Applications

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Note: Up to three latest versions are listed even though there could be more available. Run module spider name for a full list of provided versions.

Name Versions URL Description
3d-dna 20170330 [1] biology, phylogenetics
3PCLR 20150906 [2] biology, phylogenetics
4p 1.0 [3] biology,SNP
R 3.4.3, 3.5.1, 3.6 [4] statistics
Rmpi 0.6.6, 0.6.9 [5] statistics, R, mpi
ABruijn 1.0 [6] biology, assembly, ngs, pacbio, nanopore
ABySS 1.3.7, 1.5.2, 2.1.0 [7] biology, de novo
AdapterRemoval 2.2.2 [8] phylogenetics
ADMB 11.5, 12.0 [9] math, modeling, optimization
AdmixTools 20150311, 20160513 [10] biology, bioinformatics, genomics, ngs
ADMIXTURE 1.23, 1.3.0 [11] biology, bioinformatics, genomics, ngs
AEGeAn 0.14.0 [12] biology,genomics
AFNI 2016019-openmp, 2016_2_09, 2018_04_12 [13] biology,bioinformatics,neurology,imaging
AfterQC 0.9.7 [14] phylogenetics
Agalma 0.2.1, 0.3.5, 0.5.0 [15] biology, bioinformatics, genomics, SNP
AGOUTI 0.3.3 [16] biology, genomics
Albacore 2.1.10, 2.3.1, 2.3.3 [17] Biology, Phylogenetics
ALE 20150507 [18] biology,bioinformatics,assembly
ALLMAPS 20180117 [19] biology, phylogenetics
ALLPATHS-LG 42316, 44837, 49232 [20] biology,bioinformatics,ngs
Alphagenes 1.0 [21] phylogenetics
Alphaimpute 1.9.8.2 [22] phylogenetics
AltAnalyze 2.1.0 [23] Biology, genomics
AMAS 0.98 [24] biology, sequence alignment
AMBER 16, 16.0, 18 [25] Computational Chemistry, Molecular Dynamics
AMICO 1.0.1 [26] library, imaging, optimization
AMOS 3.1.0 [27] biology,bioinformatics,genomics,assembly
AMP 0.6.1, 0.6.1-1 [28] Atomistics
Amphora2 20140305 [29] biology, phylogenetics
AMPtk 0.8.0, 0.8.5, 1.2.4 [30] biology, bioinformatics, ngs
AMUSE 10.0, 6.0 [31] Astrophysics
ANGEL 2.3 [32] biology,bioinformatics,sequence
Angsd 20150306, 20150909 [33] biology, ngs
Annocript 2.0 [34] phylogenetics
ANNOVAR 20121023, 20130221, 20150322 [35] biology, bioinformatics, genomics
Ansible 2.5.5, 2.8.1 [36] automation, deployment
Ansysem 17.0 [37] Electromechanics
AntiSMASH 4.1.0 [38] phylogenetics
ANTs 2.2.0 [39] biology, phylogenetics
Anvio 2.3.2, 2.4.0, 5.5.0 [40] biology, microbial 'omics
Anylogic 1.0 [41] software tool
APT 1.15.0, 1.18.0, 1.20.5 [42] biology, bioinformatics, genomics, microarray
ARC 20130715, 20140305, 20140312 [43] biology,bioinformatics,ngs
ArcGIS 1.5.1, 10.3.1 [44] geospatial
ARCS 1.0.0, 1.0.1, 1.0.5 [45] biology, genomics
ARIBA 2.13.1 [46] phylogenetics
ARKS 1.0.2 [47] phylogenetics
Armadillo 6.200.3, 7.900.0, 9.200.6 [48] library, C++, math
ARPACK 1.0 [49] Solve eigenvalue problems
ArrayFire 3.4.2 [50] Code Optimization
ART 20160417, 20160605 [51] phylogenetics
ASE-ANI 20180712 [52] biology, bioinformatics, genomics, ngs
Assembly-stats 1.0.1 [53] biology, sequencing, genomics
AStalavista 3.2, 4.0 [54] biology, bioinformatics, genomics
ASTRAL 5.0.3, 5.6.1, 5.6.2 [55] biology,bioinformatics,ngs,phylogenetics
ASTRID 20150807 [56] biology,genomics
Astropy 2.0.8 [57] biology, bioinformatics, phylogenetics
Atac 0.3.3 [58] biology, phylogenetics
ATAT 3.23, 3.34 [59] alloy theory
ATLAS 3.10.1, 3.10.2, 3.11.17 [60] library, data
AtomEye 3 [61] Material Science
ATRAM 2.0, 2.1, 2.1.2 [62] Math
Augustus 3.2.1, 3.2.2, 3.3 [63] biology,bioinformatics,genomics
Auto3DEM 4.05.2 [64] Image Reconstruction
AutoDock 4.2.6 [65] biology
BALI-PHY 2.3.8 [66] Baesian Estimation
BAM-matcher 20161021 [67] phylogenetics
Bam-Readcount 20150616 [68] biology, genomics
BamBam 1.0 [69] biology, bioinformatics, genomics
BAMM 2.5.0 [70] bioinformatics, evolution
Bam-readcount 20150216 [71] biology, ngs
Bamstats 20140602 [72] biology,bioinformatics,ngs
Bamtools 2.4.1, 2.5.0, 2.5.1 [73] biology,bioinformatics,ngs,sequencing
BamUtil 1.0.2 [74] biology, bioinformatics, genomics
BAPS 6.0 [75] biology, bioinformatics, genomics
Barrnap 0.7, 0.9 [76] biology, RNA-Seq
Basemount 0.1.2.464, 0.12.8.1516 [77] biology,DNA Sequencing
Bashdb 4.4-0.94 [78] Debugger
BatVI 1.00 [79] biolgoy, phylogenetics
BayArea 1.0.2 [80] biology
BAYENV 2.0 [81] biolgoy, phylogenetics
BayesAss 3.0.4 [82] phylogenetics
BayeScan 2.1 [83] biology, SNP
BayeScEnv 1.1 [84] biology, phylogenetics
BayesR 20151016 [85] biology, phylogenetics
BayesRate 1.3.43 [86] biology, phylogenetics
Baypass 2.1 [87] biology, phylogenetics
Bazel 0.11.1 [88] build, development, java
BBMap 37.09, 38.26, 38.44 [89] biology, alignment
Bcbio-nextgen 0.8.7, 0.9.9 [90] biology, bioinformatics, ngs
Bcftools 1.6, 1.8, 1.9 [91] biology, bioinformatics, ngs
Bcl2fastq 2.17.1.14, 2.19.1.403, 2.20.0.422 [92] biology, ngs, illumina
BDG-SeQuila 0.5.5 [93] phylogenetics
BEAGLE 4.0, 4.1, 5.0 [94] biology, genetics, genotyping
BEAR 20170209 [95] biology, bioinformatics, metagenomics
BEAST 2.5.1, 2.5.2, 2.6.0 [96] biology,phylogeny
BEDOPS 2.4.2, 2.4.30 [97] biology,bioinformatics,sequence,ngs
BEDTools 2.26.0, 2.27.1, 2.28.0 [98] biology,bioinformatics,ngs
Bertini 1.6 [99] Mathemetics
BESST 2.2.4 [100] biology, NGS
BETA 1.0.5 [101] biology, bioinformatics, genomics, ngs, chip-seq
BFAST 0.7.0 [102] biology,bioinformatics,ngs
BinPacker 1.0 [103] biology, RNA-seq, sequence assembly
BinSanity 0.1.3, 0.2.5.9, 0.2.6.4 [104] biology, genomics
Bioawk 1.0 [105] phylogenetics
Biodiverse 2.1 [106] phylogenetics
Biolite 0.3.5.1 [107] biology, bioinformatics, genomics, SNP
BIOM 1.3.1, 2.1.5, 2.1.6 [108] biology, genomics
BIOMART 1.4 [109] biology,genomics
BiSCoT 1.0 [110] phylogenetics
Bismark 0.20.1, 0.7.4, 0.7.7 [111] biology, bioinformatics, NGS
Blackfynn 0.1.13 [112] data mining
BLASR 20160518 (5.1), 20161215 (5.3), 5.3.2 [113] biology,bioinformatics,ngs
Blast2GO 1.3.3, 2.5.0-20120705 [114] biology,bioinformatics,gene ontology
BLAT 20121105, 20140318 [115] Genomics, bioinformatics
Blender 2.63, 2.73, 2.77 [116] graphics
Blitz 0.10 [117] library
BlobTools 1.0 [118] phylogenetics
BloomTree 0.3.5 [119] data mining
BLUPF90 20160604, 20180301, 20190531 [120] biology, phylogenetics
BoltzTraP 1.2.5 [121] physics
Boost 1.63.0, 1.64.0, 1.67.0 [122] programming, library, cpp
Booster 0.1.2 [123] phylogenetics
Bowtie 1.1.1, 1.2.0, 1.2.3 [124] biology,bioinformatics,ngs,sequencing
Bowtie2 2.3.4.3, 2.3.5, 2.3.5.1 [125] biology,bioinformatics,ngs,sequencing
BPGA 1.2 [126] biology, ngs
BPP 2.2, 3.2, 3.4 [127] biology, phylogenetics
Bracken 1.0.0 [128] biology, phylogenetics
Braker 2.1.2 [129] phylogenetics
BRANCH 1.8.1 [130] biology,bioinformatics,ngs,mapping
BRATNextGen 20150505 [131] biology, bioinformatics, genomics
BreakDancer 1.4.5 [132] biology, phylogenetics
Breakseq 2.2 [133] biology, phylogenetics
Bridger 20141201 [134] NGS, Genomics, bioinformatics
BRIG 0.95 [135] biology, genomics
Bsmap 2.74, 2.87 [136] biology, bioinformatics, NGS
Bsoft 1.9.1 [137] biology, image analysis
BSseeker2 2.1.0 [138] biology, phylogenetics
Bubbleparse 20140314 [139] biology, phylogenetics
BUCKy 1.4.4 [140] biology, phylogenetics
BUSCO 2.0b, 3.01, 3.02 [141] biology, genomics
BWA 0.7.7, 0.7.8, 0.7.9a [142] biology,bioinformatics,ngs
BWA-PSSM 0.5.11 [143] phylogenetics
Bxh_xcede_tools 1.11.1 [144] biology, bioinformatics
BYOBU 5.92 [145] shell, screen, terminal
Bzip2 1.0.6 [146] archiver, library
CAFE 4.1 [147] biology, phylogenetics
Caffe 1.0, 20180607 [148] Machine Learning
Camino 20140723 [149] biology,bioinformatics,neuroscience,imaging
Cantera 2.1.1 [150] kinetics, thermodynamics
Canu 1.6, 1.7, 1.8 [151] biology, sequencing
CAP3 20120705 [152] biology,bioinformatics,assembly
Capnp 0.5.3 [153] C++
CASAVA 1.8.2 [154] biology,bioinformatics,ngs
CASM 0.2.0 [155] Statistical Mechanics
CasOFFinder 2.4 [156] phylogenetics
CAVIAR 20171218 [157] biology, phylogenetics
CD-HIT 4.6, 4.6.4, 4.6.8 [158] biology, genomics
CDO 1.7.2rc3, 1.9.4 [159] Climate
CEAS 1.0.2 [160] biology,bioinformatics,ngs,sequencing,rna-seq
CellProfiler 2.0, 2.2.0 [161] biology, phylogenetics
Cell Ranger 2.1.1, 2.2.0, 3.0.0 [162] biology, bioinformatics, ngs, rna-seq
