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 3.6.2, 4.0, 4.1 [4] statistics
Rmpi 0.6.9 [5] statistics, R, mpi
AAFTF 0.2.5 [6] Biology, Pipeline, Assembly
ABRicate 1.0.1 [7] phylogenetics
ABruijn 1.0 [8] biology, assembly, ngs, pacbio, nanopore
ABySS 1.5.2, 2.1.0, 2.2.5 [9] biology, de novo
AdapterRemoval 2.2.2 [10] phylogenetics
ADMB 11.5, 12.0 [11] math, modeling, optimization
AdmixTools 20150311 [12] biology, bioinformatics, genomics, ngs
ADMIXTURE 1.23, 1.3.0 [13] biology, bioinformatics, genomics, ngs
AEGeAn 0.14.0 [14] biology,genomics
AFNI 20.3.00, 2018_04_12 [15] biology,bioinformatics,neurology,imaging
AfterQC 0.9.7 [16] phylogenetics
AGAT 0.4.0 [17] phylogenetics
AGfusion 1.252 [18] phylogenetics
Albacore 2.3.1, 2.3.3 [19] Biology, Phylogenetics
Albumentations 1.0.3 [20] AI, Vision, Imaging
ALFA 1.1.1 [21] phylogenetics
AliStat 1.12 [22] phylogenetics
ALLMAPS 20180117 [23] biology, phylogenetics
ALLPATHS-LG 42316, 44837, 49232 [24] biology,bioinformatics,ngs
AlphaFold 2.0.0 [25] phylogenetics
Alphaimpute 0.0.2, 1.9.8.2, 1.9.8.3 [26] phylogenetics
AltAnalyze 2.1.0 [27] Biology, genomics
AMAS 1.0 [28] phylogenetics
AMBER 16.0, 18, 20 [29] Computational Chemistry, Molecular Dynamics
AMICO 1.0.1 [30] library, imaging, optimization
AMOS 3.1.0 [31] biology,bioinformatics,genomics,assembly
AMP 0.6.1 [32] phylogenetics
AmPEPpy 1.0 [33] phylogenetics
Amphora2 20140305 [34] biology, phylogenetics
AMPtk 1.2.4, 1.5.1 [35] biology, bioinformatics, ngs
Amptorch 20210313 [36] phylogenetics
Amrfinderplus 3.10.5 [37] phylogenetics
AMRPlusPlus 20180508 [38] phylogenetics
AMUSE 10.0, 13.1.0 [39] Astrophysics
ANGSD 0.933 [40] biology, ngs
Annocript 2.0 [41] phylogenetics
AnnoTALE 1.4.1 [42] phylogenetics
ANNOVAR 20121023, 20130221, 20150322 [43] biology, bioinformatics, genomics
Ansible 2.5.5, 2.8.1 [44] automation, deployment
Ansysem 17.0 [45] Electromechanics
AntiSMASH 4.1.0, 6.0.1 [46] phylogenetics
ANTs 2.2.0, 2.3.4 [47] biology, phylogenetics
Anvio 6.0, 6.1, 6.2 [48] biology, microbial 'omics
APT 1.15.0, 1.18.0, 1.20.5 [49] biology, bioinformatics, genomics, microarray
ARC 1.1.4 [50] biology,bioinformatics,ngs
Aria2 1.35.0 [51] Utility
ARKS 1.0.2 [52] phylogenetics
Armadillo 7.900.0, 9.200.6, 9.900.4 [53] library, C++, math
ARPACK 1.0 [54] Solve eigenvalue problems
ArrayFire 3.4.2 [55] Code Optimization
Arriba 2.1.0 [56] phylogenetics
ART 20160417, 20160605 [57] phylogenetics
ASE-ANI 20180712 [58] biology, bioinformatics, genomics, ngs
ASHS 2.0 [59] biology, mri
Assembly-stats 1.0.1 [60] biology, sequencing, genomics
Assemblytics 1.2.1 [61] phylogenetics
Assexon 20190814 [62] phylogenetics
AStalavista 3.2, 4.0 [63] biology, bioinformatics, genomics
ASTRAL 5.6.1, 5.6.2, 5.7.7 [64] biology,bioinformatics,ngs,phylogenetics
ASTRID 2.2.1 [65] phylogenetics
Astropy 2.0.8 [66] biology, bioinformatics, phylogenetics
ATAT 3.23, 3.34 [67] alloy theory
ATLAS 3.10.1, 3.10.2, 3.11.17 [68] library, data
Atom 1.57.0 [69] IDE
AtomEye 3 [70] Material Science
AtomMan 1.3.3 [71] phylogenetics
ATRAM 2.2.0, 2.4.3 [72] Math
Augustus 3.3.2, 3.3.3, 3.4.0 [73] biology,bioinformatics,genomics
Auto3DEM 4.05.2 [74] Image Reconstruction
AutoDock 4.2.6 [75] biology
Autometa 20190802 [76] phylogenetics
AWS CLI 2.2.30 [77] Utilities
Azoo 1.3.1 [78] phylogenetics
Badread 0.1.5 [79] phylogenetics
BALi-Phy 3.4.1, 3.5.0 [80] phylogenetics
BAM-matcher 20161021 [81] phylogenetics
Bam-Readcount 20150616 [82] biology, genomics
Bamaddrg 20120326 [83] phylogenetics
BamBam 1.0 [84] biology, bioinformatics, genomics
Bamm 2.5.0 [85] phylogenetics
Bamstats 20140602 [86] biology,bioinformatics,ngs
Bamsurgeon 1.2 [87] phylogenetics
Bamtofastq 1.3.5 [88] phylogenetics
Bamtools 2.4.1, 2.5.0, 2.5.1 [89] biology,bioinformatics,ngs,sequencing
BamUtil 1.0.2 [90] biology, bioinformatics, genomics
BAPS 6.0 [91] biology, bioinformatics, genomics
Barrnap 0.7, 0.9 [92] biology, RNA-Seq
Basemount 0.1.2.464, 0.12.8.1516, 0.15.96 [93] biology,DNA Sequencing
BatMeth2 20210720 [94] Biology, Genomics, Mapping
Bax2bam 0.0.9 [95] phylogenetics
BayArea 1.0.2 [96] biology
BAYENV 2.0 [97] biolgoy, phylogenetics
BayesAss 3.0.4, 3.0.4.2 [98] phylogenetics
BayeScan 2.1 [99] biology, SNP
BayesR 20151016 [100] biology, phylogenetics
BayesTraits 3.0.2 [101] phylogenetics
Baypass 2.1 [102] biology, phylogenetics
BBMap 38.26, 38.44, 38.90 [103] biology, alignment
Bcftools 1.13, 1.3.1, 1.9 [104] biology,bioinformatics,ngs
Bcl2fastq 2.16.0.10, 2.20.0.422 [105] biology, ngs, illumina
BDG-SeQuila 0.5.5 [106] phylogenetics
BEAGLE 4.1, 5.0, 5.2 [107] biology, genetics, genotyping
BEAR 20170209 [108] biology, bioinformatics, metagenomics
BEAST 2.6.0, 2.6.2, 2.6.3 [109] biology,phylogeny
BEAST2-XML 1.0.9 [110] phylogenetics
BEDOPS 2.4.30 [111] biology,bioinformatics,sequence,ngs
BEDTools 2.29.1, 2.29.2, 2.30.0 [112] biology,bioinformatics,ngs
Bertini 1.6 [113] Mathemetics
BERTopic 0.7, 0.8.1 [114] machine-learning
BESST 2.2.4 [115] biology, NGS
BFAST 0.7.0 [116] biology,bioinformatics,ngs
Bifrost 0.2, 1.0.3, 20200225 [117] phylogenetics
BinPacker 1.0 [118] biology, RNA-seq, sequence assembly
BinSanity 0.2.6.4 [119] biology, genomics
Bioawk 1.0 [120] phylogenetics
BioBakery 0.13.2, 0.15.1 [121] phylogenetics
Biodiverse 2.1 [122] phylogenetics
Biolite 0.3.5.1 [123] biology, bioinformatics, genomics, SNP
BIOM 2.1.5, 2.1.6 [124] biology, genomics
BIOMART 1.4 [125] biology,genomics
Bismark 0.22.3, 0.7.4, 0.7.7 [126] biology, bioinformatics, NGS
Blackfynn 0.2.7 [127] data mining
BLASR 20130815, 20161215 (5.3), 5.3.2 [128] biology,bioinformatics,ngs
Blast2GO CLI 1.3.3, 2.5.0-20120705 [129] biology, bioinformatics, gene ontology
BLAT 20121105, 20140318 [130] Genomics, bioinformatics
Blender 2.63, 2.73, 2.77 [131] graphics
Blitz 0.10 [132] library
BlobTools 1.0, 2.2 [133] phylogenetics
Bloomfiltertrie 0.8.7 [134] phylogenetics
BloomTree 0.3.5 [135] data mining
BLUPF90 20160604, 20180301, 20190531 [136] biology, phylogenetics
BMGE 1.12 [137] Biology, genetics, phylogeny
BOLT-LMM 2.3.4 [138] phylogenetics
BoltzTraP 1.2.5 [139] physics
Boost 1.67.0, 1.71.0, 1.75.0 [140] programming,library,cpp
Booster 0.1.2 [141] phylogenetics
Bowtie 1.1.1, 1.2.0, 1.2.3 [142] biology,bioinformatics,ngs,sequencing
Bowtie2 2.3.5, 2.3.5.1, 2.4.2 [143] biology,bioinformatics,ngs,sequencing
BPGA 1.2 [144] biology, ngs
BPP 3.4, 4.1.4, 4.3.8 [145] biology, phylogenetics
Bracken 1.0.0, 2.5 [146] biology, phylogenetics
Braker 2.1.2, 2.1.5, 2.1.6 [147] phylogenetics
BRANCH 1.8.1 [148] biology,bioinformatics,ngs,mapping
BRATNextGen 20150505 [149] biology, bioinformatics, genomics
BreakDancer 1.4.5 [150] biology, phylogenetics
Breakseq 2.2 [151] biology, phylogenetics
Brewery 20191205 [152] phylogenetics
Bridger 20141201 [153] NGS, Genomics, bioinformatics
BRIG 0.95 [154] biology, genomics
BRM 0.3 [155] phylogenetics
Bruker2nifti 1.0.4 [156] phylogenetics
Bsmap 2.87 [157] biology, bioinformatics, NGS
Bsoft 1.9.1 [158] biology, image analysis
BSseeker2 2.1.0, 2.1.8 [159] biology, phylogenetics
Bubbleparse 20140314 [160] biology, phylogenetics
BUCKy 1.4.4 [161] biology, phylogenetics
BUSCO 4.0.6, 4.1.4, 5.2.0 [162] biology, genomics
BWA 0.7.7, 0.7.8, 0.7.9a [163] biology,bioinformatics,ngs
Bwa-mem2 2.2.1 [164] phylogenetics
BWA-PSSM 0.5.11 [165] phylogenetics
Bxh_xcede_tools 1.11.1 [166] biology, bioinformatics
BYOBU 5.133, 5.92 [167] shell, screen, terminal
Bzip2 1.0.6 [168] archiver, library
CAFE 4.1, 5.0.0 [169] phylogenetics
Came 0.0.1 [170] phylogenetics
Camino 20140723 [171] biology,bioinformatics,neuroscience,imaging
Cantera 2.1.1 [172] kinetics, thermodynamics
Canu 1.9, 2.0, 2.1 [173] biology, sequencing
CANVAS 1.40.0.1613 [174] phylogenetics
CAP3 20120705 [175] biology,bioinformatics,assembly
Capnp 0.5.3 [176] C++
CASAVA 1.8.2 [177] biology,bioinformatics,ngs
CASM 0.2.0 [178] Statistical Mechanics
CasOFFinder 2.4 [179] phylogenetics
Catch 1.4.0 [180] Biology, Bioinformatics, Genomics, Sequencing
CAVIAR 20171218 [181] biology, phylogenetics
CBGpipe 20190702 [182] phylogenetics
CDBFasta 20181005 [183] phylogenetics
CD-HIT 4.6, 4.6.4, 4.6.8 [184] biology,genomics
CDO 1.7.2rc3, 1.9.4 [185] Climate
CellProfiler 3.1.9, 4.1.3 [186] phylogenetics
Cell Ranger 4.0.0, 5.0.0, 6.0.1 [187] biology, bioinformatics, ngs, rna-seq
Cell Ranger ATAC 1.2.0 [188] biology, bioinformatics, ngs, rna-seq
