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 3.5.1, 3.6, 3.6.2 [4] statistics
Rmpi 0.6.6, 0.6.9 [5] statistics, R, mpi
ABRicate 1.0.1 [6] phylogenetics
ABruijn 1.0 [7] biology, assembly, ngs, pacbio, nanopore
ABySS 1.3.7, 1.5.2, 2.1.0 [8] biology, de novo
AdapterRemoval 2.2.2 [9] phylogenetics
ADMB 11.5, 12.0 [10] math, modeling, optimization
AdmixTools 20150311, 20160513 [11] biology, bioinformatics, genomics, ngs
ADMIXTURE 1.23, 1.3.0 [12] biology, bioinformatics, genomics, ngs
AEGeAn 0.14.0 [13] biology,genomics
AFNI 2018_04_12 [14] biology,bioinformatics,neurology,imaging
AfterQC 0.9.7 [15] phylogenetics
AGOUTI 0.3.3 [16] biology, genomics
Albacore 2.1.10, 2.3.1, 2.3.3 [17] Biology, Phylogenetics
ALFA 1.1.1 [18] phylogenetics
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 16.0, 18, 20 [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
AMRPlusPlus 20180508 [31] phylogenetics
AMUSE 10.0 [32] Astrophysics
ANGEL 2.3 [33] biology,bioinformatics,sequence
Angsd 20150306, 20150909 [34] biology, ngs
Annocript 2.0 [35] phylogenetics
ANNOVAR 20121023, 20130221, 20150322 [36] biology, bioinformatics, genomics
Ansible 2.5.5, 2.8.1 [37] automation, deployment
Ansysem 17.0 [38] Electromechanics
AntiSMASH 4.1.0 [39] phylogenetics
ANTs 2.2.0 [40] biology, phylogenetics
Anvio 5.5.0, 6.0, 6.1 [41] biology, microbial 'omics
Anylogic 1.0 [42] software tool
APT 1.15.0, 1.18.0, 1.20.5 [43] biology, bioinformatics, genomics, microarray
ARC 1.1.4 [44] biology,bioinformatics,ngs
ArcGIS 1.5.1, 10.3.1 [45] geospatial
ARCS 1.0.0, 1.0.1, 1.0.5 [46] biology, genomics
ARIBA 2.13.1 [47] phylogenetics
ARKS 1.0.2 [48] phylogenetics
Armadillo 6.200.3, 7.900.0, 9.200.6 [49] library, C++, math
ARPACK 1.0 [50] Solve eigenvalue problems
ArrayFire 3.4.2 [51] Code Optimization
ART 20160417, 20160605 [52] phylogenetics
ASE-ANI 20180712 [53] biology, bioinformatics, genomics, ngs
ASHS 2.0 [54] biology, mri
Assembly-stats 1.0.1 [55] biology, sequencing, genomics
Assexon 20190814 [56] phylogenetics
AStalavista 3.2, 4.0 [57] biology, bioinformatics, genomics
ASTRAL 5.0.3, 5.6.1, 5.6.2 [58] biology,bioinformatics,ngs,phylogenetics
Astropy 2.0.8 [59] biology, bioinformatics, phylogenetics
Atac 0.3.3 [60] biology, phylogenetics
ATAT 3.23, 3.34 [61] alloy theory
ATLAS 3.10.1, 3.10.2, 3.11.17 [62] library, data
AtomEye 3 [63] Material Science
ATRAM 2.1, 2.1.2, 2.2.0 [64] Math
Augustus 3.2.2, 3.3, 3.3.2 [65] biology,bioinformatics,genomics
Auto3DEM 4.05.2 [66] Image Reconstruction
AutoDock 4.2.6 [67] biology
Autometa 20190802 [68] phylogenetics
BALI-PHY 2.3.8, 3.4.1 [69] Baesian Estimation
BAM-matcher 20161021 [70] phylogenetics
Bam-Readcount 20150616 [71] biology, genomics
BamBam 1.0 [72] biology, bioinformatics, genomics
BAMM 2.5.0 [73] bioinformatics, evolution
Bamstats 20140602 [74] biology,bioinformatics,ngs
Bamtools 2.4.1, 2.5.0, 2.5.1 [75] biology,bioinformatics,ngs,sequencing
BamUtil 1.0.2 [76] biology, bioinformatics, genomics
BAPS 6.0 [77] biology, bioinformatics, genomics
Barrnap 0.7, 0.9 [78] biology, RNA-Seq
Basemount 0.1.2.464, 0.12.8.1516, 0.15.96 [79] biology, DNA Sequencing
Bashdb 4.4-0.94 [80] Debugger
BatVI 1.00 [81] biolgoy, phylogenetics
Bax2bam 0.0.9 [82] phylogenetics
BayArea 1.0.2 [83] biology
BAYENV 2.0 [84] biolgoy, phylogenetics
BayesAss 3.0.4 [85] phylogenetics
BayeScan 2.1 [86] biology, SNP
BayeScEnv 1.1 [87] biology, phylogenetics
BayesR 20151016 [88] biology, phylogenetics
Baypass 2.1 [89] biology, phylogenetics
Bazel 0.11.1 [90] build, development, java
BBMap 37.09, 38.26, 38.44 [91] biology, alignment
Bcbio-nextgen 0.9.9 [92] biology, bioinformatics, ngs
Bcftools 1.6, 1.8, 1.9 [93] biology, bioinformatics, ngs
Bcl2fastq 2.17.1.14, 2.19.1.403, 2.20.0.422 [94] biology, ngs, illumina
BDG-SeQuila 0.5.5 [95] phylogenetics
BEAGLE 4.0, 4.1, 5.0 [96] biology, genetics, genotyping
BEAR 20170209 [97] biology, bioinformatics, metagenomics
BEAST 2.5.2, 2.6.0, 2.6.2 [98] biology, phylogeny
BEDOPS 2.4.30 [99] biology,bioinformatics,sequence,ngs
BEDTools 2.29.0, 2.29.1, 2.29.2 [100] biology,bioinformatics,ngs
Bertini 1.6 [101] Mathemetics
BESST 2.2.4 [102] biology, NGS
BFAST 0.7.0 [103] biology,bioinformatics,ngs
Bifrost 0.2, 1.0.3, 20200225 [104] phylogenetics
BIGSI 0.3.8 [105] phylogenetics
BinPacker 1.0 [106] biology, RNA-seq, sequence assembly
BinSanity 0.2.6.4 [107] biology, genomics
Bioawk 1.0 [108] phylogenetics
BioBakery 0.13.2 [109] phylogenetics
Biodiverse 2.1 [110] phylogenetics
Biolite 0.3.5.1 [111] biology, bioinformatics, genomics, SNP
BIOM 2.1.5, 2.1.6 [112] biology, genomics
BIOMART 1.4 [113] biology,genomics
BiSCoT 1.0 [114] phylogenetics
Bismark 0.22.3, 0.7.4, 0.7.7 [115] biology, bioinformatics, NGS
Blackfynn 0.2.7 [116] data mining
BLASR 20160518 (5.1), 20161215 (5.3), 5.3.2 [117] biology,bioinformatics,ngs
Blast2GO 1.3.3, 2.5.0-20120705 [118] biology,bioinformatics,gene ontology
BLAT 20121105, 20140318 [119] Genomics, bioinformatics
Blender 2.63, 2.73, 2.77 [120] graphics
Blitz 0.10 [121] library
BlobTools 1.0 [122] phylogenetics
Bloomfiltertrie 0.8.7 [123] phylogenetics
BloomTree 0.3.5 [124] data mining
BLUPF90 20160604, 20180301, 20190531 [125] biology, phylogenetics
BOLT-LMM 2.3.4 [126] phylogenetics
BoltzTraP 1.2.5 [127] physics
Boost 1.64.0, 1.67.0, 1.71.0 [128] programming, library, cpp
Booster 0.1.2 [129] phylogenetics
Bowtie 1.1.1, 1.2.0, 1.2.3 [130] biology,bioinformatics,ngs,sequencing
Bowtie2 2.3.4.3, 2.3.5, 2.3.5.1 [131] biology,bioinformatics,ngs,sequencing
BPGA 1.2 [132] biology, ngs
BPP 3.2, 3.4, 4.1.4 [133] biology, phylogenetics
Bracken 1.0.0, 2.5 [134] biology, phylogenetics
Braker 2.1.2 [135] phylogenetics
BRANCH 1.8.1 [136] biology,bioinformatics,ngs,mapping
BRATNextGen 20150505 [137] biology, bioinformatics, genomics
BreakDancer 1.4.5 [138] biology, phylogenetics
Breakseq 2.2 [139] biology, phylogenetics
Brewery 20191205 [140] phylogenetics
Bridger 20141201 [141] NGS, Genomics, bioinformatics
BRIG 0.95 [142] biology, genomics
Bsmap 2.87 [143] biology, bioinformatics, NGS
Bsoft 1.9.1 [144] biology, image analysis
BSseeker2 2.1.0, 2.1.8 [145] biology, phylogenetics
Bubbleparse 20140314 [146] biology, phylogenetics
BUCKy 1.4.4 [147] biology, phylogenetics
BUSCO 3.01, 3.02 [148] biology, genomics
BWA 0.7.7, 0.7.8, 0.7.9a [149] biology,bioinformatics,ngs
BWA-PSSM 0.5.11 [150] phylogenetics
Bxh_xcede_tools 1.11.1 [151] biology, bioinformatics
BYOBU 5.92 [152] shell, screen, terminal
Bzip2 1.0.6 [153] archiver, library
CAFE 4.1 [154] biology, phylogenetics
Came 0.0.1 [155] phylogenetics
Camino 20140723 [156] biology,bioinformatics,neuroscience,imaging
Cantera 2.1.1 [157] kinetics, thermodynamics
Canu 1.8, 1.9, 2.0 [158] biology, sequencing
CANVAS 1.40.0.1613 [159] phylogenetics
CAP3 20120705 [160] biology,bioinformatics,assembly
Capnp 0.5.3 [161] C++
CASAVA 1.8.2 [162] biology,bioinformatics,ngs
CASM 0.2.0 [163] Statistical Mechanics
CasOFFinder 2.4 [164] phylogenetics
CAVIAR 20171218 [165] biology, phylogenetics
CBGpipe 20190702 [166] phylogenetics
CD-HIT 4.6, 4.6.4, 4.6.8 [167] biology, genomics
CDO 1.7.2rc3, 1.9.4 [168] Climate
CellProfiler 2.2.0 [169] biology, phylogenetics
Cell Ranger 2.2.0, 3.0.0, 3.1.0 [170] biology, bioinformatics, ngs, rna-seq
Cell Ranger ATAC 1.2.0 [171] biology, bioinformatics, ngs, rna-seq
CellRanger-DNA 1.0.0, 1.1.0 [172] biology, bioinformatics, ngs, rna-seq, 10xgenomics
Centrifuge 1.0.3 [173] biology, phylogenetics
CFITSIO 3.370 [174] library, C
CGAL 4.10, 4.9, 5.02 [175] library, math
CGATools 1.6.0.43 [176] biology, bioinformatics, ngs
Cgmaptools 0.1.1, 0.1.2 [177] phylogenetics
CHARMM 36a3, 43b2 [178] chemistry, simulation
CheckM 1.0.4, 1.0.7, 1.1.2 [179] biology, genomics
ChewBBACa 0.2.5 [180] phylogenetics
Chimera 1.12 [181] biology, bioinformatics, modeling
Chipyard 1.0 [182] hardware, design
ChromEvol 2.0 [183] Biology, NGS
CIMS 4.1.2 [184] biology,genomics
CIRCexplorer 1.1.10 [185] biology, bioinformatics, rna-seq
CIRCexplorer2 2.3.5 [186] phylogenetics
Circlator 1.5.1, 1.5.5 [187] biology, genomics
