Difference between revisions of "Installed Software"

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Line 1,508: Line 1,508:
 
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|-
 
| [[TaxonDNA]] || 1.8 || [https://github.com/gaurav/taxondna] || Biology, Taxonomy
 
| [[TaxonDNA]] || 1.8 || [https://github.com/gaurav/taxondna] || Biology, Taxonomy
 +
|-
 +
| [[Tcllib]] || 1.18 || [https://www.tcl.tk/software/tcllib/] || Computer Science
 
|-
 
|-
 
| [[T-Coffee]] || 9.03.r1318 || [http://www.tcoffee.org/Projects/tcoffee/] || Biology, Genomics, Multiple Alignment  
 
| [[T-Coffee]] || 9.03.r1318 || [http://www.tcoffee.org/Projects/tcoffee/] || Biology, Genomics, Multiple Alignment  

Revision as of 23:46, 29 August 2017

  • Last updated on 2017-08-29.bes
  • 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
3PCLR 20150906 [1] Biology, Genomics
4P 1.0 [2] Biology, SNP
AbInit 6.12.3, 7.10.2, 7.10.4 [3] Quantum Chemistry, DFT
Abyss 1.5.2, 1.9.0, 2.0.0 [4] Biology, NGS
ADMB 11.5 [5] Math, Modeling, Optimization
AdmixTools 20150311, 20160513 [6] Biology, Bioinformatics, Genomics, NGS
ADMIXTURE 1.23, 1.3.0 [7] Biology, Bioinformatics, Genomics, NGS
AEGeAn 0.14.0 [8] Biology, Genomics
AFNI 2013_11_24, 2016_0_19 [9] Biology, Statistics, Imaging, Neurology
Agalma 0.2.1, 0.3.5, 0.5.0 [10] Biology, Bioinformatics, Genomics, SNP
AGOUTI 0.3.3 [11] Biology, Genomics
ALE 20150507 [12] Biology, Bioinformatics, Assembly
AltAnalyze 1.9.6 [13] Biology, Genomics
ALLPATHS-LG 42316, 44837 [14] Biology, NGS
Amber 11, 12, 14, 16 [15] Simulation, chemistry
AMAS 0.98 [16] Biology, Sequence Alignment
AMOS 3.1.0 [17] Biology, Genomics, NGS
AMPHORA2 20140305 [18] Biology, Phylogenetics
AMPtk 0.8.0, 0.8.5 [19] Biology, Bioinformatics, NGS
ANGEL 2.3 [20] Biology, Bioinformatics, NGS
ANTs 2.2.0 [21] Biology, Phylogenetics
Anvio 2.1.0, 2.3.2, 2.4.0 [22] Biology, Microbial 'omics
ANNOVAR 20120621, 20150322 [23] Biology, Genomics
AStalavista 3.2 [24] Biology, NGS, RNA-Seq, Genomics
ASTRID 20150807 [25] Biology, Genomics
ASPECT 1.5.0 [26] Simulation, Geology
Atlas 3.10.1, 3.11.17 [27] Library, Math
Amuse 6.0, 10.0 [28] Astrophysics
ANGSD 20150306, 20150909 [29] Biology, NGS
Affymetrix Power Tools 1.15.0, 1.18.0, 1.20.5 [30] Biology, Genomics, Microarray
ArrayFire 3.4.2 [31] Code Optimization
ARC 20140312 [32] Biology, NGS
ARCS 1.0.0, 1.0.1 [33] Biology, Genomics
Armadillo 6.200.3 [34] Library, C++ , Math
Astral 4.10.6, 4.10.7, 5.0.3 [35] Biology, Bioinformatics, NGS, Phylogenetics
AtomEye 3 [36] Material Science
ATRAM 20140624 [37] Biology, NGS
Augustus 3.2.1, 3.2.2, 3.3 [38] Biology, NGS
Auto3DEM 4.05.1, 4.05.2 [39] Image Reconstruction
BamBam 1.0 [40] Biology, NGS
BALI-PHY 2.3.8 [41] Bioinformatics, Bayesian Estimation
BAMM 2.5.0 [42] Biology, Phylogenetics
Bam-readcount 20150216 [43] Biology, NGS
Bamstats 20140602 [44] Biology, NGS
Bamtools 2.1.1, 2.4.1 [45] Biology, NGS
BamUtil 1.0.2 [46] Biology, NGS
Bam-Readcount 20150616 [47]] Biology, Genomics
BAPS 6.0 [48] Biology, Populaton genetics
Barrnap 0.7 [49] Biology, RNA-Seq
Basemount 0.1.2.464 [50] Biology, DNA Sequencing
BatVI 1.00 [51] Biology, Phylogenetics
BayArea 1.0.2 [52] Biology
BAYENV 2.0.0 [53] Biology, Phylogenetics
BayeScan 2.1 [54] Biology, SNP
BayesR 20151016 [55] Biology, Phylogenetics
BayeScEnv 1.1 [56]] Biology, SNP, Phylogenetics
BayesRate 1.3.43 [57] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [58] Network file transfer
BBMap 36.23, 37.09 [59] Biology, Alignment
Bcbio-nextgen 0.8.7, 0.9.9 [60] Biology, NGS
Bcftools 1.3.1, 1.4, 1.5 [61] Biology, Genomics, NGS
Bcl2fastq 2.16, 2.17, 2.19 [62] Biology, NGS, Illumina
BEAGLE 3.2.2, 4.0 [63] Biology, Genetics, Genotyping
BEAST 1.7.5, 1.8.1, 2.3.2 [64] Biology, Phylogenetics
Bedops 2.4.2 [65] Biology, Bioinformatics, Sequence, NGS
BEDTools 2.23.0, 2.24.0, 2.26.0 [66] Biology, NGS
BEST 2.3.1 [67] Biology, Phylogenetics
BESST 2.2.4 [68] Biology, Bioinformatics
BETA 1.0.5 [69] Biology, NGS
BFAST 0.7.0 [70] Biology, NGS
Bismark 0.7.7, 0.13.0, 0.17.0 [71] Biology, NGS, Methylation
BinPacker 1.0 [72] Biology, RNA-Seq, Sequence Assembly
BinSanity 0.1.3, 0.2.5.9 [73] Biology, Genomics
Bioconductor Latest [74] Biology, R, Statistics
BioPerl 1.006901 [75] Biology, Perl
BioPython 1.59 [76] Biology, Python
BLASR 20130815 [77] Biology, NGS
NCBI BLAST 2.2.27, 2.5.0, 2.6.0 [78] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [79] Biology, Annotation
BLAT 20120524, 20140318 [80] Biology, Sequence alignment
Blender 2.63 [81] Graphics
BLESS 1.02 [82] Biology, NGS
BLUPF90 20160604 [83] Biology, Phylogenetics
BloomTree 0.3.5 [84] Biology, Phylogenetics
BoltzTraP 1.2.5 [85] Physics
Boost 1.59.0, 1.63.0 [86] C++, Library
