Difference between revisions of "Installed Software"

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Line 653: Line 653:
 
| [[Olego]] || 1.1.2, 1.1.5 || [http://zhanglab.c2b2.columbia.edu/index.php/OLego_Documentation] || Biology, NGS, RNA-Seq
 
| [[Olego]] || 1.1.2, 1.1.5 || [http://zhanglab.c2b2.columbia.edu/index.php/OLego_Documentation] || Biology, NGS, RNA-Seq
 
|-
 
|-
| [[Octave]] || 3.6.4 || [http://www.gnu.org/software/octave/]|| Numerical Computation
+
| [[Octave]] || 3.6.4 || [http://www.gnu.org/software/octave/] || Numerical Computation
 +
|-
 +
| [[Oncotator]] || 1.5.1.0 || [https://github.com/broadinstitute/oncotator] || Biology, Genomics
 
|-
 
|-
 
| [[OpenBabel]] || 2.3.2 || [http://openbabel.org/wiki/Main_Page]|| Biology, Chemistry
 
| [[OpenBabel]] || 2.3.2 || [http://openbabel.org/wiki/Main_Page]|| Biology, Chemistry

Revision as of 20:25, 9 September 2015

  • Last updated on 2015-09-09.
  • Up to three latest versions are listed. The default is shown in bold if it's not the latest version.
  • See output of 'module spider module_name' for a full list of provided versions.

A B C D E F G H I J K L M N O P Q R S T U V W X Y

Name Version [1] Website Category
AbInit 6.12.3, 7.10.2 [1] Quantum Chemistry, DFT
Abyss 1.3.4, 1.3.7, 1.5.2 [2] Biology, NGS
AdmixTools 20150311 [3] Biology, Bioinformatics, Genomics, NGS
ADMIXTURE 1.23 [4] Biology, Bioinformatics, Genomics, NGS
AFNI 2011_12_21_1014 [5] Biology, Statistics, Imaging, Neurology
Agalma 0.2.1, 0.3.5, 0.5.0 [6] Biology, Bioinformatics, Genomics, SNP
ALLPATHS-LG 42316, 44837 [7] Biology, NGS
Amber 11, 12, 14 [8] Simulation, chemistry
AMOS 3.1.0 [9] Biology, Genomics, NGS
ANNOVAR 20120621, 20150322 [10] Biology, Genomics
AStalavista 3.2 [11] Biology, NGS, RNA-Seq, Genomics
ASTRID 20150807 [12] Biology, Genomics
Atlas 3.10.1, 3.11.17 [13] Library, Math
Amuse 6.0, 10.0 [14] Astrophysics
ANGSD 20150306 [15] Biology, NGS
Affymetrix Power Tools 1.15.0 [16] Biology, Genomics, Microarray
ARC 20140312 [17] Biology, NGS
Astral 4.7.6, 4.7.8, 4.7.9 [18] Biology, Bioinformatics, NGS, Phylogenetics
AtomEye 3 [19] Material Science
ATRAM 20140624 [20] Biology, NGS
Augustus 2.6 [21] Biology, NGS
BamBam 1.0 [22] Biology, NGS
Bam-readcount 20150216 [23] Biology, NGS
Bamstats 20140602 [24] Biology, NGS
Bamtools 2.1.1 [25] Biology, NGS
BamUtil 1.0.2 [26] Biology, NGS
BAPS 6.0 [27] Biology, Populaton genetics
BayesRate 1.3.43 [28] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [29] Network file transfer
Bcbio-nextgen 0.8.7 [30] Biology, NGS
Bcftools 1.0, 1.2 [31] Biology, Genomics, NGS
Bcl2fastq 2.16 [32] Biology, NGS, Illumina
BEAGLE 3.2.2, 4.0 [33] Biology, Genetics, Genotyping
BEAST 1.7.5, 1.8.1, 2.1.3 [34] Biology, Phylogenetics
Bedops 2.4.2 [35] Biology, Bioinformatics, Sequence, NGS
BEDTools 2.17.0, 2.23.0, 2.24.0 [36] Biology, NGS
BEST 2.3 [37] Biology, Phylogenetics
BETA 1.0.5 [38] Biology, NGS
BFAST 0.7.0 [39] Biology, NGS