Circleator 1.0.2 [188] phylogenetics
Circos 0.63-pre11, 0.69-2 [189] biology,genomics,ngs
CIRI 2.0.6 [190] phylogenetics
CisGenome 2.0 [191] biology, bioinformatics, genomics
CisTEM 1.0.0 [192] phylogenetics
Clairvoyante 1.02 [193] phylogenetics
Clann 3.2.3 [194] biology,bioinformatics,phylogentics
CLARK 1.2.2-b, 1.2.3 [195] biology, genomics
CLHEP 2.2.0.1 [196] High Energy Physics
Click-demultiplex 0.1.0 [197] Machine Learning
CLIFinder 4.1 [198] biology, phylogenetics
CLIPSeqTools 0.1.7 [199] biology, sequencing
ClonalFrame 1.1, 1.2 [200] biology,bioinformatics,ngs,phylogenetics
ClonalFrameML 1.0, 1.11 [201] biology, bioinformatics, ngs, phylogenetics
CloudCompare 2.10.3 [202] 3D visualization
CLUMPP 1.1.2 [203] biology, bioinformatics
ClustalO 1.2.0 [204] biology, bioinformatics, alignment
ClustalW 2.1 [205] biology,bioinformatics,alignment
Cluster3 1.52a [206] biology, genomics
ClusterFinder 313 [207] biology, bioinformatics, metabolomics
Clview 20130402 [208] biology, bioinformatics
CMake 3.14.5, 3.15.6, 3.6.3 [209] Software Development
CMS 20170518 [210] biology
CMWP 140518 [211] biology, genomics
CNSpipeline 20170827 [212] phylogenetics
CNV-Sim 0.9.2 [213] biology, phylogenetics
CNVkit 0.9.0, 0.9.6 [214] biology
CNVnator 0.3.2 [215] biology, genomics, CNV
CNV-Seq 20110715, 20140812 [216] biology,bioinformatics,genomics
Cobra-tf 0.1 [217] Nuclear Engineering
Coevol 1.3c, 1.4b [218] bio,bioinformatics,phylogenetics
Cogent 2.1 [219] biology, phylogenics
COLMAP 3.6 [220] modeling
CoMap 1.4.1 [221] Bioinformatics, Genomics
COMSOL 5.4.0 [222] General-purpose simulation software
Concaterpillar 1.8a [223] phylogenetics
CONCOCT 1.1.0 [224] biology, bioinformatics, genomics
Conda 4.7.12, 4.8.2, 4.8.3 [225] programming, development, packages
CONN 18a [226] mri,fmri,matlab
Connectomemapper3 3.0.0-rc1 [227] phylogenetics
ConPADE 1.0 [228] phylogenetics
Conpair 20161010, 20180624 [229] biology, phylogenetics
Consed 23.0, 25.0, 29.0 [230] biology, bioinformatics, genomics
CONSEL 0.20 [231] biology, phylogenetics
ContaVect 0.2 [232] biology, phylogenetics
Coot 0.8.9 [233] Modeling
Coreutils 8.23, 8.28 [234] Software tools
Corset 1.06 [235] biology, NGS
Counterr 0.1 [236] phylogenetics
CovNMR 2014 [237] Biochemistry
Cp2k 7.0.0 [238] Quantum Chemistry
CPAT 1.2.2 [239] biology, phylogenetics
CPLEX 12.6.1, 12.6.2, 12.7 [240] Meteorology
Crass 1.0.1 [241] biology, assembly
Crisflash 1.2.0 [242] phylogenetics
CRISP 20181122 [243] phylogenetics
CRISPRanalyzer 1.50 [244] biology,genomics,ngs
CRISPRCasFinder 4.2.17 [245] phylogenetics
CrossMap 0.3.9 [246] biology, genomics
Crux 1.40 [247] biology, mass-spectroscopy
CryptoMiniSat 5.0.1 [248] SAT
CryptSplice 20180111 [249] biology, phylogenetics
CUBE 4.3.4, 4.4 [250] library,c,math
Nvidia CUDA Toolkit 10.0.130 [251] programming, library, graphics, runtime
Cufflinks 2.1.1, 2.2.1, 2.2.1.1 [252] biology,bioinformatics,ngs,sequencing
CDNA_Cupcake 9.0.1 [253] biology, bioinformatics, ngs, iso-seq
Cutadapt 2.6, 2.7, 2.8 [254] biology,bioinformatics,ngs
CUTE 3.2.6 [255] astronomy
CutRunTools 20200104 [256] phylogenetics
CVXOPT 1.1.8 [257] python, optimization, module
CWLtool 1.0.20190228, 1.0.20190906, 2.0.20200126 [258] workflow, scheduler
Cytoscape 3.4.0 [259] biology, bioinformatics, ngs, phylogenetics
Dadi 1.7.0 [260] phylogenetics
DAKOTA 6.10, 6.8, 6.8-gui [261] Computational Science and Engineering
DALIGNER 1.0 [262] biology, phylogenetics
Dammit 1.0rc2 [263] biology, phylogenetics
DASTool 1.1.0, 1.1.2 [264] biology, phylogenetics
Datamash 1.1.0 [265] math
DAWGPASW 1.0 [266] biology, phylogenetics
DCC 0.4.4 [267] biology, bioinformatics, ngs
Dcm2Bids 2.1.4 [268] phylogenetics
Dcmstack 0.6.2 [269] biology, imaging
DCMTK 3.6.0 [270] biology,neuroscience,imaging
DDocent 2.7.8 [271] phylogenetics
DDSCAT 7.3.0 [272] Astrophysics
DDT 6.0, 6.1.2, 7.0.4 [273] Software Development
DealII 8.3.0 [274] Library
DeconSeq 0.4.3 [275] biology, phylogenetics
DeepGS 1.2 [276] phylogenetics
DeepLabCut 2.0.7-cpu, 2.0.7-gpu, 2.1.1 [277] phylogenetics
DeepPicker 20161102 [278] particle picking
DeepTools 2.4.3, 3.1.1 [279] biology, bioinformatics, NGS
DeFusion 20200305 [280] phylogenetics
Delft3D 7545 [281] Physics
Delly 0.7.5, 0.7.7, 0.7.8 [282] biology, phylogenetics
DeNoGAP 1.0 [283] biology, phylogenetics, ngs
DeTiN 1.7.5.9 [284] ngs, genomics
DETONATE 1.11, 1.9 [285] biology, rna-seq
DEXTRACTOR 1.0 [286] biology, sequencing
Diamond 0.8.25, 0.8.5, 0.9.15 [287] computational biology, genomics
DiCal2 2.2.0.1 [288] biology, phylogenetics
DiffReps 1.55.4 [289] Bioinformatics
DiscoSnp 2.2.10 [290] biology, phylogenetics
DISCOVAR de novo 52488 [291] biology, ngs, assembler
DiscoVista 20180906 [292] phylogenetics
Distruct 2.2 [293] phylogenetics
DIYABC 1.0.4.43b, 2.0.3, 2.1.0 [294] biology, phylogenetics
Dlib 19.19 [295] phylogenetics
DL_POLY 1.9 [296] Molecular Dynamics
DNA Clust 3.0 [297] biology,bioinformatics,genomics
DNA-ML 1.0 [298] Biology, NGS
DOCK 6.7, 6.8, 6.9 [299] chemistry
DosageConvertor 1.0.3 [300] biology
DOT 2.0 [301] biology,bioinformatics,docking
Doxygen 1.8.3.1 [302] programming, documentation
DRAP 1.91 [303] biology, phylogenetics
DRep 2.3.2 [304] phylogenetics
DSK 2.1.0, 2.3.0 [305] biology, NGS
DSSAT 4.6 [306] Agriculture
DSSP 2.2.1, 3.0.0 [307] Molecular Dynamics
Dtiprep 0.1.1 [308] phylogenetics
PHYLDOG 20130116-dbg [309] biology,bioinformatics,phylogenetics
DynamicDBG 20181003 [310] phylogenetics
Dynare 4.4.3 [311] math
EAGLE 2.0 [312] phylogenetics
Eagle-rc 1.1.1 [313] phylogenetics
Ea-utils 1.04.807.18, 1.1.2.537 [314] biology,bioinformatics,genomics,ngs
ECE 1.2 [315] ECE
EDirect 10.7, 12.2 [316] biology, phylogenetics
Edta 20190108 [317] phylogenetics
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [318] biology,bioinformatics,matlab
EGene-MVN 0.1 [319] biology, genetics
EggNOG-mapper 2.0.1 [320] phylogenetics
EGSnrc 2019 [321] phylogenetics
EIGENSOFT 4.2, 5.0.1, 6.0.1 [322] biology, bioinformatics
Elastix 4.9.0 [323] phylogenetics
ElPrep 4.1.4 [324] phylogenetics
Emacs 25.3 [325] programming, scripting, language
EMAN2 2.22, 2.31 [326] image processing
EMBOSS 6.5.7 [327] biology,bioinformatics
Embree 3.6.1 [328] ray, tracing, kernels
EMC 9.4.3 [329] Monte Carlo Simulations
EMMAX 20100307, 20120210 [330] biology, NGS, mapping
Ensembl Tools 80 [331] biology, bioinformatics
EnTAP 0.6.1.2, 20160416 [332] biology, phylogenetics
EPACTS 3.2.6, 3.4.2 [333] biology, bioinformatics, genomics
Epic 0.2.9 [334] Biology, Phylogenetics
Epiteome 1.0 [335] phylogenetics
Epoch 4.7.3 [336] astronomy,CCPP
EQTLA 1.1 [337] biology, bioinformatics, genomics
EQtlBma 1.2.2, 1.3.0r20140820 [338] biology, genotyping
Erpin 5.5.4 [339] biology, phylogenetics
ESOM 1.1 [340] biology, phylogenetics
ESPRESSO 6.2.0, 6.2.1, 6.4.1 [341] Quantum,modeling
ESPRIT 2009-nogap, 201102 [342] biology,bioinformatics
ETE2 2.1.539 [343] biology,phylogenetics
ETE3 3.0.0, 3.1.1 [344] biology, phylogenetics
Evigene 20180730 [345] phylogenetics
ExaBayes 1.5 [346] phylogenetics
Exonerate 2.2.0 [347] biology,bioinformatics,genomics
EXpress 1.3.1, 1.5.1 [348] biology,bioinformatics,ngs
Face_recognition 1.2.2 [349] phylogenetics
FALCON 20161027, 20161222, 20190601 [350] biology,bioinformatics,ngs,sequencing
FALCON_unzip 20161222 [351] biology, bioinformatics
FAR 2.15 [352] biology,bioinformatics,genomics
FAST 1.06 [353] biology phylogenetics
Fast-gep 1.0 [354] phylogenetics
Fast-Plast 1.2.6 [355] biology, phylogenetics
FASTA 34.26.5, 36.3.6d [356] biology,bioinformatics,genomics
FastANI 1.1 [357] phylogenetics
FastGEAR 20161216 [358] biology, bioinformatics, genomics
R8s 1.8 [359] phylogenetics
FastML 3.0 [360] biology,bioinformatics,phylogenetics
Fastp 0.20.0 [361] biology,bioinformatics,ngs
FASTphase 1.4.8 [362] phylogenetics
FastQ-Screen 0.14.0 [363] phylogenetics
Fastq-tools 0.8 [364] biology, NGS,
FastQC 0.11.4, 0.11.7, 0.9.6 [365] biology,bioinformatics,ngs
Fastsimcoal 2.6.0.3 [366] biology, phylogenetics
FastSpar 0.0.4 [367] biology, genomics
FastStructure 20150112 [368] biology, genomics
