Installed Software
Revision as of 16:50, 14 November 2011 by Moskalenko (talk | contribs)
The following is a list of the installed software at the UF HPC Center.
List updated 14 November 2011.
Software
Software | Version | Home Website | Category | Notes |
---|---|---|---|---|
Abaqus | 6.6-1, 6.9-2 | Abaqus | Simulation | |
ADMB | 9.1, 10.0 | 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 | 3.1.3 | Antlr | Linguistics, Parser | |
arachne | 37618 | Arachne | Biology, Genomics | |
beast | 1.6.2 | BEAST | Biology, Phylogenetics | |
bioscope | 1.0.1, 1.2.1 | ABI BioScope | Biology, NGS | |
Blast | 2.2.24, 2.2.25 | NCBI | Biology, Sequence alignment | |
Boost | 1.37.0, 1.46.1 | Boost | C++, Library | |
bwa | 0.5.9 | BWA | Biology, NGS | |
Bowtie | 0.12.7 | Bowtie | Biology, NGS | |
CAP3 | 20071015 | CAP3 | Biology, sequence assembly | |
Charmm | 35b2 | Charmm | Simulation, Chemistry | |
Circuit | Circuitscape | GIS | ||
CPMD | 3.11.1 | CPMD | Simulation, Chemistry | |
Cufflinks | 1.0.3 | Cufflinks | Biology, NGS | |
dar | 2.3.9 | Dar | Backup | |
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 | |
emboss | 6.4.0 | Emboss | Biology, multi-tool suite | |
espresso | 3.0, 3.2.2, 4.0.4 | Espresso | Modeling, Physics | |
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 | |
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 | |
Gromacs | 4.0.4, 4.0.7 | Gromacs | Physics, Modeling | |
HDF5 | 1.8.7 | HDF5 | Library, Data | |
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 | |
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 | |
mosaik | 1.1.0021 | MOSAIK | Biology,NGS | |
MPIBlast | 1.6.0 | MPIBlast | Biology, Sequence alignment | |
MrBayes | 3.1.2 | MrBayes | Biology, Phylogenetics | |
NAMD | 2.7b2 | NAMD | Simulation, Chemistry, Biology | |
netcdf | 3.6.3, 4.1.2, 4.1.3 | NetCDF | Data exchange, Tools | HDF5 support in 4.1.3 only |
Newbler | 2.5.3, 2.6 | Newbler | Biology, NGS | |
NWChem | 6.0 | NWChem | Simulation, Chemistry | |
OpenFOAM | 1.7.1 | OpenFoam | Molecular Dynamics | |
PAML | 4.4e | PAML | Biology, Phylogenetics | |
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 | |
riboPicker | 0.4.2 | riboPicker | Biology, Sequence | |
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 | |
SOAPdenovo | 1.05 | SOAPdenovo | Biology, NGS | |
SRA | 2.1.7 | SRA] | biology, NGS | |
Stata | 10 | Stata | Statistics, Data analysis | |
tau | 2.20.1 | TAU | Profiling, Tracing, Programming, Toolkit | |
TRF | 4.04 | TRF | Biology, Genomics | |
Trinity | r20110519, r20110820 | Trinity RNA-Seq | Biology, RNA-Seq | |
Tophat | 1.3.0 | Tophat | Biology, NGS | |
tuxedo | The "tuxedo suite," Bowtie, Tophat, and Cufflinks | |||
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 | 1.1.05 | 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.