Difference between revisions of "Installed Software"

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[[Category:Software]]
 
[[Category:Software]]
 
* Last updated on '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''.
 
* Last updated on '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''.
−
* Usually one to three latest versions are listed. See output of 'module spider $module' for a full list of provided modules.
+
* Up to three latest versions are listed. The default is shown in '''bold''' if it's not the latest version.
 +
* See output of 'module spider '''module_name'''' for a full list of provided versions.
  
 
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
 
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
Line 14: Line 15:
 
| <span id="A"></span> [[AbInit]] || 6.12.3, '''7.10.2''' || [http://www.abinit.org/] || Ab Initio Quantum Chemistry, Density Functional Theory
 
| <span id="A"></span> [[AbInit]] || 6.12.3, '''7.10.2''' || [http://www.abinit.org/] || Ab Initio Quantum Chemistry, Density Functional Theory
 
|-
 
|-
−
| [[Abyss]] || 1.3.4, '''1.3.7''' || [http://www.bcgsc.ca/platform/bioinfo/software/abyss] || Biology, NGS
+
| [[Abyss]] || 1.3.4, 1.3.7 || [http://www.bcgsc.ca/platform/bioinfo/software/abyss] || Biology, NGS
 
|-
 
|-
 
| [[AFNI]] || 2011_12_21_1014 || [http://afni.nimh.nih.gov/afni] || Biology, Statistics, Imaging, Neurology
 
| [[AFNI]] || 2011_12_21_1014 || [http://afni.nimh.nih.gov/afni] || Biology, Statistics, Imaging, Neurology
Line 26: Line 27:
 
| [[AMOS]] || 3.1.0 || [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS] || Biology, Genomics, NGS
 
| [[AMOS]] || 3.1.0 || [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS] || Biology, Genomics, NGS
 
|-
 
|-
−
| [[ANNOVAR]] || 20120621,20121023,'''20130321''' || [http://www.openbioinformatics.org/annovar/] || Biology, Genomics
+
| [[ANNOVAR]] || 20120621,20121023,'''20130321 || [http://www.openbioinformatics.org/annovar/] || Biology, Genomics
 
|-
 
|-
 
| [[Atlas]] || 3.10.1, 3.11.17 || [http://www.gnu.org/software/gsl] || Library, Math
 
| [[Atlas]] || 3.10.1, 3.11.17 || [http://www.gnu.org/software/gsl] || Library, Math
Line 72: Line 73:
 
| [[BFAST]] || 0.7.0 || [http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page] || Biology, NGS
 
| [[BFAST]] || 0.7.0 || [http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page] || Biology, NGS
 
|-
 
|-
−
| [[Bismark]] || 0.7.4, 0.7.7, '''0.13.0''' || [http://www.bioinformatics.babraham.ac.uk/projects/download.html#bismark] || Biology, NGS, Methylation
+
| [[Bismark]] || 0.7.4, 0.7.7, 0.13.0 || [http://www.bioinformatics.babraham.ac.uk/projects/download.html#bismark] || Biology, NGS, Methylation
 
|-
 
|-
 
| [[Bioconductor]] || Latest || [http://www.bioconductor.org/] || Biology, R, Statistics
 
| [[Bioconductor]] || Latest || [http://www.bioconductor.org/] || Biology, R, Statistics
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| [[BLASR]] || 20130815 || [https://github.com/PacificBiosciences/blasr] || Biology, NGS
 
| [[BLASR]] || 20130815 || [https://github.com/PacificBiosciences/blasr] || Biology, NGS
 
|-
 
|-
−
| [[Blast|NCBI BLAST]] || 2.2.27, 2.2.28, '''2.2.29''' || [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download ] || Biology, Sequence alignment
+
| [[Blast|NCBI BLAST]] || 2.2.27, 2.2.28, 2.2.29 || [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download ] || Biology, Sequence alignment
 
|-
 
|-
 
| [[Blast2go]] || 2.5.0-20120705 || [http://www.blast2go.com/b2ghome] || Biology, Annotation
 
| [[Blast2go]] || 2.5.0-20120705 || [http://www.blast2go.com/b2ghome] || Biology, Annotation
Line 94: Line 95:
 
| [[Blender]] || 2.63 || [http://www.blender.org/] || Graphics
 
| [[Blender]] || 2.63 || [http://www.blender.org/] || Graphics
 
|-
 
|-
−
| [[Boost]] || 1.49.0, 1.53.0, '''1.54.0''' || [http://www.boost.org/] || C++, Library
+
| [[Boost]] || 1.49.0, 1.53.0, 1.54.0 || [http://www.boost.org/] || C++, Library
 
|-
 
|-
−
| [[Bowtie]] || 0.12.9, '''1.0.0''' || [http://bowtie-bio.sourceforge.net/index.shtml] || Biology, NGS
+
| [[Bowtie]] || 0.12.9, 1.0.0, 1.1.1 || [http://bowtie-bio.sourceforge.net/index.shtml] || Biology, NGS
 
|-
 
|-
−
| [[Bowtie2]] || 2.1.0, 2.2.2, 2.2.3, '''2.2.4''' || [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml] || Biology, NGS
+
| [[Bowtie2]] || 2.2.2, 2.2.3, 2.2.4 || [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml] || Biology, NGS
 
|-
 
|-
 
| [[BPP]] || 2.2, 1.9.0 || [http://abacus.gene.ucl.ac.uk/software.html] || Biology, Phylogenetics
 
| [[BPP]] || 2.2, 1.9.0 || [http://abacus.gene.ucl.ac.uk/software.html] || Biology, Phylogenetics
Line 104: Line 105:
 
| [[BRANCH]] || 1.8.1 || [http://manuals.bioinformatics.ucr.edu/home/branch] || Biology, NGS, Mapping
 
| [[BRANCH]] || 1.8.1 || [http://manuals.bioinformatics.ucr.edu/home/branch] || Biology, NGS, Mapping
 
|-
 
|-
−
| [[Bsmap]] || 2.74, '''2.87''' || [https://code.google.com/p/bsmap/] || Biology, NGS, Methylation
+
| [[Bsmap]] || 2.74, 2.87 || [https://code.google.com/p/bsmap/] || Biology, NGS, Methylation
 
|-
 
|-
 
| [[Bwa]] || 0.6.1, 0.7.11, 0.7.12 || [http://bio-bwa.sourceforge.net/] || Biology, NGS
 
| [[Bwa]] || 0.6.1, 0.7.11, 0.7.12 || [http://bio-bwa.sourceforge.net/] || Biology, NGS
Line 170: Line 171:
 
| [[Crux]] || 1.40 || [http://cruxtoolkit.sourceforge.net/] || Biology, Mass-Spectrometry
 