Bowtie 0.12.9, 1.1.1, 1.2.0 [87] Biology, NGS
Bowtie2 2.2.9, 2.3.0, 2.3.2 [88] Biology, NGS
BPP 1.9.0, 2.2, 3.2 [89] Biology, Phylogenetics
Bracken 1.0.0 [90] Biology, Phylogenetics
BRANCH 1.8.1 [91] Biology, NGS, Mapping
BRATNextGen 20150505 [92] Biology, Genomics
BRIG 0.95 [93] Biology, Genomics
Bsoft 1.9.1 [94] Biology, Image Analysis
Bsmap 2.74, 2.87 [95] Biology, NGS, Methylation
BSSeeker2 2.1.0 [96] Biology, Phylogenetics
Bubbleparse 20140314 [97] Biology, Phylogenetics
BUCKy 1.4.4 [98] Biology, Genomics
BUSCO 1.22, 2.0b, 3.01 [99] Biology, Genomics
Bwa 0.6.1, 0.7.12, 0.7.15 [100] Biology, NGS
BXH_XCEDE_tools 1.11.1 [101] Biology, Bioinformatics
Camino 20140723 [102] Biology, Neuroscience, Imaging
Canu 1.3, 1.5, 1.6 [103] Biology, Sequencing
CASM 0.2.0 [104] Statistical Mechanics
CAP3 20120705 [105] Biology, Sequence Assembly
CASAVA 1.8.2 [106] Biology, NGS
CD-HIT 4.6, 4.6.4 [107] Biology, Genomics
CDO 1.6.1, 1.7.2rc5 [108] Climate
CEAS 1.0.2 [109] Biology, Genomics
CellProfiler 2.0, 2.2.0 [110] Biology, Image Analysis
CellRanger 1.2.1, 1.3.0 [111] Biology, Bioinformatics, NGS, RNA-Seq
CFITSIO 3.370 [112] Library, C
CGATools 1.6.0.42 [113] Biology, NGS
Charmm 36a3 [114] Simulation, Chemistry
Chartdirector 5.1.0 [115] Graphics
CheckM 1.0.4 [116] Biology, Genomics
Chimera 1.7 [117] Biology, Modeling
ChromEvol 2.0 [118] Biology, Phylogenetics
CIMS 4.1.2 [119] Biology, Genomics
Circos 0.63-pre11, 0.69-2 [120] Biology, Visualization
Circlator 1.5.1 [121] Biology, Genomics
CIRCexplorer 1.1.10 [122] Biology, Bioinformatics, RNA-Seq
CisGenome 2.0 [123] Biology, Genomics, Peak Calling
Clann 3.2.3 [124] Biology, Phylogenetics
CLARK 1.2.2-b [125] Biology, Genomics
CLHEP 2.2.0.1 [126] High Energy Physics
CLIPper 1.0 [127] Biology, Sequencing
CLIPSeqTools 0.1.7 [128] Biology, Sequencing
ClonalFrame 1.1, 1.2 [129] Biology, Genomics, NGS
ClonalFrameML 1.25 [130] Biology, Genomics, NGS
ClustalW 2.1 [131] Biology, Genomics
Cluster3 1.52 [132] Biology, Genomics
Clview 20130402 [133] Biology, Genomics
ClustalO 1.2.0 [134] Biology, Genomics
CLUMPP 1.1.2 [135]] Biology, Bioinformatics
ClusterFinder 313 [136] Biology, Metabolomics
CMake 2.9.12.1, 3.1.0, 3.6.3 [137] Programming, Build System
CMS 20170518 [138] Biology
CMWP 140518 [139] Biology, Genomics
CNVnator 0.3.2 [140] Biology, Genomics
CNVSeq 20110715 [141] Biology, NGS
CNVkit 0.9.0 [142] Biology
Cobrapy 0.3.2 [143] Biology, Metabolomics, Modeling
Coevol 1.3c, 1.4b [144] Biology, Phylogenetics
CoMap 1.4.1 [145] Biology, Genomics
CONSEL 0.20 [146] Biology, Phylogenetcs
CONCOCT 0.3.1 [147] Biology, Genomics
ContaVect 0.2 [148] Biology, Phylogenetics
CoNIFER 0.2.2 [149] Biology, Genomics
Consed 23.0 [150] Biology, Genomics
Coreutils 8.23 [151] GNU Utilities, Computer Science
Corset 1.06 [152] Biology, NGS
covNMR 2014 [153] Biochemistry
CPAT 1.2.2 [154] Biology, Phylogenetics
CPLEX 12.6.5 [155] Optimizer
CUDA 4.2, 5.5 [156] Programming, Graphics
Crass 1.0.1 [157] Biology, Assembly
CRISPRdigger 1.007 [158] Biology, Phylogenetics
CrossMap 0.2.3 [159] Biology, Genomics
Crux 1.40 [160] Biology, Mass-Spectrometry
CryptoMiniSat 5.0.1 [161] SAT
Cufflinks 1.3.0, 2.0.2, 2.2.1 [162] Biology, NGS
Cutadapt 1.7.1, 1.8.1, 1.10 [163] Biology, NGS
CUTE 20160116, 20161010 [164] Cosmology
Cytoscape 3.4.0 [165]] Biology, Bioinformatics
DAKOTA 5.4.0 [166] Computational Science
DaPars 0.9.0 [167] Biology, NGS, RNA-Seq
DALIGNER 1.0 [168] Biology, Sequencing
Datamash 1.1.0 [169] Math
DCMTK 3.6.0 [170] Biology, Neuroscience, Imaging
DSSAT 4.5 [171] Biology
dDocent 20160425 [172] Biology
DDSCAT 7.3.0 [173] Astrophysics
DDT 5.0, 6.0, 6.1.2, 7.0.4 [174] Software
Dealii 8.3.0, 8.4.1, 8.5.0 [175] Library
DeconSeq 0.4.3 [176] Biology, Phylogenetics
Delft3D 3621 [177] Hydrodynamics, Physics
DeepPicker 20161102 [178] Deep Learning, Cross-Molecule Training
DeepTools 2.4.3 [179] Biology, Bioinformatics, NGS
Desmond 3.0.3.1 [180] Simulation, Biology, Chemistry
DETONATE 1.9, 1.11 [181] Biology, NGS
DEXTRACTOR 1.0 [182] Biology, Sequencing
Dalton 2011 [183] Quantum Chemistry
Diamond 0.5.1, 0.8.5 [184] Computational Biology, Genomics
DiscoSnp 2.2.10 [185] Biology, Phylogenetics, SNP
Dibig Tools 1.0 [186] Bioinformatics, PBS, Torque, Jobs
DiffReps 1.55.4 [187] Biology, NGS, ChIP-Seq
Dindel 1.01 [188] Biology, NGS
DISCOVARdenovo 52488 [189] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [190] Biology, Genomics
Dlpoly 4.03.4 [191] Simulation, Biology, Chemistry
Dlpoly-Classic 1.9 [192] Simulation, Biology, Chemistry
DNA Clust 3.0 [193] Biology, Genomics
Dock 6.5, 6.6, 6.7 [194] Chemistry, ligand binding prediction
DOT 2.0 [195] Biology, Bioinformatics, Docking
