Difference between revisions of "Installed Software"

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Line 1,106: Line 1,106:
 
|-
 
|-
 
| [[PHITS]] || 2.52, 2.76. 2.82 || [http://www.oecd-nea.org/tools/abstract/detail/nea-1857/] || Physics
 
| [[PHITS]] || 2.52, 2.76. 2.82 || [http://www.oecd-nea.org/tools/abstract/detail/nea-1857/] || Physics
−
|-
 
−
| [[PIPE-CLIP]] || 1.1.0 || [https://github.com/QBRC/PIPE-CLIP] || Biology, NGS
 
−
|-
 
−
| [[Pipits]] || 1.3.6 || [https://github.com/hsgweon/pipits] || Biology, Sequencing
 
−
|-
 
−
| [[piPipes]] || 1.5.0 || [https://github.com/bowhan/piPipes] || Biology, Phylogenetics
 
 
|-
 
|-
 
| [[PHLAWD]] || 20170427 || [http://phlawd.net] || Biology, Phylogenetics
 
| [[PHLAWD]] || 20170427 || [http://phlawd.net] || Biology, Phylogenetics
Line 1,132: Line 1,126:
 
|-
 
|-
 
| [[Pilon]] || 1.22 || [https://github.com/broadinstitute/pilon] || Biology, Bioinformatics
 
| [[Pilon]] || 1.22 || [https://github.com/broadinstitute/pilon] || Biology, Bioinformatics
 +
|-
 +
| [[PIPE-CLIP]] || 1.1.0 || [https://github.com/QBRC/PIPE-CLIP] || Biology, NGS
 +
|-
 +
| [[Pipits]] || 1.3.6 || [https://github.com/hsgweon/pipits] || Biology, Sequencing
 +
|-
 +
| [[piPipes]] || 1.5.0 || [https://github.com/bowhan/piPipes] || Biology, Phylogenetics
 
|-
 
|-
 
| [[Piranha]] || 1.2.1 || [http://smithlabresearch.org/software/piranha/] || Biology, Phylogenetics
 
| [[Piranha]] || 1.2.1 || [http://smithlabresearch.org/software/piranha/] || Biology, Phylogenetics

