Difference between revisions of "Installed Software"

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<!-- | [[CPMD]] || 3.11.1 || [http://www.cpmd.org/] || Simulation, Chemistry || X ||
 
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| [[covNMR]] || 2014 || [http://spin.ccic.ohio-state.edu/index.php/welcome/index] || Biochemistry
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| [[CUDA]] || 4.2, 5.5 || [http://www.nvidia.com/object/cuda_home_new.html] || Programming, Graphics
 
| [[CUDA]] || 4.2, 5.5 || [http://www.nvidia.com/object/cuda_home_new.html] || Programming, Graphics
 
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Revision as of 20:54, 28 February 2014

Installed Software List

Last updated 2014-02-28.

Note: Click on the icons to the right of the column headings to sort the table.

Name Version [1] Website Category
AbInit 6.12.3 [1] Ab Initio Quantum Chemistry, Density Functional Theory
Abyss 1.3.3, 1.3.4, 1.3.4-mpi [2] Biology, NGS
ALLPATHS-LG 42316, 44837 [3] Biology, NGS
AFNI 2011_12_21_1014 [4] Biology, Statistics, Imaging, Neurology
Amber 11, Amber 12.21, AmberTools 13.23 [5] Simulation, chemistry
AMOS 3.1.0 [6] Biology, Genomics, NGS
ANNOVAR 20120621,20121023,20130321 [7] Biology, Genomics
Amuse 6.0 [8] Astrophysics
Affymetrix Power Tools 1.15.0 [9] Biology, Genomics, Microarray
AtomEye 3 [10] Material Science
Augustus 2.6 [11] Biology, NGS
BamBam 1.0 [12] Biology, NGS
Bamtools 2.1.1 [13] Biology, NGS
BamUtil 1.0.2 [14] Biology, NGS
BayesRate 1.3.43 [15] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [16] Network file transfer
BEAGLE 3.2.2 [17] Biology, Genetics, Genotyping
BEAST 1.7.5, 2.0.1, 2.0.2.pre [18] Biology, Phylogenetics
BEDTools 2.16.2, 2.17.0 [19] Biology, NGS
BEST 2.3 [20] Biology, Phylogenetics
BETA 1.0.5 [21] Biology, NGS
BFAST 0.7.0 [22] Biology, NGS
Bismark 0.7.4, 0.7.7 [23] Biology, Methylation, NGS
Bioconductor Latest [24] Biology, R, Statistics
BioPerl 1.006901 [25] Biology, Perl
BioPython 1.59 [26] Biology, Python
BLASR 20130815 [27] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [28] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [29] Biology, Annotation
BLAT 20120524 [30] Biology, Sequence alignment
Boost 1.49.0, 1.53.0, 1.54.0 [31] C++, Library
Bwa 0.6.1, 0.7.2, 0.7.6a [32] Biology, NGS
Bowtie 0.12.8, 0.12.9, 2.1.0 [33] Biology, NGS
CAP3 20120705 [34] Biology, sequence assembly
CASAVA 1.8.2 [35] Biology, NGS
CD-HIT 4.6 [36] Biology, Genomics
CDO 1.6.1 [37] Climate
CellProfiler 2.0 [38] Biology, Image Analysis
Charmm 36a3 [39] Simulation, Chemistry
Circos 0.63-pre11 [40] Biology, Visualization
CisGenome 2.0 [41] Biology, Genomics, Peak Calling
ClustalW 2.1 [42] Biology, Genomics
Clview 20130402 [43] Biology, Genomics
CMake 2.8.8 [44] Programming, Build System
CoMap 1.4.1 [45] Biology, Genomics
Consed 23.0 [46] Biology, Genomics
covNMR 2014 [47] Biochemistry
CUDA 4.2, 5.5 [48] Programming, Graphics
