Installed Software
Revision as of 13:48, 6 July 2012 by Moskalenko (talk | contribs)
The following is a list of the installed software at the UF HPC Center.
Last updated 2012-07-06.
Note: Click on the icons to the right of the column headings to sort the table.
Software
Name | Version [1] | Website | Category | EL5 [2] | EL6[3] |
---|---|---|---|---|---|
Abaqus | 6.6-1, 6.9-2 | [1] | Simulation | X | |
Abyss | 1.3.1 | [2] | Biology, NGS | X | X |
ADMB | 9.1, 10.0, 10.1 | [3] | Modeling, math | X | |
ALLPATHS-LG | 39099, 40122, 41655, 42316 (EL6) | [4] | Biology, NGS | X | X |
Amber | 10,11.old, 11, 12 | [5] | Simulation, chemistry | X | X |
Amos | 3.0.0 | [6] | Biology, Genomics | X | |
ANNOVAR | 20120308 | [7] | Biology, Genomics | X | |
Ansys | 9.0, 10.0 | [8] | Simulation, Engineering | X | |
antlr | 2.7.7, 3.1.3 | [9] | Linguistics, Parser | X | |
arachne | 37618 | [10] | Biology, Genomics | X | |
Augustus | 2.6 | [11] | Biology, NGS | X | X |
Bamtools | 2.1.0 | [12] | Biology, NGS | X | X |
BamUtil | 1.0.2 | [13] | Biology, NGS | X | |
BayesPhylogenies | 2.0 | [14] | Biology, Phylogenetics | X | |
beast | 1.6.2, 1.7.0, 1.7.1 | [15] | Biology, Phylogenetics | X | |
BEDTools | 2.16.2 | [16] | Biology, NGS | X | X |
BFAST | 0.7.0 | [17] | Biology, NGS | X | |
Bismark | 0.7.4 | [18] | Biology, Methylation, NGS | X | X |
Bioconductor | 2011-11-16 | [19] | Biology, R, Statistics | X | |
BioPerl | 1.006901 | [20] | Biology, Perl | X | X |
Biopython | 1.59 | [21] | Biology, Python | X | X |
bioscope | 1.0.1, 1.2.1 | ABI | Biology, NGS | X | |
Blast | 2.2.24, 2.2.25, 2.2.26 | [22] | Biology, Sequence alignment | X | X |
Blast2go | 2.5.0-20120220, 2.5.0-20120705 (EL6) | [23] | Biology, Annotation | X | X |
BLAT | 34 | [24] | Biology, Sequence alignment | X | X |
Boost | 1.38.0, 1.46.1, 1.48.0, 1.49.0 | [25] | C++, Library | X | X |
bwa | 0.5.9, 0.5.10, 0.6.0 (default) | [26] | Biology, NGS | X | X |
Bowtie | 0.12.8 (default), 2.0.0-beta5 | [27] | Biology, NGS | X | X |
BreakDancer | 1.1 | [28] | Biology, NGS, Genomics | X | |
CAP3 | 20071015 | [29] | Biology, sequence assembly | X | X |
CASAVA | 1.8.2 | [30] | Biology, NGS | X | |
CD-HIT | 4.5.7, 4.6 (EL6) | [31] | Biology, Genomics | X | X |
CEGMA | 2.3 | [32] | Biology, Genomics, Annotation | X | |
CGATools | 1.5.0.31 | [33] | Biology, Genomics | X | |
Charmm | 35b2 | [34] | Simulation, Chemistry | X | |
Circuit | 3.5.1, 3.5.7 | [35] | GIS | X | |
CisGenome | 2.0 | [36] | Biology, Genomics, Peak Calling | X | |
CMake | 2.8.5 | [37] | Programming | X | X |
CNV-seq | 07.15.11 | [38] | Biology, NGS | X | |
CNVnator | 0.2.5 | [39] | Biology, NGS | X | |
Consed | 23.0 | [40] | Biology, Genomics | X | X |
CPMD | 3.11.1 | [41] | Simulation, Chemistry | X | |
Cufflinks | 1.0.3, 1.1.0, 1.3.0 | [42] | Biology, NGS | X | X |
Cutadapt | 1.1 | [43] | Biology, NGS | X | X |