Bismark 0.7.4, 0.7.7, 0.13.0 [40] Biology, NGS, Methylation
Bioconductor Latest [41] Biology, R, Statistics
BioPerl 1.006901 [42] Biology, Perl
BioPython 1.59 [43] Biology, Python
BLASR 20130815 [44] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [45] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [46] Biology, Annotation
BLAT 20120524 [47] Biology, Sequence alignment
Blender 2.63 [48] Graphics
Boost 1.49.0, 1.53.0, 1.54.0 [49] C++, Library
Bowtie 0.12.9, 1.0.0, 1.1.1 [50] Biology, NGS
Bowtie2 2.2.2, 2.2.3, 2.2.4, 2.2.5 [51] Biology, NGS
BPP 2.2, 1.9.0 [52] Biology, Phylogenetics
BRANCH 1.8.1 [53] Biology, NGS, Mapping
BRATNextGen 20150505 [54] Biology, Genomics
Bsmap 2.74, 2.87 [55] Biology, NGS, Methylation
Bwa 0.6.1, 0.7.11, 0.7.12 [56] Biology, NGS
Camino 20140723 [57] Biology, Neuroscience, Imaging
CAP3 20120705 [58] Biology, sequence assembly
CASAVA 1.8.2 [59] Biology, NGS
CD-HIT 4.6, 4.6.4 [60] Biology, Genomics
CDO 1.6.1 [61] Climate
CEAS 1.0.2 [62] Biology, Genomics
CellProfiler 2.0 [63] Biology, Image Analysis
CGATools 1.6.0.42 [64] Biology, NGS
Charmm 36a3 [65] Simulation, Chemistry
Chartdirector 5.1.0 [66] Graphics
Chimera 1.7 [67] Biology, Modeling
ChromEvol 2.0 [68] Biology, Phylogenetics
CIMS 4.1.2 [69] Biology, Genomics
Circos 0.63-pre11 [70] Biology, Visualization
CisGenome 2.0 [71] Biology, Genomics, Peak Calling
Clann 3.2.3 [72] Biology, Phylogenetics
CLHEP 2.2.0.1 [73] High Energy Physics
ClonalFrame 1.1, 1.2 [74] Biology, Genomics, NGS
ClonalFrameML 1.25 [75] Biology, Genomics, NGS
ClustalW 2.1 [76] Biology, Genomics
Cluster3 1.52 [77] Biology, Genomics
Clview 20130402 [78] Biology, Genomics
ClustalO 1.2.0 [79] Biology, Genomics
CMake 2.8.8, 2.9.12.1, 3.1.0 [80] Programming, Build System
CNVSeq 20110715 [81] Biology, NGS
Cobrapy 0.3.2 [82] Biology, Metabolomics, Modeling
Coevol 1.3c, 1.4b [83] Biology, Phylogenetics
CoMap 1.4.1 [84] Biology, Genomics
CONCOCT 0.3.1 [85] Biology, Genomics
CoNIFER 0.2.2 [86] Biology, Genomics
Consed 23.0 [87] Biology, Genomics
Coreutils 8.23 [88] GNU Utilities, Computer Science
covNMR 2014 [89] Biochemistry
CPLEX 12.6.5 [90] Optimizer
CUDA 4.2, 5.5 [91] Programming, Graphics
Crux 1.40 [92] Biology, Mass-Spectrometry
Cufflinks 1.3.0, 2.0.2, 2.2.1 [93] Biology, NGS
Cutadapt 1.1, 1.7.1, 1.8.1 [94] Biology, NGS
DAKOTA 5.4.0 [95] Computational Science
DaPars 0.9.0 [96] Biology, NGS, RNA-Seq
DCMTK 3.6.0 [97] Biology, Neuroscience, Imaging
DSSAT 4.5 [98] Biology
DDSCAT 7.3.0 [99] Astrophysics
DDT 4.1.0, 4.2.1 [100] Software
Delft3D 3621 [101] Hydrodynamics, Physics
Desmond 3.0.3.1 [102] Simulation, Biology, Chemistry
DETONATE 1.9 [103] Biology, NGS
Dalton 2011 [104] Quantum Chemistry
Diamond 0.5.1 [105] Computational Biology, Genomics
Dibig Tools 1.0 [106] Bioinformatics, PBS, Torque, Jobs
DiffReps 1.55.4 [107] Biology, NGS, ChIP-Seq
Dindel 1.01 [108] Biology, NGS
DISCOVARdenovo 52488 [109] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [110] Biology, Genomics
