The following is a list of the installed software at the UF HPC Center.
List updated 07 October 2011.
Software
| Software |
Version |
Home Website |
Category |
Notes
|
| Abaqus |
6.6-1, 6.9-2 |
|
Simulation |
|
| ADMB |
9.1, 10.0 |
admb-project.org |
Modeling, math |
|
| Amber |
10,11.old, 11 |
amber.scripps.edu |
Simulation, chemistry |
|
| Amos |
3.0.0 |
AMOS SourceForge |
Biology, Genomics |
|
| Ansys |
10.0 |
www.ansys.com |
Simulation, Engineering |
|
| antlr |
3.1.3 |
http://www.antlr.org/ |
Linguistics, Parser |
|
| arachne |
37618 |
Broadinstitute page |
Biology, Genomics |
|
| bioscope |
1.0.1, 1.2.1 |
ABI BioScope |
Biology, NGS |
|
| Blast |
2.2.24, 2.2.25 |
NCBI page |
Biology, Sequence alignment |
|
| Boost |
1.37.0, 1.46.1 |
Boost.org |
C++, Library |
|
| Bowtie |
0.12.7 |
http://bowtie-bio.sourceforge.net/ |
Biology, NGS |
|
| Charmm |
35b2 |
[1] |
Simulation, Chemistry |
|
| Circuit |
|
circuitscape.org |
GIS |
|
| CPMD |
3.11.1 |
www.cpmd.org |
Simulation, Chemistry |
|
| Crystal |
1.0.2 |
|
|
Will be removed on 2011-10-30
|
| Cufflinks |
1.0.3 |
http://cufflinks.cbcb.umd.edu/ |
Biology, NGS |
|
| dar |
2.3.9 |
SF.net |
Backup |
|
| denovo |
2.5.3, 2.6 |
Newbler |
Biology, NGS |
|
| Desmond |
2.4.2.1 |
www.deshawresearch.com/resources_desmond.html Desmond |
Simulation, Biology, Chemistry |
|
| dlpoly |
3.0.9 |
www.cse.clrc.ac.uk |
Simulation, Biology, Chemistry |
|
| dock |
6.3, 6.4 |
dock.compbio.ucsf.edu |
Chemistry, ligand binding prediction |
|
| emboss |
6.4.0 |
emboss.sourceforge.net |
Biology, multi-tool suite |
|
| espresso |
3.0, 3.2.2, 4.0.4 |
quantum-espresso.org
|
| fastqc |
0.10.0 |
FastQC website
|
| fftw |
2.1.5, 3.1.2 |
www.gaussian.com
|
| fluent |
6.3.26 |
|
| gadget |
2.0.4, 2.0.5 |
Atlassian Gadgets website
|
| gamess |
11-Aug11 |
www.msg.ameslab.gov/gamess
|
| gaussian |
03,09 |
www.gaussian.com
|
| Gromacs |
4.0.4, 4.0.7 |
www.gromacs.org
|
| hypre |
2.0.0 |
Lawrence Livermore National Labs
|
| Inelastica |
1.1 |
|
| IE3D |
15.1 |
|
| lammps |
17-Sept11 |
LAMPPS Home Page
|
| madness |
0.9 |
MADNESS Home Page
|
| mafft |
6.859 |
MAFFT Home Page
|
| MACS |
1.4.1 |
MACS Home Page
|
| Matlab |
2009b |
www.mathworks.com
|
| meep |
0.10.0, 0.20.3 |
|
| meme |
3.0.13, 4.3.0 |
|
| metis |
4.0 |
glaros.dtc.umn.edu
|
| mira |
3.2.0 |
|
| MrBayes |
3.1.2 |
mrbayes.scs.fsu.edu
|
| NAMD |
2.7b2 |
www.ks.uiuc.edu
|
| netcdf |
3.6.3, 4.1.2 |
|
| Newbler |
2.5.3, 2.6 |
|
| NWChem |
6.0 |
http://www.nwchem-sw.org
|
| OpenFOAM |
1.7.1 |
|
| papi |
4.1.2.1 |
|
| PeakSplitter |
1.0 |
Upstream sofware page
|
| pdt |
3.16 |
|
| petsc |
2.3.3-p8, 3.0.0-p12 |
|
| pqs |
3.3-19 |
|
| pyopencl |
0.92 |
|
| python |
2.5.1, 2.6.4, 2.6.5 |
|
| RAxML |
7.3.0 |
RAxML
|
| RAxML-Light |
1.0.5 |
RAxML
|
| RepeatMasker |
3.3.0 |
Repeat Masker
|
| Rosetta |
2.1.1, 2.1.2 |
www.rosettacommons.org
|
| rsm |
2961 |
|
| samtools |
0.1.16 |
http://samtools.sourceforge.net/
|
| SAS |
9.2, 9.3 |
SAS
|
| Siesta |
2.0, 2.0.2, 3.0b |
www.uam.es
|
| Stata |
10 |
Stata
|
| tau |
2.20.1 |
|
| TRF |
4.04 |
Tandem Repeats Finder
|
| Tophat |
1.3.0 |
http://tophat.cbcb.umd.edu/
|
| tuxedo |
|
The "tuxedo suite," Bowtie, Tophat, and Cufflinks
|
| VASP |
4.6.34,5.2.0 |
cms.mpi.univie.ac.at
|
| velvet |
1.1.05 |
www.ebi.ac.uk/~zerbino/velvet/
|
| vmd |
1.9 |
|
| weka |
3.6.2 |
|
| wublast |
2.0 |
WU-Blast WU-BLAST Readme file
|
- 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.