Difference between revisions of "Installed Software"

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! scope="col" | Name  
 
! scope="col" | Name  
 
! scope="col" class="unsortable" | Version  
 
! scope="col" class="unsortable" | Version  
−
! scope="col" | Project/Vendor Website
+
! scope="col" | Website
 
! scope="col" | Category
 
! scope="col" | Category
 
! scope="col" class="unsortable" style="text-align: center;" | EL5 <ref name="el5">Operating system: CentOS 5 - currently in production at UF HPC</ref>
 
! scope="col" class="unsortable" style="text-align: center;" | EL5 <ref name="el5">Operating system: CentOS 5 - currently in production at UF HPC</ref>
−
! scope="col" class="unsortable" style="text-align: center;" | EL6<ref  name="el6">Operating system: RedHat Enterprise Linux 6 - scheduled for production at UF HPC for the Fall of 2012</ref>
+
! scope="col" class="unsortable" style="text-align: center;" | EL6<ref  name="el6">Operating system: RedHat Enterprise Linux 6 - scheduled for production at UF HPC for the Fall of 2012. EL5 software we provide will not be automatically installed on EL6. Please file a [http://support.hpc.ufl.edu Support Request Ticket] for EL6 software installation.</ref>
 
|-
 
|-
 
| [[Abaqus]] || 6.6-1, 6.9-2 || [http://www.simulia.com/products/abaqus_standard.html] || Simulation || X ||
 
| [[Abaqus]] || 6.6-1, 6.9-2 || [http://www.simulia.com/products/abaqus_standard.html] || Simulation || X ||
Line 41: Line 41:
 
| [[BayesPhylogenies]] || 2.0 || [http://www.evolution.reading.ac.uk/BayesPhy.html] || Biology, Phylogenetics || X ||
 
| [[BayesPhylogenies]] || 2.0 || [http://www.evolution.reading.ac.uk/BayesPhy.html] || Biology, Phylogenetics || X ||
 
|-
 
|-
−
| [[beast]] || 1.6.2, 1.7.0, 1.7.1 || [http://beast.bio.ed.ac.uk/Main_Page] || Biology, Phylogenetics || X ||
+
| [[beast]] || 1.6.2, 1.7.0, 1.7.1 || [http://beast.bio.ed.ac.uk/Main_Page]|| Biology, Phylogenetics || X ||
 
|-
 
|-
−
| [[Bedtools|BEDTools]] || 2.16.2 || [http://code.google.com/p/bedtools/ BEDTools] || Biology, NGS ||
+
| [[Bedtools|BEDTools]] || 2.16.2 || [http://code.google.com/p/bedtools/]|| Biology, NGS || X ||
 
|-
 
|-
−
| [[BFAST]] || 0.7.0 || [http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page BFAST] || Biology, NGS ||
+
| [[BFAST]] || 0.7.0 || [http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page] || Biology, NGS || X ||
 
|-
 
|-
−
| [[Bioconductor]] || 2011-11-16 || [http://www.bioconductor.org/ Bioconductor] || Biology, R, Statistics ||
+
| [[Bioconductor]] || 2011-11-16 || [http://www.bioconductor.org/] || Biology, R, Statistics || X ||
 
|-
 
|-
−
| [[Perl|BioPerl]] || 1.006901 || [http://bioperl.org/ BioPerl] || Biology, Perl ||
+
| [[Perl|BioPerl]] || 1.006901 || [http://bioperl.org/] || Biology, Perl || X ||
 
|-
 
|-
−
| [[Python|Biopython]] || 1.59 || [http://biopython.org/ BioPython] || Biology, Python ||
+
| [[Python|Biopython]] || 1.59 || [http://biopython.org/] || Biology, Python || X ||
 
|-
 
|-
−
| [[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 ||
+
| [[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] || Biology, NGS || X ||
 
|-
 
|-
−
| [[Blast]] || 2.2.24, 2.2.25, 2.2.26 || [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download NCBI] || Biology, Sequence alignment ||
+
| [[Blast]] || 2.2.24, 2.2.25, 2.2.26 || [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download ] || Biology, Sequence alignment || X ||
 
|-
 
|-
−
| [[Blast2go]] || 2.5.0 || [http://www.blast2go.com/b2ghome Blast2go] || Biology, Annotation ||
+
| [[Blast2go]] || 2.5.0 || [http://www.blast2go.com/b2ghome] || Biology, Annotation || X ||
 
|-
 
|-
−
| [[BLAT]] || 34 || [http://genome.ucsc.edu/goldenPath/help/blatSpec.html BLAT] || Biology, Sequence alignment ||
+
| [[BLAT]] || 34 || [http://genome.ucsc.edu/goldenPath/help/blatSpec.html] || Biology, Sequence alignment || X ||
 
|-
 
|-
−
| [[Boost]] || 1.38.0, 1.46.1, 1.48.0, 1.49.0 || [http://www.boost.org/ Boost] || C++, Library ||
+
| [[Boost]] || 1.38.0, 1.46.1, 1.48.0, 1.49.0 || [http://www.boost.org/] || C++, Library || X ||
 
|-
 
|-
−
| [[bwa]] || 0.5.9, 0.5.10, 0.6.0 (default) || [http://bio-bwa.sourceforge.net/ BWA] || Biology, NGS ||
+
| [[bwa]] || 0.5.9, 0.5.10, 0.6.0 (default) || [http://bio-bwa.sourceforge.net/] || Biology, NGS || X ||
 
|-
 
|-
−
| [[Bowtie]] || 0.12.7, 0.12.8 (default), 2.0.0-beta3, 2.0.0-beta5 || [http://bowtie-bio.sourceforge.net/index.shtml Bowtie] || Biology, NGS ||
+
| [[Bowtie]] || 0.12.7, 0.12.8 (default), 2.0.0-beta3, 2.0.0-beta5 || [http://bowtie-bio.sourceforge.net/index.shtml] || Biology, NGS || X ||
 
|-
 
|-
−
| [[BreakDancer]] || 1.1 || [http://breakdancer.sourceforge.net/index.html BreakDancer] || Biology, NGS, Genomics ||
+
| [[BreakDancer]] || 1.1 || [http://breakdancer.sourceforge.net/index.html] || Biology, NGS, Genomics || X ||
 
|-
 
|-
−
| [[CAP3]] || 20071015 || [http://seq.cs.iastate.edu/ CAP3] || Biology, sequence assembly ||
+
| [[CAP3]] || 20071015 || [http://seq.cs.iastate.edu/] || Biology, sequence assembly || X ||
 
|-
 
|-
−
| [[CASAVA]] || 1.8.2 || [http://www.illumina.com/software/genome_analyzer_software.ilmn CASAVA] || Biology, NGS ||
+
| [[CASAVA]] || 1.8.2 || [http://www.illumina.com/software/genome_analyzer_software.ilmn] || Biology, NGS || X ||
 
|-
 
|-
−
| [[CD-HIT]] || 4.5.7 || [http://weizhong-lab.ucsd.edu/cd-hit/ CD-HIT] || Biology, Genomics ||
+
| [[CD-HIT]] || 4.5.7 || [http://weizhong-lab.ucsd.edu/cd-hit/] || Biology, Genomics || X ||
 
|-
 
|-
−
| [[CEGMA]] || 2.3 || [http://korflab.ucdavis.edu/Datasets/cegma/ CEGMA] || Biology, Genomics, Annotation ||
+
| [[CEGMA]] || 2.3 || [http://korflab.ucdavis.edu/Datasets/cegma/] || Biology, Genomics, Annotation || X ||
 
|-
 
|-
−
| [[CGATools]] || 1.5.0.31 || [http://cgatools.sourceforge.net/ CGA Tools] || Biology, Genomics ||
+
| [[CGATools]] || 1.5.0.31 || [http://cgatools.sourceforge.net/] || Biology, Genomics || X ||
 