Dlpoly 4.03.4 [111] Simulation, Biology, Chemistry
DNA Clust 3.0 [112] Biology, Genomics
Dock 6.5, 6.6, 6.7 [113] Chemistry, ligand binding prediction
DOT 2.0 [114] Biology, Bioinformatics, Docking
Doxygen 1.8.3.1 [115] Programming, Documentation
DSSP 2.2.1 [116] Biology, Molecular Dynamics
DTI-TK 2.3.1 [117] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [118] Biology, NGS
ECTools 20140311, 20141201 [119] Biology, Sequencing, Bioinformatics
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [120] Biology, Matlab
EIGENSOFT 4.2, 5.0.1, 6.0.1 [121] Biology, Population
emboss 6.5.7 [122] Biology, multi-tool suite
EMIRGE 20130727 [123] Biology, NGS
Ensembl_Tools 80 [124] Biology, Bioinformatics
EPACTS 3.2.6 [125] Biology, Bioinformatics, Genomics
eQTLA 1.1 [126] Biology, Genomics
Eqtlbma 1.2.2 [127] Biology, Genotyping
Esmf 6.3.0rp1 [128] Climate
Espresso 5.0.1, 5.2.0 [129] Modeling, Physics
ESPRIT 201211 [130] Biology, NGS, Metagenomics
ETE2 2.1 [131] Biology, Phylogenetics
Eval 2.2.8 [132] Biology, Genomics, GUI
ExaBayes 1.2.1 [133] Biology, Phylogenetics
ExaML 1.0.5, 1.0.12, 3.0.14 [134] Biology, Phylogenetics
ExomeCNV 1.4 [135] Biology, NGS, Genomics
Exonerate 2.2.0 [136] Biology, Genomics
eXpress 1.3.1 [137] Biology, NGS
FAR 2.15 [138] Biology, Genomics
FASTA 34.26.5, 36.3.6d [139] Biology, Genomics
FastML 3.0 [140] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [141] Biology, NGS
Fastq-tools 0.7, 0.8 [142] Biology, NGS
FastTree 2.1.7 [143] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [144] Biology, NGS
fcGENE 1.0.7 [145] Biology, Genomics, SNP
Ferret 6.82 [146] Oceanography, Meteorology
FFmpeg 2.1.3 [147] Multimedia, audio, video
FFTW 3.3.2, 3.3.3 [148] Math, Library, C++
FLASH 1.2.10, 1.2.11 [149] Biology, Genomics, NGS
Flexbar 2.3 [150] Biology, Genomics, NGS
Fluent 14.5.7, 15.0.7, 16.0 [151] Simulation, Fluid Dynamics
FragGeneScan 1.16 [152] Biology, NGS, Genomics
FreeBayes 0.9.6, 0.9.15, 0.9.21 [153] Biology, NGS, SNP Calling
Freesurfer 5.2.0 [154] Biology, Neurology, Imaging
FSL 5.0.2.2 [155] Biology, Neurology, Imaging
Galaxy latest [156] Biology, Chemistry, Other
GapFiller 1.11 [157] Biology, NGS
Garli 2.0, 2.01 [158] Biology, Phylogenetics
GAML 20150610 [159] Biology, NGS
GARM 0.7.4 [160] Biology, NGS
GASVPro 201310 [161] Biology, NGS, Genomics
GATE 7.0 [162] Data Analysis
GATK 1.6.9, 2.7.4, 3.1.1, 3.3.0 [163] Biology, NGS
Gaussian G03, G09-A.02, G09-C.01 [164] Modeling, Computational Chemistry
Gblocks 0.91b [165] Genomics, Alignment tool
GCTA 1.24.7 [166] Biology, Genomics, SNP
GDAL 1.11.2 [167] Geospatial Data Modeling, Geospatial Library
Geant4 4.10 [168] Physics
GEM 20130406 [169] Biology, NGS
GEMINI 4.6.6a, 0.13.1 [170] Biology, Genomics, Genetics
GenBank Tools 20140130 [171] BIology< Genomics
GeneMark 2012.04 [172] Biology, Genomics, Metagenomics
GeneSeqer 20140226 [173] Biology, Genomics
Genewise 2.2.0 [174] Biology, Genomics, Annotation
Genome STRiP 2.00.1602 [175] Biology, genomics, NGS