dar | 2.3.9 | [44] | Backup | X | |
deFuse | 0.4.3 | [45] | Biology, RNA-seq | X | |
Desmond | 2.4.2.1 | [46] | Simulation, Biology, Chemistry | X | |
Dindel | 1.01 | [47] | Biology, NGS, Genomics | X | |
dlpoly | 3.0.9 | [48] | Simulation, Biology, Chemistry | X | |
dock | 6.3, 6.4, 6.5 | [49] | Chemistry, ligand binding prediction | X | |
emacs | 21.4.1, 23.4.1 | [50] | The Emacs editor | X | |
EMAN2 | 2.04 | [51] | Biology, image processing | X | |
emboss | 6.4.0 | [52] | Biology, multi-tool suite | X | |
espresso | 3.0, 3.2.2, 4.0.4, 5.0 | [53] | Modeling, Physics | X | |
Exonerate | 2.2 | [54] | Biology, Genomics | X | X |
FAR | 2.15 | [55] | Biology, Genomics | X | X |
FASTA | 34.26.5 | [56] | Biology, Genomics | X | X |
FastQC | 0.9.6, 0.10.0 | [57] | Biology, NGS | X | X |
fastx_toolkit | 0.0.13.1 | [58] | Biology, NGS | X | X |
fftw | 2.1.5, 3.1.2 | [59] | Math, Library, C++ | X | |
fluent | 6.3.26 | [60] | Simulation | X | |
FragGeneScan | 1.16 | [61] | Biology, NGS | X | |
FreeBayes | 0.9.4 | [62] | Biology | X | X |
gadget | 2.0.4, 2.0.5 | [63] | Software Development | X | |
gamess | 11-Aug11 | [64] | Quantum Chemistry | X | |
garli | 2.0 | [65] | Biology, Phylogenetics | X | |
GATK | 1.4.30 | [66] | Biology, NGS | X | |
gulp | 4.0.3 | [67] | Modeling/simulation, Chemistry | X | |
gaussian | E01, G03, G09-A.02, G09-C.01 | [68] | Modeling, Computational Chemistry | X | X |
Geneid | 1.4 | [69] | Biology, Genomics, Annotation | X | |
GeneMark | 2012.04 | [70] | Biology, Genomics, Metagenomics | X | X |
Genewise | 2.2.3 | [71] | Biology, Genomics, Annotation | X | |
GMAP | 20070928, 20120612, 20120703 | [72] | Biology, Genomics | X | X |
Grace | 5.1.22 | [73] | Graphics, plotting, 2D | X | |
Gromacs | 4.0.4, 4.0.7 | [74] | Physics, Modeling | X | |
HDF5 | 1.8.7, 1.8.8 | [75] | Library, Data | X | |
HMMER3 | 3.0 | [76] | Biology, Genomics | X | |
HTSeq | 0.5.3p3 | [77] | Biology, NGS | X | |
HugeSeq | 1.0.1 | [78] | Biology, NGS, Genomics | X | |
hypre | 2.8.0 | [79] | Library, Math, Physics | X | X |
IM and IMa | 2009.12.17 | [80] | Biology, Population | X | |
IMa2 | 8.26.11 | [81] | Biology, Population | X | |
Inelastica | 1.1 (python/2.7.2) | [82] | Quantum Chemistry | X | |
IE3D | 15.1 | [83] | Simulation, Design | X | |
Iprscan | 4.8 | [84] | BIology, Genomics | X | |
JDK | 1.6.0_12, 1.7.0 | [85] | Java Development Kit | X | |
Kent | 20120423 | [86] | Biology, NGS | X | X |
Khmer | 20120321 | [87] | Biology, NGS, Utilities | X | |
Kmer | r1909 | [88] | Biology, NGS, genome alignment | X | X |
lammps | 17-Sept11 | [89] | Simulation | X | |
Last | 193 | [90] | Biology, Sequence alignment | X | |
libxc | 1.1.0 | [91] | Math, funtionals | X | |
MACS | 1.4.1 | [92] | Biology, ChIP-Seq | X | |
madness | 1769 | [93] | Math, DIff. Equation solving | X | |
mafft | 6.859 | [94] | Biology, Multiple sequence alignment | X | X |