Revision as of 03:07, 13 July 2017

  • Last updated on 2017-07-13.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
Anvio 2.0.2, 2.1.0, 2.3.2 [21] Biology, Microbial 'omics
ANNOVAR 20120621, 20150322 [22] Biology, Genomics
AStalavista 3.2 [23] Biology, NGS, RNA-Seq, Genomics
ASTRID 20150807 [24] Biology, Genomics
Atlas 3.10.1, 3.11.17 [25] Library, Math
Amuse 6.0, 10.0 [26] Astrophysics
ANGSD 20150306, 20150909 [27] Biology, NGS
Affymetrix Power Tools 1.15.0, 1.18.0 [28] Biology, Genomics, Microarray
ArrayFire 3.4.2 [29] Code Optimization
ARC 20140312 [30] Biology, NGS
ARCS 1.0.0, 1.0.1 [31] Biology, Genomics
Armadillo 6.200.3 [32] Library, C++ , Math
Astral 4.10.6, 4.10.7, 5.0.3 [33] Biology, Bioinformatics, NGS, Phylogenetics
AtomEye 3 [34] Material Science
ATRAM 20140624 [35] Biology, NGS
Augustus 2.6, 3.2.1, 3.2.2 [36] Biology, NGS
Auto3DEM 4.05.1, 4.05.2 [37] Image Reconstruction
BamBam 1.0 [38] Biology, NGS
BALI-PHY 2.3.8 [39] Bioinformatics, Bayesian Estimation
BAMM 2.5.0 [40] Biology, Phylogenetics
Bam-readcount 20150216 [41] Biology, NGS
Bamstats 20140602 [42] Biology, NGS
Bamtools 2.1.1 [43] Biology, NGS
BamUtil 1.0.2 [44] Biology, NGS
Bam-Readcount 20150616 [45]] Biology, Genomics
BAPS 6.0 [46] Biology, Populaton genetics
Barrnap 0.7 [47] Biology, RNA-Seq
Basemount 0.1.2.464 [48] Biology, DNA Sequencing
BatVI 1.00 [49] Biology, Phylogenetics
BayArea 1.0.2 [50] Biology
BayeScan 2.1 [51] Biology, SNP
BayesR 20151016 [52] Biology, Phylogenetics
BayeScEnv 1.1 [53]] Biology, SNP, Phylogenetics
BayesRate 1.3.43 [54] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [55] Network file transfer
BBMap 36.23, 37.09 [56] Biology, Alignment
Bcbio-nextgen 0.8.7, 0.9.9 [57] Biology, NGS
Bcftools 1.2, 1.3.1, 1.4 [58] Biology, Genomics, NGS
Bcl2fastq 2.16 [59] Biology, NGS, Illumina
BEAGLE 3.2.2, 4.0 [60] Biology, Genetics, Genotyping
BEAST 1.7.5, 1.8.1, 2.3.2 [61] Biology, Phylogenetics
Bedops 2.4.2 [62] Biology, Bioinformatics, Sequence, NGS
BEDTools 2.23.0, 2.24.0, 2.26.0 [63] Biology, NGS
BEST 2.3.1 [64] Biology, Phylogenetics
BESST 2.2.4 [65] Biology, Bioinformatics
BETA 1.0.5 [66] Biology, NGS
BFAST 0.7.0 [67] Biology, NGS
Bismark 0.7.7, 0.13.0, 0.17.0 [68] Biology, NGS, Methylation
BinPacker 1.0 [69] Biology, RNA-Seq, Sequence Assembly
BinSanity 0.1.3, 0.2.5.9 [70] Biology, Genomics
Bioconductor Latest [71] Biology, R, Statistics
BioPerl 1.006901 [72] Biology, Perl
BioPython 1.59 [73] Biology, Python
BLASR 20130815 [74] Biology, NGS
NCBI BLAST 2.2.27, 2.5.0, 2.6.0 [75] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [76] Biology, Annotation
BLAT 20120524, 20140318 [77] Biology, Sequence alignment
Blender 2.63 [78] Graphics
BLESS 1.02 [79] Biology, NGS
BLUPF90 20160604 [80] Biology, Phylogenetics
BoltzTraP 1.2.5 [81] Physics
Boost 1.49.0, 1.59.0, 1.63.0 [82] C++, Library
Bowtie 0.12.9, 1.1.1, 1.2.0 [83] Biology, NGS
Bowtie2 2.2.9, 2.3.0, 2.3.2 [84] Biology, NGS
BPP 1.9.0, 2.2, 3.2 [85] Biology, Phylogenetics
Bracken 1.0.0 [86] Biology, Phylogenetics
BRANCH 1.8.1 [87] Biology, NGS, Mapping
BRATNextGen 20150505 [88] Biology, Genomics
BRIG 0.95 [89] Biology, Genomics
Bsoft 1.9.1 [90] Biology, Image Analysis
Bsmap 2.74, 2.87 [91] Biology, NGS, Methylation
BSSeeker2 2.1.0 [92] Biology, Phylogenetics
BUCKy 1.4.4 [93] Biology, Genomics
BUSCO 1.1b1, 1.22, 2.0b [94] Biology, Genomics
Bwa 0.6.1, 0.7.12, 0.7.15 [95] Biology, NGS
BXH_XCEDE_tools 1.11.1 [96] Biology, Bioinformatics
Camino 20140723 [97] Biology, Neuroscience, Imaging
Canu 1.1, 1.3, 1.5 [98] Biology, Sequencing
CASM 0.2.0 [99] Statistical Mechanics
CAP3 20120705 [100] Biology, Sequence Assembly
CASAVA 1.8.2 [101] Biology, NGS
CD-HIT 4.6, 4.6.4 [102] Biology, Genomics
CDO 1.6.1, 1.7.2rc5 [103] Climate
CEAS 1.0.2 [104] Biology, Genomics
CellProfiler 2.0 [105] Biology, Image Analysis
CellRanger 1.2.1, 1.3.0 [106] Biology, Bioinformatics, NGS, RNA-Seq
CFITSIO 3.370 [107] Library, C
CGATools 1.6.0.42 [108] Biology, NGS
Charmm 36a3 [109] Simulation, Chemistry
Chartdirector 5.1.0 [110] Graphics
CheckM 1.0.4 [111] Biology, Genomics
Chimera 1.7 [112] Biology, Modeling
ChromEvol 2.0 [113] Biology, Phylogenetics
CIMS 4.1.2 [114] Biology, Genomics
Circos 0.63-pre11, 0.69-2 [115] Biology, Visualization
Circlator 1.5.1 [116] Biology, Genomics
CIRCexplorer 1.1.10 [117] Biology, Bioinformatics, RNA-Seq
CisGenome 2.0 [118] Biology, Genomics, Peak Calling
Clann 3.2.3 [119] Biology, Phylogenetics
CLARK 1.2.2-b [120] Biology, Genomics
CLHEP 2.2.0.1 [121] High Energy Physics
CLIPper 1.0 [122] Biology, Sequencing
CLIPSeqTools 0.1.7 [123] Biology, Sequencing
ClonalFrame 1.1, 1.2 [124] Biology, Genomics, NGS
ClonalFrameML 1.25 [125] Biology, Genomics, NGS
ClustalW 2.1 [126] Biology, Genomics
Cluster3 1.52 [127] Biology, Genomics
Clview 20130402 [128] Biology, Genomics
ClustalO 1.2.0 [129] Biology, Genomics
CLUMPP 1.1.2 [130]] Biology, Bioinformatics
ClusterFinder 313 [131] Biology, Metabolomics
CMake 2.8.8, 2.9.12.1, 3.1.0 [132] Programming, Build System