|-
 
|-
−
| [[Charmm]] || 35b2 || [http://www.charmm.org/ Charmm] || Simulation, Chemistry ||
+
| [[Charmm]] || 35b2 || [http://www.charmm.org/] || Simulation, Chemistry || X ||
 
|-
 
|-
−
| [[Circuit]] || 3.5.1, 3.5.7 || [http://www.circuitscape.org/Circuitscape/Welcome.html Circuitscape] || GIS ||
+
| [[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 CisGenome] || Biology, Genomics, Peak Calling ||
+
| [[CisGenome]] || 2.0 || [http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm] || Biology, Genomics, Peak Calling || X ||
 
|-
 
|-
−
| [[CMake]] || 2.8.5 || [http://www.cmake.org/ Cmake] || Programming ||
+
| [[CMake]] || 2.8.5 || [http://www.cmake.org/] || Programming || X ||
 
|-
 
|-
−
| [[CNV-seq]] || 07.15.11 || [http://tiger.dbs.nus.edu.sg/cnv-seq/ CNV-seq] || Biology, NGS ||
+
| [[CNV-seq]] || 07.15.11 || [http://tiger.dbs.nus.edu.sg/cnv-seq/] || Biology, NGS || X ||
 
|-
 
|-
−
| [[CNVnator]] || 0.2.5 || [http://sv.gersteinlab.org/ CNVnator] || Biology, NGS ||
+
| [[CNVnator]] || 0.2.5 || [http://sv.gersteinlab.org/] || Biology, NGS || X ||
 
|-
 
|-
−
| [[CPMD]] || 3.11.1 || [http://www.cpmd.org/ CPMD] || Simulation, Chemistry ||
+
| [[CPMD]] || 3.11.1 || [http://www.cpmd.org/] || Simulation, Chemistry || X ||
 
|-
 
|-
−
<!--| [[Crystal]] || 1.0.2 || || || Will be removed on 2011-10-30 |- -->
+
| [[Cufflinks|Cufflinks]] || 1.0.3, 1.1.0, 1.3.0 || [http://cufflinks.cbcb.umd.edu/] || Biology, NGS ||  X ||
−
| [[Cufflinks|Cufflinks]] || 1.0.3, 1.1.0, 1.3.0 || [http://cufflinks.cbcb.umd.edu/ Cufflinks] || Biology, NGS ||  
 
 
|-
 
|-
−
| [[Cutadapt]] || 1.1 || [http://code.google.com/p/cutadapt/ Cutadapt] || Biology, NGS ||
+
| [[Cutadapt]] || 1.1 || [http://code.google.com/p/cutadapt/] || Biology, NGS || X ||
 
|-
 
|-
−
| [[dar]] || 2.3.9 || [http://sourceforge.net/projects/dar/ Dar] || Backup ||
+
| [[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 deFuse] || Biology, RNA-seq ||
+
| [[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 Desmond] || Simulation, Biology, Chemistry ||
+
| [[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/ Dindel] || Biology, NGS, Genomics ||
+
| [[Dindel]] || 1.01 || [http://www.sanger.ac.uk/resources/software/dindel/] || Biology, NGS, Genomics || X ||
 
|-
 
|-
−
| [[dlpoly]] || 3.0.9 || [http://www.cse.clrc.ac.uk/ccg/software/DL_POLY/index.shtml DL_POLY]  || Simulation, Biology, Chemistry ||
+
| [[dlpoly]] || 3.0.9 || [http://www.cse.clrc.ac.uk/ccg/software/DL_POLY/index.shtml]  || Simulation, Biology, Chemistry || X ||
 
|-
 
|-
−
| [[dock]] || 6.3, 6.4, 6.5 || [http://dock.compbio.ucsf.edu/ Dock] || Chemistry, ligand binding prediction ||
+
| [[dock]] || 6.3, 6.4, 6.5 || [http://dock.compbio.ucsf.edu/] || Chemistry, ligand binding prediction || X ||
 
|-
 
|-
−
| [[emacs]] || 21.4.1, 23.4.1 || [http://www.gnu.org/software/emacs/ Gnu Website] || The Emacs editor ||
+
| [[emacs]] || 21.4.1, 23.4.1 || [http://www.gnu.org/software/emacs/] || The Emacs editor || X ||
 
|-
 
|-
−
| [[EMAN2]] || 2.04 || [http://blake.bcm.tmc.edu/emanwiki/EMAN2 EMAN2] || Biology, image processing ||
+
| [[EMAN2]] || 2.04 || [http://blake.bcm.tmc.edu/emanwiki/EMAN2] || Biology, image processing || X ||
 
|-
 
|-
−
| [[emboss]] || 6.4.0 || [http://emboss.sourceforge.net/ Emboss] || Biology, multi-tool suite ||
+
| [[emboss]] || 6.4.0 || [http://emboss.sourceforge.net/] || Biology, multi-tool suite || X ||
 
|-
 
|-
−
| [[espresso]] || 3.0, 3.2.2, 4.0.4, 5.0 || [http://www.quantum-espresso.org/ Espresso] || Modeling, Physics ||
+
| [[espresso]] || 3.0, 3.2.2, 4.0.4, 5.0 || [http://www.quantum-espresso.org/] || Modeling, Physics || X ||
 
|-
 
|-
−
| [[Exonerate]] || 2.2 || [http://www.ebi.ac.uk/~guy/exonerate/ Exonerate] || Biology, Genomics ||
+
| [[Exonerate]] || 2.2 || [http://www.ebi.ac.uk/~guy/exonerate/] || Biology, Genomics || X ||
 
|-
 
|-
 +
| [[FAR]] || 2.15 || [http://sourceforge.net/apps/mediawiki/theflexibleadap/index.php?title=Main_Page] || Biology, Genomics || X ||
 
|-
 
|-
−
| [[FAR]] || 2.15 || [http://sourceforge.net/apps/mediawiki/theflexibleadap/index.php?title=Main_Page FAR] || Biology, Genomics ||
+
| [[FASTA]] || 34.26.5 || [http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml] || Biology, Genomics || X ||
 
|-
 
|-
−
| [[FASTA]] || 34.26.5 || [http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml FASTA] || Biology, Genomics ||
+
| [[fastx_toolkit]]|| 0.0.13.1|| [http://hannonlab.cshl.edu/fastx_toolkit/] || Biology, NGS || X ||
 
|-
 
|-
−
| [[fastx_toolkit]]|| 0.0.13.1|| [http://hannonlab.cshl.edu/fastx_toolkit/ Fastx Tolkit] || Biology, NGS ||
+
| [[FastQC]] || 0.9.6, 0.10.0 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/] || Biology, NGS || X ||
 
|-
 
|-
−
| [[FastQC]] || 0.9.6, 0.10.0 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ FastQC] || Biology, NGS ||
+
| [[fftw]] || 2.1.5, 3.1.2 || [http://www.fftw.org/] || Math, Library, C++ || X ||
 
|-
 
|-
−
| [[fftw]] || 2.1.5, 3.1.2 || [http://www.fftw.org/ FFTW Gaussian] || Math, Library, C++ ||
+
| [[fluent]] || 6.3.26 || [http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+FLUENT] || Simulation || X ||
 
|-
 
|-
−
| [[fluent]] || 6.3.26 || [http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+FLUENT ANSYS FLUENT] || Simulation ||
+
| [[FragGeneScan]] || 1.16 || [http://omics.informatics.indiana.edu/FragGeneScan/] || Biology, NGS || X ||
 
|-
 
|-
−
| [[FragGeneScan]] || 1.16 || [http://omics.informatics.indiana.edu/FragGeneScan/ FragGeneScan] || Biology, NGS
+
| [[FreeBayes]] || 0.9.4 || [http://bioinformatics.bc.edu/marthlab/FreeBayes] || Biology || X ||
 
