Installed Software

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

Last updated: 12 May 2012.

Note: Click on the icons to the right of the column headings to sort the table.

Software

Name	Version	Website	Category	Notes
Abaqus	6.6-1, 6.9-2	Abaqus	Simulation
Abyss	1.3.1	Abyss	Biology, NGS
ADMB	9.1, 10.0, 10.1	ADMB	Modeling, math
ALLPATHS-LG	39099, 40122, 41655	ALLPATHS-LG	Biology, NGS
Amber	10,11.old, 11, 12	Amber	Simulation, chemistry
Amos	3.0.0	AMOS	Biology, Genomics
ANNOVAR	20120308	ANNOVAR	Biology, Genomics
Ansys	9.0, 10.0	Ansys	Simulation, Engineering
antlr	2.7.7, 3.1.3	Antlr	Linguistics, Parser
arachne	37618	Arachne	Biology, Genomics
Bamtools	2.1.0	Bamtools	Biology, NGS
BayesPhylogenies	2.0	BayesPhylogenies	Biology, Phylogenetics
beast	1.6.2	BEAST	Biology, Phylogenetics
BEDTools	2.16.2	BEDTools	Biology, NGS
BFAST	0.7.0	BFAST	Biology, NGS
Bioconductor	2011-11-16	Bioconductor	Biology, R, Statistics
BioPerl	1.006901	BioPerl	Biology, Perl
Biopython	1.59	BioPython	Biology, Python
bioscope	1.0.1, 1.2.1	ABI BioScope	Biology, NGS
Blast	2.2.24, 2.2.25, 2.2.26	NCBI	Biology, Sequence alignment
Blast2go	2.5.0	Blast2go	Biology, Annotation
BLAT	34	BLAT	Biology, Sequence alignment
Boost	1.38.0, 1.46.1, 1.48.0, 1.49.0	Boost	C++, Library
bwa	0.5.9, 0.5.10, 0.6.0 (default)	BWA	Biology, NGS
Bowtie	0.12.7 (default), 2.0.0-beta3	Bowtie	Biology, NGS
BreakDancer	1.1	BreakDancer	Biology, NGS, Genomics
CAP3	20071015	CAP3	Biology, sequence assembly
CASAVA	1.8.2	CASAVA	Biology, NGS
CD-HIT	4.5.7	CD-HIT	Biology, Genomics
CEGMA	2.3	CEGMA	Biology, Genomics, Annotation
Charmm	35b2	Charmm	Simulation, Chemistry
Circuit	3.5.1, 3.5.7	Circuitscape	GIS
CisGenome	2.0	CisGenome	Biology, Genomics, Peak Calling
Cmake	2.8.5	Cmake	Programming
CNV-seq	07.15.11	CNV-seq	Biology, NGS
CNVnator	0.2.5	CNVnator	Biology, NGS
CPMD	3.11.1	CPMD	Simulation, Chemistry
Cufflinks	1.0.3, 1.1.0, 1.3.0	Cufflinks	Biology, NGS
Cutadapt	1.0	Cutadapt	Biology, NGS
dar	2.3.9	Dar	Backup
deFuse	0.4.3	deFuse	Biology, RNA-seq
Desmond	2.4.2.1	Desmond	Simulation, Biology, Chemistry
dlpoly	3.0.9	DL_POLY	Simulation, Biology, Chemistry
dock	6.3, 6.4, 6.5	Dock	Chemistry, ligand binding prediction
emacs	21.4.1, 23.4.1	Gnu Website	The Emacs editor
EMAN2	2.04	EMAN2	Biology, image processing
emboss	6.4.0	Emboss	Biology, multi-tool suite
espresso	3.0, 3.2.2, 4.0.4	Espresso	Modeling, Physics
FASTA	34.26.5	FASTA	Biology, Genomics
fastx_toolkit	0.0.13.1	Fastx Tolkit	Biology, NGS
fastqc	0.10.0	FastQC	Biology, NGS
fftw	2.1.5, 3.1.2	FFTW Gaussian	Math, Library, C++
fluent	6.3.26	ANSYS FLUENT	Simulation
