Difference between revisions of "Installed Software"

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Line 17: Line 17:
 
| [[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 ||
 
|-
 
|-
−
| [[Abyss]] || 1.3.1 || [http://www.bcgsc.ca/platform/bioinfo/software/abyss] || Biology, NGS || X ||
+
| [[Abyss]] || 1.3.1 || [http://www.bcgsc.ca/platform/bioinfo/software/abyss] || Biology, NGS || X || X
 
|-
 
|-
 
| [[ADMB]] || 9.1, 10.0, 10.1 || [http://admb-project.org/] || Modeling, math || X ||
 
| [[ADMB]] || 9.1, 10.0, 10.1 || [http://admb-project.org/] || Modeling, math || X ||
Line 23: Line 23:
 
| [[ALLPATHS-LG]] || 39099, 40122, 41655 || [http://www.broadinstitute.org/software/allpaths-lg/blog/] || Biology, NGS || X ||
 
| [[ALLPATHS-LG]] || 39099, 40122, 41655 || [http://www.broadinstitute.org/software/allpaths-lg/blog/] || Biology, NGS || X ||
 
|-
 
|-
−
| [[Amber]] || 10,11.old, 11, 12 || [http://amber.scripps.edu/] || Simulation, chemistry || X ||
+
| [[Amber]] || 10,11.old, 11, 12 || [http://amber.scripps.edu/] || Simulation, chemistry || X || X
 
|-
 
|-
 
| [[Amos]] || 3.0.0 || [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS] || Biology, Genomics || X ||
 
| [[Amos]] || 3.0.0 || [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS] || Biology, Genomics || X ||
Line 35: Line 35:
 
| [[arachne]] || 37618 || [http://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational] || Biology, Genomics || X ||
 
| [[arachne]] || 37618 || [http://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational] || Biology, Genomics || X ||
 
|-
 
|-
−
| [[Bamtools]] || 2.1.0 || [https://github.com/pezmaster31/bamtools/wiki] || Biology, NGS || X ||
+
| [[Augustus]] || 2.6 || [http://augustus.gobics.de/]|| Biology, NGS || || X
 +
|-
 +
| [[Bamtools]] || 2.1.0 || [https://github.com/pezmaster31/bamtools/wiki] || Biology, NGS || X || X
 
|-
 
|-
 
| [[BamUtil]] || 1.0.2 || [http://genome.sph.umich.edu/wiki/BamUtil] || Biology, NGS || X ||
 
| [[BamUtil]] || 1.0.2 || [http://genome.sph.umich.edu/wiki/BamUtil] || Biology, NGS || X ||
Line 43: Line 45:
 
| [[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/]|| Biology, NGS || X ||
+
| [[Bedtools|BEDTools]] || 2.16.2 || [http://code.google.com/p/bedtools/]|| Biology, NGS || X || X
 
|-
 
|-
 
| [[BFAST]] || 0.7.0 || [http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page] || Biology, NGS || X ||
 
| [[BFAST]] || 0.7.0 || [http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page] || Biology, NGS || X ||
 +
|-
 +
| [[Bismark]] || 0.7.4 || [http://www.bioinformatics.babraham.ac.uk/projects/download.html#bismark] || Biology, Methylation, NGS || || X ||
 
|-
 
|-
 
| [[Bioconductor]] || 2011-11-16 || [http://www.bioconductor.org/] || Biology, R, Statistics || X ||
 
| [[Bioconductor]] || 2011-11-16 || [http://www.bioconductor.org/] || Biology, R, Statistics || X ||
 
|-
 
|-
−
| [[Perl|BioPerl]] || 1.006901 || [http://bioperl.org/] || Biology, Perl || X ||
+
| [[Perl|BioPerl]] || 1.006901 || [http://bioperl.org/] || Biology, Perl || X || X
 