|-
 
|-
−
| [[FreeBayes]] || 0.9.4 || [http://bioinformatics.bc.edu/marthlab/FreeBayes 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 ||
 
|-
 
|-
−
| [[gadget]] || 2.0.4, 2.0.5 || [http://confluence.atlassian.com/display/GADGETS/Atlassian+Gadgets+2.0.5+Release+Notes Atlassian Gadgets] || Software Development ||
+
| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/]|| Quantum Chemistry|| X ||
 
|-
 
|-
−
| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/ GAMESS]|| Quantum Chemistry||
+
| [[garli]] || 2.0 || [https://www.nescent.org/wg_garli/Main_Page]||Biology, Phylogenetics|| X ||
 
|-
 
|-
−
| [[garli]] || 2.0 || [https://www.nescent.org/wg_garli/Main_Page GARLI]||Biology, Phylogenetics||
+
| [[GATK]] || 1.4.30 || [http://www.broadinstitute.org/gsa/wiki/index.php/GATK] || Biology, NGS || X ||
 
|-
 
|-
−
| [[GATK]] || 1.4.30 || [http://www.broadinstitute.org/gsa/wiki/index.php/GATK GATK] || Biology, NGS ||
+
| [[gulp]] || 4.0.3 || [http://projects.ivec.org/gulp/] || Modeling/simulation, Chemistry || X ||
 
|-
 
|-
−
| [[gulp]] || 4.0.3 || [http://projects.ivec.org/gulp/ GULP] || Modeling/simulation, Computational Chemistry ||
+
| [[gaussian]] || E01, G03, G09-A.02, G09-C.01 || [http://www.gaussian.com/]||Modeling, Computational Chemistry|| X ||
 
|-
 
|-
−
| [[gaussian]] || E01, G03, G09-A.02, G09-C.01 || [http://www.gaussian.com/ Gaussian]||Modeling, Computational Chemistry||
+
| [[Geneid]] || 1.4 || [http://genome.crg.es/software/geneid/]||Biology, Genomics, Annotation|| X ||
 
|-
 
|-
−
| [[Geneid]] || 1.4 || [http://genome.crg.es/software/geneid/ geneid]||Biology, Genomics, Annotation||
+
|| [[GeneMark]] || 2012.04 || [http://exon.gatech.edu/] || Biology, Genomics, Metagenomics || X ||
 
|-
 
|-
−
|| [[GeneMark]] || 2012.04 || [http://exon.gatech.edu/ GeneMark] || Biology, Genomics, Metagenomics ||
+
| [[Genewise]] || 2.2.3 || [http://www.ebi.ac.uk/Tools/Wise2]||Biology, Genomics, Annotation|| X ||
 
|-
 
|-
−
| [[Genewise]] || 2.2.3 || [http://www.ebi.ac.uk/Tools/Wise2/ Wise2]||Biology, Genomics, Annotation||
+
| [[GMAP]] || 20070928, 20120524, 20120612 || [http://research-pub.gene.com/gmap/] || Biology, Genomics || X ||
 
|-
 
|-
−
| [[GMAP]] || 20070928, 20120111, 20120323, 20120427, 20120524, 20120612 || [http://research-pub.gene.com/gmap/ GMAP] || Biology, Genomics ||
+
| [[Grace]] || 5.1.22 || [http://plasma-gate.weizmann.ac.il/Grace/] || Graphics, plotting, 2D || X ||
 
|-
 
|-
−
| [[Grace]] || 5.1.22 || [http://plasma-gate.weizmann.ac.il/Grace/ Grace] || Graphics, plotting, 2D ||
+
| [[Gromacs]] || 4.0.4, 4.0.7 || [http://www.gromacs.org/]||Physics, Modeling|| X ||
 
|-
 
|-
−
| [[Gromacs]] || 4.0.4, 4.0.7 || [http://www.gromacs.org/ Gromacs]||Physics, Modeling||
+
| [[HDF5]] || 1.8.7, 1.8.8 || [http://www.hdfgroup.org/HDF5/]||Library, Data|| X ||
 
|-
 
|-
−
| [[HDF5]] || 1.8.7, 1.8.8 || [http://www.hdfgroup.org/HDF5/ HDF5]||Library, Data||
+
| [[HMMER3]] || 3.0 || [http://hmmer.janelia.org/]||Biology, Genomics|| X ||
 
|-
 
|-
−
| [[HMMER3]] || 3.0 || [http://hmmer.janelia.org/ HMMER3]||Biology, Genomics||
+
| [[HTSeq]] || 0.5.3p3 || [http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html] || Biology, NGS || X ||
 
|-
 
|-
−
| [[HTSeq]] || 0.5.3p3 || [http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html HTSeq] || Biology, NGS ||
+
| [[HugeSeq]] || 1.0.1 || [http://hugeseq.hugolam.com/]|| Biology, NGS, Genomics || X ||
 
|-
 
|-
−
| [[HugeSeq]] || 1.0.1 || [http://hugeseq.hugolam.com/ HugeSeq] || Biology, NGS, Genomics ||
+
| [[hypre]] || 2.8.0 || [http://www.llnl.gov/casc/hypre/software.html]||Library, Math, Physics|| X ||
 
|-
 
|-
−
| [[hypre]] || 2.8.0 || [http://www.llnl.gov/casc/hypre/software.html HYPRE]||Library, Math, Physics||
+
| [[IM and IMa]] || 2009.12.17 || [http://genfaculty.rutgers.edu/hey/software]||Biology, Population|| X ||
 
|-
 
|-
−
| [[IM and IMa]] || 2009.12.17 || [http://genfaculty.rutgers.edu/hey/software IM&IMa]||Biology, Population||
+
| [[IMa2]] || 8.26.11 || [http://genfaculty.rutgers.edu/hey/software#IMa2]||Biology, Population|| X ||
 
|-
 
|-
−
| [[IMa2]] || 8.26.11 || [http://genfaculty.rutgers.edu/hey/software#IMa2 IMa2]||Biology, Population||
+
| [[Inelastica]] || 1.1 (python/2.7.2) || [http://sourceforge.net/projects/inelastica/]||Quantum Chemistry|| X ||
 
|-
 
|-
−
| [[Inelastica]] || 1.1 (python/2.7.2) || [http://sourceforge.net/projects/inelastica/ Inelastica]||Quantum Chemistry||
+
| [[IE3D]] || 15.1 || [http://www.mentor.com/electromagnetic-simulation/]||Simulation, Design|| X ||
 
|-
 
|-
−
| [[IE3D]] || 15.1 || [http://www.mentor.com/electromagnetic-simulation/ IE3D]||Simulation, Design||
+
| [[JDK]] || 1.6.0_12, 1.7.0 || [http://java.com] || Java Development Kit || X ||
 
|-
 
|-
−
| [[JDK]] || 1.6.0_12, 1.7.0 || [http://java.com Oracle JDK] || Java Development Kit ||
+
| [[Khmer]] || 20120321 || [https://github.com/ctb/khmer] || Biology, NGS, Utilities || X ||
 
|-
 
|-
−
| [[Khmer]] || 20120321 || [https://github.com/ctb/khmer Khmer] || Biology, NGS, Utilities ||
+
| [[Kmer]] || r1909 || [http://sourceforge.net/apps/mediawiki/kmer/index.php?title=Main_Page] || Biology, NGS, genome alignment || X ||
 
|-
 
|-
−
| [[Kmer]] || r1909 || [http://sourceforge.net/apps/mediawiki/kmer/index.php?title=Main_Page Kmer package] || Biology, NGS, genome alignment ||
+
| [[lammps]] || 17-Sept11 || [http://lammps.sandia.gov/]||Simulation|| X ||
 