| [[Crux]] || 1.40 || [http://cruxtoolkit.sourceforge.net/] || Biology, Mass-Spectrometry
 
|-
 
|-
−
| [[Cufflinks|Cufflinks]] || 1.3.0, 2.0.2, '''2.2.1''' || [http://cufflinks.cbcb.umd.edu/] || Biology, NGS
+
| [[Cufflinks|Cufflinks]] || 1.3.0, 2.0.2, 2.2.1 || [http://cufflinks.cbcb.umd.edu/] || Biology, NGS
 
|-
 
|-
 
| [[Cutadapt]] || 1.1, 1.7.1 || [http://code.google.com/p/cutadapt/] || Biology, NGS
 
| [[Cutadapt]] || 1.1, 1.7.1 || [http://code.google.com/p/cutadapt/] || Biology, NGS
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| [[EEGLAB]] || 12.0.2.1b || [http://sccn.ucsd.edu/wiki/EEGLAB] || Biology, Matlab
 
| [[EEGLAB]] || 12.0.2.1b || [http://sccn.ucsd.edu/wiki/EEGLAB] || Biology, Matlab
 
|-
 
|-
−
| [[EIGENSOFT]] || 4.2, '''5.0.1''' || [http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html] || Biology, Population
+
| [[EIGENSOFT]] || 4.2, 5.0.1 || [http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html] || Biology, Population
 
|-
 
|-
 
| [[emboss]] || 6.5.7 || [http://emboss.sourceforge.net/] || Biology, multi-tool suite
 
| [[emboss]] || 6.5.7 || [http://emboss.sourceforge.net/] || Biology, multi-tool suite
Line 252: Line 253:
 
| <span id="F"></span> [[FAR]] || 2.15 || [http://sourceforge.net/apps/mediawiki/theflexibleadap/index.php?title=Main_Page] || Biology, Genomics
 
| <span id="F"></span> [[FAR]] || 2.15 || [http://sourceforge.net/apps/mediawiki/theflexibleadap/index.php?title=Main_Page] || Biology, Genomics
 
|-
 
|-
−
| [[FASTA]] || 34.26.5, '''36.3.6d''' || [http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml] || Biology, Genomics
+
| [[FASTA]] || 34.26.5, 36.3.6d || [http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml] || Biology, Genomics
 
|-
 
|-
 
| [[FastML]] || 3.0 || [http://fastml.tau.ac.il/overview.php] || Biology, Phylogenetics, ML
 
| [[FastML]] || 3.0 || [http://fastml.tau.ac.il/overview.php] || Biology, Phylogenetics, ML
Line 364: Line 365:
 
| [[HTMLDoc]] || 1.2.82 || [http://www.msweet.org/projects.php?Z1] || Documentation, PDF, HTML
 
| [[HTMLDoc]] || 1.2.82 || [http://www.msweet.org/projects.php?Z1] || Documentation, PDF, HTML
 
|-
 
|-
−
| [[HTSeq]] || 0.5.3p3, '''0.6.1p1''' || [http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html] || Biology, NGS
+
| [[HTSeq]] || 0.5.3p3, 0.6.1p1 || [http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html] || Biology, NGS
 
|-
 
|-
 
| [[HyPhy]] || 2.1.2.28 || [http://www.datam0nk3y.org/hyphywiki/index.php/Main_Page] || Biology, Phylogenetics
 
| [[HyPhy]] || 2.1.2.28 || [http://www.datam0nk3y.org/hyphywiki/index.php/Main_Page] || Biology, Phylogenetics
Line 422: Line 423:
 
| [[LIBSVM]] || 3.12 || [http://www.csie.ntu.edu.tw/~cjlin/libsvm/] || Machine Learning
 
| [[LIBSVM]] || 3.12 || [http://www.csie.ntu.edu.tw/~cjlin/libsvm/] || Machine Learning
 
|-
 
|-
−
| [[LSC]] || 0.3, '''0.3.1''' || [http://www.stanford.edu/~kinfai/LSC/LSC.html] || Biology, NGS, Error correction
+
| [[LSC]] || 0.3, 0.3.1 || [http://www.stanford.edu/~kinfai/LSC/LSC.html] || Biology, NGS, Error correction
 
|-
 
|-
 
| [[Loci]] || 3.3 || [http://www.tetraresearch.com/locichem/about-locichem/] || Fluid Dynamics
 
| [[Loci]] || 3.3 || [http://www.tetraresearch.com/locichem/about-locichem/] || Fluid Dynamics
 
|-
 
|-
−
| [[LS-DYNA]] || 700, '''711''' || [http://www.lstc.com/products/ls-dyna] || Physics
+
| [[LS-DYNA]] || 700, 711 || [http://www.lstc.com/products/ls-dyna] || Physics
 
|-
 
|-
 
| [[Lumpy]] || 0.2.1 || [https://github.com/timflutre/eqtlbma] || Biology, SNP
 
| [[Lumpy]] || 0.2.1 || [https://github.com/timflutre/eqtlbma] || Biology, SNP
Line 488: Line 489:
 
| [[Migrate-n]] || 3.3.0 || [http://popgen.sc.fsu.edu/Migrate/Migrate-n.html] || Biology, Population
 
| [[Migrate-n]] || 3.3.0 || [http://popgen.sc.fsu.edu/Migrate/Migrate-n.html] || Biology, Population
 
|-
 
|-
−
| [[mira]] || 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, '''4.0.rc1''' || [http://mira-assembler.sourceforge.net/]||Biology, NGS
+
| [[mira]] || 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 || [http://mira-assembler.sourceforge.net/]||Biology, NGS
 
|-
 
|-
−
| [[MISO]] || 0.4.4, '''0.4.9''' || [http://genes.mit.edu/burgelab/miso/] || Biology, NGS
+
| [[MISO]] || 0.4.4, 0.4.9 || [http://genes.mit.edu/burgelab/miso/] || Biology, NGS
 
|-
 
|-
 
| [[MMSEQ]] || 1.0.8 || [https://github.com/eturro/mmseq] || Biology, NGS
 
| [[MMSEQ]] || 1.0.8 || [https://github.com/eturro/mmseq] || Biology, NGS
Line 498: Line 499:
 
| [[MOABS]] || 1.2.9 || [https://code.google.com/p/moabs/] || Biology, NGS, Genomics
 
| [[MOABS]] || 1.2.9 || [https://code.google.com/p/moabs/] || Biology, NGS, Genomics
 
|-
 
|-
−
| [[Modeller]] || 9.11, 9.13, '''9.14''' || [http://salilab.org/modeller] || Biology, Modeling
+
| [[Modeller]] || 9.11, 9.13, 9.14 || [http://salilab.org/modeller] || Biology, Modeling
 
