Installed Software

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

List updated 07 October 2011.

Software

Software Version Home Website
Abaqus 6.6-1, 6.9-2
ADMB 9.1, 10.0 admb-project.org
Amber 10,11.old, 11 amber.scripps.edu
Amos 3.0.0 AMOS SourceForge
Ansys 10.0 www.ansys.com
antlr 3.1.3 http://www.antlr.org/
arachne 37618
bioscope 1.0.1, 1.2.1
Blast 2.2.24
Boost 1.37.0, 1.46.1
Bowtie 0.12.7 http://bowtie-bio.sourceforge.net/
Charmm 35b2
Circuit  
CPMD 3.11.1 www.cpmd.org
Crystal 1.0.2  
Cufflinks 1.0.3 http://cufflinks.cbcb.umd.edu/
dar 2.3.9
denovo 2.5.3, 2.6
Desmond 2.4.2.1 www.deshawresearch.com/resources_desmond.html
dlpoly 3.0.9 www.cse.clrc.ac.uk
dock 6.3, 6.4 dock.compbio.ucsf.edu
emboss 6.4.0 emboss.sourceforge.net
espresso 3.0, 3.2.2, 4.0.4 quantum-espresso.org
fastqc 0.10.0 FastQC website
fftw 2.1.5, 3.1.2 www.gaussian.com
fluent 6.3.26
gadget 2.0.4, 2.0.5 Atlassian Gadgets website
gamess 11-Aug11 www.msg.ameslab.gov/gamess
gaussian 03,09 www.gaussian.com
Gromacs 4.0.4, 4.0.7 www.gromacs.org
hypre 2.0.0 Lawrence Livermore National Labs
Inelastica 1.1
IE3D 15.1
lammps 17-Sept11 LAMPPS Home Page
madness 0.9 MADNESS Home Page
mafft 6.859 MAFFT Home Page
MACS 1.4.1 MACS Home Page
Matlab 2009b www.mathworks.com
meep 0.10.0, 0.20.3
meme 3.0.13, 4.3.0
metis 4.0 glaros.dtc.umn.edu
mira 3.2.0
MrBayes 3.1.2 mrbayes.scs.fsu.edu
NAMD 2.7b2 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
OpenFOAM 1.7.1
papi 4.1.2.1
PeakSplitter 1.0 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 RAxML
RAxML-Light 1.0.5 RAxML
RepeatMasker 3.3.0 Repeat Masker
Rosetta 2.1.1, 2.1.2 www.rosettacommons.org
rsm 2961
samtools 0.1.16 http://samtools.sourceforge.net/
SAS 9.2, 9.3 SAS
Siesta 2.0, 2.0.2, 3.0b www.uam.es
Stata 10 Stata
tau 2.20.1
TRF 4.04 Tandem Repeats Finder
Tophat 1.3.0 http://tophat.cbcb.umd.edu/
tuxedo The "tuxedo suite," Bowtie, Tophat, and Cufflinks
VASP 4.6.34,5.2.0 cms.mpi.univie.ac.at
velvet 1.1.05 www.ebi.ac.uk/~zerbino/velvet/
vmd 1.9
weka 3.6.2
wublast 2.0 WU-Blast WU-BLAST Readme file
  • Many versions available. /scratch/hpc/osg/app/etc/grid3-locations.txt may have an up-to-date list. Or look underneath /scratch/hpc/osg/app/cmssoft.