Installed Software

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

Last updated 2012-07-09.

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
QIIME 1.5.0 [142] Biology, Ecology X X
R 2.14.1-MPI, 2.14.2, 2.15.0 [143] Statistics, Programming X X
RAxML 7.3.0,7.3.2 [144] Biology, Phylogenetics X X
RAxML-Light 1.0.5 [145] Biology, Phylogenetics X
RepeatMasker 3.3.0 [146] Biology, Genomics X X
Reptile 1.1, 1.1-omp [147] Biology, NGS, error correction X X
riboPicker 0.4.2 [148] Biology, Sequence X
Rosetta 2.1.1, 2.1.2 [149] Biology, Structural, Modeling X
Ruby 1.9.3 [150] Programming, Language, Scripting X
RSMToolkit 2961 [151] Math, Modeling, Geometry X
samtools 0.1.16, 0.1.18 [152] Biology, NGS X X
SAS 9.2, 9.3 [153] Statistics, Graphing X X
SATe 2.1.0 [154] Biology, Phylogenetics X
Scala 2.9.1 [155] Programming, language, java X
Segminator 0.0.2 [156] Biology, NGS X
SeqPrep 0.4, 0.5 (EL6) [157] Biology, NGS X X
Siesta 2.0, 2.0.2, 3.0b [158] Simulation, physics, ab-initio X
Silo 4.7 [159] Library, Data X X
Snap 20100728 [160] Biology, Genomics X X
SOAPdenovo 1.05 [161] Biology, NGS X X
SPARTA+ 2.60 [162] Chemistry X
SRA 2.1.7 [163]] biology, NGS X X
SRNAPredict 3.0 [164] Biology, Genomics X
SRNAScanner 200903 [165] Biology, Genomics X
Staden 2.0.0b9 [166] Biology, Genomics, Sequencing X X
Stata 10 [167] Statistics, Data analysis X
Structure 2.3.3 [168] Biology, Population X X
TAU 2.20.1 [169] Profiling, Tracing, Programming X
tgicl 2.1 [170] Biology, sequencing, clustering X X
TRF 4.04 [171] Biology, Genomics X X
Trimal 1.2 [172] Biology, NGS X
Trinity r20120125, r20120317, r20120608 [173] Biology, RNA-Seq X X
Tophat 1.3.0, 1.3.3, 1.4.1 [174] Biology, NGS X X
Twinscan 3.5,4.1.2 [175] Biology, Genomics X
usearch 5.0.151,5.1.221, 5.2.32 (EL6) [176] Biology, Sequence analysis X X
VASP 4.6.34,5.2.0 [177] Quantum Chemistry, ab initio X
VCFtools 0.1.7 (EL5), 0.1.9 [178] Biology, SNPs X X
velvet 1.2.06,1.2.02,1.2.01,1.1.05 [179] Biology, NGS X X
vmd 1.9 [180] Biology, Visualization X
weka 3.6.2 [181] Data mining algorithms X
wgs 6.1, 6.1-20110830 [182] Biology,Assembler,Genome X X
wublast 2.0 [183] Biology, Sequence Alignment X X
  1. ↑ 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.
  2. ↑ Operating system: CentOS 5 - currently in production at UF HPC. Please file a Support Request Ticket for EL5 software installation
  3. ↑ 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.

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