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| The following is a list of the installed software at the UF HPC Center.
| | #REDIRECT [[Applications]] |
| | |
| List updated '''11 September 2011'''.
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| ==Software==
| |
| {| border="1"
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| ! Software !! Version !! Home Website
| |
| |-
| |
| | [[Abaqus]] || 6.6-1, 6.9-2 ||
| |
| |-
| |
| | [[ADMB]] || 9.1, 10.0 || [http://admb-project.org/ admb-project.org]
| |
| |-
| |
| | [[Amber]] || 10,11.old, 11 || [http://amber.scripps.edu/ amber.scripps.edu]
| |
| |-
| |
| | [[Amos]] || 3.0.0 || [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS AMOS SourceForge]
| |
| |-
| |
| | [[Ansys]] || 10.0 || [http://www.ansys.com/ www.ansys.com]
| |
| |-
| |
| | [[antlr]] || 3.1.3 || [http://www.antlr.org/ http://www.antlr.org/]
| |
| |-
| |
| | [[arachne]] || 37618 ||
| |
| |-
| |
| | [[bioscope]] || 1.0.1, 1.2.1 ||
| |
| |-
| |
| | [[Blast]] || 2.2.24 ||
| |
| |-
| |
| | [[Boost]] || 1.37.0, 1.46.1 ||
| |
| |-
| |
| | [[tuxedo|Bowtie]] || 0.12.7 || [http://bowtie-bio.sourceforge.net/index.shtml http://bowtie-bio.sourceforge.net/]
| |
| |-
| |
| | [[Charmm]] || 35b2 ||
| |
| |-
| |
| | [[Circuit]] || ||
| |
| |-
| |
| | [[CPMD]] || 3.11.1 || [http://www.cpmd.org/ www.cpmd.org]
| |
| |-
| |
| | [[Crystal]] || 1.0.2 ||
| |
| |-
| |
| | [[tuxedo|Cufflinks]] || 1.0.3 || [http://cufflinks.cbcb.umd.edu/ http://cufflinks.cbcb.umd.edu/]
| |
| |-
| |
| | [[dar]] || 2.3.9 ||
| |
| |-
| |
| | [[Newbler|denovo]] || 2.5.3, 2.6 ||
| |
| |-
| |
| | [[Desmond]] || 2.4.2.1 || [http://www.deshawresearch.com/resources_desmond.html www.deshawresearch.com/resources_desmond.html]
| |
| |-
| |
| | [[dlpoly]] || 3.0.9 || [http://www.cse.clrc.ac.uk/ccg/software/DL_POLY/index.shtml www.cse.clrc.ac.uk]
| |
| |-
| |
| | [[dock]] || 6.3, 6.4 || [http://dock.compbio.ucsf.edu/ dock.compbio.ucsf.edu]
| |
| |-
| |
| | [[emboss]] || 6.4.0 || [http://emboss.sourceforge.net/ emboss.sourceforge.net]
| |
| |-
| |
| | [[espresso]] || 3.0, 3.2.2, 4.0.4 ||
| |
| |-
| |
| | [[fftw]] || 2.1.5, 3.1.2 || [http://www.fftw.org/ www.gaussian.com]
| |
| |-
| |
| | [[fluent]] || 6.3.26 ||
| |
| |-
| |
| | [[gadget]] || 2.0.4, 2.0.5 ||
| |
| |-
| |
| | [[gaussian]] || 03,09 || [http://www.gaussian.com/ www.gaussian.com]
| |
| |-
| |
| | [[Gromacs]] || 4.0.4, 4.0.7 || [http://www.gromacs.org/ www.gromacs.org]
| |
| |-
| |
| | [[hypre]] || 2.0.0 || [http://www.llnl.gov/casc/hypre/software.html Lawrence Livermore National Labs]
| |
| |-
| |
| | [[Inelastica]] || 1.1 ||
| |
| |-
| |
| | [[IE3D]] || 15.1 ||
| |
| |-
| |
| | [[madness]] || ||
| |
| |-
| |
| | [[mafft]] || 6.859 || [http://mafft.cbrc.jp/alignment/software/ MAFFT Home Page]
| |
| |-
| |
| | [[MACS]] || 1.4.1 || [http://liulab.dfci.harvard.edu/MACS/ MACS Home Page]