CellRanger-DNA 1.0.0, 1.1.0 [189] biology, bioinformatics, ngs, rna-seq, 10xgenomics
Centrifuge 1.0.3 [190] biology, phylogenetics
CFITSIO 3.370 [191] library, C
CGAL 4.10, 4.9, 5.02 [192] library, math
CGATools 1.6.0.43 [193] biology, bioinformatics, ngs
Cgmaptools 0.1.1, 0.1.2 [194] phylogenetics
CHARMM 36a3, 43b2 [195] chemistry, simulation
CheckM 1.0.4, 1.0.7, 1.1.2 [196] biology, genomics
Chimera 1.12 [197] biology, bioinformatics, modeling
Chipyard 1.0 [198] hardware, design
ChromEvol 2.0 [199] Biology, NGS
CIMS 4.1.2 [200] biology,genomics
CIRCexplorer 1.1.10 [201] biology, bioinformatics, rna-seq
CIRCexplorer2 2.3.5 [202] phylogenetics
Circlator 1.5.5 [203] phylogenetics
Circleator 1.0.2 [204] phylogenetics
Circos 0.63-pre11, 0.69-2, 0.69-9 [205] biology,genomics,ngs
CIRI 2.0.6 [206] phylogenetics
CisGenome 2.0 [207] biology, bioinformatics, genomics
CisTEM 1.0.0 [208] phylogenetics
Clairvoyante 1.02 [209] phylogenetics
Clann 3.2.3 [210] biology,bioinformatics,phylogentics
Clara v4.0 [211] AI, machine learning
CLARK 1.2.2-b, 1.2.3 [212] biology, genomics
CLHEP 2.2.0.1 [213] High Energy Physics
CLIFinder 4.1 [214] biology, phylogenetics
CLIPper 2.1.0 [215] phylogenetics
CLIPSeqTools 0.1.7 [216] biology, sequencing
ClonalFrame 1.1, 1.2 [217] biology,bioinformatics,ngs,phylogenetics
ClonalFrameML 1.0, 1.11 [218] biology, bioinformatics, ngs, phylogenetics
CloudCompare 2.10.3 [219] 3D visualization
GFCloveram 2.0 [220] biology, genomics, assembly
CLUMPP 1.1.2 [221] biology, bioinformatics
ClustalO 1.2.0 [222] biology, bioinformatics, alignment
ClustalW 2.1 [223] biology,bioinformatics,alignment
Cluster3 1.52a [224] biology, genomics
Clview 20130402 [225] biology, bioinformatics
CMake 3.19.1, 3.21.3 [226] Software Development
CMS 20170518 [227] biology
CMWP 140518 [228] biology, genomics
CNCI 20180305 [229] phylogenetics
CNSpipeline 20170827 [230] phylogenetics
CNV-Sim 0.9.2 [231] biology, phylogenetics
CNVkit 0.9.6 [232] phylogenetics
CNVnator 0.3.2 [233] biology, genomics, CNV
CNV-Seq 20110715, 20140812 [234] biology,bioinformatics,genomics
Cobra-tf 0.1 [235] Nuclear Engineering
CodonPhyML 20150303 [236] phylogenetics
Coevol 1.3c, 1.4b, 1.6 [237] bio,bioinformatics,phylogenetics
Cogent 2.1 [238] biology, phylogenics
COLMAP 3.6 [239] modeling
CoMap 1.4.1 [240] Bioinformatics, Genomics
Comp-D_MPI 1.0 [241] Statistics
COMSOL 5.4.0 [242] General-purpose simulation software
Concaterpillar 1.8a [243] phylogenetics
CONCOCT 1.1.0 [244] biology, bioinformatics, genomics
Conda 4.10.1 [245] programming, development, packages
CONN 18a [246] mri,fmri,matlab
CONNECT 20200614 [247] phylogenetics
Connectomemapper3 3.0.0-rc1 [248] phylogenetics
ConPADE 1.0 [249] phylogenetics
Conpair 20161010, 20180624 [250] biology, phylogenetics
Consed 23.0, 25.0, 29.0 [251] biology, bioinformatics, genomics
CONSEL 0.20 [252] biology, phylogenetics
ContaVect 0.2 [253] biology, phylogenetics
Coot 0.9.5 [254] Modeling
Coreutils 8.23, 8.28 [255] Software tools
Corset 1.06 [256] biology, NGS
Counterr 0.1 [257] phylogenetics
CovNMR 2014 [258] Biochemistry
Cp2k 7.0.0 [259] Quantum Chemistry
CPAT 3.0.2 [260] phylogenetics
Cpc2 2.0 [261] phylogenetics
CPLEX 12.6.1, 12.6.2, 12.7 [262] Meteorology
Crass 1.0.1 [263] biology, assembly
Crisflash 1.2.0 [264] phylogenetics
CRISP 20181122 [265] phylogenetics
CRISPRanalyzer 1.50 [266] biology,genomics,ngs
CRISPRCasFinder 4.2.17 [267] phylogenetics
CrossMap 0.3.9 [268] biology, genomics
Crux 1.40 [269] biology, mass-spectroscopy
CryptoMiniSat 5.0.1 [270] SAT
CUBE 4.4 [271] library,c,math
Nvidia CUDA Toolkit 10.0.130, 11.0.207, 11.1.0 [272] programming, library, graphics, runtime
Cufflinks 2.1.1, 2.2.1, 2.2.1.1 [273] biology,bioinformatics,ngs,sequencing
CDNA_Cupcake 22.0.0, 9.0.1 [274] biology, bioinformatics, ngs, iso-seq
Cupy 8.3.0 [275] phylogenetics
Cutadapt 1.18, 2.8, 3.4 [276] biology,bioinformatics,ngs
CutRunTools 20200104 [277] phylogenetics
Cvbio 3.0.0 [278] phylogenetics
CWLtool 1.0.20190906, 2.0.20200126, 3.0.20210124104916 [279] workflow, scheduler
CycleGan 20201015 [280] phylogenetics
Cytoscape 3.4.0 [281] biology, bioinformatics, ngs, phylogenetics
D2go 20210702 [282] ml, dl, ai
DAKOTA 6.10, 6.8, 6.8-gui [283] Computational Science and Engineering
DALIGNER 1.0 [284] biology, phylogenetics
Dammit 1.0rc2 [285] biology, phylogenetics
DASTool 1.1.0, 1.1.2 [286] biology, phylogenetics
Datamash 1.1.0 [287] math
DAWGPASW 1.0 [288] biology, phylogenetics
DCC 0.4.4 [289] biology, bioinformatics, ngs
Dcmstack 0.6.2 [290] biology, imaging
DCMTK 3.6.0 [291] biology,neuroscience,imaging
DDocent 2.7.8 [292] phylogenetics
DDSCAT 7.3.0 [293] Astrophysics
DDT 18.2, 20.0, 20.2 [294] Software Development
DealII 8.3.0 [295] Library
DeconSeq 0.4.3 [296] biology, phylogenetics
DecontaMiner 1.4 [297] genomics, biology
DECX 20180205 [298] phylogenetics
DeepARG 1.0.1 [299] phylogenetics
Deepbgc 0.1.18 [300] phylogenetics
DeepGS 1.2 [301] phylogenetics
DeepLabCut 2.0.7-cpu, 2.0.7-gpu, 2.1.1 [302] phylogenetics
Deepmicrobes 20200219 [303] biology, genomics, metagenomics, ML
DeepPicker 20161102 [304] particle picking
DeepTools 2.4.3, 3.1.1 [305] biology, bioinformatics, NGS
DeFusion 20200305 [306] phylogenetics
Delft3D 7545 [307] Physics
Delineate 1.2.2 [308] Biology, genomics
Delly 0.7.5, 0.7.7, 0.7.8 [309] biology, phylogenetics
DeNoGAP 1.0 [310] biology, phylogenetics, ngs
DERIVA 1.5.0 [311] phylogenetics
Detectron2 0.4 [312] library
DeTiN 1.7.5.9 [313] ngs, genomics
DEXTRACTOR 1.0 [314] biology, sequencing
Diamond 0.9.15, 0.9.34, 2.0.9 [315] computational biology, genomics
DiCal2 2.2.0.1 [316] biology, phylogenetics
DiffReps 1.55.4 [317] Bioinformatics
DISCOVAR de novo 52488 [318] biology, ngs, assembler
DiscoVista 20180906 [319] phylogenetics
Distruct 2.3 [320] phylogenetics
DIYABC 1.0.4.43b, 2.0.3, 2.1.0 [321] biology, phylogenetics
Dlib 19.19 [322] phylogenetics
DL_POLY 1.9 [323] Molecular Dynamics
DNA Clust 3.0 [324] biology,bioinformatics,genomics
DOCK 6.7, 6.8, 6.9 [325] chemistry
DoGFinder 20201103 [326] phylogenetics
DosageConvertor 1.0.3 [327] biology
DOT 2.0 [328] biology,bioinformatics,docking
Doxygen 1.8.3.1 [329] programming, documentation
DRAP 1.91 [330] biology, phylogenetics
DRep 2.3.2 [331] phylogenetics
Dropseq 2.4.0 [332] phylogenetics
Dsistudio 20210123 [333] Machine Learning
DSK 2.1.0, 2.3.0 [334] biology, NGS
DSRC 2.0 [335] phylogenetics
DSSAT 4.6 [336] Agriculture
DSSP 2.2.1, 3.0.0 [337] Molecular Dynamics
DSuite 0.4, 0.4-r41 [338] Biology, Genomics
Dtiprep 0.1.1 [339] phylogenetics
PHYLDOG 20130116-dbg [340] biology,bioinformatics,phylogenetics
Duchamp 1.6.2 [341] phylogenetics
DynamicDBG 20181003 [342] phylogenetics
Dynare 4.4.3 [343] math
EAGLE 2.0 [344] phylogenetics
Eagle-rc 1.1.1 [345] phylogenetics
Ea-utils 1.04.807.18, 1.1.2.537 [346] biology,bioinformatics,genomics,ngs
ECE 1.2 [347] ECE
EDirect 10.7, 12.2 [348] biology, phylogenetics
EDTA 1.9.6 [349] phylogenetics
Edyeet 0.1, 0.3 [350] phylogenetics
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [351] biology,bioinformatics,matlab
EGene-MVN 0.1 [352] biology, genetics
EggNOG-mapper 2.0.1 [353] phylogenetics
EGSnrc 2019 [354] phylogenetics
EIGENSOFT 4.2, 5.0.1, 6.0.1 [355] biology, bioinformatics
Elastix 4.9.0 [356] phylogenetics
ELPA 2019.11.001 [357] library,c,math
ElPrep 4.1.4 [358] phylogenetics
Emacs 27.2 [359] programming, scripting, language
EMAN2 2.22, 2.31 [360] image processing
EMBOSS 6.6.0 [361] biology,bioinformatics
Embree 3.6.1 [362] ray, tracing, kernels
EMC 9.4.3 [363] Monte Carlo Simulations
EMMAX 20100307, 20120210 [364] biology, NGS, mapping
EnergyPlus 9.3.0 [365] simulation
Ensembl Tools 100, 80 [366] biology, bioinformatics
EnTAP 0.6.1.2, 20160416 [367] biology, phylogenetics
EPACTS 3.2.6, 3.4.2, 3.4.2.hg38 [368] biology, bioinformatics, genomics
Epiteome 1.0 [369] phylogenetics
Epoch 4.7.3 [370] astronomy,CCPP
EQTLA 1.1 [371] biology, bioinformatics, genomics
EQtlBma 1.2.2, 1.3.0r20140820 [372] biology, genotyping
Erpin 5.5.4 [373] biology, phylogenetics
ESOM 1.1 [374] biology, phylogenetics
ESPRESSO 6.2.0, 6.2.1, 6.4.1 [375] Quantum,modeling
ESPRIT 2009-nogap, 201102 [376] biology,bioinformatics
ETE3 3.0.0, 3.1.1 [377] biology, phylogenetics
EVidenceModeler 1.1.1 [378] phylogenetics
Evigene 20180730, 20200520 [379] phylogenetics
ExaBayes 1.5 [380] phylogenetics