GenomicTools 2.7.0 [176] Biology, NGS
GenSel 4.90 [177] Biology, Genetics
GET_HOMOLOGUES 20150529 [178] Biology, Genomics
GKNO 1.30.18 [179] Biology, NGS,
Git 1.8.2.1, 1.9.0 [180] Development, Revision Control
Globus 2.1.3 [181] Data Transfer
GLPK 4.55 [182] Biology, Genomics
Gmap 20150612, 20150723 [183] Biology, Genomics
GNU 4.4.6, 4.7.2 [184] Compilers, Programming
GnuPlot 4.6.0 [185] Graphics, Plotting, Programming
Grace 5.1.22 [186] Graphics, plotting, 2D
GrADS 2.0.1 [187] Earth Science
GramCluster 1.3 [188] Biology, Sequencing
GraphViz 2.38.0 [189] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5 [190] Chemistry, Modeling, Simulation
GSNP 1.0 [191] Biology, Bioinformatics, NGS
GSL 1.15 [192] Library, Math, C++, C
Gubbins 20150519 [193] Biology, Phylogenetics, Genomics
GULP 4.0 [194] Material Science
HaMStR 13.2.2, 13.2.3, 13.2.4 [195] Biology, Genomics
HapCompass 0.7.7 [196] Biology, NGS, Genomics
Hapsembler 2.21 [197] Biology, Genomics, NGS
HapTree 1.0 [198] Biology, Genomics, NGS
HDF4 4.2.11 [199] Library, Data
HDF5 1.8.9, 1.8.12, 1.8.15 [200] Library, Data
HMMER3 3.0, 3.1b1, 3.1b2 [201] Biology, Genomics
HMMSplicer 0.9.5 [202] Biology, Genomics
HOMER 4.2 [203] Biology, Genomics
HTMLDoc 1.2.82 [204] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [205] Biology, NGS
Hyb 20141126 [206] Biology, NGS, RNA-Seq
HyPhy 2.1.2.28 [207] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [208] Library, Math, Physics
IBDNe 20150815 [209] Biology, NGS
IDBA-UD 1.0.9, 1.1.0, 1.1.1 [210] Biology, NGS
IEP 3.6 [211] Programming, Python, Editor
IGB 8.4.1 [212] Biology, Genomics, NGS
iGTP 1.1 [213] Biology, Bioinformatics, Phylogenetics
IM and IMa 20091217 [214] Biology, Population
IMa2 20120827 [215] Biology, Population
ImageJ 1.48 [216] Image manipulation
ImageMagick 6.8.8-9 [217] Image manipulation
Intel Compilers 11.1, 2012 [218] Programming, Compilers
IOAPI 3.1 [219] Meteorology
Iprscan 4.8 [220] Biology, Genomics
IQ-TREE 1.3.4 [221] Biology, Phylogenetics
ITK 4.3.1 [222] Biology, Genomics
ITK-SNAP 3.0.0 [223] Biology, Neuroscience, Imaging
JAGS 3.3.0 [224] Statistics
Java 1.6.0_31, 1.7.0_02, 1.8.0_31 [225] Java Development Kit
Jellyfish 2.1.1 [226] Biology, NGS
JModelTest 2.1.1 [227] Biology, Phylogenetics, Genomics
Julia 0.3.11 [228] Programming, Languages
KaKs 1.2 [229] Biology, Phylogenetics
Kent 20120524 [230] Biology, NGS
Khmer 1.1 [231] Biology, NGS
KING 1.4 [232] Biology, Genomics
Kmer 1934 [233] Biology, NGS
KmerGenie 1.6741 [234] Biology, NGS, Utilities
Kraken 0.10.4b [235] Biology, Genomics, Phylogenetics
LAMMPS 28Oct12, 30Sep13, 28Jun14,15May15 [236] Molecular Dynamics Simulation
LAMP 2.5 [237] Biology, Genomics
Last 193, 247 [238] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [239] Biology, NGS
LIBSVM 3.12 [240] Machine Learning
LSC 0.3, 0.3.1 [241] Biology, NGS, Error correction
Loci 3.3 [242] Fluid Dynamics
LS-DYNA 700, 711, 800 [243] Physics
Lumpy 0.2.1 [244] Biology, SNP
