Installed Software
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The following is a list of the installed software at the UF HPC Center.
Last updated 2012-06-18.
Note: Click on the icons to the right of the column headings to sort the table.
Software
Name | Version | Project/Vendor 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 | |
BamUtil | 1.0.2 | BamUtil | 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, 0.12.8 (default), 2.0.0-beta3, 2.0.0-beta5 | 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 | |
CGATools | 1.5.0.31 | CGA Tools | Biology, Genomics | |
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 | |
Dindel | 1.01 | Dindel | Biology, NGS, Genomics | |
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, 5.0 | Espresso | Modeling, Physics | |
Exonerate | 2.2 | Exonerate | Biology, Genomics | |
FAR | 2.15 | [1] | Biology, Genomics | |
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, 20120524, 20120612 | 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 | |
MapSplice | 1.15.2 | MapSplice | Biology, Genomics | |
Matlab | 2009b | MathWorks | Math, Simulation, Programming | |
MATS | 2.1.0 | MATS | BIology, NGS | |
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 | 3.1.2,3.2.1 | 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 | |
Segminator | 0.0.2 | Segminator | Biology, NGS | |
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 | |
SPARTA+ | 2.60 | [URL: http://spin.niddk.nih.gov/bax/software/SPARTA+/] | Chemistry | |
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 | |
tgicl | 2.1 | TGICL | Biology, sequencing, clustering | |
TRF | 4.04 | TRF | Biology, Genomics | |
Trimal | 1.2 | Trimal | Biology, NGS | |
Trinity | r20110820, r20120125, r20120317, r20120608 | 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, 0.1.9 | VCFtools | Biology, SNPs | |
velvet | 1.2.06,1.2.02,1.2.01,1.1.05 | 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.