|-
 
|-
−
| [[lammps]] || 17-Sept11 || [http://lammps.sandia.gov/ LAMPPS]||Simulation||
+
| [[Last]] || 193 || [http://last.cbrc.jp/] || Biology, Sequence alignment || X ||
 
|-
 
|-
−
| [[Last]] || 193 || [http://last.cbrc.jp/ Last] || Biology, Sequence alignment ||
+
| [[libxc]] || 1.1.0 || [http://www.tddft.org/programs/octopus/wiki/index.php/Libxc] || Math, funtionals || X ||
 
|-
 
|-
−
| [[libxc]] || 1.1.0 || [http://www.tddft.org/programs/octopus/wiki/index.php/Libxc libxc] || Math, funtionals ||
+
| [[MACS]] || 1.4.1 || [http://liulab.dfci.harvard.edu/MACS/]||Biology, ChIP-Seq|| X ||
 
|-
 
|-
−
| [[MACS]] || 1.4.1 || [http://liulab.dfci.harvard.edu/MACS/ MACS]||Biology, ChIP-Seq||
+
| [[madness]] || 1769 || [http://code.google.com/p/m-a-d-n-e-s-s/]||Math, DIff. Equation solving|| X ||
 
|-
 
|-
−
| [[madness]] || 1769 || [http://code.google.com/p/m-a-d-n-e-s-s/ MADNESS]||Math, DIff. Equation solving||
+
| [[mafft]] || 6.859 || [http://mafft.cbrc.jp/alignment/software/]||Biology, Multiple sequence alignment|| X ||
 
|-
 
|-
−
| [[mafft]] || 6.859 || [http://mafft.cbrc.jp/alignment/software/ MAFFT]||Biology, Multiple sequence alignment||
+
| [[Maker]] || 2.10 || [http://www.yandell-lab.org/software/maker.html] || Biology, Annotation, Genomics || X ||
 
|-
 
|-
−
| [[Maker]] || 2.10 || [http://www.yandell-lab.org/software/maker.html Maker] || Biology, Annotation, Genomics ||
+
| [[MapSplice]] || 1.15.2 || [http://www.netlab.uky.edu/p/bioinfo/MapSplice]|| Biology, Genomics || X ||
 
|-
 
|-
−
| [[MapSplice]] || 1.15.2 || [http://www.netlab.uky.edu/p/bioinfo/MapSplice MapSplice] || Biology, Genomics ||
+
| [[Matlab]] || 2009b || [http://www.mathworks.com]||Math, Simulation, Programming|| X ||
 
|-
 
|-
−
| [[Matlab]] || 2009b || [http://www.mathworks.com MathWorks]||Math, Simulation, Programming||
+
| [[MATS]] || 2.1.0 || [http://rnaseq-mats.sourceforge.net/index.html]||BIology, NGS|| X ||
 
|-
 
|-
−
| [[MATS]] || 2.1.0 || [http://rnaseq-mats.sourceforge.net/index.html MATS]||BIology, NGS||
+
| [[Mauve]] || 2.3.1 || [http://gel.ahabs.wisc.edu/mauve/]||Biology, Multiple genome alignments || X ||
 
|-
 
|-
−
| [[Mauve]] || 2.3.1 || [http://gel.ahabs.wisc.edu/mauve/ Mauve]||Biology, Multiple genome alignments ||
+
| [[MCL]] || 11-335 || [http://www.micans.org/mcl/] || Biology, Genomics, Clustering|| X ||
 
|-
 
|-
−
| [[MCL]] || 11-335 || [http://www.micans.org/mcl/ MCL] || Biology, Genomics, Clustering||
+
| [[meme]] || 3.0.13, 4.3.0 || [http://meme.nbcr.net/meme/intro.html]||Biology, Motifs, Sequence analysis|| X ||
 
|-
 
|-
−
| [[meme]] || 3.0.13, 4.3.0 || [http://meme.nbcr.net/meme/intro.html MEME]||Biology, Motifs, Sequence analysis||
+
| [[MetaPhyler]] || 1.13 || [http://www.cbcb.umd.edu/~boliu/metaphyler/] || Biology, Metagenomics || X ||
 
|-
 
|-
−
| [[MetaPhyler]] || 1.13 || [http://www.cbcb.umd.edu/~boliu/metaphyler/ MetaPhyler ] || Biology, Metagenomics ||
+
| [[metis]] || 4.0 || [http://glaros.dtc.umn.edu/gkhome/views/metis]||Math, Graph partitioning|| X ||
 
|-
 
|-
−
| [[metis]] || 4.0 || [http://glaros.dtc.umn.edu/gkhome/views/metis Metis]||Math, Graph partitioning||
+
| [[Migrate-n]] || 3.2.16 || [http://popgen.sc.fsu.edu/Migrate/Migrate-n.html] || Biology, Population || X ||
 
|-
 
|-
−
| [[Migrate-n]] || 3.2.16 || [http://popgen.sc.fsu.edu/Migrate/Migrate-n.html Migrate-n] || Biology, Population ||
+
| [[mira]] || 3.2.0, 3.4.0.1 || [http://mira-assembler.sourceforge.net/]||Biology, NGS|| X ||
 
|-
 
|-
−
| [[mira]] || 3.2.0, 3.4.0.1 || [http://mira-assembler.sourceforge.net/ MIRA]||Biology, NGS||
+
| [[mosaik]] || 1.1.0021 || [http://code.google.com/p/mosaik-aligner/]||Biology,NGS|| X ||
 
|-
 
|-
−
| [[mosaik]] || 1.1.0021 || [http://code.google.com/p/mosaik-aligner/ MOSAIK]||Biology,NGS||
+
| [[MPIBlast]] || 1.6.0 || [http://www.mpiblast.org/]||Biology, Sequence alignment|| X ||
 
|-
 
|-
−
| [[MPIBlast]] || 1.6.0 || [http://www.mpiblast.org/ MPIBlast]||Biology, Sequence alignment||
+
| [[MrBayes]] || 3.1.2,3.2.1 || [http://mrbayes.scs.fsu.edu/]||Biology, Phylogenetics|| X ||
 
|-
 
|-
−
| [[MrBayes]] || 3.1.2,3.2.1 || [http://mrbayes.scs.fsu.edu/ MrBayes]||Biology, Phylogenetics||
+
| [[MUMmer]] || 3.22 || [http://mummer.sourceforge.net/]|| Biology, Genomics || X ||
 
|-
 
|-
−
| [[MUMmer]] || 3.22 || [http://mummer.sourceforge.net/ MUMmer] || Biology, Genomics ||
+
| [[MUSCLE]] || 3.8.31 || [http://www.drive5.com/muscle/]|| Biology, Genomics ||  X ||
 
|-
 
|-
−
| [[MUSCLE]] || 3.8.31 || [http://www.drive5.com/muscle/ MUSCLE] || Biology, Genomics ||  
+
| [[NAMD]] || 2.7b2 || [http://www.ks.uiuc.edu/Research/namd/]||Simulation, Chemistry, Biology|| X ||
 
|-
 
|-
−
| [[NAMD]] || 2.7b2 || [http://www.ks.uiuc.edu/Research/namd/ NAMD]||Simulation, Chemistry, Biology||
+
| [[NCO]] || 4.0.9 || [http://nco.sourceforge.net/]|| Data exchange tools ||  X ||
 
|-
 
|-
−
| [[NCO]] || 4.0.9 || [http://nco.sourceforge.net/ NCO] || Data exchange tools ||  
+
| [[netcdf]] || 3.6.3, 4.1.2, 4.1.3 || [http://www.unidata.ucar.edu/software/netcdf/]|| Data exchange, Tools || X ||
 
