Difference between revisions of "Installed Software"

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| [[GASVPro]] || 201310 || [https://code.google.com/p/gasv/] || Biology, NGS, Genomics
 
| [[GASVPro]] || 201310 || [https://code.google.com/p/gasv/] || Biology, NGS, Genomics
 +
|-
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| [[GATE]] || 7.0 || [http://wiki.opengatecollaboration.org/index.php/Main_Page] || Data Analysis
 
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| [[GATK]] || 1.6.9, 2.7.4, '''3.1.1''' || [http://www.broadinstitute.org/gsa/wiki/index.php/GATK] || Biology, NGS
 
| [[GATK]] || 1.6.9, 2.7.4, '''3.1.1''' || [http://www.broadinstitute.org/gsa/wiki/index.php/GATK] || Biology, NGS

Revision as of 20:48, 9 July 2014

Installed Software List

Last updated 2014-07-09.

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 1.3.4, 1.3.7 [2] Biology, NGS
ALLPATHS-LG 42316, 44837 [3] Biology, NGS
AFNI 2011_12_21_1014 [4] Biology, Statistics, Imaging, Neurology
Amber 11, 12, 14 [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
Bamstats 20140602 [13] Biology, NGS
Bamtools 2.1.1 [14] Biology, NGS
BamUtil 1.0.2 [15] Biology, NGS
BayesRate 1.3.43 [16] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [17] Network file transfer
Bcftools 20140618 [18]] Biology, Genomics, NGS
BEAGLE 3.2.2 [19] Biology, Genetics, Genotyping
BEAST 1.7.5, 2.0.1, 2.0.2.pre [20] Biology, Phylogenetics
BEDTools 2.16.2, 2.17.0 [21] Biology, NGS
BEST 2.3 [22] Biology, Phylogenetics
BETA 1.0.5 [23] Biology, NGS
BFAST 0.7.0 [24] Biology, NGS
Bismark 0.7.4, 0.7.7 [25] Biology, Methylation, NGS
Bioconductor Latest [26] Biology, R, Statistics
BioPerl 1.006901 [27] Biology, Perl
BioPython 1.59 [28] Biology, Python
BLASR 20130815 [29] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [30] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [31] Biology, Annotation
BLAT 20120524 [32] Biology, Sequence alignment
Boost 1.49.0, 1.53.0, 1.54.0 [33] C++, Library
Bwa 0.6.1, 0.7.8, 0.7.9a [34] Biology, NGS
Bowtie 0.12.8, 0.12.9, 1.0.0 [35] Biology, NGS
Bowtie2 2.1.0, 2.2.2, 2.2.3 [36] Biology, NGS
CAP3 20120705 [37] Biology, sequence assembly
CASAVA 1.8.2 [38] Biology, NGS
CD-HIT 4.6 [39] Biology, Genomics
CDO 1.6.1 [40] Climate
CEAS 1.0.2 [41] Biology, Genomics
CellProfiler 2.0 [42] Biology, Image Analysis
Charmm 36a3 [43] Simulation, Chemistry
Circos 0.63-pre11 [44] Biology, Visualization
CisGenome 2.0 [45] Biology, Genomics, Peak Calling
CLHEP 2.2.0.1 [46] High Energy Physics
ClustalW 2.1 [47] Biology, Genomics
Clview 20130402 [48] Biology, Genomics
CMake 2.8.8 [49] Programming, Build System
CoMap 1.4.1 [50] Biology, Genomics
CONCOCT 0.3.1 [51] Biology, Genomics
Consed 23.0 [52] Biology, Genomics
covNMR 2014 [53] Biochemistry
CUDA 4.2, 5.5 [54] Programming, Graphics
Cufflinks 1.3.0, 2.1.1, 2.2.0 [55] Biology, NGS
Cutadapt 1.1 [56] Biology, NGS
DAKOTA 5.4.0 [57] Computational Science
DDSCAT 7.3.0 [58] Astrophysics
Delft3D 3621 [59] Hydrodynamics, Physics
Desmond 3.0.3.1 [60] Simulation, Biology, Chemistry
Dalton 2011 [61] Quantum Chemistry
DiffReps 1.55.4 [62] Biology, NGS, ChIP-Seq
Dindel 1.01 [63] Biology, NGS
DIYABC many [64] Biology, Genomics
