Difference between revisions of "Installed Software"
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| [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html TRF]||Biology, Genomics|| | | [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html TRF]||Biology, Genomics|| | ||
| + | | [[Trinity]] || r20110519, r20110820 || [http://trinityrnaseq.sourceforge.net/ Trinity RNA-Seq]|| | ||
|- | |- | ||
| [[tuxedo|Tophat]] || 1.3.0 || [http://tophat.cbcb.umd.edu/ Tophat]||Biology, NGS|| | | [[tuxedo|Tophat]] || 1.3.0 || [http://tophat.cbcb.umd.edu/ Tophat]||Biology, NGS|| | ||
Revision as of 16:18, 14 October 2011
The following is a list of the installed software at the UF HPC Center.
List updated 12 October 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 | |||||
| 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 | |||||
| Bowtie | 0.12.7 | Bowtie | Biology, NGS | |||||
| Charmm | 35b2 | Charmm | Simulation, Chemistry | |||||
| Circuit | Circuitscape | GIS | ||||||
| CPMD | 3.11.1 | CPMD | Simulation, Chemistry | |||||
| Crystal | 1.0.2 | Will be removed on 2011-10-30 | ||||||
| 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 | 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 | |||||
| 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 | |||||
| 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 | |||||
| meep | 0.10.0, 0.20.3 | Will be removed on 2011-10-30 | ||||||
| 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 | |||||
| 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 | |||||
| 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 | |||||
| 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 | |||||
| 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 | ||
| Tophat | 1.3.0 | Tophat | Biology, NGS | |||||
| tuxedo | The "tuxedo suite," Bowtie, Tophat, and Cufflinks | |||||||
| VASP | 4.6.34,5.2.0 | VASP | Quantum Chemistry, ab initio | |||||
| velvet | 1.1.05 | Velvet | Biology, NGS | |||||
| vmd | 1.9 | VMD | Biology, Visualization | |||||
| weka | 3.6.2 | WEKA | Data mining algorithms | |||||
| 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.