DosageConvertor 1.0.3 [196] Biology, Converter
Doxygen 1.8.3.1 [197] Programming, Documentation
DSK 2.1.0 [198] Biology, NGS
DSSP 2.2.1 [199] Biology, Molecular Dynamics
DTI-TK 2.3.1 [200] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [201] Biology, NGS
ECTools 20140311, 20141201 [202] Biology, Sequencing, Bioinformatics
ECE 1.0 [203] Ece
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [204] Biology, Matlab
ED2 2.1 [205] Biology
eGene-MVN 0.1 [206] Biology, Genetics
eigenMT 20160228 [207] Biology, Genetics
EIGENSOFT 4.2, 5.0.1, 6.0.1 [208] Biology, Population
emboss 6.5.7 [209] Biology, multi-tool suite
EMAN2 2.11 [210] Biology
EMMAX 20100307, 20120210 [211] Biology, NGS, Mapping
EMC 9.3.9 [212] Monte Carlo Simulations
EMIRGE 20130727 [213] Biology, NGS
Ensembl_Tools 80 [214] Biology, Bioinformatics
EPACTS 3.2.6 [215] Biology, Bioinformatics, Genomics
EPOCH 4.7.3 [216] Astronomy, CPPP
eQTLA 1.1 [217] Biology, Genomics
Eqtlbma 1.2.2 [218] Biology, Genotyping
Esmf 6.3.0rp1 [219] Climate
Espresso 5.0.1, 5.2.0, 5.2.1, 5.3.0 [220] Modeling, Physics
ESPRIT 201211 [221] Biology, NGS, Metagenomics
ETE2 2.1 [222] Biology, Phylogenetics
ETE3 3.0.0 [223] Biology, Phylogenetics
Eval 2.2.8 [224] Biology, Genomics, GUI
ExaBayes 1.4.1, 1.5 [225] Biology, Phylogenetics
ExaML 1.0.5, 1.0.12, 3.0.14, 3.0.17 [226] Biology, Phylogenetics
ExomeCNV 1.4 [227] Biology, NGS, Genomics
Exonerate 2.2.0 [228] Biology, Genomics
eXpress 1.3.1 [229] Biology, NGS
FALCON 20160828, 20161222 [230] Biology, Bioinformatics, NGS, Sequencing
FALCON_unzip 20160623, 20161222 [231] Biology, Bioinformatics
FAR 2.15 [232] Biology, Genomics
FASTA 34.26.5, 36.3.6d [233] Biology, Genomics
FAST-iCLIP 0.9.1 [234] Biology, Sequencing
FastML 3.0 [235] Biology, Phylogenetics, ML
FastSpar 0.0.4 [236] Biology, Genomics
FastQC 0.10.1, 0.11.2, 0.11.4 [237] Biology, NGS
Fastq-tools 0.7, 0.8 [238] Biology, NGS
FastStructure 20150112 [239] Biology, Genomics
FastTree 2.1.7 [240] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [241] Biology, NGS
Fathmm 20150225 [242] Biology, Genomics
fcGENE 1.0.7 [243] Biology, Genomics, SNP
Ferret 6.82 [244] Oceanography, Meteorology
FFmpeg 2.1.3, 2.8.3 [245] Multimedia, audio, video
FFTW 3.3.2, 3.3.3, 3.3.4 [246] Math, Library, C++
FineSTRUCTURE 2.0.7 [247] Biology, Populatiopn Genetics
FLASH 1.2.10, 1.2.11 [248] Biology, Genomics, NGS
Flexbar 2.3 [249] Biology, Genomics, NGS
Fluent 14.5.7, 15.0.7, 16.0, 17.2 [250] Simulation, Fluid Dynamics
fqtools 20160224 [251] Biology, Bioinformatics, NGS
FragGeneScan 1.16 [252] Biology, NGS, Genomics
FrameDP 1.2.2 [253] Biology, Sequencing
Frealign 9.11 [254] Image Reconsctruction
FreeBayes 1.0.1, 1.0.2, 1.1.0 [255] Biology, NGS, SNP Calling
FREEC 9.6 [256] Biology, Sequencing
Freesurfer 5.2.0, 5.3.0 [257] Biology, Neurology, Imaging
FSL 5.0.2.2 [258] Biology, Neurology, Imaging
Galaxy latest [259] Biology, Chemistry, Other
GapFiller 1.11 [260] Biology, NGS
Garli 2.0, 2.01 [261] Biology, Phylogenetics
GAML 20150610 [262] Biology, NGS
GAMBIT 15.1.0, 16.0.0 [263] Game Theory
GARM 0.7.4 [264] Biology, NGS
GASVPro 201310 [265] Biology, NGS, Genomics
GATE 7.0 [266] Data Analysis
GATK 3.4.46, 3.5.0, 3.7.0 [267] Biology, NGS
Gaussian G03, G09-A.02, G09-C.01 [268] Modeling, Computational Chemistry
Gblocks 0.91b [269] Genomics, Alignment tool
GCTA 1.24.7, 1.26.0 [270] Biology, Genomics, SNP
GDAL 1.11.2 [271] Geospatial Data Modeling, Geospatial Library
GDC-Client 1.0.1 [272] Biology, Bioinformatics, Sequencing, NGS
Geant4 4.10 [273] Physics
GEM 20130406 [274] Biology, NGS
gem5 2.0 [275]] Computer Simulator
GEMINI 4.6.6a, 0.13.1, 0.18.0 [276] Biology, Genomics, Genetics
GenBank Tools 20140130 [277] Biology, Genomics
GeneMark 2012.04 [278] Biology, Genomics, Metagenomics
GeneSeqer 20140226 [279] Biology, Genomics
Genewise 2.2.0 [280] Biology, Genomics, Annotation
GenGen 1.0.1 [281] Biology, Phylogenetics
Genome STRiP 2.00.1602 [282] Biology, genomics, NGS
GenomicConsensus 20160523 [283] Biology, Phylogenetics
GenomicTools 2.7.0 [284] Biology, NGS
GenomeTools 1.5.7 [285] Biology, Bioinformatics
GenotypeHarmonizer 1.4.18 [286] Biology, Bioinformatics
GenSel 4.90 [287] Biology, Genetics
GET_HOMOLOGUES 20150529 [288] Biology, Genomics
GFOLD 1.1.4 [289] Biology, RNA-seq
Gffread 0.9.8c [290] Biology, Bioinformatics
GKNO 1.30.18 [291] Biology, NGS,
Git 1.8.2.1, 1.9.0 [292] Development, Revision Control
Glimmer 3.02 [293] Biology, Microbial Annotation
Globus 2.1.3 [294] Data Transfer
GLPK 4.55 [295] Biology, Genomics
Gmap 20150723, 20160501, 20160816 [296] Biology, Genomics
GNU Compilers 5.2.0 [297] Compilers, Programming
GnuPlot 4.6.0, 5.0.3 [298] Graphics, Plotting, Programming