|-
 
|-
−
| [[Python|Biopython]] || 1.59 || [http://biopython.org/] || Biology, Python || X ||
+
| [[Python|Biopython]] || 1.59 || [http://biopython.org/] || Biology, Python || X || 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] || Biology, NGS || 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] || Biology, NGS || X ||
Line 61: Line 65:
 
| [[BLAT]] || 34 || [http://genome.ucsc.edu/goldenPath/help/blatSpec.html] || Biology, Sequence alignment || X ||
 
| [[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/] || C++, Library || X ||
+
| [[Boost]] || 1.38.0, 1.46.1, 1.48.0, 1.49.0 || [http://www.boost.org/] || C++, Library || X || X
 
|-
 
|-
−
| [[bwa]] || 0.5.9, 0.5.10, 0.6.0 (default) || [http://bio-bwa.sourceforge.net/] || Biology, NGS || X ||
+
| [[bwa]] || 0.5.9, 0.5.10, 0.6.0 (default) || [http://bio-bwa.sourceforge.net/] || Biology, NGS || X || X
 
|-
 
|-
−
| [[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 ||
+
| [[Bowtie]] || 0.12.8 (default), 2.0.0-beta5 || [http://bowtie-bio.sourceforge.net/index.shtml] || Biology, NGS || X || X
 
|-
 
|-
 
| [[BreakDancer]] || 1.1 || [http://breakdancer.sourceforge.net/index.html] || Biology, NGS, Genomics || X ||
 
| [[BreakDancer]] || 1.1 || [http://breakdancer.sourceforge.net/index.html] || Biology, NGS, Genomics || X ||
Line 85: Line 89:
 
| [[CisGenome]] || 2.0 || [http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm] || Biology, Genomics, Peak Calling || X ||
 
| [[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/] || Programming || X ||
+
| [[CMake]] || 2.8.5 || [http://www.cmake.org/] || Programming || X || X
 
|-
 
|-
 
| [[CNV-seq]] || 07.15.11 || [http://tiger.dbs.nus.edu.sg/cnv-seq/] || Biology, NGS || X ||
 
| [[CNV-seq]] || 07.15.11 || [http://tiger.dbs.nus.edu.sg/cnv-seq/] || Biology, NGS || X ||
 
|-
 
|-
 
| [[CNVnator]] || 0.2.5 || [http://sv.gersteinlab.org/] || Biology, NGS || X ||
 
| [[CNVnator]] || 0.2.5 || [http://sv.gersteinlab.org/] || Biology, NGS || X ||
 +
|-
 +
| [[Consed]] || 23.0 || [http://bozeman.mbt.washington.edu/consed/consed.html] || Biology, Genomics || || X
 
|-
 
|-
 
| [[CPMD]] || 3.11.1 || [http://www.cpmd.org/] || Simulation, Chemistry || X ||
 
| [[CPMD]] || 3.11.1 || [http://www.cpmd.org/] || Simulation, Chemistry || X ||
 
|-
 
|-
−
| [[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/] || Biology, NGS ||  X || X
 
|-
 
|-
−
| [[Cutadapt]] || 1.1 || [http://code.google.com/p/cutadapt/] || Biology, NGS || X ||
+
| [[Cutadapt]] || 1.1 || [http://code.google.com/p/cutadapt/] || Biology, NGS || X || X
 
|-
 
|-
 
| [[dar]] || 2.3.9 || [http://sourceforge.net/projects/dar/] || Backup || X ||
 
| [[dar]] || 2.3.9 || [http://sourceforge.net/projects/dar/] || Backup || X ||
Line 117: Line 123:
 
| [[espresso]] || 3.0, 3.2.2, 4.0.4, 5.0 || [http://www.quantum-espresso.org/] || Modeling, Physics || X ||
 
| [[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/] || Biology, Genomics || X ||
+
| [[Exonerate]] || 2.2 || [http://www.ebi.ac.uk/~guy/exonerate/] || Biology, Genomics || X || 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] || Biology, Genomics || X ||
 