Maker | 2.10 | [95] | Biology, Annotation, Genomics | X | X |
MapSplice | 1.15.2 | [96] | Biology, Genomics | X | |
Matlab | 2009b | [97] | Math, Simulation, Programming | X | |
MATS | 2.1.0 | [98] | BIology, NGS | X | |
Mauve | 2.3.1 | [99] | Biology, Multiple genome alignments | X | |
MCL | 11-335 | [100] | Biology, Genomics, Clustering | X | |
MCNP | 5, 6beta2 | [101] | Physics | X | |
MCNPX | 2.7.0 | [102] | Physics | X | |
meme | 3.0.13, 4.3.0 | [103] | Biology, Motifs, Sequence analysis | X | |
MetaPhyler | 1.13 | [104] | Biology, Metagenomics | X | |
metis | 4.0 | [105] | Math, Graph partitioning | X | |
Migrate-n | 3.2.16 | [106] | Biology, Population | X | |
mira | 3.2.0, 3.4.0.1 | [107] | Biology, NGS | X | |
mosaik | 1.1.0021 | [108] | Biology,NGS | X | X |
MPIBlast | 1.6.0 | [109] | Biology, Sequence alignment | X | |
MrBayes | 3.1.2,3.2.1 | [110] | Biology, Phylogenetics | X | |
MUMmer | 3.22, 3.23 | [111] | Biology, Genomics | X | X |
MUSCLE | 3.8.31 | [112] | Biology, Genomics | X | X |
NAMD | 2.7b2 | [113] | Simulation, Chemistry, Biology | X | |
NCO | 4.0.9 | [114] | Data exchange tools | X | |
netcdf | 3.6.3, 4.1.2, 4.1.3 | [115] | Data exchange, Tools | X | |
NetLogo | 4.1.3 | [116] | Modeling | X | |
Newbler | 2.5.3, 2.6 | [117] | Biology, NGS | X | X |
NFFT | 3.1.3 | [118] | NDFT, library, math | X | |
Novoalign | 2.07.15 | [119] | Biology, NGS | X | |
NWChem | 6.0 | [120] | Simulation, Chemistry | X | |
Oases | 0.2.04 | [121] | Biology, NGS | X | |
OpenFOAM | 1.7.1 | [122] | Molecular Dynamics | X | |
OrthoMCL | 2.0 | [123] | Biology, Genomics | X | |
PAL2NAL | 14 | [124] | Biology, Genomics | X | |
PAML | 4.4e | [125] | Biology, Phylogenetics | X | |
PAPI | 4.1.2.1 | [126] | CPU API | X | |
Parflow | v615 | [127] | Ecology, Modeling | X | |
PASA | 20110520 | [128] | Biology, Genomics | X | X |
PeakSplitter | 1.0 | [129] | Biology, Chip-Seq | X | |
PDT | 3.16 | [130] | Programming, Profiler | X | |
Perl | 5.14.1 | [131] | Programming, Language | X | X |
PETSc | 2.3.3-p8, 3.0.0-p12 | [132] | MPI toolkit | X | |
Phred | 020425 | [133] | Biology, Genomics, Sequencing | X | |
PhyloBayes | 3.3b | [134] | Biology, Phylogenetics | X | |
PhyML | 3.0 | [135] | Biology, Phylogenetics | X | |
Picard | 1.54 | [136] | Biology, NGS | X | X |
Pindel | 0.2.8 | [137] | Biology, NGS | X | |
PQS | 3.3-19 | [138] | Modeling, Chemistry | X | |
Prinseq | 0.17 | [139] | Biology, NGS | X | |
PyOpenCL | 2012.04 | [140] | python, parallel programming | X | |
python | 2.6.5, 2.7.2, 2.7.3 | [141] | Programming, scripting, language | X | X |
R | 2.14.1, 2.14.1-MPI, 2.14.2 | [142] | Statistics, Programming | X | X |
RAxML | 7.3.0,7.3.1 | [143] | Biology, Phylogenetics | X | X |
RAxML-Light | 1.0.5 | [144] | Biology, Phylogenetics | X | |
RepeatMasker | 3.3.0 | [145] | Biology, Genomics | X | X |