FastTree 2.1.7 [369] biology,bioinformatics,phylogenetics
FastUniq 1.1 [370] biology, phylogenetics
Fastx Toolkit 0.0.13.2, 0.0.14 [371] biology,ngs
FcGENE 1.0.7, 1.0.7.1 [372] biology,bioinformatics,genomics,snp
Fdupes 1.51 [373] file management
FEniCS 2018.1.0 [374] biology, phylogenetics
Ferret 6.82 [375] Data Visualization and Analysis, Oceanography, Meteorology
FFmpeg 2.1.3, 2.8.3 [376] Audio, Video
FFTW 3.3.4, 3.3.6, 3.3.7 [377] library,c,math
Fgbio 0.5.0, 0.7.0 [378] phylogenetics
FGMP 1.0.1 [379] phylogenetics
Fiji 2.0.0rc59 [380] ImageJ
Filtlong 0.2.0 [381] biology, phylogenetics
FineSTRUCTURE 1.8, 2.0.7, 2.1.3 [382] biology, population genetics
Flappie 1.1.0, 2.1.3 [383] phylogenetics
FLASh 1.2.10, 1.2.11 [384] biology, genomics
FLEA 2.0.0 [385] phylogenetics
Flex 2.6.4 [386] programming tool
Flexbar 2.3, 2.34 [387] biology, bioinformatics, genomics, ngs
FLEXLm 1.0 [388] Administration
Fluent 17.2, 19.1, 2020R1 [389] CFD
Flye 2.3.3, 2.6, 2.7.1 [390] Biology, NGS
FMRIPrep 1.3.2, 1.4.0a1, 1.5.4 [391] data mining
ForeSeqs 1.0.4 [392] phylogenetics
Pascal 3.0.0 [393] Compiler, Programming
Fqtools 20160224 [394] biology,bioinformatics,ngs,sequencing
FragGeneScan 1.16 [395] biology,genomics
FRAMA 20151019 [396] biology
FrameDP 1.2.2 [397] biology, sequencing
FreeBayes 1.3.1, 1.3.2, v0.9.15-1-g076a2a2 [398] biology,genomics
FREEC 11.0, 9.6 [399] biology, sequencing
Freesurfer 5.3.0, 6.0.0, 7.1.0 [400] biology,bioinformatics,neuroscience,imaging
FSL 5.0.8, 5.0.9, 6.0.1 [401] biology,bioinformatics,neuroscience,imaging
FusionInspector 1.1.0 [402] biology, phylogenetics
GAL 20180906 [403] phylogenetics
Galaxy 1.0 [404] biology,bioinformatics
GAMBIT 15.1.0, 16.0.0 [405]
GAML 20150610 [406] biology, bioinformatics, genomics
GapCloser 1.12r6 [407] biology, genomics, ngs
GapFiller 1.10, 1.11 [408] biology, genomics
GARLI 2.0, 2.01 [409] biology,bioinformatics,phylogeny
GASVPro 201310 [410] biology, bioinformatics, ngs
GATE 7.0 [411] Date analysis and visualization
GATK 4.1.2.0, 4.1.3.0, 4.1.4.0 [412] biology,bioinformatics,ngs
Gaussian 09, 09 A.02, 09 D.01 [413] Computational Chemistry
Gawk 4.2.0 [414] Software tools
Gblocks 0.91b [415] biology,bioinformatics
GNU Compiler Collection 6.3.0, 7.3.0, 8.2.0 [416] compilers
GCT 6.2.1 [417] gridftp, globus, toolkit
GCTA 1.24.7, 1.26.0, 1.92.4beta [418] biology, genomics, SNP,
GDAL 2.2.1, 2.2.4, 2.3.1 [419] Geospatial library
GDB 8.3 [420] Software Development
GDC-Client 1.0.1 [421] biology, bioinformatics, sequence, ngs
GDSL 1.18 [422] library
Geant4 4.10, 4.10.03, 4.10.5 [423] Physics
GEM 20130406 [424] biology,bioinformatics,ngs,sequencing
Gem5 2.0 [425] Computer Simulator
GEMMA 0.98.1 [426] phylogenetics
NCBI GenBank Tools 20140130 [427] Biology,bioinformatics,NCBI,GenBank
GeneMark-ES 4.33 [428] biology, genomics
GeneMarkS 2012.04, 3.10.001 [429] biology,genomics
GenePainter 2.0.4 [430] biology, phylogenetics
GeneSeqer 2014-02-26 [431] biology, genomics
Genesum 0.1.0 [432] biology,genomics
GeneTorrent 3.8.7 [433] biology,bioinformatics,data download
GenGen 1.0.1 [434] biology, phylogenetics
Genome_Graph_Annotation 20190131 [435] phylogenetics
Genome STRiP 2.00.1602 [436] biology, genomics, ngs
GenomeTools 1.5.7, 1.5.9 [437] biology, bioinformatics
Genomic-fluidity 20151109 [438] phylogenetics
GenomicNeuralnet 20161030 [439] phylogenetics
GenomicConsensus 2.3.3 [440] biology, phylogenetics
GenomicTools 2.7.0 [441] biology,bioinformatics,ngs,chip-seq,rna-seq
GenotypeHarmonizer 1.4.18 [442] biology, bioinformatics
Genrich 0.5 [443] phylogenetics
GenSel 4.90 [444] population genetics
Geopython 1.0.0, 1.0.1 [445] python, geospatial, cartography
GEOS 3.3.8, 3.6.2 [446] library, data
GeP 2.1 [447] biology, phylogenetics
Gepard 1.40.0 [448] phylogenetics
Gerbil 1.11 [449] phylogenetics
Get_homologues 20150529 [450] biology, genome
GetOrganelle 1.6.2e [451] phylogenetics
Gffread 0.9.8c [452] biology, bioinformatics
Gflags 2.2.1, 20150520 [453] google,libraries
GFOLD 1.1.4 [454] biology, RNA-seq
GHOST-MP 1.3.4 [455] phylogenetics
Ghostscript 9.21, 9.22 [456] PDF
Git 2.14.1 [457] Revision Control
Glactools 1.0.8 [458] phylogenetics
Glimmer 3.02 [459] biology, microbial annotation
GlimmerHMM 3.0.4 [460] biology, microbial annotation
Globus 1.10.1, 2.1.3 [461] Data Transfer
Glog 0.3.5 [462] google,libraries
GLPK 4.55, 4.65 [463] Programming
Glueviz 0.15.2 [464] phylogenetics
GMAP 20180212, 20180212_sse2, 20190610 [465] biology, bioinformatics, genomics, ngs
GMcloser 1.6 [466] Biology, NGS
GMP 6.1.2 [467] library, crypto
GnuPlot 4.6.0, 5.2.2, 5.2.3 [468] graphics,plotting,math
Go 1.11.1, 1.12.9, 1.13.6 [469] programming language
GOMAP 1.3 [470] biology, bioinformatics, ngs
Gotcloud 1.17.5 [471] phylogenetics
GPA 1.1 [472] phylogenetics
GPhoCS 1.2.3 [473] phylogenetics
Grace 5.1.22 [474] graphics, statistics, 2D
GRACKLE 3.1 [475] library,c,astrophysics
GrADS 2.0.1 [476] environment, grid analysis
Graftm 0.12.2 [477] phylogenetics
GramCluster 1.3 [478] biology,sequencing,
Graph_annotation 0.1 [479] phylogenetics
GraPhlAn 0.9.7 [480] biology, phylogenetics
GraphMap 0.4.0 [481] biology, nanopore sequencing
GraphViz 2.38.0 [482] biology,bioinformatics,neuroscience,imaging
GRASS 7.0, 7.4 [483] Geography
Grf 1.0.0 [484] genomics, bioinformatics
Grib_api 1.10.1, 1.15.1, 1.26.1 [485] C, fortran, library
GRIDSS 2.6.2 [486] phylogenetics
GROCSVs 0.2.5 [487] phylogenetics
GROMACS 2018.0, 2019.2 [488] Computational Chemistry, Molecular Dynamics
GroopM 0.3.5 [489] biology, phylogenetics
Groovy 2.4.15 [490] Programming
Gscripts 1.1 [491] scripts
GSEA 3.0.0 [492] biology, bioinformatics, genomics
GSL 2.4, 2.5, 2.6 [493] library, data
GSNP 1.0 [494] biology,bioinformatics,ngs
GTDBTk 0.1.3 [495] phylogenetics
GUAVA 1.0 [496] phylogenetics
Gubbins 20150519, 20150902, 20160421 [497] biology, bioinformatics, genomics, phylogenetics
Guile 2.2.2 [498] Programming Language
GULP 4.4, 5.0 [499] Material Science
Guppy 3.5.1, 3.6.0, 3.6.1 [500] phylogenetics
GWAMA 2.2.2 [501] phylogenetics
HALC 1.1 [502] biology, phylogenetics
HaMStR 13.2.3, 13.2.4, v8b [503] biology, genome
HapCompass 0.7.7 [504] ngs, genomics
HAPCUT 0.7 [505] biology, assembly
HAPLOSWEEP 1.0 [506] biology, phylogenetics
HapQTL 1.00 [507] biology
Hapsembler 2.21 [508] biology, bioinformatics, assembly
HDF4 4.2.11 [509] library, data
HDF5 1.8.19, 1.8.20, 1.8.9 [510] library, data
HECIL 20180926 [511] phylogenetics
HELEN 0.0.1 [512] phylogenetics
HelitronScanner 1.1 [513] phylogenetics
HGCoLoR 1.1.1 [514] phylogenetics
HGTFinder 20160720 [515] biology, genomics
Hifiasm 0.4 [516] phylogenetics
HISAT2 2.0.5, 2.1.0, 2.2.0 [517] Biology, Sequence Alignment, NGS
HLAHD 1.1.1 [518] biology, phylogenetics
HLAminer 1.3.1 [519] biology, phylogenetics
HMM-FRAME 20140724 [520] phylogenetics
HMMER 3.1b1, 3.1b2, 3.2.1 [521] biology, genome
HomBlocks 1.0 [522] biology, phylogenetics
HOMER 4.10, 4.8 [523] biology,bioinformatics,sequence,ngs
HOOMD 2.1.7 [524] library, math
HPL 2.1 [525] parallel programming, benchmarks, MPI
HTMLDoc 1.8.28, 1.9.3 [526] pdf, docs, html
HTSeq 0.11.0, 0.11.2, 0.9.1 [527] biology, bioinformatics, ngs
Humann2 0.11.2, 2.8.1 [528] phylogenetics
Hyb 20141126 [529] biology, ngs, RNA-Seq
HybPhyloMaker 1.5 [530] biology, phylogenetics
HybPiper 1.2, 1.3.1 [531] biology, phylogenetics
HyPhy 2.5.4, 2.5.7, 2.5.8 [532] biology,bioinformatics,evolution
HYPRE 2.11.2, 2.18.2 [533] Math, Numerical Solvers
IAnnotateSV 1.0.6, 1.0.9 [534] Biology, Phylogenetics
IAssembler 1.3.2 [535] biology, assembly
Ibdne 20150815 [536] biology,ngs
ICallSV 0.0.6 [537] Biology, Phylogenetics
Icommands 3.3.1 [538] iRods
ICORN2 0.95 [539] biology, sequencing
IDBA-MT 1.0 [540] biology,NGS
IDBA-UD 1.1.1, 1.1.1-512, 1.1.1-512-mem [541] Genomics, bioinformatics, phylogenetics
IDL 8.3 [542] language, programming, science
IDR 2.0.3 [543] phylogenetics
IGB 8.4.1 [544] biology, bioinformatics, genomics
IgBLAST 1.5.0, 1.7.0 [545] biology, bioinformatics
IGoR 1.4.0 [546] phylogenetics
IGTP 1.1 [547] biology, bioinformatics, phylogenetics