|-
 
|-
−
| [[netcdf]] || 3.6.3, 4.1.2, 4.1.3 || [http://www.unidata.ucar.edu/software/netcdf/ NetCDF]|| Data exchange, Tools ||
+
| [[NetLogo]] || 4.1.3 || [http://ccl.northwestern.edu/netlogo/] || Modeling || X ||
 
|-
 
|-
−
| [[NetLogo]] || 4.1.3 || [http://ccl.northwestern.edu/netlogo/ NetLogo] || Modeling ||
+
| [[Newbler]] || 2.5.3, 2.6 || [http://my454.com/products/analysis-software/index.asp] || Biology, NGS || X ||
 
|-
 
|-
−
| [[Newbler]] || 2.5.3, 2.6 || [http://my454.com/products/analysis-software/index.asp Newbler] || Biology, NGS ||
+
| [[NFFT]] || 3.1.3 || [http://www-user.tu-chemnitz.de/~potts/nfft/] || NDFT, library, math || X ||
 
|-
 
|-
−
| [[NFFT]] || 3.1.3 || [http://www-user.tu-chemnitz.de/~potts/nfft/ nfft] || NDFT, library, math ||
+
| [[Novoalign]] || 2.07.15 || [http://www.novocraft.com/main/page.php?s=novoalign] || Biology, NGS || X ||
 
|-
 
|-
−
| [[Novoalign]] || 2.07.15 || [http://www.novocraft.com/main/page.php?s=novoalign Novoalign] || Biology, NGS ||
+
| [[NWChem]] || 6.0 || [http://www.nwchem-sw.org/index.php/Main_Page]||Simulation, Chemistry|| X ||
 
|-
 
|-
−
| [[NWChem]] || 6.0 || [http://www.nwchem-sw.org/index.php/Main_Page NWChem]||Simulation, Chemistry||
+
| [[Oases]] || 0.2.04 || [http://www.ebi.ac.uk/~zerbino/oases/] || Biology, NGS || X ||
 
|-
 
|-
−
| [[Oases]] || 0.2.04 || [http://www.ebi.ac.uk/~zerbino/oases/ Oases] || Biology, NGS ||
+
| [[OpenFOAM]] || 1.7.1 || [http://www.openfoam.com/]||Molecular Dynamics|| X ||
 
|-
 
|-
−
| [[OpenFOAM]] || 1.7.1 || [http://www.openfoam.com/ OpenFoam]||Molecular Dynamics||
+
| [[OrthoMCL]] || 2.0 || [http://orthomcl.org/]|| Biology, Genomics || X ||
 
|-
 
|-
−
| [[OrthoMCL]] || 2.0 || [http://orthomcl.org/ OrthoMCL] || Biology, Genomics ||
+
| [[PAL2NAL]] || 14 || [http://www.bork.embl.de/pal2nal/]|| Biology, Genomics|| X ||
 
|-
 
|-
−
| [[PAL2NAL]] || 14 || [http://www.bork.embl.de/pal2nal/ PAL2NAL] || Biology, bioinformatics, multiple sequence alignment ||
+
| [[PAML]] || 4.4e || [http://abacus.gene.ucl.ac.uk/software/paml.html]||Biology, Phylogenetics|| X ||
 
|-
 
|-
−
| [[PAML]] || 4.4e || [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]||Biology, Phylogenetics||
+
| [[TAU|PAPI]] || 4.1.2.1 || [http://icl.cs.utk.edu/papi/software/index.html]||CPU API|| X ||
 
|-
 
|-
−
| [[TAU|PAPI]] || 4.1.2.1 || [http://icl.cs.utk.edu/papi/software/index.html PAPI]||CPU API||
+
| [[PASA]] || 20110520 || [http://http://pasa.sourceforge.net/]|| Biology, Genomics || X ||
 
|-
 
|-
−
| [[PASA]] || 20110520 || [http://http://pasa.sourceforge.net/ PASA]|| Biology, Genomics ||
+
| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html]||Biology, Chip-Seq|| X ||
 
|-
 
|-
−
| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html PeakSplitter]||Biology, Chip-Seq||
+
| [[TAU|PDT]] || 3.16 || [http://www.cs.uoregon.edu/Research/tau/home.php]||Programming, Profiler|| X ||
 
|-
 
|-
−
| [[TAU|PDT]] || 3.16 || [http://www.cs.uoregon.edu/Research/tau/home.php PDT]||Programming, Profiler||
+
| [[Perl]] || 5.14.1 || [http://www.perl.org/]||Programming, Language || X ||
 
|-
 
|-
−
| [[Perl]] || 5.14.1 || [http://www.perl.org/ Perl]||Programming, Language ||
+
| [[PETSc]] || 2.3.3-p8, 3.0.0-p12 || [http://www.mcs.anl.gov/petsc/petsc-as/]||MPI toolkit|| X ||
 
|-
 
|-
−
| [[PETSc]] || 2.3.3-p8, 3.0.0-p12 || [http://www.mcs.anl.gov/petsc/petsc-as/ PETSc]||MPI toolkit||
+
| [[Phred]] || 020425 || [http://www.phrap.com/]|| Biology, Genomics, Sequencing || X ||
 
|-
 
|-
−
| [[Phred]] || 020425 || [http://www.phrap.com/ Phred] || Biology, Genomics, Sequencing ||
+
| [[PhyloBayes]] || 3.3b || [http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm] || Biology, Phylogenetics || X ||
 
|-
 
|-
−
| [[PhyloBayes]] || 3.3b || [http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm PhyloBayes] || Biology, Phylogenetics ||
+
| [[PhyML]] || 3.0 || [http://code.google.com/p/phyml/] || Biology, Phylogenetics || X ||
 
|-
 
|-
−
| [[PhyML]] || 3.0 || [http://code.google.com/p/phyml/ PhyML] || Biology, Phylogenetics ||
+
| [[Picard]] || 1.54 || [http://picard.sourceforge.net/] || Biology, NGS || X ||
 
|-
 
|-
−
| [[Picard]] || 1.54 || [http://picard.sourceforge.net/ Picard] || Biology, NGS ||
+
| [[Pindel]] || 0.2.8 || [https://trac.nbic.nl/pindel/] || Biology, NGS || X ||
 
|-
 
|-
−
| [[Pindel]] || 0.2.8 || [https://trac.nbic.nl/pindel/ Pindel] || Biology, NGS ||
+
| [[PQS]] || 3.3-19 ||[http://www.pqs-chem.com/software.php]||Modeling, Chemistry|| X ||
 
|-
 
|-
−
| [[PQS]] || 3.3-19 ||[http://www.pqs-chem.com/software.php PQS]||Modeling, Chemistry||
+
| [[Prinseq]] || 0.17 || [http://prinseq.sourceforge.net/index.html] || Biology, NGS || X ||
 
|-
 
|-
−
| [[Prinseq]] || 0.17 || [http://prinseq.sourceforge.net/index.html Prinseq] || Biology, NGS ||
+
| [[PyOpenCL]] || 2012.04 || [http://mathema.tician.de/software/pyopencl]||python, parallel programming|| X ||
 
|-
 
|-
−
| [[PyOpenCL]] || 2012.04 || [http://mathema.tician.de/software/pyopencl PyOpenCL]||python, parallel programming||
+
| [[python]] || 2.6.5, 2.7.2, 2.7.3 || [http://python.org]||Programming, scripting, language|| X || X
 
|-
 
|-
−
| [[python]] || 2.6.5, 2.7.2, 2.7.3 || [http://python.org Python]||Programming, scripting, language||
+
| [[R]] || 2.14.1, 2.14.1-MPI, 2.14.2 || [http://www.r-project.org/]|| Statistics, Programming || X || X
 