Reptile | 1.1, 1.1-omp | [146] | Biology, NGS, error correction | X | X |
riboPicker | 0.4.2 | [147] | Biology, Sequence | X | |
Rosetta | 2.1.1, 2.1.2 | [148] | Biology, Structural, Modeling | X | |
Ruby | 1.9.3 | [149] | Programming, Language, Scripting | X | |
RSMToolkit | 2961 | [150] | Math, Modeling, Geometry | X | |
samtools | 0.1.16, 0.1.18 | [151] | Biology, NGS | X | X |
SAS | 9.2, 9.3 | [152] | Statistics, Graphing | X | X |
SATe | 2.1.0 | [153] | Biology, Phylogenetics | X | |
Scala | 2.9.1 | [154] | Programming, language, java | X | |
Segminator | 0.0.2 | [155] | Biology, NGS | X | |
SeqPrep | 0.4, 0.5 (EL6) | [156] | Biology, NGS | X | X |
Siesta | 2.0, 2.0.2, 3.0b | [157] | Simulation, physics, ab-initio | X | |
Silo | 4.7 | [158] | Library, Data | X | X |
Snap | 20100728 | [159] | Biology, Genomics | X | X |
SOAPdenovo | 1.05 | [160] | Biology, NGS | X | X |
SPARTA+ | 2.60 | [161] | Chemistry | X | |
SRA | 2.1.7 | [162]] | biology, NGS | X | X |
SRNAPredict | 3.0 | [163] | Biology, Genomics | X | |
SRNAScanner | 200903 | [164] | Biology, Genomics | X | |
Staden | 2.0.0b9 | [165] | Biology, Genomics, Sequencing | X | X |
Stata | 10 | [166] | Statistics, Data analysis | X | |
Structure | 2.3.3 | [167] | Biology, Population | X | X |
TAU | 2.20.1 | [168] | Profiling, Tracing, Programming | X | |
tgicl | 2.1 | [169] | Biology, sequencing, clustering | X | X |
TRF | 4.04 | [170] | Biology, Genomics | X | X |
Trimal | 1.2 | [171] | Biology, NGS | X | |
Trinity | r20120125, r20120317, r20120608 | [172] | Biology, RNA-Seq | X | X |
Tophat | 1.3.0, 1.3.3, 1.4.1 | [173] | Biology, NGS | X | X |
Twinscan | 3.5,4.1.2 | [174] | Biology, Genomics | X | |
usearch | 5.0.151,5.1.221, 5.2.32 (EL6) | [175] | Biology, Sequence analysis | X | X |
VASP | 4.6.34,5.2.0 | [176] | Quantum Chemistry, ab initio | X | |
VCFtools | 0.1.7 (EL5), 0.1.9 | [177] | Biology, SNPs | X | X |
velvet | 1.2.06,1.2.02,1.2.01,1.1.05 | [178] | Biology, NGS | X | X |
vmd | 1.9 | [179] | Biology, Visualization | X | |
weka | 3.6.2 | [180] | Data mining algorithms | X | |
wgs | 6.1, 6.1-20110830 | [181] | Biology,Assembler,Genome | X | X |
wublast | 2.0 | [182] | Biology, Sequence Alignment | X | X |
- ↑ Up to 3 most recent/important releases are listed. See the software wiki pages and the output of "module spider software" for full version listing.
- ↑ Operating system: CentOS 5 - currently in production at UF HPC. Please file a Support Request Ticket for EL5 software installation
- ↑ Operating system: RedHat Enterprise Linux 6 - scheduled for production at UF HPC for the Fall of 2012. EL5 software we provide will not be automatically installed on EL6. Please file a Support Request Ticket for EL6 software installation.
To add a documentation page for a new piece of software installed into /apps please go to Add New App Page.