Grace 5.1.22 [299] Graphics, plotting, 2D
GrADS 2.0.1 [300] Earth Science
GramCluster 1.3 [301] Biology, Sequencing
GRASS 7.0 [302] Geography
GraphViz 2.38.0 [303] Graphics, plotting, visualization
GraphMap 0.4.0 [304] Biology, Sequencing
Gromacs 4.5.5, 4.6.5, 5.1.2 [305] Chemistry, Modeling, Simulation
GSNP 1.0 [306] Biology, Bioinformatics, NGS
GSL 1.15 [307] Library, Math, C++, C
Gsutil 4.15 [308] Cloud, Storage, Google
Gubbins 20150519, 20160421 [309] Biology, Phylogenetics, Genomics
GULP 4.0 [310] Material Science
HaMStR 13.2.2, 13.2.3, 13.2.4 [311] Biology, Genomics
HapCompass 0.7.7 [312] Biology, NGS, Genomics
HAPCUT 0.7 [313] Biology, Assembly
Hapsembler 2.21 [314] Biology, Genomics, NGS
HapTree 1.0 [315] Biology, Genomics, NGS
hapQTL 1.00 [316] Biology, Genomics
HDF4 4.2.11 [317] Library, Data
HDF5 1.8.9, 1.8.15, 1.10.1 [318] Library, Data
HGTFinder 20160720 [319] Biology, Genomics
HISAT2 2.0.0b, 2.0.1b, 2.0.3b [320] Biology, Sequence Alignment, NGS
HMMER3 3.0, 3.1b1, 3.1b2 [321] Biology, Genomics
HMMSplicer 0.9.5 [322] Biology, Genomics
HOMER 4.2, 4.7, 4.8 [323] Biology, Genomics
HOOMD 1.3.3 [324] Chemistry
HTMLDoc 1.2.82 [325] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [326] Biology, NGS
Hyb 20141126 [327] Biology, NGS, RNA-Seq
HybPiper 1.2 [328] Biology, Phylogenetics
HyPhy 2.1.2.28, 2.2.6.1, 2.3.0 [329] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [330] Library, Math, Physics
iAssembler 1.32 [331] Biology, Assembly
IBDNe 20150815 [332] Biology, NGS
iCommands 3.3.1 [333] Biology, iPlant, Data Tansfer
ICORN2 0.95 [334] Biology, Sequencing
IDBA-UD 1.0.9, 1.1.0, 1.1.1 [335] Biology, NGS
IDBA-MT 1.0 [336] Biology, NGS
IEP 3.6 [337] Programming, Python, Editor
IGB 8.4.1 [338] Biology, Genomics, NGS
IGV 2.3.91 [339] Biology, Bioinformatics, NGS
iGTP 1.1 [340] Biology, Bioinformatics, Phylogenetics
illumiprocessor 20150803 [341] Biology, Sequencing
IM and IMa 20091217 [342] Biology, Population
IMa2 20120827 [343] Biology, Population
ImageJ 1.48 [344] Image manipulation
ImageMagick 6.8.8-9, 7.0.5-5 [345] Image manipulation
IMOD 4.7.15 [346] 3D modeling, Image Reconstruction
InParanoid 4.1 [347] Biology, Bioinformatics
Intel Compilers 2016.0.109 [348] Programming, Compilers
IOAPI 3.1 [349] Meteorology
Interproscan 4.8 [350] Biology, Genomics, Iprscan, Interproscan
ipyrad 0.4.4, 0.6.20 [351] Biology, bioinformatics, NGS
IQ-TREE 1.4.0, 1.4.2, 1.5.3 [352] Biology, Phylogenetics
IRAP 0.8.1p7 [353] Biology, NGS, RNA-seq
iRep 20161015 [354] Biology,
IRFinder 1.0.0, 1.2.0 [355] Biology, RNA-Seq
ITK 4.3.1 [356] Biology, Genomics
ITK-SNAP 3.0.0 [357] Biology, Neuroscience, Imaging
JACUSA 1.2.0 [358] Biology, NGS
JAGS 3.3.0 [359] Statistics
Java 1.7.0_79, 1.8.0_31 [360] Java Development Kit
Je 1.0. [361] Biology, NGS
Jellyfish 2.1.1 [362] Biology, NGS
JModelTest 2.1.1 [363] Biology, Phylogenetics, Genomics
Julia 0.3.11, 0.4.6 [364] Programming, Languages
KaKs 1.2 [365] Biology, Phylogenetics
Kent 20120524 [366] Biology, NGS
Khmer 1.1, 2.0, 2.1 [367] Biology, NGS
KIM 1.7.2 [368] Library
KING 1.4, 1.9 [369] Biology, Genomics
Kinfin 1.0.1 [370] Biology, Phylogenetics
KisSplice 2.4.0-p1 [371] Biology, NGS
Kallisto 0.42.3, 0.42.4 [372] Biology, NGS, RNA-Seq
KERAS 1.0.8 [373] Deep Learning
Kmer 1934 [374] Biology, NGS
KmerGenie 1.6741 [375] Biology, NGS, Utilities
Kraken 0.10.4b [376] Biology, Genomics, Phylogenetics
Krona 20161019 [377] Biology, Bioinformatics
kSNP 3.021 [378] Biology, Phylogenetics, SNP
Lace 0.99 [379] Biology, NGS
LAMMPS 28Oct12, 30Sep13, 28Jun14 [380] Molecular Dynamics Simulation
LAMP 2.5 [381] Biology, Genomics
Last 247, 531, 801 [382] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [383] Biology, NGS
LDhat 2.2a [384] Biology, Genomics
LIBSVM 3.12 [385] Machine Learning
LIGR 2.05 [386] Biology, Assembly
LINKS 1.8.5 [387] Biology, Genomics
LFMM 1.4 [388] Biology, Genomics
LSC 0.3, 0.3.1 [389] Biology, NGS, Error correction
lobSTR 4.0.6 [390] Biology, Phylogenetics
Loci 3.3 [391] Fluid Dynamics
LongRanger 2.1.5 [392] Biology, Phylogenetics
LoRMA 0.3 [393] Biology, NGS
LS-DYNA 700, 711, 800 [394] Physics
LTRReteriever 20170514 [395] Biology, Phyloegenetics
Lumpy 0.2.1 [396] Biology, SNP
LZO 2.09 [397] Library, Data Compression
MACH 1.0.18 [398] Biology, Genomics
Mach2VCF 20150515 [399] Biology
M5tools 20121126 [400] Biology, Bioinformatics, Genomics
MACS 1.4.2, 2.1.1 [401] Biology, ChIP-Seq
mafft 7.215, 7.245, 7.294 [402] Biology, Multiple sequence alignment
Mash 1.1 [403] Biology, Genomics
Maker 2.25b, 2.31.6, 2.31.8 [404] Biology, Annotation, Genomics
MapSplice 2.1.7 [405] Biology, NGS, RNA-Seq
MAPminer 1.1 [406] Biology, Phylogenetics
MassMine 0.9.5, 0.10.0, 0.11.0 [407] Data Mining