CMS 20170518 [133] Biology
CMWP 140518 [134] Biology, Genomics
CNVnator 0.3.2 [135] Biology, Genomics
CNVSeq 20110715 [136] Biology, NGS
Cobrapy 0.3.2 [137] Biology, Metabolomics, Modeling
Coevol 1.3c, 1.4b [138] Biology, Phylogenetics
CoMap 1.4.1 [139] Biology, Genomics
CONSEL 0.20 [140] Biology, Phylogenetcs
CONCOCT 0.3.1 [141] Biology, Genomics
ContaVect 0.2 [142] Biology, Phylogenetics
CoNIFER 0.2.2 [143] Biology, Genomics
Consed 23.0 [144] Biology, Genomics
Coreutils 8.23 [145] GNU Utilities, Computer Science
Corset 1.06 [146] Biology, NGS
covNMR 2014 [147] Biochemistry
CPAT 1.2.2 [148] Biology, Phylogenetics
CPLEX 12.6.5 [149] Optimizer
CUDA 4.2, 5.5 [150] Programming, Graphics
Crass 1.0.1 [151] Biology, Assembly
CRISPRdigger 1.007 [152] Biology, Phylogenetics
CrossMap 0.2.3 [153] Biology, Genomics
Crux 1.40 [154] Biology, Mass-Spectrometry
CryptoMiniSat 5.0.1 [155] SAT
Cufflinks 1.3.0, 2.0.2, 2.2.1 [156] Biology, NGS
Cutadapt 1.7.1, 1.8.1, 1.10 [157] Biology, NGS
CUTE 20160116, 20161010 [158] Cosmology
Cytoscape 3.4.0 [159]] Biology, Bioinformatics
DAKOTA 5.4.0 [160] Computational Science
DaPars 0.9.0 [161] Biology, NGS, RNA-Seq
DALIGNER 1.0 [162] Biology, Sequencing
Datamash 1.1.0 [163] Math
DCMTK 3.6.0 [164] Biology, Neuroscience, Imaging
DSSAT 4.5 [165] Biology
dDocent 20160425 [166] Biology
DDSCAT 7.3.0 [167] Astrophysics
DDT 5.0, 6.0, 6.1.2, 7.0.4 [168] Software
Dealii 8.3.0, 8.4.1 [169] Library
DeconSeq 0.4.3 [170] Biology, Phylogenetics
Delft3D 3621 [171] Hydrodynamics, Physics
DeepPicker 20161102 [172] Deep Learning, Cross-Molecule Training
DeepTools 2.4.3 [173] Biology, Bioinformatics, NGS
Desmond 3.0.3.1 [174] Simulation, Biology, Chemistry
DETONATE 1.9, 1.11 [175] Biology, NGS
DEXTRACTOR 1.0 [176] Biology, Sequencing
Dalton 2011 [177] Quantum Chemistry
Diamond 0.5.1, 0.8.5 [178] Computational Biology, Genomics
DiscoSnp 2.2.10 [179] Biology, Phylogenetics, SNP
Dibig Tools 1.0 [180] Bioinformatics, PBS, Torque, Jobs
DiffReps 1.55.4 [181] Biology, NGS, ChIP-Seq
Dindel 1.01 [182] Biology, NGS
DISCOVARdenovo 52488 [183] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [184] Biology, Genomics
Dlpoly 4.03.4 [185] Simulation, Biology, Chemistry
Dlpoly-Classic 1.9 [186] Simulation, Biology, Chemistry
DNA Clust 3.0 [187] Biology, Genomics
Dock 6.5, 6.6, 6.7 [188] Chemistry, ligand binding prediction
DOT 2.0 [189] Biology, Bioinformatics, Docking
DosageConvertor 1.0.3 [190] Biology, Converter
Doxygen 1.8.3.1 [191] Programming, Documentation
DSK 2.1.0 [192] Biology, NGS
DSSP 2.2.1 [193] Biology, Molecular Dynamics
DTI-TK 2.3.1 [194] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [195] Biology, NGS
ECTools 20140311, 20141201 [196] Biology, Sequencing, Bioinformatics
ECE 1.0 [197] Ece
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [198] Biology, Matlab
ED2 2.1 [199] Biology
eGene-MVN 0.1 [200] Biology, Genetics
eigenMT 20160228 [201] Biology, Genetics
EIGENSOFT 4.2, 5.0.1, 6.0.1 [202] Biology, Population
emboss 6.5.7 [203] Biology, multi-tool suite
EMAN2 2.11 [204] Biology
EMMAX 20100307, 20120210 [205] Biology, NGS, Mapping
EMC 9.3.9 [206] Monte Carlo Simulations
EMIRGE 20130727 [207] Biology, NGS
Ensembl_Tools 80 [208] Biology, Bioinformatics
EPACTS 3.2.6 [209] Biology, Bioinformatics, Genomics
EPOCH 4.7.3 [210] Astronomy, CPPP
eQTLA 1.1 [211] Biology, Genomics
Eqtlbma 1.2.2 [212] Biology, Genotyping
Esmf 6.3.0rp1 [213] Climate
Espresso 5.0.1, 5.2.0, 5.2.1, 5.3.0 [214] Modeling, Physics
ESPRIT 201211 [215] Biology, NGS, Metagenomics
ETE2 2.1 [216] Biology, Phylogenetics
ETE3 3.0.0 [217] Biology, Phylogenetics
Eval 2.2.8 [218] Biology, Genomics, GUI
ExaBayes 1.4.1, 1.5 [219] Biology, Phylogenetics
ExaML 1.0.5, 1.0.12, 3.0.14, 3.0.17 [220] Biology, Phylogenetics
ExomeCNV 1.4 [221] Biology, NGS, Genomics
Exonerate 2.2.0 [222] Biology, Genomics
eXpress 1.3.1 [223] Biology, NGS
FALCON 20160828, 20161222 [224] Biology, Bioinformatics, NGS, Sequencing
FALCON_unzip 20160623, 20161222 [225] Biology, Bioinformatics
FAR 2.15 [226] Biology, Genomics
FASTA 34.26.5, 36.3.6d [227] Biology, Genomics
FAST-iCLIP 0.9.1 [228] Biology, Sequencing
FastML 3.0 [229] Biology, Phylogenetics, ML
FastSpar 0.0.4 [230] Biology, Genomics
FastQC 0.10.1, 0.11.2, 0.11.4 [231] Biology, NGS
Fastq-tools 0.7, 0.8 [232] Biology, NGS
FastStructure 20150112 [233] Biology, Genomics
FastTree 2.1.7 [234] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [235] Biology, NGS
Fathmm 20150225 [236] Biology, Genomics
fcGENE 1.0.7 [237] Biology, Genomics, SNP
Ferret 6.82 [238] Oceanography, Meteorology
FFmpeg 2.1.3, 2.8.3 [239] Multimedia, audio, video
FFTW 3.3.2, 3.3.3, 3.3.4 [240] Math, Library, C++
FineSTRUCTURE 2.0.7 [241] Biology, Populatiopn Genetics
FLASH 1.2.10, 1.2.11 [242] Biology, Genomics, NGS
Flexbar 2.3 [243] Biology, Genomics, NGS
Fluent 14.5.7, 15.0.7, 16.0, 17.2 [244] Simulation, Fluid Dynamics
fqtools 20160224 [245] Biology, Bioinformatics, NGS
FragGeneScan 1.16 [246] Biology, NGS, Genomics
FrameDP 1.2.2 [247] Biology, Sequencing