CellRanger-DNA 1.0.0, 1.1.0 [163] biology, bioinformatics, ngs, rna-seq, 10xgenomics
Centrifuge 1.0.3 [164] biology, phylogenetics
Cerulean 0.1 [165] biology, phylogenetics
CFITSIO 3.370 [166] library, C
CGAL 4.10, 4.9 [167] library, math
CGAT 0.2.0, 0.2.3 [168] biology,bioinformatics,genomics
CGATools 1.6.0.43 [169] biology, bioinformatics, ngs
Cgmaptools 0.1.1 [170] phylogenetics
CHARMM 36a3, 43b2 [171] chemistry, simulation
CheckM 1.0.4, 1.0.7 [172] biology, genomics
ChewBBACa 0.2.5 [173] phylogenetics
Chimera 1.12 [174] biology, bioinformatics, modeling
ChromEvol 2.0 [175] Biology, NGS
CIMS 4.1.2 [176] biology,genomics
CIRCexplorer 1.1.10 [177] biology, bioinformatics, rna-seq
CIRCexplorer2 2.3.5 [178] phylogenetics
Circlator 1.5.1 [179] biology, genomics
Circos 0.63-pre11, 0.69-2 [180] biology,genomics,ngs
CIRI 2.0.6 [181] phylogenetics
CisGenome 2.0 [182] biology, bioinformatics, genomics
CisTEM 1.0.0 [183] phylogenetics
Clann 3.2.3 [184] biology,bioinformatics,phylogentics
CLARK 1.2.2-b, 1.2.3 [185] biology, genomics
CLHEP 2.2.0.1 [186] High Energy Physics
Click-demultiplex 0.1.0 [187] Machine Learning
CLIFinder 4.1 [188] biology, phylogenetics
CLIPper 1.0 [189] biology, sequencing
CLIPSeqTools 0.1.7 [190] biology, sequencing
ClonalFrame 1.1, 1.2 [191] biology,bioinformatics,ngs,phylogenetics
ClonalFrameML 1.0, 1.11 [192] biology, bioinformatics, ngs, phylogenetics
CLUMPP 1.1.2 [193] biology, bioinformatics
ClustalO 1.2.0 [194] biology, bioinformatics, alignment
ClustalW 2.1 [195] biology,bioinformatics,alignment
Cluster3 1.52a [196] biology, genomics
ClusterFinder 313 [197] biology, bioinformatics, metabolomics
Clview 20130402 [198] biology, bioinformatics
CMake 3.12.3, 3.14.5, 3.6.3 [199] Software Development
CMS 20170518 [200] biology
CMWP 140518 [201] biology, genomics
CNSpipeline 20170827 [202] phylogenetics
CNV-Sim 0.9.2 [203] biology, phylogenetics
CNVkit 0.9.0 [204] biology
CNVnator 0.3.2 [205] biology, genomics, CNV
CNV-Seq 20110715, 20140812 [206] biology,bioinformatics,genomics
Cobra-tf 0.1 [207] Nuclear Engineering
Cobrapy 0.3.2 [208] biology, bioinformatics, metabolomics, modeling
CodeBlocks 13.12 [209] programming, c++, gui
Coevol 1.3c, 1.4b [210] bio,bioinformatics,phylogenetics
Cogent 2.1 [211] biology, phylogenics
COLMAP 3.6 [212] modeling
CoMap 1.4.1 [213] Bioinformatics, Genomics
Concaterpillar 1.8a [214] phylogenetics
CONCOCT 0.3.1 [215] biology, bioinformatics, genomics
Conda 4.6.14, 4.6.3, 4.7.5 [216] programming, development, packages
CoNIFER 0.2.2 [217] biology,bioinformatics,genomics
CONN 18a [218] mri,fmri,matlab
ConPADE 1.0 [219] phylogenetics
Conpair 20161010, 20180624 [220] biology, phylogenetics
Consed 23.0, 25.0, 29.0 [221] biology, bioinformatics, genomics
CONSEL 0.20 [222] biology, phylogenetics
ContaVect 0.2 [223] biology, phylogenetics
Coot 0.8.9 [224] Modeling
Coreutils 8.23, 8.28 [225] Software tools
Corset 1.06 [226] biology, NGS
Counterr 0.1 [227] phylogenetics
CovNMR 2014 [228] Biochemistry
Cp2k 7.0.0 [229] Quantum Chemistry
CPAT 1.2.2 [230] biology, phylogenetics
CPLEX 12.6.1, 12.6.2, 12.7 [231] Meteorology
Crass 1.0.1 [232] biology, assembly
Crisflash 1.2.0 [233] phylogenetics
CRISP 20181122 [234] phylogenetics
CRISPRanalyzer 1.50 [235] biology,genomics,ngs
CRISPRCasFinder 4.2.17 [236] phylogenetics
CrossMap 0.2.3 [237] biology, genomics
Crux 1.40 [238] biology, mass-spectroscopy
CryptoMiniSat 5.0.1 [239] SAT
CryptSplice 20180111 [240] biology, phylogenetics
CUBE 4.3.4, 4.4 [241] library,c,math
Nvidia CUDA Toolkit 9.0.176, 9.1.85, 9.2.88 [242] programming, library, graphics, runtime
Cufflinks 2.2.0, 2.2.1, 2.2.1.1 [243] biology,bioinformatics,ngs,sequencing
Cutadapt 1.8.1, 2.1, 2.4 [244] biology,bioinformatics,ngs
CUTE 3.2.6 [245] astronomy
CVXOPT 1.1.8 [246] python, optimization, module
CWLtool 1.0.20181217 [247] workflow, scheduler
Cytoscape 3.4.0 [248] biology, bioinformatics, ngs, phylogenetics
Dadi 1.7.0 [249] phylogenetics
DAKOTA 6.8, 6.8-gui [250] Computational Science and Engineering
DALIGNER 1.0 [251] biology, phylogenetics
Dammit 1.0rc2 [252] biology, phylogenetics
DaPars 0.9.0 [253] biology,bioinformatics,ngs
DASTool 1.1.0 [254] biology, phylogenetics
Datamash 1.1.0 [255] math
DAWGPASW 1.0 [256] biology, phylogenetics
DBG2OLC 0.6 [257] biology, bioinformatics, NGS
DCC 0.4.4 [258] biology, bioinformatics, ngs
Dcmstack 0.6.2 [259] biology, imaging
DCMTK 3.6.0 [260] biology,neuroscience,imaging
DDocent 20160425 [261] biology
DDSCAT 7.3.0 [262] Astrophysics
DDT 6.0, 6.1.2, 7.0.4 [263] Software Development
DealII 8.3.0 [264] Library
DeconSeq 0.4.3 [265] biology, phylogenetics
DeepGS 1.2 [266] phylogenetics
DeepLabCut 2.0.7-cpu, 2.0.7-gpu [267] phylogenetics
DeepPicker 20161102 [268] particle picking
DeepTools 2.4.3, 3.1.1 [269] biology, bioinformatics, NGS
Delft3D 7545 [270] Physics
Delly 0.7.5, 0.7.7, 0.7.8 [271] biology, phylogenetics
DeNoGAP 1.0 [272] biology, phylogenetics, ngs
DeTiN 1.7.5.9 [273] ngs, genomics
DETONATE 1.11, 1.9 [274] biology, rna-seq
DEXTRACTOR 1.0 [275] biology, sequencing
Diamond 0.8.25, 0.8.5, 0.9.15 [276] computational biology, genomics
DiCal2 2.2.0.1 [277] biology, phylogenetics
DiffReps 1.55.4 [278] Bioinformatics
Dindel 1.01 [279] biology,bioinformatics,ngs,sequencing
DiscoSnp 2.2.10 [280] biology, phylogenetics
DISCOVAR de novo 52488 [281] biology, ngs, assembler
Distruct 2.2 [282] phylogenetics
DIYABC 1.0.4.43b, 2.0.3, 2.1.0 [283] biology, phylogenetics
DL_POLY 1.9 [284] Molecular Dynamics
DNA Clust 3.0 [285] biology,bioinformatics,genomics
DNA-ML 1.0 [286] Biology, NGS
DOCK 3.6, 6.7, 6.8 [287] chemistry
DosageConvertor 1.0.3 [288] biology
DOT 2.0 [289] biology,bioinformatics,docking
Doxygen 1.8.3.1 [290] programming, documentation
DRAP 1.91 [291] biology, phylogenetics
DRep 2.3.2 [292] phylogenetics
DSK 2.1.0 [293] biology, NGS
DSSAT 4.6 [294] Agriculture
DSSP 2.2.1, 3.0.0 [295] Molecular Dynamics
PHYLDOG 20130116-dbg [296] biology,bioinformatics,phylogenetics
DynamicDBG 20181003 [297] phylogenetics
Dynare 4.4.3 [298] math
EAGLE 2.0 [299] phylogenetics
Ea-utils 1.04.807.18, 1.1.2.537 [300] biology,bioinformatics,genomics,ngs
ECE 1.2 [301] ECE
ECTools 20140311, 20141201 [302] biology,bioinformatics,ngs,sequencing
EDirect 10.7, 20120820 [303] biology, phylogenetics
Edta 20190108 [304] phylogenetics
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [305] biology,bioinformatics,matlab
EGene-MVN 0.1 [306] biology, genetics
EigenMT 20160228 [307] biology, genetics
EIGENSOFT 4.2, 5.0.1, 6.0.1 [308] biology, bioinformatics
ElPrep 4.1.4 [309] phylogenetics
Emacs 25.3 [310] programming, scripting, language
EMAN2 2.11, 2.12, 2.22 [311] biology
EMBOSS 6.5.7 [312] biology,bioinformatics
EMC 9.4.3 [313] Monte Carlo Simulations
EMIRGE 20130727 [314] biology,bioinformatics,ngs
EMMAX 20100307, 20120210 [315] biology, NGS, mapping
Ensembl Tools 80 [316] biology, bioinformatics
EnTAP 0.6.1.2, 20160416 [317] biology, phylogenetics
EPACTS 3.2.6 [318] biology, bioinformatics, genomics
Epic 0.2.9 [319] Biology, Phylogenetics
Epoch 4.7.3 [320] astronomy,CCPP
EQTLA 1.1 [321] biology, bioinformatics, genomics
EQtlBma 1.2.2, 1.3.0r20140820 [322] biology, genotyping
Erpin 5.5.4 [323] biology, phylogenetics
ESOM 1.1 [324] biology, phylogenetics
ESPRESSO 5.3.0, 6.2.0, 6.2.1 [325] Quantum,modeling
ESPRIT 2009-nogap, 201102 [326] biology,bioinformatics
ETE2 2.1.539 [327] biology,phylogenetics
ETE3 3.0.0 [328] biology, phylogenetics
Eval 2.2.8 [329] biology,bioinformatics,genoimcs
Evigene 20180730 [330] phylogenetics
ExaBayes 1.5 [331] phylogenetics
ExomeCNV 1.4 [332] ngs, genomics
Exonerate 2.2.0 [333] biology,bioinformatics,genomics
EXpress 1.3.1, 1.5.1 [334] biology,bioinformatics,ngs
Face_recognition 1.2.2 [335] phylogenetics
FALCON 20161027, 20161222, 20190601 [336] biology,bioinformatics,ngs,sequencing