|-
 
|-
 
| [[Molden]] || 5.0 || [http://www.cmbi.ru.nl/molden/] || Molecular, electronic structure
 
| [[Molden]] || 5.0 || [http://www.cmbi.ru.nl/molden/] || Molecular, electronic structure
Line 532: Line 533:
 
| [[NCL]] || 6.1.2 || [http://www.ncl.ucar.edu] || Atmosphere Science
 
| [[NCL]] || 6.1.2 || [http://www.ncl.ucar.edu] || Atmosphere Science
 
|-
 
|-
−
| [[NCO]] || 4.2.1, '''4.4.3'''|| [http://nco.sourceforge.net/] || Data exchange tools
+
| [[NCO]] || 4.2.1, 4.4.3 || [http://nco.sourceforge.net/] || Data exchange tools
 
|-
 
|-
 
| [[Ncview]] || 2.1.2 || [http://meteora.ucsd.edu/~pierce/ncview_home_page.html] || Data visualization
 
| [[Ncview]] || 2.1.2 || [http://meteora.ucsd.edu/~pierce/ncview_home_page.html] || Data visualization
Line 556: Line 557:
 
| <span id="O"></span> [[Oases]] || 0.2.08 || [http://www.ebi.ac.uk/~zerbino/oases/] || Biology, NGS
 
| <span id="O"></span> [[Oases]] || 0.2.08 || [http://www.ebi.ac.uk/~zerbino/oases/] || Biology, NGS
 
|-
 
|-
−
| [[Olego]] || 1.1.2, '''1.1.5''' || [http://zhanglab.c2b2.columbia.edu/index.php/OLego_Documentation] || Biology, NGS, RNA-Seq
+
| [[Olego]] || 1.1.2, 1.1.5 || [http://zhanglab.c2b2.columbia.edu/index.php/OLego_Documentation] || Biology, NGS, RNA-Seq
 
|-
 
|-
 
| [[Octave]] || 3.6.4 || [http://www.gnu.org/software/octave/]|| Numerical Computation
 
| [[Octave]] || 3.6.4 || [http://www.gnu.org/software/octave/]|| Numerical Computation
Line 570: Line 571:
 
| [[OpenMM]] || 6.2.0 || [https://simtk.org/home/openmm]||Quantum Chemistry
 
| [[OpenMM]] || 6.2.0 || [https://simtk.org/home/openmm]||Quantum Chemistry
 
|-
 
|-
−
| [[OrthoMCL]] || 2.0.2, 2.0.3, '''2.0.7''' || [http://orthomcl.org/]|| Biology, Genomics
+
| [[OrthoMCL]] || 2.0.2, 2.0.3, 2.0.7 || [http://orthomcl.org/]|| Biology, Genomics
 
|-
 
|-
 
| [[p4vasp]] || 0.3.29 || [http://www.p4vasp.at/] || Molecular, Electronic Structure
 
| [[p4vasp]] || 0.3.29 || [http://www.p4vasp.at/] || Molecular, Electronic Structure
Line 592: Line 593:
 
| [[Parflow]] || v615 || [https://computation.llnl.gov/casc/parflow/parflow_home.html] || Ecology, Modeling
 
| [[Parflow]] || v615 || [https://computation.llnl.gov/casc/parflow/parflow_home.html] || Ecology, Modeling
 
|-
 
|-
−
| [[PASA]] || 1.5, 2.0-r20130605p1, '''2.0-r20130907''' || [http://http://pasa.sourceforge.net/]|| Biology, Genomics
+
| [[PASA]] || 1.5, 2.0-r20140714, 2.0-r20150209 || [http://http://pasa.sourceforge.net/]|| Biology, Genomics
 
|-
 
|-
 
| [[PAUP]] || 4.0b10 || [http://paup.csit.fsu.edu/] || Biology, Phylogenetics
 
| [[PAUP]] || 4.0b10 || [http://paup.csit.fsu.edu/] || Biology, Phylogenetics
Line 662: Line 663:
 
| [[Quickquartet]] || 1.0.0 || [https://code.google.com/p/quickquartet/] || Biology, Phylogenetics
 
| [[Quickquartet]] || 1.0.0 || [https://code.google.com/p/quickquartet/] || Biology, Phylogenetics
 
|-
 
|-
−
| <span id="R"></span> [[R]] || 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0, 3.0.1, 3.0.2 || [http://www.r-project.org/] || Statistics, Programming
+
| <span id="R"></span> [[R]] || Rmpi/2.15.1, 33.0.2 || [http://www.r-project.org/] || Statistics, Programming
 
|-
 
|-
 
| [[R8S]] || 1.71 || [http://loco.biosci.arizona.edu/r8s/] || Biology, Evolution
 
| [[R8S]] || 1.71 || [http://loco.biosci.arizona.edu/r8s/] || Biology, Evolution
Line 668: Line 669:
 
| [[RADICAL]] || 0.2 || [http://desalle.amnh.org/software.html] || Biology, Phylogenetics, Genomics
 
| [[RADICAL]] || 0.2 || [http://desalle.amnh.org/software.html] || Biology, Phylogenetics, Genomics
 
|-
 
|-
−
| [[RAxML]] || 7.9.1, 8.0.25, '''8.1.12''' || [http://sco.h-its.org/exelixis/software.html] || Biology, Phylogenetics
+
| [[RAxML]] || 7.9.1, 8.0.25, 8.1.12 || [http://sco.h-its.org/exelixis/software.html] || Biology, Phylogenetics
 
|-
 
|-
 
| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/] || Biology, Genomics
 
| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/] || Biology, Genomics
Line 696: Line 697:
 
| [[Samblaster]] || 0.1.14 || [https://github.com/GregoryFaust/samblaster] || Biology, NGS
 
| [[Samblaster]] || 0.1.14 || [https://github.com/GregoryFaust/samblaster] || Biology, NGS
 
|-
 
|-
−
| [[samtools]] || 0.1.16, 0.1.18, '''0.1.19''', 1.0, 1.1, 1.2 || [http://samtools.sourceforge.net/] || Biology, NGS
+
| [[samtools]] || 1.0, 1.1, 1.2 || [http://samtools.sourceforge.net/] || Biology, NGS
 
|-
 
|-
 
| [[SAS]] || 9.3 || [http://www.sas.com] || Statistics, Graphing
 
| [[SAS]] || 9.3 || [http://www.sas.com] || Statistics, Graphing
Line 758: Line 759:
 
| [[SparCC]] || 201402 || [https://bitbucket.org/yonatanf/sparcc/overview] || Microbial Ecology
 
| [[SparCC]] || 201402 || [https://bitbucket.org/yonatanf/sparcc/overview] || Microbial Ecology
 