Frealign 9.11 [248] Image Reconsctruction
FreeBayes 1.0.1, 1.0.2, 1.1.0 [249] Biology, NGS, SNP Calling
FREEC 9.6 [250] Biology, Sequencing
Freesurfer 5.2.0, 5.3.0 [251] Biology, Neurology, Imaging
FSL 5.0.2.2 [252] Biology, Neurology, Imaging
Galaxy latest [253] Biology, Chemistry, Other
GapFiller 1.11 [254] Biology, NGS
Garli 2.0, 2.01 [255] Biology, Phylogenetics
GAML 20150610 [256] Biology, NGS
GAMBIT 15.1.0, 16.0.0 [257] Game Theory
GARM 0.7.4 [258] Biology, NGS
GASVPro 201310 [259] Biology, NGS, Genomics
GATE 7.0 [260] Data Analysis
GATK 1.6.9, 3.4.46, 3.5.0 [261] Biology, NGS
Gaussian G03, G09-A.02, G09-C.01 [262] Modeling, Computational Chemistry
Gblocks 0.91b [263] Genomics, Alignment tool
GCTA 1.24.7, 1.26.0 [264] Biology, Genomics, SNP
GDAL 1.11.2 [265] Geospatial Data Modeling, Geospatial Library
GDC-Client 1.0.1 [266] Biology, Bioinformatics, Sequencing, NGS
Geant4 4.10 [267] Physics
GEM 20130406 [268] Biology, NGS
gem5 2.0 [269]] Computer Simulator
GEMINI 4.6.6a, 0.13.1, 0.18.0 [270] Biology, Genomics, Genetics
GenBank Tools 20140130 [271] Biology, Genomics
GeneMark 2012.04 [272] Biology, Genomics, Metagenomics
GeneSeqer 20140226 [273] Biology, Genomics
Genewise 2.2.0 [274] Biology, Genomics, Annotation
GenGen 1.0.1 [275] Biology, Phylogenetics
Genome STRiP 2.00.1602 [276] Biology, genomics, NGS
GenomicConsensus 20160523 [277] Biology, Phylogenetics
GenomicTools 2.7.0 [278] Biology, NGS
GenomeTools 1.5.7 [279] Biology, Bioinformatics
GenotypeHarmonizer 1.4.18 [280] Biology, Bioinformatics
GenSel 4.90 [281] Biology, Genetics
GET_HOMOLOGUES 20150529 [282] Biology, Genomics
GFOLD 1.1.4 [283] Biology, RNA-seq
Gffread 0.9.8c [284] Biology, Bioinformatics
GKNO 1.30.18 [285] Biology, NGS,
Git 1.8.2.1, 1.9.0 [286] Development, Revision Control
Glimmer 3.02 [287] Biology, Microbial Annotation
Globus 2.1.3 [288] Data Transfer
GLPK 4.55 [289] Biology, Genomics
Gmap 20150723, 20160501, 20160816 [290] Biology, Genomics
GNU Compilers 5.2.0 [291] Compilers, Programming
GnuPlot 4.6.0, 5.0.3 [292] Graphics, Plotting, Programming
Grace 5.1.22 [293] Graphics, plotting, 2D
GrADS 2.0.1 [294] Earth Science
GramCluster 1.3 [295] Biology, Sequencing
GRASS 7.0 [296] Geography
GraphViz 2.38.0 [297] Graphics, plotting, visualization
GraphMap 0.4.0 [298] Biology, Sequencing
Gromacs 4.5.5, 4.6.5, 5.1.2 [299] Chemistry, Modeling, Simulation
GSNP 1.0 [300] Biology, Bioinformatics, NGS
GSL 1.15 [301] Library, Math, C++, C
Gsutil 4.15 [302] Cloud, Storage, Google
Gubbins 20150519, 20160421 [303] Biology, Phylogenetics, Genomics
GULP 4.0 [304] Material Science
HaMStR 13.2.2, 13.2.3, 13.2.4 [305] Biology, Genomics
HapCompass 0.7.7 [306] Biology, NGS, Genomics
HAPCUT 0.7 [307] Biology, Assembly
Hapsembler 2.21 [308] Biology, Genomics, NGS
HapTree 1.0 [309] Biology, Genomics, NGS
hapQTL 1.00 [310] Biology, Genomics
HDF4 4.2.11 [311] Library, Data
HDF5 1.8.9, 1.8.15, 1.10.1 [312] Library, Data
HGTFinder 20160720 [313] Biology, Genomics
HISAT2 2.0.0b, 2.0.1b, 2.0.3b [314] Biology, Sequence Alignment, NGS
HMMER3 3.0, 3.1b1, 3.1b2 [315] Biology, Genomics
HMMSplicer 0.9.5 [316] Biology, Genomics
HOMER 4.2, 4.7, 4.8 [317] Biology, Genomics
HOOMD 1.3.3 [318] Chemistry
HTMLDoc 1.2.82 [319] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [320] Biology, NGS
Hyb 20141126 [321] Biology, NGS, RNA-Seq
HybPiper 1.2 [322] Biology, Phylogenetics
HyPhy 2.1.2.28, 2.2.6.1 [323] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [324] Library, Math, Physics
iAssembler 1.32 [325] Biology, Assembly
IBDNe 20150815 [326] Biology, NGS
iCommands 3.3.1 [327] Biology, iPlant, Data Tansfer
ICORN2 0.95 [328] Biology, Sequencing
IDBA-UD 1.0.9, 1.1.0, 1.1.1 [329] Biology, NGS
IDBA-MT 1.0 [330] Biology, NGS
IEP 3.6 [331] Programming, Python, Editor
IGB 8.4.1 [332] Biology, Genomics, NGS
IGV 2.3.91 [333] Biology, Bioinformatics, NGS
iGTP 1.1 [334] Biology, Bioinformatics, Phylogenetics
illumiprocessor 20150803 [335] Biology, Sequencing
IM and IMa 20091217 [336] Biology, Population
IMa2 20120827 [337] Biology, Population
ImageJ 1.48 [338] Image manipulation
ImageMagick 6.8.8-9, 7.0.5-5 [339] Image manipulation
IMOD 4.7.15 [340] 3D modeling, Image Reconstruction
InParanoid 4.1 [341] Biology, Bioinformatics
Intel Compilers 2016.0.109 [342] Programming, Compilers
IOAPI 3.1 [343] Meteorology
Iprscan 4.8 [344] Biology, Genomics
ipyrad 0.4.4, 0.6.20 [345] Biology, bioinformatics, NGS
IQ-TREE 1.4.0, 1.4.2, 1.5.3 [346] Biology, Phylogenetics
IRAP 0.8.1p7 [347] Biology, NGS, RNA-seq
iRep 20161015 [348] Biology,
IRFinder 1.0.0, 1.2.0 [349] Biology, RNA-Seq
ITK 4.3.1 [350] Biology, Genomics
ITK-SNAP 3.0.0 [351] Biology, Neuroscience, Imaging
JACUSA 1.2.0 [352] Biology, NGS
JAGS 3.3.0 [353] Statistics
Java 1.7.0_79, 1.8.0_31 [354] Java Development Kit
Je 1.0. [355] Biology, NGS
Jellyfish 2.1.1 [356] Biology, NGS
JModelTest 2.1.1 [357] Biology, Phylogenetics, Genomics
Julia 0.3.11, 0.4.6 [358] Programming, Languages
KaKs 1.2 [359] Biology, Phylogenetics