|-
 
|-
−
| [[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] || Biology, Genomics || X || X
 
|-
 
|-
−
| [[fastx_toolkit]]|| 0.0.13.1|| [http://hannonlab.cshl.edu/fastx_toolkit/] || Biology, NGS || X ||
+
| [[FastQC]] || 0.9.6, 0.10.0 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/] || Biology, NGS || X || X
 
|-
 
|-
−
| [[FastQC]] || 0.9.6, 0.10.0 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/] || Biology, NGS || X ||
+
| [[fastx_toolkit]]|| 0.0.13.1|| [http://hannonlab.cshl.edu/fastx_toolkit/] || Biology, NGS || X || X
 
|-
 
|-
 
| [[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/] || Math, Library, C++ || X ||
Line 133: Line 139:
 
| [[FragGeneScan]] || 1.16 || [http://omics.informatics.indiana.edu/FragGeneScan/] || Biology, NGS || X ||
 
| [[FragGeneScan]] || 1.16 || [http://omics.informatics.indiana.edu/FragGeneScan/] || Biology, NGS || X ||
 
|-
 
|-
−
| [[FreeBayes]] || 0.9.4 || [http://bioinformatics.bc.edu/marthlab/FreeBayes] || Biology || X ||
+
| [[FreeBayes]] || 0.9.4 || [http://bioinformatics.bc.edu/marthlab/FreeBayes] || Biology || X || X
 
|-
 
|-
 
| [[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] || Software Development || X ||
Line 145: Line 151:
 
| [[gulp]] || 4.0.3 || [http://projects.ivec.org/gulp/] || Modeling/simulation, Chemistry || X ||
 
| [[gulp]] || 4.0.3 || [http://projects.ivec.org/gulp/] || Modeling/simulation, Chemistry || X ||
 
|-
 
|-
−
| [[gaussian]] || E01, G03, G09-A.02, G09-C.01 || [http://www.gaussian.com/]||Modeling, Computational Chemistry|| X ||
+
| [[gaussian]] || E01, G03, G09-A.02, G09-C.01 || [http://www.gaussian.com/]||Modeling, Computational Chemistry|| X || X
 
|-
 
|-
 
| [[Geneid]] || 1.4 || [http://genome.crg.es/software/geneid/]||Biology, Genomics, Annotation|| X ||
 
| [[Geneid]] || 1.4 || [http://genome.crg.es/software/geneid/]||Biology, Genomics, Annotation|| X ||
 
|-
 
|-
−
|| [[GeneMark]] || 2012.04 || [http://exon.gatech.edu/] || Biology, Genomics, Metagenomics || X ||
+
| [[GeneMark]] || 2012.04 || [http://exon.gatech.edu/] || Biology, Genomics, Metagenomics || X || X
 
|-
 
|-
 
| [[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]||Biology, Genomics, Annotation|| X ||
 
|-
 
|-
−
| [[GMAP]] || 20070928, 20120524, 20120612 || [http://research-pub.gene.com/gmap/] || Biology, Genomics || X ||
+
| [[GMAP]] || 20070928, 20120524, 20120612 || [http://research-pub.gene.com/gmap/] || Biology, Genomics || X || X
 
|-
 
|-
 
| [[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/] || Graphics, plotting, 2D || X ||
Line 167: Line 173:
 
| [[HugeSeq]] || 1.0.1 || [http://hugeseq.hugolam.com/]|| Biology, NGS, Genomics || X ||
 
| [[HugeSeq]] || 1.0.1 || [http://hugeseq.hugolam.com/]|| Biology, NGS, Genomics || X ||
 
|-
 
|-
−
| [[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]||Library, Math, Physics|| X || X
 
|-
 
|-
 
| [[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]||Biology, Population|| X ||
Line 176: Line 182:
 
|-
 
|-
 
| [[IE3D]] || 15.1 || [http://www.mentor.com/electromagnetic-simulation/]||Simulation, Design|| X ||
 