FragGeneScan	1.16	FragGeneScan	Biology, NGS
FreeBayes	0.9.4	FreeBayes	Biology,
gadget	2.0.4, 2.0.5	Atlassian Gadgets	Software Development
gamess	11-Aug11	GAMESS	Quantum Chemistry
garli	2.0	GARLI	Biology, Phylogenetics
GATK	1.4.30	GATK	Biology, NGS
gulp	4.0.3	GULP	Modeling/simulation, Computational Chemistry
gaussian	E01, G03, G09-A.02, G09-C.01	Gaussian	Modeling, Computational Chemistry
Geneid	1.4	geneid	Biology, Genomics, Annotation
GeneMark	2012.04	GeneMark	Biology, Genomics, Metagenomics
Genewise	2.2.3	Wise2	Biology, Genomics, Annotation
GMAP	20070928, 20120111, 20120323, 20120427	GMAP	Biology, Genomics
Grace	5.1.22	Grace	Graphics, plotting, 2D
Gromacs	4.0.4, 4.0.7	Gromacs	Physics, Modeling
HDF5	1.8.7, 1.8.8	HDF5	Library, Data
HMMER3	3.0	HMMER3	Biology, Genomics
HTSeq	0.5.3p3	HTSeq	Biology, NGS
HugeSeq	1.0.1	HugeSeq	Biology, NGS, Genomics
hypre	2.8.0	HYPRE	Library, Math, Physics
IMa2	8.26.11	IMa2	Biology, Population
Inelastica	1.1 (python/2.7.2)	Inelastica	Quantum Chemistry
IE3D	15.1	IE3D	Simulation, Design
JDK	1.6.0_12, 1.7.0	Oracle JDK	Java Development Kit
Khmer	20120321	Khmer	Biology, NGS, Utilities
Kmer	r1909	Kmer package	Biology, NGS, genome alignment
lammps	17-Sept11	LAMPPS	Simulation
Last	193	Last	Biology, Sequence alignment
libxc	1.1.0	libxc	Math, funtionals
MACS	1.4.1	MACS	Biology, ChIP-Seq
madness	1769	MADNESS	Math, DIff. Equation solving
mafft	6.859	MAFFT	Biology, Multiple sequence alignment
Maker	2.10	Maker	Biology, Annotation, Genomics
Matlab	2009b	MathWorks	Math, Simulation, Programming
Mauve	2.3.1	Mauve	Biology, Multiple genome alignments
MCL	11-335	MCL	Biology, Genomics, Clustering
meme	3.0.13, 4.3.0	MEME	Biology, Motifs, Sequence analysis
MetaPhyler	1.13	MetaPhyler	Biology, Metagenomics
metis	4.0	Metis	Math, Graph partitioning
Migrate-n	3.2.16	Migrate-n	Biology, Population
mira	3.2.0, 3.4.0.1	MIRA	Biology, NGS
mosaik	1.1.0021	MOSAIK	Biology,NGS
MPIBlast	1.6.0	MPIBlast	Biology, Sequence alignment
MrBayes	3.1.2	MrBayes	Biology, Phylogenetics
MUMmer	3.22	MUMmer	Biology, Genomics
MUSCLE	3.8.31	MUSCLE	Biology, Genomics
NAMD	2.7b2	NAMD	Simulation, Chemistry, Biology
NCO	4.0.9	NCO	Data exchange tools
netcdf	3.6.3, 4.1.2, 4.1.3	NetCDF	Data exchange, Tools	HDF5 support in 4.1.3 only
NetLogo	4.1.3	NetLogo	Modeling
Newbler	2.5.3, 2.6	Newbler	Biology, NGS
NFFT	3.1.3	nfft	NDFT, library, math
Novoalign	2.07.15	Novoalign	Biology, NGS
NWChem	6.0	NWChem	Simulation, Chemistry
Oases	0.2.04	Oases	Biology, NGS
OpenFOAM	1.7.1	OpenFoam	Molecular Dynamics
OrthoMCL	2.0	OrthoMCL	Biology, Genomics