Kent 20120524 [360] Biology, NGS
Khmer 1.1, 2.0, 2.1 [361] Biology, NGS
KIM 1.7.2 [362] Library
KING 1.4, 1.9 [363] Biology, Genomics
Kinfin 1.0.1 [364] Biology, Phylogenetics
KisSplice 2.4.0-p1 [365] Biology, NGS
Kallisto 0.42.3, 0.42.4 [366] Biology, NGS, RNA-Seq
KERAS 1.0.8 [367] Deep Learning
Kmer 1934 [368] Biology, NGS
KmerGenie 1.6741 [369] Biology, NGS, Utilities
Kraken 0.10.4b [370] Biology, Genomics, Phylogenetics
Krona 20161019 [371] Biology, Bioinformatics
kSNP 3.021 [372] Biology, Phylogenetics, SNP
Lace 0.99 [373] Biology, NGS
LAMMPS 28Oct12, 30Sep13, 28Jun14 [374] Molecular Dynamics Simulation
LAMP 2.5 [375] Biology, Genomics
Last 247, 531, 801 [376] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [377] Biology, NGS
LDhat 2.2a [378] Biology, Genomics
LIBSVM 3.12 [379] Machine Learning
LIGR 2.05 [380] Biology, Assembly
LINKS 1.8.5 [381] Biology, Genomics
LFMM 1.4 [382] Biology, Genomics
LSC 0.3, 0.3.1 [383] Biology, NGS, Error correction
lobSTR 4.0.6 [384] Biology, Phylogenetics
Loci 3.3 [385] Fluid Dynamics
LoRMA 0.3 [386] Biology, NGS
LS-DYNA 700, 711, 800 [387] Physics
LTRReteriever 20170514 [388] Biology, Phyloegenetics
Lumpy 0.2.1 [389] Biology, SNP
LZO 2.09 [390] Library, Data Compression
MACH 1.0.18 [391] Biology, Genomics
Mach2VCF 20150515 [392] Biology
M5tools 20121126 [393] Biology, Bioinformatics, Genomics
MACS 1.4.2, 2.1.1 [394] Biology, ChIP-Seq
mafft 7.215, 7.245, 7.294 [395] Biology, Multiple sequence alignment
Mash 1.1 [396] Biology, Genomics
Maker 2.25b, 2.31.6, 2.31.8 [397] Biology, Annotation, Genomics
MapSplice 2.1.7 [398] Biology, NGS, RNA-Seq
MAPminer 1.1 [399] Biology, Phylogenetics
MassMine 0.9.5, 0.10.0, 0.11.0 [400] Data Mining
Maq 0.7.1 [401] Biology, NGS
MARK 2.0.1 [402] Statistics
MarkerMiner 20150429, 20150511 [403] Biology, Genomics
MaryGold 0.2 [404] Biology, NGS
MaSuRCA 2.3.2, 3.2.1 [405] Biology, NGS
Matlab 2012a, 2013a, 2014a [406] Math, Simulation, Programming
MATS 3.0.8, 3.0.9, 3.2.5 [407] BIology, NGS
Mauve 2.3.1 [408] Biology, NGS
MaxBin 2.1.1 [409] Biology, NGS
MCarts 1.0.2 [410] Biology, Genomics, Markov models
MCNP 5, 6b2, 6, 6.1 [411] Physics
MCNPX 2.7.0, 2.7.0-i8 [412] Physics
MEGAN 5.10.3, 6.4.15 [413] Biology, NGS
MEGAHIT 1.1.1 [414] Biology, NGS
Megraft 1.0.2 [415] Biology, Sequencing
Melting 4.3.1 [416] Biology, Genome, RNA, Folding
Meme 4.11.1, 4.11.2 [417] Biology, Motifs, Sequence analysis
Meraculous 2.0.5 [418] Biology, NGS
Mercurial 4.0.2 [419] Development, Revision Control
Merlin 1.1.2 [420] Biogolgy, SNP
Meta-Tissue 0.4 [421] Biology, Genetics
Metabin 1.0 [422] Biology, Metagenomics
MetaCluster 5.0b [423] Biology, Metagenomics
MetaCV 2.3.0 [424] Biology, NGS
METAL 20110325 [425] Biology, Genomics
MetAMOS 1.5.0rc4-20140827 [426] Biology, Bioinformatics, Genomics, Assembly
Metassembler 1.5 [427] Biology, Genomics
MetaVelvet 1.2.01 [428] Biology, NGS
Metaxa2 2.0.2, 2.1.1 [429] Biology, NGS
MetaGeneMark 2012.04 [430] Biology, Genomics
Mfold 3.6 [431] Biology, Genomics
MGEScan 1.1 [432] Biology, Genomics
MHAP 1.6 [433] Biology, Sequencing
MIA 20130301 [434] Biology, NGS
MicrobeCensus 1.0.7 [435] Biology, NGS
MIDAS 20160830 [436] Biology, Phylogenetics
Midnight Commander 4.6.1 [437] Tools, Utilities
Migrate-n 3.3.0, 3.6.6, 3.6.11 [438] Biology, Population
Minced 0.2.0 [439] Biology, Genomics
Minimac 2-20140915, 3-20151015 [440] Biology, Genomics
Minimap 0.2 [441] Biology, Phylogenetics
mira 3.9.18, 4.0.rc1, 4.0.2 [442] Biology, NGS
MIReNA 2.0 [443] Biology, Phylogenetics
MISO 0.4.9, 0.5.2, 0.5.3 [444] Biology, NGS
MMSEQ 1.0.8 [445] Biology, NGS
MSMBuilder 2.5.1 [446] Molecular Dynamics
MOABS 1.2.9, 1.3.2, 1.3.4 [447] Biology, NGS, Genomics
Modeller 9.11, 9.13, 9.14 [448] Biology, Modeling
Molden 5.0 [449] Molecular, electronic structure
MolPro 2012.1p22 [450] Quantum Chemistry, Ab Initio
mosaik 2.1.33, 2.2.3 [451] Biology,NGS
Mothur 1.36.1, 1.37.0, 1.38.1 [452] Biology, Microbial Ecology
MotionCorr 2.1 [453] Motion Correction
MotionCor2 01302017 [454] Motion Correction
MOTU 1.1 [455] Biology, Bioinformatics, Genomics
MOST 20170721 [456] Biology, Genomics
MPE2 2.4.9b [457] MPI
MP-EST 1.4, 1.5 [458] Biology, Phylogenetics
mpiP 3.4.1 [459] Parallel Computing
MrBayes 3.2.1, 3.2.4, 3.2.5 [460] Biology, Phylogenetics
MRIcron 201306, 20161012 [461] Biology, MRI, Imaging
MUMmer 3.23 [462] Biology, Genomics
MUSCLE 3.8.31 [463] Biology, Genomics
MuTect 1.1.4, 1.1.7 [464] Biology, Genomics
MutSig 1.4, 1.41 [465] Biology, Genomics
MZMine 2.19, 2.20, 2.21 [466] Biology, Spectroscopy
NAMD 2.9, 2.11, 2.12 [467] Molecular Dynamics, Chemistry
Nanocorrect 20150727 [468] Biology, NGS
Nanopolish 20150904 [469] Biology
Nbody 6 [470] Astronomy
NCBI C++ Toolkit 12.0.0 [471] Biology, C++, Development
NCL 6.1.2, 6.3.0 [472] Atmosphere Science
NCO 4.2.1, 4.4.3 [473] Data exchange tools
Ncview 2.1.2 [474] Data visualization
NeEstimator 2.01 [475] Biology, Bioinformatics
NetCDF 4.2, 4.3, 4.4.1.1 [476] Data exchange, Tools
NEURON 7.4 [477] Biology, Neuroscience
