Difference between revisions of "Installed Software"
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| [[HTSeq]] || 0.5.3p3 || [http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html HTSeq] || Biology, NGS || | | [[HTSeq]] || 0.5.3p3 || [http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html HTSeq] || Biology, NGS || | ||
| + | |- | ||
| + | | [[HugeSeq]] || 1.0.1 || [http://hugeseq.hugolam.com/ HugeSeq] || Biology, NGS, Genomics || | ||
|- | |- | ||
| [[hypre]] || 2.0.0 || [http://www.llnl.gov/casc/hypre/software.html HYPRE]||Library, Math, Physics|| | | [[hypre]] || 2.0.0 || [http://www.llnl.gov/casc/hypre/software.html HYPRE]||Library, Math, Physics|| | ||
Revision as of 18:57, 18 April 2012
The following is a list of the installed software at the UF HPC Center.
List updated 18 April 2012.
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, 10.1 | ADMB | Modeling, math | |
| ALLPATHS-LG | 39099 | ALLPATHS-LG | Biology, NGS | |
| Amber | 10,11.old, 11, 12 | Amber | Simulation, chemistry | |
| Amos | 3.0.0 | AMOS | Biology, Genomics | |
| ANNOVAR | 20120308 | ANNOVAR | Biology, Genomics | |
| Ansys | 10.0 | Ansys | Simulation, Engineering | |
| antlr | 2.7.7, 3.1.3 | Antlr | Linguistics, Parser | |
| arachne | 37618 | Arachne | Biology, Genomics | |
| Bamtools | 2.1.0 | Bamtools | Biology, NGS | |
| beast | 1.6.2 | BEAST | Biology, Phylogenetics | |
| BEDTools | 2.16.2 | BEDTools | Biology, NGS | |
| BFAST | 0.7.0 | BFAST | Biology, NGS | |
| Bioconductor | 2011-11-16 | Bioconductor | Biology, R, Statistics | |
| BioPerl | BioPerl | Biology, Perl | ||
| Biopython | BioPython | Biology, Python | ||
| bioscope | 1.0.1, 1.2.1 | ABI BioScope | Biology, NGS | |
| Blast | 2.2.24, 2.2.25, 2.2.26 | NCBI | Biology, Sequence alignment | |
| Blast2go | 2.5.0 | Blast2go | Biology, Annotation | |
| 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 | |
| BreakDancer | 1.1 | BreakDancer | Biology, NGS, Genomics | |
| CAP3 | 20071015 | CAP3 | Biology, sequence assembly | |
| CASAVA | 1.8.2 | CASAVA | Biology, NGS | |
| CD-HIT | 4.5.7 | CD-HIT | Biology, Genomics | |
| CEGMA | 2.3 | CEGMA | Biology, Genomics, Annotation | |
| Charmm | 35b2 | Charmm | Simulation, Chemistry | |
| Circuit | Circuitscape | GIS | ||
| CisGenome | 2.0 | CisGenome | Biology, Genomics, Peak Calling | |
| Cmake | 2.8.5 | Cmake | Programming | |
| CNV-seq | 07.15.11 | CNV-seq | Biology, NGS | |
| CNVnator | 0.2.5 | CNVnator | Biology, NGS | |
| CPMD | 3.11.1 | CPMD | Simulation, Chemistry | |
| Cufflinks | 1.0.3, 1.1.0, 1.3.0 | Cufflinks | Biology, NGS | |
| Cutadapt | 1.0 | Cutadapt | 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 | |
| emacs | 21.4.1, 23.4.1 | Gnu Website | The Emacs editor | |
| 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 | |
| FASTA | 34.26.5 | FASTA | Biology, Genomics | |
| 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 | |
| FreeBayes | 0.9.4 | FreeBayes | Biology, | |
| gadget | 2.0.4, 2.0.5 | Atlassian Gadgets | Software Development | |
| gamess | 11-Aug11 | GAMESS | Quantum Chemistry | |
| garli | 2.0 | GARLI | Biology, Phylogenetics | |
| GATK | 1.4.30 | GATK | Biology, NGS | |
| gaussian | 03,09 | Gaussian | Modeling, Physics | |
| Geneid | 1.4 | geneid | Biology, Genomics, Annotation | |
| Genewise | 2.2.3 | Wise2 | Biology, Genomics, Annotation | |
| GMAP | 20070928, 20120111, 20120323 | GMAP | Biology, Genomics | |
| Grace | 5.1.22 | Grace | Graphics, plotting, 2D | |
| Gromacs | 4.0.4, 4.0.7 | Gromacs | Physics, Modeling | |
| HDF5 | 1.8.7, 1.8.8 | HDF5 | Library, Data | |
| HMMER3 | 3.0 | HMMER3 | Biology, Genomics | |
| HTSeq | 0.5.3p3 | HTSeq | Biology, NGS | |
| HugeSeq | 1.0.1 | HugeSeq | Biology, NGS, Genomics | |
| hypre | 2.0.0 | HYPRE | Library, Math, Physics | |
| IMa2 | 8.26.11 | IMa2 | Biology, Population | |
| Inelastica | 1.1 (python/2.7.2) | Inelastica | Quantum Chemistry | |
| IE3D | 15.1 | IE3D | Simulation, Design | |
| JDK | 1.6.0_12, 1.7.0 | Oracle JDK | Java Development Kit | |
| Khmer | 20120321 | Khmer | Biology, NGS, Utilities | |