|-
 
|-
−
| [[Spades]] || 2.5.0, 2.5.1, 3.0.0, 3.1.0, '''3.5.0''' || [http://bioinf.spbau.ru/en/spades] || Biology, NGS
+
| [[Spades]] || 3.0.0, 3.1.0, 3.5.0 || [http://bioinf.spbau.ru/en/spades] || Biology, NGS
 
|-
 
|-
−
| [[Spanki]] || 0.4.1, '''0.4.3''' || [http://www.cbcb.umd.edu/software/spanki/] || Biology, NGS, RNA-Seq
+
| [[Spanki]] || 0.4.1, 0.4.3 || [http://www.cbcb.umd.edu/software/spanki/] || Biology, NGS, RNA-Seq
 
|-
 
|-
 
| [[SPARTA+]] || 2.60 || [http://spin.niddk.nih.gov/bax/software/SPARTA+/]||Chemistry
 
| [[SPARTA+]] || 2.60 || [http://spin.niddk.nih.gov/bax/software/SPARTA+/]||Chemistry
Line 784: Line 785:
 
| [[STAR-CCM+]] || 8.06 || [http://wiki.hpc.ufl.edu/doc/STAR-CCM+]||Mechanical Engineering
 
| [[STAR-CCM+]] || 8.06 || [http://wiki.hpc.ufl.edu/doc/STAR-CCM+]||Mechanical Engineering
 
|-
 
|-
−
| [[Stata]] || 10.1, '''13''' || [http://www.stata.com/]||Statistics, Data analysis
+
| [[Stata]] || 10.1, 13 || [http://www.stata.com/]||Statistics, Data analysis
 
|-
 
|-
 
| [[Stringtie]] || 0.97 || [http://ccb.jhu.edu/software/stringtie/] || Biology, NGS, Alignment
 
| [[Stringtie]] || 0.97 || [http://ccb.jhu.edu/software/stringtie/] || Biology, NGS, Alignment
 
|-
 
|-
−
| [[Structure]] || 2.3.3, '''2.3.4''' || [http://pritch.bsd.uchicago.edu/structure_software/release_versions/v2.3.3/html/structure.html]|| Biology, Population
+
| [[Structure]] || 2.3.3, 2.3.4 || [http://pritch.bsd.uchicago.edu/structure_software/release_versions/v2.3.3/html/structure.html]|| Biology, Population
 
|-
 
|-
−
| [[SUNDIALS]] || 2.3.0, '''2.5.0''' || [https://computation.llnl.gov/casc/sundials/main.html] || Numerical Solver
+
| [[SUNDIALS]] || 2.3.0, 2.5.0 || [https://computation.llnl.gov/casc/sundials/main.html] || Numerical Solver
 
|-
 
|-
 
| [[SVDetect]] || 0.8b || [http://svdetect.sourceforge.net/Site/Home.html] || Biology, NGS, SNP
 
| [[SVDetect]] || 0.8b || [http://svdetect.sourceforge.net/Site/Home.html] || Biology, NGS, SNP
Line 816: Line 817:
 
| [[TomoPy]] || 0.0.3 || [https://github.com/tomopy/tomopy] || Biology, Neuroimaging
 
| [[TomoPy]] || 0.0.3 || [https://github.com/tomopy/tomopy] || Biology, Neuroimaging
 
|-
 
|-
−
| [[Tophat]] || 1.4.1, '''2.0.13''' || [http://tophat.cbcb.umd.edu/] || Biology, NGS
+
| [[Tophat]] || 1.4.1, 2.0.13 || [http://tophat.cbcb.umd.edu/] || Biology, NGS
 
|-
 
|-
 
| [[Totalview]] || 8.12.0 || [http://www.roguewave.com/products/totalview.aspx] || Computer Science
 
| [[Totalview]] || 8.12.0 || [http://www.roguewave.com/products/totalview.aspx] || Computer Science
Line 856: Line 857:
 
| <span id="V"></span> [[Valgrind]] || 3.9.0 || [http://valgrind.org] || Computer Science
 
| <span id="V"></span> [[Valgrind]] || 3.9.0 || [http://valgrind.org] || Computer Science
 
|-
 
|-
−
| [[VASP]] || 4.6.34, 5.2.12, 5.3.2, 5.3.3, '''5.3.5''' || [http://cms.mpi.univie.ac.at/vasp/] || Quantum Chemistry, Ab Initio
+
| [[VASP]] || 5.3.2, 5.3.3, 5.3.5 || [http://cms.mpi.univie.ac.at/vasp/] || Quantum Chemistry, Ab Initio
 
|-
 
|-
 
| [[VarScan]] || 2.3.6 || [http://varscan.sourceforge.net/] || Biology, NGS, Genomics
 
| [[VarScan]] || 2.3.6 || [http://varscan.sourceforge.net/] || Biology, NGS, Genomics
Line 874: Line 875:
 
| [[VTK]] ||  6.1.0 || [http://www.vtk.org/] || Visualization, Graphics
 
| [[VTK]] ||  6.1.0 || [http://www.vtk.org/] || Visualization, Graphics
 
|-
 
|-
−
| <span id="W"></span> [[Wannier90]] || 1.2, '''2.0.0''' ||[http://www.wannier.org/index.html]||Computational Physics
+
| <span id="W"></span> [[Wannier90]] || 1.2, 2.0.0 ||[http://www.wannier.org/index.html]||Computational Physics
 
|-  
 
|-  
 
| [[WebLogo]] || 3.3 || [http://code.google.com/p/weblogo/] || Biology, Genomics
 
| [[WebLogo]] || 3.3 || [http://code.google.com/p/weblogo/] || Biology, Genomics

Revision as of 21:14, 6 March 2015

  • Last updated on 2015-03-06.
  • Up to three latest versions are listed. The default is shown in bold if it's not the latest version.
  • See output of 'module spider module_name' for a full list of provided versions.