|-
 
|-
−
| [[R]] || 2.14.1, 2.14.1-MPI, 2.14.2 || [http://www.r-project.org/ R] || Statistics, Programming ||
+
| [[RAxML]] || 7.3.0 || [http://sco.h-its.org/exelixis/software.html]||Biology, Phylogenetics|| X ||
 
|-
 
|-
−
| [[RAxML]] || 7.3.0 || [http://sco.h-its.org/exelixis/software.html RAxML]||Biology, Phylogenetics||
+
| [[RAxML-Light]]|| 1.0.5 ||[http://sco.h-its.org/exelixis/software.html]||Biology, Phylogenetics|| X ||
 
|-
 
|-
−
| [[RAxML-Light]]|| 1.0.5 ||[http://sco.h-its.org/exelixis/software.html RAxML]||Biology, Phylogenetics||
+
| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/]||Biology, Genomics|| X ||
 
|-
 
|-
−
| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/ Repeat Masker]||Biology, Genomics||
+
| [[Reptile]] || 1.1, 1.1-omp || [http://aluru-sun.ece.iastate.edu/doku.php?id=reptile]||Biology, NGS, error correction|| X ||
 
|-
 
|-
−
| [[Reptile]] || 1.1, 1.1-omp || [http://aluru-sun.ece.iastate.edu/doku.php?id=reptile Reptile]||Biology, NGS, error correction||
+
| [[riboPicker]] || 0.4.2 || [http://ribopicker.sourceforge.net/]||Biology, Sequence|| X ||
 
|-
 
|-
−
| [[riboPicker]] || 0.4.2 || [http://ribopicker.sourceforge.net/ riboPicker]||Biology, Sequence||
+
| [[Rosetta]] || 2.1.1, 2.1.2 || [https://www.rosettacommons.org/]||Biology, Structural, Modeling|| X ||
 
|-
 
|-
−
| [[Rosetta]] || 2.1.1, 2.1.2 || [https://www.rosettacommons.org/ Rosetta]||Biology, Structural, Modeling||
+
| [[Ruby]] || 1.9.3 || [http://www.ruby-lang.org/en]||Programming, Language, Scripting|| X ||
 
|-
 
|-
−
| [[Ruby]] || 1.9.3 || [http://www.ruby-lang.org/en Ruby]||Programming, Language, Scripting||
+
| [[RSMToolkit]] || 2961 || [http://www.adoptech.com/software/RSMToolkit.htm]||Math, Modeling, Geometry|| X ||
 
|-
 
|-
−
| [[RSMToolkit]] || 2961 || [http://www.adoptech.com/software/RSMToolkit.htm RSM]||Math, Modeling, Geometry||
+
| [[samtools]] || 0.1.16, 0.1.18 || [http://samtools.sourceforge.net/]||Biology, NGS|| X || X
 
|-
 
|-
−
| [[samtools]] || 0.1.16, 0.1.18 || [http://samtools.sourceforge.net/ Samtools]||Biology, NGS||
+
| [[SAS]] || 9.2, 9.3 || [http://www.sas.com]||Statistics, Graphing|| X || X
 
|-
 
|-
−
| [[SAS]] || 9.2, 9.3 || [http://www.sas.com SAS]||Statistics, Graphing||
+
| [[SATe]] || 2.1.0 || [http://phylo.bio.ku.edu/software/sate/sate2.html] ||Biology, Phylogenetics|| X ||
 
|-
 
|-
−
| [[SATe]] || 2.1.0 || [http://phylo.bio.ku.edu/software/sate/sate2.html SATe] ||Biology, Phylogenetics||
+
| [[Scala]] || 2.9.1 || [http://www.scala-lang.org/]|| Programming, language, java || X ||
 
|-
 
|-
−
| [[Scala]] || 2.9.1 || [http://www.scala-lang.org/ Scala] || Programming, language, java ||
+
| [[Segminator]] || 0.0.2 || [http://www.bioinf.manchester.ac.uk/segminator/index.html]|| Biology, NGS || X ||
 
|-
 
|-
−
| [[Segminator]] || 0.0.2 || [http://www.bioinf.manchester.ac.uk/segminator/index.html Segminator] || Biology, NGS ||
+
| [[SeqPrep]] || 0.4 || [https://github.com/jstjohn/SeqPrep] ||Biology, NGS || X ||
 
|-
 
|-
−
| [[SeqPrep]] || 0.4 || [https://github.com/jstjohn/SeqPrep SeqPrep] ||Biology, NGS ||
+
| [[Siesta]] || 2.0, 2.0.2, 3.0b || [http://www.icmab.es/siesta/]||Simulation, physics, ab-initio|| X ||
 
|-
 
|-
−
| [[Siesta]] || 2.0, 2.0.2, 3.0b || [http://www.icmab.es/siesta/ Siesta]||Simulation, physics, ab-initio||
+
| [[SOAPdenovo]] || 1.05 || [http://soap.genomics.org.cn/soapdenovo.html]||Biology, NGS|| X ||
 
|-
 
|-
−
| [[SOAPdenovo]] || 1.05 || [http://soap.genomics.org.cn/soapdenovo.html SOAPdenovo] ||Biology, NGS||
+
| [[SPARTA+]] || 2.60 || [http://spin.niddk.nih.gov/bax/software/SPARTA+/]||Chemistry|| X ||
 
|-
 
|-
−
| [[SPARTA+]] || 2.60 || [http://spin.niddk.nih.gov/bax/software/SPARTA+/] ||Chemistry||
+
| [[SRA]] || 2.1.7 || [http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software]]||biology, NGS|| X || X
 
|-
 
|-
−
| [[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||
+
| [[SRNAPredict]] || 3.0 || [http://www.tufts.edu/sackler/waldorlab/sRNAPredict.html]|| Biology, Genomics || X ||
 
|-
 
|-
−
| [[SRNAPredict]] || 3.0 || [http://www.tufts.edu/sackler/waldorlab/sRNAPredict.html sRNAPredict] || Biology, Genomics ||
+
| [[SRNAScanner]] || 200903 || [http://cluster.physics.iisc.ernet.in/sRNAscanner/]|| Biology, Genomics || X ||
 
|-
 
|-
−
| [[SRNAScanner]] || 200903 || [http://cluster.physics.iisc.ernet.in/sRNAscanner/ sRNAScanner] || Biology, Genomics ||
+
| [[Staden]] || 2.0.0b9 || [http://staden.sourceforge.net/]|| Biology, Genomics, Sequencing || X || X ||
 
|-
 
|-
−
| [[Staden]] || 2.0.0b9 || [http://staden.sourceforge.net/ Staden] || Biology, Genomics, Sequencing ||
+
| [[Stata]] || 10 || [http://www.stata.com/]||Statistics, Data analysis|| X ||
 
|-
 
|-
−
| [[Stata]] || 10 || [http://www.stata.com/ Stata]||Statistics, Data analysis||
+
| [[Structure]] || 2.3.3 || [http://pritch.bsd.uchicago.edu/structure_software/release_versions/v2.3.3/html/structure.html]|| Biology, Population || X ||
 
|-
 
|-
−
| [[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]||Profiling, Tracing, Programming|| X ||
 
|-
 
|-
−
| [[TAU]] || 2.20.1 ||[http://www.cs.uoregon.edu/Research/tau/home.php TAU]||Profiling, Tracing, Programming, Toolkit||
+
| [[tgicl]] || 2.1 || [http://compbio.dfci.harvard.edu/tgi/software/]|| Biology, sequencing, clustering || X ||
 
|-
 
|-
−
| [[tgicl]] || 2.1 || [http://compbio.dfci.harvard.edu/tgi/software/ TGICL] || Biology, sequencing, clustering ||
+
| [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html]||Biology, Genomics|| X ||
 