LZO 2.09 [245] Library, Data Compression
MACH 1.0.18 [246] Biology, Genomics
Mach2VCF 20150515 [247] Biology
M5tools 20121126 [248] Biology, Bioinformatics, Genomics
MACS 1.4.2 [249] Biology, ChIP-Seq
mafft 6.903, 7.215, 7.245 [250] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [251] Biology, Annotation, Genomics
MapSplice 2.1.7 [252] Biology, NGS, RNA-Seq
MAPminer 1.1 [253] Biology, Phylogenetics
MassMine 0.9.5 [254] Data Mining
Maq 0.7.1 [255] Biology, NGS
MARK 2.0.1 [256] Statistics
MarkerMiner 20150429, 20150511 [257] Biology, Genomics
MaSuRCA 2.3.2 [258] Biology, NGS
Matlab 2012a, 2013a, 2014a [259] Math, Simulation, Programming
MATS 2.1.0, 3.0.8, 3.0.9 [260] BIology, NGS
Mauve 2.3.1 [261] Biology, NGS
MCarts 1.0.2 [262] Biology, Genomics, Markov models
MCNP 5, 6b2 [263] Physics
MCNPX 2.7.0, 2.7.0-i8 [264] Physics
MEGAN 5.10.3 [265] Biology, NGS
Megraft 1.0.2 [266] Biology, Sequencing
Melting 4.3.1 [267] Biology, Genome, RNA, Folding
Meme 4.8.1 [268] Biology, Motifs, Sequence analysis
Mercurial 2.7 [269] Development, Revision Control
Merlin 1.1.2 [270] Biogolgy, SNP
Metabin 1.0 [271] Biology, Metagenomics
MetaCluster 5.0b [272] Biology, Metagenomics
MetaCV 2.3.0 [273] Biology, NGS
METAL 20110325 [274] Biology, Genomics
MetAMOS 1.5.0rc4-20140827 [275] Biology, Bioinformatics, Genomics, Assembly
MetaVelvet 1.2.01 [276] Biology, NGS
Metaxa2 2.0.2 [277] Biology, NGS
MetaGeneMark 2012.04 [278] Biology, Genomics
Mfold 3.6 [279] Biology, Genomics
MIA 20130301 [280] Biology, NGS
Midnight Commander 4.6.1 [281] Tools, Utilities
Migrate-n 3.3.0, 3.6.6 [282] Biology, Population
Minimac 1-20130717, 2-20140915, 3-20150727 [283] Biology, Genomics
mira 3.9.18, 4.0.rc1, 4.0.2 [284] Biology, NGS
MISO 0.4.9, 0.5.2, 0.5.3 [285] Biology, NGS
MMSEQ 1.0.8 [286] Biology, NGS
MSMBuilder 2.5.1 [287] Molecular Dynamics
MOABS 1.2.9 [288] Biology, NGS, Genomics
Modeller 9.11, 9.13, 9.14 [289] Biology, Modeling
Molden 5.0 [290] Molecular, electronic structure
MolPro 2012.1p22 [291] Quantum Chemistry, Ab Initio
mosaik 2.1.33, 2.2.3 [292] Biology,NGS
Mothur 1.31.2 [293] Biology, Microbial Ecology
MOTU 1.1 [294] Biology, Bioinformatics, Genomics
MP-EST 1.4 [295] Biology, Phylogenetics
mpiP 3.4.1 [296] Parallel Computing
MrBayes 3.2.1, 3.2.4, 3.2.5 [297] Biology, Phylogenetics
MRIcron 201306 [298] Biology, MRI, Imaging
MUMmer 3.23 [299] Biology, Genomics
MUSCLE 3.8.31 [300] Biology, Genomics
MZMine 2.10, 2.14.2, 2.15 [301] Biology, Spectroscopy
NAMD 2.9 [302] Simulation, Chemistry, Biology
Nbody 6 [303] Astronomy
NCBI C++ Toolkit 12.0.0 [304] Biology, C++, Development
NCL 6.1.2 [305] Atmosphere Science
NCO 4.2.1, 4.4.3 [306] Data exchange tools
Ncview 2.1.2 [307] Data visualization
NetCDF 3.4.2, 4.2, 4.3 [308] Data exchange, Tools
Newbler 2.7, 2.8, 2.9 [309] Biology, NGS
Newick utils 1.6 [310] Biology, Phylogenetics
Nextallele 20140718 [311] Biology, Genomics
Nexus NCL 2.1.18 [312] Biology, Phylogenetics, Library
ngsCAT 0.1 [313] Biology, Bioinformatics, NGS