Newbler 2.7, 2.8, 2.9 [478] Biology, NGS
Newick utils 1.6 [479] Biology, Phylogenetics
Nextallele 20140718 [480] Biology, Genomics
NextGenMap 0.5.3 [481] Biology, Bioinformatics, NGS
Nexus NCL 2.1.18 [482] Biology, Phylogenetics, Library
NGS-bits 0.1 [483] Biology, Sequencing
ngsCAT 0.1 [484] Biology, Bioinformatics, NGS
ngsTools 20150816 [485] Biology, NGS
NGSUtils 20130722, 20150206 [486] Biology, NGS
Nipype 0.10.0, 0.12.1, 0.13.1 [487] Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe 7.9 [488] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [489] Biology, NGS
NWChem 6.5, 6.6 [490] Chemistry
NxTrim 0.4.1 [491] Biology, Bioinformatics, NGS
Oases 0.2.08 [492] Biology, NGS
OBITools 1.2.11 [493] Biology, Phylogenetics
Olego 1.1.2, 1.1.5, 1.1.6 [494] Biology, NGS, RNA-Seq
OCaml 4.02.3 [495] Programming Languages, Scripting, Development
Octave 3.6.4 [496] Numerical Computation
Oncotator 1.5.2.0, 1.5.3.0, 1.8.0.0 [497] Biology, Genomics
OpenBabel 2.3.2, 2.4.1 [498] Biology, Chemistry
OpenCL 1.1 [499] Programming, Library
OpenCV 2.4.8 [500] Computervision
OpenFOAM 2.1.1, 3.0.1, 4.0 [501] Fluid Dynamics
OpenMM 6.2.0 [502] Quantum Chemistry
Orange3 3.3.6 [503] Data Mining, Visualization
OrthoFinder 0.2.5, 0.6.0, 1.0.2 [504] Biology, Genomics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [505] Biology, Genomics
OTB 5.6.1 [506] Geospacial Imaging
p4vasp 0.3.29 [507] Molecular, Electronic Structure
p53MH 20020901 [508] Biology, Sequencing
Pacbio 2.2.0, 2.3.0p5 [509] Biology, Bioinformatics, NGS
Package-GFE 20150701 [510] Biology, Genomics
PALES 122 [511] Physics
PALADIN 1.3.1 [512] Biology, Phylogenetics
PAML 4.7, 4.8a, 4.9a [513] Biology, Phylogenetics
Pandaseq 20140808, 20150627 [514] Biology, Bioinformatics, NGS, Sequencing
PAPI 5.1.0.2 [515] Software, Computing
Parallel 20150122, 20170322 [516] Programming, Languages
ParaView 4.1.0, 4.2.0, 4.3.0 [517] Data Analysis
Parsimonator 1.0.2 [518] Biology, Bioinformatics
PartitionFinder 1.1.1, 2.1.1 [519] Biology, Phylogenetics, Evolution
Parflow v615 [520] Ecology, Modeling
PASA 1.5, 2.0-r20150209 [521] Biology, Genomics
PASTA 20160616 [522] Biology, Sequence alignment,
PAUP 4.0b10, 4.1a147, 4.0a152 [523] Biology, Phylogenetics
PAUDA 1.0.1 [524] Biology, Bioinformatics, Sequence alignment
PBalign 20160921 [525] Biology, Bioinformatics
PBCore 20151201 [526] Biology, Bioinformatics
PBCommand 20151203 [527] Biology, Library
PBJelly 14.7.14, 15.2.20, 15.8.24 [528] Biology, Bioinformatics
pbsdrmaa 1.0.17 [529] Libraries, Torque
p4est 1.1 [530] Library
pbsmrtpipe 20151202 [531] Biology
PeakSplitter 1.0 [532] Biology, Chip-Seq
PEAR 0.9.2, 0.9.6 [533] Biology, NGS
PECaller 1.0.0 [534] Biology, NGS
PDT 3.18, 3.20, 3.22 [535] Programming, Profiler
Perl 5.16.0 [536] Programming, Language
PerM 0.4.0 [537] Biology, NGS
PETSc 2.3, 3.3 [538] Math, Numerical solvers
PGDSpider 2.0.9.0 [539] Biology, NGS
PHAST 1.4 [540] Biology, Phylogenetics
Phenix 1.8.1069, 1.10.2155 [541] Crystallography
PHYLDOG 20130418 [542] Biology, Genomics, Phylogenetics
Phyluce 20140427, 20151103, 20160715 [543] Biology, Phylogenetics
Phyutility 2.7.1 [544] Biology, Bioinformatics
Phyx 0.99 [545] Biology, Phylogenetics
PfamScan 1.3 [546] Biology, Genomics
PHITS 2.52, 2.76. 2.82 [547] Physics
PHLAWD 20170427 [548] Biology, Phylogenetics
Phonopy 1.9.2 [549] Chemistry
PHYLIP 3.696 [550] Biology, Phylogenetics
PhyloBayes 3.3f, 1.4f MPI [551] Biology, Phylogenetics
PhyloNet 3.5.7 [552] Biology, Phylogenetics
Phylosift 1.1 [553] Biology, Genomics, Phylogenetics, Taxonomy
PhyML 3.0, 3.1 [554] Biology, Phylogenetics
Picard 2.0.1, 2.5.0, 2.9.2 [555] Biology, NGS
PICRUSt 1.0.0, 1.1.0 [556] Biology, Phylogenetics
Pilon 1.22 [557] Biology, Bioinformatics
PIPE-CLIP 1.1.0 [558] Biology, NGS
Pipits 1.3.6 [559] Biology, Sequencing
piPipes 1.5.0 [560] Biology, Phylogenetics
Piranha 1.2.1 [561] Biology, Phylogenetics
PLAST 1.0 [562] Biology, Bioinformatics
Platypus 0.8.1 [563] Biology, NGS
PLEK 1.2 [564]] Biology, Phylogenetics
Plink 1.07, 1.90b3, 1.90b3.39 [565] Biology, GWAS
PLINKSEQ 0.10 [566] Biology, Genomics
PluMiST 1.1 [567] Biology, Phylogenetics, Genomics
PolyPhen 2.2.2.r405b [568] Biology, Genomics
PonyTools 0.1 [569] Biology, Genomics
Poretools 0.5.0 [570] Biology, Sequencing
POV-Ray 3.7 [571] 3D, Graphics
Prank 20150803 [572] Biology, Bioinformatics, Alignment
Preseq 0.0.4 [573] Biology, NGS
PRICE 1.2 [574] Biology, NGS
Primer3 2.3.4 [575] Biology, Genomics
PRIMUS 1.8.0 [576] Biology, Phylogenetics
PRINSEQ 0.20.4 [577] Biology, Sequencing
Prodigal 2.6.3 [578] Biology, Genomics
ProfessAtQE 2014 [579] Material Science, Molecular Dynamics
Prokka 1.10, 1.11 [580] Biology, Genomics, Bioinformatics, Assembly
ProBABEL 0.4.2, 0.4.3, 0.4.5 [581] Biology, Genomics, GWAS
Probalign 1.4 [582] Biology, Genomics
Proovread 1.03rcl [583] Biology, Genomics, NGS
Proteinortho 4.26, 5.11, 5.16 [584] Biology, Genomics
PROVEAN 1.1.5 [585] Biology, Genomics
PyAni 0.2.1 [586] Bilogy, Genomics
PyHDF 0.9.0 [587] Library, HDF4