|-
 
|-
−
| [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html TRF]||Biology, Genomics||
+
| [[Trimal]] || 1.2 || [http://trimal.cgenomics.org/] || Biology, NGS || X ||
 
|-
 
|-
−
| [[Trimal]] || 1.2 || [http://trimal.cgenomics.org/ Trimal] || Biology, NGS ||
+
| [[Trinity]] || r20120125, r20120317, r20120608 || [http://trinityrnaseq.sourceforge.net/] || Biology, RNA-Seq|| X ||
 
|-
 
|-
−
| [[Trinity]] || r20110820, r20120125, r20120317, r20120608 || [http://trinityrnaseq.sourceforge.net/ Trinity RNA-Seq] || Biology, RNA-Seq||
+
| [[tuxedo|Tophat]] || 1.3.0, 1.3.3, 1.4.1 || [http://tophat.cbcb.umd.edu/]||Biology, NGS|| X ||
 
|-
 
|-
−
| [[tuxedo|Tophat]] || 1.3.0, 1.3.3, 1.4.1 || [http://tophat.cbcb.umd.edu/ Tophat]||Biology, NGS||
+
| [[tuxedo]] ||colspan="3"|The "tuxedo suite" - Bowtie, Tophat, and Cufflinks|| X ||
 
|-
 
|-
−
| [[tuxedo]] ||colspan="3"|The "tuxedo suite" - Bowtie, Tophat, and Cufflinks||
+
| [[Twinscan]] || 3.5,4.1.2 || [http://mblab.wustl.edu/software.html#twinscanLink]|| Biology, Genomics || X ||
 
|-
 
|-
−
| [[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/]||Biology, Sequence analysis|| X ||
 
|-
 
|-
−
| [[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/]||Quantum Chemistry, ab initio|| X ||
 
|-
 
|-
−
| [[VASP]] || 4.6.34,5.2.0 || [http://cms.mpi.univie.ac.at/vasp/ VASP]||Quantum Chemistry, ab initio||
+
| [[VCFtools]] || 0.1.7, 0.1.9 || [http://vcftools.sourceforge.net/]||Biology, SNPs || X ||
 
|-
 
|-
−
| [[VCFtools]] || 0.1.7, 0.1.9 || [http://vcftools.sourceforge.net/ VCFtools] ||Biology, SNPs ||
+
| [[velvet]] || 1.2.06,1.2.02,1.2.01,1.1.05 || [http://www.ebi.ac.uk/~zerbino/velvet/]||Biology, NGS|| X || X
 
|-
 
|-
−
| [[velvet]] || 1.2.06,1.2.02,1.2.01,1.1.05 || [http://www.ebi.ac.uk/~zerbino/velvet/ Velvet]||Biology, NGS||
+
| [[vmd]] || 1.9 ||[http://ftp.ks.uiuc.edu/Research/vmd/]||Biology, Visualization|| X ||
 
|-
 
|-
−
| [[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/]||Data mining algorithms|| X ||
 
|-
 
|-
−
| [[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]||Biology,Assembler,Genome|| X ||
 
|-
 
|-
−
| [[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/]||Biology, Sequence Alignment|| X ||
−
|-
 
−
| [[wublast]] || 2.0 || [http://blast.wustl.edu/ WU-Blast]||Biology, Sequence Alignment||
 
 
|}
 
|}
  

Revision as of 04:05, 29 June 2012

The following is a list of the installed software at the UF HPC Center.

Last updated 2012-06-29.