Exonerate 2.2.0 [381] biology,bioinformatics,genomics
Export2graphlan 0.22 [382] statistics, mapping, graphing
EXpress 1.3.1, 1.5.1 [383] biology,bioinformatics,ngs
Face_morpher 20190630 [384] phylogenetics
Face_recognition 1.2.2 [385] phylogenetics
FALCON 20161027, 20161222, 20190601 [386] biology,bioinformatics,ngs,sequencing
FALCON_unzip 20161222 [387] biology, bioinformatics
FAR 2.15 [388] biology,bioinformatics,genomics
FAST 1.06 [389] biology phylogenetics
Fast-gep 1.0 [390] phylogenetics
Fast-Plast 1.2.6 [391] biology, phylogenetics
FASTA 34.26.5, 36.3.6d [392] biology,bioinformatics,genomics
Fastai 2.1.5 [393] phylogenetics
FastANI 1.1 [394] phylogenetics
FastGEAR 20161216 [395] biology, bioinformatics, genomics
Fastix 0.1.0 [396] biology sequence fasta
R8s 1.8 [397] phylogenetics
FastML 3.0 [398] biology,bioinformatics,phylogenetics
Fastp 0.20.0 [399] biology,bioinformatics,ngs
FASTphase 1.4.8 [400] phylogenetics
FastPlast 1.2.8 [401] phylogenetics
Fastq-pair 1.0 [402] phylogenetics
FastQ-Screen 0.14.0 [403] phylogenetics
Fastq-tools 0.8 [404] biology, NGS,
FastQC 0.11.4, 0.11.7, 0.9.6 [405] biology,bioinformatics,ngs
FastqPuri 1.0.7 [406] phylogenetics
FastQTL 2.184 [407] phylogenetics
Fastsimcoal 2.6.0.3 [408] biology, phylogenetics
FastSpar 0.0.4 [409] biology, genomics
FastStructure 20150112 [410] biology, genomics
FastTree 2.1.11 [411] biology,bioinformatics,phylogenetics
FastUniq 1.1 [412] biology, phylogenetics
Fastx Toolkit 0.0.13.2, 0.0.14 [413] biology,ngs
FcGENE 1.0.7, 1.0.7.1 [414] biology,bioinformatics,genomics,snp
FDSTools 1.2.0 [415] phylogenetics
Fdupes 1.51 [416] file management
FEELnc 0.1.1 [417] phylogenetics
FEniCS 2018.1.0 [418] biology, phylogenetics
Ferret 6.82 [419] Data Visualization and Analysis, Oceanography, Meteorology
FFmpeg 2.1.3, 2.8.3, 4.3.1 [420] Audio, Video
FFTW 3.3.6, 3.3.7, 3.3.8 [421] library,c,math
Fgbio 0.5.0, 0.7.0 [422] phylogenetics
FGMP 1.0.1 [423] phylogenetics
Fiji 2.0.0rc59 [424] ImageJ
BIRDS 1.0 [425] fiji, plugin, imaging
Filtlong 0.2.0 [426] biology, phylogenetics
Finder 20210503, 20210609 [427] biology, bioinformatics, finder
Finemap 1.4 [428] phylogenetics
Finesse 2.3.1 [429] simulation
R8s 1.8 [430] phylogenetics
Fit-sne 1.2.1 [431] phylogenetics
FLAIR 1.5 [432] phylogenetics
Flappie 1.1.0, 2.1.3 [433] phylogenetics
FLASh 1.2.10, 1.2.11 [434] biology, genomics
FLEA 2.0.0 [435] phylogenetics
Flex 2.6.4 [436] programming tool
Flexbar 2.3, 2.34, 3.5.0 [437] biology, bioinformatics, genomics, ngs
FLEXLm 1.0 [438] Administration
FlowCraft 1.4.1 [439] phylogenetics
Fluent 17.2, 19.1, 2020R1 [440] CFD
Flye 2.6, 2.7.1, 2.8.1 [441] Biology, NGS
FMRIPrep 1.4.0a1, 1.5.4, 20.2.3 [442] data mining
ForeSeqs 1.0.4 [443] phylogenetics
Pascal 3.0.0 [444] Compiler, Programming
Fqtools 20160224 [445] biology,bioinformatics,ngs,sequencing
FragGeneScan 1.16 [446] biology,genomics
FRAMA 20151019 [447] biology
FrameDP 1.2.2 [448] biology, sequencing
FRAPOSA 20200421 [449] phylogenetics
FreeBayes 1.1.0-20170823, 1.3.1, 1.3.2 [450] biology,genomics
Freesurfer 6.0.0, 7.1.0, 7.1.1 [451] biology,bioinformatics,neuroscience,imaging
FSA 1.15.9 [452] phylogenetics
FSL 6.0.1, 6.0.3, 6.0.4 [453] biology,bioinformatics,neuroscience,imaging
Funannotate 1.8.7 [454] phylogenetics
Fusion_twas 20210218 [455] phylogenetics
GAL 20180906 [456] phylogenetics
Galaxy 1.0 [457] biology,bioinformatics
GAML 20150610 [458] biology, bioinformatics, genomics
GapCloser 1.12r6 [459] biology, genomics, ngs
GapFiller 1.10, 1.11 [460] biology, genomics
GARLI 2.0, 2.01 [461] biology,bioinformatics,phylogeny
GASVPro 201310 [462] biology, bioinformatics, ngs
GATE 7.0 [463] Date analysis and visualization
GATK 4.1.4.0, 4.1.8.1, 4.1.9.0 [464] biology,bioinformatics,ngs
Gaussian 09 A.02, 09 D.01, 16 [465] Computational Chemistry
Gawk 4.2.0 [466] Software tools
Gblocks 0.91b [467] biology,bioinformatics
GNU Compiler Collection 7.3.0, 8.2.0, 9.3.0 [468] compilers
Kmerfreq 1.0.2 [469] biology, bioinformatics, genomics
GCT 6.2.1 [470] gridftp, globus, toolkit
GCTA 1.26.0, 1.92.4beta, 1.93.2beta [471] biology, genomics, SNP,
GDAL 2.2.1, 2.2.4, 2.3.1 [472] Geospatial library
GDB 8.3, 9.2 [473] Software Development
GDC-Client 1.0.1, 1.5.0 [474] biology, bioinformatics, sequence, ngs
GDrive 2.1.0 [475] Applications, Utilities, Data Transfer
GDSL 1.18 [476] library
Geant4 4.10, 4.10.03, 4.10.5 [477] Physics
GEM 20130406 [478] biology,bioinformatics,ngs,sequencing
Gem5 2.0 [479] Computer Simulator
GEMMA 0.98.1 [480] phylogenetics
NCBI GenBank Tools 20140130 [481] Biology,bioinformatics,NCBI,GenBank
GeneMark-ES 4.33, 4.58, 4.65 [482] biology, genomics
GeneMarkS-T 2012.04, 3.10.001 [483] biology,genomics
GenePainter 2.0.4 [484] biology, phylogenetics
GeneRax 1.2.2 [485] phylogenetics
GeneSeqer 2014-02-26 [486] biology, genomics
Genesum 0.1.0 [487] biology,genomics
GeneTorrent 3.8.7 [488] biology,bioinformatics,data download
GenGen 1.0.1 [489] biology, phylogenetics
Genome_Graph_Annotation 20190131 [490] phylogenetics
Genome STRiP 2.00.1602 [491] biology, genomics, ngs
GenomeTools 1.5.7, 1.5.9 [492] biology, bioinformatics
Genomic-fluidity 20151109 [493] phylogenetics
GenomicNeuralnet 20161030 [494] phylogenetics
GenomicConsensus 2.3.3 [495] biology, phylogenetics
GenomicTools 2.7.0 [496] biology,bioinformatics,ngs,chip-seq,rna-seq
GenotypeHarmonizer 1.4.18 [497] biology, bioinformatics
Genrich 0.5 [498] phylogenetics
GenSel 4.90 [499] population genetics
Geopython 1.0.0, 1.0.1 [500] python, geospatial, cartography
GEOS 3.3.8, 3.6.2 [501] library, data
GeP 2.1 [502] biology, phylogenetics
Gepard 1.40.0 [503] phylogenetics
Gerbil 1.11 [504] phylogenetics
Get_homologues 3.3.3 [505] biology, genome
GetOrganelle 1.7.3.5, 1.7.5.0 [506] phylogenetics
GFam 1.1 [507] biology, genomics, annotation
GFF-Ex 2.3 [508] phylogenetics
GFF3toolkit 2.0.3 [509] phylogenetics
Gffcompare 0.12.2 [510] phylogenetics
Gffread 0.11.8, 0.12.7, 0.9.8c [511] biology, bioinformatics
Gflags 2.2.1, 20150520 [512] google,libraries
GFOLD 1.1.4 [513] biology, RNA-seq
Ggsashimi 0.5.0 [514] phylogenetics
GHOST-MP 1.3.4 [515] phylogenetics
Ghostscript 9.22 [516] PDF
Giotto 0.1.0 [517] phylogenetics
Git 2.14.1, 2.30.1 [518] Revision Control
Glactools 1.0.8 [519] phylogenetics
Glimmer 3.02 [520] biology, microbial annotation
GlimmerHMM 3.0.4 [521] biology, microbial annotation
Globus 1.10.1, 2.1.3 [522] Data Transfer
Glog 0.3.5 [523] google,libraries
GLPK 4.55, 4.65 [524] Programming
Glueviz 0.15.2 [525] phylogenetics
GMAP 20180212, 20180212_sse2, 20190610 [526] biology, bioinformatics, genomics, ngs
GMcloser 1.6 [527] Biology, NGS
GMP 6.1.2 [528] library, crypto
GnuPlot 4.6.0, 5.2.2, 5.2.3 [529] graphics,plotting,math
Go 1.12.9, 1.13.6, 1.15.4 [530] programming language
GOMAP 1.3 [531] biology, bioinformatics, ngs
GoPHY 201030 [532] phylogenetics
Gotcloud 1.17.5 [533] phylogenetics
GPA 1.1 [534] phylogenetics
GPhoCS 1.2.3 [535] phylogenetics
Gpufit 20201127 [536] phylogenetics
Grace 5.1.22 [537] graphics, statistics, 2D
GRACKLE 3.1 [538] library,c,astrophysics
GrADS 2.0.1 [539] environment, grid analysis
Graftm 0.12.2 [540] phylogenetics
GramCluster 1.3 [541] biology,sequencing,
Graph-tool 2.32 [542] phylogenetics
Graph_annotation 0.1 [543] phylogenetics
GraPhlAn 1.1.3 [544] phylogenetics
GraphaMap 0.6.5 [545] phylogenetics
GraphSplitting 2.4 [546] phylogenetics
GraphViz 2.38.0, 2.46.1 [547] biology,bioinformatics,neuroscience,imaging
GRASS 7.0, 7.4 [548] Geography
Grf 1.0.0 [549] genomics, bioinformatics
Grib_api 1.10.1, 1.15.1, 1.26.1 [550] C, fortran, library
GRIDSS 2.6.2 [551] phylogenetics
GROCSVs 0.2.5 [552] phylogenetics
GROMACS 2019.2, 2020.3, 2021.2 [553] Computational Chemistry, Molecular Dynamics
GroopM 0.3.5 [554] biology, phylogenetics
Groovy 2.4.15 [555] Programming
Gscripts 1.1 [556] scripts
GSEA 3.0.0 [557] biology, bioinformatics, genomics
GSL 2.4, 2.5, 2.6 [558] library, data
GSNP 1.0 [559] biology,bioinformatics,ngs
GTDBTk 0.1.3 [560] phylogenetics
GTOOL 0.7.5 [561] phylogenetics
GUAVA 1.0 [562] phylogenetics
Gubbins 2.4.1 [563] phylogenetics
Guile 2.2.2 [564] Programming Language
GULP 4.4, 5.0 [565] Material Science
Guppy 4.2.2, 4.4.1, 4.5.4 [566] phylogenetics
GWAMA 2.2.2 [567] phylogenetics
HALC 1.1 [568] biology, phylogenetics
HaMStR 13.2.3, 13.2.4, v8b [569] biology, genome