| Kmer | r1909 | Kmer package | Biology, NGS, genome alignment | |
| lammps | 17-Sept11 | LAMPPS | Simulation | |
| Last | 193 | Last | Biology, Sequence alignment | |
| libxc | 1.1.0 | libxc | Math, funtionals | |
| MACS | 1.4.1 | MACS | Biology, ChIP-Seq | |
| madness | 1769 | MADNESS | Math, DIff. Equation solving | |
| mafft | 6.859 | MAFFT | Biology, Multiple sequence alignment | |
| Maker | 2.10 | Maker | Biology, Annotation, Genomics | |
| Matlab | 2009b | MathWorks | Math, Simulation, Programming | |
| Mauve | 2.3.1 | Mauve | Biology, Multiple genome alignments | |
| MCL | 11-335 | MCL | Biology, Genomics, Clustering | |
| meme | 3.0.13, 4.3.0 | MEME | Biology, Motifs, Sequence analysis | |
| MetaPhyler | 1.13 | MetaPhyler | Biology, Metagenomics | |
| metis | 4.0 | Metis | Math, Graph partitioning | |
| Migrate-n | 3.2.16 | Migrate-n | Biology, Population | |
| mira | 3.2.0, 3.4.0.1 | MIRA | Biology, NGS | |
| mosaik | 1.1.0021 | MOSAIK | Biology,NGS | |
| MPIBlast | 1.6.0 | MPIBlast | Biology, Sequence alignment | |
| MrBayes | 3.1.2 | MrBayes | Biology, Phylogenetics | |
| MUMmer | 3.22 | MUMmer | Biology, Genomics | |
| MUSCLE | 3.8.31 | MUSCLE | Biology, Genomics | |
| NAMD | 2.7b2 | NAMD | Simulation, Chemistry, Biology | |
| NCO | 4.0.9 | NCO | Data exchange tools | |
| netcdf | 3.6.3, 4.1.2, 4.1.3 | NetCDF | Data exchange, Tools | HDF5 support in 4.1.3 only |
| NetLogo | 4.1.3 | NetLogo | Modeling | |
| Newbler | 2.5.3, 2.6 | Newbler | Biology, NGS | |
| NFFT | 3.1.3 | nfft | NDFT, library, math | |
| Novoalign | 2.07.15 | Novoalign | Biology, NGS | |
| NWChem | 6.0 | NWChem | Simulation, Chemistry | |
| Oases | 0.2.04 | Oases | Biology, NGS | |
| OpenFOAM | 1.7.1 | OpenFoam | Molecular Dynamics | |
| OrthoMCL | 2.0 | OrthoMCL | Biology, Genomics | |
| PAL2NAL | 14 | PAL2NAL | Biology, bioinformatics, multiple sequence alignment | |
| PAML | 4.4e | PAML | Biology, Phylogenetics | |
| papi | 4.1.2.1 | PAPI | CPU API | |
| PASA | 20110520 | PASA | Biology, Genomics | |
| PeakSplitter | 1.0 | PeakSplitter | Biology, Chip-Seq | |
| pdt | 3.16 | PDT | Programming, Profiler | |
| Perl | 5.14.1 | Perl | Programming, Language | |
| petsc | 2.3.3-p8, 3.0.0-p12 | PETSc | MPI toolkit | |
| Phred | 020425 | Phred | Biology, Genomics, Sequencing | |
| PhyloBayes | 3.3b | PhyloBayes | Biology, Phylogenetics | |
| PhyML | 3.0 | PhyML | Biology, Phylogenetics | |
| Picard | 1.54 | Picard | Biology, NGS | |
| Pindel | 0.2.8 | Pindel | Biology, NGS | |
| pqs | 3.3-19 | PQS | Modeling, Chemistry | |
| Prinseq | 0.17 | Prinseq | Biology, NGS | |
| pyopencl | 0.92 | PyOpenCL | python, parallel programming | |
| python | 2.6.5, 2.7.2 | Python | Programming, scripting, language | |
| R | 2.13.1, 2.14.1, 2.14.1-MPI, 2.14.2 | R | Statistics, Programming | |
| RAxML | 7.3.0 | RAxML | Biology, Phylogenetics | |
| RAxML-Light | 1.0.5 | RAxML | Biology, Phylogenetics | |
| RepeatMasker | 3.3.0 | Repeat Masker | Biology, Genomics | |
| Reptile | 1.1, 1.1-omp | Reptile | Biology, NGS, error correction | |
| 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, 0.1.18 | Samtools | Biology, NGS | |
| SAS | 9.2, 9.3 | SAS | Statistics, Graphing | |
| SATe | 2.1.0 | SATe | Biology, Phylogenetics | |
| Scala | 2.9.1 | Scala | Programming, language, java | |
| SeqPrep | 0.4 | SeqPrep | Biology, NGS | |
| 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 | |
| SRNAPredict | 3.0 | sRNAPredict | Biology, Genomics | |
| SRNAScanner | 200903 | sRNAScanner | Biology, Genomics | |
| Staden | 2.0.0b9 | Staden | Biology, Genomics, Sequencing | |
| 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 | |
| Trimal | 1.2 | Trimal | Biology, NGS | |
| Trinity | r20110519, r20110820, r20120125 | Trinity RNA-Seq | Biology, RNA-Seq | |
| Tophat | 1.3.0, 1.3.3, 1.4.1 | Tophat | Biology, NGS | |
| tuxedo | The "tuxedo suite" - Bowtie, Tophat, and Cufflinks | |||
| Twinscan | 3.5,4.1.2 | Twinscan | Biology, Genomics | |
| 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 | 1.2.02,1.2.01,1.1.05 | 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.