Installed Software

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.