Cufflinks 1.3.0, 2.0.0, 2.0.2 [49] Biology, NGS
Cutadapt 1.1 [50] Biology, NGS
DDSCAT 7.3.0 [51] Astrophysics
Desmond 3.0.3.1 [52] Simulation, Biology, Chemistry
Dalton 2011 [53] Quantum Chemistry
DiffReps 1.55.4 [54] Biology, NGS, ChIP-Seq
Dindel 1.01 [55] Biology, NGS
DIYABC many [56] Biology, Genomics
Dlpoly 4.03.4 [57] Simulation, Biology, Chemistry
DNA Clust 3.0 [58] Biology, Genomics
Dock 6.5, 6.6 [59] Chemistry, ligand binding prediction
DTI-TK 2.3.1 [60] Biology, Neurology, Imaging
EIGENSOFT 4.2, 5.0.1 [61] Biology, Population
emboss 6.5.7 [62] Biology, multi-tool suite
Espresso 5.0.1 [63] Modeling, Physics
ESPRIT 201211 [64] Biology, NGS, Metagenomics
ETE2 2.1 [65] Biology, Phylogenetics
Eval 2.2.8 [66] Biology, Genomics, GUI
ExaML 20130314 [67] Biology, Phylogenetics
Exonerate 2.2.0 [68] Biology, Genomics
FAR 2.15 [69] Biology, Genomics
FASTA 34.26.5, 36.3.6d [70] Biology, Genomics
FastML 3.0 [71] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [72] Biology, NGS
Fastx_toolkit 0.0.13.2 [73] Biology, NGS
fcGENE 1.0.7 [74] Biology, Genomics, SNP
Ferret 6.82 [75] Oceanography, Meteorology
FFTW 3.3.2, 3.3.3 [76] Math, Library, C++
Fluent 14.5.7 [77] Simulation, Fluid Dynamics
FragGeneScan 1.16 [78] Biology, NGS, Genomics
FreeBayes 0.9.6 [79] Biology, NGS, SNP Calling
FSL 5.0.2.2 [80] Biology, Neurology, Imaging
Garli 2.0, 2.01 [81] Biology, Phylogenetics
GATK 1.6.9, 2.2.15, 2.6.5 [82] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [83] Modeling, Computational Chemistry
GEMINI 4.6.0a [84] Biology, Genomics, Genetics
GenBank Tools 20140130 [85] BIology< Genomics
GeneMark 2012.04 [86] Biology, Genomics, Metagenomics
Genewise 2.2.0 [87] Biology, Genomics, Annotation
GenomicTools 2.7.0 [88] Biology, NGS
Git 1.8.2.1 [89] Development, Revision Control
Gmap 20120712, 20130331, 20130618 [90] Biology, Genomics
GnuPlot 4.6.0 [91] Graphics, Plotting, Programming
Grace 5.1.22 [92] Graphics, plotting, 2D
GrADS 2.0.1 [93] Earth Science
Gromacs 4.5.5, 4.6.5 [94] Chemistry, Modeling, Simulation
GSL 1.15 [95] Library, Math, C++, C
GULP 4.0 [96] Material Science
HaMStR v8b [97] Biology, Genomics
HDF5 1.8.9, 1.8.12 [98] Library, Data
HMMER3 3.0 [99] Biology, Genomics
HOMER 4.2 [100] Biology, Genomics
HTSeq 0.5.3p3 [101] Biology, NGS
HyPhy 2.1.2.28 [102] Biology, Phylogenetics
Hypre 2.8.0b [103] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [104] Biology, NGS
IM and IMa 20091217 [105] Biology, Population
IMa2 20120827 [106] Biology, Population
Intel Compilers 11.1, 2012 [107] Programming, Compilers
IOAPI 3.1 [108] Meteorology
Iprscan 4.8 [109] Biology, Genomics
LS-DYNA 700 [110] Physics
ITK 4.3.1 [111] Biology, Genomics
JAGS 3.3.0 [112] Statistics
Java 1.6.0_31, 1.7.0_02 [113] Java Development Kit
Kent 20120524 [114] Biology, NGS
Kmer 1934 [115] Biology, NGS
LAMMPS 28Oct12, 30Sep13 [116] Molecular Dynamics Simulation
Last 193, 247 [117] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [118] Biology, NGS