Dlpoly 4.03.4 [65] Simulation, Biology, Chemistry
DNA Clust 3.0 [66] Biology, Genomics
Dock 6.5, 6.6 [67] Chemistry, ligand binding prediction
DSSP 2.2.1 [68] Biology, Molecular Dynamics
DTI-TK 2.3.1 [69] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [70] Biology, NGS
EIGENSOFT 4.2, 5.0.1 [71] Biology, Population
emboss 6.5.7 [72] Biology, multi-tool suite
eQTLA 1.1 [73] Biology, Genomics
Espresso 5.0.1 [74] Modeling, Physics
ESPRIT 201211 [75] Biology, NGS, Metagenomics
ETE2 2.1 [76] Biology, Phylogenetics
Eval 2.2.8 [77] Biology, Genomics, GUI
ExaML 1.0.3, 1.0.5, 1.0.12 [78] Biology, Phylogenetics
Exonerate 2.2.0 [79] Biology, Genomics
FAR 2.15 [80] Biology, Genomics
FASTA 34.26.5, 36.3.6d [81] Biology, Genomics
FastML 3.0 [82] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [83] Biology, NGS
FastTree 2.1.7 [84] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [85] Biology, NGS
fcGENE 1.0.7 [86] Biology, Genomics, SNP
Ferret 6.82 [87] Oceanography, Meteorology
FFmpeg 2.1.3 [88] Multimedia, audio, video
FFTW 3.3.2, 3.3.3 [89] Math, Library, C++
FLASH 1.2.10 [90] Biology, Genomics, NGS
Fluent 14.5.7, 15.0 [91] Simulation, Fluid Dynamics
FragGeneScan 1.16 [92] Biology, NGS, Genomics
FreeBayes 0.9.6 [93] Biology, NGS, SNP Calling
Freesurfer 5.2.0 [94] Biology, Neurology, Imaging
FSL 5.0.2.2 [95] Biology, Neurology, Imaging
Garli 2.0, 2.01 [96] Biology, Phylogenetics
GASVPro 201310 [97] Biology, NGS, Genomics
GATE 7.0 [98] Data Analysis
GATK 1.6.9, 2.7.4, 3.1.1 [99] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [100] Modeling, Computational Chemistry
Geant4 4.10 [101] Physics
GEMINI 4.6.6a [102] Biology, Genomics, Genetics
GenBank Tools 20140130 [103] BIology< Genomics
GeneMark 2012.04 [104] Biology, Genomics, Metagenomics
Genewise 2.2.0 [105] Biology, Genomics, Annotation
GenomicTools 2.7.0 [106] Biology, NGS
Git 1.8.2.1 [107] Development, Revision Control
Gmap 20130618, 20130720, 20140530 [108] Biology, Genomics
GnuPlot 4.6.0 [109] Graphics, Plotting, Programming
Grace 5.1.22 [110] Graphics, plotting, 2D
GrADS 2.0.1 [111] Earth Science
Gromacs 4.5.5, 4.6.5 [112] Chemistry, Modeling, Simulation
GSL 1.15 [113] Library, Math, C++, C
GULP 4.0 [114] Material Science
HaMStR v8b [115] Biology, Genomics
HDF5 1.8.9, 1.8.12 [116] Library, Data
HMMER3 3.0 [117] Biology, Genomics
HMMSplicer 0.9.5 [118] Biology, Genomics
HOMER 4.2 [119] Biology, Genomics
HTSeq 0.5.3p3, 0.6.1p1 [120] Biology, NGS
HyPhy 2.1.2.28 [121] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [122] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [123] Biology, NGS
IM and IMa 20091217 [124] Biology, Population
IMa2 20120827 [125] Biology, Population
ImageMagick 6.8.8-9 [126] Image manipulation
Intel Compilers 11.1, 2012 [127] Programming, Compilers
IOAPI 3.1 [128] Meteorology
Iprscan 4.8 [129] Biology, Genomics
ITK 4.3.1 [130] Biology, Genomics
JAGS 3.3.0 [131] Statistics
Java 1.6.0_31, 1.7.0_02 [132] Java Development Kit
Kent 20120524 [133] Biology, NGS
Kmer 1934 [134] Biology, NGS
LAMMPS 28Oct12, 30Sep13 [135] Molecular Dynamics Simulation
Last 193, 247 [136] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [137] Biology, NGS