Maq 0.7.1 [408] Biology, NGS
MARK 2.0.1 [409] Statistics
MarkerMiner 20150429, 20150511 [410] Biology, Genomics
MaryGold 0.2 [411] Biology, NGS
MaSuRCA 2.3.2, 3.2.1 [412] Biology, NGS
Matlab 2012a, 2013a, 2014a [413] Math, Simulation, Programming
MATS 3.0.8, 3.0.9, 3.2.5 [414] BIology, NGS
Mauve 2.3.1 [415] Biology, NGS
MaxBin 2.1.1 [416] Biology, NGS
MCarts 1.0.2 [417] Biology, Genomics, Markov models
MCNP 5, 6b2, 6, 6.1 [418] Physics
MCNPX 2.7.0, 2.7.0-i8 [419] Physics
MEGAN 5.10.3, 6.4.15 [420] Biology, NGS
MEGAHIT 1.1.1 [421] Biology, NGS
Megraft 1.0.2 [422] Biology, Sequencing
Melting 4.3.1 [423] Biology, Genome, RNA, Folding
Meme 4.11.1, 4.11.2 [424] Biology, Motifs, Sequence analysis
Meraculous 2.0.5 [425] Biology, NGS
Mercurial 4.0.2 [426] Development, Revision Control
Merlin 1.1.2 [427] Biogolgy, SNP
Meta-Tissue 0.4 [428] Biology, Genetics
Metabin 1.0 [429] Biology, Metagenomics
MetaCluster 5.0b [430] Biology, Metagenomics
MetaCV 2.3.0 [431] Biology, NGS
METAL 20110325 [432] Biology, Genomics
MetAMOS 1.5.0rc4-20140827 [433] Biology, Bioinformatics, Genomics, Assembly
Metassembler 1.5 [434] Biology, Genomics
MetaVelvet 1.2.01 [435] Biology, NGS
Metaxa2 2.0.2, 2.1.1 [436] Biology, NGS
MetaGeneMark 2012.04 [437] Biology, Genomics
Mfold 3.6 [438] Biology, Genomics
MGEScan 1.1 [439] Biology, Genomics
MHAP 1.6 [440] Biology, Sequencing
MIA 20130301 [441] Biology, NGS
MicrobeCensus 1.0.7 [442] Biology, NGS
MIDAS 20160830 [443] Biology, Phylogenetics
Midnight Commander 4.6.1 [444] Tools, Utilities
Migrate-n 3.3.0, 3.6.6, 3.6.11 [445] Biology, Population
Minced 0.2.0 [446] Biology, Genomics
Minimac 2-20140915, 3-20151015 [447] Biology, Genomics
Minimap 0.2 [448] Biology, Phylogenetics
mira 3.9.18, 4.0.rc1, 4.0.2 [449] Biology, NGS
MIReNA 2.0 [450] Biology, Phylogenetics
MISO 0.4.9, 0.5.2, 0.5.3 [451] Biology, NGS
MKL 2016.0.109, 2017.1.132 [452] Library, Math
MMSEQ 1.0.8 [453] Biology, NGS
MSMBuilder 2.5.1 [454] Molecular Dynamics
MOABS 1.2.9, 1.3.2, 1.3.4 [455] Biology, NGS, Genomics
Modeller 9.11, 9.13, 9.14 [456] Biology, Modeling
Molden 5.0 [457] Molecular, electronic structure
MolPro 2012.1p22 [458] Quantum Chemistry, Ab Initio
mosaik 2.1.33, 2.2.3 [459] Biology,NGS
Mothur 1.36.1, 1.37.0, 1.38.1 [460] Biology, Microbial Ecology
MotionCorr 2.1 [461] Motion Correction
MotionCor2 01302017 [462] Motion Correction
MOTU 1.1 [463] Biology, Bioinformatics, Genomics
MOST 20170721 [464] Biology, Genomics
MPE2 2.4.9b [465] MPI
MP-EST 1.4, 1.5 [466] Biology, Phylogenetics
mpiP 3.4.1 [467] Parallel Computing
MrBayes 3.2.1, 3.2.4, 3.2.5 [468] Biology, Phylogenetics
MRIcron 201306, 20161012 [469] Biology, MRI, Imaging
MUMmer 3.23 [470] Biology, Genomics
MUSCLE 3.8.31 [471] Biology, Genomics
MuTect 1.1.4, 1.1.7 [472] Biology, Genomics
MutSig 1.4, 1.41 [473] Biology, Genomics
MZMine 2.19, 2.20, 2.21 [474] Biology, Spectroscopy
NAMD 2.9, 2.11, 2.12 [475] Molecular Dynamics, Chemistry
Nanocorrect 20150727 [476] Biology, NGS
Nanopolish 20150904 [477] Biology
Nbody 6 [478] Astronomy
NCBI C++ Toolkit 12.0.0 [479] Biology, C++, Development
NCL 6.1.2, 6.3.0 [480] Atmosphere Science
NCO 4.2.1, 4.4.3 [481] Data exchange tools
Ncview 2.1.2 [482] Data visualization
NeEstimator 2.01 [483] Biology, Bioinformatics
NetCDF 4.2, 4.3, 4.4.1.1 [484] Data exchange, Tools
NEURON 7.4 [485] Biology, Neuroscience
Newbler 2.7, 2.8, 2.9 [486] Biology, NGS
Newick utils 1.6 [487] Biology, Phylogenetics
Nextallele 20140718 [488] Biology, Genomics
NextGenMap 0.5.3 [489] Biology, Bioinformatics, NGS
Nexus NCL 2.1.18 [490] Biology, Phylogenetics, Library
NGS-bits 0.1 [491] Biology, Sequencing
ngsCAT 0.1 [492] Biology, Bioinformatics, NGS
ngsTools 20150816 [493] Biology, NGS
NGSUtils 20130722, 20150206 [494] Biology, NGS
Nipype 0.10.0, 0.12.1, 0.13.1 [495] Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe 7.9 [496] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [497] Biology, NGS
NWChem 6.5, 6.6 [498] Chemistry
NxTrim 0.4.1 [499] Biology, Bioinformatics, NGS
Oases 0.2.08 [500] Biology, NGS
OBITools 1.2.11 [501] Biology, Phylogenetics
Olego 1.1.2, 1.1.5, 1.1.6 [502] Biology, NGS, RNA-Seq
OCaml 4.02.3 [503] Programming Languages, Scripting, Development
OCE 0.18.1 [504] Library, 3D
Octave 3.6.4 [505] Numerical Computation
Oncotator 1.5.2.0, 1.5.3.0, 1.8.0.0 [506] Biology, Genomics
OpenBabel 2.3.2, 2.4.1 [507] Biology, Chemistry
OpenCL 1.1 [508] Programming, Library
OpenCV 2.4.8 [509] Computervision
OpenFOAM 2.1.1, 3.0.1, 4.0 [510] Fluid Dynamics
OpenMM 6.2.0 [511] Quantum Chemistry
Orange3 3.3.6 [512] Data Mining, Visualization
OrthoFinder 0.2.5, 0.6.0, 1.0.2 [513] Biology, Genomics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [514] Biology, Genomics