| [[IE3D]] || 15.1 || [http://www.mentor.com/electromagnetic-simulation/]||Simulation, Design|| X ||
 +
|-
 +
| [[Iprscan]] || 4.8 || [http://www.ebi.ac.uk/Tools/pfa/iprscan/] || BIology, Genomics || || X
 
|-
 
|-
 
| [[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] || Java Development Kit || X ||
 +
|-
 +
| [[Kent]] || 20120423 || [http://genomewiki.cse.ucsc.edu/index.php/The_source_tree] || Biology, NGS || X || X
 
|-
 
|-
 
| [[Khmer]] || 20120321 || [https://github.com/ctb/khmer] || Biology, NGS, Utilities || X ||
 
| [[Khmer]] || 20120321 || [https://github.com/ctb/khmer] || Biology, NGS, Utilities || X ||
 
|-
 
|-
−
| [[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] || Biology, NGS, genome alignment || X || X
 
|-
 
|-
 
| [[lammps]] || 17-Sept11 || [http://lammps.sandia.gov/]||Simulation|| X ||
 
| [[lammps]] || 17-Sept11 || [http://lammps.sandia.gov/]||Simulation|| X ||
Line 193: Line 203:
 
| [[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/]||Math, DIff. Equation solving|| X ||
 
|-
 
|-
−
| [[mafft]] || 6.859 || [http://mafft.cbrc.jp/alignment/software/]||Biology, Multiple sequence alignment|| X ||
+
| [[mafft]] || 6.859 || [http://mafft.cbrc.jp/alignment/software/]||Biology, Multiple sequence alignment|| X || X
 
|-
 
|-
−
| [[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] || Biology, Annotation, Genomics || X || X
 
|-
 
|-
 
| [[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]|| Biology, Genomics || X ||
Line 217: Line 227:
 
| [[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/]||Biology, NGS|| X ||
 
|-
 
|-
−
| [[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/]||Biology,NGS|| X || X
 
|-
 
|-
 
| [[MPIBlast]] || 1.6.0 || [http://www.mpiblast.org/]||Biology, Sequence alignment|| X ||
 
| [[MPIBlast]] || 1.6.0 || [http://www.mpiblast.org/]||Biology, Sequence alignment|| X ||
Line 235: Line 245:
 
| [[NetLogo]] || 4.1.3 || [http://ccl.northwestern.edu/netlogo/] || Modeling || X ||
 
| [[NetLogo]] || 4.1.3 || [http://ccl.northwestern.edu/netlogo/] || Modeling || X ||
 
|-
 
|-
−
| [[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] || Biology, NGS || X || X
 
|-
 
|-
 
| [[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/] || NDFT, library, math || X ||
Line 255: Line 265:
 
| [[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]||CPU API|| X ||
 
|-
 
|-
−
| [[PASA]] || 20110520 || [http://http://pasa.sourceforge.net/]|| Biology, Genomics || X ||
+
| [[Parflow]] || v615 || [https://computation.llnl.gov/casc/parflow/parflow_home.html] || Ecology, Modeling || || X
 +
|-
 +
| [[PASA]] || 20110520 || [http://http://pasa.sourceforge.net/]|| Biology, Genomics || X || X
 
|-
 
|-
 
| [[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]||Biology, Chip-Seq|| X ||
Line 261: Line 273:
 
| [[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]||Programming, Profiler|| X ||
 
|-
 
|-
−
| [[Perl]] || 5.14.1 || [http://www.perl.org/]||Programming, Language || X ||
+
| [[Perl]] || 5.14.1 || [http://www.perl.org/]||Programming, Language || X || X
 
|-
 
|-
 
| [[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/]||MPI toolkit|| X ||
Line 271: Line 283:
 
| [[PhyML]] || 3.0 || [http://code.google.com/p/phyml/] || Biology, Phylogenetics || X ||
 
| [[PhyML]] || 3.0 || [http://code.google.com/p/phyml/] || Biology, Phylogenetics || X ||
 