LIBSVM 3.12 [138] Machine Learning
LSC 0.3, 0.3.1 [139] Biology, NGS, Error correction
Loci 3.3 [140] Fluid Dynamics
LS-DYNA 700, 711 [141] Physics
MACH 1.0.18 [142] Biology, Genomics
MACS 1.4.2 [143] Biology, ChIP-Seq
mafft 7.037, 6.903 [144] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [145] Biology, Annotation, Genomics
Maq 0.7.1 [146] Biology, NGS
Matlab 2012a, 2013a, 2014a [147] Math, Simulation, Programming
MATS 2.1.0, 3.0.6b, 3.0.8 [148] BIology, NGS
Mauve 2.3.1 [149] Biology, Genomics, Multiple genome alignments
MCNP 5, 6b2 [150] Physics
MCNPX 2.7.0, 2.7.0-i8 [151] Physics
Meme 4.8.1 [152] Biology, Motifs, Sequence analysis
Mercurial 2.7 [153] Development, Revision Control
Metabin 1.0 [154] Biology, Metagenomics
MetaCluster 5.0beta [155] Biology, Metagenomics
MetaVelvet 1.2.01 [156] Biology, NGS
MetaGeneMark 2012.04 [157] Biology, Genomics
Mfold 3.6 [158] Biology, Genomics
Midnight Commander 4.6.1 [159] Tools, Utilities
Migrate-n 3.3.0 [160] Biology, Population
mira 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 [161] Biology, NGS
MISO 0.4.4, 0.4.9 [162] Biology, NGS
MSMBuilder 2.5.1 [163] Molecular Dynamics
Molden 5.0 [164] Molecular, electronic structure
mosaik 2.1.33 [165] Biology,NGS
Mothur 1.31.2 [166] Biology, Microbial Ecology
mpiP 3.4.1 [167] Parallel Computing
MrBayes 3.2.1 [168] Biology, Phylogenetics
MUMmer 3.23 [169] Biology, Genomics
MUSCLE 3.8.31 [170] Biology, Genomics
NAMD 2.9 [171] Simulation, Chemistry, Biology
Nbody 6 [172] Astronomy
NCBI C++ Toolkit 12.0.0 [173] Biology, C++, Development
NCL 6.1.2 [174] Atmosphere Science
NCO 4.2.1, 4.4.3 [175] Data exchange tools
NetCDF 4.2 [176] Data exchange, Tools
Newbler 2.6, 2.7 [177] Biology, NGS
Nexus NCL 2.1.18 [178] Biology, Phylogenetics, Library
NMRPipe 7.9 [179] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [180] Biology, NGS
Oases 0.2.08 [181] Biology, NGS
Olego 1.1.2 [182] Biology, NGS, RNA-Seq
Octave 3.6.4 [183] Numerical Computation
OpenBabel 2.3.2 [184] Biology, Chemistry
OpenCV 2.4.8 [185] Computervision
OpenFOAM 2.1.1 [186] Fluid Dynamics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [187] Biology, Genomics
PAML 4.7 [188] Biology, Phylogenetics
PartitionFinder 1.0.1, 1.1.1 [189] Biology, Phylogenetics, Evolution
Parflow v615 [190] Ecology, Modeling
PASA 1.5, 2.0-r20130605p1, 2.0-r20130907 [191] Biology, Genomics
PeakSplitter 1.0 [192] Biology, Chip-Seq
PDT 3.18 [193] Programming, Profiler
Perl 5.16.0 [194] Programming, Language
PerM 0.4.0 [195] Biology, NGS
PETSc 2.3, 3.3 [196] Math, Numerical solvers
Phenix 1.8.1069 [197] Crystallography
PHITS 2.52 [198] Physics
PhyloBayes 3.3f, 1.4f MPI [199] Biology, Phylogenetics
PhyML 3.0, 20121109 [200] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [201] Biology, NGS
Preseq 0.0.4 [202] Biology, NGS
ProBABEL 0.4.2 [203] Biology, Genomics, GWAS
Proteinortho 4.26 [204] Biology, Genomics
python 2.6.8, 2.7.3 [205] Programming, scripting, language
QIIME 1.5.0 [206] Biology, Ecology
QT 4.8.3 [207] Computer Science
Quickquartet 1.0.0 [208] Biology, Phylogenetics
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 [209] Statistics, Programming
R8S 1.71 [210] Biology, Evolution