PyVCF 0.6.0 [588] Biology
Python 2.7.6, 3.5.0 [589] Biology, Genomics, NGS
Pyfasta 0.5.2 [590] Biology, Phylogenetics
Pyrad 3.0.63 [591] Biology, Sequencing Alignment, Assembly
QDD 3.1.2 [592] Programming, scripting, language
QGIS 2.18.0 [593] Geography
QIIME 1.9.0, 1.9.1 [594] Biology, Ecology
QIIME2 2.0.6 [595] Biology, Ecology
QT 4.8.3 [596] Computer Science
QUAST 2.3, 4.4 [597] Biology, NGS
Quake 0.3 [598] Biology, Sequencing
Quantas 1.0.4, 1.0.8 [599] Biology, Bioinformatics, NGS
QualiMap 2.1.1 [600] Biology, Sequence alignment
Quickquartet 1.0.0 [601] Biology, Phylogenetics
R Rmpi/3.3.1, 3.2.0, 3.3.0 [602] Statistics, Programming
R2R 1.0.4 [603] Biology, RNA
R8S 1.71, 1.8 [604] Biology, Evolution
Racon 20161013 [605] Biology, Sequencing
RADICAL 0.2 [606] Biology, Phylogenetics, Genomics
Randfold 2.0.1 [607] Biology, RNA
Rascaf 1.0.2 [608] Biology, RNA-Seq
RAxML 8.2.3, 8.2.8, 8.2.10 [609] Biology, Phylogenetics
Ray 2.3.1 [610] Biology, Genomics, NGS
REAGO 1.1 [611] Biology, Assembly
REAPR 1.0.18 [612] Biology, Bioinformatics, Assembly
Recycler 0.62 [613] Biology, Bioinformatics
Regtools 0.4.0 [614] Biology, RNA-seq
RELION 1.4 [615] Biology, Bioinformatics
REPdenovo 20170222 [616] Biology, Phylogenetics
RepeatExplorer 20150506 [617] Biology, Genomics
RepeatMasker 3.3.0 [618] Biology, Genomics
RepeatModeler 1.0.8 [619] Biology, Bioinformatics
Reptile 1.1 [620] Biology, NGS, error correction
RevBayes 1.0.0, 1.0.3 [621] Biology, Phylogenetics
riboPicker 0.4.3 [622] Biology, Sequence
RNAhybrid 2.1.1 [623] Biology, Genomics
rRNASelector 1.0.0 [624] Biology, Sequencing
rnaseqlib 20150721 [625] Biology, Phylogenetics, RNA-Seq
rnaQUAST 1.2.0 [626] Biology, NGS, Sequencing
ROOT 6.0 [627] Data Analysis
Roary 3.4.1 [628] Biology, Genomics
Rosetta 2014wk4 [629] Biology, Structure, Modelling
RSEG 0.4.8 [630] Biology, NGS
RSEM 1.2.19, 1.2.28, 1.2.29 [631] Biology, NGS, RNA-Seq
RSeQC 2.3.7, 2.6.2 [632] Biology, NGS, RNA-Seq
RStudio 0.99.902, 0.99.903 [633] R, Statistics, Programming
RTGTools 3.7.1 [634] Biology, NGS
Ruby 1.9.3-p0 [635] Programming, Scripting, Language
Sailfish 0.6.3 [636] Biology, NGS, RNA-Seq
Salmon 0.6.0, 0.7.2 [637] Biology, RNA-seq
SMC++ 1.7.0 [638] Biology, NGS
Sambamba 0.5.0-dev, 0.5.10, 0.6.3 [639] Biology, NGS
Samstat 1.08 [640] Biology, NGS, Bioinformatics, Sequencing
Samblaster 0.1.14 [641] Biology, NGS
samtools 1.1, 1.2, 1.3.1 [642] Biology, NGS
SAS 9.3 [643] Statistics, Graphing
SATe 2.2.7 [644] Biology, Phylogenetics
Scala 2.11.5 [645] Programming, Language
Scalablast 2.4.53 [646] Biology, Genomics
Scalpel 0.1.1, 0.5.3 [647] Biology, NGS
SCRIPTURE 20101211 [648] Biology, Bioinformatics, Genomics
Shannon 20160211 [649] Biology, RNA-Seq
SHAPEIT 2.5.5 [650] Biology, SNP
SHAPE-MaP 1.2 [651] Biology, Phylogenetics
Sharcgs 1.2.11 [652] Biology, NGS, Assembly
SHEsisPlus 1.0 [653] Biology, Phylogenetics
shustring 2.6 [654] Biology, Sequencing
SCons 2.3.0 [655] Programming
Scoary 1.6.10 [656] Biology, Bioinformatics, Genomics
SCRATCH1D 1.0 [657] Biology, Genomics
Scythe 0.991 [658] Biology, NGS
SDT 1.2 [659] Biology, Sequencing
Segemehl 0.1.9 [660] Biology, NGS, Mapper
SEPP 1.0, 3.0 [661] Biology, Phylogenetics, HMM
SGA 0.10.14 [662] Biology, Assembly
Seq-Gen 1.3.3 [663] Biology, Phylogenetics
SeqPrep 0.5 [664] Biology, NGS
Seqmagick 20150923 [665] Biology, Phylogenetics
SeqMap 1.0.13 [666] Biology, NGS
Seqtk 20140729 [667] Biology, NGS
SEQuel 1.0.1 [668] Biology, NGS
SeqyClean 1.8.10 [669] Biology, NGS, Bioinformatics
ShoRAH 20131204 [670] Biology, NGS, quality filter
SHRiMP 2.2.3 [671] Biology, NGS
SICER 1.1 [672] Biology, ChIP-Seq
Sickle 1.200, 1.33 [673] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [674] Simulation, Physics, Ab Initio
Sisl 0.8.3 [675] Physics, Tight-binding
SIFT 4.0.3b [676] Biology, Genomics
SignalP 4.1c [677] Biology, NGS
Silo 4.7 [678] Library, Data
SIPeS 2.0 [679] Biology, Bioinformatics, ChIP-Seq
Slicer 4.3.1 [680] Biology, Imaging
SMALT 0.7.6 [681] Biology, NGS
Snap 20100728, 0.15.4 [682] Biology, Genomics
SNAPE-pooled 20130407 [683] Biology, SNP
SNeP 1.1 [684] Biology, Phylogenics
SnpEff 4.2, 4.3, 4.3p [685] Biology, NGS, Genomics
SNPhylo 20140701 [686] Bilogy, Phylogenetics
SNP-sites 2.0.3 [687] Biology, SNP
Snippy 20160419 [688] Biology, Phylogenetics
SOAPdenovo 1.05 [689] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [690] Biology, NGS
SOAPec 2.03 [691] Biology, Phylogenetics
SOAPsplice 1.10 [692] Biology, NGS
SortMeRNA 2.1 [693] Biology, Sequencing, NGS
SparCC 201402 [694] Microbial Ecology
Spades 3.9.0, 3.10.0, 3.10.1 [695] Biology, NGS
Spanki 0.4.1, 0.4.3, 0.5.0 [696] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [697] Chemistry
Spidey 20150922 [698] Biology, Genomics
SPIMAP 1.1 [699] Biology, Phylogenetics
SpliceTrap 0.90.5 [700] Biology, NGS, RNA-Seq
SPM 8 [701] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [702] Biology, Genomics
SQLite 3.8.8.2 [703] Database
SQL_Developer 4.1.2 [704] Programming, Oracle, Sql
SRA 2.1.10 [705] biology, NGS