FALCON_unzip 20160623, 20161222 [337] biology, bioinformatics
FAR 2.15 [338] biology,bioinformatics,genomics
FAST 1.06 [339] biology phylogenetics
Fast-gep 1.0 [340] phylogenetics
FAST-iCLIP 0.9.1 [341] biology, sequencing
Fast-Plast 1.2.6 [342] biology, phylogenetics
FASTA 34.26.5, 36.3.6d [343] biology,bioinformatics,genomics
FastANI 1.1 [344] phylogenetics
FastaRegexFinder 0.1.1 [345] biology, phylogenetics
FastGEAR 20161216 [346] biology, bioinformatics, genomics
R8s 1.8 [347] phylogenetics
FastML 3.0 [348] biology,bioinformatics,phylogenetics
Fastq-tools 0.8 [349] biology, NGS,
FastQC 0.11.4, 0.11.7, 0.9.6 [350] biology,bioinformatics,ngs
Fastsimcoal 2.6.0.3 [351] biology, phylogenetics
FastSpar 0.0.4 [352] biology, genomics
FastStructure 20150112 [353] biology, genomics
FastTree 2.1.7 [354] biology,bioinformatics,phylogenetics
FastUniq 1.1 [355] biology, phylogenetics
Fastx Toolkit 0.0.13.2, 0.0.14 [356] biology,ngs
Fathmm-MKL 20150225 [357] Genomics
FcGENE 1.0.7, 1.0.7.1 [358] biology,bioinformatics,genomics,snp
Fdupes 1.51 [359] file management
FEniCS 2018.1.0 [360] biology, phylogenetics
Ferret 6.82 [361] Data Visualization and Analysis, Oceanography, Meteorology
FFmpeg 2.1.3, 2.8.3 [362] Audio, Video
FFTW 3.3.4, 3.3.6, 3.3.7 [363] library,c,math
Fgbio 0.5.0, 0.7.0 [364] phylogenetics
FGENESB 2012 [365] biology,bioinformatics,ngs
FGMP 1.0.1 [366] phylogenetics
Fiji 2.0.0rc59 [367] ImageJ
Filtlong 0.2.0 [368] biology, phylogenetics
FineSTRUCTURE 2.0.7, 2.1.3 [369] biology, population genetics
Flappie 1.1.0 [370] phylogenetics
FLASh 1.2.10, 1.2.11 [371] biology, genomics
FLEA 2.0.0 [372] phylogenetics
Flex 2.6.4 [373] programming tool
Flexbar 2.3, 2.34 [374] biology, bioinformatics, genomics, ngs
FLEXLm 1.0 [375] Administration
Fluent 17.2, 19.1 [376] CFD
Flye 2.3.3 [377] Biology, NGS
FMRIPrep 1.3.2, 1.4.0a1 [378] data mining
Pascal 3.0.0 [379] Compiler, Programming
Fqtools 20160224 [380] biology,bioinformatics,ngs,sequencing
FragGeneScan 1.16 [381] biology,genomics
FRAMA 20151019 [382] biology
FrameDP 1.2.2 [383] biology, sequencing
Frealign 9.11 [384] Image Reconstruction
FreeBayes 1.2.0-20180409, 1.3.1, v0.9.15-1-g076a2a2 [385] biology,genomics
FREEC 11.0, 9.6 [386] biology, sequencing
Freesurfer 5.2.0, 5.3.0, 6.0.0 [387] biology,bioinformatics,neuroscience,imaging
FSL 5.0.8, 5.0.9, 6.0.1 [388] biology,bioinformatics,neuroscience,imaging
FusionInspector 1.1.0 [389] biology, phylogenetics
GAL 20180906 [390] phylogenetics
Galaxy 1.0 [391] biology,bioinformatics
GAMBIT 15.1.0, 16.0.0 [392]
GAML 20150610 [393] biology, bioinformatics, genomics
GapCloser 1.12r6 [394] biology, genomics, ngs
GapFiller 1.10, 1.11 [395] biology, genomics
GARLI 2.0, 2.01 [396] biology,bioinformatics,phylogeny
GARM 0.7.4 [397] biology,bioinformatics,genomics,assembly
GASVPro 201310 [398] biology, bioinformatics, ngs
GATE 7.0 [399] Date analysis and visualization
GATK 4.1.1.0, 4.1.2.0, 4.1.3.0 [400] biology,bioinformatics,ngs
Gaussian 09, 09 A.02, 09 D.01 [401] Computational Chemistry
Gawk 4.2.0 [402] Software tools
Gblocks 0.91b [403] biology,bioinformatics
GNU Compiler Collection 6.3.0, 7.3.0, 8.2.0 [404] compilers
GCTA 1.24.7, 1.26.0 [405] biology, genomics, SNP,
GDAL 2.2.1, 2.2.4, 2.3.1 [406] Geospatial library
GDB 8.3 [407] Software Development
GDC-Client 1.0.1 [408] biology, bioinformatics, sequence, ngs
GDSL 1.18 [409] library
Geant4 4.10, 4.10.03, 4.10.5 [410] Physics
GEM 20130406 [411] biology,bioinformatics,ngs,sequencing
Gem5 2.0 [412] Computer Simulator
GEMINI 0.13.1, 0.18.0, 0.6.4 [413] biology,genomics,genetics
GEMMA 0.98.1 [414] phylogenetics
NCBI GenBank Tools 20140130 [415] Biology,bioinformatics,NCBI,GenBank
GeneMark-ES 4.33 [416] biology, genomics
GeneMarkS 2012.04, 3.10.001 [417] biology,genomics
GenePainter 2.0.4 [418] biology, phylogenetics
GeneSeqer 2014-02-26 [419] biology, genomics
Genesum 0.1.0 [420] biology,genomics
GeneTorrent 3.8.7 [421] biology,bioinformatics,data download
GenGen 1.0.1 [422] biology, phylogenetics
Genome_Graph_Annotation 20190131 [423] phylogenetics
Genome STRiP 2.00.1602 [424] biology, genomics, ngs
GenomeTools 1.5.7, 1.5.9 [425] biology, bioinformatics
Genomic-fluidity 20151109 [426] phylogenetics
GenomicNeuralnet 20161030 [427] phylogenetics
GenomicConsensus 2.3.3 [428] biology, phylogenetics
GenomicTools 2.7.0 [429] biology,bioinformatics,ngs,chip-seq,rna-seq
GenotypeHarmonizer 1.4.18 [430] biology, bioinformatics
Genrich 0.5 [431] phylogenetics
GenSel 4.90 [432] population genetics
Geopython 1.0.0 [433] python, geospatial, cartography
GEOS 3.3.8, 3.6.2 [434] library, data
GeP 2.1 [435] biology, phylogenetics
Get_homologues 20150529 [436] biology, genome
Gffread 0.9.8c [437] biology, bioinformatics
Gflags 2.2.1, 20150520 [438] google,libraries
GFOLD 1.1.4 [439] biology, RNA-seq
Ghmm 0.9rc3 [440] library
Ghostscript 9.21 [441] PDF
Git 2.14.1 [442] Revision Control
GKNO 1.30.18 [443] biology,genomics
Glimmer 3.02 [444] biology, microbial annotation
GlimmerHMM 3.0.4 [445] biology, microbial annotation
Globus 1.10.1, 2.1.3 [446] Data Transfer
Glog 0.3.5 [447] google,libraries
GLPK 4.55, 4.65 [448] Programming
GMAP 20180212, 20180212_sse2, 20190610 [449] biology, bioinformatics, genomics, ngs
GMcloser 1.6 [450] Biology, NGS
GMP 6.1.2 [451] library, crypto
GnuPlot 4.6.0, 5.2.2, 5.2.3 [452] graphics,plotting,math
Go 1.10, 1.11.1 [453] programming language
Grace 5.1.22 [454] graphics, statistics, 2D
GRACKLE 3.1 [455] library,c,astrophysics
GrADS 2.0.1 [456] environment, grid analysis
Graftm 0.12.2 [457] phylogenetics
GramCluster 1.3 [458] biology,sequencing,
GraPhlAn 0.9.7 [459] biology, phylogenetics
GraphMap 0.4.0 [460] biology, nanopore sequencing
GraphViz 2.38.0 [461] biology,bioinformatics,neuroscience,imaging
GRASS 7.0, 7.4 [462] Geography
Grf 1.0.0 [463] genomics, bioinformatics
Grib_api 1.10.1, 1.15.1, 1.26.1 [464] C, fortran, library
GROCSVs 0.2.5 [465] phylogenetics
GROMACS 2018.0, 2019.2 [466] Computational Chemistry, Molecular Dynamics
GroopM 0.3.5 [467] biology, phylogenetics
Groovy 2.4.15 [468] Programming
Gscripts 1.1 [469] scripts
GSEA 3.0.0 [470] biology, bioinformatics, genomics
GSL 2.2.1, 2.4, 2.5 [471] library, data
GSNP 1.0 [472] biology,bioinformatics,ngs
Gsutil 4.15 [473] cloud, storage, google
GTDBTk 0.1.3 [474] phylogenetics
GUAVA 1.0 [475] phylogenetics
Gubbins 20150519, 20150902, 20160421 [476] biology, bioinformatics, genomics, phylogenetics
Guile 2.2.2 [477] Programming Language
GULP 4.4, 5.0 [478] Material Science
Guppy 3.1.5, 3.2.1, 3.2.2 [479] phylogenetics
HALC 1.1 [480] biology, phylogenetics
HaMStR 13.2.3, 13.2.4, v8b [481] biology, genome
HapCompass 0.7.7 [482] ngs, genomics
HAPCUT 0.7 [483] biology, assembly
HAPLOSWEEP 1.0 [484] biology, phylogenetics
HapQTL 1.00 [485] biology
Hapsembler 2.21 [486] biology, bioinformatics, assembly
HapTree 1.0 [487] ngs, genomics
HDF4 4.2.11 [488] library, data
HDF5 1.8.19, 1.8.20, 1.8.9 [489] library, data
HECIL 20180926 [490] phylogenetics
HelitronScanner 1.1 [491] phylogenetics
HGCoLoR 1.1.1 [492] phylogenetics
HGTFinder 20160720 [493] biology, genomics
HISAT2 2.0.4, 2.0.5, 2.1.0 [494] Biology, Sequence Alignment, NGS
HLAHD 1.1.1 [495] biology, phylogenetics
HLAminer 1.3.1 [496] biology, phylogenetics
HMM-FRAME 20140724 [497] phylogenetics
HMMER 3.1b1, 3.1b2, 3.2.1 [498] biology, genome
HMMSplicer 0.9.5 [499] biology,bioinformatics,ngs
HomBlocks 1.0 [500] biology, phylogenetics
HOMER 4.6, 4.7, 4.8 [501] biology,bioinformatics,sequence,ngs
HOOMD 2.1.7 [502] library, math
HPL 2.1 [503] parallel programming, benchmarks, MPI
HTMLDoc 1.8.28, 1.9.3 [504] pdf, docs, html
HTSeq 0.5.3p3, 0.6.1p1, 0.9.1 [505] biology, bioinformatics, ngs
Humann2 0.11.2, 2.8.1 [506] phylogenetics
Hyb 20141126 [507] biology, ngs, RNA-Seq
HybPhyloMaker 1.5 [508] biology, phylogenetics
HybPiper 1.2 [509] biology, phylogenetics