HapCompass 0.7.7 [570] ngs, genomics
HAPCUT 0.7 [571] biology, assembly
HAPLOSWEEP 1.0 [572] biology, phylogenetics
HapQTL 1.00 [573] biology
Hapsembler 2.21 [574] biology, bioinformatics, assembly
HASLR 0.8a1 [575] phylogenetics
Hclust2 1.0.0 [576] statistics, mapping
HDF4 4.2.11 [577] library, data
HDF5 1.8.19, 1.8.20, 1.8.9 [578] library, data
HELEN 20200516 [579] phylogenetics
HelitronScanner 1.1 [580] phylogenetics
HiC-Pro 3.0.0 [581] Biology, Pipeline, Genomics
Hifiasm 0.16.1, 0.4, 0.8 [582] phylogenetics
HipSTR 0.7 [583] phylogenetics
HISAT2 2.2.0, 2.2.1, 2.2.1-3n [584] Biology, Sequence Alignment, NGS
HLAminer 1.3.1, 1.4 [585] biology, phylogenetics
HMM-FRAME 20140724 [586] phylogenetics
HmmCleaner 0.180750 [587] phylogenetics
HMMER 3.1b1, 3.1b2, 3.2.1 [588] biology, genome
HMMRATAC 1.2.10 [589] phylogenetics
HOMER 4.10, 4.11, 4.8 [590] biology,bioinformatics,sequence,ngs
HOOMD 2.1.7 [591] library, math
HPL 2.1 [592] parallel programming, benchmarks, MPI
HTMLDoc 1.8.28, 1.9.3 [593] pdf, docs, html
HTSeq 0.11.2 [594] biology,bioinformatics,ngs
Humann2 0.11.2, 2.8.1 [595] phylogenetics
Hyb 20141126 [596] biology, ngs, RNA-Seq
HybPiper 1.2, 1.3.1 [597] biology, phylogenetics
HyDe 0.4.3 [598] phylogenetics
HyPhy 2.5.4, 2.5.7, 2.5.8 [599] biology,bioinformatics,evolution
HYPRE 2.15.1, 2.18.2, 2.19.0 [600] Math, Numerical Solvers
IAnnotateSV 1.0.6, 1.0.9 [601] Biology, Phylogenetics
IAssembler 1.3.2 [602] biology, assembly
Ibdne 20150815 [603] biology,ngs
Icommands 3.3.1 [604] iRods
IDBA-MT 1.0 [605] biology,NGS
IDBA-UD 1.1.1, 1.1.1-512, 1.1.1-512-mem [606] Genomics, bioinformatics, phylogenetics
IDL 8.3 [607] language, programming, science
IDR 2.0.3 [608] phylogenetics
IGB 8.4.1 [609] biology, bioinformatics, genomics
IgBLAST 1.5.0, 1.7.0 [610] biology, bioinformatics
IGoR 1.4.0 [611] phylogenetics
IGTP 1.1 [612] biology, bioinformatics, phylogenetics
IGV 2.3.91, 2.4.16, 2.8.6 [613] biology, bioinformatics, ngs, phylogenetics
Illumina-utils 2.11 [614] phylogenetics
Illumiprocessor 2.0.9 [615] phylogenetics
IM and IMa 20091217 [616] biology,bioinformatics,population genetics
Ima2 20120827 [617] biology,bioinformatics,population genetics
IMa2p 20170712 [618] biology, phylogenetics
IMA3 22Aug18 [619] Molecular Dynamics
ImageJ 1.48 [620] imaging
ImageMagick 7.0.8-20 [621] Imaging
Imaginaire 20201229 [622] Imaging, Video, AI, synthesis
IMOD 4.7.15, 4.9.10 [623] 3D modeling, image reconstruction
Imoka 1.0 [624] biology, genomics
Intel MPI 5.1.1 [625] parallel programming, development, MPI, library
IMPUTE2 2.3.2 [626] phylogenetics
INDELible 1.03 [627] phylogenetics
Infernal 1.1.1, 1.1.4 [628] biology, sequence alignment
INLA 20160718, 20170620 [629] statistics, modeling, R
InParanoid 4.1 [630] biology, biology
InStruct 20160723 [631] phylogenetics
Intel Compilers and Libraries 2018.1.163, 2019.1.144, 2020.0.166 [632] programming languages, development, library, math, intel
Intervene 0.6.2 [633] biology, phylogenetics
IOAPI 3.1, 3.2 [634] Meteorology
IPOPT 3.12.10, 3.12.6 [635] library, c/c++,math, solver, optimization
InterProScan 5.35-74.0, 5.50-84.0, 5.52-86.0 [636] biology,bioinformatics
Ipyrad 0.7.24, 0.7.30, 0.9.53 [637] phylogenetics
IQ-TREE 2.0.6, 2.1.0, 2.1.2 [638] biology, phylogenetics,
IRAP 0.8.1p7 [639] biology, ngs, pacbio
IRFinder 1.2.0, 1.3.0, 1.3.1 [640] biology, RNA-Seq
IsONclust 0.0.6 [641] phylogenetics
IsoSel 1.0 [642] phylogenetics
IsoSeq3 3.1.0, 3.2.2, 3.4.0 [643] biology, bioinformatics, ngs, pacbio
ISOWN 20180820 [644] phylogenetics
IsPcr 3.3 [645] biology, phylogenetics
ITK 3.20.1, 4.10.1 [646] Bioinformatics
ITK-SNAP 3.0.0, 3.8.0 [647] biology,bioinformatics,neuroscience,imaging
ITSx 1.1b [648] phylogenetics
IVar 1.3.1 [649] biology
Jabba 1.0 [650] biology, phylogenetics
JACUSA 1.2.0 [651] biology, bioinformatics, ngs, phylogenetics
JAGS 3.3.0, 3.4.0, 4.2.0 [652] Statistics
NpScarf 1.7 [653] phylogenetics
JDK 11.0.1, 14, 9.0.1 [654] programming,runtime
JCVI 0.8.12, 1.0.13 [655] phylogenetics
Je 1.0 [656] biology, NGS
Jellyfish 2.2.4, 2.2.6, 2.3.0 [657] biology,ngs
JModelTest 2.1.1 [658] biology, bioinformatics, genomics, phylogenetics
Jo 1.3 [659] Software
Jq 1.6 [660] Software
Juicer 1.22.01 [661] phylogenetics
Julia 1.5.0, 1.5.3, 1.6.2 [662] programming, language, statistics
Jupyter 5.7.8, 6.0.3, 6.2.0 [663] python, R, jupyter
JVARKIT 20180405 [664] biology, phylogenetics
Kaiju 1.6.2, 1.7.2 [665] biology, phylogenetics
KaKs 1.2, 2.0 [666] biology, bioinformatics, evolution, phylogenetics
Kalign 3.3.1 [667] Biology, Bioinformatics, Sequencing, Alignment
Kallisto 0.42.4, 0.43.0, 0.44.0 [668] biology,NGS,RNA-Seq
Khmer 2.0, 2.1 [669] Biology, NGS
KIM 1.7.2, 1.8.2, 1.9.3 [670] Simulation
KING 2.1.2 [671] biology, genome, gwas
KisSplice 2.4.0-p1 [672] biology, RNA
KLayout 0.26.7 [673] phylogenetics
KMC 3.1.0, 3.1.1 [674] phylogenetics
Kmerfreq 4.0 [675] biology, bioinformatics, genomics
KMOS 0.3.21 [676] phylogenetics
Kneaddata 0.7.4, 0.9.0 [677] phylogenetics
Knitro 12.2.0 [678] Mathematical Optimization Problems
KofamScan 1.3.0 [679] phylogenetics
Kover 2.0.3 [680] phylogenetics
Kraken 1.0, 2.0.6b, 2.0.8b [681] biology, ngs
KrakenUniq 0.5.8 [682] phylogenetics
Krona 20161019 [683] biology, bioinformatics
Ksnp 3.021 [684] biology, phylogenetics, SNP
LACHESIS 2.1 [685] phylogenetics
Lambda 0.9.4, 1.0.3, 2.0.0 [686] biology, sequencing, phylogenetics
LAMMPS 30Jul16, 7Aug19, 7Dec15 [687] Molecular Dynamics
LAMP 2.5 [688] biology, bioinformatics, genomics
LAPACK 3.8.0 [689] programming,library,fortran
Last 916, 979 [690] biology,bioinformatics,sequence,alignment
LAStools 20200114 [691] LiDAR
LASTZ 1.02.00, 1.03.02, 1.04.00 [692] biology,bioinformatics,ngs
Lazypipe 1.2 [693] genomics,taxonomy,binning
Lbzip 2.5 [694] compression
LCModel 6.3 [695] Biology, NMR
LDhat 2.2a [696] biology,genomics
LEfSe 20180219 [697] phylogenetics
LFMM 1.4, 1.5 [698] biology, phylogenetics
ChartDirector 5.1.0 [699] library, data
Libint 2.5.0, 2.5.0b [700] library
LEMON 1.2.3 [701] library
LibMesh 1.5.0 [702] Math, Numerical Solvers
Libunistring 0.9.7 [703] library
Libvips 8.5.4 [704] image processing
LIBXC 4.2.3, 4.3.4 [705] library, density function
LIBXSMM 1.13 [706] library,c,math
LIBZMQ 4.3.1 [707] library
Liftoff 1.4.2 [708] phylogenetics
LIGR 2.05 [709] biology,assembly
Lima 2.0.0 [710] phylogenetics
LINKS 1.8.5, 1.8.6 [711] biology, genomics
Linksbrowser 2.14 [712] web browser
LIQA 1.0.0 [713] phylogenetics
LMAP 1.0.2 [714] biology, phylogenetics
LncScore 1.0.2 [715] biolgoy, phylogenetics
LobSTR 4.0.6 [716] biology, phylogenetics
Localbrainage 20210415 [717] bioinformatics, ml
Localizer 1.0.4 [718] phylogenetics
LocusZoom 1.4 [719] phylogenetics
LoFreq 2.1.3.1 [720] phylogenetics
LongRanger 2.1.5, 2.2.2 [721] biology, phylogenetics
LoRDEC 0.9 [722] phylogenetics
LORMA 0.3, 0.5 [723] biology, ngs, pacbio
LS-DYNA 700, 711, 901 [724] Physics
LSD2 1.6.5 [725] phylogenetics
Ltr_finder 1.07 [726] biology, phylogenetics
LTRRetriever 2.1, 2.5, 20170514 [727] biology, phylogenetics
Lua 3.5.2 [728] programming, scripting, language
Lumpy-sv 0.2.1, 0.2.13, 0.3.1 [729] biology, genotyping
LZO 2.09 [730] library, compression
M5nr 20121126 [731] biology, bioinformatics, genomics
Macaulay2 1.15 [732] phylogenetics
MACH 1.0.18 [733] biology,bioinformatics,genomics,ngs
Mach2VCF 20150515 [734] biology
MACS 2.0.10, 2.1.2, 2.2.7.1 [735] biology, bioinformatics, CHiP-Seq
MafFilter 1.3.0 [736] phylogenetics
MAFFT 7.245, 7.294, 7.397 [737] bio,bioinformatics,sequence
MAGeCK 0.5.9.4 [738] phylogenetics
MAGeCK-VISPR 0.5.6 [739] phylogenetics
MAGMA-GWAS 1.09 [740] phylogenetics
MAJIQ 2.1 [741] phylogenetics
Maker 2.31.10, 2.31.6, 3.01.03 [742] biology,bioinformatics
MAnorm 20120316 [743] biology, phylogenetics
MANTA 1.6.0 [744] phylogenetics
Mantis 1.0.4 [745] phylogenetics
Mapclassify 2.4.2 [746] statistics, mapping, geography
MapThin 1.11 [747] phylogenetics
Maq 0.7.1 [748] biology,bioinformatics,ngs
MarginPolish 1.0.0 [749] phylogenetics
MARK 2.0.1 [750] application, data, capture
MarkerMiner 20150710 [751] biology, bioinformatics, genomics
Mash 1.1, 2.3 [752] biology, genomics
MasHmap 2.0 [753] phylogenetics
MASSMINE 0.10.0, 0.11.0, 0.9.5 [754] data mining
MaSuRCA 2.3.2, 3.3.4, 3.4.2 [755] biology,bioinformatics,short read alignment
Mathematica 12.1.1.0 [756] Mathematica - a category of its own!