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

Software

Name Version Website Category EL5 [1] EL6[2]
Abaqus 6.6-1, 6.9-2 [1] Simulation X
Abyss 1.3.1 [2] Biology, NGS X
ADMB 9.1, 10.0, 10.1 [3] Modeling, math X
ALLPATHS-LG 39099, 40122, 41655 [4] Biology, NGS X
Amber 10,11.old, 11, 12 [5] Simulation, chemistry X
Amos 3.0.0 [6] Biology, Genomics X
ANNOVAR 20120308 [7] Biology, Genomics X
Ansys 9.0, 10.0 [8] Simulation, Engineering X
antlr 2.7.7, 3.1.3 [9] Linguistics, Parser X
arachne 37618 [10] Biology, Genomics X
Bamtools 2.1.0 [11] Biology, NGS X
BamUtil 1.0.2 [12] Biology, NGS X
BayesPhylogenies 2.0 [13] Biology, Phylogenetics X
beast 1.6.2, 1.7.0, 1.7.1 [14] Biology, Phylogenetics X
BEDTools 2.16.2 [15] Biology, NGS X
BFAST 0.7.0 [16] Biology, NGS X
Bioconductor 2011-11-16 [17] Biology, R, Statistics X
BioPerl 1.006901 [18] Biology, Perl X
Biopython 1.59 [19] Biology, Python X
bioscope 1.0.1, 1.2.1 ABI Biology, NGS X
Blast 2.2.24, 2.2.25, 2.2.26 [20] Biology, Sequence alignment X
Blast2go 2.5.0 [21] Biology, Annotation X
BLAT 34 [22] Biology, Sequence alignment X
Boost 1.38.0, 1.46.1, 1.48.0, 1.49.0 [23] C++, Library X
bwa 0.5.9, 0.5.10, 0.6.0 (default) [24] Biology, NGS X
Bowtie 0.12.7, 0.12.8 (default), 2.0.0-beta3, 2.0.0-beta5 [25] Biology, NGS X
BreakDancer 1.1 [26] Biology, NGS, Genomics X
CAP3 20071015 [27] Biology, sequence assembly X
CASAVA 1.8.2 [28] Biology, NGS X
CD-HIT 4.5.7 [29] Biology, Genomics X
CEGMA 2.3 [30] Biology, Genomics, Annotation X
CGATools 1.5.0.31 [31] Biology, Genomics X
Charmm 35b2 [32] Simulation, Chemistry X
Circuit 3.5.1, 3.5.7 [33] GIS X
CisGenome 2.0 [34] Biology, Genomics, Peak Calling X
CMake 2.8.5 [35] Programming X
CNV-seq 07.15.11 [36] Biology, NGS X
CNVnator 0.2.5 [37] Biology, NGS X
CPMD 3.11.1 [38] Simulation, Chemistry X
Cufflinks 1.0.3, 1.1.0, 1.3.0 [39] Biology, NGS X
Cutadapt 1.1 [40] Biology, NGS X
dar 2.3.9 [41] Backup X
deFuse 0.4.3 [42] Biology, RNA-seq X
Desmond 2.4.2.1 [43] Simulation, Biology, Chemistry X
Dindel 1.01 [44] Biology, NGS, Genomics X
dlpoly 3.0.9 [45] Simulation, Biology, Chemistry X
dock 6.3, 6.4, 6.5 [46] Chemistry, ligand binding prediction X
emacs 21.4.1, 23.4.1 [47] The Emacs editor X
EMAN2 2.04 [48] Biology, image processing X
emboss 6.4.0 [49] Biology, multi-tool suite X
espresso 3.0, 3.2.2, 4.0.4, 5.0 [50] Modeling, Physics X
Exonerate 2.2 [51] Biology, Genomics X
FAR 2.15 [52] Biology, Genomics X
FASTA 34.26.5 [53] Biology, Genomics X
fastx_toolkit 0.0.13.1 [54] Biology, NGS X
FastQC 0.9.6, 0.10.0 [55] Biology, NGS X
fftw 2.1.5, 3.1.2 [56] Math, Library, C++ X
fluent 6.3.26 [57] Simulation X
FragGeneScan 1.16 [58] Biology, NGS X
FreeBayes 0.9.4 [59] Biology X
gadget 2.0.4, 2.0.5 [60] Software Development X
gamess 11-Aug11 [61] Quantum Chemistry X
garli 2.0 [62] Biology, Phylogenetics X
GATK 1.4.30 [63] Biology, NGS X
gulp 4.0.3 [64] Modeling/simulation, Chemistry X
gaussian E01, G03, G09-A.02, G09-C.01 [65] Modeling, Computational Chemistry X
Geneid 1.4 [66] Biology, Genomics, Annotation X
GeneMark 2012.04 [67] Biology, Genomics, Metagenomics X
Genewise 2.2.3 [68] Biology, Genomics, Annotation X
GMAP 20070928, 20120524, 20120612 [69] Biology, Genomics X
Grace 5.1.22 [70] Graphics, plotting, 2D X
Gromacs 4.0.4, 4.0.7 [71] Physics, Modeling X
HDF5 1.8.7, 1.8.8 [72] Library, Data X
HMMER3 3.0 [73] Biology, Genomics X
HTSeq 0.5.3p3 [74] Biology, NGS X
HugeSeq 1.0.1 [75] Biology, NGS, Genomics X
hypre 2.8.0 [76] Library, Math, Physics X
IM and IMa 2009.12.17 [77] Biology, Population X
IMa2 8.26.11 [78] Biology, Population X
Inelastica 1.1 (python/2.7.2) [79] Quantum Chemistry X
IE3D 15.1 [80] Simulation, Design X
JDK 1.6.0_12, 1.7.0 [81] Java Development Kit X
Khmer 20120321 [82] Biology, NGS, Utilities X
Kmer r1909 [83] Biology, NGS, genome alignment X
lammps 17-Sept11 [84] Simulation X
Last 193 [85] Biology, Sequence alignment X
libxc 1.1.0 [86] Math, funtionals X
MACS 1.4.1 [87] Biology, ChIP-Seq X
madness 1769 [88] Math, DIff. Equation solving X
mafft 6.859 [89] Biology, Multiple sequence alignment X
Maker 2.10 [90] Biology, Annotation, Genomics X
MapSplice 1.15.2 [91] Biology, Genomics X
Matlab 2009b [92] Math, Simulation, Programming X
MATS 2.1.0 [93] BIology, NGS X
Mauve 2.3.1 [94] Biology, Multiple genome alignments X
MCL 11-335 [95] Biology, Genomics, Clustering X
meme 3.0.13, 4.3.0 [96] Biology, Motifs, Sequence analysis X
MetaPhyler 1.13 [97] Biology, Metagenomics X
metis 4.0 [98] Math, Graph partitioning X
Migrate-n 3.2.16 [99] Biology, Population X
mira 3.2.0, 3.4.0.1 [100] Biology, NGS X
mosaik 1.1.0021 [101] Biology,NGS X
MPIBlast 1.6.0 [102] Biology, Sequence alignment X
MrBayes 3.1.2,3.2.1 [103] Biology, Phylogenetics X
MUMmer 3.22 [104] Biology, Genomics X
MUSCLE 3.8.31 [105] Biology, Genomics X
NAMD 2.7b2 [106] Simulation, Chemistry, Biology X
NCO 4.0.9 [107] Data exchange tools X
netcdf 3.6.3, 4.1.2, 4.1.3 [108] Data exchange, Tools X
NetLogo 4.1.3 [109] Modeling X
Newbler 2.5.3, 2.6 [110] Biology, NGS X
NFFT 3.1.3 [111] NDFT, library, math X
Novoalign 2.07.15 [112] Biology, NGS X
NWChem 6.0 [113] Simulation, Chemistry X
Oases 0.2.04 [114] Biology, NGS X
OpenFOAM 1.7.1 [115] Molecular Dynamics X
OrthoMCL 2.0 [116] Biology, Genomics X
PAL2NAL 14 [117] Biology, Genomics X
PAML 4.4e [118] Biology, Phylogenetics X
PAPI 4.1.2.1 [119] CPU API X
PASA 20110520 [120] Biology, Genomics X
PeakSplitter 1.0 [121] Biology, Chip-Seq X
PDT 3.16 [122] Programming, Profiler X
Perl 5.14.1 [123] Programming, Language X
PETSc 2.3.3-p8, 3.0.0-p12 [124] MPI toolkit X
Phred 020425 [125] Biology, Genomics, Sequencing X
PhyloBayes 3.3b [126] Biology, Phylogenetics X
PhyML 3.0 [127] Biology, Phylogenetics X
Picard 1.54 [128] Biology, NGS X
Pindel 0.2.8 [129] Biology, NGS X
PQS 3.3-19 [130] Modeling, Chemistry X
Prinseq 0.17 [131] Biology, NGS X
PyOpenCL 2012.04 [132] python, parallel programming X
python 2.6.5, 2.7.2, 2.7.3 [133] Programming, scripting, language X X
R 2.14.1, 2.14.1-MPI, 2.14.2 [134] Statistics, Programming X X
RAxML 7.3.0 [135] Biology, Phylogenetics X
RAxML-Light 1.0.5 [136] Biology, Phylogenetics X
RepeatMasker 3.3.0 [137] Biology, Genomics X
Reptile 1.1, 1.1-omp [138] Biology, NGS, error correction X
riboPicker 0.4.2 [139] Biology, Sequence X
Rosetta 2.1.1, 2.1.2 [140] Biology, Structural, Modeling X
Ruby 1.9.3 [141] Programming, Language, Scripting X
RSMToolkit 2961 [142] Math, Modeling, Geometry X
samtools 0.1.16, 0.1.18 [143] Biology, NGS X X
SAS 9.2, 9.3 [144] Statistics, Graphing X X
SATe 2.1.0 [145] Biology, Phylogenetics X
Scala 2.9.1 [146] Programming, language, java X
Segminator 0.0.2 [147] Biology, NGS X
SeqPrep 0.4 [148] Biology, NGS X
Siesta 2.0, 2.0.2, 3.0b [149] Simulation, physics, ab-initio X
SOAPdenovo 1.05 [150] Biology, NGS X
SPARTA+ 2.60 [151] Chemistry X
SRA 2.1.7 [152]] biology, NGS X X
SRNAPredict 3.0 [153] Biology, Genomics X
SRNAScanner 200903 [154] Biology, Genomics X
Staden 2.0.0b9 [155] Biology, Genomics, Sequencing X X
Stata 10 [156] Statistics, Data analysis X
Structure 2.3.3 [157] Biology, Population X
TAU 2.20.1 [158] Profiling, Tracing, Programming X
tgicl 2.1 [159] Biology, sequencing, clustering X
TRF 4.04 [160] Biology, Genomics X
Trimal 1.2 [161] Biology, NGS X
Trinity r20120125, r20120317, r20120608 [162] Biology, RNA-Seq X
Tophat 1.3.0, 1.3.3, 1.4.1 [163] Biology, NGS X
tuxedo The "tuxedo suite" - Bowtie, Tophat, and Cufflinks X
Twinscan 3.5,4.1.2 [164] Biology, Genomics X
usearch 5.0.151,5.1.221 [165] Biology, Sequence analysis X
VASP 4.6.34,5.2.0 [166] Quantum Chemistry, ab initio X
VCFtools 0.1.7, 0.1.9 [167] Biology, SNPs X
velvet 1.2.06,1.2.02,1.2.01,1.1.05 [168] Biology, NGS X X
vmd 1.9 [169] Biology, Visualization X
weka 3.6.2 [170] Data mining algorithms X
wgs 6.1, 6.1-20110830 [171] Biology,Assembler,Genome X
wublast 2.0 [172] Biology, Sequence Alignment X
  1. ↑ Operating system: CentOS 5 - currently in production at UF HPC
  2. ↑ Operating system: RedHat Enterprise Linux 6 - scheduled for production at UF HPC for the Fall of 2012. EL5 software we provide will not be automatically installed on EL6. Please file a Support Request Ticket for EL6 software installation.

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

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