OTB 5.6.1 [515] Geospacial Imaging
p4vasp 0.3.29 [516] Molecular, Electronic Structure
p53MH 20020901 [517] Biology, Sequencing
Pacbio 4.0.0, 5.0.1 [518] Biology, Bioinformatics, NGS
Package-GFE 20150701 [519] Biology, Genomics
PALES 122 [520] Physics
PALADIN 1.3.1 [521] Biology, Phylogenetics
PAML 4.7, 4.8a, 4.9a [522] Biology, Phylogenetics
Pandaseq 20140808, 20150627 [523] Biology, Bioinformatics, NGS, Sequencing
PAPI 5.1.0.2 [524] Software, Computing
Parallel 20150122, 20170322 [525] Programming, Languages
ParaView 4.1.0, 4.2.0, 4.3.0 [526] Data Analysis
Parsimonator 1.0.2 [527] Biology, Bioinformatics
PartitionFinder 1.1.1, 2.1.1 [528] Biology, Phylogenetics, Evolution
Parflow v615 [529] Ecology, Modeling
PASA 1.5, 2.0-r20150209 [530] Biology, Genomics
PASTA 20160616 [531] Biology, Sequence alignment,
PAUP 4.0b10, 4.1a147, 4.0a152 [532] Biology, Phylogenetics
PAUDA 1.0.1 [533] Biology, Bioinformatics, Sequence alignment
PBalign 20160921 [534] Biology, Bioinformatics
PBCore 20151201 [535] Biology, Bioinformatics
PBCommand 20151203 [536] Biology, Library
PBJelly 14.7.14, 15.2.20, 15.8.24 [537] Biology, Bioinformatics
pbsdrmaa 1.0.17 [538] Libraries, Torque
p4est 1.1, 2.0 [539] Library
pbsmrtpipe 20151202 [540] Biology
PeakSplitter 1.0 [541] Biology, Chip-Seq
PEAR 0.9.2, 0.9.6 [542] Biology, NGS
PECaller 1.0.0 [543] Biology, NGS
PDT 3.18, 3.20, 3.22 [544] Programming, Profiler
Perl 5.16.0 [545] Programming, Language
PerM 0.4.0 [546] Biology, NGS
PETSc 2.3, 3.3 [547] Math, Numerical solvers
PGDSpider 2.0.9.0 [548] Biology, NGS
PHAST 1.4 [549] Biology, Phylogenetics
Phenix 1.8.1069, 1.10.2155 [550] Crystallography
PHYLDOG 20130418 [551] Biology, Genomics, Phylogenetics
Phyluce 20140427, 20151103, 20160715 [552] Biology, Phylogenetics
Phyutility 2.7.1 [553] Biology, Bioinformatics
Phyx 0.99 [554] Biology, Phylogenetics
PfamScan 1.3 [555] Biology, Genomics
PHITS 2.52, 2.76. 2.82 [556] Physics
PHLAWD 20170427 [557] Biology, Phylogenetics
Phonopy 1.9.2 [558] Chemistry
PHYLIP 3.696 [559] Biology, Phylogenetics
PhyloBayes 3.3f, 1.4f MPI [560] Biology, Phylogenetics
PhyloNet 3.5.7 [561] Biology, Phylogenetics
Phylosift 1.1 [562] Biology, Genomics, Phylogenetics, Taxonomy
PhyML 3.0, 3.1, 3.3 [563] Biology, Phylogenetics
Picard 2.5.0, 2.9.2, 2.10.3 [564] Biology, NGS
PICRUSt 1.0.0, 1.1.0 [565] Biology, Phylogenetics
Pilon 1.22 [566] Biology, Bioinformatics
PIPE-CLIP 1.1.0 [567] Biology, NGS
Pipits 1.3.6 [568] Biology, Sequencing
piPipes 1.5.0 [569] Biology, Phylogenetics
Piranha 1.2.1 [570] Biology, Phylogenetics
PLAST 1.0 [571] Biology, Bioinformatics
Platypus 0.8.1 [572] Biology, NGS
PLEK 1.2 [573]] Biology, Phylogenetics
Plink 1.07, 1.90b3, 1.90b3.39 [574] Biology, GWAS
PLINKSEQ 0.10 [575] Biology, Genomics
PluMiST 1.1 [576] Biology, Phylogenetics, Genomics
PolyPhen 2.2.2.r405b [577] Biology, Genomics
PonyTools 0.1 [578] Biology, Genomics
Poretools 0.5.0 [579] Biology, Sequencing
POV-Ray 3.7 [580] 3D, Graphics
Prank 20150803 [581] Biology, Bioinformatics, Alignment
Preseq 0.0.4 [582] Biology, NGS
PRICE 1.2 [583] Biology, NGS
Primer3 2.3.4 [584] Biology, Genomics
PRIMUS 1.8.0 [585] Biology, Phylogenetics
PRINSEQ 0.20.4 [586] Biology, Sequencing
Prodigal 2.6.3 [587] Biology, Genomics
ProfessAtQE 2014 [588] Material Science, Molecular Dynamics
Prokka 1.10, 1.11 [589] Biology, Genomics, Bioinformatics, Assembly
ProBABEL 0.4.2, 0.4.3, 0.4.5 [590] Biology, Genomics, GWAS
Probalign 1.4 [591] Biology, Genomics
Proovread 1.03rcl [592] Biology, Genomics, NGS
Proteinortho 4.26, 5.11, 5.16 [593] Biology, Genomics
PROVEAN 1.1.5 [594] Biology, Genomics
PyAni 0.2.1 [595] Bilogy, Genomics
PyHDF 0.9.0 [596] Library, HDF4
PyVCF 0.6.0 [597] Biology
Python 2.7.6, 2.7.10, 2.7.11 [598] Biology, Genomics, NGS
Python3 3.5.1, 3.6.1 [599] Biology, Genomics, NGS
Python-core 2.7.13 [600] Biology, Genomics, NGS
Python3-core 3.6.2 [601] Biology, Genomics, NGS
Pyfasta 0.5.2 [602] Biology, Phylogenetics
Pyrad 3.0.63 [603] Biology, Sequencing Alignment, Assembly
QDD 3.1.2 [604] Programming, scripting, language
QGIS 2.18.0 [605] Geography
QIIME 1.9.0, 1.9.1 [606] Biology, Ecology
QIIME2 2.0.6 [607] Biology, Ecology
QT 4.8.3 [608] Computer Science
QUAST 2.3, 4.4 [609] Biology, NGS
Quake 0.3 [610] Biology, Sequencing
Quantas 1.0.4, 1.0.8 [611] Biology, Bioinformatics, NGS
QualiMap 2.1.1 [612] Biology, Sequence alignment
Quickquartet 1.0.0 [613] Biology, Phylogenetics
R Rmpi/3.3.1, 3.2.0, 3.3.0 [614] Statistics, Programming
R2R 1.0.4 [615] Biology, RNA
R8S 1.71, 1.8 [616] Biology, Evolution
Racon 20161013 [617] Biology, Sequencing
RADICAL 0.2 [618] Biology, Phylogenetics, Genomics