0-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Name Version [1] Website Category
AbInit 6.12.3, 7.10.2 [1] Ab Initio Quantum Chemistry, Density Functional Theory
Abyss 1.3.4, 1.3.7 [2] Biology, NGS
AFNI 2011_12_21_1014 [3] Biology, Statistics, Imaging, Neurology
Agalma 0.2.1, 0.3.5, 0.5.0 [4] Biology, Bioinformatics, Genomics, SNP
ALLPATHS-LG 42316, 44837 [5] Biology, NGS
Amber 11, 12, 14 [6] Simulation, chemistry
AMOS 3.1.0 [7] Biology, Genomics, NGS
ANNOVAR 20120621,20121023,20130321 [8] Biology, Genomics
Atlas 3.10.1, 3.11.17 [9] Library, Math
Amuse 6.0 [10] Astrophysics
Affymetrix Power Tools 1.15.0 [11] Biology, Genomics, Microarray
ARC 20140312 [12] Biology, NGS
Astral 4.4.4, 4.7.6 [13] Biology, Bioinformatics, NGS, Phylogenetics
AtomEye 3 [14] Material Science
ATRAM 20140624 [15] Biology, NGS
Augustus 2.6 [16] Biology, NGS
BamBam 1.0 [17] Biology, NGS
Bamstats 20140602 [18] Biology, NGS
Bamtools 2.1.1 [19] Biology, NGS
BamUtil 1.0.2 [20] Biology, NGS
BayesRate 1.3.43 [21] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [22] Network file transfer
Bcftools 20140618 [23] Biology, Genomics, NGS
BEAGLE 3.2.2 [24] Biology, Genetics, Genotyping
BEAST 1.7.5, 1.8.1, 2.1.3 [25] Biology, Phylogenetics
Bedops 2.4.2 [26] Biology, Bioinformatics, Sequence, NGS
BEDTools 2.16.2, 2.17.0, 2.23.0 [27] Biology, NGS
BEST 2.3 [28] Biology, Phylogenetics
BETA 1.0.5 [29] Biology, NGS
BFAST 0.7.0 [30] Biology, NGS
Bismark 0.7.4, 0.7.7, 0.13.0 [31] Biology, NGS, Methylation
Bioconductor Latest [32] Biology, R, Statistics
BioPerl 1.006901 [33] Biology, Perl
PHYLDOG 20130418 [34] Biology, Genomics, Phylogenetics
Phyluce c561dd9 [35] Biology, Phylogenetics
BioPython 1.59 [36] Biology, Python
BLASR 20130815 [37] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [38] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [39] Biology, Annotation
BLAT 20120524 [40] Biology, Sequence alignment
Blender 2.63 [41] Graphics
Boost 1.49.0, 1.53.0, 1.54.0 [42] C++, Library
Bowtie 0.12.9, 1.0.0, 1.1.1 [43] Biology, NGS
Bowtie2 2.2.2, 2.2.3, 2.2.4 [44] Biology, NGS
BPP 2.2, 1.9.0 [45] Biology, Phylogenetics
BRANCH 1.8.1 [46] Biology, NGS, Mapping
Bsmap 2.74, 2.87 [47] Biology, NGS, Methylation
Bwa 0.6.1, 0.7.11, 0.7.12 [48] Biology, NGS
Camino 20140723 [49] Biology, Neuroscience, Imaging
CAP3 20120705 [50] Biology, sequence assembly
CASAVA 1.8.2 [51] Biology, NGS
CD-HIT 4.6 [52] Biology, Genomics
CDO 1.6.1 [53] Climate
CEAS 1.0.2 [54] Biology, Genomics
CellProfiler 2.0 [55] Biology, Image Analysis
CGATools 1.6.0.42 [56] Biology, NGS
Charmm 36a3 [57] Simulation, Chemistry
Chartdirector 5.1.0 [58] Graphics
Chimera 1.7 [59] Biology, Modeling
ChromEvol 2.0 [60] Biology, Phylogenetics
CIMS 4.1.2 [61] Biology, Genomics
Circos 0.63-pre11 [62] Biology, Visualization
CisGenome 2.0 [63] Biology, Genomics, Peak Calling
Clann 3.2.3 [64] Biology, Phylogenetics
CLHEP 2.2.0.1 [65] High Energy Physics
ClonalFrame 1.1, 1.2 [66] Biology, Genomics, NGS
ClustalW 2.1 [67] Biology, Genomics
Cluster3 1.52 [68]] Biology, Genomics
Clview 20130402 [69] Biology, Genomics
CMake 2.8.8, 2.9.12.1, 3.1.0 [70] Programming, Build System
CNVSeq 20110715 [71] Biology, NGS
Coevol 1.3c, 1.4b [72] Biology, Phylogenetics
CoMap 1.4.1 [73] Biology, Genomics
CONCOCT 0.3.1 [74] Biology, Genomics
Consed 23.0 [75] Biology, Genomics
Coreutils 8.23 [76] GNU Utilities, Computer Science
covNMR 2014 [77] Biochemistry
CUDA 4.2, 5.5 [78] Programming, Graphics
Crux 1.40 [79] Biology, Mass-Spectrometry
Cufflinks 1.3.0, 2.0.2, 2.2.1 [80] Biology, NGS
Cutadapt 1.1, 1.7.1 [81] Biology, NGS
DAKOTA 5.4.0 [82] Computational Science
DaPars 0.9.0 [83] Biology, NGS, RNA-Seq
DCMTK 3.6.0 [84] Biology, Neuroscience, Imaging
DSSAT 4.5 [85] Biology
DDSCAT 7.3.0 [86] Astrophysics
DDT 4.1.0, 4.2.1 [87] Software
Delft3D 3621 [88] Hydrodynamics, Physics
Desmond 3.0.3.1 [89] Simulation, Biology, Chemistry
Dalton 2011 [90] Quantum Chemistry
Diamond 0.5.1 [91] Computational Biology, Genomics
Dibig Tools 1.0 [92] Bioinformatics, PBS, Torque, Jobs
DiffReps 1.55.4 [93] Biology, NGS, ChIP-Seq
Dindel 1.01 [94] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [95] Biology, Genomics
Dlpoly 4.03.4 [96] Simulation, Biology, Chemistry
DNA Clust 3.0 [97] Biology, Genomics
Dock 6.5, 6.6 [98] Chemistry, ligand binding prediction
DOT 2.0 [99] Biology, Bioinformatics, Docking
Doxygen 1.8.3.1 [100] Programming, Documentation
DSSP 2.2.1 [101] Biology, Molecular Dynamics
DTI-TK 2.3.1 [102] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [103] Biology, NGS
ECTools 20140311, 20141201 [104] Biology, Sequencing, Bioinformatics
EEGLAB 12.0.2.1b [105] Biology, Matlab
EIGENSOFT 4.2, 5.0.1 [106] Biology, Population
emboss 6.5.7 [107] Biology, multi-tool suite
EMIRGE 20130727 [108] Biology, NGS
eQTLA 1.1 [109] Biology, Genomics
Eqtlbma 1.2.2 [110] Biology, Genotyping
Espresso 5.0.1 [111] Modeling, Physics