SSPACE 2.0, 3.0 [706] Biology, NGS
SST-Core 6.0.0 [707] MPI
SSR_pipeline 0.951 [708] Bilogy, DNA Sequencing
Stacks 1.24, 1.35, 1.45 [709] Biology, Genomics, NGS
Staden 1.14.6 [710] Biology, Sequencing
Stampy 1.0.31 [711] Biology, Bioinformatics, Sequencing
STAR 2.4.0j, 2.5.1b [712] Biology, NGS, Alignment
STAR-CCM+ 8.06 [713] Mechanical Engineering
Stata 10.1, 13 [714] Statistics, Data analysis
Statsmodels 0.8.0 [715] Biology, Library, Math
Stringtie 1.1.2, 1.2.1, 1.3.3 [716] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [717] Biology, Population
stringMLST 0.4 [718] Biology, Genomics, NGS
Subread 1.5.0-p1, 1.5.1 [719] Biology, Sequencing, SNP
Supercell 20170602 [720] Biology, NGS
Supernova 1.1.5 [721]] Biology, Phylogeneitcs, NGS
SUNDIALS 2.3.0, 2.5.0 [722] Numerical Solver
SVDetect 0.8b [723] Biology, NGS, SNP
swak4Foam 2.x [724] Fluid Dynamics
swarm 1.2.11 [725] Data Analysis
SWEEP 20160722 [726] Biology, SNP
Swig 2.0.9 [727] Programming, C, C++, Python
SwitchSeq 20140907 [728] Biology, NGS
Syzygy 1.2.7 [729] Biology, Genomics
TetGen 1.5.0 [730] Tetrahedral Meshes 3D
tapir 20160825 [731] Biology, Phylogenetics
TAPIS 1.2.1 [732] Biology, Sequencing
TASSEL 5.0, 5.2.29 [733] Biology, Genomics
TAU 2.21.4, 2.23, 2.24, 2.52 [734] Profiling, Tracing, Programming
taxMap 0.1 [735] Biology, Phylogenetics, Taxonomy
TaxonDNA 1.8 [736] Biology, Taxonomy
T-Coffee 9.03.r1318 [737] Biology, Genomics, Multiple Alignment
TEToolkit 1.5.1 [738] Biology, Bioinformatics, Sequencing
TensorFlow 1.0.0, 1.2.0 [739] Library, Math
TESS 2.3.1 [740] Biology, Genomics, Markov
tgicl 2.1 [741] Biology, sequencing, clustering
Tmux 2.0 [742] GNU, Terminal Multiplexer
TomoPy 0.0.3 [743] Biology, Neuroimaging
Tophat 1.4.1, 2.0.13, 2.1.0 [744] Biology, NGS
Torch 20160704, 20171102 [745] Lua
Totalview 8.12.0 [746] Computer Science
TPP 4.7.0 [747] Bioinformatics, MassSpec
TrackTools 2011 [748] Bioinformatics
TrackVis 0.5.2.2 [749] Biology, Spectroscopy
Tracula 5.3.2014_05_26 [750] Biology, Bioinformatics, Neuroscience, Imaging
TraitRate 1.1 [751] Biology, Evolution
Trans-ABySS 1.5.4 [752] Biology, Phylogenetics
TransDecoder 20140704, 2.0.1, 3.0.0 [753] Biology, NGS
Transrate 1.0.1 [754] Biology, Assembly
TransVar 2.3.3 [755] Biology, Phylogenetics
TraCeR 20160519 [756] Biology, Bioinformatics
TreeCorr 3.2.3 [757] Physics
TreeFix 1.1.7, 1.1.10 [758] Biology, Phylogenetics
TreeMix 1.12 [759] Biology, Phylogenetics
TreePL 20150305 [760] Biology, Phylogenetics
TREEPUZZLE 5.3 [761] Biology, Phylogenetics
TriMetAss 1.1 [762] Biology, Bioinformatics, NGS
TRF 4.04 [763] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [764] Math Algorithm
trimAl 1.2 [765] Biology, Genomics, Sequence Alignment
Trim Galore 0.2.8, 0.4.1, 0.4.4 [766] Biology, NGS
Trimmomatic 0.32, 0.33, 0.36 [767] Biology, NGS
Trinity r20160329-2.2.0, r20161120-2.3.2 [768] Biology, NGS, RNA-Seq
Trinotate 2.0.1, 3.0.1 [769] Biology
TRNAscan-SE 1.23 [770] Biology, NGS, Bioinformatics
Twinscan 4.1.2 [771] Biology, Genomics
usearch 7.0.1001-64, 8.0.1517, 9.2.64 [772] Biology, Sequence analysis
UDUNITS 2.2.17 [773] Library, Units, Programming
UFITS 0.7.2 [774] Biology, NGS
UNAFold 3.8 [775] Biology, Genome, RNA, Folding
UProC 1.2.0 [776] Biology, Genomics
Valgrind 3.9.0 [777] Computer Science
VarDictJava 20160521 [778] Biology, NGS
Varnorm 0.21 [779] Biology, Phylogenetics
VarScan 2.3.6 [780] Biology, NGS, Genomics
VASP 5.3.2, 5.3.3, 5.3.5, 5.4.1 [781] Quantum Chemistry, Ab Initio
VAST-TOOLS 20150506 [782] Biology, NGS, RNA-Seq
VCFLib 20141119, 20150313 [783] Biology, NGS, Genomics
VCFtools 0.1.12a, 0.1.12b, 0.1.14 [784] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [785] Biology, Genomics, NGS
VEP 74, 83 [786] Biology, NGS
VICUNA 1.3 [787] Biology, Assembly
ViennaRNA 2.2.6 [788] Biology, RNA-seq
Vim 7.4.5 [789] Programming, Scripting, Language
vmd 1.9.1, 1.9.3 [790] Biology, Visualization
VSearch 20151022, 20161209-2.3.4 [791] Biology, NGS
VT 20140903, 20160129 [792] Biology, Genomics
VTC 0.9.3 [793] Biology, Bioinformatics, VCF
VTK 6.1.0 [794] Visualization, Graphics
V-Phaser2 02112013 [795] Biology, Phylogenetics
Virsorter 1.0.3 [796] Biology, Phylogenetics
w2rap-contiger 20161124 [797] Biology, Genomics
Wannier90 1.2, 2.0.0 [798] Computational Physics
WebLogo 3.3, 3.5.0 [799] Biology, Genomics
WEVOTE 1.5.0, 1.8.0 [800] Biology, Genomics
WDSSII 1 [801] Meteorology
WIEN2k 12.1 [802] Material Science, Chemistry
Wgs or Celera 8.2, 8.3rc1, 8.3rc1.r4638 [803] Biology, NGS
wublast 2.0 [804] Biology, Sequence Alignment
YAHA 0.1.82 [805] Biology NGS
Xander 20151222 [806] Biology, Phylogenetics
XCrySDen 1.5.60 [807] Computational Material Science
Yambo 3.3.0 [808] Physics
YASM 1.3.0 [809] Computer Science
Yasra 2.32 [810] Biology, NGS
Zagros 1.0.0 [811] Biology, NGS
Zeo++ 0.2.2 [812] Chemistry
Zorro 2.2 [813] 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.

Add New App

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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