HyPhy 2.1.2.28, 2.2.6.1, 2.3.13 [510] biology,bioinformatics,evolution
IAnnotateSV 1.0.6, 1.0.9 [511] Biology, Phylogenetics
IAssembler 1.3.2 [512] biology, assembly
Ibdne 20150815 [513] biology,ngs
ICallSV 0.0.6 [514] Biology, Phylogenetics
ICLIPro 0.1.1 [515] biology,
Icommands 3.3.1 [516] iRods
ICORN2 0.95 [517] biology, sequencing
IDBA-MT 1.0 [518] biology,NGS
IDBA-UD 1.1.1, 1.1.1-512, 1.1.1-512-mem [519] Genomics, bioinformatics, phylogenetics
IDL 8.3 [520] language, programming, science
IDP-fusion 1.1.1 [521] biology, phylogenetics
IEP 3.6 [522] programming, python, qt
IGB 8.4.1 [523] biology, bioinformatics, genomics
IgBLAST 1.5.0, 1.7.0 [524] biology, bioinformatics
IGTP 1.1 [525] biology, bioinformatics, phylogenetics
IGV 2.3.91, 2.4.16 [526] biology, bioinformatics, ngs, phylogenetics
Illumina-utils 2.0.2, 2.3 [527] biology
Illumiprocessor 20150803 [528] biology, sequencing
IM and IMa 20091217 [529] biology,bioinformatics,population genetics
Ima2 20120827 [530] biology,bioinformatics,population genetics
IMa2p 20170712 [531] biology, phylogenetics
ImageJ 1.48 [532] imaging
ImageMagick 7.0.8-20 [533] Imaging
IMOD 4.7.15, 4.9.10 [534] 3D modeling, image reconstruction
Intel MPI 5.1.1 [535] parallel programming, development, MPI, library
Infernal 1.1.1 [536] biology, sequence alignment
INLA 20160718, 20170620 [537] statistics, modeling, R
InParanoid 4.1 [538] biology, biology
Intel Compilers and Libraries 2018.1.163, 2019, 2019.1.144 [539] programming languages, development, library, math, intel
Intervene 0.6.2 [540] biology, phylogenetics
IOAPI 3.1, 3.2 [541] Meteorology
IPOPT 3.12.10, 3.12.6 [542] library, c/c++,math, solver, optimization
InterProScan 5.31-70.0, 5.34-73.0, 5.35-74.0 [543] biology,bioinformatics
Ipyrad 0.7.24, 0.7.30 [544] biology, bioinformatics, NGS
IQ-TREE 1.6.6, 1.6.7, 1.6.9 [545] biology, phylogenetics,
IRAP 0.8.1p7 [546] biology, ngs, pacbio
IRep 20161025 [547] biology, microbiology
IRFinder 1.0.0, 1.2.0 [548] biology, RNA-Seq
IsoSeq3 0.7.2, 3.0.0, 3.1.0 [549] biology, bioinformatics, ngs, pacbio
ISOWN 20180820 [550] phylogenetics
IsPcr 3.3 [551] biology, phylogenetics
ITK 3.20.1, 4.10.1 [552] Bioinformatics
ITK-SNAP 3.0.0 [553] biology,bioinformatics,neuroscience,imaging
Jabba 1.0 [554] biology, phylogenetics
JACUSA 1.2.0 [555] biology, bioinformatics, ngs, phylogenetics
JAGS 3.3.0, 3.4.0, 4.2.0 [556] Statistics
NpScarf 1.7 [557] phylogenetics
JDK 1.8.0_31, 11.0.1, 9.0.1 [558] programming,runtime
JCVI 0.8.12 [559] phylogenetics
Je 1.0 [560] biology, NGS
Jellyfish 2.2.4, 2.2.6, 2.3.0 [561] biology,ngs
JModelTest 2.1.1 [562] biology, bioinformatics, genomics, phylogenetics
Julia 0.4.6, 0.6.4, 1.0.0 [563] programming, language, statistics
Jupyter 5.6.0, 5.7.0, 5.7.8 [564] python, R, jupyter
JVARKIT 20180405 [565] biology, phylogenetics
Kaiju 1.6.2 [566] biology, phylogenetics
KaKs 1.2, 2.0 [567] biology, bioinformatics, evolution, phylogenetics
Kallisto 0.42.4, 0.43.0, 0.44.0 [568] biology,NGS,RNA-Seq
KAT 2.3.4 [569] biology, phylogenetics
Kent 20120524, 20141111, 20180816 [570] Genomics, bioinformatics
Khmer 1.1, 2.0, 2.1 [571] Biology, NGS
KIM 1.8.0, 1.8.2, 1.9.3 [572] Simulation
KINFIN 1.0.1 [573] biology, phylogenetics
KING 1.4.9, 1.9, 2.1.2 [574] biology, genome, gwas
KisSplice 2.4.0-p1 [575] biology, RNA
KMC 3.1.0 [576] phylogenetics
Kmer 1934 [577] biology,bioinformatics,ngs,sequencing
KmerGenie 1.6741 [578] bioinformatics,ngs
Kraken 1.0, 2.0.6b, 2.0.8b [579] biology, ngs
Krocus 1.0.1 [580] phylogenetics
Krona 20161019 [581] biology, bioinformatics
Ksnp 3.021 [582] biology, phylogenetics, SNP
Lace 0.99 [583] biology, NGS
LACHESIS 2.1 [584] phylogenetics
Lambda 0.9.4 [585] biology, sequencing, phylogenetics
LAMMPS 22Aug18, 30Jul16, 7Dec15 [586] Molecular Dynamics
LAMP 2.5 [587] biology, bioinformatics, genomics
Last 801, 916, 979 [588] biology,bioinformatics,sequence,alignment
LASTZ 1.02.00, 1.03.02, 1.04.00 [589] biology,bioinformatics,ngs
Lbzip 2.5 [590] compression
LDhat 2.2a [591] biology,genomics
LEfSe 20180219 [592] phylogenetics
LFMM 1.4, 1.5 [593] biology, phylogenetics
ChartDirector 5.1.0 [594] library, data
Gdata 2.0.18 [595] library, google
Libint 2.5.0, 2.5.0b [596] library
LEMON 1.2.3 [597] library
Libunistring 0.9.7 [598] library
Libvips 8.5.4 [599] image processing
LIBXC 4.2.3, 4.3.4 [600] library, density function
LIBXSMM 1.13 [601] library,c,math
LIBZMQ 4.3.1 [602] library
LIGR 2.05 [603] biology,assembly
LINKS 1.8.5, 1.8.6 [604] biology, genomics
Linksbrowser 2.14 [605] web browser
LMAP 1.0.2 [606] biology, phylogenetics
LncScore 1.0.2 [607] biolgoy, phylogenetics
LobSTR 4.0.6 [608] biology, phylogenetics
LocusZoom 1.4 [609] phylogenetics
LoFreq 2.1.3.1 [610] phylogenetics
LongRanger 2.1.5, 2.2.2 [611] biology, phylogenetics
LORMA 0.3, 0.5 [612] biology, ngs, pacbio
LS-DYNA 700, 711, 901 [613] Physics
LSC 1alpha, 1beta, 2.0 [614] biology, bioinformatics, ngs
Ltr_finder 1.07 [615] biology, phylogenetics
LTRRetriever 2.1, 2.5, 20170514 [616] biology, phylogenetics
Lua 3.5.2 [617] programming, scripting, language
Lumpy-sv 0.2.1, 0.2.13 [618] biology, genotyping
LZO 2.09 [619] library, compression
M5nr 20121126 [620] biology, bioinformatics, genomics
MACE 1.2 [621] phylogenetics
MACH 1.0.18 [622] biology,bioinformatics,genomics,ngs
Mach2VCF 20150515 [623] biology
MACS 1.4.3, 2.0.10, 2.1.2 [624] biology, bioinformatics, CHiP-Seq
MAFFT 7.245, 7.294, 7.397 [625] bio,bioinformatics,sequence
MafTools 0.1 [626] phylogenetics
MAGeCK 0.5.7 [627] phylogenetics
Majiq 1.0.5 [628] biology, phylogenetics
Maker 2.25b, 2.31.10, 2.31.6 [629] biology,bioinformatics
MAnorm 20120316 [630] biology, phylogenetics
Manta 1.2.2 [631] biology, phylogenetics
Mantis 1.0.4 [632] phylogenetics
MapSplice 2.1.5, 2.1.7 [633] biology,ngs,rna-seq
MapThin 1.11 [634] phylogenetics
Maq 0.7.1 [635] biology,bioinformatics,ngs
MarginPolish 1.0.0 [636] phylogenetics
MARK 2.0.1 [637] application, data, capture
MarkerMiner 20150429, 20150511, 20150710 [638] biology, bioinformatics, genomics
MaryGold 0.2 [639] biology, phylogenetics
Mash 1.1 [640] biology, genomics
MASSMINE 0.10.0, 0.11.0, 0.9.5 [641] data mining
MaSuRCA 3.2.1, 3.2.4, 3.3.0 [642] biology, bioinformatics, short read alignment
MATLAB 2018a, 2018b, 2019a [643] math,language
MATS 3.2.5, 4.0.1, 4.0.2 [644] biology,bioinformatics,ngs,rna-seq
Mauve 2.3.1 [645] biology,ngs,genomics
Mawk 1.3.4-20150503 [646] programming language
Maxbin 2.1.1 [647] biology,NGS
Maxima 5.41.0 [648] Math
MC 4.6.1 [649] shell
MCarts 1.0.2 [650] biology, genomics, markov
Mccortex 1.0 [651] phylogenetics
MCL 12-135, 14-137 [652] biology, genomics
MCNP 6, 6.1 [653] Physics
MCNPX 2.7.0 [654] Physics
MCR 2016b, 2017a, 2018a [655] math, language
MCScanX 20130328 [656] biology, phylogenetics
MECAT 20180308 [657] phylogenetics
Medaka 0.2.0, 0.6.2, 0.7.1 [658] biology, phylogenetics
Medusa 1.6 [659] phylogenetics
MEGA 7.0.26 [660] biology, phylogenetics
Mega2 4.9.2 [661] biology, phylogenetics
MEGAHIT 1.1.1, 1.1.4 [662] biology, phylogenetics
MEGAN 5.10.3, 6.4.15 [663] biology, bioinformatics, ngs
Megraft 1.0.2 [664] biology,sequencing,
MELTING 4.3.1 [665] biology, genome, RNA, folding
MEME 4.9.1, 5.0.2, 5.0.5 [666] biology,bioinformatics,sequence
MentaLiST 0.1.3 [667] biology, phylogenetics
Meraculous 2.0.5 [668] Biology,NGS
Mercurial 4.8.2 [669] Revision Control
Merlin 1.1.2 [670] biology,SNP
Meta-Tissue 0.4 [671] biology, genetics
MetaBAT 0.32.4, 2.13 [672] biology, genomics
Metabin 1.0 [673] Genomics, bioinformatics, metagenomics
MetaCherchant 0.1.0 [674] biology, phylogenetics
MetaCluster 5.0b [675] biology,bioinformatics,genomics
MetaCV 2.3.0 [676] Biology, NGS
MetaGeneMark 2.10, 3.26 [677] biology,genomics
METAL 20110325 [678] biology, ngs, genomics
MetAMOS 1.3.1, 1.5.0rc4-20140827 [679] biology,bioinformatics,genomics,assembly
METANNOT 20171129 [680] phylogenetics
Metaphinder 20161215 [681] biology, phylogenetics