IGV 2.3.91, 2.4.16 [548] biology, bioinformatics, ngs, phylogenetics
Illumina-utils 2.0.2, 2.3 [549] biology
IM and IMa 20091217 [550] biology,bioinformatics,population genetics
Ima2 20120827 [551] biology,bioinformatics,population genetics
IMa2p 20170712 [552] biology, phylogenetics
IMA3 22Aug18 [553] Molecular Dynamics
ImageJ 1.48 [554] imaging
ImageMagick 7.0.8-20 [555] Imaging
IMOD 4.7.15, 4.9.10 [556] 3D modeling, image reconstruction
Intel MPI 5.1.1 [557] parallel programming, development, MPI, library
Infernal 1.1.1 [558] biology, sequence alignment
INLA 20160718, 20170620 [559] statistics, modeling, R
InParanoid 4.1 [560] biology, biology
InStruct 20160723 [561] phylogenetics
Intel Compilers and Libraries 2018.1.163, 2019.1.144, 2020.0.166 [562] programming languages, development, library, math, intel
Intervene 0.6.2 [563] biology, phylogenetics
IOAPI 3.1, 3.2 [564] Meteorology
IPOPT 3.12.10, 3.12.6 [565] library, c/c++,math, solver, optimization
InterProScan 5.31-70.0, 5.34-73.0, 5.35-74.0 [566] biology,bioinformatics
Ipyrad 0.7.24, 0.7.30, 0.9.53 [567] phylogenetics
IQ-TREE 2.0-rc1, 2.0-rc2, 2.0.3 [568] biology, phylogenetics,
IRAP 0.8.1p7 [569] biology, ngs, pacbio
IRep 20161025 [570] biology, microbiology
IRFinder 1.0.0, 1.2.0 [571] biology, RNA-Seq
IsoSeq3 3.0.0, 3.1.0, 3.2.2 [572] biology, bioinformatics, ngs, pacbio
ISOWN 20180820 [573] phylogenetics
IsPcr 3.3 [574] biology, phylogenetics
ITK 3.20.1, 4.10.1 [575] Bioinformatics
ITK-SNAP 3.0.0, 3.8.0 [576] biology,bioinformatics,neuroscience,imaging
ITSx 1.1b [577] phylogenetics
Jabba 1.0 [578] biology, phylogenetics
JACUSA 1.2.0 [579] biology, bioinformatics, ngs, phylogenetics
JAGS 3.3.0, 3.4.0, 4.2.0 [580] Statistics
NpScarf 1.7 [581] phylogenetics
JDK 11.0.1, 14, 9.0.1 [582] programming,runtime
JCVI 0.8.12 [583] phylogenetics
Je 1.0 [584] biology, NGS
Jellyfish 2.2.4, 2.2.6, 2.3.0 [585] biology,ngs
JModelTest 2.1.1 [586] biology, bioinformatics, genomics, phylogenetics
Jo 1.3 [587] Software
Jq 1.6 [588] Software
Julia 0.4.6, 0.6.4, 1.0.0 [589] programming, language, statistics
Jupyter 5.6.0, 5.7.0, 5.7.8 [590] python, R, jupyter
JVARKIT 20180405 [591] biology, phylogenetics
Kaiju 1.6.2, 1.7.2 [592] biology, phylogenetics
KaKs 1.2, 2.0 [593] biology, bioinformatics, evolution, phylogenetics
Kallisto 0.42.4, 0.43.0, 0.44.0 [594] biology,NGS,RNA-Seq
KAT 2.3.4 [595] biology, phylogenetics
Khmer 2.0, 2.1 [596] Biology, NGS
KIM 1.8.0, 1.8.2, 1.9.3 [597] Simulation
KINFIN 1.0.1 [598] biology, phylogenetics
KING 2.1.2 [599] biology, genome, gwas
KisSplice 2.4.0-p1 [600] biology, RNA
KMC 3.1.0, 3.1.1 [601] phylogenetics
Kmer 1934 [602] biology,bioinformatics,ngs,sequencing
KMOS 0.3.21 [603] phylogenetics
Kneaddata 0.7.4 [604] phylogenetics
Kraken 1.0, 2.0.6b, 2.0.8b [605] biology, ngs
Krocus 1.0.1 [606] phylogenetics
Krona 20161019 [607] biology, bioinformatics
Ksnp 3.021 [608] biology, phylogenetics, SNP
Lace 0.99 [609] biology, NGS
LACHESIS 2.1 [610] phylogenetics
Lambda 0.9.4, 1.0.3, 2.0.0 [611] biology, sequencing, phylogenetics
LAMMPS 30Jul16, 7Aug19, 7Dec15 [612] Molecular Dynamics
LAMP 2.5 [613] biology, bioinformatics, genomics
LAPACK 3.8.0 [614] programming,library,fortran
Last 801, 916, 979 [615] biology,bioinformatics,sequence,alignment
LAStools 20200114 [616] LiDAR
LASTZ 1.02.00, 1.03.02, 1.04.00 [617] biology,bioinformatics,ngs
Lbzip 2.5 [618] compression
LDhat 2.2a [619] biology,genomics
LEfSe 20180219 [620] phylogenetics
LFMM 1.4, 1.5 [621] biology, phylogenetics
ChartDirector 5.1.0 [622] library, data
Libint 2.5.0, 2.5.0b [623] library
LEMON 1.2.3 [624] library
Libunistring 0.9.7 [625] library
Libvips 8.5.4 [626] image processing
LIBXC 4.2.3, 4.3.4 [627] library, density function
LIBXSMM 1.13 [628] library,c,math
LIBZMQ 4.3.1 [629] library
LIGR 2.05 [630] biology,assembly
LINKS 1.8.5, 1.8.6 [631] biology, genomics
Linksbrowser 2.14 [632] web browser
LMAP 1.0.2 [633] biology, phylogenetics
LncScore 1.0.2 [634] biolgoy, phylogenetics
LobSTR 4.0.6 [635] biology, phylogenetics
Localizer 1.0.4 [636] phylogenetics
LocusZoom 1.4 [637] phylogenetics
LoFreq 2.1.3.1 [638] phylogenetics
LongRanger 2.1.5, 2.2.2 [639] biology, phylogenetics
LORMA 0.3, 0.5 [640] biology, ngs, pacbio
LS-DYNA 700, 711, 901 [641] Physics
LSD2 1.6.5 [642] phylogenetics
Ltr_finder 1.07 [643] biology, phylogenetics
LTRRetriever 2.1, 2.5, 20170514 [644] biology, phylogenetics
Lua 3.5.2 [645] programming, scripting, language
Lumpy-sv 0.2.1, 0.2.13 [646] biology, genotyping
LZO 2.09 [647] library, compression
M5nr 20121126 [648] biology, bioinformatics, genomics
Macaulay2 1.15 [649] phylogenetics
MACE 1.2 [650] phylogenetics
MACH 1.0.18 [651] biology,bioinformatics,genomics,ngs
Mach2VCF 20150515 [652] biology
MACS 2.0.10, 2.1.2 [653] biology, bioinformatics, CHiP-Seq
MafFilter 1.3.0 [654] phylogenetics
MAFFT 7.245, 7.294, 7.397 [655] bio,bioinformatics,sequence
MafTools 0.1 [656] phylogenetics
MAGeCK 0.5.7 [657] phylogenetics
Majiq 1.0.5, 2.1 [658] biology, phylogenetics
Maker 2.31.10, 2.31.6 [659] biology,bioinformatics
MAnorm 20120316 [660] biology, phylogenetics
Mantis 1.0.4 [661] phylogenetics
MapThin 1.11 [662] phylogenetics
Maq 0.7.1 [663] biology,bioinformatics,ngs
MarginPolish 1.0.0 [664] phylogenetics
MARK 2.0.1 [665] application, data, capture
MarkerMiner 20150710 [666] biology, bioinformatics, genomics
Mash 1.1 [667] biology, genomics
MASSMINE 0.10.0, 0.11.0, 0.9.5 [668] data mining
MaSuRCA 3.2.4, 3.3.0, 3.3.4 [669] biology, bioinformatics, short read alignment
MATLAB 2018b, 2019a, 2019b [670] math,language
MATS 3.2.5, 4.0.1, 4.0.2 [671] biology,bioinformatics,ngs,rna-seq
Mauve 2.3.1 [672] biology,ngs,genomics
Mawk 1.3.4-20150503 [673] programming language
Maxbin 2.1.1 [674] biology,NGS
Maxima 5.41.0 [675] Math
MC 4.6.1 [676] shell
MCarts 1.0.2 [677] biology, genomics, markov
Mccortex 1.0 [678] phylogenetics
MCL 12-135, 14-137 [679] biology, genomics
MCNP 6, 6.1 [680] Physics
MCNPX 2.7.0 [681] Physics
MCR 2018a, 2018b, 2019b [682] math, language
MCScanX 20130328 [683] biology, phylogenetics
MECAT 20180308 [684] phylogenetics
Medaka 0.6.2, 0.7.1, 1.0.1 [685] biology, phylogenetics
Medusa 1.6 [686] phylogenetics
MEGA 7.0.26 [687] biology, phylogenetics
Mega2 4.9.2 [688] biology, phylogenetics
MEGAHIT 1.1.1, 1.1.4 [689] biology, phylogenetics
MEGAN 5.10.3, 6.4.15 [690] biology, bioinformatics, ngs
Megraft 1.0.2 [691] biology,sequencing,
MELTING 4.3.1 [692] biology, genome, RNA, folding
MEME 4.9.1, 5.0.2, 5.0.5 [693] biology,bioinformatics,sequence
MentaLiST 0.1.3 [694] biology, phylogenetics
Meraculous 2.0.5 [695] Biology,NGS
Mercurial 4.8.2 [696] Revision Control
Merlin 1.1.2 [697] biology,SNP
Meshroom 2019.2.0 [698] phylogenetics
Meta-Tissue 0.4 [699] biology, genetics
MetaBAT 0.32.4, 2.13 [700] biology, genomics
Metabin 1.0 [701] Genomics, bioinformatics, metagenomics
MetaCherchant 0.1.0 [702] biology, phylogenetics
MetaCluster 5.0b [703] biology,bioinformatics,genomics
MetaCompare 20181016 [704] phylogenetics
MetaCV 2.3.0 [705] Biology, NGS
MetaGeneMark 2.10, 3.26 [706] biology,genomics
METAL 20110325 [707] biology, ngs, genomics
METANNOT 20171129 [708] phylogenetics
Metaphinder 20161215 [709] biology, phylogenetics
MetaPhlAn2 2.7.7, 2.96.1 [710] biology, phylogenetics
MetaPhysicl 1.0.0 [711] Math, Astronomy, Numerical Simulation
MetaSUB_Utils 3.0.0 [712] phylogenetics
MetaSV 0.5.4 [713] biology, phylogenetics, NGS
MetaVelvet 1.2.06 [714] computational biology, genomics
MetaWRAP 1.2 [715] phylogenetics
Metaxa2 2.1.1, 2.1.3 [716] biology,bioinformatics,ngs,sequencing
MethylDackel 0.5.0 [717] phylogenetics
Methylpy 1.2.9 [718] Biology, Phylogenetics
Metilene 0.2.8 [719] biology, genomics, methylation
METIS 5.1.0 [720] software
Mfannot 20180405 [721] biology, phylogenetics
Mfold 3.6 [722] bioinformatics,structure,RNA
Mg-rast 20150919 [723] biolgoy, genomics
MGEScan 20160416 [724] biology, genomics
MHAP 1.6 [725] biology, sequencing
MHCflurry 1.4.3 [726] phylogenetics
MIA 20130201 [727] biology, ngs
MicrobeCensus 1.0.7 [728] biology, NGS
MIDAS 20160830 [729] biology, phylogenetics