MATLAB 2019b, 2020a, 2020b [757] math,language
MATS 4.0.1, 4.0.2, 4.1.0 [758] biology,bioinformatics,ngs,rna-seq
Mauve 2.3.1 [759] biology,ngs,genomics
Mawk 1.3.4-20150503 [760] programming language
Maxbin 2.1.1 [761] biology,NGS
Maxima 5.41.0 [762] Math
MC 4.6.1 [763] shell
MCarts 1.0.2 [764] biology, genomics, markov
Mccortex 1.0 [765] phylogenetics
MCL 12-135, 14-137 [766] biology, genomics
MCNP 6, 6.1 [767] Physics
MCNPX 2.7.0 [768] Physics
MCR 2019b, 2020a, 2020b [769] math, language
MCScanX 20130328 [770] biology, phylogenetics
MECAT 20180308 [771] phylogenetics
Medaka 0.7.1, 1.0.1, 1.2.1 [772] biology, phylogenetics
Medusa 1.6 [773] phylogenetics
MEGA 7.0.26 [774] biology, phylogenetics
Mega2 4.9.2, 6.0.0 [775] biology, phylogenetics
MEGAHIT 1.1.1, 1.1.4 [776] biology, phylogenetics
Megalodon 2.0.0 [777] phylogenetics
MEGAN 5.10.3, 6.4.15 [778] biology, bioinformatics, ngs
MEGASAT 1.0 [779] phylogenetics
Megraft 1.0.2 [780] biology,sequencing,
MELD 0.4.14, 0.4.19 [781] Computational Chemistry, Molecular Dynamics
MELTING 4.3.1 [782] biology, genome, RNA, folding
MEME 4.9.1, 5.0.2, 5.0.5 [783] biology,bioinformatics,sequence
MentaLiST 0.1.3 [784] biology, phylogenetics
Meraculous 2.0.5 [785] Biology,NGS
Mercurial 4.8.2 [786] Revision Control
Merge_peaks 0.1.0 [787] workflow
Merlin 1.1.2 [788] biology,SNP
Merqury 1.1, 1.3 [789] phylogenetics
Meryl 1.0 [790] phylogenetics
MeShClust 1.2.0 [791] biology
Meshroom 2019.2.0 [792] phylogenetics
Meta-Marc 1.0.0 [793] phylogenetics
Meta-Tissue 0.4 [794] biology, genetics
MetaBAT 0.32.4, 2.13 [795] biology, genomics
Metabin 1.0 [796] Genomics, bioinformatics, metagenomics
MetaCherchant 0.1.0 [797] biology, phylogenetics
MetaCluster 5.0b [798] biology,bioinformatics,genomics
MetaCompare 20181016 [799] phylogenetics
Metacrast 20200309 [800] phylogenetics
MetaGeneMark 2.10, 3.26 [801] biology,genomics
METAL 20110325 [802] biology, ngs, genomics
METANNOT 20171129 [803] phylogenetics
MetaPhlAn2 2.7.7, 2.96.1, 3.0.3 [804] biology, phylogenetics
MetaPhysicl 1.0.0 [805] Math, Astronomy, Numerical Simulation
MetaSV 0.5.4 [806] biology, phylogenetics, NGS
MetaVelvet 1.2.06 [807] computational biology, genomics
MetaWRAP 1.2 [808] phylogenetics
Metaxa2 2.1.1, 2.1.3 [809] biology,bioinformatics,ngs,sequencing
MethylDackel 0.5.0 [810] phylogenetics
Methylpy 1.2.9 [811] Biology, Phylogenetics
Metilene 0.2.8 [812] biology, genomics, methylation
METIS 5.1.0 [813] software
Mfannot 20180405 [814] biology, phylogenetics
Mfold 3.6 [815] bioinformatics,structure,RNA
Mg-rast 20150919 [816] biolgoy, genomics
MGEfinder 1.0.5 [817] phylogenetics
MGERT 1.0.1 [818] phylogenetics
MGEScan 20160416 [819] biology, genomics
MHAP 1.6 [820] biology, sequencing
MHCflurry 1.4.3 [821] phylogenetics
MIA 20130201 [822] biology, ngs
MIDAS 20160830 [823] biology, phylogenetics
MIGRATE-N 3.3.0, 3.6.6, 4.2.14 [824] biology,bioinformatics,population genetics
MIKE 1.0 [825] environment,water,modeling
Minced 0.2.0 [826] biology, genomics
Miniasm 0.2-r168, 0.3-r179 [827] biology, phylogenetics
MiniCaller 20161201 [828] biology,bioinformatics,ngs,phylogenetics
Minigraph 0.15 [829] phylogenetics
Minimac2 1-20130717, 2-20140915, 3-20150727 [830] biology, NGS,
Minimap 2.1t, 2.21, 2.9-r720 [831] biology, phylogenetics
MinkowskiEngine 0.5.3 [832] Machine Learning, Deep Learning
MinPath 1.4 [833] biology, phylogenetics
MIRA 4.0.rc1, 4.9.6, 5rc2 [834] biology,bioinformatics,genomics,assembly
MiRanda 1.9 [835] phylogenetics
MiRBShunter 0.2 [836] phylogenetics
Mirdeep 0.1.0, 0.1.1, 2.0.1.3 [837] phylogenetics
MiRDP2 1.1.4 [838] Biology, Genomics
Mireap 0.20 [839] biology
MiRge 2.0 [840] phylogenetics
Misa 1.0 [841] biology, bioinformatics, genomics
MISO 0.5.3 [842] biology,bioinformatics,ngs,sequencing,rna-seq
MITE-Hunter 20111101 [843] biology, phylogenetics
MITObim 1.9.1 [844] phylogenetics
MitoFinder 1.0.2, 1.1, 1.4 [845] phylogenetics
MitoPhAST 3.0 [846] phylogenetics
MiXCR 2.1.8, 3.0.13 [847] biolgoy, phylogenetics
MixMHC2pred 1.2 [848] phylogenetics
MixMHCpred 2.0.2 [849] phylogenetics
Mixmogam 20190322 [850] phylogenetics
Intel Compilers and Libraries 2018.1.163, 2019.1.144, 2020.0.166 [851] programming languages, development, library, math, intel
Mlcoalsim 1.9916b [852] biology, phylogenetics
Mlpack 3.4.2 [853] library
Mlst 2.15.2 [854] phylogenetics
Mlstcheck 2.1 [855] phylogenetics
MMSEQ 1.0.8 [856] biology,bioinformatics,genomics
MMseqs2 11, 12 [857] phylogenetics
MNEtools 0.22.0 [858] phylogenetics
MOABS 1.2.9, 1.3.2, 1.3.4 [859] biology, ngs
MODELLER 9.14, 9.23 [860] biology,bioinformatics,modelling,structure
MODELTEST 0.1.2 [861] biology, phylogenetics
Molden 5.0 [862] Molecular, Electronic Structure
Monai 0.5.3 [863] Data Science in Healthcare
MongoDB 4.0.3 [864] db, mongodb, mongo
Mono 5.18 [865] linux, runtime
Monolix 4.3.2 [866] modeling, pharmacokinetics
MOOSE 20200316, 20200722, 20210726 [867] physics, simulation
MOSAIK 2.1.33, 2.2.3, 2.2.30 [868] biology,bioinformatics,short read alignment
Mosdepth 0.2.3, 0.3.1 [869] biology, phylogenetics
Mothur 1.37.0, 1.38.1, 1.41.3 [870] biology, microbial ecology
MotionCor2 1.2.3, 1.3.1 [871] Motion Correction
MOTU 1.1 [872] biology, bioinformatics, genomics
MOTUs 2.5.1 [873] phylogenetics
MountainSort 0.9.0 [874] library
MPACK 0.8.0 [875] library
MPB 1.5 [876] library, math
MPBoot 1.1.0 [877] biology, phylogenetics
MP-EST 1.4 [878] biology,bioinformatics,ngs,sequencing
MPFR 3.1.6 [879] library, math
Mpinterfaces 20170613 [880] DFT
MrBayes 3.2.4, 3.2.5, 3.2.6 [881] application, biology, phylogenetics
MRIcroGL 20200420, 20201102, 20210327 [882] biology, mri, imaging
MRIcron 201306, 20161012, 20190911 [883] biology, mri, imaging
Mriqc 0.11.0, 0.16.1 [884] mri, imaging, biology
MRtrix 0.2.13, 3.0.1, 3.0rc2 [885] biology, mri, imaging
Ms 20171108 [886] phylogenetics
Ms-dial 4.4.8 [887] biology, bioinformatics, metabolomics
MSINGS 20180810 [888] phylogenetics
MSMC-Tools 20190614 [889] phylogenetics
Msprime 0.7.4 [890] phylogenetics
MstatX 1.0 [891] biology, phylogenetics
MSTmap 1.0 [892] phylogenetics
Msvar 1.3 [893] biology,bioinformatics,population genetics
MTG2 2.15 [894] phylogenetics
MTR 20210526 [895] Biology, Genomics
Mugsy 1.2.3 [896] biology, phylogenetics
MultiQC 1.7 [897] biology, bioinformatics, CHiP-Seq
MUMmer 3.23, 4.0.0beta2 [898] biology,bioinformatics,genomics
MUSCLE 3.8.31 [899] biology, bioinformatics, alignment
MuSE 1.0rc [900] phylogenetics
Musket 1.1 [901] biology, genomics, ngs
MuTect 1.1.4, 1.1.7 [902] biology,genomics
MutSig 1.4, 1.41 [903] biology,genomics
Mvftools 20191124 [904] phylogenetics
MZMine 2.41, 2.52, 2.53 [905] biology, bioinformatics, spectrometry, NMR
NAMD 2.14, 2.14b2, 3.0 Alpha [906] Molecular Dynamics
NANO 2.8.2 [907] Text Editor
NanoCount 0.2.1 [908] phylogenetics
Nanodisco 1.0.3 [909] phylogenetics
Nanofilt 2.7.1 [910] phylogenetics
NanoPlot 1.30.1 [911] phylogenetics
Nanopolish 0.11.1, 0.13.2, 20171006 [912] biology
NanoSV 1.2.0, 1.2.3, 1.2.4 [913] biology, genomics
NanoVar 1.3.9 [914] phylogenetics
Napari 0.3.8, 0.4.7 [915] phylogenetics
NBODY 6 [916] Astronomy
Ncbi-vdb 2.6.3, 2.8.2 [917] SRA toolkit library
NCBI BLAST+ 2.7.1, 2.8.1, 2.9.0 [918] biology, bioinformatics
NCBI C++ Toolkit 12.0.0, 21.0.0, 7.0.0 [919] Biology,bioinformatics,NCBI,programming,library,cpp
Nccl 20.11 [920] development, library, communication, nvidia
Ncftp 3.2.5 [921] file transfer
NCL 6.1.2, 6.3.0 [922] Atmosphere Science
NCO 4.2.1, 4.4.3 [923] data tools
Ncview 2.1.2, 2.1.7 [924] data visualization
NECAT 202001019 [925] phylogenetics
Necklace 1.00 [926] biology, phylogenetics
NeEstimator 2.1 [927] Biology, Bioinformatics
Nemo 1.0.0rc1, 1.0.1, 1.2.0 [928] AI, machine learning
Neovim 0.2.0 [929] editor, text, ide, vim
NetCDF 4.3.3, 4.4.3, 4.7.2 [930] data, exchange
NetCDF-C 4.5.0, 4.6.1, 4.7.4 [931] data, exchange
NetCDF-Fortran 4.4.3, 4.4.4, 4.5.3 [932] data, exchange
NetLogo 5.3.64, 6.1.1, 6.2.0 [933] modeling
NEURON 7.6.2, 7.7.2, 8.0.0 [934] biology, neuroscience
Newbler 2.7, 2.8, 2.9 [935] biology,bioinformatics,ngs,454,assembly,denovo
Newick_utils 1.6, 1.7 [936] biology, phylogenetics
Newick-utils 1.6 [937] biology, bioinformatics, genomics, phylogenetics
NewTargets 20210215 [938] biinformatics
NextDenovo 2.4.0 [939] phylogenetics
Nextflow 20.07.1, 20.10.0, 24.04.0 [940] biology, bioinformatics, workflow
NextGenMap 0.5.5 [941] phylogenetics
NextPolish 1.3.1 [942] phylogenetics
Nextstrain 1.16.1 [943] phylogenetics
Nf-core 1.12.1 [944] biology, bioinformatics, workflow
LAMMPS 10Feb2021 [945] Molecular Dynamics