RADICAL 0.2 [211] Biology, Phylogenetics, Genomics
RAxML 7.9.1, 8.0.0, 8.0.25 [212] Biology, Phylogenetics
RepeatMasker 3.3.0 [213] Biology, Genomics
Reptile 1.1 [214] Biology, NGS, error correction
riboPicker 0.4.3 [215] Biology, Sequence
RNAhybrid 2.1.1 [216] Biology, Genomics
ROOT 6.0 [217] Data Analysis
RSEG 0.4.8 [218] Biology, NGS
Sailfish 0.6.3 [219] Biology, NGS, RNA-Seq
samtools 0.1.16, 0.1.18, 0.1.19 [220] Biology, NGS
SAS 9.3 [221] Statistics, Graphing
SATe 2.2.7 [222] Biology, Phylogenetics
Sharcgs 1.2.11 [223] Biology, NGS, de novo assembly
Schrodinger 2012, 2013 [224] Simulation, chemistry
SCons 2.3.0 [225] Programming, Build System
SeqPrep 0.5 [226] Biology, NGS
SEQuel 1.0.1 [227] Biology, NGS
SeqyClean 1.8.10 [228] Biology, NGS, quality filter
Sickle 1.200 [229] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [230] Simulation, Physics, Ab Initio
SIFT 4.0.3b [231] Biology, Genomics
Silo 4.7 [232] Library, Data
Snap 20100728 [233] Biology, Genomics
SOAPdenovo 1.05 [234] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [235] Biology, NGS
SparCC 201402 [236] Microbial Ecology
Spades 2.5.0, 2.5.1, 3.0.0 [237] Biology, NGS
Spanki 0.4.1, 0.4.3 [238] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [239] Chemistry
SPIMAP 1.1 [240] Biology, Phylogenetics
SpliceTrap 0.90.5 [241] Biology, NGS, RNA-Seq
SPM 8 [242] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [243] Biology, Genomics
SRA 2.1.10 [244]] biology, NGS
SSPACE 2.0 [245] Biology, NGS
Stacks 0.9995 [246] Biology, Genomics, NGS
STAR 2.3.0e [247] Biology, NGS, Alignment
STAR-CCM+ 8.06 [248] Mechanical Engineering
Stata 10.1, 13 [249] Statistics, Data analysis
Stringtie 0.97 [250] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [251] Biology, Population
SUNDIALS 2.3.0, 2.5.0 [252] Numerical Solver
swak4Foam 2.x [253] Fluid Dynamics
Swig 2.0.9 [254] Programming, C, C++, Python
Syzygy 1.2.7 [255] Biology, Genomics
TAU 2.21.4, 2.23 [256] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [257] Biology, Genomics, Multiple Alignment
tgicl 2.1 [258] Biology, sequencing, clustering
Tophat 1.4.1, 2.0.1, 2.0.8b [259] Biology, NGS
Totalview 8.12.0 [260] Computer Science
TPP 4.7.0 [261] Bioinformatics, MassSpec
TreeFix 1.1.7 [262] Biology, Phylogenetics
TRF 4.04 [263] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [264] Math Algorithm
Trimmomatic 0.22, 0.32 [265] Biology, NGS
Trinity r20131110, r20140413 [266] Biology, NGS, RNA-Seq
Twinscan 4.1.2 [267] Biology, Genomics
usearch 5.2.32, 7.0.959, 7.0.1001-64 (licensed 64-bit) [268] Biology, Sequence analysis
Valgrind 3.9.0 [269] Computer Science
VASP 4.6.34, 5.2.12, 5.3.2, 5.3.3 [270] Quantum Chemistry, Ab Initio
VCFtools 0.1.9, 0.1.10 [271] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [272] Biology, NGS
vmd 1.9.1 [273] Biology, Visualization
Wannier90 2.0.0 [274] Computational Physics
WebLogo 3.3 [275] Biology, Genomics
WDSSII 1 [276] Meteorology
WIEN2k 12.1 [277] Material Science, Chemistry
wgs 7.0.1.22 [278] Biology, NGS
wublast 2.0 [279] Biology, Sequence Alignment
Yambo 3.3.0 [280] Physics
Yasra 2.32 [281] 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.

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