UFRC Help and Documentation

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

List updated 07 October 2011.

Software

Software	Version	Home Website	Category	Notes
Abaqus	6.6-1, 6.9-2	Abaqus	Simulation
ADMB	9.1, 10.0	admb-project.org	Modeling, math
Amber	10,11.old, 11	amber.scripps.edu	Simulation, chemistry
Amos	3.0.0	AMOS SourceForge	Biology, Genomics
Ansys	10.0	www.ansys.com	Simulation, Engineering
antlr	3.1.3	http://www.antlr.org/	Linguistics, Parser
arachne	37618	Broadinstitute page	Biology, Genomics
bioscope	1.0.1, 1.2.1	ABI BioScope	Biology, NGS
Blast	2.2.24, 2.2.25	NCBI page	Biology, Sequence alignment
Boost	1.37.0, 1.46.1	Boost.org	C++, Library
Bowtie	0.12.7	http://bowtie-bio.sourceforge.net/	Biology, NGS
Charmm	35b2	[1]	Simulation, Chemistry
Circuit		circuitscape.org	GIS
CPMD	3.11.1	www.cpmd.org	Simulation, Chemistry
Crystal	1.0.2			Will be removed on 2011-10-30
Cufflinks	1.0.3	http://cufflinks.cbcb.umd.edu/	Biology, NGS
dar	2.3.9	SF.net	Backup
Desmond	2.4.2.1	www.deshawresearch.com/resources_desmond.html Desmond	Simulation, Biology, Chemistry
dlpoly	3.0.9	www.cse.clrc.ac.uk	Simulation, Biology, Chemistry
dock	6.3, 6.4	dock.compbio.ucsf.edu	Chemistry, ligand binding prediction
emboss	6.4.0	emboss.sourceforge.net	Biology, multi-tool suite
espresso	3.0, 3.2.2, 4.0.4	quantum-espresso.org	Modeling, Physics
fastqc	0.10.0	FastQC website	Biology, NGS
fftw	2.1.5, 3.1.2	FFTW Gaussian	Math, Library, C++
fluent	6.3.26	ANSYS FLUENT	Simulation
gadget	2.0.4, 2.0.5	Atlassian Gadgets	Software Development
gamess	11-Aug11	www.msg.ameslab.gov/gamess GAMESS	Quantum Chemistry
gaussian	03,09	Gaussian	Modeling, Physics
Gromacs	4.0.4, 4.0.7	www.gromacs.org	Physics, Modeling
hypre	2.0.0	HYPRE	Library, Math, Physics
Inelastica	1.1	Inelastica	Quantum Chemistry
IE3D	15.1	IE3D	Simulation, Design
lammps	17-Sept11	LAMPPS	Simulation
madness	0.9	MADNESS Home Page	Math, DIff. Equation solving
mafft	6.859	MAFFT	Biology, Multiple sequence alignment
MACS	1.4.1	MACS	Biology, ChIP-Seq
Matlab	2009b	MathWorks	Math, Simulation, Programming
meep	0.10.0, 0.20.3		Will be removed on 2011-10-30
meme	3.0.13, 4.3.0	MEME	Biology, Motifs, Sequence analysis
metis	4.0	Metis	Math, Graph partitioning
mira	3.2.0	MIRA Guide	Biology, NGS
MrBayes	3.1.2	MrBayes	Biology, Phylogenetics
NAMD	2.7b2	NAMD	Simulation, Chemistry, Biology
netcdf	3.6.3, 4.1.2	[http://www.unidata.ucar.edu/software/netcdf/ NetCDF	Data exchange, Tools
Newbler	2.5.3, 2.6	Newbler	Biology, NGS
NWChem	6.0	NWChem	Simulation, Chemistry
OpenFOAM	1.7.1	OpenFoam	Molecular Dynamics
papi	4.1.2.1	PAPI	CPU API
PeakSplitter	1.0	PeakSplitter	Biology, Chip-Seq
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.