PyTorch 1.9.0 [946] library, math
TensorFlow 1.15.5, 2.4.0 [947] library, math
NGmerge 0.3 [948] phylogenetics
Ngmlr 0.2.6, 0.2.7 [949] biology, phylogenetics
NGS-SDK 1.2.4, 1.3.0 [950] biology,bioinformatics,ncbi,sdk,library
Ngs-bits 0.1 [951] biology, sequencing
Ngscheckmate 1.0 [952] phylogenetics
Ngstools 20150816 [953] biology, ngs
Nilearn 0.7.0 [954] phylogenetics
Nimare 0.0.5 [955] neuroimaging
Nipype 1.2.0, 1.4.1, 1.6.0 [956] biology,bioinformatics,neuroscience,imaging
Nlp 1.0 [N/A] Machine Learning
Nlr-annotator 0.7 [957] phylogenetics
NLR-Parser 1.0 [958] phylogenetics
NMRPipe 7.9, 8.2 [959] Biochemistry
NONMEM 7.3.0, 7.4.4 [960] Modeling
Nonpareil 3.3.4 [961] phylogenetics
Novoalign 2.08.02, 3.00.02 [962] biology,bioinformatics,ngs
NOVOPlasty 3.7, 4.2, 4.3 [963] phylogenetics
NPhase 1.1.3 [964] bioinformatics,pipeline,phasing,polyploid
NQuire 20180405 [965] phylogenetics
NtEdit 1.2.1 [966] phylogenetics
Nubeamdedup 20200907 [967] phylogenetics
NucDiff 2.0.3 [968] phylogenetics
NucleoATAC 0.3.1 [969] biology, bioinformatics
Nullarbor 1.41 [970] biology, phylogenetics
Numba 0.36.2, 0.43.1, 0.48.0 [971] Compiler
NUPACK 3.2.2 [972] phylogenetics
Nvhpc 11.1, 21.7 [973] programming languages, development, library, math, nvidia
NVidia HPC Compilers 20.11 [974] compilers
NWChem 6.8 [975] Chemistry
NxTrim 0.4.1 [976] biology, bioinformatics, ngs
Oases 0.2.08 [977] biology,ngs,assembler
OCaml 4.02.3 [978] programming languages, scripting, development
OCOCO 0.1.2.6 [979] biology, phylogenetics
Octave 4.2.1 [980] numerical computation
Odgi 0.6 [981] phylogenetics
Olego 1.1.2, 1.1.5, 1.1.6 [982] biology,bioinformatics,ngs,rna-seq
OmicsBox 1.1.78 [983] Image Processing
OMindel 20180129 [984] phylogenetics
OmniCLIP 0.1.0 [985] phylogenetics
OMSV 1.0.1 [986] phylogenetics
ONT-Bonito 0.0.5, 0.1.5 [987] phylogenetics
Ont_fast5_api 2.0.1 [988] phylogenetics
Ont_tutorial_cas9 20190705 [989] phylogenetics
Open-cravat 2.0.1 [990] bioinformatics, genomics
Open3d 0.12.0 [991] phylogenetics
OPENACC 16.7 [992] Programming, Accelerator toolkit
OpenBabel 2.3.2, 2.4.1 [993] biology, bioinformatics
OpenBLAS 0.2.20 [994] programming,library
OpenCL 18.1.0.013 [995] phylogenetics
OpenCV 4.5.2 [996] computer vision
OpenFOAM 4.1, 5.0, 8.0 [997] Computational Fluid Dynamics
OPENMM 7.4.2, 7.5, 7.5.0 [998] Computational Chemistry, Molecular Dynamics
OpenMPI 4.0.4, 4.0.5, 4.1.1 [999] parallel programming, development, MPI, library
OpenNeuro 3.17.4 [1,000] biology, data
OpenPIV-python-gpu 0.21.2, 20190506-gpu [1,001] python, imaging
OpenSlide 3.4.1 [1,002] imaging
OptiType 1.3.1 [1,003] biology, phylogenetics
Orange3 3.3.6 [1,004] data mining
ORCA 4.0.1.2 [1,005] Molecular, Electronic Structure
OrganellePBA 20180904 [1,006] phylogenetics
OrthoFiller 1.1.4 [1,007] phylogenetics
OrthoFinder 1.1.10, 2.3.11, 2.5.2 [1,008] biology, ngs
Orthofisher 0.1.2 [1,009] Biology, Genetics
Orthograph 0.6.3 [1,010] Orthology
Orthologer 2.2.0 [1,011] biology,
OrthoMCL 2.0.3, 2.0.7 [1,012] biology,genomics
OTB 5.8.0 [1,013] Geospatial Data Modeling
P4est 1.1 [1,014] Library
P4vasp 0.3.29, 0.3.30 [1,015] Visualization
P53MH 20020901 [1,016] biology, DNA-sequencing
P7zip 9.20.1 [1,017] archiver
PacBio 10.1.0.119588, 7.0.1 [1,018] biology, bioinformatics, ngs, pacbio, smrtlink
Package-GFE 20150701 [1,019] biology,genomics
PALADIN 1.3.1 [1,020] biology, phylogenetics
PALES 122 [1,021] physics
PAML 4.8a, 4.9a, 4.9h [1,022] biology, phylogenetics
Pandaseq 20140808, 20150627 [1,023] biology,bioinformatics,ngs,sequencing
Pandoc 2.2.2.1 [1,024] Converter
Pangolin 2 [1,025] phylogenetics
PanX 1.6.0 [1,026] phylogenetics
PAPI 5.5.1, 5.7.0 [1,027] programming interface, performance analysis
Parabricks 3.5.0 [1,028] phylogenetics
Parallel 20150122, 20170322 [1,029] shell, process management
Paralyzer 1.5 [1,030] phylogenetics
ParaView 5.4.1, 5.7.0, 5.9.1 [1,031] Data Analysis
ParGenes 1.2.0 [1,032] phylogenetics
ParlAI 1.3.0 [1,033] phylogenetics
Parsnp 1.2, 1.5.0 [1,034] biology, phylogenetics
PartitionFinder 2.0.0-pre-20160513, 2.1.1-20161205, 2.1.1.0 [1,035] biology,phylogenetics,evolution
PASA 2.0.2-r20151207, 2.2.0-r20171013, 2.4.1 [1,036] biology, bioinformatics, genomics, ngs
PASTA 0.2.0, 1.7.8, 20160616 [1,037] biology, sequence alignment
PATHd8 1.0 [1,038] biology, phylogenetics
PATRIC 1.034 [1,039] Machine Learning
PAUDA 1.0.1 [1,040] biology,bioinformatics,ngs,phylogenetics
PAUP 4.0a165, 4.0a166, 4.0b10 [1,041] inferring and interpreting phylogenetic trees
PB-Assembly 0.0.6 [1,042] biology,bioinformatics,ngs,sequencing,pacbio
Pbalign 20160921, 20161221 [1,043] biology, bioinformatics
PBCCS 5.0.0 [1,044] phylogenetics
Pbcore 1.7.1 [1,045] biology,bioinformatics
PBGCpp 1.9.0 [1,046] phylogenetics
PBJelly 15.8.24 [1,047] biology,bioinformatics,ngs
Pbmm2 1.3.0 [1,048] phylogenetics
Pbrt 20181017 [1,049] phylogenetics
Pbsmrtpipe 0.63.0 [1,050] biology,API
Pbtranscript-tofu 20150317, 20160119 [1,051] biology, bioinformatics, ngs, pacbio
PCIT 2014 [1,052] Bioinformatics
PCRE 8.38, 8.39 [1,053] perl, library
PDA 1.0.3 [1,054] biology, phylogenetics
Pdb2pqr 2.1.0 [1,055] protein, modeling, pdb
Program Database Toolkit 3.20, 3.22, 3.24 [1,056] programming languages, development, performance analysis
PeakSplitter 1.0 [1,057] biology, bioinformatics, CHiP-Seq
PEAR 0.9.2 [1,058] biology, genomics, ngs
Peneasy 20150530 [1,059] physics
PennCNV 1.0.5 [1,060] phylogenetics
Perl 5.16.0, 5.20.0, 5.24.1 [1,061] programming,scripting,language
PerM 0.4.0 [1,062] biology,bioinformatics,ngs,mapping
PETSc 3.8.1, 3.8.3, 3.8.4 [1,063] Math, Numerical Solvers
PfamScan 1.3, 1.5 [1,064] biology, genomics
PGDSpider 2.0.9.0, 2.1.1.5 [1,065] biology, NGS
Pggb 0.1.3, 20201106, 20210121 [1,066] phylogenetics
PhaME 1.0.3 [1,067] phylogenetics
PHASE 2.1.1 [1,068] phylogenetics
PHAST 1.5 [1,069] biology,phylogeny
Phenix 1.10.2155, 1.17.1, 1.8.1069 [1,070] crystallography
PHI 3.1.1, 3.1.2b [1,071] Calculations
PhiSpy 3.2 [1,072] phylogenetics
PHITS 2.76, 2.82, 2.84 [1,073] Physics
PHLAWD 20170427 [1,074] biology, phylogenetics
PhotoScan 1.4.1, 1.4.5 [1,075] Image Processing
Photutils 0.5 [1,076] astronomy, photometry
PHYling 1.0 [1,077] Biology, Phylogenetics, Markers, Genomics
PHYLIP 3.696 [1,078] biology,phylogenetics
PhyloAcc 1.0 [1,079] phylogenetics
PhyloBayes 3.3f [1,080] biology,bioinformatics,phylogenetics
PhyloFlash 3.3b4 [1,081] phylogenetics
Phylonet 3.5.7 [1,082] biology, phylogenetics
PhyloParser 20180404 [1,083] phylogenetics
PhyloPhlAn2 0.41 [1,084] phylogenetics
Phylopypruner 1.2.3 [1,085] phylogenetics
PhyloSift 1.1 [1,086] biology, genomics, phylogenetics, taxonomy
Phyluce 20180727, 20190308, 20191015 [1,087] biology,bioinformatics,ngs,sequencing
PhyML 3.0, 3.1 [1,088] biology,bioinformatics,phylogenetics
Phynd 20200409 [1,089] phylogenetics
PHYUTILITY 2.7.1 [1,090] biology, bioinformatics
Phyx 1.1 [1,091] phylogenetics
PIA2 20180305 [1,092] biology, phylogenetics
Picard-tools 2.5.0, 2.9.0, 2.9.2 [1,093] biology, bioinformatics, ngs
PICRUSt 1.1.0, 1.1.3, 1.1.4 [1,094] biology, phylogenics
PICRUSt 2.3.0b [1,095] biology,phylogenics
Piggy 20171220 [1,096] biology, bioinformatics, ngs
Pigz 2.4 [1,097] Compression
PILON 1.22, 1.24 [1,098] biology, bioinformatics, ngs, phylogenetics
Pindel 0.2.5b8 [1,099] biology, phylogenetics
Pipe-clip 1.1.0 [1,100] biology,NGS
Pipits 1.3.6, 1.4.0 [1,101] biology, sequencing
Piranha 1.2.1 [1,102] biology,phylogenetics
Plasflow 1.1 [1,103] biology, phylogenetics
PLAST 1.0, 2.3.2 [1,104] biology,bioinformatics
Platanus 1.2.4 [1,105] phylogenetics
Platypus 0.8.1 [1,106] biology,bioinformatics,ngs
PLEK 1.2.2 [1,107] biology, phylogenetics
Plink 1.90b3, 1.90b3.39, 2.00a2 [1,108] biology,bioinformatics,genomics,phylogenetics
Plinkseq 0.10 [1,109] biology, bioinformatics, library
PolyGembler 1.0 [1,110] phylogenetics
PolyPHen 2.2.2.r405b [1,111] biology, genomics
Pomoxis 0.1.11, 0.2.5, 0.3.2 [1,112] biology, phylogenetics
PopLDdecay 3.40 [1,113] phylogenetics
Popoolation 1.2.2 [1,114] biology, phylogenetics
Porechop 0.2.4 [1,115] phylogenetics
Poretools 0.6.1 [1,116] phylogenetics
PosiGene 20171113 [1,117] biology, phylogenetics
POV-Ray 3.7 [1,118] 3D Graphics
Pplacer 1.1.alpha19 [1,119] biology, bioinformatics, phylogenics, taxonomy
PRANK 170427, 20150803 [1,120] biology, bioinformatics, alignment
Predector 20201110 [1,121] phylogenetics
Preplot 14.0.2 []
Preseq 0.0.4 [1,122] biology, bioinformatics, ngs
PRICE 1.2 [1,123] biology, bioinformatics, ngs
Primer3 2.3.4 [1,124] biology,bioinformatics,genomics
Primus 1.8.0 [1,125] biology, phylogenetics