MIGRATE-N 3.3.0, 3.6.6, 4.2.14 [730] biology,bioinformatics,population genetics
MIKE 1.0 [731] environment,water,modeling
Minced 0.2.0 [732] biology, genomics
Miniasm 0.2-r168, 0.3-r179 [733] biology, phylogenetics
MiniCaller 20161201 [734] biology,bioinformatics,ngs,phylogenetics
Minimac2 1-20130717, 2-20140915, 3-20150727 [735] biology, NGS,
Minimap 2.17, 2.1t, 2.9-r720 [736] biology, phylogenetics
Minipolish 0.1.2 [737] phylogenetics
MinPath 1.4 [738] biology, phylogenetics
MIRA 4.0.rc1, 4.9.6, 5rc2 [739] biology,bioinformatics,genomics,assembly
MiRanda 1.9 [740] phylogenetics
MiRBShunter 0.2 [741] phylogenetics
Mirdeep 0.1.0, 0.1.1 [742] phylogenetics
Mireap 0.20 [743] biology
MIReNA 2.0 [744] biology, phylogenetics
MiRge 2.0 [745] phylogenetics
Misa 1.0 [746] biology, bioinformatics, genomics
MISO 0.5.3 [747] biology,bioinformatics,ngs,sequencing,rna-seq
MITE-Hunter 20111101 [748] biology, phylogenetics
MITObim 1.9.1 [749] phylogenetics
MitoFinder 1.0.2, 1.1 [750] phylogenetics
MitoPhAST 3.0 [751] phylogenetics
MiXCR 2.1.8 [752] biolgoy, phylogenetics
MixMHC2pred 1.2 [753] phylogenetics
MixMHCpred 2.0.2 [754] phylogenetics
Mixmogam 20190322 [755] phylogenetics
MKL 2018.1.163, 2019.1.144, 2020.0.166 [756] programming, development, library, math, intel
Mlcoalsim 1.9916b [757] biology, phylogenetics
Mlst 2.15.2 [758] phylogenetics
Mlstcheck 2.1 [759] phylogenetics
MMSEQ 1.0.8 [760] biology,bioinformatics,genomics
MOABS 1.2.9, 1.3.2, 1.3.4 [761] biology, ngs
MODELLER 9.14, 9.23 [762] biology,bioinformatics,modelling,structure
MODELTEST 0.1.2 [763] biology, phylogenetics
Molden 5.0 [764] Molecular, Electronic Structure
MongoDB 4.0.3 [765] db, mongodb, mongo
Mono 5.18 [766] linux, runtime
Monolix 4.3.2 [767] modeling, pharmacokinetics
MOOSE 20180404, 20200316 [768] physics, simulation
MOSAIK 2.1.33, 2.2.3, 2.2.30 [769] biology,bioinformatics,short read alignment
Mosdepth 0.2.3 [770] biology, phylogenetics
Mothur 1.37.0, 1.38.1, 1.41.3 [771] biology, microbial ecology
MotionCor2 1.2.3, 1.3.1 [772] Motion Correction
MOTU 1.1 [773] biology, bioinformatics, genomics
MOTUs 2.5.1 [774] phylogenetics
MountainSort 0.9.0 [775] library
MPACK 0.8.0 [776] library
MPB 1.5 [777] library, math
MPBoot 1.1.0 [778] biology, phylogenetics
MP-EST 1.4, 1.5 [779] biology,bioinformatics,ngs,sequencing
MPFR 3.1.6 [780] library, math
Mpinterfaces 20170613 [781] DFT
MrBayes 3.2.4, 3.2.5, 3.2.6 [782] application, biology, phylogenetics
MRIcroGL 20180623 [783] biology, mri, imaging
MRIcron 201306, 20161012 [784] biology, mri, imaging
Mriqc 0.11.0 [785] mri, imaging, biology
MRtrix 3.0rc2 [786] biology, mri, imaging
Ms 20171108 [787] phylogenetics
MSINGS 20180810 [788] phylogenetics
MstatX 1.0 [789] biology, phylogenetics
MSTmap 1.0 [790] phylogenetics
Msvar 1.3 [791] biology,bioinformatics,population genetics
MTG2 2.15 [792] phylogenetics
Mugsy 1.2.3 [793] biology, phylogenetics
MultiGeneBlast 1.1.13 [794] phylogenetics
MultiQC 1.1, 1.5, 1.7 [795] biology, bioinformatics, CHiP-Seq
MUMmer 3.23, 4.0.0beta2 [796] biology,bioinformatics,genomics
MUSCLE 3.8.31 [797] biology, bioinformatics, alignment
Musket 1.1 [798] biology, genomics, ngs
MuTect 1.1.4, 1.1.7 [799] biology,genomics
MutSig 1.4, 1.41 [800] biology,genomics
Mvftools 20191124 [801] phylogenetics
MZMine 2.41, 2.52, 2.53 [802] biology, bioinformatics, spectrometry, NMR
NAMD 2.12, 2.13 [803] Molecular Dynamics
NANO 2.8.2 [804] Text Editor
NanoCount 0.2.1 [805] phylogenetics
Nanofilt 20180408 [806] biology, bioinformatics
Nanopack 1.0.0 [807] phylogenetics
NanoPlot 1.0.0 [808] Biology, Plotting
Nanopolish 0.11.1, 0.13.2, 20171006 [809] biology
NanoSV 1.2.0, 1.2.3, 1.2.4 [810] biology, genomics
NanoVar 1.0.1 [811] phylogenetics
NBODY 6 [812] Astronomy
Ncbi-vdb 2.6.3, 2.8.2 [813] SRA toolkit library
NCBI BLAST+ 2.7.1, 2.8.1, 2.9.0 [814] biology, bioinformatics
NCBI C++ Toolkit 12.0.0, 21.0.0, 7.0.0 [815] Biology,bioinformatics,NCBI,programming,library,cpp
Ncftp 3.2.5 [816] file transfer
NCL 6.1.2, 6.3.0 [817] Atmosphere Science
NCO 4.2.1, 4.4.3 [818] data tools
Ncview 2.1.2, 2.1.7 [819] data visualization
Neat-genreads 20171102, 20190331 [820] biology, bioinformatics, phylogenetics
Necklace 1.00 [821] biology, phylogenetics
NeEstimator 2.01, 2.1 [822] Biology, Bioinformatics
Neovim 0.2.0 [823] editor, text, ide, vim
NetCDF 4.3.3, 4.4.3, 4.7.2 [824] data, exchange
NetCDF-C 4.4.1.1, 4.5.0, 4.6.1 [825] data, exchange
NetCDF-Fortran 4.4.3, 4.4.4 [826] data, exchange
NetLogo 5.3.64, 6.1.1 [827] modeling
NEURON 7.4, 7.6.2, 7.7.2 [828] biology, neuroscience
Newbler 2.7, 2.8, 2.9 [829] biology,bioinformatics,ngs,454,assembly,denovo
Newick_utils 1.6 [830] biology, phylogenetics
Newick-utils 1.6 [831] biology, bioinformatics, genomics, phylogenetics
Nextflow 19.07.0, 19.10.0, 20.01.0 [832] biology, bioinformatics, workflow
NextGenMap 0.5.3, 0.5.5 [833] biology, bioinformatics, ngs
Nextstrain 1.16.1 [834] phylogenetics
NGmerge 0.3 [835] phylogenetics
Ngmlr 0.2.6, 0.2.7 [836] biology, phylogenetics
NGS-SDK 1.2.4, 1.3.0 [837] biology,bioinformatics,ncbi,sdk,library
Ngs-bits 0.1 [838] biology, sequencing
Ngscheckmate 1.0 [839] phylogenetics
Ngstools 20150816 [840] biology, ngs
NGSUtils 20160507 [841] biology, ngs
Nipype 1.2.0, 1.4.1 [842] biology,bioinformatics,neuroscience,imaging
Nlr-annotator 0.7 [843] phylogenetics
NLR-Parser 1.0 [844] phylogenetics
NMRPipe 7.9, 8.2 [845] Biochemistry
NONMEM 7.2, 7.3.0 [846] Modeling
NORGAL 1.0.0 [847] phylogenetics
Novoalign 2.08.02, 3.00.02 [848] biology,bioinformatics,ngs
NOVOPlasty 3.2, 3.7 [849] phylogenetics
NQuire 20180405 [850] phylogenetics
NtEdit 1.2.1 [851] phylogenetics
NucDiff 2.0.2 [852] phylogenetics
NucleoATAC 0.3.1 [853] biology, bioinformatics
Nullarbor 1.41 [854] biology, phylogenetics
Numba 0.36.2, 0.43.1, 0.48.0 [855] Compiler
NUPACK 3.2.2 [856] phylogenetics
NWChem 6.8 [857] Chemistry
NxTrim 0.4.1 [858] biology, bioinformatics, ngs
Oases 0.2.08 [859] biology,ngs,assembler
Obitools 1.2.11 [860] biology, bioinformatics, phylogenetics
OCaml 4.02.3 [861] programming languages, scripting, development
OCOCO 0.1.2.6 [862] biology, phylogenetics
Octave 4.2.1 [863] numerical computation
Olego 1.1.2, 1.1.5, 1.1.6 [864] biology,bioinformatics,ngs,rna-seq
OmicsBox 1.1.78 [865] Image Processing
OMindel 20180129 [866] phylogenetics
OMSV 1.0.1 [867] phylogenetics
ONT-Bonito 0.0.5, 0.1.5 [868] phylogenetics
Ont_fast5_api 2.0.1 [869] phylogenetics
Ont_tutorial_cas9 20190705 [870] phylogenetics
OPENACC 16.7 [871] Programming, Accelerator toolkit
OpenBabel 2.3.2, 2.4.1 [872] biology, bioinformatics
OpenBLAS 0.2.20 [873] programming,library
OpenCL 18.1.0.013 [874] phylogenetics
OpenCV 2.4.13, 2.4.8 [875] Computervision
OpenFOAM 4.1, 5.0 [876] Computational Fluid Dynamics
OpenMPI 4.0.0, 4.0.1, 4.0.3 [877] parallel programming, development, MPI, library
OpenPIV-python-gpu 0.21.2, 20190506-gpu [878] python, imaging
OpenSlide 3.4.1 [879] imaging
Opera 2.0.6 [880] biology, phylogenetics
OptiType 1.3.1 [881] biology, phylogenetics
Orange3 3.3.6 [882] data mining
ORCA 4.0.1.2 [883] Molecular, Electronic Structure
OrganellePBA 20180904 [884] phylogenetics
OrthoFiller 1.1.4 [885] phylogenetics
OrthoFinder 1.0.2, 1.1.10, 2.3.11 [886] biology, ngs
Orthograph 0.6.3 [887] Orthology
OrthoMCL 2.0.3, 2.0.7 [888] biology,genomics
OTB 5.8.0 [889] Geospatial Data Modeling
P4est 1.1 [890] Library
P4vasp 0.3.29, 0.3.30 [891] Molecular, Electronic Structure
P53MH 20020901 [892] biology, DNA-sequencing
P7zip 9.20.1 [893] archiver
PacBio 7.0.0.63985, 7.0.1.66975, 8.0.0.79519 [894] biology, bioinformatics, ngs
Package-GFE 20150701 [895] biology,genomics
PALADIN 1.3.1 [896] biology, phylogenetics
PALES 122 [897] physics
PAML 4.8a, 4.9a, 4.9h [898] biology, phylogenetics
Pandaseq 20140808, 20150627 [899] biology,bioinformatics,ngs,sequencing
Pandoc 2.2.2.1 [900] Converter
PanX 1.6.0 [901] phylogenetics
PAPI 5.5.1, 5.7.0 [902] programming interface, performance analysis
Parallel 20150122, 20170322 [903] shell, process management