|-
 
|-
−
| [[Picard]] || 1.54 || [http://picard.sourceforge.net/] || Biology, NGS || X ||
+
| [[Picard]] || 1.54 || [http://picard.sourceforge.net/] || Biology, NGS || X || X
 
|-
 
|-
 
| [[Pindel]] || 0.2.8 || [https://trac.nbic.nl/pindel/] || Biology, NGS || X ||
 
| [[Pindel]] || 0.2.8 || [https://trac.nbic.nl/pindel/] || Biology, NGS || X ||
Line 289: Line 301:
 
| [[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]||Biology, Phylogenetics|| X ||
 
|-
 
|-
−
| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/]||Biology, Genomics|| X ||
+
| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/]||Biology, Genomics|| X || X
 
|-
 
|-
−
| [[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]||Biology, NGS, error correction|| X || X
 
|-
 
|-
 
| [[riboPicker]] || 0.4.2 || [http://ribopicker.sourceforge.net/]||Biology, Sequence|| X ||
 
| [[riboPicker]] || 0.4.2 || [http://ribopicker.sourceforge.net/]||Biology, Sequence|| X ||
Line 315: Line 327:
 
| [[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/]||Simulation, physics, ab-initio|| X ||
 
|-
 
|-
−
| [[SOAPdenovo]] || 1.05 || [http://soap.genomics.org.cn/soapdenovo.html]||Biology, NGS|| X ||
+
| [[Silo]] || 4.7 || [https://wci.llnl.gov/codes/silo/index.html] || Library, Data || X || X
 +
|-
 +
| [[Snap]] || 20100728 || [http://homepage.mac.com/iankorf] || Biology, Genomics || X || X
 +
|-
 +
| [[SOAPdenovo]] || 1.05 || [http://soap.genomics.org.cn/soapdenovo.html]||Biology, NGS|| X || X
 
|-
 
|-
 
| [[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|| X ||
Line 333: Line 349:
 
| [[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]||Profiling, Tracing, Programming|| X ||
 
|-
 
|-
−
| [[tgicl]] || 2.1 || [http://compbio.dfci.harvard.edu/tgi/software/]|| Biology, sequencing, clustering || X ||
+
| [[tgicl]] || 2.1 || [http://compbio.dfci.harvard.edu/tgi/software/]|| Biology, sequencing, clustering || X || X
 
|-
 
|-
−
| [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html]||Biology, Genomics|| X ||
+
| [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html]||Biology, Genomics|| X || X
 
|-
 
|-
 
| [[Trimal]] || 1.2 || [http://trimal.cgenomics.org/] || Biology, NGS || X ||
 
| [[Trimal]] || 1.2 || [http://trimal.cgenomics.org/] || Biology, NGS || X ||
Line 341: Line 357:
 
| [[Trinity]] || r20120125, r20120317, r20120608 || [http://trinityrnaseq.sourceforge.net/] || Biology, RNA-Seq|| X ||
 
| [[Trinity]] || r20120125, r20120317, r20120608 || [http://trinityrnaseq.sourceforge.net/] || Biology, RNA-Seq|| X ||
 
|-
 
|-
−
| [[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/]||Biology, NGS|| X || X
−
|-
 
−
| [[tuxedo]] ||colspan="3"|The "tuxedo suite" - Bowtie, Tophat, and Cufflinks|| X ||
 
 
|-
 
|-
 
| [[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]|| Biology, Genomics || X ||
Line 359: Line 373:
 
| [[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/]||Data mining algorithms|| X ||
 
|-
 
|-
−
| [[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]||Biology,Assembler,Genome|| X || X
 
|-
 
|-
−
| [[wublast]] || 2.0 || [http://blast.wustl.edu/]||Biology, Sequence Alignment|| X ||
+
| [[wublast]] || 2.0 || [http://blast.wustl.edu/]||Biology, Sequence Alignment|| X || X
 
