Installed Software
Revision as of 14:50, 16 November 2011 by Moskalenko (talk | contribs)
The following is a list of the installed software at the UF HPC Center.
List updated 15 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, 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 | ||
| Charmm | 35b2 | Charmm | Simulation, Chemistry | ||
| Circuit | Circuitscape | GIS | |||
| CPMD | 3.11.1 | CPMD | Simulation, Chemistry | ||
| Cufflinks | 1.0.3, 1.1.0 | Cufflinks | Biology, NGS | ||
| dar | 2.3.9 | Dar | Backup | ||
| [[DeFuse | 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 | ||
| 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.txtmay 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.