Paralyzer 1.5 [904] phylogenetics
ParaView 5.4.0, 5.4.1, 5.7.0 [905] Data Analysis
PARSIMONATOR 1.0.2 [906] biology, bioinformatics
Parsnp 1.2 [907] biology, phylogenetics
PartitionFinder 2.1.1, 2.1.1-20161205, 2.1.1.0 [908] biology,phylogenetics,evolution
PASA 2.0.2-r20150209, 2.0.2-r20151207, 2.2.0-r20171013 [909] biology, bioinformatics, genomics, ngs
PASTA 0.2.0, 20160616 [910] biology, sequence alignment
PATHd8 1.0 [911] biology, phylogenetics
PAUDA 1.0.1 [912] biology,bioinformatics,ngs,phylogenetics
PAUP 4.0a165, 4.0a166, 4.0b10 [913] inferring and interpreting phylogenetic trees
Pauvre 0.1.86 [914] biology, phylogenetics
PB-Assembly 0.0.6 [915] biology,bioinformatics,ngs,sequencing,pacbio
Pbalign 20160921, 20161221 [916] biology, bioinformatics
Pbcore 1.7.1 [917] biology,bioinformatics
PBJelly 15.8.24 [918] biology,bioinformatics,ngs
Pbrt 20181017 [919] phylogenetics
Pbsmrtpipe 0.63.0 [920] biology,API
Pbtranscript-tofu 20150317, 20160119 [921] biology, bioinformatics, ngs, pacbio
PCIT 2014 [922] Bioinformatics
PCRE 8.38, 8.39 [923] perl, library
PDA 1.0.3 [924] biology, phylogenetics
Pdb2pqr 2.1.0 [925] protein, modeling, pdb
Program Database Toolkit 3.20, 3.22, 3.24 [926] programming languages, development, performance analysis
PeakSplitter 1.0 [927] biology, bioinformatics, CHiP-Seq
PEAR 0.9.2 [928] biology, genomics, ngs
PECaller 1.0.0 [929] biology, NGS
PennCNV 1.0.5 [930] phylogenetics
Perl 5.16.0, 5.20.0, 5.24.1 [931] programming,scripting,language
PerM 0.4.0 [932] biology,bioinformatics,ngs,mapping
PETSc 3.8.1, 3.8.3, 3.8.4 [933] Math, Numerical Solvers
PfamScan 1.3, 1.5 [934] biology, genome
PGDSpider 2.0.9.0 [935] biology, NGS
PhaME 1.0.3 [936] phylogenetics
PHASE 2.1.1 [937] phylogenetics
PHAST 1.4, 1.5 [938] biology,phylogeny
Phenix 1.10.2155, 1.17.1, 1.8.1069 [939] crystallography
PHI 3.1.1, 3.1.2b [940] Calculations
PhiSpy 3.2 [941] phylogenetics
PHITS 2.76, 2.82, 2.84 [942] Physics
PHLAWD 20170427 [943] biology, phylogenetics
PhotoScan 1.4.1, 1.4.5 [944] Image Processing
Photutils 0.5 [945] astronomy, photometry
PHYLIP 3.696 [946] biology,phylogenetics
PhyloBayes 3.3f [947] biology,bioinformatics,phylogenetics
Phylonet 3.5.7 [948] biology, phylogenetics
PhyloParser 20180404 [949] phylogenetics
PhyloPhlAn 0.99 [950] phylogenetics
PhyloPhlAn2 0.41 [951] phylogenetics
PhyloSift 1.1 [952] biology, genomics, phylogenetics, taxonomy
Phyluce 20180727, 20190308, 20191015 [953] biology,bioinformatics,ngs,sequencing
PhyML 3.0, 3.1 [954] biology,bioinformatics,phylogenetics
Phynd 20200409 [955] phylogenetics
PHYUTILITY 2.7.1 [956] biology, bioinformatics
Phyx 20190403 [957] phylogenetics
PIA2 20180305 [958] biology, phylogenetics
Picard-tools 2.5.0, 2.9.0, 2.9.2 [959] biology,bioinformatics,ngs
PICRUSt 1.0.0, 1.1.0, 1.1.3 [960] biology, phylogenics
PICRUSt 2.3.0b [961] biology,phylogenics
Piggy 20171220 [962] biology, bioinformatics, ngs
Pigz 2.4 [963] Compression
PILON 1.22 [964] biology, bioinformatics, ngs, phylogenetics
Pindel 0.2.5b8 [965] biology, phylogenetics
Pipe-clip 1.1.0 [966] biology,NGS
PiPipes 1.5.0 [967] phylogenetics
Pipits 1.3.6, 1.4.0 [968] biology, sequencing
Piranha 1.2.1 [969] biology,phylogenetics
PIRS 2.0.2 [970] biolgoy, phylogenetics
Plasflow 1.1 [971] biology, phylogenetics
PLAST 1.0, 2.3.2 [972] biology,bioinformatics
Platanus 1.2.4 [973] phylogenetics
Platypus 0.8.1 [974] biology,bioinformatics,ngs
PLEK 1.2.2 [975] biology, phylogenetics
Plink 1.90b3, 1.90b3.39, 2.00a2 [976] biology,bioinformatics,genomics,phylogenetics
Plinkseq 0.10 [977] biology, bioinformatics, library
PloidyNGS 3.1.2 [978] phylogenetics
PolyPHen 2.2.2.r405b [979] biology, genomics
Pomoxis 0.1.11, 0.2.5, 0.3.2 [980] biology, phylogenetics
Ponytools 0.1 [981] biology, genomics
PopLDdecay 3.40 [982] phylogenetics
Popoolation 1.2.2 [983] biology, phylogenetics
Porechop 0.2.3, 0.2.4 [984] biology, bioinformatics
PosiGene 20171113 [985] biology, phylogenetics
POTION 1.1.2 [986] phylogenetics
POV-Ray 3.7 [987] 3D Graphics
PRANK 170427, 20150803 [988] biology, bioinformatics, alignment
Preplot 14.0.2 []
Preseq 0.0.4 [989] biology, bioinformatics, ngs
PRICE 1.2 [990] biology, bioinformatics, ngs
Primer3 2.3.4 [991] biology,bioinformatics,genomics
Primus 1.8.0 [992] biology, phylogenetics
PRINSEQ 0.20.4 [993] biology, sequencing
PRINSEQ++ 1.2 [994] phylogenetics
ProbABEL 0.4.2, 0.4.3, 0.4.5 [995] Genomics, bioinformatics, gwas
Probalign 1.4 [996] biology, bioinformatics, ngs
Processing 3.4 [997] java, language, programming, visual
Prodigal 2.6.2, 2.6.3 [998] biology, genomics
Libproj4 4.9.2, 4.9.3, 5.1.0 [999] library, geospatial, cartography
Prokka 1.10, 1.12 [1,000] biology,bioinformatics,genomics,assembly
Proovread 1.03rcl, 2.12, 2.13 [1,001] biology, genomics, ngs
ProSplign 1.0.0 [1,002] phylogenetics
Protege 5.1.0 [1,003] Ontology
Proteinortho 4.26, 5.11, 5.16 [1,004] biology, genomics
ProtExcluder 1.2 [1,005] biology, phylogenetics
Protobuf 2.5.0, 3.5.1 [1,006] google, libraries
PROVEAN 1.1.5 [1,007] biology, genomics
PSMC 0.6.5 [1,008] phylogenetics
PsRobot 1.2 [1,009] phylogenetics
PureCLIP 1.1.1 [1,010] phylogenetics
PurgeDups 1.0.1 [1,011] phylogenetics
PVACtools 1.0.4 [1,012] biology, phylogenetics
Pyani 0.2.1, 0.2.7 [1,013] biology, genomics
PyCharm 2018.3 [1,014] editor, ide, programming, python
PyCogent 1.9 [1,015] biology, genomics
PyDeface 2.0.0 [1,016] mri, imaging
Pyfaidx 0.5.2 [1,017] biology, bioinformatics, ngs, sequencing
Pyfasta 0.5.2 [1,018] biology, phylogenetics
Pygot 20170518 [1,019] biology, phylogenetics
Pyhdf 0.9.0 [1,020] library, hdf4
PyPHLAWD 20180416, 20190414 [1,021] biology, phylogenetics
PyRosetta r56324 [1,022] biology,structure,modeling
Pyrpipe 0.0.3 [1,023] phylogenetics
PyScaf 0.12a [1,024] Biology, NGS
PySLURM 18.08.04 [1,025] SLURM
Python 3.6.5, 3.7, 3.8 [1,026] programming languages, scripting, development
Python-core 3.6.5, 3.7, 3.8 [1,027] programming languages, scripting, development
Pytorch 1.3.0 [1,028] library, math
PyVCF 0.6.0 [1,029] biology, phylogenetics
Pyweka 0.3.18 [1,030] phylogenetics
Qcat 1.1.0 [1,031] phylogenetics
Qctool 2.0.1 [1,032] phylogenetics
QDD 3.1.2 [1,033] biology, genomics, ngs
QGIS 2.18.0 [1,034] GIS
QIIME 1.9.1 [1,035] biology, bioinformatics, metagenomics
QIIME2 2019.1, 2019.10, 2019.7 [1,036] biology, bioinformatics, metagenomics
QMCPACK 3.4.0 [1,037] Library
QRNA 2.0.4 [1,038] phylogenetics
QT 4.8.3 [1,039] UI Framework
Quake 0.3 [1,040] biology, sequencing
QualiMap 2.1.2 [1,041] biology,sequence alignment
Quantas 1.0.4, 1.0.8, 1.0.9 [1,042] biology,bioinformatics,ngs
QuartetScores 1.0.0 [1,043] phylogenetics
QUAST 2.3, 4.4, 5.0.0 [1,044] biology, bioinformatics, ngs, sequencing, rna-seq
Quickmerge 0.3 [1,045] phylogenetics
Quickquartet 1.0.0 [1,046] biology,bioinformatics,ngs
QuorUM 1.0.0 [1,047] biology
Quota-alignment 20170905 [1,048] biology, phylogenetics
R-index 20190711 [1,049] phylogenetics
R2R 1.0.4 [1,050] biology, RNA
R8s 1.8, 1.81 [1,051] phylogenetics
RACA 0.9.1.1 [1,052] biology, ngs
Racon 1.3.3, 1.4.10, 20161013 [1,053] biolgoy, sequencing
RADICAL 0.2 [1,054] biology, bioinformatics, genomics
RaGOO 1.11 [1,055] phylogenetics
Rainbow 2.0.4 [1,056] biology, sequencing
Rainbowfish 0.1.0 [1,057] phylogenetics
Randfold 2.0.1 [1,058] biology, RNA
Rapidtide 1.9.0 [1,059] phylogenetics
RAPSearch 2.24 [1,060] biology, phylogenetics
Unrar 0.0.1, 4.20 [1,061] unarchiver, utility
Rascaf 1.0.2 [1,062] biology, bioinformatics
RAVE 2.1 [1,063] biology, phylogenetics
RAxML 8.2.10, 8.2.12, 8.2.8 [1,064] application, biology, philogenetics
RAxML-NG 0.7.0b, 0.8.0b, 0.9.0 [1,065] phylogenetics
Razers3 3.5.7 [1,066] biology, phylogenetics
Rcorrector 1.0.2 [1,067] biology, phylogenetics
RDnaTools 0.1.3 [1,068] phylogenetics
REAPR 1.0.18 [1,069] biology,bioinformatics,assembly
Rebaler 0.2.0 [1,070] phylogenetics
Recon 1.08 [1,071] biology,sequencing
Recycler 0.62 [1,072] biology, bioinformatics
Redis 2.8.13, 2.8.19 [1,073] daemon, data, server
Redundans 0.14a [1,074] biology, phylogenetics
Regtools 0.4.0 [1,075] biolgoy, RNA-seq
