 
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| [[Cmake]] || 2.8.5 || [http://www.cmake.org/ Cmake] || Programming ||
 
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|-
 
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| [[CNV-seq]] || 07.15.11 || [http://tiger.dbs.nus.edu.sg/cnv-seq/ CNV-seq] || Biology, NGS ||
 
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|-
 
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| [[CPMD]] || 3.11.1 || [http://www.cpmd.org/ CPMD] || Simulation, Chemistry ||
 
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|-
 
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<!--| [[Crystal]] || 1.0.2 || || || Will be removed on 2011-10-30 |- -->
 
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| [[Cufflinks|Cufflinks]] || 1.0.3, 1.1.0, 1.3.0 || [http://cufflinks.cbcb.umd.edu/ Cufflinks] || Biology, NGS ||
 
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|-
 
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| [[Cutadapt]] || 1.0 || [http://code.google.com/p/cutadapt/ Cutadapt] || Biology, NGS ||
 
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|-
 
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| [[dar]] || 2.3.9 || [http://sourceforge.net/projects/dar/ Dar] || Backup ||
 
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|-
 
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| [[DeFuse|deFuse]] || 0.4.3 || [http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page deFuse] || Biology, RNA-seq ||
 
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|-
 
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| [[Desmond]] || 2.4.2.1 || [http://www.deshawresearch.com/resources_desmond.html Desmond] || Simulation, Biology, Chemistry ||
 
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|-
 
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| [[dlpoly]] || 3.0.9 || [http://www.cse.clrc.ac.uk/ccg/software/DL_POLY/index.shtml DL_POLY]  || Simulation, Biology, Chemistry ||
 
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|-
 
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| [[dock]] || 6.3, 6.4, 6.5 || [http://dock.compbio.ucsf.edu/ Dock] || Chemistry, ligand binding prediction ||
 
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|-
 
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| [[EMAN2]] || 2.04 || [http://blake.bcm.tmc.edu/emanwiki/EMAN2 EMAN2] || Biology, image processing ||
 
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|-
 
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| [[emboss]] || 6.4.0 || [http://emboss.sourceforge.net/ Emboss] || Biology, multi-tool suite ||
 
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| [[espresso]] || 3.0, 3.2.2, 4.0.4 || [http://www.quantum-espresso.org/ Espresso] || Modeling, Physics ||
 
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|-
 
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| [[FASTA]] || 34.26.5 || [http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml FASTA] || Biology, Genomics ||
 
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|-
 
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| [[fastx_toolkit]]|| 0.0.13.1|| [http://hannonlab.cshl.edu/fastx_toolkit/ Fastx Tolkit] || Biology, NGS ||
 
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| [[fastqc]] || 0.10.0 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ FastQC] || Biology, NGS ||
 
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|-
 
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| [[fftw]] || 2.1.5, 3.1.2 || [http://www.fftw.org/ FFTW Gaussian] || Math, Library, C++ ||
 
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| [[fluent]] || 6.3.26 || [http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+FLUENT ANSYS FLUENT] || Simulation ||
 
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|-
 
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| [[FreeBayes]] || 0.9.4 || [http://bioinformatics.bc.edu/marthlab/FreeBayes 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 Atlassian Gadgets] || Software Development ||
 
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|-
 
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| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/ GAMESS]|| Quantum Chemistry||
 
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| [[garli]] || 2.0 || [https://www.nescent.org/wg_garli/Main_Page GARLI]||Biology, Phylogenetics||
 
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| [[gaussian]] || 03,09 || [http://www.gaussian.com/ Gaussian]||Modeling, Physics||
 
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|-
 
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| [[Geneid]] || 1.4 || [http://genome.crg.es/software/geneid/ geneid]||Biology, Genomics, Annotation||
 
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| [[Genewise]] || [http://www.ebi.ac.uk/Tools/Wise2/ Wise2]||Biology, Genomics, Annotation||
 
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|-
 
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| [[GMAP]] || [http://research-pub.gene.com/gmap/ GMAP] || Biology, Genomics ||
 
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|-
 
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| [[Gromacs]] || 4.0.4, 4.0.7 || [http://www.gromacs.org/ Gromacs]||Physics, Modeling||
 
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| [[HDF5]] || 1.8.7, 1.8.8 || [http://www.hdfgroup.org/HDF5/ HDF5]||Library, Data||
 
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|-
 
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| [[HMMER3]] || 3.0 || [http://hmmer.janelia.org/ HMMER3]||Biology, Genomics||
 
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|-
 
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| [[HTSeq]] || 0.5.3p3 || [http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html HTSeq] || Biology, NGS ||
 
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|-
 
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| [[hypre]] || 2.0.0 || [http://www.llnl.gov/casc/hypre/software.html HYPRE]||Library, Math, Physics||
 