NGSUtils 20130722, 20150206 [314] Biology, NGS
Nipype 0.10.0 [315] Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe 7.9 [316] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [317] Biology, NGS
NWChem 6.5 [318] Chemistry
Oases 0.2.08 [319] Biology, NGS
Olego 1.1.2, 1.1.5 [320] Biology, NGS, RNA-Seq
Octave 3.6.4 [321] Numerical Computation
Oncotator 1.5.1.0 [322] Biology, Genomics
OpenBabel 2.3.2 [323] Biology, Chemistry
OpenCL 1.1 [324] Programming, Library
OpenCV 2.4.8 [325] Computervision
OpenFOAM 2.1.1 [326] Fluid Dynamics
OpenMM 6.2.0 [327] Quantum Chemistry
OrthoFinder 0.2.5 [328] Biology, Genomics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [329] Biology, Genomics
p4vasp 0.3.29 [330] Molecular, Electronic Structure
Pacbio 2.2.0, 2.3.0 [331] Biology, Bioinformatics, NGS
PALES 122 [332] Physics
PAML 4.7, 4.8a [333] Biology, Phylogenetics
Pandaseq 20140808, 20150627 [334] Biology, Bioinformatics, NGS, Sequencing
PAPI 5.1.0.2 [335] Software, Computing
Parallel 20150122 [336] Programming, Languages
ParaView 4.1.0, 4.2.0, 4.3.0 [337] Data Analysis
PartitionFinder 1.0.1, 1.1.1 [338] Biology, Phylogenetics, Evolution
Parflow v615 [339] Ecology, Modeling
PASA 1.5, 2.0-r20150209 [340] Biology, Genomics
PAUP 4.0b10 [341] Biology, Phylogenetics
PAUDA 1.0.1 [342] Biology, Bioinformatics, Sequence alignment
PBJelly 14.7.14, 15.2.20 [343] Biology, Bioinformatics
pbsdrmaa 1.0.17 [344] Libraries, Torque
PeakSplitter 1.0 [345] Biology, Chip-Seq
PEAR 0.9.2, 0.9.6 [346] Biology, NGS
PDT 3.18 [347] Programming, Profiler
Perl 5.16.0 [348] Programming, Language
PerM 0.4.0 [349] Biology, NGS
PETSc 2.3, 3.3 [350] Math, Numerical solvers
Phenix 1.8.1069 [351] Crystallography
PHYLDOG 20130418 [352] Biology, Genomics, Phylogenetics
Phyluce c561dd9 [353] Biology, Phylogenetics
PfamScan 1.3 [354] Biology, Genomics
PHITS 2.52 [355] Physics
Phonopy 1.9.2 [356] Chemistry
PHYLIP 3.696 [357] Biology, Phylogenetics
PhyloBayes 3.3f, 1.4f MPI [358] Biology, Phylogenetics
Phylosift 1.1 [359] Biology, Genomics, Phylogenetics, Taxonomy
PhyML 3.0, 20121109 [360] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [361] Biology, NGS
PLAST 1.0 [362] Biology, Bioinformatics
Plink 1.07, 1.90b3 [363] Biology, GWAS
PLINKSEQ 0.10 [364] Biology, Genomics
PluMiST 1.1 [365] Biology, Phylogenetics, Genomics
POV-Ray 3.7 [366] 3D, Graphics
PolyPhen 2.2.2.r405b [367] Biology, Genomics
Preseq 0.0.4 [368] Biology, NGS
Primer3 2.3.4 [369] Biology, Genomics
ProfessAtQE 2014 [370] Material Science, Molecular Dynamics
Prokka 1.10 [371] Biology, Genomics, Bioinformatics, Assembly
ProBABEL 0.4.2, 0.4.3, 0.4.5 [372] Biology, Genomics, GWAS
Probalign 1.4 [373] Biology, Genomics
Proovread 1.03rcl [374] Biology, Genomics, NGS
Proteinortho 4.26 [375] Biology, Genomics
PROVEAN 1.1.5 [376] Biology, Genomics
Python 2.7.3, 2.7.5, 2.7.6, 2.7.8 [377] Biology, Genomics, NGS
QDD 3.1.2 [378] Programming, scripting, language
QIIME 1.5.0 [379] Biology, Ecology