MetaPhlAn2 2.7.7 [682] biology, phylogenetics
Metassembler 1.5 [683] biology,genomics
MetaSV 0.5.4 [684] biology, phylogenetics, NGS
MetaVelvet 1.2.06 [685] computational biology, genomics
Metaxa2 2.1.1, 2.1.3 [686] biology,bioinformatics,ngs,sequencing
Methylpy 1.2.9 [687] Biology, Phylogenetics
METIS 5.1.0 [688] software
Mfannot 20180405 [689] biology, phylogenetics
Mfold 3.6 [690] bioinformatics,structure,RNA
Mg-rast 20150919 [691] biolgoy, genomics
MGEScan 20160416 [692] biology, genomics
MHAP 1.6 [693] biology, sequencing
MIA 20130201 [694] biology, ngs
MicrobeCensus 1.0.7 [695] biology, NGS
MIDAS 20160830 [696] biology, phylogenetics
MIGRATE-N 3.3.0, 3.6.6, 4.2.14 [697] biology,bioinformatics,population genetics
Minced 0.2.0 [698] biology, genomics
Miniasm 0.2-r168, 0.3-r179 [699] biology, phylogenetics
MiniCaller 20161201 [700] biology,bioinformatics,ngs,phylogenetics
Minimac2 1-20130717, 2-20140915, 3-20150727 [701] biology, NGS,
Minimap 2.17, 2.1t, 2.9-r720 [702] biology, phylogenetics
MinPath 1.4 [703] biology, phylogenetics
MIRA 4.0.2, 4.0.rc1, 4.9.6 [704] biology,bioinformatics,genomics,assembly
MiRanda 1.9 [705] phylogenetics
MiRBShunter 0.2 [706] phylogenetics
Mirdeep 0.1.0, 0.1.1 [707] phylogenetics
MIReNA 2.0 [708] biology, phylogenetics
MiRge 2.0 [709] phylogenetics
Misa 1.0 [710] biology, bioinformatics, genomics
MISO 0.4.9, 0.5.2, 0.5.3 [711] biology,bioinformatics,ngs,sequencing,rna-seq
MITE-Hunter 20111101 [712] biology, phylogenetics
MitoFinder 1.0.2 [713] phylogenetics
MiXCR 2.1.8 [714] biolgoy, phylogenetics
MKL 2016.0.109, 2017.1.132, 2018.1.163 [715] programming, development, library, math, intel
Mlcoalsim 1.9916b [716] biology, phylogenetics
Mlst 2.15.2 [717] phylogenetics
Mlstcheck 2.1 [718] phylogenetics
MMSEQ 1.0.8 [719] biology,bioinformatics,genomics
MOABS 1.2.9, 1.3.2, 1.3.4 [720] biology, ngs
MOCAT 1.3r2, 2.0 [721] biology, genomics
MODELLER 9.11, 9.13, 9.14 [722] biology,bioinformatics,modelling,structure
MODELTEST 0.1.2 [723] biology, phylogenetics
Molden 5.0 [724] Molecular, Electronic Structure
Mono 5.18 [725] linux, runtime
Monolix 4.3.2 [726] modeling, pharmacokinetics
MOOSE 20180404 [727] physics, simulation
MOSAIK 2.1.33, 2.2.3, 2.2.30 [728] biology,bioinformatics,short read alignment
Mosdepth 0.2.3 [729] biology, phylogenetics
MOST 20160721 [730] biology, sequencing
Mothur 1.37.0, 1.38.1, 1.41.3 [731] biology, microbial ecology
MotionCor2 1.1.6e [732] Motion Correction
MOTU 1.1 [733] biology, bioinformatics, genomics
MountainSort 0.9.0 [734] library
MPACK 0.8.0 [735] library
MPB 1.5 [736] library, math
MPBoot 1.1.0 [737] biology, phylogenetics
MP-EST 1.4, 1.5 [738] biology,bioinformatics,ngs,sequencing
MPFR 3.1.6 [739] library, math
Mpinterfaces 20170613 [740] DFT
MrBayes 3.2.4, 3.2.5, 3.2.6 [741] application, biology, phylogenetics
MRIcroGL 20180623 [742] biology, mri, imaging
MRIcron 201306, 20161012 [743] biology, mri, imaging
Mriqc 0.11.0 [744] mri, imaging, biology
MRtrix 3.0rc2 [745] biology, mri, imaging
Ms 20171108 [746] phylogenetics
MSINGS 20180810 [747] phylogenetics
MSMBuilder 2.5.1 [748] biology, bioinformatics, bayesian
MstatX 1.0 [749] biology, phylogenetics
Msvar 1.3 [750] biology,bioinformatics,population genetics
MTG2 2.15 [751] phylogenetics
Mugsy 1.2.3 [752] biology, phylogenetics
MultiGeneBlast 1.1.13 [753] phylogenetics
MultiQC 1.1, 1.5 [754] biology, bioinformatics, CHiP-Seq
MUMmer 3.23, 4.0.0beta2 [755] biology,bioinformatics,genomics
MUSCLE 3.8.31 [756] biology, bioinformatics, alignment
Musket 1.1 [757] biology, genomics, ngs
MuTect 1.1.4, 1.1.7 [758] biology,genomics
MutSig 1.4, 1.41 [759] biology,genomics
MyCC 20150710 [760] biology, genomics
MZMine 2.37, 2.38, 2.41 [761] biology, bioinformatics, spectrometry, NMR
NAMD 2.12, 2.13 [762] Molecular Dynamics
NANO 2.8.2 [763] Text Editor
Nanocorrect 20150727 [764] biology,NGS
Nanofilt 20180408 [765] biology, bioinformatics
Nanopack 1.0.0 [766] phylogenetics
NanoPlot 1.0.0 [767] Biology, Plotting
Nanopolish 0.11.1, 20150904, 20171006 [768] biology
NanoSV 1.2.0, 1.2.3 [769] biology, genomics
NanoVar 1.0.1 [770] phylogenetics
NBODY 6 [771] Astronomy
Ncbi-vdb 2.6.3, 2.8.2 [772] SRA toolkit library
NCBI BLAST+ 2.6.0, 2.7.1, 2.8.1 [773] biology, bioinformatics
NCBI C++ Toolkit 12.0.0, 21.0.0, 7.0.0 [774] Biology,bioinformatics,NCBI,programming,library,cpp
Ncftp 3.2.5 [775] file transfer
NCL 6.1.2, 6.3.0 [776] Atmosphere Science
NCO 4.2.1, 4.4.3 [777] data tools
Ncview 2.1.2, 2.1.7 [778] data visualization
Neat-genreads 20171102, 20190331 [779] biology, bioinformatics, phylogenetics
Necklace 1.00 [780] biology, phylogenetics
NeEstimator 2.01, 2.1 [781] Biology, Bioinformatics
Neovim 0.2.0 [782] editor, text, ide, vim
NetCDF 4.3, 4.3.3, 4.4.3 [783] data, exchange
NetCDF-C 4.4.1.1, 4.5.0, 4.6.1 [784] data, exchange
NetCDF-Fortran 4.4.3, 4.4.4 [785] data, exchange
NetLogo 5.3.64 [786] modeling
NEURON 7.4, 7.6.2 [787] biology, neuroscience
Newbler 2.7, 2.8, 2.9 [788] biology,bioinformatics,ngs,454,assembly,denovo
Newick_utils 1.6 [789] biology, phylogenetics
Newick-utils 1.6 [790] biology, bioinformatics, genomics, phylogenetics
Nextallele 20140718 [791] Biology, Genomics
Nextflow 0.32.0, 18.10.1, 19.04.1 [792] biology, bioinformatics, workflow
NextGenMap 0.5.3, 0.5.5 [793] biology, bioinformatics, ngs
Nexus Class Library (NCL) 2.1.18 [794] biology,bioinformatics,evolution
NGmerge 0.3 [795] phylogenetics
Ngmlr 0.2.6, 0.2.7 [796] biology, phylogenetics
NGS-SDK 1.2.4, 1.3.0 [797] biology,bioinformatics,ncbi,sdk,library
Ngs-bits 0.1 [798] biology, sequencing
NgsCAT 0.1 [799] biology,bioinformatics,ngs
Ngscheckmate 1.0 [800] phylogenetics
Ngstools 20150816 [801] biology, ngs
NGSUtils 20130722, 20150206, 20160507 [802] biology, ngs
Nipype 0.8, 0.9.2, 1.2.0 [803] biology, bioinformatics, neuroscience, imaging
NMRPipe 7.9, 8.2 [804] Biochemistry
NONMEM 7.2, 7.3.0 [805] Modeling
NORGAL 1.0.0 [806] phylogenetics
Novoalign 2.08.02, 3.00.02 [807] biology,bioinformatics,ngs
NOVOPlasty 3.2 [808] phylogenetics
NtEdit 1.2.1 [809] phylogenetics
NucDiff 2.0.2 [810] phylogenetics
NucleoATAC 0.3.1 [811] biology, bioinformatics
Nullarbor 1.41 [812] biology, phylogenetics
Numba 0.36.2, 0.43.1 [813] Compiler
NUPACK 3.2.2 [814] phylogenetics
NWChem 6.8 [815] Chemistry
NxTrim 0.4.1 [816] biology, bioinformatics, ngs
Oases 0.2.08 [817] biology,ngs,assembler
Obitools 1.2.11 [818] biology, bioinformatics, phylogenetics
OCaml 4.02.3 [819] programming languages, scripting, development
OCOCO 0.1.2.6 [820] biology, phylogenetics
Octave 3.6.4 [821] numerical computation
Olego 1.1.2, 1.1.5, 1.1.6 [822] biology,bioinformatics,ngs,rna-seq
OmicsBox 1.1.78 [823] Image Processing
OMindel 20180129 [824] phylogenetics
OMSV 1.0.1 [825] phylogenetics
Oncotator 1.5.2.0, 1.5.3.0, 1.8.0.0 [826] biology,genomics
Ont_tutorial_cas9 20190705 [827] phylogenetics
OPENACC 16.7 [828] Programming, Accelerator toolkit
OpenBabel 2.3.2, 2.4.1 [829] biology, bioinformatics
OpenCL 18.1.0.013 [830] phylogenetics
OpenCV 2.4.13, 2.4.8 [831] Computervision
OpenFOAM 4.1, 5.0 [832] Computational Fluid Dynamics
OpenMPI 3.1.0, 3.1.2, 4.0.0 [833] parallel programming, development, MPI, library
OpenSlide 3.4.1 [834] imaging
Opera 2.0.6 [835] biology, phylogenetics
OptiType 1.3.1 [836] biology, phylogenetics
Orange3 3.3.6 [837] data mining
ORCA 4.0.1.2 [838] Molecular, Electronic Structure
OrganellePBA 20180904 [839] phylogenetics
OrthoFinder 2.2.6, 2.2.7, 2.3.3 [840] biology, ngs
OrthoMCL 2.0.3, 2.0.7 [841] biology,genomics
OTB 5.8.0 [842] Geospatial Data Modeling
P4est 1.1 [843] Library
P4vasp 0.3.29, 0.3.30 [844] Molecular, Electronic Structure
P53MH 20020901 [845] biology, DNA-sequencing
P7zip 9.20.1 [846] archiver
PacBio 5.0.1.9585, 7.0.0.63985, 7.0.1.66975 [847] biology, bioinformatics, ngs
Package-GFE 20150701 [848] biology,genomics
PALADIN 1.3.1 [849] biology, phylogenetics