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|-
 
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| [[IMa2]] || 8.26.11 || [http://genfaculty.rutgers.edu/hey/software#IMa2 IMa2]||Biology, Population||
 
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|-
 
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| [[Inelastica]] || 1.1 || [http://sourceforge.net/projects/inelastica/ Inelastica]||Quantum Chemistry||
 
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|-
 
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| [[IE3D]] || 15.1 || [http://www.mentor.com/electromagnetic-simulation/ IE3D]||Simulation, Design||
 
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| [[JDK]] || 1.6.0_12, 1.7.0 || [http://java.com Oracle JDK] || Java Development Kit ||
 
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|-
 
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| [[Khmer]] || 20120321 || [https://github.com/ctb/khmer Khmer] || Biology, NGS, Utilities ||
 
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|-
 
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| [[Kmer]] || r1909 || [http://sourceforge.net/apps/mediawiki/kmer/index.php?title=Main_Page Kmer package] || Biology, NGS, genome alignment ||
 
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|-
 
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| [[lammps]] || 17-Sept11 || [http://lammps.sandia.gov/ LAMPPS]||Simulation||
 
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|-
 
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| [[Last]] || 193 || [http://last.cbrc.jp/ Last] || Biology, Sequence alignment ||
 
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|-
 
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| [[libxc]] || 1.1.0 || [http://www.tddft.org/programs/octopus/wiki/index.php/Libxc libxc] || Math, funtionals ||
 
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|-
 
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| [[MACS]] || 1.4.1 || [http://liulab.dfci.harvard.edu/MACS/ MACS]||Biology, ChIP-Seq||
 
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|-
 
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| [[madness]] || 1769 || [http://code.google.com/p/m-a-d-n-e-s-s/ MADNESS]||Math, DIff. Equation solving||
 
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|-
 
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| [[mafft]] || 6.859 || [http://mafft.cbrc.jp/alignment/software/ MAFFT]||Biology, Multiple sequence alignment||
 
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|-
 
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| [[Maker]] || 2.10 || [http://www.yandell-lab.org/software/maker.html Maker] || Biology, Annotation, Genomics ||
 
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|-
 
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| [[Matlab]] || 2009b || [http://www.mathworks.com MathWorks]||Math, Simulation, Programming||
 
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|-
 
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| [[MCL]] || 11-335 || [http://www.micans.org/mcl/ MCL] || Biology, Genomics, Clustering||
 
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|-
 
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| [[meme]] || 3.0.13, 4.3.0 || [http://meme.nbcr.net/meme/intro.html MEME]||Biology, Motifs, Sequence analysis||
 
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|-
 
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| [[MetaPhyler]] || 1.13 || [http://www.cbcb.umd.edu/~boliu/metaphyler/ MetaPhyler ] || Biology, Metagenomics ||
 
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|-
 
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| [[metis]] || 4.0 || [http://glaros.dtc.umn.edu/gkhome/views/metis Metis]||Math, Graph partitioning||
 
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|-
 
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| [[Migrate-n]] || 3.2.16 || [http://popgen.sc.fsu.edu/Migrate/Migrate-n.html Migrate-n] || Biology, Population ||
 
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|-
 
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| [[mira]] || 3.2.0 || [http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_intro_whatismira MIRA Guide]||Biology, NGS||
 
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|-
 
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| [[mosaik]] || 1.1.0021 || [http://code.google.com/p/mosaik-aligner/ MOSAIK]||Biology,NGS||
 
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|-
 
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| [[MPIBlast]] || 1.6.0 || [http://www.mpiblast.org/ MPIBlast]||Biology, Sequence alignment||
 
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|-
 
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| [[MrBayes]] || 3.1.2 || [http://mrbayes.scs.fsu.edu/ MrBayes]||Biology, Phylogenetics||
 
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|-
 
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| [[MUMmer]] || 3.22 || [http://mummer.sourceforge.net/ MUMmer] || Biology, Genomics ||
 
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|-
 
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| [[NAMD]] || 2.7b2 || [http://www.ks.uiuc.edu/Research/namd/ NAMD]||Simulation, Chemistry, Biology||
 
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|-
 
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| [[NCO]] || 4.0.9 || [http://nco.sourceforge.net/ NCO] || Data exchange tools ||
 
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|-
 
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| [[netcdf]] || 3.6.3, 4.1.2, 4.1.3 || [http://www.unidata.ucar.edu/software/netcdf/ NetCDF]|| Data exchange, Tools || HDF5 support in 4.1.3 only
 
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| [[NetLogo]] || 4.1.3 || [http://ccl.northwestern.edu/netlogo/ NetLogo] || Modeling ||
 