PRINSEQ 0.20.4 [1,126] biology, sequencing
PRINSEQ++ 1.2 [1,127] phylogenetics
ProbABEL 0.4.2, 0.4.3, 0.4.5 [1,128] Genomics, bioinformatics, gwas
Probalign 1.4 [1,129] biology, bioinformatics, ngs
Processing 3.4 [1,130] java, language, programming, visual
Prodigal 2.6.2, 2.6.3 [1,131] biology, genomics
Libproj4 4.9.3, 5.1.0, 8.0.1 [1,132] library, geospatial, cartography
Prokka 1.12, 1.14.6 [1,133] biology, bioinformatics, genomics, assembly
Proovread 1.03rcl, 2.12, 2.13 [1,134] biology, genomics, ngs
ProSplign 1.0.0 [1,135] phylogenetics
Protege 5.1.0 [1,136] Ontology
Proteinortho 4.26, 5.11, 5.16 [1,137] biology, genomics
ProtExcluder 1.2 [1,138] biology, phylogenetics
ProtHint 2.6.0 [1,139] biology, bioinformatics, genomics
Protobuf 2.5.0, 3.5.1 [1,140] google, libraries
PROVEAN 1.1.5 [1,141] biology, genomics
PRSice 2.3.3 [1,142] phylogenetics
PsiCLASS 1.0.1 [1,143] phylogenetics
PSMC 0.6.5 [1,144] phylogenetics
PsRobot 1.2 [1,145] phylogenetics
Pufferfish 20200417 [1,146] phylogenetics
PureCLIP 1.1.1 [1,147] phylogenetics
PurgeDups 1.0.1 [1,148] phylogenetics
Pyani 0.2.10 [1,149] phylogenetics
PyBSASeq 20200623 [1,150] phylogenetics
PyCharm 2018.3 [1,151] editor, ide, programming, python
PyCogent 1.9 [1,152] biology, genomics
PyDeface 2.0.0 [1,153] mri, imaging
PyEGA3 3.4.1 [1,154] Biology, Genomics, Utility
Pyfaidx 0.5.2 [1,155] biology, bioinformatics, ngs, sequencing
Pyfasta 0.5.2 [1,156] phylogenetics
Pygot 20170518 [1,157] biology, phylogenetics
Pyhdf 0.9.0 [1,158] library, hdf4
PyHIST 1.0 [1,159] Biology, Histology, Image segmentation
PyPHLAWD 20180416, 20190414 [1,160] biology, phylogenetics
PyRosetta r56324 [1,161] biology,structure,modeling
Pyrpipe 0.0.3 [1,162] phylogenetics
Pysamstats 1.1.2 [1,163] phylogenetics
PySLURM 18.08.04 [1,164] SLURM
Python 3.6.3, 3.6.5, 3.8 [1,165] programming languages, scripting, development
Python-core 3.6.5, 3.7, 3.8 [1,166] programming languages, scripting, development
Pytorch 1.7.1, 1.8.1, 1.9.0 [1,167] library, math
PyVCF 0.6.0 [1,168] biology, phylogenetics
PyVista 0.26.1 [1,169] phylogenetics
Pyweka 0.3.18 [1,170] phylogenetics
QAPA 1.3.1 [1,171] phylogenetics
Qcat 1.1.0 [1,172] phylogenetics
Qctool 2.0.1 [1,173] phylogenetics
QD 2.3.22 [1,174] library,c,math
QDD 3.1.2 [1,175] biology, genomics, ngs
QGIS 2.18.0, 3.14.0 [1,176] GIS
QIIME 1.9.1 [1,177] biology, bioinformatics, metagenomics
QIIME2 2020.11, 2020.8, 2021.4 [1,178] biology, bioinformatics, metagenomics
QMCPACK 3.4.0 [1,179] Library
QRNA 2.0.4 [1,180] phylogenetics
QT 4.8.3, 5.12.9 [1,181] UI Framework
QTLtools 1.2 [1,182] phylogenetics
Quake 0.3 [1,183] biology, sequencing
QualiMap 2.1.2 [1,184] biology,sequence alignment
Quantas 1.0.4, 1.0.8, 1.0.9 [1,185] biology,bioinformatics,ngs
QuartetScores 1.0.0 [1,186] phylogenetics
QUAST 4.4, 5.0.0, 5.0.2 [1,187] biology, bioinformatics, ngs, sequencing, rna-seq
Quickmerge 0.3 [1,188] phylogenetics
Quickquartet 1.0.0 [1,189] biology,bioinformatics,ngs
QUIP 20201029 [1,190] phylogenetics
QuorUM 1.0.0 [1,191] biology
R-index 20190711 [1,192] phylogenetics
R8s 1.8, 1.81 [1,193] phylogenetics
RACA 0.9.1.1 [1,194] biology, ngs
Racon 1.3.3, 1.4.10, 1.4.13 [1,195] phylogenetics
RADICAL 0.2 [1,196] biology, bioinformatics, genomics
RaGOO 1.11 [1,197] phylogenetics
RagTag 1.0.0 [1,198] phylogenetics
Rainbow 2.0.4 [1,199] biology, sequencing
Rainbowfish 0.1.0 [1,200] phylogenetics
RAiSD 2.8 [1,201] phylogenetics
Randfold 2.0.1 [1,202] biology, RNA
Rapidsai 0.14.1, 0.19 [1,203] Data Science
Rapidtide 1.9.0 [1,204] phylogenetics
RAPSearch 2.24 [1,205] biology, phylogenetics
Unrar 0.0.1, 4.20 [1,206] unarchiver, utility
Rascaf 1.0.2 [1,207] biology, bioinformatics
RAVE 2.1 [1,208] biology, phylogenetics
RAxML 8.2.10, 8.2.12, 8.2.8 [1,209] application, biology, philogenetics
RAxML-NG 0.8.0b, 0.9.0, 1.0.2 [1,210] phylogenetics
Razers3 3.5.7 [1,211] biology, phylogenetics
Rbp-maps 0.1.4 [1,212] phylogenetics
Rcorrector 1.0.4 [1,213] phylogenetics
RDKit 2020092 [1,214] Chemiformatics
RDnaTools 0.1.3 [1,215] phylogenetics
READemption 1.0.0 [1,216] phylogenetics
REAPR 1.0.18 [1,217] biology,bioinformatics,assembly
Rebaler 0.2.0 [1,218] phylogenetics
ReCOGnizer 1.3.3 [1,219] phylogenetics
Recon 1.08 [1,220] biology,sequencing
Redis 2.8.13, 2.8.19 [1,221] daemon, data, server
REDItools2 20200701 [1,222] phylogenetics
Redundans 0.14a [1,223] biology, phylogenetics
ReFrame 3.2 [1,224] hpc, internal
Regtools 0.5.2 [1,225] Biology, RNA-seq, Genitics
RELION 3.0.2, 3.0b, 3.1.0 [1,226] biology, imaging
RelocaTE2 2.0.1 [1,227] phylogenetics
REMORA 1.8.2, 1.8.3 [1,228] System, profiler
REPdenovo 20170222 [1,229] biology, phylogenetics
RepeatAnalysis 0.10.0, 0.12.2 [] biology, phylogenetics
RepeatAnalysisTools 20210506 [1,230] Biology, Genomics, Sequencing, Utility
RepeatExplorer 20150506, 20180517 [1,231] biology, bioinformatics, ngs
RepeatMasker 4.0.5, 4.0.9, 4.1.1 [1,232] biology,bioinformatics
RepeatModeler 1.0.8, 2.0 [1,233] biology,bioinformatics
Repeatscout 1.0.5 [1,234] biology
RepeatSeq 0.8.2 [1,235] phylogenetics
Reptile 1.1 [1,236] biology,NGS,error correction
ResFinder 4.0 [1,237] biology, genomics
Resistome 20170111 [1,238] phylogenetics
RevBayes 1.0.7, 1.0.9, 1.1.1 [1,239] biology, phylogenetics
RFMIX 2.03 [1,240] phylogenetics
RGI 4.2.2, 5.1.1 [1,241] phylogenetics
RGIS 20180211, 20180814 [1,242] RiverGIS
RHash 1.3.3 [1,243] GNU
RiboCode 1.2.11 [1,244] phylogenetics
RiboPicker 0.4.3 [1,245] biology,sequence
RiboTaper 1.3.1a [1,246] phylogenetics
RIGERJ 2.0.2 [1,247] phylogenetics
Rmats2sashimiplot 2.0.3 [1,248] phylogenetics
Rmpi 0.6.9 [1,249] statistics, R, mpi
RNAhybrid 2.1.1 [1,250] biology, bioinformatics, genomics
RNAmmer 1.2 [1,251] biology, RNA-seq
RnaQUAST 1.5.1 [1,252] biology,bioinformatics,ngs,sequencing,rna-seq
RNAsalsa 0.8.1 [1,253] biology, phylogenetics
Rnaseqlib 20150721 [1,254] biology, phylogenetics, RNA-seq
RNAstructure 6.3 [1,255] Biology, sequencing
RDnaTools 0.1.3 [1,256] phylogenetics
Roary 3.12.0, 3.4.1 [1,257] biology,genomics
ROOT 5.34.17, 6.0, 6.06.02 [1,258] Data Analysis
ROOTPy 20160323 [1,259] Data Analysis
Rosetta 2014wk4, 2019.35.60890 [1,260] biology,structure,modeling
RoseTTAFold 1.0.0 [1,261] phylogenetics
Rrnaselector 1.0 [1,262] biology, sequencing
RSEG 0.4.8 [1,263] biology, bioinformatics, genomics
RSEM 1.2.31, 1.2.7, 1.3.3 [1,264] biology,bioinformatics,ngs,sequencing
RSeQC 2.6.4, 3.0.0 [1,265] biology,ngs,rna-seq
RStudio 1.3, 1.4 [1,266] statistics
RTGTools 3.7.1 [1,267] biology, NGS
Ruby 2.5.1 [1,268] programming,scripting,language
Rust 1.31.0, 1.48.0, 1.52.1 [1,269] programming
S.A.G.E 6.4.2 [1,270] phylogenetics
Sabre 1.0 [1,271] phylogenetics
Saffrontree 0.1.2 [1,272] phylogenetics
Sailfish 0.6.3 [1,273] biology,genomics,ngs,rna-seq
Salmon 0.6.0, 0.7.2, 1.1.0 [1,274] biology, RNA-seq
SALSA 20171009, 20191001 [1,275] biology, ngs, pacbio
Sambamba 0.6.3, 0.6.6, 0.6.9 [1,276] Biology, NGS
Samblaster 0.1.14, 0.1.24 [1,277] biology,bioinformatics,ngs,sequencing
SAMStat 1.08 [1,278] biology,bioinformatics,ngs,sequencing
Samtools 1.7, 1.8, 1.9 [1,279] biology,bioinformatics,ngs,sequencing
DS9 7.5, 8.0.1 [1,280] Imaging
SAS 9.3, 9.4 [1,281] statistics, data analysis
Sate 2.2.7 [1,282] biology, bioinformatics, phylogenetics
Satsuma 3.0 [1,283] phylogenetics
Satsuma2 20161123, 3.1 [1,284] phylogenetics
Scala 2.11.5, 3.0.1 [1,285] programming, language, java
Scalablast 2.4.53 [1,286] application, biology, genomics
ScaLAPACK 2.0.2, 2.1.0 [1,287] programming,library
Scallop 0.10.5 [1,288] phylogenetics
Scalpel 0.1.1, 0.5.3 [1,289] Biology, NGS
Schrodinger Suite 2019-3, 2020-4, 2021-2 [1,290] Computational Chemistry, Molecular Dynamics
Scipion 1.2 [1,291] Image Processing
SCIrun 5.0.Z [1,292] phylogenetics
Scoary 1.6.16 [1,293] phylogenetics
Scons 2.5.1, 3.1.2 [1,294] Programming
Scrappie 1.4.2 [1,295] Biology, Genomics
SCRATCH-1D 1.0 [1,296] biology, bioinformatics, ngs
Screen 4.8.0 [1,297] GNU, Terminal Multiplerxer
SCRIPTURE 20101211 [1,298] biology, bioinformatics, genomics
Scythe 0.991 [1,299] Biology, NGS
Sdsl 2.1.1 [1,300] library, c++
SeCaPr 1.1.12, 2.0.2, 2.1.1 [1,301] phylogenetics
Segemehl 0.1.9, 0.3.4 [1,302] biology,bioinformatics,ngs,sequencing
SEPP 20160614 [1,303] biology, phylogenetics
Seq-Gen 1.3.3 [1,304] biology,phylogenetics
Seq_crumbs 20150120 [1,305] biology, sequence, genomics, utilities
SeqKit 0.10.2, 0.8.0 [1,306] biology, phylogenetics
Seqmagick 0.8.4 [1,307] biology, bioinformatics
SeqMap 1.0.13 [1,308] biology,bioinformatics,sequence,ngs
SEQPower 1.1.1 [1,309] Genomics, bioinformatics, phylogenetics
