Difference between revisions of "Installed Software"

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The following is a list of the installed software at the UF HPC Center.
+
#REDIRECT [[Applications]]
 
 
List updated '''07 October 2011'''.
 
==Software==
 
{| border="1"
 
! 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 || [http://www.quantum-espresso.org/ quantum-espresso.org]
 
|-
 
| [[fastqc]] || 0.10.0 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ FastQC website]
 
|-
 
| [[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 || [http://confluence.atlassian.com/display/GADGETS/Atlassian+Gadgets+2.0.5+Release+Notes Atlassian Gadgets website]
 
|-
 
| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/ www.msg.ameslab.gov/gamess]
 
|-
 
| [[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 ||
 
|-
 
| [[lammps]] || 17-Sept11 || [http://lammps.sandia.gov/ LAMPPS Home Page]
 
|-
 
| [[madness]] || 0.9 || [http://code.google.com/p/m-a-d-n-e-s-s/ MADNESS Home Page]
 
|-
 
| [[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]] || 9.2, 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>.
 
 
 
{{App Add Page}}
 

Latest revision as of 17:41, 28 September 2017

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