PALES 122 [850] physics
PAML 4.8a, 4.9a, 4.9h [851] biology, phylogenetics
Pandaseq 20140808, 20150627 [852] biology,bioinformatics,ngs,sequencing
Pandoc 2.2.2.1 [853] Converter
PanX 1.6.0 [854] phylogenetics
PAPI 5.5.1 [855] programming interface, performance analysis
Parallel 20150122, 20170322 [856] shell, process management
Paralyzer 1.5 [857] phylogenetics
ParaView 5.3, 5.4.0, 5.4.1 [858] Data Analysis
PARSIMONATOR 1.0.2 [859] biology, bioinformatics
Parsnp 1.2 [860] biology, phylogenetics
PartitionFinder 2.0.0-pre8, 2.1.1, 2.1.1-20161205 [861] biology,phylogenetics,evolution
PASA 2.0.2-r20150209, 2.0.2-r20151207, 2.2.0-r20171013 [862] biology, bioinformatics, genomics, ngs
PASTA 20160616 [863] biology, sequence alignment
PATHd8 1.0 [864] biology, phylogenetics
PAUDA 1.0.1 [865] biology,bioinformatics,ngs,phylogenetics
PAUP 4.0a165, 4.0b10 [866] inferring and interpreting phylogenetic trees
Pauvre 0.1.86 [867] biology, phylogenetics
Pbalign 20160921, 20161221 [868] biology, bioinformatics
Pbcommand 20151203 [869] biology,API
Pbcore 20151201 [870] biology,bioinformatics
PBJelly 15.2.20, 15.8.24, 20140305 [871] biology,bioinformatics,ngs
Pbrt 20181017 [872] phylogenetics
Pbsmrtpipe 0.63.0, 20151202 [873] biology,API
Pbtranscript-tofu 20150317, 20160119 [874] biology, bioinformatics, ngs, pacbio
PCIT 2014 [875] Bioinformatics
PCRE 8.38, 8.39 [876] perl, library
PDA 1.0.3 [877] biology, phylogenetics
Pdb2pqr 2.1.0 [878] protein, modeling, pdb
Program Database Toolkit 3.20, 3.22, 3.24 [879] programming languages, development, performance analysis
PeakSplitter 1.0 [880] biology, bioinformatics, CHiP-Seq
PEAR 0.9.2 [881] biology, genomics, ngs
PECaller 1.0.0 [882] biology, NGS
PEER 20120508 [883] biology
PennCNV 1.0.5 [884] phylogenetics
Perl 5.16.0, 5.20.0, 5.24.1 [885] programming,scripting,language
PerM 0.4.0 [886] biology,bioinformatics,ngs,mapping
PETSc 3.8.1, 3.8.3, 3.8.4 [887] Math, Numerical Solvers
PfamScan 1.3, 1.5 [888] biology, genome
PGDSpider 2.0.9.0 [889] biology, NGS
PHASE 2.1.1 [890] phylogenetics
PHAST 1.4, 1.5 [891] biology,phylogeny
Phenix 1.10.2155, 1.8.1069 [892] crystallography
PHI 3.1.1, 3.1.2b [893] Calculations
PHITS 2.76, 2.82, 2.84 [894] Physics
PHLAWD 20170427 [895] biology, phylogenetics
Phonopy 1.9.2 [896] chemistry,phonon calculations
PhotoScan 1.4.1, 1.4.5 [897] Image Processing
Photutils 0.5 [898] astronomy, photometry
Phycas 1.2.0 [899] biology, bioinformatics, phylogenetics
PHYLIP 3.696 [900] biology,phylogenetics
PhyloBayes 3.3f [901] biology,bioinformatics,phylogenetics
Phylonet 3.5.7 [902] biology, phylogenetics
PhyloParser 20180404 [903] phylogenetics
PhyloSift 1.1 [904] biology, genomics, phylogenetics, taxonomy
Phyluce 20180413, 20180727, 20190308 [905] biology,bioinformatics,ngs,sequencing
PhyML 3.0, 3.1 [906] biology,bioinformatics,phylogenetics
PHYUTILITY 2.7.1 [907] biology, bioinformatics
Phyx 20190403 [908] phylogenetics
PIA2 20180305 [909] biology, phylogenetics
Picard-tools 2.5.0, 2.9.0, 2.9.2 [910] biology,bioinformatics,ngs
PICRUSt 1.0.0, 1.1.0, 1.1.3 [911] biology, phylogenics
Piggy 20171220 [912] biology, bioinformatics, ngs
Pigz 2.4 [913] Compression
PILON 1.22 [914] biology, bioinformatics, ngs, phylogenetics
Pindel 0.2.5b8 [915] biology, phylogenetics
Pipe-clip 1.1.0 [916] biology,NGS
PiPipes 1.5.0 [917] phylogenetics
Pipits 1.3.6, 1.4.0 [918] biology, sequencing
Piranha 1.2.1 [919] biology,phylogenetics
PIRS 2.0.2 [920] biolgoy, phylogenetics
Plasflow 1.1 [921] biology, phylogenetics
PLAST 1.0 [922] biology,bioinformatics
Platanus 1.2.4 [923] phylogenetics
Platypus 0.8.1 [924] biology,bioinformatics,ngs
PLEK 1.2.2 [925] biology, phylogenetics
Plink 1.90b3, 1.90b3.39, 2.00a2 [926] biology,bioinformatics,genomics,phylogenetics
Plinkseq 0.10 [927] biology, bioinformatics, library
PloidyNGS 3.1.2 [928] phylogenetics
PluMiST 1.1 [929] biology,genomics,phylogenetics
PolyPHen 2.2.2.r405b [930] biology, genomics
Pomoxis 0.1.11 [931] biology, phylogenetics
Ponytools 0.1 [932] biology, genomics
PopLDdecay 3.40 [933] phylogenetics
Popoolation 1.2.2 [934] biology, phylogenetics
Porechop 0.2.3, 0.2.4 [935] biology, bioinformatics
Poretools 0.5.0 [936] biology,
PosiGene 20171113 [937] biology, phylogenetics
POTION 1.1.2 [938] phylogenetics
POV-Ray 3.7 [939] 3D Graphics
PRANK 20150803 [940] biology, bioinformatics, alignment
Preplot 14.0.2 []
Preseq 0.0.4 [941] biology, bioinformatics, ngs
PRICE 1.2 [942] biology, bioinformatics, ngs
Primer3 2.3.4 [943] biology,bioinformatics,genomics
Primus 1.8.0 [944] biology, phylogenetics
PRINSEQ 0.20.4 [945] biology, sequencing
ProbABEL 0.4.2, 0.4.3, 0.4.5 [946] Genomics, bioinformatics, gwas
Probalign 1.4 [947] biology, bioinformatics, ngs
Processing 3.4 [948] java, language, programming, visual
Prodigal 2.6.2, 2.6.3 [949] biology, genomics
Libproj4 4.9.2, 4.9.3, 5.1.0 [950] library, geospatial, cartography
Prokka 1.10, 1.12 [951] biology,bioinformatics,genomics,assembly
Proovread 1.03rcl, 2.12, 2.13 [952] biology, genomics, ngs
ProSplign 1.0.0 [953] phylogenetics
Protege 5.1.0 [954] Ontology
Proteinortho 4.26, 5.11, 5.16 [955] biology, genomics
ProtExcluder 1.2 [956] biology, phylogenetics
Protobuf 2.5.0, 3.5.1 [957] google, libraries
PROVEAN 1.1.5 [958] biology, genomics
PureCLIP 1.1.1 [959] phylogenetics
PVACtools 1.0.4 [960] biology, phylogenetics
Pyani 0.2.1, 0.2.7 [961] biology, genomics
PyCharm 2018.3 [962] editor, ide, programming, python
Pyfaidx 0.5.2 [963] biology, bioinformatics, ngs, sequencing
Pyfasta 0.5.2 [964] biology, phylogenetics
Pygot 20170518 [965] biology, phylogenetics
Pyhdf 0.9.0 [966] library, hdf4
PyPHLAWD 20180416, 20190414 [967] biology, phylogenetics
Pyrad 3.0.63 [968] biology,sequencing alignment,assembly
PyRosetta r56324 [969] biology,structure,modeling
PyScaf 0.12a [970] Biology, NGS
PySLURM 18.08.04 [971] SLURM
Python2 2.7.5, 2.7.6, 2.7.8 [972] programming languages, scripting, development
Python2-core 2.7.11, 2.7.13, 2.7.14 [973] programming languages, scripting, development
Python3 3.6.1, 3.6.3, 3.6.5 [974] programming languages, scripting, development
Python3-core 3.6.2, 3.6.5 [975] programming languages, scripting, development
Pytorch 1.0, 1.0py2, 1.1.0 [976] library, math
PyVCF 0.6.0 [977] biology, phylogenetics
Qctool 2.0.1, 20160918 [978] phylogenetics
QDD 3.1.2 [979] biology, genomics, ngs
QGIS 2.18.0 [980] GIS
QIIME 1.9.1 [981] biology, bioinformatics, metagenomics
QIIME2 2018.8, 2019.1, 2019.7 [982] biology, bioinformatics, metagenomics
QMCPACK 3.4.0 [983] Library
QT 4.8.3 [984] UI Framework
Quake 0.3 [985] biology, sequencing
QualiMap 2.1.2 [986] biology,sequence alignment
Quantas 1.0.4, 1.0.8, 1.0.9 [987] biology,bioinformatics,ngs
QUAST 2.3, 4.4, 5.0.0 [988] biology, bioinformatics, ngs, sequencing, rna-seq
Quickquartet 1.0.0 [989] biology,bioinformatics,ngs
QuorUM 1.0.0 [990] biology
Quota-alignment 20170905 [991] biology, phylogenetics
R-index 20190711 [992] phylogenetics
R2R 1.0.4 [993] biology, RNA
R8s 1.8, 1.81 [994] phylogenetics
RACA 0.9.1.1 [995] biology, ngs
Racon 1.3.2, 1.3.3, 20161013 [996] biolgoy, sequencing
RADICAL 0.2 [997] biology, bioinformatics, genomics
Rainbow 2.0.4 [998] biology, sequencing
Rainbowfish 0.1.0 [999] phylogenetics
Randfold 2.0.1 [1,000] biology, RNA
RAPSearch 2.24 [1,001] biology, phylogenetics
Unrar 0.0.1, 4.20 [1,002] unarchiver, utility
Rascaf 1.0.2 [1,003] biology, bioinformatics
RAVE 2.1 [1,004] biology, phylogenetics
RAxML 8.2.10, 8.2.12, 8.2.8 [1,005] application, biology, philogenetics
RAxML-NG 0.7.0b, 0.8.0b, 0.9.0 [1,006] phylogenetics
Razers3 3.5.7 [1,007] biology, phylogenetics
Rcorrector 1.0.2 [1,008] biology, phylogenetics
RDnaTools 0.1.3 [1,009] phylogenetics
Reago 1.1 [1,010] biology, phylogenetics
REAPR 1.0.18 [1,011] biology,bioinformatics,assembly
Recon 1.08 [1,012] biology,sequencing
Recycler 0.62 [1,013] biology, bioinformatics