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|-
 
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| [[Newbler]] || 2.5.3, 2.6 || [http://my454.com/products/analysis-software/index.asp Newbler] || Biology, NGS ||
 
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|-
 
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| [[NFFT]] || 3.1.3 || [http://www-user.tu-chemnitz.de/~potts/nfft/ nfft] || NDFT, library, math ||
 
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|-
 
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| [[Novoalign]] || 2.07.15 || [http://www.novocraft.com/main/page.php?s=novoalign Novoalign] || Biology, NGS ||
 
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|-
 
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| [[NWChem]] || 6.0 || [http://www.nwchem-sw.org/index.php/Main_Page NWChem]||Simulation, Chemistry||
 
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|-
 
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| [[Oases]] || 0.2.04 || [http://www.ebi.ac.uk/~zerbino/oases/ Oases] || Biology, NGS ||
 
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|-
 
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| [[OpenFOAM]] || 1.7.1 || [http://www.openfoam.com/ OpenFoam]||Molecular Dynamics||
 
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|-
 
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| [[OrthoMCL]] || 2.0 || [http://orthomcl.org/ OrthoMCL] || Biology, Genomics ||
 
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|-
 
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| [[PAL2NAL]] || 14 || [http://www.bork.embl.de/pal2nal/ PAL2NAL] || Biology, bioinformatics, multiple sequence alignment ||
 
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|-
 
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| [[PAML]] || 4.4e || [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]||Biology, Phylogenetics||
 
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|-
 
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| [[papi]] || 4.1.2.1 || [http://icl.cs.utk.edu/papi/software/index.html PAPI]||CPU API||
 
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|-
 
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| [[PASA]] || 20110520 || [http://http://pasa.sourceforge.net/ PASA]|| Biology, Genomics ||
 
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|-
 
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| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html PeakSplitter]||Biology, Chip-Seq||
 
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|-
 
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| [[pdt]] || 3.16 || [http://www.cs.uoregon.edu/Research/tau/home.php PDT]||Programming, Profiler||
 
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|-
 
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| [[Perl]] || 5.14.1 || [http://www.perl.org/ Perl]||Programming, Language ||
 
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|-
 
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| [[petsc]] || 2.3.3-p8, 3.0.0-p12 || [http://www.mcs.anl.gov/petsc/petsc-as/ PETSc]||MPI toolkit||
 
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|-
 
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| [[Phred]] || 020425 || [http://www.phrap.com/ Phred] || Biology, Genomics, Sequencing ||
 
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|-
 
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| [[PhyloBayes]] || 3.3b || [http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm PhyloBayes] || Biology, Phylogenetics ||
 
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|-
 
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| [[PhyML]] || 3.0 || [http://code.google.com/p/phyml/ PhyML] || Biology, Phylogenetics ||
 
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|-
 
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| [[pqs]] || 3.3-19 ||[http://www.pqs-chem.com/software.php PQS]||Modeling, Chemistry||
 
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|-
 
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| [[Prinseq]] || 0.17 || [http://prinseq.sourceforge.net/index.html Prinseq] || Biology, NGS ||
 
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|-
 
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| [[pyopencl]] || 0.92 || [http://mathema.tician.de/software/pyopencl PyOpenCL]||python, parallel programming||
 
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|-
 
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| [[python]] || 2.5.1, 2.6.4, 2.6.5 || [http://python.org Python]||Programming, scripting, language||
 
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|-
 
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| [[R]] || 2.13.1, 2.14.1, 2.14.1-MPI || [http://www.r-project.org/ R] || Statistics, Programming ||
 
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|-
 
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| [[RAxML]] || 7.3.0 || [http://sco.h-its.org/exelixis/software.html RAxML]||Biology, Phylogenetics||
 
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|-
 
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| [[RAxML-Light]]|| 1.0.5 ||[http://sco.h-its.org/exelixis/software.html RAxML]||Biology, Phylogenetics||
 
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|-
 
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| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/ Repeat Masker]||Biology, Genomics||
 
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|-
 
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| [[riboPicker]] || 0.4.2 || [http://ribopicker.sourceforge.net/ riboPicker]||Biology, Sequence||
 
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|-
 
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| [[Rosetta]] || 2.1.1, 2.1.2 || [https://www.rosettacommons.org/ Rosetta]||Biology, Structural, Modeling||
 
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|-
 
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| [[Ruby]] || 1.9.3 || [http://www.ruby-lang.org/en Ruby]||Programming, Language, Scripting||
 
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|-
 
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| [[rsm]] || 2961 || [http://www.adoptech.com/software/RSMToolkit.htm RSM]||Math, Modeling, Geometry||
 
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|-
 
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| [[samtools]] || 0.1.16, 0.1.18 || [http://samtools.sourceforge.net/ Samtools]||Biology, NGS||
 
