UFRC Help and Documentation

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

List updated 11 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	Cufflinks	Biology, NGS
dar	2.3.9	SF.net	Backup
Desmond	2.4.2.1	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	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	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	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	PDT	Programming, Profiler
petsc	2.3.3-p8, 3.0.0-p12	PETSc	MPI toolkit
pqs	3.3-19	PQS	Modeling, Chemistry
pyopencl	0.92	PyOpenCL	python, parallel programming
python	2.5.1, 2.6.4, 2.6.5	Python	Programming, scripting, language
RAxML	7.3.0	RAxML	Biology, Phylogenetics
RAxML-Light	1.0.5	RAxML	Biology, Phylogenetics
RepeatMasker	3.3.0	Repeat Masker	Biology, Genomics
Rosetta	2.1.1, 2.1.2	Rosetta	Biology, Structural, Modeling
rsm	2961	RSM	Math, Modeling, Geometry
samtools	0.1.16	Samtools	Biology, NGS
SAS	9.2, 9.3	SAS	Statistics, Graphing
Siesta	2.0, 2.0.2, 3.0b	Siesta	Simulation, physics, ab-initio
Stata	10	Stata	Statistics, Data analysis
tau	2.20.1	TAU	Profiling, Tracing, Programming, Toolkit
TRF	4.04	TRF	Biology, Genomics
Tophat	1.3.0	Tophat	Biology, NGS
tuxedo	The "tuxedo suite," Bowtie, Tophat, and Cufflinks
VASP	4.6.34,5.2.0	VASP	Quantum Chemistry, ab initio
velvet	1.1.05	Velvet	Biology, NGS
vmd	1.9	VMD	Biology, Visualization
weka	3.6.2	WEKA	Data mining algorithms
wublast	2.0	WU-Blast	Biology, Sequence Alignment

• 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.