|}
 
|}
  

Revision as of 04:22, 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 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 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
Augustus 2.6 [11] Biology, NGS X
Bamtools 2.1.0 [12] Biology, NGS X X
BamUtil 1.0.2 [13] Biology, NGS X
BayesPhylogenies 2.0 [14] Biology, Phylogenetics X
beast 1.6.2, 1.7.0, 1.7.1 [15] Biology, Phylogenetics X
BEDTools 2.16.2 [16] Biology, NGS X X
BFAST 0.7.0 [17] Biology, NGS X
Bismark 0.7.4 [18] Biology, Methylation, NGS X
Bioconductor 2011-11-16 [19] Biology, R, Statistics X
BioPerl 1.006901 [20] Biology, Perl X X
Biopython 1.59 [21] Biology, Python X X
bioscope 1.0.1, 1.2.1 ABI Biology, NGS X
Blast 2.2.24, 2.2.25, 2.2.26 [22] Biology, Sequence alignment X
Blast2go 2.5.0 [23] Biology, Annotation X
BLAT 34 [24] Biology, Sequence alignment X
Boost 1.38.0, 1.46.1, 1.48.0, 1.49.0 [25] C++, Library X X
bwa 0.5.9, 0.5.10, 0.6.0 (default) [26] Biology, NGS X X
Bowtie 0.12.8 (default), 2.0.0-beta5 [27] Biology, NGS X X
BreakDancer 1.1 [28] Biology, NGS, Genomics X
CAP3 20071015 [29] Biology, sequence assembly X
CASAVA 1.8.2 [30] Biology, NGS X
CD-HIT 4.5.7 [31] Biology, Genomics X
CEGMA 2.3 [32] Biology, Genomics, Annotation X
CGATools 1.5.0.31 [33] Biology, Genomics X
Charmm 35b2 [34] Simulation, Chemistry X
Circuit 3.5.1, 3.5.7 [35] GIS X
CisGenome 2.0 [36] Biology, Genomics, Peak Calling X
CMake 2.8.5 [37] Programming X X
CNV-seq 07.15.11 [38] Biology, NGS X
CNVnator 0.2.5 [39] Biology, NGS X
Consed 23.0 [40] Biology, Genomics X
CPMD 3.11.1 [41] Simulation, Chemistry X
Cufflinks 1.0.3, 1.1.0, 1.3.0 [42] Biology, NGS X X
Cutadapt 1.1 [43] Biology, NGS X X
dar 2.3.9 [44] Backup X
deFuse 0.4.3 [45] Biology, RNA-seq X
Desmond 2.4.2.1 [46] Simulation, Biology, Chemistry X
Dindel 1.01 [47] Biology, NGS, Genomics X
dlpoly 3.0.9 [48] Simulation, Biology, Chemistry X
dock 6.3, 6.4, 6.5 [49] Chemistry, ligand binding prediction X
emacs 21.4.1, 23.4.1 [50] The Emacs editor X
EMAN2 2.04 [51] Biology, image processing X
emboss 6.4.0 [52] Biology, multi-tool suite X
espresso 3.0, 3.2.2, 4.0.4, 5.0 [53] Modeling, Physics X
Exonerate 2.2 [54] Biology, Genomics X X
FAR 2.15 [55] Biology, Genomics X
FASTA 34.26.5 [56] Biology, Genomics X X
FastQC 0.9.6, 0.10.0 [57] Biology, NGS X X
fastx_toolkit 0.0.13.1 [58] Biology, NGS X X
fftw 2.1.5, 3.1.2 [59] Math, Library, C++ X
fluent 6.3.26 [60] Simulation X
FragGeneScan 1.16 [61] Biology, NGS X
FreeBayes 0.9.4 [62] Biology X X
gadget 2.0.4, 2.0.5 [63] Software Development X
gamess 11-Aug11 [64] Quantum Chemistry X
garli 2.0 [65] Biology, Phylogenetics X
GATK 1.4.30 [66] Biology, NGS X