−
|-
 
−
| [[SAS]] || 9.2, 9.3 || [http://www.sas.com SAS]||Statistics, Graphing||
 
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|-
 
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| [[SATe]] || 2.1.0 || [http://phylo.bio.ku.edu/software/sate/sate2.html SATe] ||Biology, Phylogenetics||
 
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|-
 
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| [[Scala]] || 2.9.1 || [http://www.scala-lang.org/ Scala] || Programming, language, java ||
 
−
|-
 
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| [[SeqPrep]] || 0.4 || [https://github.com/jstjohn/SeqPrep SeqPrep] ||Biology, NGS ||
 
−
|-
 
−
| [[Siesta]] || 2.0, 2.0.2, 3.0b || [http://www.icmab.es/siesta/ Siesta]||Simulation, physics, ab-initio||
 
−
|-
 
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| [[SOAPdenovo]] || 1.05 || [http://soap.genomics.org.cn/soapdenovo.html SOAPdenovo] ||Biology, NGS||
 
−
|-
 
−
| [[SRA]] || 2.1.7 || [http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software SRA]]||biology, NGS||
 
−
|-
 
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| [[SRNAPredict]] || 3.0 || [http://www.tufts.edu/sackler/waldorlab/sRNAPredict.html sRNAPredict] || Biology, Genomics ||
 
−
|-
 
−
| [[SRNAScanner]] || 200903 || [http://cluster.physics.iisc.ernet.in/sRNAscanner/ sRNAScanner] || Biology, Genomics ||
 
−
|-
 
−
| [[Staden]] || 2.0.0b9 || [http://staden.sourceforge.net/ Staden] || Biology, Genomics, Sequencing ||
 
−
|-
 
−
| [[Stata]] || 10 || [http://www.stata.com/ Stata]||Statistics, Data analysis||
 
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|-
 
−
| [[Structure]] || 2.3.3 || [http://pritch.bsd.uchicago.edu/structure_software/release_versions/v2.3.3/html/structure.html Structure] || Biology, Population ||
 
−
|-
 
−
| [[tau]] || 2.20.1 ||[http://www.cs.uoregon.edu/Research/tau/home.php TAU]||Profiling, Tracing, Programming, Toolkit||
 
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|-
 
−
| [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html TRF]||Biology, Genomics||
 
−
|-
 
−
| [[Trimal]] || 1.2 || [http://trimal.cgenomics.org/ Trimal] || Biology, NGS ||
 
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|-
 
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| [[Trinity]] || r20110519, r20110820, r20120125 || [http://trinityrnaseq.sourceforge.net/ Trinity RNA-Seq] || Biology, RNA-Seq||
 
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|-
 
−
| [[tuxedo|Tophat]] || 1.3.0 || [http://tophat.cbcb.umd.edu/ Tophat]||Biology, NGS||
 
−
|-
 
−
| [[tuxedo]] ||colspan="3"|The "tuxedo suite," Bowtie, Tophat, and Cufflinks||
 
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|-
 
−
| [[Twinscan]] || 3.5,4.1.2 || [http://mblab.wustl.edu/software.html#twinscanLink Twinscan] || Biology, Genomics ||
 
−
|-
 
−
| [[usearch]] || 5.0.151,5.1.221 || [http://www.drive5.com/usearch/ USEARCH]||Biology, Sequence analysis||
 
−
|-
 
−
| [[VASP]] || 4.6.34,5.2.0 || [http://cms.mpi.univie.ac.at/vasp/ VASP]||Quantum Chemistry, ab initio||
 
−
|-
 
−
| [[VCFtools]] || 0.1.7 || [http://vcftools.sourceforge.net/ VCFtools] ||Biology, SNPs ||
 
−
|-
 
−
| [[velvet]] || 1.2.02,1.2.01,1.1.05 || [http://www.ebi.ac.uk/~zerbino/velvet/ Velvet]||Biology, NGS||
 
−
|-
 
−
| [[vmd]] || 1.9 ||[http://ftp.ks.uiuc.edu/Research/vmd/ VMD]||Biology, Visualization||
 
−
|-
 
−
| [[weka]] || 3.6.2 ||[http://www.cs.waikato.ac.nz/ml/weka/ WEKA]||Data mining algorithms||
 
−
|-
 
−
| [[wgs]] || 6.1, 6.1-20110830||[http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page Celera WGS Assembler]||Biology,Assembler,Genome||
 
−
|-
 
−
| [[wublast]] || 2.0 || [http://blast.wustl.edu/ WU-Blast]||Biology, Sequence Alignment||
 
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|}
 
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* Many versions available.  <code>/scratch/hpc/osg/app/etc/grid3-locations.txt</code> may have an up-to-date list.  Or look underneath <code>/scratch/hpc/osg/app/cmssoft</code>.
 
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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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