QT 4.8.3 [380] Computer Science
QUAST 2.3 [381] Biology, NGS
Quantas 1.0.4, 1.0.8 [382] Biology, Bioinformatics, NGS
Quickquartet 1.0.0 [383] Biology, Phylogenetics
R Rmpi/2.15.1, 3.0.2, 3.2.0 [384] Statistics, Programming
R8S 1.71, 1.8 [385] Biology, Evolution
RADICAL 0.2 [386] Biology, Phylogenetics, Genomics
RAxML 8.1.12, 8.1.23, 8.2.2 [387] Biology, Phylogenetics
RepeatExplorer 20150506 [388] Biology, Genomics
RepeatMasker 3.3.0 [389] Biology, Genomics
Reptile 1.1 [390] Biology, NGS, error correction
riboPicker 0.4.3 [391] Biology, Sequence
RNAhybrid 2.1.1 [392] Biology, Genomics
ROOT 6.0 [393] Data Analysis
Rosetta 2014wk4 [394] Biology, Structure, Modelling
RSEG 0.4.8 [395] Biology, NGS
RSEM 1.1.17, 1.2.7, 1.2.19 [396] Biology, NGS, RNA-Seq
RSeQC 2.3.7 [397] Biology, NGS, RNA-Seq
Ruby 1.9.3-p0 [398] Programming, Scripting, Language
Sailfish 0.6.3 [399] Biology, NGS, RNA-Seq
Sambamba 0.5.0-dev, 0.5.1 [400] Biology, NGS
Samstat 1.08 [401] Biology, NGS, Bioinformatics, Sequencing
Samblaster 0.1.14 [402] Biology, NGS
samtools 1.0, 1.1, 1.2 [403] Biology, NGS
SAS 9.3 [404] Statistics, Graphing
SATe 2.2.7 [405] Biology, Phylogenetics
Scala 2.11.5 [406] Programming, Language
Scalablast 2.4.53 [407] Biology, Genomics
Scalpel 0.1.1 [408] Biology, NGS
SHAPEIT 2.5.5 [409] Biology, SNP
Sharcgs 1.2.11 [410] Biology, NGS, Assembly
Schrodinger 2012, 2013 [411] Simulation, chemistry
SCons 2.3.0 [412] Programming
SCRATCH1D 1.0 [413] Biology, Genomics
Scythe 0.991 [414] Biology, NGS
Segemehl 0.1.9 [415] Biology, NGS, Mapper
SEPP 1.0, 3.0 [416] Biology, Phylogenetics, HMM
SeqPrep 0.5 [417] Biology, NGS
SeqMap 1.0.13 [418] Biology, NGS
Seqtk 20140729 [419] Biology, NGS
SEQuel 1.0.1 [420] Biology, NGS
SeqyClean 1.8.10 [421] Biology, NGS, Bioinformatics
ShoRAH 20131204 [422] Biology, NGS, quality filter
SHRiMP 2.2.3 [423] Biology, NGS
Sickle 1.200, 1.33 [424] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [425] Simulation, Physics, Ab Initio
SIFT 4.0.3b [426] Biology, Genomics
Silo 4.7 [427] Library, Data
SIPeS 2.0 [428] Biology, Bioinformatics, ChIP-Seq
Slicer 4.3.1 [429] Biology, Imaging
SMALT 0.7.6 [430] Biology, NGS
Snap 20100728 [431] Biology, Genomics
SNAPE-pooled 20130407 [432] Biology, SNP
SNeP 1.1 [433] Biology, Phylogenics
SnpEff 3.3h, 4.0e, 4.1i [434] Biology, NGS, Genomics
SNPhylo 20140701 [435] Bilogy, Phylogenetics
SOAPdenovo 1.05 [436] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [437] Biology, NGS
SOAPsplice 1.10 [438] Biology, NGS
SparCC 201402 [439] Microbial Ecology
Spades 3.0.0, 3.1.0, 3.5.0 [440] Biology, NGS
Spanki 0.4.1, 0.4.3, 0.5.0 [441] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [442] Chemistry
SPIMAP 1.1 [443] Biology, Phylogenetics
SpliceTrap 0.90.5 [444] Biology, NGS, RNA-Seq
SPM 8 [445] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [446] Biology, Genomics
SQLite 3.8.8.2 [447] Database
SRA 2.1.10 [448] biology, NGS
SSPACE 2.0 [449] Biology, NGS