gulp 4.0.3 [67] Modeling/simulation, Chemistry X
gaussian E01, G03, G09-A.02, G09-C.01 [68] Modeling, Computational Chemistry X X
Geneid 1.4 [69] Biology, Genomics, Annotation X
GeneMark 2012.04 [70] Biology, Genomics, Metagenomics X X
Genewise 2.2.3 [71] Biology, Genomics, Annotation X
GMAP 20070928, 20120524, 20120612 [72] Biology, Genomics X X
Grace 5.1.22 [73] Graphics, plotting, 2D X
Gromacs 4.0.4, 4.0.7 [74] Physics, Modeling X
HDF5 1.8.7, 1.8.8 [75] Library, Data X
HMMER3 3.0 [76] Biology, Genomics X
HTSeq 0.5.3p3 [77] Biology, NGS X
HugeSeq 1.0.1 [78] Biology, NGS, Genomics X
hypre 2.8.0 [79] Library, Math, Physics X X
IM and IMa 2009.12.17 [80] Biology, Population X
IMa2 8.26.11 [81] Biology, Population X
Inelastica 1.1 (python/2.7.2) [82] Quantum Chemistry X
IE3D 15.1 [83] Simulation, Design X
Iprscan 4.8 [84] BIology, Genomics X
JDK 1.6.0_12, 1.7.0 [85] Java Development Kit X
Kent 20120423 [86] Biology, NGS X X
Khmer 20120321 [87] Biology, NGS, Utilities X
Kmer r1909 [88] Biology, NGS, genome alignment X X
lammps 17-Sept11 [89] Simulation X
Last 193 [90] Biology, Sequence alignment X
libxc 1.1.0 [91] Math, funtionals X
MACS 1.4.1 [92] Biology, ChIP-Seq X
madness 1769 [93] Math, DIff. Equation solving X
mafft 6.859 [94] Biology, Multiple sequence alignment X X
Maker 2.10 [95] Biology, Annotation, Genomics X X
MapSplice 1.15.2 [96] Biology, Genomics X
Matlab 2009b [97] Math, Simulation, Programming X
MATS 2.1.0 [98] BIology, NGS X
Mauve 2.3.1 [99] Biology, Multiple genome alignments X
MCL 11-335 [100] Biology, Genomics, Clustering X
meme 3.0.13, 4.3.0 [101] Biology, Motifs, Sequence analysis X
MetaPhyler 1.13 [102] Biology, Metagenomics X
metis 4.0 [103] Math, Graph partitioning X
Migrate-n 3.2.16 [104] Biology, Population X
mira 3.2.0, 3.4.0.1 [105] Biology, NGS X
mosaik 1.1.0021 [106] Biology,NGS X X
MPIBlast 1.6.0 [107] Biology, Sequence alignment X
MrBayes 3.1.2,3.2.1 [108] Biology, Phylogenetics X
MUMmer 3.22 [109] Biology, Genomics X
MUSCLE 3.8.31 [110] Biology, Genomics X
NAMD 2.7b2 [111] Simulation, Chemistry, Biology X
NCO 4.0.9 [112] Data exchange tools X
netcdf 3.6.3, 4.1.2, 4.1.3 [113] Data exchange, Tools X
NetLogo 4.1.3 [114] Modeling X
Newbler 2.5.3, 2.6 [115] Biology, NGS X X
NFFT 3.1.3 [116] NDFT, library, math X
Novoalign 2.07.15 [117] Biology, NGS X
NWChem 6.0 [118] Simulation, Chemistry X
Oases 0.2.04 [119] Biology, NGS X
OpenFOAM 1.7.1 [120] Molecular Dynamics X
OrthoMCL 2.0 [121] Biology, Genomics X
PAL2NAL 14 [122] Biology, Genomics X
PAML 4.4e [123] Biology, Phylogenetics X
PAPI 4.1.2.1 [124] CPU API X
Parflow v615 [125] Ecology, Modeling X
PASA 20110520 [126] Biology, Genomics X X