ESPRIT 201211 [112] Biology, NGS, Metagenomics
ETE2 2.1 [113] Biology, Phylogenetics
Eval 2.2.8 [114] Biology, Genomics, GUI
ExaBayes 1.2.1 [115] Biology, Phylogenetics
ExaML 1.0.3, 1.0.5, 1.0.12 [116] Biology, Phylogenetics
ExomeCNV 1.4 [117] Biology, NGS, Genomics
Exonerate 2.2.0 [118] Biology, Genomics
eXpress 1.3.1 [119] Biology, NGS
FAR 2.15 [120] Biology, Genomics
FASTA 34.26.5, 36.3.6d [121] Biology, Genomics
FastML 3.0 [122] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [123] Biology, NGS
FastTree 2.1.7 [124] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [125] Biology, NGS
fcGENE 1.0.7 [126] Biology, Genomics, SNP
Ferret 6.82 [127] Oceanography, Meteorology
FFmpeg 2.1.3 [128] Multimedia, audio, video
FFTW 3.3.2, 3.3.3 [129] Math, Library, C++
FLASH 1.2.10, 1.2.11 [130] Biology, Genomics, NGS
Flexbar 2.3 [131] Biology, Genomics, NGS
Fluent 14.5.7, 15.0 [132] Simulation, Fluid Dynamics
FragGeneScan 1.16 [133] Biology, NGS, Genomics
FreeBayes 0.9.6, 0.9.15 [134] Biology, NGS, SNP Calling
Freesurfer 5.2.0 [135] Biology, Neurology, Imaging
FSL 5.0.2.2 [136] Biology, Neurology, Imaging
GapFiller 1.11 [137] Biology, NGS
Garli 2.0, 2.01 [138] Biology, Phylogenetics
GASVPro 201310 [139] Biology, NGS, Genomics
GATE 7.0 [140] Data Analysis
GATK 1.6.9, 2.7.4, 3.1.1, 3.3.0 [141] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [142] Modeling, Computational Chemistry
Gblocks 0.91b [143] Genomics, Alignment tool
Geant4 4.10 [144] Physics
GEM 20130406 [145] Biology, NGS
GEMINI 4.6.6a [146] Biology, Genomics, Genetics
GenBank Tools 20140130 [147] BIology< Genomics
GeneMark 2012.04 [148] Biology, Genomics, Metagenomics
GeneSeqer 20140226 [149] Biology, Genomics
Genewise 2.2.0 [150] Biology, Genomics, Annotation
GenomicTools 2.7.0 [151] Biology, NGS
GenSel 4.90 [152] Biology, Genetics
GKNO 1.30.18 [153] Biology, NGS
Git 1.8.2.1 [154] Development, Revision Control
Globus 2.1.3 [155] Data Transfer
GLPK 4.55 [156] Biology, Genomics
Gmap 20141222 [157] Biology, Genomics
GNU 4.4.6, 4.7.2 [158] Compilers, Programming
GnuPlot 4.6.0 [159] Graphics, Plotting, Programming
Grace 5.1.22 [160] Graphics, plotting, 2D
GrADS 2.0.1 [161] Earth Science
GraphViz 2.38.0 [162] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5 [163] Chemistry, Modeling, Simulation
GSNP 1.0 [164] Biology, Bioinformatics, NGS
GSL 1.15 [165] Library, Math, C++, C
GULP 4.0 [166] Material Science
HaMStR v8b [167] Biology, Genomics
HapCompass 0.7.7 [168] Biology, NGS, Genomics
Hapsembler 2.21 [169] Biology, Genomics, NGS
HapTree 1.0 [170] Biology, Genomics, NGS
HDF4 4.2.11 [171] Library, Data
HDF5 1.8.9, 1.8.12 [172] Library, Data
HMMER3 3.0, 3.1b1 [173] Biology, Genomics
HMMSplicer 0.9.5 [174] Biology, Genomics
HOMER 4.2 [175] Biology, Genomics
HTMLDoc 1.2.82 [176] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [177] Biology, NGS
HyPhy 2.1.2.28 [178] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [179] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [180] Biology, NGS
iGTP 1.1 [181] Biology, Bioinformatics, Phylogenetics
IM and IMa 20091217 [182] Biology, Population
IMa2 20120827 [183] Biology, Population
ImageJ 1.48 [184] Image manipulation
ImageMagick 6.8.8-9 [185] Image manipulation
Intel Compilers 11.1, 2012 [186] Programming, Compilers
IOAPI 3.1 [187] Meteorology
Iprscan 4.8 [188] Biology, Genomics
ITK 4.3.1 [189] Biology, Genomics
ITK-SNAP 3.0.0 [190] Biology, Neuroscience, Imaging
JAGS 3.3.0 [191] Statistics
Java 1.6.0_31, 1.7.0_02, 1.8.0_31 [192] Java Development Kit
Jellyfish 2.1.1 [193] Biology, NGS
JModelTest 2.1.1. [194] Biology, Phylogenetics, Genomics
KaKs 1.2 [195] Biology, Phylogenetics
Kent 20120524 [196] Biology, NGS
Khmer 1.1 [197] Biology, NGS
KING 1.4 [198] Biology, Genomics
Kmer 1934 [199] Biology, NGS
KmerGenie 1.6741 [200] Biology, NGS, Utilities
Kraken 0.10.4b [201] Biology, Genomics, Phylogenetics
LAMMPS 28Oct12, 30Sep13, 28Jun14 [202] Molecular Dynamics Simulation
Last 193, 247 [203] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [204] Biology, NGS
LIBSVM 3.12 [205] Machine Learning
LSC 0.3, 0.3.1 [206] Biology, NGS, Error correction
Loci 3.3 [207] Fluid Dynamics
LS-DYNA 700, 711 [208] Physics
Lumpy 0.2.1 [209] Biology, SNP
MACH 1.0.18 [210] Biology, Genomics
M5tools 20121126 [211] Biology, Bioinformatics, Genomics
MACS 1.4.2 [212] Biology, ChIP-Seq
mafft 7.037, 6.903, 7.215 [213] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [214] Biology, Annotation, Genomics
MapSplice 2.1.7 [215] Biology, NGS, RNA-Seq
Maq 0.7.1 [216] Biology, NGS
MARK 2.0.1 [217] Statistics
MaSuRCA 2.3.2 [218] Biology, NGS
Matlab 2012a, 2013a, 2014a [219] Math, Simulation, Programming
MATS 2.1.0, 3.0.6b, 3.0.8, 3.0.9 [220] BIology, NGS
Mauve 2.3.1 [221] Biology, NGS
MCarts 1.0.2 [222] Biology, Genomics, Markov models
MCNP 5, 6b2 [223] Physics
MCNPX 2.7.0, 2.7.0-i8 [224] Physics