Stacks 0.9995 [450] Biology, Genomics, NGS
STAR 2.3.0e [451] Biology, NGS, Alignment
STAR-CCM+ 8.06 [452] Mechanical Engineering
Stata 10.1, 13 [453] Statistics, Data analysis
Stringtie 0.97 [454] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [455] Biology, Population
SUNDIALS 2.3.0, 2.5.0 [456] Numerical Solver
SVDetect 0.8b [457] Biology, NGS, SNP
swak4Foam 2.x [458] Fluid Dynamics
swarm 1.2.11 [459] Data Analysis
Swig 2.0.9 [460] Programming, C, C++, Python
SwitchSeq 20140907 [461] Biology, NGS
Syzygy 1.2.7 [462] Biology, Genomics
TASSEL 5.0 [463] Biology, Genomics
TAU 2.21.4, 2.23 [464] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [465] Biology, Genomics, Multiple Alignment
TESS 2.3.1 [466] Biology, Genomics, Markov
tgicl 2.1 [467] Biology, sequencing, clustering
Tmux 2.0 [468] GNU
TomoPy 0.0.3 [469] Biology, Neuroimaging
Tophat 1.4.1, 2.0.13 [470] Biology, NGS
Totalview 8.12.0 [471] Computer Science
TPP 4.7.0 [472] Bioinformatics, MassSpec
TrackTools 2011 [473] Bioinformatics
TrackVis 0.5.2.2 [474] Biology, Spectroscopy
Tracula 5.3.2014_05_26 [475] Biology, Bioinformatics, Neuroscience, Imaging
TraitRate 1.1 [476] Biology, Evolution
TransDecoder 20140704, 2.0.1 [477] Biology, NGS
Transrate 1.0.1 [478] Biology, Assembly
TreeFix 1.1.7, 1.1.10 [479] Biology, Phylogenetics
TreePL 20150305 [480] Biology, Phylogenetics
TRF 4.04 [481] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [482] Math Algorithm
Trim Galore 0.2.8 [483] Biology, NGS
Trimmomatic 0.22, 0.32 [484] Biology, NGS
Trinity r20150215-2.0.4 [485] Biology, NGS, RNA-Seq
Trinotate 2.0.1 [486] Biology
TRNAscan-SE 1.23 [487] Biology, NGS, Bioinformatics
Twinscan 4.1.2 [488] Biology, Genomics
usearch 7.0.1001-64, 8.0.1517 [489] Biology, Sequence analysis
UDUNITS 2.2.17 [490] Library, Units, Programming
UNAFold 3.8 [491] Biology, Genome, RNA, Folding
UProC 1.2.0 [492] Biology, Genomics
Valgrind 3.9.0 [493] Computer Science
VarScan 2.3.6 [494] Biology, NGS, Genomics
VASP 5.3.2, 5.3.3, 5.3.5 [495] Quantum Chemistry, Ab Initio
VAST-TOOLS 20150506 [496] Biology, NGS, RNA-Seq
VCFLib 20141119, 20150313 [497] Biology, NGS, Genomics
VCFtools 0.1.11, 0.1.12a, 0.1.12b [498] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [499] Biology, Genomics, NGS
VEP 74 [500] Biology, NGS
VICUNA 1.3 [501] Biology, Assembly
Vim 7.4.5 [502] Programming, Scripting, Language
vmd 1.9.1 [503] Biology, Visualization
VTK 6.1.0 [504] Visualization, Graphics
Wannier90 1.2, 2.0.0 [505] Computational Physics
WebLogo 3.3 [506] Biology, Genomics
WDSSII 1 [507] Meteorology
WIEN2k 12.1 [508] Material Science, Chemistry
Wgs or Celera 8.2, 8.3rc1, 8.3rc1.r4638 [509] Biology, NGS
wublast 2.0 [510] Biology, Sequence Alignment
YAHA 0.1.82 [511] Biology NGS
XCrySDen 1.5.60 [512] Computational Material Science
Yambo 3.3.0 [513] Physics
YASM 1.3.0 [514] Computer Science
Yasra 2.32 [515] 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.

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