Difference between revisions of "Installed Software"

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| [[dock]] || 6.3, 6.4, 6.5 || [http://dock.compbio.ucsf.edu/ Dock] || Chemistry, ligand binding prediction ||
 
| [[dock]] || 6.3, 6.4, 6.5 || [http://dock.compbio.ucsf.edu/ Dock] || Chemistry, ligand binding prediction ||
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| [[EMAN2]] || 2.04 || [http://blake.bcm.tmc.edu/emanwiki/EMAN2 EMAN2] || Biology, image processing ||
 
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| [[emboss]] || 6.4.0 || [http://emboss.sourceforge.net/ Emboss] || Biology, multi-tool suite ||
 
| [[emboss]] || 6.4.0 || [http://emboss.sourceforge.net/ Emboss] || Biology, multi-tool suite ||

Revision as of 18:01, 2 December 2011

The following is a list of the installed software at the UF HPC Center.

List updated 01 December 2011.

Software

Software Version Home Website Category Notes
Abaqus 6.6-1, 6.9-2 Abaqus Simulation
Abyss 1.3.1 Abyss Biology, NGS
ADMB 9.1, 10.0 ADMB Modeling, math
ALLPATHS-LG 39099 ALLPATHS-LG Biology, NGS
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
BFAST 0.7.0 BFAST Biology, NGS
Bioconductor 2011-11-16 Bioconductor Biology, R, Statistics
bioscope 1.0.1, 1.2.1 ABI BioScope Biology, NGS
Blast 2.2.24, 2.2.25 NCBI Biology, Sequence alignment
BLAT 34 BLAT 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
CASAVA 1.8.2 CASAVA Biology, NGS
CEGMA 2.3 CEGMA Biology, Genomics, Annotation
Charmm 35b2 Charmm Simulation, Chemistry
Circuit   Circuitscape GIS
Cmake 2.8.5 Cmake Programming
CPMD 3.11.1 CPMD Simulation, Chemistry
Cufflinks 1.0.3, 1.1.0 Cufflinks 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
dlpoly 3.0.9 DL_POLY Simulation, Biology, Chemistry
dock 6.3, 6.4, 6.5 Dock Chemistry, ligand binding prediction
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 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
Geneid 1.4 geneid Biology, Genomics, Annotation
Genewise Wise2 Biology, Genomics, Annotation
Gromacs 4.0.4, 4.0.7 Gromacs Physics, Modeling
HDF5 1.8.7 HDF5 Library, Data
HMMER3 3.0 HMMER3 Biology, Genomics
hypre 2.0.0 HYPRE Library, Math, Physics
IMa2 8.26.11 IMa2 Biology, Population
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
Migrate-n 3.2.16 Migrate-n Biology, Population
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
Novoalign 2.07.15 Novoalign 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
PhyloBayes 3.3b PhyloBayes Biology, Phylogenetics
pqs 3.3-19 PQS Modeling, Chemistry
Prinseq 0.17 Prinseq Biology, NGS
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
Ruby 1.9.3 Ruby Programming, Language, Scripting
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
Structure 2.3.3 Structure Biology, Population
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.

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