LIBSVM 3.12 [119] Machine Learning
LSC 0.3, 0.3.1 [120] Biology, NGS, Error correction
MACH 1.0.18 [121] Biology, Genomics
MACS 1.4.2 [122] Biology, ChIP-Seq
mafft 7.037, 6.903 [123] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [124] Biology, Annotation, Genomics
Maq 0.7.1 [125] Biology, NGS
Matlab 2012a [126] Math, Simulation, Programming
MATS 2.1.0, 3.0.6b, 3.0.8 [127] BIology, NGS
Mauve 2.3.1 [128] Biology, Genomics, Multiple genome alignments
MCNP 5, 6b2 [129] Physics
MCNPX 2.7.0, 2.7.0-i8 [130] Physics
Meme 4.8.1 [131] Biology, Motifs, Sequence analysis
Mercurial 2.7 [132] Development, Revision Control
Metabin 1.0 [133] Biology, Metagenomics
MetaCluster 5.0beta [134] Biology, Metagenomics
MetaVelvet 1.2.01 [135] Biology, NGS
MetaGeneMark 2012.04 [136] Biology, Genomics
Mfold 3.6 [137] Biology, Genomics
Midnight Commander 4.6.1 [138] Tools, Utilities
Migrate-n 3.3.0 [139] Biology, Population
mira 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 [140] Biology, NGS
MISO 0.4.4, 0.4.9 [141] Biology, NGS
MSMBuilder 2.5.1 [142] Molecular Dynamics
Molden 5.0 [143] Molecular, electronic structure
mosaik 2.1.33 [144] Biology,NGS
Mothur 1.31.2 [145] Biology, Microbial Ecology
MrBayes 3.2.1 [146] Biology, Phylogenetics
MUMmer 3.23 [147] Biology, Genomics
MUSCLE 3.8.31 [148] Biology, Genomics
NAMD 2.9 [149] Simulation, Chemistry, Biology
Nbody 6 [150] Astronomy
NCBI C++ Toolkit 12.0.0 [151] Biology, C++, Development
NCL 6.1.2 [152] Atmosphere Science
NCO 4.2.1 [153] Data exchange tools
NetCDF 4.2 [154] Data exchange, Tools
Newbler 2.6, 2.7 [155] Biology, NGS
Nexus NCL 2.1.18 [156] Biology, Phylogenetics, Library
NMRPipe 7.9 [157] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [158] Biology, NGS
Oases 0.2.08 [159] Biology, NGS
Olego 1.1.2 [160] Biology, NGS, RNA-Seq
Octave 3.6.4 [161] Numerical Computation
OpenBabel 2.3.2 [162] Biology, Chemistry
OpenFOAM 2.1.1 [163] Fluid Dynamics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [164] Biology, Genomics
PAML 4.7 [165] Biology, Phylogenetics
PartitionFinder 1.0.1 [166] Biology, Phylogenetics, Evolution
Parflow v615 [167] Ecology, Modeling
PASA 1.5, 2.0-r20130605p1, 2.0-r20130907 [168] Biology, Genomics
PeakSplitter 1.0 [169] Biology, Chip-Seq
PDT 3.18 [170] Programming, Profiler
Perl 5.16.0 [171] Programming, Language
PerM 0.4.0 [172] Biology, NGS
PETSc 2.3, 3.3 [173] Math, Numerical solvers
Phenix 1.8.1069 [174] Crystallography
PHITS 2.52 [175] Physics
PhyloBayes 3.3f, 1.4f MPI [176] Biology, Phylogenetics
PhyML 3.0, 20121109 [177] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [178] Biology, NGS
Preseq 0.0.4 [179] Biology, NGS
ProBABEL 0.4.2 [180] Biology, Genomics, GWAS
Proteinortho 4.26 [181] Biology, Genomics
python 2.6.8, 2.7.3 [182] Programming, scripting, language
QIIME 1.5.0 [183] Biology, Ecology
QT 4.8.3 [184] Computer Science
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 [185] Statistics, Programming
R8S 1.71 [186] Biology, Evolution