Melting 4.3.1 [225] Biology, Genome, RNA, Folding
Meme 4.8.1 [226] Biology, Motifs, Sequence analysis
Mercurial 2.7 [227] Development, Revision Control
Metabin 1.0 [228] Biology, Metagenomics
MetaCluster 5.0beta [229] Biology, Metagenomics
MetaCV 2.3.0 [230] Biology, NGS
METAL 20110325 [231] Biology, Genomics
MetAMOS 1.5.0rc4-20140827 [232] Biology, Bioinformatics, Genomics, Assembly
MetaVelvet 1.2.01 [233] Biology, NGS
MetaGeneMark 2012.04 [234] Biology, Genomics
Mfold 3.6 [235] Biology, Genomics
MIA 20130301 [236] Biology, NGS
Midnight Commander 4.6.1 [237] Tools, Utilities
Migrate-n 3.3.0 [238] Biology, Population
mira 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 [239] Biology, NGS
MISO 0.4.4, 0.4.9 [240] Biology, NGS
MMSEQ 1.0.8 [241] Biology, NGS
MSMBuilder 2.5.1 [242] Molecular Dynamics
MOABS 1.2.9 [243] Biology, NGS, Genomics
Modeller 9.11, 9.13, 9.14 [244] Biology, Modeling
Molden 5.0 [245] Molecular, electronic structure
MolPro 2012.1p22 [246] Quantum Chemistry, Ab Initio
mosaik 2.1.33 [247] Biology,NGS
Mothur 1.31.2 [248] Biology, Microbial Ecology
MOTU 1.1 [249] Biology, Bioinformatics, Genomics
MP-EST 1.4 [250] Biology, Phylogenetics
mpiP 3.4.1 [251] Parallel Computing
MrBayes 3.2.1 [252] Biology, Phylogenetics
MRIcron 201306 [253] Biology, MRI, Imaging
MUMmer 3.23 [254] Biology, Genomics
MUSCLE 3.8.31 [255] Biology, Genomics
MZMine 2.10 [256] Biology, Spectroscopy
NAMD 2.9 [257] Simulation, Chemistry, Biology
Nbody 6 [258] Astronomy
NCBI C++ Toolkit 12.0.0 [259] Biology, C++, Development
NCL 6.1.2 [260] Atmosphere Science
NCO 4.2.1, 4.4.3 [261] Data exchange tools
Ncview 2.1.2 [262] Data visualization
NetCDF 3.4.2, 4.2, 4.3 [263] Data exchange, Tools
Newbler 2.6, 2.7 [264] Biology, NGS
Nextallele 20140718 [265] Biology, Genomics
Nexus NCL 2.1.18 [266] Biology, Phylogenetics, Library
ngsCAT 0.1 [267] Biology, Bioinformatics, NGS
NGSUtils 20130722 [268] Biology, NGS
Nipype 0.10.0 [269] Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe 7.9 [270] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [271] Biology, NGS
Oases 0.2.08 [272] Biology, NGS
Olego 1.1.2, 1.1.5 [273] Biology, NGS, RNA-Seq
Octave 3.6.4 [274] Numerical Computation
OpenBabel 2.3.2 [275] Biology, Chemistry
OpenCL 1.1 [276] Programming, Library
OpenCV 2.4.8 [277] Computervision
OpenFOAM 2.1.1 [278] Fluid Dynamics
OpenMM 6.2.0 [279] Quantum Chemistry
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [280] Biology, Genomics
p4vasp 0.3.29 [281] Molecular, Electronic Structure
Pacbio 2.2.0.133377 [282] Biology, Bioinformatics, NGS
PALES 122 [283] Physics
PAML 4.7, 4.8a [284] Biology, Phylogenetics
Pandaseq 20140808 [285] Biology, Bioinformatics, NGS, Sequencing
PAPI 5.1.0.2 [286] Software, Computing
Parallel 20150122 [287] Programming, Languages
ParaView 4.1.0 [288] Data Analysis
PartitionFinder 1.0.1, 1.1.1 [289] Biology, Phylogenetics, Evolution
Parflow v615 [290] Ecology, Modeling
PASA 1.5, 2.0-r20140714, 2.0-r20150209 [291] Biology, Genomics
PAUP 4.0b10 [292] Biology, Phylogenetics
PBJelly 14.7.14 [293] Biology, Bioinformatics
pbsdrmaa 1.0.17 [294] Libraries, Torque
PeakSplitter 1.0 [295] Biology, Chip-Seq
PEAR 0.9.2, 0.9.6 [296] Biology, NGS
PDT 3.18 [297] Programming, Profiler
Perl 5.16.0 [298] Programming, Language
PerM 0.4.0 [299] Biology, NGS
PETSc 2.3, 3.3 [300] Math, Numerical solvers
Phenix 1.8.1069 [301] Crystallography
PfamScan 1.3 [302] Biology, Genomics
PHITS 2.52 [303] Physics
Phonopy 1.9.2 [304] Chemistry
PhyloBayes 3.3f, 1.4f MPI [305] Biology, Phylogenetics
Phylosift 1.1 [306] Biology, Genomics, Phylogenetics, Taxonomy
PhyML 3.0, 20121109 [307] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [308] Biology, NGS
PLAST 1.0 [309] Biology, Bioinformatics
Plink 1.07 [310] Biology, GWAS
PLINKSEQ 0.10 [311] Biology, Genomics
PluMiST 1.1 [312] Biology, Phylogenetics, Genomics
Preseq 0.0.4 [313] Biology, NGS
Primer3 2.3.4 [314] Biology, Genomics
Prokka 1.10 [315] Biology, Genomics, Bioinformatics, Assembly
ProBABEL 0.4.2, 0.4.3 [316] Biology, Genomics, GWAS
Probalign 1.4 [317] Biology, Genomics
Proovread 1.03rcl [318] Biology, Genomics, NGS
Proteinortho 4.26 [319] Biology, Genomics
python 2.6.8, 2.7.3, 2.7.5, 2.7.6, 2.7.8 [320] Biology, Genomics, NGS
QDD 3.1.2 [321] Programming, scripting, language
QIIME 1.5.0 [322] Biology, Ecology
QT 4.8.3 [323] Computer Science
QUAST 2.3 [324] Biology, NGS
Quickquartet 1.0.0 [325] Biology, Phylogenetics
R Rmpi/2.15.1, 33.0.2 [326] Statistics, Programming
R8S 1.71 [327] Biology, Evolution
RADICAL 0.2 [328] Biology, Phylogenetics, Genomics
RAxML 7.9.1, 8.0.25, 8.1.12 [329] Biology, Phylogenetics
RepeatMasker 3.3.0 [330] Biology, Genomics
Reptile 1.1 [331] Biology, NGS, error correction
riboPicker 0.4.3 [332] Biology, Sequence
RNAhybrid 2.1.1 [333] Biology, Genomics
ROOT 6.0 [334] Data Analysis
Rosetta 2014wk4 [335] Biology, Structure, Modelling