PeakSplitter 1.0 [127] Biology, Chip-Seq X
PDT 3.16 [128] Programming, Profiler X
Perl 5.14.1 [129] Programming, Language X X
PETSc 2.3.3-p8, 3.0.0-p12 [130] MPI toolkit X
Phred 020425 [131] Biology, Genomics, Sequencing X
PhyloBayes 3.3b [132] Biology, Phylogenetics X
PhyML 3.0 [133] Biology, Phylogenetics X
Picard 1.54 [134] Biology, NGS X X
Pindel 0.2.8 [135] Biology, NGS X
PQS 3.3-19 [136] Modeling, Chemistry X
Prinseq 0.17 [137] Biology, NGS X
PyOpenCL 2012.04 [138] python, parallel programming X
python 2.6.5, 2.7.2, 2.7.3 [139] Programming, scripting, language X X
R 2.14.1, 2.14.1-MPI, 2.14.2 [140] Statistics, Programming X X
RAxML 7.3.0 [141] Biology, Phylogenetics X
RAxML-Light 1.0.5 [142] Biology, Phylogenetics X
RepeatMasker 3.3.0 [143] Biology, Genomics X X
Reptile 1.1, 1.1-omp [144] Biology, NGS, error correction X X
riboPicker 0.4.2 [145] Biology, Sequence X
Rosetta 2.1.1, 2.1.2 [146] Biology, Structural, Modeling X
Ruby 1.9.3 [147] Programming, Language, Scripting X
RSMToolkit 2961 [148] Math, Modeling, Geometry X
samtools 0.1.16, 0.1.18 [149] Biology, NGS X X
SAS 9.2, 9.3 [150] Statistics, Graphing X X
SATe 2.1.0 [151] Biology, Phylogenetics X
Scala 2.9.1 [152] Programming, language, java X
Segminator 0.0.2 [153] Biology, NGS X
SeqPrep 0.4 [154] Biology, NGS X
Siesta 2.0, 2.0.2, 3.0b [155] Simulation, physics, ab-initio X
Silo 4.7 [156] Library, Data X X
Snap 20100728 [157] Biology, Genomics X X
SOAPdenovo 1.05 [158] Biology, NGS X X
SPARTA+ 2.60 [159] Chemistry X
SRA 2.1.7 [160]] biology, NGS X X
SRNAPredict 3.0 [161] Biology, Genomics X
SRNAScanner 200903 [162] Biology, Genomics X
Staden 2.0.0b9 [163] Biology, Genomics, Sequencing X X
Stata 10 [164] Statistics, Data analysis X
Structure 2.3.3 [165] Biology, Population X
TAU 2.20.1 [166] Profiling, Tracing, Programming X
tgicl 2.1 [167] Biology, sequencing, clustering X X
TRF 4.04 [168] Biology, Genomics X X
Trimal 1.2 [169] Biology, NGS X
Trinity r20120125, r20120317, r20120608 [170] Biology, RNA-Seq X
Tophat 1.3.0, 1.3.3, 1.4.1 [171] Biology, NGS X X
Twinscan 3.5,4.1.2 [172] Biology, Genomics X
usearch 5.0.151,5.1.221 [173] Biology, Sequence analysis X
VASP 4.6.34,5.2.0 [174] Quantum Chemistry, ab initio X
VCFtools 0.1.7, 0.1.9 [175] Biology, SNPs X
velvet 1.2.06,1.2.02,1.2.01,1.1.05 [176] Biology, NGS X X
vmd 1.9 [177] Biology, Visualization X
weka 3.6.2 [178] Data mining algorithms X
wgs 6.1, 6.1-20110830 [179] Biology,Assembler,Genome X X
wublast 2.0 [180] Biology, Sequence Alignment X 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.

Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=Installed_Software&oldid=6801"