Redis 2.8.13, 2.8.19 [1,014] daemon, data, server
Redundans 0.14a [1,015] biology, phylogenetics
Regtools 0.4.0 [1,016] biolgoy, RNA-seq
RELION 2.1 Beta, 3.0 Beta, 3.0.2 [1,017] biology, imaging
REMORA 1.8.2, 1.8.3 [1,018] System, profiler
REPdenovo 20170222 [1,019] biology, phylogenetics
RepeatAnalysis 0.10.0, 0.12.2 [] biology, phylogenetics
RepeatExplorer 20150506, 20180517 [1,020] biology, bioinformatics, ngs
RepeatMasker 3.3.0, 4.0.3, 4.0.5 [1,021] biology,bioinformatics
RepeatModeler 1.0.8 [1,022] biology,bioinformatics
Repeatscout 1.0.5 [1,023] biology
Reptile 1.1 [1,024] biology,NGS,error correction
Resistome 20170111 [1,025] phylogenetics
RevBayes 1.0.3, 1.0.7, 1.0.9 [1,026] biology, phylogenetics
RGI 4.2.2 [1,027] phylogenetics
RGIS 20180211, 20180814 [1,028] RiverGIS
RHash 1.3.3 [1,029] GNU
RiboPicker 0.4.3 [1,030] biology,sequence
RIGERJ 2.0.2 [1,031] phylogenetics
Rmats2sashimiplot 2.0.3 [1,032] phylogenetics
RNAhybrid 2.1.1 [1,033] biology, bioinformatics, genomics
RNAmmer 1.2 [1,034] biology, RNA-seq
RnaQUAST 1.2.0 [1,035] biology,bioinformatics,ngs,sequencing,rna-seq
RNAsalsa 0.8.1 [1,036] biology, phylogenetics
Rnaseqlib 20150721 [1,037] biology, phylogenetics, RNA-seq
RNASkim 20140625 [1,038] biology, ngs
RDnaTools 0.1.3 [1,039] phylogenetics
Roary 3.4.1 [1,040] biology,genomics
ROOT 5.34.17, 6.0, 6.06.02 [1,041] Data Analysis
ROOTPy 20160323 [1,042] Data Analysis
Rosetta 2014wk4 [1,043] biology,structure,modeling
Rpy 2.6.2 [1,044] biology, bioinformatics, genomics, ngs, chip-seq
Rrnaselector 1.0 [1,045] biology, sequencing
RSEG 0.4.8 [1,046] biology, bioinformatics, genomics
RSEM 1.2.29, 1.2.31, 1.2.7 [1,047] biology,bioinformatics,ngs,sequencing
RSeQC 2.6.2, 2.6.4, 3.0.0 [1,048] biology,ngs,rna-seq
RStudio 1.1.419, 1.1.453, 1.2.1335 [1,049] statistics
RTGTools 3.7.1 [1,050] biology, NGS
Ruby 2.5.1 [1,051] programming,scripting,language
Rust 1.31.0 [1,052] programming
Saffrontree 0.1.2 [1,053] phylogenetics
Sailfish 0.6.3 [1,054] biology,genomics,ngs,rna-seq
Salmon 0.13.1, 0.6.0, 0.7.2 [1,055] biology, RNA-seq
SALSA 20171009 [1,056] biology, ngs, pacbio
Sambamba 0.6.3, 0.6.6, 0.6.9 [1,057] Biology, NGS
Samblaster 0.1.14, 0.1.24 [1,058] biology,bioinformatics,ngs,sequencing
SAMStat 1.08 [1,059] biology,bioinformatics,ngs,sequencing
Samtools 1.7, 1.8, 1.9 [1,060] biology,bioinformatics,ngs,sequencing
DS9 7.5, 8.0.1 [1,061] Imaging
SAS 9.3, 9.4 [1,062] statistics, data analysis
Sate 2.2.7 [1,063] biology, bioinformatics, phylogenetics
Satsuma 3.0 [1,064] phylogenetics
Satsuma2 20161123 [1,065] phylogenetics
Scala 2.11.5 [1,066] programming, language, java
Scalablast 2.4.53 [1,067] application, biology, genomics
SCALAPACK 2.0.2 [1,068] library,c,math,mpi
Scalpel 0.1.1, 0.5.3 [1,069] Biology, NGS
Schrodinger Suite 2015, 2017, 2017-2 [1,070] Computational Chemistry, Molecular Dynamics
Scipion 1.2 [1,071] Image Processing
Scoary 1.6.10 [1,072] biology, bioinformatics, genomics
Scons 2.3.0, 2.5.1 [1,073] Programming
SCRATCH-1D 1.0 [1,074] biology, bioinformatics, ngs
Screen 4.6.2 [1,075] GNU, Terminal Multiplerxer
SCRIPTURE 20101211 [1,076] biology, bioinformatics, genomics
Scythe 0.991 [1,077] Biology, NGS
Sdsl 2.1.1 [1,078] library, c++
Sdt 1.2 [1,079] Biology, Sequencing
SeCaPr 1.1.12 [1,080] phylogenetics
Segemehl 0.1.9 [1,081] biology,bioinformatics,ngs,sequencing
SEPP 1.0, 20160614, 3.0 [1,082] biology, phylogenetics
Seq-Gen 1.3.3 [1,083] biology,phylogenetics
Seq_crumbs 20150120 [1,084] biology, sequence, genomics, utilities
SeqKit 0.8.0 [1,085] biology, phylogenetics
Seqmagick 20150923 [1,086] biology, phylogenetics
SeqMap 1.0.13 [1,087] biology,bioinformatics,sequence,ngs
SEQPower 1.1.1 [1,088] Genomics, bioinformatics, phylogenetics
SeqPrep 0.5, 1.1 [1,089] biology,bioinformatics,ngs,sequencing
Seqtk 1.3, 20140729 [1,090] Bioinformatics, Genomics, NGS
SEQuel 1.0.1 [1,091] biology,bioinformatics,ngs
Seqwish 20190509 [1,092] phylogenetics
SeqyClean 1.8.10 [1,093] biology,bioinformatics,ngs,sequencing
SEXCMD 20170823 [1,094] biology, phylogenetics
SExtractor 2.19.5 [1,095] Astronomy
SGA 0.10.14 [1,096] biology, assembly
Shannon 20160211 [1,097] biology, RNA-Seq
SHAPEIT 2.12, 2.5 [1,098] biology,SNP
SHAPE-MaP 1.2 [1,099] biology, phylogenetics
ShapeMapper 2.1.3 [1,100] biology, phylogenetics
SHARCGS 1.2.11 [1,101] biology, NGS, de novo assembly
Shasta 0.1.0 [1,102] phylogenetics
SHEsisPlus 1.0, 1.01 [1,103] biology, genetics
Shogun 6.1.3 [1,104] phylogenetics
ShoRAH 20130830, 20131204 [1,105] biology,bioinformatics,ngs
SHRiMP 2.2.3 [1,106] biology, genomics, ngs
Shustring 2.6 [1,107] biology, sequencing
SICER 1.1 [1,108] biology, ChIP-Seq
Sickle 1.200, 1.33 [1,109] biology, bioinformatics, ngs
Siesta 3.2, 4.1b2, 4.1b3 [1,110] Chemistry
SIFT 4.0.3b [1,111] biology,bioinformatics,genomics
SignalP 4.1c, 5.0b [1,112] biology, phylogenetics
SiLiX 1.2.11 [1,113] phylogenetics
Silo 4.7 [1,114] io,library
Sim4 20121010 [1,115] biology, bioinformatics, genomics
SimSeq 4.12.2011 [1,116] biology, bioinformatics, ngs, phylogenetics
SInC 20140120 [1,117] biology, phylogenetics
Sine_scan 1.1.1 [1,118] phylogenetics
Singularity 2.6.1, 3.2.0, 3.3.0 [1,119] Containers
SIPeS 2.0 [1,120] biology, bioinformatics, ChIP-Seq
Sisl 0.8.3 [1,121] Physics, Tight-binding
Slicer 4.3.1 [1,122] biology,bioinformatics,neuroscience,imaging
Slurm-drmaa 1.2.1, 1.2.1.18, 1.2.1.19 [1,123] libraries, slurm, api, drmaa
Smalt 0.7.6 [1,124] application, biology, phylogenetics
SMARTdenovo 20180219 [1,125] biology, phylogenetics
Smartie-sv 20180308 [1,126] phylogenetics
SMC++ 1.8.0 [1,127] biology, NGS
SMRT-SV 2.0.0 [1,128] biology, bioinformatics, ngs
SMS 1.7 [1,129] biology, bioinformatics
SNAP 0.15.4, 20100728 [1,130] biology,bioinformatics,sequencing
SPANE-pooled 20130407 [1,131] biology,SNP
Snappy 1.1.7, 1.2.1 [1,132] library
SNeP 1.1 [1,133] biology,phylogenetics
Sniffles 1.0.11, 1.0.6, 1.0.8 [1,134] phylogenetics
Snippy 20160419 [1,135] biology, phylogenetics
SNP-Pipeline 1.0.1 [1,136] biology, phylogenics
SNP-sites 2.0.3 [1,137] biology, SNP
SnpEff 4.3q, 4.3r, 4.3t [1,138] biology,bioinformatics,variant annotation
SNPGenie 20190620 [1,139] phylogenetics
SNPhylo 20140701 [1,140] biology,phylogenetics
SOAPaligner 2.21 [1,141] phylogenetics
SOAPdenovo 1.05, 2.04 [1,142] biology,ngs
SOAPdenovo-Trans 1.01, 1.03 [1,143] biology,ngs
SOAPec 2.03 [1,144] biology, phylogenetics
SOAPsplice 1.10 [1,145] biology,ngs
SOLAR 8.4.2 [1,146] phylogenetics
SortMeRNA 2.1 [1,147] biology, sequencing, NGS
Sourmash 2.0.1 [1,148] phylogenetics
SPAdes 3.7.1, 3.8.0, 3.9.0 [1,149] biology,bioinformatics,ngs
Spanki 0.4.1, 0.4.3, 0.5.0 [1,150] biology, bioinformatics, genomics
SparCC 201402, 201608 [1,151] Microbial Ecology
Spark 2.1.0, 2.2.0 [1,152] spark, hadoop
Sparsehash 2.0.3 [1,153] Google, API
SPARTA+ 2.60 [1,154] Chemistry
Spidey 20150922 [1,155] biology, genomics, bioinformatics
SPIMAP 1.1 [1,156] biology, bioinformatics, phylogenetics
SpliceGrapher 0.2.5 [1,157] biology, sequencing
SpliceTrap 0.90.5 [1,158] biology, bioinformatics, genomics, NGS
SPM 12b, 8, 8r5236 [1,159] biology,bioinformatics,matlab
Sputnik 1.0 [1,160] biology,bioinformatics,repeats
SQANTI 1.2 [1,161] phylogenetics
SQL Developer 4.1.2 [1,162] programming, oracle, sql
SQLite 3.8.8.2 [1,163] database
SRA 2.8.0 [1,164] biology,bioinformatics,sra
SRST2 0.2.0 [1,165] biology,bioinformatics,ngs
SSPACE 2.0, 3.0 [1,166] biology,bioinformatics,ngs
Ssr_pipeline 0.951 [1,167] biology, DNA sequencing,
Stacks 2.1, 2.3e, 2.41 [1,168] biology, bioinformatics, genomics, ngs
Staden 1.14.6 [1,169] biology, phylogenetics
Stampy 1.0.31 [1,170] biology, bioinformatics, sequencing
Rnastar 2.6.1a, 2.6.1b, 2.7.0b [1,171] biology, ngs, rna-seq
STAR-Fusion 1.1.0, 1.3.1 [1,172] biology, transcriptome
STAR-CCM+ 13.06.012, 14.04.011, 8.06 [1,173] Mechanical Engineering
Starseqr 0.6.7 [1,174] phylogenetics
