Installed Software

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

List updated 04 April 2012.


Software Version Home 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
Amber 10,11.old, 11 Amber Simulation, chemistry
Amos 3.0.0 AMOS Biology, Genomics
Ansys 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
beast 1.6.2 BEAST Biology, Phylogenetics
BFAST 0.7.0 BFAST Biology, NGS
Bioconductor 2011-11-16 Bioconductor Biology, R, Statistics
BioPerl BioPerl Biology, Perl
Biopython 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 1.37.0, 1.46.1 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
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   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
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 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 [1] 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 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
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
gaussian 03,09 Gaussian Modeling, Physics
Geneid 1.4 geneid Biology, Genomics, Annotation
Genewise 2.2.3 Wise2 Biology, Genomics, Annotation
GMAP 20070928, 20120111, 20120323 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
hypre 2.0.0 HYPRE Library, Math, Physics
IMa2 8.26.11 IMa2 Biology, Population
Inelastica 1.1 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
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 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
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
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
pqs 3.3-19 PQS Modeling, Chemistry
Prinseq 0.17 Prinseq Biology, NGS
pyopencl 0.92 PyOpenCL python, parallel programming
python 2.5.1, 2.6.4, 2.6.5 Python Programming, scripting, language
R 2.13.1, 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
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
rsm 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 r20110519, r20110820, r20120125 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.