RADICAL 0.2 [187] Biology, Phylogenetics, Genomics
RAxML 7.3.2.0705, 7.9.1, 8.0.0 [188] Biology, Phylogenetics
RepeatMasker 3.3.0 [189] Biology, Genomics
Reptile 1.1 [190] Biology, NGS, error correction
riboPicker 0.4.3 [191] Biology, Sequence
RSEG 0.4.8 [192] Biology, NGS
samtools 0.1.16, 0.1.18, 0.1.19 [193] Biology, NGS
SAS 9.3 [194] Statistics, Graphing
SATe 2.2.7 [195] Biology, Phylogenetics
Sharcgs 1.2.11 [196] Biology, NGS, de novo assembly
Schrodinger 2012, 2013 [197] Simulation, chemistry
SCons 2.3.0 [198] Programming, Build System
SeqPrep 0.5 [199] Biology, NGS
SEQuel 1.0.1 [200] Biology, NGS
SeqyClean 1.8.10 [201] Biology, NGS, quality filter
Sickle 1.200 [202] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [203] Simulation, Physics, Ab Initio
SIFT 4.0.3b [204] Biology, Genomics
Silo 4.7 [205] Library, Data
Snap 20100728 [206] Biology, Genomics
SOAPdenovo 1.05 [207] Biology, NGS
SOAPdenovo-Trans 1.01 [208] Biology, NGS
SparCC 201402 [209] Microbial Ecology
Spades 2.5.0, 2.5.1, 3.0.0 [210] Biology, NGS
Spanki 0.4.1 [211] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [212] Chemistry
SPIMAP 1.1 [213] Biology, Phylogenetics
SpliceTrap 0.90.5 [214] Biology, NGS, RNA-Seq
SPM 8 [215] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [216] Biology, Genomics
SRA 2.1.10 [217]] biology, NGS
SSPACE 2.0 [218] Biology, NGS
Stacks 0.9995 [219] Biology, Genomics, NGS
Stata 10.1 [220] Statistics, Data analysis
Structure 2.3.3, 2.3.4 [221] Biology, Population
SUNDIALS 2.5.0 [222] Numerical Solver
swak4Foam 2.x [223] Fluid Dynamics
Swig 2.0.9 [224] Programming, C, C++, Python
TAU 2.21.4 [225] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [226] Biology, Genomics, Multiple Alignment
tgicl 2.1 [227] Biology, sequencing, clustering
Tophat 1.4.1, 2.0.1, 2.0.8b [228] Biology, NGS
Totalview 8.12.0 [229] Computer Science
TreeFix 1.1.7 [230] Biology, Phylogenetics
TRF 4.04 [231] Biology, Genomics
Trilinos 11.4.1 [232] Math Algorithm
Trimmomatic 0.22 [233] Biology, NGS
Trinity r20120905, r20121005, r20120225 [234] Biology, NGS, RNA-Seq
Twinscan 4.1.2 [235] Biology, Genomics
usearch 5.2.32, 7.0.959, 7.0.1001-64 (licensed 64-bit) [236] Biology, Sequence analysis
Valgrind 3.9.0 [237] Computer Science
VASP 4.6.34, 5.2.12, 5.3.2, 5.3.3 [238] Quantum Chemistry, Ab Initio
VCFtools 0.1.9, 0.1.10 [239] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [240] Biology, NGS
vmd 1.9.1 [241] Biology, Visualization
WebLogo 3.3 [242] Biology, Genomics
WDSSII 1 [243] Meteorology
WIEN2k 12.1 [244] Material Science, Chemistry
wgs 7.0.1.22 [245] Biology, NGS
wublast 2.0 [246] Biology, Sequence Alignment
Yambo 3.3.0 [247] Physics
Yasra 2.32 [248] Biology, NGS
  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.

To add a documentation page for a new piece of software installed into /apps please go to Add New App Page.

Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=Installed_Software&oldid=12093"