PAL2NAL	14	PAL2NAL	Biology, bioinformatics, multiple sequence alignment
PAML	4.4e	PAML	Biology, Phylogenetics
PAPI	4.1.2.1	PAPI	CPU API
PASA	20110520	PASA	Biology, Genomics
PeakSplitter	1.0	PeakSplitter	Biology, Chip-Seq
PDT	3.16	PDT	Programming, Profiler
Perl	5.14.1	Perl	Programming, Language
PETSc	2.3.3-p8, 3.0.0-p12	PETSc	MPI toolkit
Phred	020425	Phred	Biology, Genomics, Sequencing
PhyloBayes	3.3b	PhyloBayes	Biology, Phylogenetics
PhyML	3.0	PhyML	Biology, Phylogenetics
Picard	1.54	Picard	Biology, NGS
Pindel	0.2.8	Pindel	Biology, NGS
PQS	3.3-19	PQS	Modeling, Chemistry
Prinseq	0.17	Prinseq	Biology, NGS
PyOpenCL	2012.04	PyOpenCL	python, parallel programming
python	2.6.5, 2.7.2, 2.7.3	Python	Programming, scripting, language
R	2.14.1, 2.14.1-MPI, 2.14.2	R	Statistics, Programming
RAxML	7.3.0	RAxML	Biology, Phylogenetics
RAxML-Light	1.0.5	RAxML	Biology, Phylogenetics
RepeatMasker	3.3.0	Repeat Masker	Biology, Genomics
Reptile	1.1, 1.1-omp	Reptile	Biology, NGS, error correction
riboPicker	0.4.2	riboPicker	Biology, Sequence
Rosetta	2.1.1, 2.1.2	Rosetta	Biology, Structural, Modeling
Ruby	1.9.3	Ruby	Programming, Language, Scripting
RSMToolkit	2961	RSM	Math, Modeling, Geometry
samtools	0.1.16, 0.1.18	Samtools	Biology, NGS
SAS	9.2, 9.3	SAS	Statistics, Graphing
SATe	2.1.0	SATe	Biology, Phylogenetics
Scala	2.9.1	Scala	Programming, language, java
SeqPrep	0.4	SeqPrep	Biology, NGS
Siesta	2.0, 2.0.2, 3.0b	Siesta	Simulation, physics, ab-initio
SOAPdenovo	1.05	SOAPdenovo	Biology, NGS
SRA	2.1.7	SRA]	biology, NGS
SRNAPredict	3.0	sRNAPredict	Biology, Genomics
SRNAScanner	200903	sRNAScanner	Biology, Genomics
Staden	2.0.0b9	Staden	Biology, Genomics, Sequencing
Stata	10	Stata	Statistics, Data analysis
Structure	2.3.3	Structure	Biology, Population
TAU	2.20.1	TAU	Profiling, Tracing, Programming, Toolkit
TRF	4.04	TRF	Biology, Genomics
Trimal	1.2	Trimal	Biology, NGS
Trinity	r20110820, r20120125, r20120317	Trinity RNA-Seq	Biology, RNA-Seq
Tophat	1.3.0, 1.3.3, 1.4.1	Tophat	Biology, NGS
tuxedo	The "tuxedo suite" - Bowtie, Tophat, and Cufflinks
Twinscan	3.5,4.1.2	Twinscan	Biology, Genomics
usearch	5.0.151,5.1.221	USEARCH	Biology, Sequence analysis
VASP	4.6.34,5.2.0	VASP	Quantum Chemistry, ab initio
VCFtools	0.1.7	VCFtools	Biology, SNPs
velvet	1.2.02,1.2.01,1.1.05	Velvet	Biology, NGS
vmd	1.9	VMD	Biology, Visualization
weka	3.6.2	WEKA	Data mining algorithms
wgs	6.1, 6.1-20110830	Celera WGS Assembler	Biology,Assembler,Genome
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.

To add a documentation page for a new piece of software installed into /apps please go to Add New App Page.