Randfold 2.0.1 [619] Biology, RNA
Rascaf 1.0.2 [620] Biology, RNA-Seq
RAxML 8.2.3, 8.2.8, 8.2.10 [621] Biology, Phylogenetics
Ray 2.3.1 [622] Biology, Genomics, NGS
REAGO 1.1 [623] Biology, Assembly
REAPR 1.0.18 [624] Biology, Bioinformatics, Assembly
Recycler 0.62 [625] Biology, Bioinformatics
Regtools 0.4.0 [626] Biology, RNA-seq
RELION 1.4 [627] Biology, Bioinformatics
REPdenovo 20170222 [628] Biology, Phylogenetics
RepeatExplorer 20150506 [629] Biology, Genomics
RepeatMasker 3.3.0 [630] Biology, Genomics
RepeatModeler 1.0.8 [631] Biology, Bioinformatics
Reptile 1.1 [632] Biology, NGS, error correction
RevBayes 1.0.0, 1.0.3 [633] Biology, Phylogenetics
riboPicker 0.4.3 [634] Biology, Sequence
RNAhybrid 2.1.1 [635] Biology, Genomics
rRNASelector 1.0.0 [636] Biology, Sequencing
rnaseqlib 20150721 [637] Biology, Phylogenetics, RNA-Seq
rnaQUAST 1.2.0 [638] Biology, NGS, Sequencing
ROOT 6.0 [639] Data Analysis
Roary 3.4.1 [640] Biology, Genomics
Rosetta 2014wk4 [641] Biology, Structure, Modelling
RSEG 0.4.8 [642] Biology, NGS
RSEM 1.2.19, 1.2.28, 1.2.29 [643] Biology, NGS, RNA-Seq
RSeQC 2.3.7, 2.6.2 [644] Biology, NGS, RNA-Seq
RStudio 0.99.902, 0.99.903 [645] R, Statistics, Programming
RTGTools 3.7.1 [646] Biology, NGS
Ruby 1.9.3-p0 [647] Programming, Scripting, Language
Sailfish 0.6.3 [648] Biology, NGS, RNA-Seq
Salmon 0.6.0, 0.7.2 [649] Biology, RNA-seq
SMC++ 1.7.0 [650] Biology, NGS
Sambamba 0.5.0-dev, 0.5.10, 0.6.3 [651] Biology, NGS
Samstat 1.08 [652] Biology, NGS, Bioinformatics, Sequencing
Samblaster 0.1.14, 0.1.24 [653] Biology, NGS
samtools 1.3.1, 1.4, 1.5 [654] Biology, NGS
SAS 9.4 [655] Statistics, Graphing
SATe 2.2.7 [656] Biology, Phylogenetics
Scala 2.11.5 [657] Programming, Language
Scalablast 2.4.53 [658] Biology, Genomics
Scalpel 0.1.1, 0.5.3 [659] Biology, NGS
SCRIPTURE 20101211 [660] Biology, Bioinformatics, Genomics
Shannon 20160211 [661] Biology, RNA-Seq
SHAPEIT 2.5.5 [662] Biology, SNP
SHAPE-MaP 1.2 [663] Biology, Phylogenetics
Sharcgs 1.2.11 [664] Biology, NGS, Assembly
SHEsisPlus 1.0 [665] Biology, Phylogenetics
shustring 2.6 [666] Biology, Sequencing
SCons 2.3.0 [667] Programming
Scoary 1.6.10 [668] Biology, Bioinformatics, Genomics
SCRATCH1D 1.0 [669] Biology, Genomics
Scythe 0.991 [670] Biology, NGS
SDT 1.2 [671] Biology, Sequencing
Segemehl 0.1.9 [672] Biology, NGS, Mapper
SEPP 1.0, 3.0 [673] Biology, Phylogenetics, HMM
SGA 0.10.14 [674] Biology, Assembly
Seq-Gen 1.3.3 [675] Biology, Phylogenetics
SeqPrep 0.5 [676] Biology, NGS
Seqmagick 20150923 [677] Biology, Phylogenetics
SeqMap 1.0.13 [678] Biology, NGS
Seqtk 20140729 [679] Biology, NGS
SEQuel 1.0.1 [680] Biology, NGS
SeqyClean 1.8.10 [681] Biology, NGS, Bioinformatics
ShoRAH 20131204 [682] Biology, NGS, quality filter
SHRiMP 2.2.3 [683] Biology, NGS
SICER 1.1 [684] Biology, ChIP-Seq
Sickle 1.200, 1.33 [685] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [686] Simulation, Physics, Ab Initio
Sisl 0.8.3 [687] Physics, Tight-binding
SIFT 4.0.3b [688] Biology, Genomics
SignalP 4.1c [689] Biology, NGS
Silo 4.7 [690] Library, Data
SIPeS 2.0 [691] Biology, Bioinformatics, ChIP-Seq
Slicer 4.3.1 [692] Biology, Imaging
SMALT 0.7.6 [693] Biology, NGS
Snap 20100728, 0.15.4 [694] Biology, Genomics
SNAPE-pooled 20130407 [695] Biology, SNP
SNeP 1.1 [696] Biology, Phylogenics
SnpEff 4.2, 4.3, 4.3p [697] Biology, NGS, Genomics
SNPhylo 20140701 [698] Bilogy, Phylogenetics
SNP-sites 2.0.3 [699] Biology, SNP
Snippy 20160419 [700] Biology, Phylogenetics
SOAPdenovo 1.05 [701] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [702] Biology, NGS
SOAPec 2.03 [703] Biology, Phylogenetics
SOAPsplice 1.10 [704] Biology, NGS
SortMeRNA 2.1 [705] Biology, Sequencing, NGS
SparCC 201402 [706] Microbial Ecology
Spades 3.9.0, 3.10.0, 3.10.1 [707] Biology, NGS
Spanki 0.4.1, 0.4.3, 0.5.0 [708] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [709] Chemistry
Spidey 20150922 [710] Biology, Genomics
SPIMAP 1.1 [711] Biology, Phylogenetics
SpliceTrap 0.90.5 [712] Biology, NGS, RNA-Seq
SPM 8 [713] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [714] Biology, Genomics
SQLite 3.8.8.2 [715] Database
SQL_Developer 4.1.2 [716] Programming, Oracle, Sql
SRA 2.1.10 [717] biology, NGS
SSPACE 2.0, 3.0 [718] Biology, NGS
SST-Core 6.0.0, 7.1.0 [719] MPI
SSR_pipeline 0.951 [720] Bilogy, DNA Sequencing
Stacks 1.24, 1.35, 1.45 [721] Biology, Genomics, NGS
Staden 1.14.6 [722] Biology, Sequencing
Stampy 1.0.31 [723] Biology, Bioinformatics, Sequencing
STAR 2.4.0j, 2.5.1b [724] Biology, NGS, Alignment
STAR-CCM+ 8.06 [725] Mechanical Engineering
Stata 10.1, 13 [726] Statistics, Data analysis
Statsmodels 0.8.0 [727] Biology, Library, Math