RSEG 0.4.8 [336] Biology, NGS
RSEM 1.1.17, 1.2.7, 1.2.19 [337] Biology, NGS, RNA-Seq
Ruby 1.9.3-p0 [338] Programming, Scripting, Language
Sailfish 0.6.3 [339] Biology, NGS, RNA-Seq
Sambamba 0.5.0-dev, 0.5.1 [340] Biology, NGS
Samstat 1.08 [341] Biology, NGS, Bioinformatics, Sequencing
Samblaster 0.1.14 [342] Biology, NGS
samtools 1.0, 1.1, 1.2 [343] Biology, NGS
SAS 9.3 [344] Statistics, Graphing
SATe 2.2.7 [345] Biology, Phylogenetics
Scalablast 2.4.53, 2.11.5 [346] Biology, Genomics
Scalpel 0.1.1 [347] Biology, NGS
Sharcgs 1.2.11 [348] Biology, NGS, Assembly
Schrodinger 2012, 2013 [349] Simulation, chemistry
SCons 2.3.0 [350] Programming
SCRATCH1D 1.0 [351] Biology, Genomics
Scythe 0.991 [352] Biology, NGS
Segemehl 0.1.9 [353] Biology, NGS, Mapper
SeqPrep 0.5 [354] Biology, NGS
SeqMap 1.0.13 [355] Biology, NGS
Seqtk 20140729 [356] Biology, NGS
SEQuel 1.0.1 [357] Biology, NGS
SeqyClean 1.8.10 [358] Biology, NGS, Bioinformatics
ShoRAH 20131204 [359] Biology, NGS, quality filter
SHRiMP 2.2.3 [360] Biology, NGS
Sickle 1.200, 1.33 [361] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [362] Simulation, Physics, Ab Initio
SIFT 4.0.3b [363] Biology, Genomics
Silo 4.7 [364] Library, Data
SIPeS 2.0 [365] Biology, Bioinformatics, ChIP-Seq
Slicer 4.3.1 [366] Biology, Imaging
SMALT 0.7.6 [367] Biology, NGS
Snap 20100728 [368] Biology, Genomics
SnpEff 3.3h, 4.0e [369] Biology, NGS, Genomics
SOAPdenovo 1.05 [370] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [371] Biology, NGS
SOAPsplice 1.10 [372] Biology, NGS
SparCC 201402 [373] Microbial Ecology
Spades 3.0.0, 3.1.0, 3.5.0 [374] Biology, NGS
Spanki 0.4.1, 0.4.3 [375] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [376] Chemistry
SPIMAP 1.1 [377] Biology, Phylogenetics
SpliceTrap 0.90.5 [378] Biology, NGS, RNA-Seq
SPM 8 [379] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [380] Biology, Genomics
SQLite 3.8.8.2 [381] Database
SRA 2.1.10 [382]] biology, NGS
SSPACE 2.0 [383] Biology, NGS
Stacks 0.9995 [384] Biology, Genomics, NGS
STAR 2.3.0e [385] Biology, NGS, Alignment
STAR-CCM+ 8.06 [386] Mechanical Engineering
Stata 10.1, 13 [387] Statistics, Data analysis
Stringtie 0.97 [388] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [389] Biology, Population
SUNDIALS 2.3.0, 2.5.0 [390] Numerical Solver
SVDetect 0.8b [391] Biology, NGS, SNP
swak4Foam 2.x [392] Fluid Dynamics
swarm 1.2.11 [393] Data Analysis
Swig 2.0.9 [394] Programming, C, C++, Python
SwitchSeq 20140907 [395] Biology, NGS
Syzygy 1.2.7 [396] Biology, Genomics
TASSEL 5.0 [397] Biology, Genomics
TAU 2.21.4, 2.23 [398] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [399] Biology, Genomics, Multiple Alignment
TESS 2.3.1 [400] Biology, Genomics, Markov
tgicl 2.1 [401] Biology, sequencing, clustering
TomoPy 0.0.3 [402] Biology, Neuroimaging
Tophat 1.4.1, 2.0.13 [403] Biology, NGS
Totalview 8.12.0 [404] Computer Science
TPP 4.7.0 [405] Bioinformatics, MassSpec
TrackTools 2011 [406] Bioinformatics
TrackVis 0.5.2.2 [407] Biology, Spectroscopy
Tracula 5.3.2014_05_26 [408] Biology, Bioinformatics, Neuroscience, Imaging
TraitRate 1.1 [409] Biology, Evolution
TransDecoder 20140704 [410] Biology, NGS
TreeFix 1.1.7 [411] Biology, Phylogenetics
TRF 4.04 [412] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [413] Math Algorithm
Trim Galore 0.2.8 [414] Biology, NGS
Trimmomatic 0.22, 0.32 [415] Biology, NGS
Trinity r20131110, r20140413, r20150215-2.0.4 [416] Biology, NGS, RNA-Seq
TRNAscan-SE 1.23 [417] Biology, NGS, Bioinformatics
Twinscan 4.1.2 [418] Biology, Genomics
usearch 7.0.1001-64, 8.0.1517 [419] Biology, Sequence analysis
UDUNITS 2.2.17 [420] Library, Units, Programming
UNAFold 3.8 [421] Biology, Genome, RNA, Folding
Valgrind 3.9.0 [422] Computer Science
VASP 5.3.2, 5.3.3, 5.3.5 [423] Quantum Chemistry, Ab Initio
VarScan 2.3.6 [424] Biology, NGS, Genomics
VCFLib 20121207 [425] Biology, NGS, Genomics
VCFtools 0.1.9, 0.1.10 [426] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [427] Biology, Genomics, NGS
VEP 74 [428] Biology, NGS
Vim 7.4.5-minimal, 7.4.5-py2, 7.4.5 [429] Programming, Scripting, Language
vmd 1.9.1 [430] Biology, Visualization
VTK 6.1.0 [431] Visualization, Graphics
Wannier90 1.2, 2.0.0 [432] Computational Physics
WebLogo 3.3 [433] Biology, Genomics
WDSSII 1 [434] Meteorology
WIEN2k 12.1 [435] Material Science, Chemistry
Wgs or Celera 8.1, 8.2, 8.3rc1 [436] Biology, NGS
wublast 2.0 [437] Biology, Sequence Alignment
YAHA 0.1.82 [438] Biology NGS
XCrySDen 1.5.60 [439] Computational Material Science
Yambo 3.3.0 [440] Physics
Yasra 2.32 [441] Biology, NGS
  1. ↑ Up to 3 most recent/important releases are listed. See the software wiki pages and the output of "module spider software" for full version listing.

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

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