RELION 3.0.2, 3.0b, 3.1.0 [1,076] biology, imaging
RelocaTE2 2.0.1 [1,077] phylogenetics
REMORA 1.8.2, 1.8.3 [1,078] System, profiler
REPdenovo 20170222 [1,079] biology, phylogenetics
RepeatAnalysis 0.10.0, 0.12.2 [] biology, phylogenetics
RepeatExplorer 20150506, 20180517 [1,080] biology, bioinformatics, ngs
RepeatMasker 4.0.3, 4.0.5, 4.0.9 [1,081] biology, bioinformatics
RepeatModeler 1.0.8, 2.0 [1,082] biology,bioinformatics
Repeatscout 1.0.5 [1,083] biology
Reptile 1.1 [1,084] biology,NGS,error correction
Resistome 20170111 [1,085] phylogenetics
RevBayes 1.0.3, 1.0.7, 1.0.9 [1,086] biology, phylogenetics
RGI 4.2.2 [1,087] phylogenetics
RGIS 20180211, 20180814 [1,088] RiverGIS
RHash 1.3.3 [1,089] GNU
RiboCode 1.2.11 [1,090] phylogenetics
RiboPicker 0.4.3 [1,091] biology,sequence
RiboTaper 1.3.1a [1,092] phylogenetics
RIGERJ 2.0.2 [1,093] phylogenetics
Rmats2sashimiplot 2.0.3 [1,094] phylogenetics
RNAhybrid 2.1.1 [1,095] biology, bioinformatics, genomics
RNAmmer 1.2 [1,096] biology, RNA-seq
RnaQUAST 1.5.1 [1,097] biology,bioinformatics,ngs,sequencing,rna-seq
RNAsalsa 0.8.1 [1,098] biology, phylogenetics
Rnaseqlib 20150721 [1,099] biology, phylogenetics, RNA-seq
RDnaTools 0.1.3 [1,100] phylogenetics
Roary 3.12.0, 3.4.1 [1,101] biology,genomics
ROOT 5.34.17, 6.0, 6.06.02 [1,102] Data Analysis
ROOTPy 20160323 [1,103] Data Analysis
Rosetta 2014wk4, 2019.35.60890 [1,104] biology,structure,modeling
Rrnaselector 1.0 [1,105] biology, sequencing
RSEG 0.4.8 [1,106] biology, bioinformatics, genomics
RSEM 1.2.29, 1.2.31, 1.2.7 [1,107] biology,bioinformatics,ngs,sequencing
RSeQC 2.6.4, 3.0.0 [1,108] biology,ngs,rna-seq
RStudio 1.1.419, 1.1.453, 1.2.1335 [1,109] statistics
RTGTools 3.7.1 [1,110] biology, NGS
Ruby 2.5.1 [1,111] programming,scripting,language
Rust 1.31.0 [1,112] programming
Saffrontree 0.1.2 [1,113] phylogenetics
Sailfish 0.6.3 [1,114] biology,genomics,ngs,rna-seq
Salmon 0.6.0, 0.7.2, 1.1.0 [1,115] biology, RNA-seq
SALSA 20171009 [1,116] biology, ngs, pacbio
Sambamba 0.6.3, 0.6.6, 0.6.9 [1,117] Biology, NGS
Samblaster 0.1.14, 0.1.24 [1,118] biology,bioinformatics,ngs,sequencing
SAMStat 1.08 [1,119] biology,bioinformatics,ngs,sequencing
Samtools 1.7, 1.8, 1.9 [1,120] biology,bioinformatics,ngs,sequencing
DS9 7.5, 8.0.1 [1,121] Imaging
SAS 9.3, 9.4 [1,122] statistics, data analysis
Sate 2.2.7 [1,123] biology, bioinformatics, phylogenetics
Satsuma 3.0 [1,124] phylogenetics
Satsuma2 20161123 [1,125] phylogenetics
Scala 2.11.5 [1,126] programming, language, java
Scalablast 2.4.53 [1,127] application, biology, genomics
ScaLAPACK 2.0.2 [1,128] programming,library
Scalpel 0.1.1, 0.5.3 [1,129] Biology, NGS
Schrodinger Suite 2017, 2017-2, 2019-3 [1,130] Computational Chemistry, Molecular Dynamics
Scipion 1.2 [1,131] Image Processing
Scoary 1.6.10 [1,132] biology, bioinformatics, genomics
Scons 2.5.1, 3.1.2 [1,133] Programming
SCRATCH-1D 1.0 [1,134] biology, bioinformatics, ngs
Screen 4.7.0, 4.8.0 [1,135] GNU, Terminal Multiplerxer
SCRIPTURE 20101211 [1,136] biology, bioinformatics, genomics
Scythe 0.991 [1,137] Biology, NGS
Sdsl 2.1.1 [1,138] library, c++
SeCaPr 1.1.12 [1,139] phylogenetics
Segemehl 0.1.9, 0.3.4 [1,140] biology,bioinformatics,ngs,sequencing
SEPP 20160614 [1,141] biology, phylogenetics
Seq-Gen 1.3.3 [1,142] biology,phylogenetics
Seq_crumbs 20150120 [1,143] biology, sequence, genomics, utilities
SeqKit 0.10.2, 0.8.0 [1,144] biology, phylogenetics
SeqMap 1.0.13 [1,145] biology,bioinformatics,sequence,ngs
SEQPower 1.1.1 [1,146] Genomics, bioinformatics, phylogenetics
SeqPrep 0.5, 1.1 [1,147] biology,bioinformatics,ngs,sequencing
Seqtk 1.3, 20140729 [1,148] Bioinformatics, Genomics, NGS
SEQuel 1.0.1 [1,149] biology,bioinformatics,ngs
SequelQC 1.1.0 [1,150] phylogenetics
Seqwish 20190509 [1,151] phylogenetics
SeqyClean 1.8.10 [1,152] biology,bioinformatics,ngs,sequencing
SEXCMD 20170823 [1,153] biology, phylogenetics
SExtractor 2.19.5 [1,154] Astronomy
SHAPEIT 2.12, 2.5 [1,155] biology,SNP
SHAPE-MaP 1.2 [1,156] biology, phylogenetics
ShapeMapper 2.1.3, 2.1.5 [1,157] biology, phylogenetics
SHARCGS 1.2.11 [1,158] biology, NGS, de novo assembly
Shasta 0.1.0 [1,159] phylogenetics
SHEsisPlus 1.0, 1.01 [1,160] biology, genetics
Shogun 6.1.3 [1,161] phylogenetics
SHRiMP 2.2.3 [1,162] biology, genomics, ngs
Shustring 2.6 [1,163] biology, sequencing
SICER 1.1 [1,164] biology, ChIP-Seq
Sickle 1.200, 1.33 [1,165] biology, bioinformatics, ngs
Siesta 3.2, 4.1b2, 4.1b3 [1,166] Chemistry
SIFT 4.0.3b [1,167] biology,bioinformatics,genomics
SignalP 4.1c, 5.0b [1,168] biology, phylogenetics
SiLiX 1.2.11 [1,169] phylogenetics
Silo 4.7 [1,170] io,library
Sim4 20121010 [1,171] biology, bioinformatics, genomics
SimSeq 4.12.2011 [1,172] biology, bioinformatics, ngs, phylogenetics
SInC 20140120 [1,173] biology, phylogenetics
Sine_scan 1.1.1 [1,174] phylogenetics
Singularity 3.4.2, 3.5.2 [1,175] Containers
SIPeS 2.0 [1,176] biology, bioinformatics, ChIP-Seq
Sisl 0.8.3 [1,177] Physics, Tight-binding
SKESA 2.3.0 [1,178] phylogenetics
Slamdunk 0.4.1, 0.4.2 [1,179] phylogenetics
Slicer 4.10.2, 4.3.1 [1,180] biology,bioinformatics,neuroscience,imaging
Slurm-drmaa 1.2.1.19, 1.2.1.20 [1,181] libraries, slurm, api, drmaa
Smalt 0.7.6 [1,182] application, biology, phylogenetics
SMARTdenovo 20180219 [1,183] biology, phylogenetics
Smartie-sv 20180308 [1,184] phylogenetics
SMC++ 1.8.0 [1,185] biology, NGS
SMRT-SV 2.0.0 [1,186] biology, bioinformatics, ngs
SMS 1.7 [1,187] biology, bioinformatics
Snakemake 5.17.0 [1,188] biology, bioinformatics, workflow
SNAP 0.15.4, 20100728 [1,189] biology,bioinformatics,sequencing
SPANE-pooled 20130407 [1,190] biology,SNP
Snappy 1.1.7 [1,191] library
SNeP 1.1 [1,192] biology,phylogenetics
Sniffles 1.0.11, 1.0.6, 1.0.8 [1,193] phylogenetics
Snippy 20160419 [1,194] biology, phylogenetics
SNP-Pipeline 1.0.1 [1,195] biology, phylogenics
SNP-sites 2.0.3 [1,196] biology, SNP
SnpEff 4.3q, 4.3r, 4.3t [1,197] biology,bioinformatics,variant annotation
SNPGenie 20190620 [1,198] phylogenetics
SNPhylo 20140701 [1,199] biology,phylogenetics
SNPTEST 2.5.2 [1,200] phylogenetics
SOAPaligner 2.21 [1,201] phylogenetics
SOAPdenovo 1.05, 2.04 [1,202] biology,ngs
SOAPdenovo-Trans 1.01, 1.03 [1,203] biology,ngs
SOAPec 2.03 [1,204] biology, phylogenetics
SOAPnuke 2.1.0 [1,205] phylogenetics
SOAPsplice 1.10 [1,206] biology,ngs
SOLAR 8.4.2 [1,207] phylogenetics
SortaDate 20190705 [1,208] phylogenetics
SortMeRNA 2.1, 4.0 [1,209] biology, sequencing, NGS
Sourmash 2.0.1 [1,210] phylogenetics
SoX 14.4.2 [1,211] phylogenetics
SPAdes 3.13.0, 3.7.1, 3.8.0 [1,212] biology,bioinformatics,ngs
SparCC 201608 [1,213] Microbial Ecology
Spark 2.2.0 [1,214] spark, hadoop
Sparsehash 2.0.3 [1,215] Google, API
SPARTA+ 2.60 [1,216] Chemistry
Spidey 20150922 [1,217] biology, genomics, bioinformatics
SplAdder 2.4.2 [1,218] phylogenetics
SpliceGrapher 0.2.5 [1,219] biology, sequencing
SpliceTrap 0.90.5 [1,220] biology, bioinformatics, genomics, NGS
SPM 12b, 8, 8r5236 [1,221] biology,bioinformatics,matlab
Spruceup 2019.2.3 [1,222] phylogenetics
Sputnik 1.0 [1,223] biology,bioinformatics,repeats
Spyder 4.1.0 [1,224] ide, editor, programming, scripting
SQANTI 1.2 [1,225] phylogenetics
SQANTI2 5.0 [1,226] phylogenetics
SQL Developer 4.1.2 [1,227] programming, oracle, sql
SQLite 3.8.8.2 [1,228] database
SRA 2.10.3, 2.10.4 [1,229] biology,bioinformatics,sra
SSPACE 2.0, 3.0 [1,230] biology,bioinformatics,ngs
Ssr_pipeline 0.951 [1,231] biology, DNA sequencing,
Stacks 2.3e, 2.41, 20190403 [1,232] biology, bioinformatics, genomics, ngs
Staden 1.14.6 [1,233] biology, phylogenetics
Stampy 1.0.31 [1,234] biology, bioinformatics, sequencing
Rnastar 2.6.1b, 2.7.0b, 2.7.3a [1,235] biology, ngs, rna-seq
STAR-Fusion 1.1.0, 1.3.1 [1,236] biology, transcriptome
STAR-CCM+ 14.04.011, 15.02.009, 8.06 [1,237] Mechanical Engineering
Starseqr 0.6.7 [1,238] phylogenetics
Stata 10.1, 13 [1,239] Statistics
Statsmodels 0.8.0 [1,240] biology, library, math
StringMLST 0.4 [1,241] biology, bioinformatics, CHiP-Seq