| |
| |-
| |
| | [[Matlab]] || 2009b || [http://www.mathworks.com www.mathworks.com]
| |
| |-
| |
| | [[meep]] || 0.10.0, 0.20.3 ||
| |
| |-
| |
| | [[meme]] || 3.0.13, 4.3.0 ||
| |
| |-
| |
| | [[metis]] || 4.0 || [http://glaros.dtc.umn.edu/gkhome/views/metis glaros.dtc.umn.edu]
| |
| |-
| |
| | [[mira]] || 3.2.0 ||
| |
| |-
| |
| | [[MrBayes]] || 3.1.2 || [http://mrbayes.scs.fsu.edu/ mrbayes.scs.fsu.edu]
| |
| |-
| |
| | [[NAMD]] || 2.7b2 || [http://www.ks.uiuc.edu/Research/namd/ www.ks.uiuc.edu]
| |
| |-
| |
| | [[netcdf]] || 3.6.3, 4.1.2 ||
| |
| |-
| |
| | [[Newbler]] || 2.5.3, 2.6 ||
| |
| |-
| |
| | [[NWChem]] || 6.0 || [http://www.nwchem-sw.org/index.php/Main_Page http://www.nwchem-sw.org]
| |
| |-
| |
| | [[OpenFOAM]] || 1.7.1 ||
| |
| |-
| |
| | [[papi]] || 4.1.2.1 ||
| |
| |-
| |
| | [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html Upstream sofware page]
| |
| |-
| |
| | [[pdt]] || 3.16 ||
| |
| |-
| |
| | [[petsc]] || 2.3.3-p8, 3.0.0-p12 ||
| |
| |-
| |
| | [[pqs]] || 3.3-19 ||
| |
| |-
| |
| | [[pyopencl]] || 0.92 ||
| |
| |-
| |
| | [[python]] || 2.5.1, 2.6.4, 2.6.5 ||
| |
| |-
| |
| | [[RAxML]] || 7.3.0 || [http://wwwkramer.in.tum.de/exelixis/software.html RAxML]
| |
| |-
| |
| | [[RAxML-Light]] || 1.0.5 || [http://wwwkramer.in.tum.de/exelixis/software.html RAxML]
| |
| |-
| |
| | [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/ Repeat Masker]
| |
| |-
| |
| | [[Rosetta]] || 2.1.1, 2.1.2 || [https://www.rosettacommons.org/ www.rosettacommons.org]
| |
| |-
| |
| | [[rsm]] || 2961 ||
| |
| |-
| |
| | [[samtools]] || 0.1.16 || [http://samtools.sourceforge.net/ http://samtools.sourceforge.net/]
| |
| |-
| |
| | [[SAS]] || 9.1, 9.2, 9.3 || [http://www.sas.com SAS]
| |
| |-
| |
| | [[Siesta]] || 2.0, 2.0.2, 3.0b || [http://www.uam.es/departamentos/ciencias/fismateriac/siesta/ www.uam.es]
| |
| |-
| |
| | [[Stata]] || 10 || [http://www.stata.com/ Stata]
| |
| |-
| |
| | [[tau]] || 2.20.1 ||
| |
| |-
| |
| | [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html Tandem Repeats Finder]
| |
| |-
| |
| | [[tuxedo|Tophat]] || 1.3.0 || [http://tophat.cbcb.umd.edu/ http://tophat.cbcb.umd.edu/]
| |
| |-
| |
| | [[tuxedo]] || || The "tuxedo suite," Bowtie, Tophat, and Cufflinks
| |
| |-
| |
| | [[VASP]] || 4.6.34,5.2.0 || [http://cms.mpi.univie.ac.at/vasp/ cms.mpi.univie.ac.at]
| |
| |-
| |
| | [[velvet]] || 1.1.05 || [http://www.ebi.ac.uk/~zerbino/velvet/ www.ebi.ac.uk/~zerbino/velvet/]
| |
| |-
| |
| | [[vmd]] || 1.9 ||
| |
| |-
| |
| | [[weka]] || 3.6.2 ||
| |
| |-
| |
| | [[wublast]] || 2.0 || [http://blast.wustl.edu/ WU-Blast] [[WUBLAST|WU-BLAST Readme file]]
| |
| |}
| |
| | |
| * Many versions available. <code>/scratch/hpc/osg/app/etc/grid3-locations.txt</code> may have an up-to-date list. Or look underneath <code>/scratch/hpc/osg/app/cmssoft</code>.
| |