Stata 10.1, 13 [1,175] Statistics
Statsmodels 0.8.0 [1,176] biology, library, math
Strelka 1.0.15, 2.9.2 [1,177] biology, phylogenetics
StringMLST 0.4 [1,178] biology, bioinformatics, CHiP-Seq
Stringtie 1.2.3, 1.3.3, 1.3.4d [1,179] biology,bioinformatics,ngs,sequencing,alignment
Structure 2.3.3, 2.3.4 [1,180] biology,bioinformatics,population genetics
Subread 1.5.1, 1.5.3, 1.6.2 [1,181] biology, sequencing, SNP
Subversion 1.9.7 [1,182] Revision Control
SUNDIALS 2.3.0, 2.5.0, 3.0.0 [1,183] Math, Numerical Solvers
Supercell 20170602 [1,184] biology, NGS
Supernova 1.2.1, 2.0.0, 2.1.1 [1,185] biology, phylogenetics, ngs
SUPPA 2.3 [1,186] phylogenetics
SURVIVOR 1.0.6 [1,187] phylogenetics
SVDetect 0.8b [1,188] biology,ngs,genomics
SVM-BPfinder 20160920 [1,189] biology, sequence, genomics, utilities
Swarm 1.2.11 [1,190] Data Analysis
Sweed 3.3.2 [1,191] biology, phylogenetics
SWEEP 20160722 [1,192] biology, SNP
SWIG 2.0.9, 3.0.12, 3.0.8 [1,193] library, development, C++, python
SwitchSeq 20140907 [1,194] biology,bioinformatics,genomics
Syzygy 1.2.7 [1,195] biology, ngs
Taiyaki 3.0.1, 4.1.0 [1,196] phylogenetics
Talesf 20160814 [1,197] phylogenetics
Tandem-Genotypes 1.4.0 [1,198] phylogenetics
Tantan 13 [1,199] ngs, genomics
Tapir 20160825 [1,200] biology, phylogenetics
TAPIS 1.2.1 [1,201] biology, sequencing
TARGeT 2.10 [1,202] phylogenetics
TASSEL 5.0, 5.2.20, 5.2.29 [1,203] biology,bioinformatics,genomics,wga
Tuning Analysis Utilities 2.23, 2.26, 2.26.3 [1,204] library, profiling and optimization
TaxMaps 0.1 [1,205] biology, phylogenetics, taxonomy
Taxtastic 0.5.7 [1,206] biology, taxonomy
Tbb 2017_20161128 [1,207] library
Tcllib 1.18 [1,208] library
Tcoffee 10.00.r1613, 9.03.r1318 [1,209] Bioinformatics
Tecplot 360 EX 2015R1 [1,210] plotting, animation, cfd, simulations
TEMP 20170731 [1,211] phylogenetics
TensorFlow 1.14.0, 1.7.0, 1.7.0.0 [1,212] library, math
TESS 2.3.1 [1,213] biology, bioinformatics, genomics, markov
Test 1.0 [1,214] shell
TetGen 1.5.0 [1,215] tetrahedral meshes
TEToolkit 1.5.1 [1,216] biology, bioinformatics, sequencing
TEtools 20180213 [1,217] biology, phylogenetics
Texlive 2015.20160320 [1,218] formatting, typesetting, document preparataion
TGICL 2.1 [1,219] biology,bioinformatics,ngs,sequencing
Theano 1.0.4 [1,220] library, math, gpu
Tiff 4.0.10 [1,221] imaging
Tigmint 1.1.2 [1,222] phylogenetics
Tmux 2.0 [1,223] GNU
ToFU2 20180629, v17 [1,224] biology, bioinformatics, ngs, iso-seq
Toil 3.3.0, 3.3.3 [1,225] biology, bioinformatics
Tombo 1.4, 1.5 [1,226] biology, genomics, ngs
TomoPy 0.0.3 [1,227] biology,neuroscience,imaging
Tophat 2.1.0, 2.1.1, 2.1.2 [1,228] biology,bioinformatics,ngs,sequencing
TotalView 8.12 [1,229] Parallel Computing
TPP 4.7.0, 4.7.1, 5.0.0 [1,230] biology, chemistry, nmr
TraCeR 0.5.1, 20160519 [1,231] Biology, Phylogenetics
TrackTools 2011 [1,232] Software
TrackVis/DTK 0.5.2.2, 0.6.0.1 [1,233] biology,bioinformatics,neuroscience,imaging
Tracula 5.3.2014_05_26 [1,234] biology,bioinformatics,neuroscience,imaging
TraitRate 1.1 [1,235] biology, evolution
Trans-ABySS 1.5.4, 2.0.1 [1,236] biology, phylogenetics
TransDecoder 5.3.0, 5.4.0, 5.5.0 [1,237] biology, ngs
TRANSIT 2.5.2 [1,238] phylogenetics
Transrate 1.0.1 [1,239] biology,assembly
TransVar 2.3.3 [1,240] biology, bioinformatics, phylogenetics
TreeBreaker 20160621 [1,241] biology, phylogenetics
TreeCorr 3.2.3 [1,242] physics
TreeFix 1.1.10, 1.1.7 [1,243] biology,bioinformatics,phylogenetics
TreeMix 1.12 [1,244] biology, phylogenetics
TreePL 20150305 [1,245] biology, bioinformatics, phylogenetics
TREEPUZZLE 5.3 [1,246] biology, phylogenetics
Trelis 16.3 [1,247] Geometry
TRF 4.04 [1,248] biology,bioinformatics,genomics
Trilinos 12.12.1, 12.4.1, 12.6.4 [1,249] Mathematical Algorithms
Trim Galore 0.4.1, 0.4.4, 0.5.0 [1,250] biology,bioinformatics,ngs
TrimAl 1.2 [1,251] biology,genomics,sequence alignment
TriMetAss 1.1 [1,252] biology,bioinformatics,ngs
Trimmomatic 0.32, 0.33, 0.36 [1,253] biology,bioinformatics,ngs
Trinity r20130225, r20131110, r20140413 [1,254] biology,bioinformatics,ngs,sequencing,rna-seq
Trinotate 3.0.1 [1,255] biology
TRIPLEC 1.0 [1,256] biology, bioinformatics
TRNAscan-Se 1.23 [1,257] biology,bioinformatics,ngs
TWINSCAN 4.1.2 [1,258] biology,genomics
Ubuntu 18.04 [1,259] Ubuntu Linux
Ucsc 20120524 [1,260] biology,bioinformatics,genomics
UDUNITS 2.2.17 [1,261] library, data, units
UFITS 0.7.2 [1,262] biology,bioinformatics,ngs
Ufraw 0.22 [1,263] data mining
Ugtm 1.1.6 [1,264] statistics, modeling
Umi-tools 0.5.5 [1,265] phylogenetics
UNAFold 3.8 [1,266] biology, genome, RNA, folding
Unanimity 20171108, 3.4.1 [1,267] programming,library,cpp
Uproc 1.2.0 [1,268] biology, genome
USEARCH 9.0.2132, 9.1.13, 9.2.64 [1,269] biology,bioinformatics,alignment,sequence analysis
Valgrind 3.11.0, 3.8.1 [1,270] Computer Programming
Valouev 20160325 [1,271] Biology, Phylogenetics
VAMPIR 9.1 [1,272] High Performance Computing
VarDictJava 1.6.0, 20160521, 20170531 [1,273] biology, phylogenetics
Varnorm 0.21 [1,274] biology, bioinformatics
VarScan 2.3.6 [1,275] biology,bioinformatics,ngs
VarSimLab 20180220, 20180921 [1,276] biology, simulation, genomics
Vasp 5.4.1, 5.4.4 [1,277] Quantum Chemistry
VAST-TOOLS 20150506 [1,278] biology, rna-seq, ngs, splicing
VCF-kit 0.1.2 [1,279] biology, phylogenetics
Vcfanno 0.2.8 [1,280] biology, phylogenetics
Vcflib 20121207, 20141119, 20150313 [1,281] biology,bioinformatics,genomics
Vcftools 0.1.15, 0.1.16, 0.1.9 [1,282] biology,bioinformatics,genomics
Vcf-validator 0.6 [1,283] biology, phylogenetics
Vcontact 20190512 [1,284] phylogenetics
VDJtools 1.1.7 [1,285] biolgoy, phylogenetics
Velvet 1.2.06, 1.2.07, 1.2.10 [1,286] computational biology, genomics
VEP 83, 88.8, 92 [1,287] biology, genomics, ngs
Vidjil 201703 [1,288] biology, genomics
ViennaRNA 2.2.6 [1,289] biology, RNA-seq
Vim 8.1.1566 [1,290] programming,scripting,language
VirSorter 1.0.3 [1,291] biology, phylogenetics
VirtualCell 7.1 [1,292] phylogenetics
VirusFinder 2.0 [1,293] biology, phylogenetics
Visit 2.12.2, 2.13.3, 3.0.1 [1,294] Visualization, Animation and Analysis
VISPR 0.4.14 [1,295] phylogenetics
VMD 1.9.1, 1.9.3 [1,296] visualization, animation, 3d
V-Phaser 02112013 [1,297] biology, phylogenetics
VSearch 20151022, 20161209-2.3.4 [1,298] biology,NGS
Vt 20140903, 20160129 [1,299] biology, genomics
VTC 0.9.3 [1,300] biology, bioinformatics, VCF
VTK 6.1.0, 7.1.0, 7.1.1 [1,301] biology,bioinformatics,neuroscience,imaging
VULCAN 6.3.1 [1,302] Fluid Dynamics
W2rap-contigger 20161124 [1,303] biology, genomics
Wannier90 1.2, 2.1.0 [1,304] Computational Physics
WDSSII 5 [1,305] Weather, Meteorology
WebLogo 2.8.2, 3.3, 3.5.0 [1,306] biology,bioinformatics,sequence,graphics
Weka 3.8 [1,307] statistics,machine learning
WEVOTE 1.5.0, 1.8.0 [1,308] biology, phylogenetics
WGS Assembler 8.3rc1, 8.3rc1.r4638, 8.3rc2 [1,309] biology, bioinformatics, genomics
Wgsim 0.3.1-r13 [1,310] biology, phylogenetics
WHAMM 0.14a [1,311] biology, phylogenetics
WhatsHap 0.14.1 [1,312] biology, phylogenetics
Wine 1.6.2, 1.9.6, 4.0.0 [1,313] windows, emulator
Wise 2.2.0, 2.4.1 [1,314] biology, genome
WIsH 1.0 [1,315] phylogenetics
WoLFPSort 0.2 [1,316] phylogenetics
WOMBAT 20180118 [1,317] biology, phylogenetics
Wtdbg 2.1, 2.4 [1,318] phylogenetics
Wub 0.2.0 [1,319] biology, genomics, ngs
WU BLAST 2.0 [1,320] biology, bioinformatics
Xander 20151222 [1,321] biology, phylogenetics
Xapian 1.4.4 [1,322] library
XCrySDen 1.5.60 [1,323] Computational Material Science
Xerces 3.1.4 [1,324] phylogenetics
Xpclr 1.1.1 [1,325] phylogenetics
Xterm 1.1 [1,326] terminal emulator
XZ 5.2.2 [1,327] compression, library
YAHA 0.1.82 [1,328] biology, ngs
YASM 1.3.0 [1,329] Computer Programming
YASRA 2.33 [1,330] biology,bioinformatics,ngs,sequencing
Zagros 1.0.0 [1,331] biology,phylogenetics
ZEO++ 0.2.2 [1,332] chemistry
Zorro 2.2 [1,333] biology, sequencing