Stringtie 1.3.3, 1.3.4d, 2.0.4 [1,242] biology,bioinformatics,ngs,sequencing,alignment
Structure 2.3.3, 2.3.4 [1,243] biology,bioinformatics,population genetics
Subread 1.5.3, 1.6.2, 2.0.0 [1,244] biology, sequencing, SNP
Subversion 1.9.7 [1,245] Revision Control
SUMO 1.2.0 [1,246] phylogenetics
SUNDIALS 2.3.0, 2.5.0, 3.0.0 [1,247] Math, Numerical Solvers
Supercell 20170602 [1,248] biology, NGS
SuperCRUNCH 1.2.1 [1,249] phylogenetics
Supernova 1.2.1, 2.0.0, 2.1.1 [1,250] biology, phylogenetics, ngs
SUPPA 2.3 [1,251] phylogenetics
SURVIVOR 1.0.6 [1,252] phylogenetics
SVDetect 0.8b [1,253] biology,ngs,genomics
Swarm 1.2.11 [1,254] Data Analysis
Sweed 3.3.2 [1,255] biology, phylogenetics
SWIG 2.0.9, 3.0.12, 3.0.8 [1,256] library, development, C++, python
SwitchSeq 20140907 [1,257] biology,bioinformatics,genomics
SWSC-EN 1.0.0 [1,258] phylogenetics
TACO 0.7.3 [1,259] phylogenetics
Taiyaki 3.0.1, 4.1.0, 5.0.1 [1,260] phylogenetics
Talesf 20160814 [1,261] phylogenetics
Tandem-Genotypes 1.4.0 [1,262] phylogenetics
Tantan 13 [1,263] ngs, genomics
Tapir 20160825 [1,264] biology, phylogenetics
TAPIS 1.2.1 [1,265] biology, sequencing
TARGeT 2.10 [1,266] phylogenetics
TASSEL 5.0, 5.2.20, 5.2.29 [1,267] biology,bioinformatics,genomics,wga
Tuning Analysis Utilities 2.23, 2.26, 2.26.3 [1,268] library, profiling and optimization
Tax4Fun 0.3.1 [1,269] phylogenetics
TaxMaps 0.1 [1,270] biology, phylogenetics, taxonomy
Taxtastic 0.5.7 [1,271] biology, taxonomy
Tbb 2017_20161128 [1,272] library
Tcllib 1.18 [1,273] library
Tcoffee 10.00.r1613, 9.03.r1318 [1,274] Bioinformatics
Tecplot 360 EX 2015R1 [1,275] plotting, animation, cfd, simulations
TEMP 20170731 [1,276] phylogenetics
TensorFlow 1.14.0, 2.0, 2.1.0 [1,277] library, math
TESS 2.3.1 [1,278] biology, bioinformatics, genomics, markov
Test 1.0 [1,279] shell
TetGen 1.5.0 [1,280] tetrahedral meshes
TEToolkit 1.5.1 [1,281] biology, bioinformatics, sequencing
TEtools 20180213 [1,282] biology, phylogenetics
Texlive 2015.20160320, 20191127 [1,283] formatting, typesetting, document preparataion
TGICL 2.1 [1,284] biology,bioinformatics,ngs,sequencing
Theano 1.0.4 [1,285] library, math, gpu
Tiff 3.8.0, 4.0.10 [1,286] imaging
Tigmint 1.1.2 [1,287] phylogenetics
Tmux 2.4, 2.9 [1,288] GNU
TNTBLAST 2.04 [1,289] Biology
ToFU2 20180629, v17 [1,290] biology, bioinformatics, ngs, iso-seq
Toil 3.3.0, 3.3.3 [1,291] biology, bioinformatics
Tombo 1.4, 1.5 [1,292] biology, genomics, ngs
Tophat 2.1.0, 2.1.1, 2.1.2 [1,293] biology,bioinformatics,ngs,sequencing
TotalView 8.12 [1,294] Parallel Computing
TPMcalculator 0.0.3 [1,295] phylogenetics
TPP 4.7.0, 4.7.1, 5.0.0 [1,296] biology, chemistry, nmr
TraCeR 0.5.1, 20160519 [1,297] Biology, Phylogenetics
TrackTools 2011 [1,298] Software
TrackVis/DTK 0.5.2.2, 0.6.0.1 [1,299] biology,bioinformatics,neuroscience,imaging
Tracula 5.3.2014_05_26 [1,300] biology,bioinformatics,neuroscience,imaging
TraitRate 1.1 [1,301] biology, evolution
Trans-ABySS 2.0.1 [1,302] biology, phylogenetics
TransDecoder 5.3.0, 5.4.0, 5.5.0 [1,303] biology, ngs
TRANSIT 2.5.2 [1,304] phylogenetics
Transrate 1.0.1 [1,305] biology,assembly
TransVar 2.3.3 [1,306] biology, bioinformatics, phylogenetics
TreeBreaker 20160621 [1,307] biology, phylogenetics
TreeMix 1.12 [1,308] biology, phylogenetics
TreePL 20150305 [1,309] biology, bioinformatics, phylogenetics
TREEPUZZLE 5.3 [1,310] biology, phylogenetics
TreeShrink 1.3.1, 1.3.2 [1,311] phylogenetics
Trelis 16.3 [1,312] Geometry
TRF 4.04 [1,313] biology,bioinformatics,genomics
Trilinos 12.12.1, 12.18.1, 12.6.4 [1,314] Mathematical Algorithms
Trim Galore 0.4.4, 0.5.0, 0.6.5 [1,315] biology,bioinformatics,ngs
TrimAl 1.2 [1,316] biology,genomics,sequence alignment
TriMetAss 1.1 [1,317] biology,bioinformatics,ngs
Trimmomatic 0.33, 0.36, 0.39 [1,318] biology,bioinformatics,ngs
Trinity r20130225, r20131110, r20140413 [1,319] biology,bioinformatics,ngs,sequencing,rna-seq
Trinotate 3.0.1, 3.2.0 [1,320] biology
TRIPLEC 1.0 [1,321] biology, bioinformatics
TRNAscan-Se 1.23 [1,322] biology,bioinformatics,ngs
TURBOMOLE 7.4.1 [1,323] Quantum Chemistry
TWINSCAN 4.1.2 [1,324] biology,genomics
Ubuntu 18.04 [1,325] Ubuntu Linux
Kent 20141111, 20180816, 20200320 [1,326] Genomics, bioinformatics
UDUNITS 2.2.17 [1,327] library, data, units
UFITS 0.7.2 [1,328] biology,bioinformatics,ngs
Ufraw 0.22 [1,329] data mining
Ugtm 1.1.6 [1,330] statistics, modeling
Umi-tools 0.5.5 [1,331] phylogenetics
UNAFold 3.8 [1,332] biology, genome, RNA, folding
Unanimity 20171108, 3.4.1 [1,333] programming,library,cpp
Unicycler 0.4.8 [1,334] phylogenetics
Uproc 1.2.0 [1,335] biology, genome
USEARCH 9.0.2132, 9.1.13, 9.2.64 [1,336] biology,bioinformatics,alignment,sequence analysis
Valgrind 3.11.0, 3.15.0, 3.8.1 [1,337] Computer Programming
Valouev 20160325 [1,338] Biology, Phylogenetics
VAMPIR 9.1 [1,339] High Performance Computing
VarDictJava 1.6.0, 20160521, 20170531 [1,340] biology, phylogenetics
VAIR 0.7.0 [1,341] Geospatial Data Modeling
Varnorm 0.21 [1,342] biology, bioinformatics
VarScan 2.3.6 [1,343] biology,bioinformatics,ngs
VarSim 0.8.4 [1,344] phylogenetics
VarSimLab 20180220, 20180921 [1,345] biology, simulation, genomics
Vasp 5.4.1, 5.4.4 [1,346] Quantum Chemistry
VAST-TOOLS 20150506 [1,347] biology, rna-seq, ngs, splicing
VCF-kit 0.1.2 [1,348] biology, phylogenetics
Vcfanno 0.2.8 [1,349] biology, phylogenetics
Vcflib 20150313 [1,350] biology,bioinformatics,genomics
Vcftools 0.1.15, 0.1.16, 0.1.9 [1,351] biology,bioinformatics,genomics
Vcf-validator 0.6 [1,352] biology, phylogenetics
Vcontact 20190512 [1,353] phylogenetics
VDJtools 1.1.7 [1,354] biolgoy, phylogenetics
Velvet 1.2.10, 1.2.10-long [1,355] computational biology, genomics
VEP 83, 88.8, 92 [1,356] biology, genomics, ngs
Vg 1.20.0 [1,357] phylogenetics
Vidjil 201703 [1,358] biology, genomics
ViennaRNA 2.2.6 [1,359] biology, RNA-seq
ViewBS 0.1.9 [1,360] phylogenetics
Vim 8.1.1566 [1,361] programming,scripting,language
VirSorter 1.0.3 [1,362] biology, phylogenetics
VirtualCell 7.1 [1,363] phylogenetics
VIRULIGN 1.0.2 [1,364] phylogenetics
VirusFinder 2.0 [1,365] biology, phylogenetics
Visit 2.12.2, 2.13.3, 3.0.1 [1,366] Visualization, Animation and Analysis
VISPR 0.4.14 [1,367] phylogenetics
VMD 1.9.1, 1.9.3 [1,368] visualization, animation, 3d
V-Phaser 02112013 [1,369] biology, phylogenetics
Vscode 1.38.1 [1,370] ide, editor, programming, scripting
VSearch 20151022, 20161209-2.3.4 [1,371] biology,NGS
Vt 0.57721, 20140903, 20160129 [1,372] biology, genomics
VTC 0.9.3 [1,373] biology, bioinformatics, VCF
VTK 7.1.0, 7.1.1 [1,374] biology,bioinformatics,neuroscience,imaging
VULCAN 6.3.1 [1,375] Fluid Dynamics
W2rap-contigger 20161124 [1,376] biology, genomics
Wannier90 1.2, 2.1.0 [1,377] Computational Physics
WDSSII 5 [1,378] Weather, Meteorology
WebLogo 2.8.2, 3.3, 3.5.0 [1,379] biology,bioinformatics,sequence,graphics
Weka 3.8 [1,380] statistics,machine learning
WEVOTE 1.5.0, 1.8.0 [1,381] biology, phylogenetics
WGS Assembler 8.3rc1.r4638, 8.3rc2 [1,382] biology, bioinformatics, genomics
Wgsim 0.3.1-r13 [1,383] biology, phylogenetics
WHAMM 0.14a [1,384] biology, phylogenetics
WhatsHap 0.14.1 [1,385] biology, phylogenetics
Wine 1.6.2, 1.9.6, 4.0.0 [1,386] windows, emulator
Wise 2.2.0, 2.4.1 [1,387] biology, genome
WIsH 1.0 [1,388] phylogenetics
WoLFPSort 0.2 [1,389] phylogenetics
WOMBAT 20180118 [1,390] biology, phylogenetics
Wtdbg 2.1, 2.4 [1,391] phylogenetics
Wub 0.2.0, 0.4.0 [1,392] biology, genomics, ngs
WU BLAST 2.0 [1,393] biology, bioinformatics
Xander 20151222 [1,394] biology, phylogenetics
Xapian 1.4.4 [1,395] library
XCrySDen 1.5.60 [1,396] Computational Material Science
Xerces 3.1.4 [1,397] phylogenetics
Xpclr 1.1.1 [1,398] phylogenetics
Xterm 1.1 [1,399] terminal emulator
XZ 5.2.2 [1,400] compression, library
YAHA 0.1.82 [1,401] biology, ngs
YASM 1.3.0 [1,402] Computer Programming
YASRA 2.33 [1,403] biology,bioinformatics,ngs,sequencing
Zagros 1.0.0 [1,404] biology,phylogenetics
ZEO++ 0.2.2 [1,405] chemistry
Zorro 2.2 [1,406] biology, sequencing
ZUMIS 2.6.0 [1,407] biology, bioinformatics, ngs, sequencing