Stringtie 1.1.2, 1.2.1, 1.3.3 [728] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [729] Biology, Population
stringMLST 0.4 [730] Biology, Genomics, NGS
Subread 1.5.0-p1, 1.5.1, 1.5.3 [731] Biology, Sequencing, SNP
Supercell 20170602 [732] Biology, NGS
Supernova 1.1.5, 1.2.1 [733]] Biology, Phylogeneitcs, NGS
SUNDIALS 2.3.0, 2.5.0 [734] Numerical Solver
SVDetect 0.8b [735] Biology, NGS, SNP
swak4Foam 2.x [736] Fluid Dynamics
swarm 1.2.11 [737] Data Analysis
SWEEP 20160722 [738] Biology, SNP
Swig 2.0.9 [739] Programming, C, C++, Python
SwitchSeq 20140907 [740] Biology, NGS
Syzygy 1.2.7 [741] Biology, Genomics
TetGen 1.5.0 [742] Tetrahedral Meshes 3D
tapir 20160825 [743] Biology, Phylogenetics
TAPIS 1.2.1 [744] Biology, Sequencing
TASSEL 5.0, 5.2.29 [745] Biology, Genomics
TAU 2.21.4, 2.23, 2.24, 2.52 [746] Profiling, Tracing, Programming
taxMap 0.1 [747] Biology, Phylogenetics, Taxonomy
TaxonDNA 1.8 [748] Biology, Taxonomy
Tcllib 1.18 [749] Computer Science
T-Coffee 9.03.r1318 [750] Biology, Genomics, Multiple Alignment
TEToolkit 1.5.1 [751] Biology, Bioinformatics, Sequencing
TensorFlow 1.0.0, 1.2.1, 1.3.0 [752] Library, Math
TESS 2.3.1 [753] Biology, Genomics, Markov
tgicl 2.1 [754] Biology, sequencing, clustering
Tmux 2.0 [755] GNU, Terminal Multiplexer
TomoPy 0.0.3 [756] Biology, Neuroimaging
Tophat 1.4.1, 2.0.13, 2.1.0 [757] Biology, NGS
Torch 20160704, 20171102 [758] Lua
Totalview 8.12.0 [759] Computer Science
TPP 4.7.0 [760] Bioinformatics, MassSpec
TrackTools 2011 [761] Bioinformatics
TrackVis 0.5.2.2 [762] Biology, Spectroscopy
Tracula 5.3.2014_05_26 [763] Biology, Bioinformatics, Neuroscience, Imaging
TraitRate 1.1 [764] Biology, Evolution
Trans-ABySS 1.5.4 [765] Biology, Phylogenetics
TransDecoder 20140704, 2.0.1, 3.0.0 [766] Biology, NGS
Transrate 1.0.1 [767] Biology, Assembly
TransVar 2.3.3 [768] Biology, Phylogenetics
TraCeR 20160519 [769] Biology, Bioinformatics
TreeCorr 3.2.3 [770] Physics
TreeFix 1.1.7, 1.1.10 [771] Biology, Phylogenetics
TreeMix 1.12 [772] Biology, Phylogenetics
TreePL 20150305 [773] Biology, Phylogenetics
TREEPUZZLE 5.3 [774] Biology, Phylogenetics
TriMetAss 1.1 [775] Biology, Bioinformatics, NGS
TRF 4.04 [776] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [777] Math Algorithm
trimAl 1.2 [778] Biology, Genomics, Sequence Alignment
Trim Galore 0.2.8, 0.4.1, 0.4.4 [779] Biology, NGS
Trimmomatic 0.32, 0.33, 0.36 [780] Biology, NGS
Trinity r20161120-2.3.2, r20170205-2.4.0 [781] Biology, NGS, RNA-Seq
Trinotate 2.0.1, 3.0.1 [782] Biology
TRNAscan-SE 1.23 [783] Biology, NGS, Bioinformatics
Twinscan 4.1.2 [784] Biology, Genomics
usearch 7.0.1001-64, 8.0.1517, 9.2.64 [785] Biology, Sequence analysis
UDUNITS 2.2.17 [786] Library, Units, Programming
UFITS 0.7.2 [787] Biology, NGS
UNAFold 3.8 [788] Biology, Genome, RNA, Folding
UProC 1.2.0 [789] Biology, Genomics
Valgrind 3.9.0 [790] Computer Science
VarDictJava 20160521 [791] Biology, NGS
Varnorm 0.21 [792] Biology, Phylogenetics
VarScan 2.3.6 [793] Biology, NGS, Genomics
VASP 5.3.2, 5.3.3, 5.3.5, 5.4.1 [794] Quantum Chemistry, Ab Initio
VAST-TOOLS 20150506 [795] Biology, NGS, RNA-Seq
VCFLib 20141119, 20150313 [796] Biology, NGS, Genomics
VCFtools 0.1.12a, 0.1.12b, 0.1.14 [797] Biology, SNPs
VCF-kit 0.1.2 [798] Biology, Phylogenetics
velvet 1.2.06, 1.2.07, 1.2.10 [799] Biology, Genomics, NGS
VEP 74, 83, 88.8 [800] Biology, NGS
VICUNA 1.3 [801] Biology, Assembly
ViennaRNA 2.2.6 [802] Biology, RNA-seq
Vim 7.4.5 [803] Programming, Scripting, Language
vmd 1.9.1, 1.9.3 [804] Biology, Visualization
VSearch 20151022, 20161209-2.3.4 [805] Biology, NGS
VT 20140903, 20160129 [806] Biology, Genomics
VTC 0.9.3 [807] Biology, Bioinformatics, VCF
VTK 6.1.0 [808] Visualization, Graphics
V-Phaser2 02112013 [809] Biology, Phylogenetics
Virsorter 1.0.3 [810] Biology, Phylogenetics
w2rap-contiger 20161124 [811] Biology, Genomics
Wannier90 1.2, 2.0.0 [812] Computational Physics
WebLogo 3.3, 3.5.0 [813] Biology, Genomics
WEVOTE 1.5.0, 1.8.0 [814] Biology, Genomics
WDSSII 1 [815] Meteorology
WIEN2k 12.1 [816] Material Science, Chemistry
Wgs or Celera 8.2, 8.3rc1, 8.3rc1.r4638 [817] Biology, NGS
wublast 2.0 [818] Biology, Sequence Alignment
YAHA 0.1.82 [819] Biology NGS
Xander 20151222 [820] Biology, Phylogenetics
XCrySDen 1.5.60 [821] Computational Material Science
Yambo 3.3.0 [822] Physics
YASM 1.3.0 [823] Computer Science
Yasra 2.32 [824] Biology, NGS
Zagros 1.0.0 [825] Biology, NGS
Zeo++ 0.2.2 [826] Chemistry
Zorro 2.2 [827] Biology, Sequencing
  1. Up to 3 most recent/important releases are listed. See the individual application pages and the output of "module spider software" for full version listing.

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