SeqPrep 0.5, 1.1 [1,310] biology,bioinformatics,ngs,sequencing
Seqtk 1.3, 20140729 [1,311] Bioinformatics, Genomics, NGS
SEQuel 1.0.1 [1,312] biology,bioinformatics,ngs
SequelQC 1.1.0 [1,313] phylogenetics
Seqwish 0.7, 20190509 [1,314] phylogenetics
SeqyClean 1.8.10 [1,315] biology,bioinformatics,ngs,sequencing
SeSiMCMC 4.36 [1,316] Biology, Sequencing
SExtractor 2.19.5 [1,317] Astronomy
SHAPEIT 2.12, 2.5 [1,318] biology,SNP
SHAPE-MaP 1.2 [1,319] biology, phylogenetics
ShapeMapper 2.1.3, 2.1.5 [1,320] biology, phylogenetics
SHARCGS 1.2.11 [1,321] biology, NGS, de novo assembly
Shasta 0.1.0 [1,322] phylogenetics
SHEsisPlus 1.0, 1.01 [1,323] biology, genetics
Shogun 6.1.3 [1,324] phylogenetics
Shortbred 0.9.4 [1,325] phylogenetics
SHRiMP 2.2.3 [1,326] biology, genomics, ngs
Shustring 2.6 [1,327] biology, sequencing
SibeliaZ 1.2.2, 1.2.3 [1,328] bioinformatics, genomics, alignment
SICER 1.1 [1,329] biology, ChIP-Seq
Sickle 1.200, 1.33 [1,330] biology, bioinformatics, ngs
Siesta 3.2, 4.1b2, 4.1b3 [1,331] Chemistry
SIFT 4.0.3b [1,332] biology,bioinformatics,genomics
SignalP 4.1c, 5.0b [1,333] biology, phylogenetics
SiLiX 1.2.11 [1,334] phylogenetics
Silo 4.7 [1,335] io,library
Sim4 20121010 [1,336] biology, bioinformatics, genomics
Simka 1.5.3 [1,337] phylogenetics
SimNIBS 3.2.1 [1,338] phylogenetics
SimSeq 4.12.2011 [1,339] biology, bioinformatics, ngs, phylogenetics
Simulia 2019 [1,340] simulation, visualization
SInC 20140120 [1,341] biology, phylogenetics
Sine_scan 1.1.1 [1,342] phylogenetics
Singularity 3.7.4 [1,343] Containers
SIPeS 2.0 [1,344] biology, bioinformatics, ChIP-Seq
Sisl 0.8.3 [1,345] Physics, Tight-binding
Slamdunk 0.4.1, 0.4.2 [1,346] phylogenetics
Slicer 4.10.2, 4.3.1 [1,347] biology,bioinformatics,neuroscience,imaging
Slurm-drmaa 1.1.1.20, 1.1.2 [1,348] libraries, slurm, api, drmaa
Smalt 0.7.6 [1,349] application, biology, phylogenetics
SMARTdenovo 20180219 [1,350] biology, phylogenetics
Smartie-sv 20180308 [1,351] phylogenetics
Smetana 1.1.0 [1,352] phylogenetics
SMR 1.03 [1,353] Biology, Genomics
SMRT-SV 2.0.0 [1,354] biology, bioinformatics, ngs
SMS 1.7 [1,355] biology, bioinformatics
Smudgeplot 0.2.4 [1,356] phylogenetics
Snakemake 5.17.0, 6.4.1 [1,357] biology, bioinformatics, workflow
SNAP 0.15.4, 20100728 [1,358] biology,bioinformatics,sequencing
SPANE-pooled 20130407 [1,359] biology,SNP
SNeP 1.1 [1,360] biology,phylogenetics
Sniffles 1.0.11, 1.0.6, 1.0.8 [1,361] phylogenetics
Snippy 20160419 [1,362] biology, phylogenetics
SNP-Pipeline 1.0.1 [1,363] biology, phylogenics
SNP-sites 2.0.3 [1,364] biology, SNP
SnpEff 4.3r, 4.3t, 5.0 [1,365] biology,bioinformatics,variant annotation
SNPGenie 20190620 [1,366] phylogenetics
SNPhylo 20140701 [1,367] biology,phylogenetics
SNPTEST 2.5.2 [1,368] phylogenetics
SOAPaligner 2.21 [1,369] phylogenetics
SOAPdenovo 1.05, 2.04 [1,370] biology,ngs
SOAPdenovo-Trans 1.01, 1.03 [1,371] biology,ngs
SOAPec 2.03 [1,372] biology, phylogenetics
SOAPnuke 2.1.0 [1,373] phylogenetics
SOAPsplice 1.10 [1,374] biology,ngs
SODA 20200930 [1,375] biology
SOLAR 8.4.2 [1,376] phylogenetics
SomaticSeq 3.6.2 [1,377] phylogenetics
SortaDate 20190705 [1,378] phylogenetics
SortMeRNA 2.1, 4.0 [1,379] biology, sequencing, NGS
SourceTracker2 2.0.1 [1,380] phylogenetics
Sourmash 2.0.1 [1,381] phylogenetics
SoX 14.4.2 [1,382] phylogenetics
SPAdes 3.15.3, 3.7.1, 3.8.0 [1,383] biology,bioinformatics,ngs
SparCC 201608 [1,384] Microbial Ecology
Spark 2.2.0, 3.1.1 [1,385] spark, hadoop
Sparsehash 2.0.3 [1,386] Google, API
SPARTA+ 2.60 [1,387] Chemistry
Spec2nii 0.3.4 [1,388] phylogenetics
SpeedSeq 0.1.2 [1,389] phylogenetics
Spidey 20150922 [1,390] biology, genomics, bioinformatics
SplAdder 2.4.2 [1,391] phylogenetics
SpliceGrapher 0.2.5 [1,392] biology, sequencing
SpliceTrap 0.90.5 [1,393] biology, bioinformatics, genomics, NGS
SPM 12b, 8, 8r5236 [1,394] biology,bioinformatics,matlab
Spruceup 2019.2.3 [1,395] phylogenetics
Sputnik 1.0 [1,396] biology,bioinformatics,repeats
Spyder 4.1.4, 5.1.1 [1,397] ide, editor, programming, scripting
SQANTI 1.2 [1,398] phylogenetics
SQANTI2 5.0 [1,399] phylogenetics
SQANTI3 0.1, 1.6 [1,400] phylogenetics
SQL Developer 4.1.2 [1,401] programming, oracle, sql
SQLite 3.33.0, 3.8.8.2 [1,402] database
SqueezeMeta 1.4.0 [1,403] phylogenetics
SRA 2.10.4, 2.10.8, 2.10.9 [1,404] biology,bioinformatics,sra
SRAssembler 1.0.0 [1,405] phylogenetics
SSM 20210511 [1,406] phylogenetics
SSPACE 2.0, 3.0 [1,407] biology,bioinformatics,ngs
Ssr_pipeline 0.951 [1,408] biology, DNA sequencing,
Stacks 2.53, 2.55, 20190403 [1,409] biology, bioinformatics, genomics, ngs
Staden 1.14.6 [1,410] biology, phylogenetics
Stampy 1.0.31 [1,411] biology, bioinformatics, sequencing
Staphb-toolkit 1.2.0 [1,412] biology
Rnastar 2.7.5c, 2.7.6a, 2.7.9a [1,413] biology, ngs, rna-seq
STAR-Fusion 1.1.0, 1.3.1, 1.9.1 [1,414] biology, transcriptome
STAR-CCM+ 14.04.011, 15.02.009, 8.06 [1,415] Mechanical Engineering
Starseqr 0.6.7 [1,416] phylogenetics
Stata 10.1, 13 [1,417] Statistics
StringMLST 0.4 [1,418] biology, bioinformatics, CHiP-Seq
Stringtie 1.3.4d, 2.0.4, 2.1.3b [1,419] biology,bioinformatics,ngs,sequencing,alignment
Structure 2.3.3, 2.3.4 [1,420] biology,bioinformatics,population genetics
SU2 7.0.6 [1,421] phylogenetics
Subread 1.5.3, 1.6.2, 2.0.0 [1,422] biology, sequencing, SNP
Subversion 1.9.7 [1,423] Revision Control
SUMO 1.2.0, 1.9.2 [1,424] simulation, traffic, engineering
SUNDIALS 2.3.0, 2.5.0, 3.0.0 [1,425] Math, Numerical Solvers
Supercell 20170602 [1,426] biology, NGS
SuperCRUNCH 1.2.1 [1,427] phylogenetics
Supernova 1.2.1, 2.0.0, 2.1.1 [1,428] biology, phylogenetics, ngs
SUPPA 2.3 [1,429] phylogenetics
Survival_Kit 6.12 [1,430] Clinical Biometrics
SURVIVOR 1.0.6 [1,431] phylogenetics
SVDetect 0.8b [1,432] biology,ngs,genomics
Svim 1.4.2 [1,433] biology
Svim-asm 1.0.2 [1,434] biology
Swarm 1.2.11 [1,435] Data Analysis
Sweed 3.3.2 [1,436] biology, phylogenetics
SWIG 2.0.9, 3.0.12, 3.0.8 [1,437] library, development, C++, python
SWSC-EN 1.0.0 [1,438] phylogenetics
Synima 20210908 [1,439] phylogenetics
TACO 0.7.3 [1,440] phylogenetics
Taiyaki 5.0.1 [1,441] phylogenetics
Talesf 20160814 [1,442] phylogenetics
Tandem-Genotypes 1.4.0 [1,443] phylogenetics
Tantan 13 [1,444] ngs, genomics
Tapestri 2.0.1 [1,445] phylogenetics
Tapir 20160825 [1,446] biology, phylogenetics
TAPIS 1.2.1 [1,447] biology, sequencing
TASSEL 5.0, 5.2.20, 5.2.29 [1,448] biology,bioinformatics,genomics,wga
Tuning Analysis Utilities 2.23, 2.26, 2.26.3 [1,449] library, profiling and optimization
Tax4Fun 0.3.1 [1,450] phylogenetics
TaxMaps 0.1 [1,451] biology, phylogenetics, taxonomy
Taxtastic 0.5.7, 0.9.1 [1,452] biology, taxonomy
Tbb 2017_20161128 [1,453] library
Tcllib 1.18 [1,454] library
Tcoffee 10.00.r1613, 9.03.r1318 [1,455] Bioinformatics
Tecplot 360 EX 2015R1 [1,456] plotting, animation, cfd, simulations
TEMP 20170731 [1,457] phylogenetics
TensorFlow 2.3.1, 2.4.1, 2.5.0 [1,458] library, math
TESS 2.3.1 [1,459] biology, bioinformatics, genomics, markov
Test 1.0 [1,460] shell
TetGen 1.5.0 [1,461] tetrahedral meshes
TEToolkit 1.5.1 [1,462] biology, bioinformatics, sequencing
TEtools 20180213 [1,463] biology, phylogenetics
Texlive 20191127, 2020 [1,464] formatting, typesetting, document preparataion
TGICL 2.1 [1,465] biology,bioinformatics,ngs,sequencing
TGSGapCloser 1.0.3 [1,466] phylogenetics
The_silver_searcher 2.2.0 [1,467] search
Theano 1.0.4 [1,468] library, math, gpu
Themisto 0.2.0, 1.1.0 [1,469] Genomics, Alignment
Tiff 3.8.0, 4.0.10 [1,470] imaging
Tigmint 1.1.2 [1,471] phylogenetics
Tmux 2.9, 3.1 [1,472] GNU
TNTBLAST 2.04 [1,473] Biology
CDNA_Cupcake 20180629, v17 [1,474] biology, bioinformatics, ngs, iso-seq
Toil 3.3.0, 3.3.3 [1,475] biology, bioinformatics
Tombo 1.4, 1.5, 1.5.1 [1,476] biology, genomics, ngs
Tophat 2.1.0, 2.1.1, 2.1.2 [1,477] biology,bioinformatics,ngs,sequencing
Torch-geometric 1.3.2 [1,478] phylogenetics
TotalView 8.12 [1,479] Parallel Computing
TPMcalculator 0.0.3 [1,480] phylogenetics
TPP 4.7.0, 4.7.1, 5.0.0 [1,481] biology, chemistry, nmr
TraCeR 20160519 [1,482] biology, phylogenetics
TrackTools 2011 [1,483] Software
TrackVis/DTK 0.5.2.2, 0.6.0.1 [1,484] biology,bioinformatics,neuroscience,imaging
Tracula 5.3.2014_05_26 [1,485] biology,bioinformatics,neuroscience,imaging
TraitRate 1.1 [1,486] biology, evolution
Trans-ABySS 2.0.1 [1,487] biology, phylogenetics
TransDecoder 5.3.0, 5.4.0, 5.5.0 [1,488] biology, ngs
TRANSIT 2.5.2 [1,489] phylogenetics
Transrate 1.0.1 [1,490] biology,assembly
TransVar 2.3.3 [1,491] biology, bioinformatics, phylogenetics
TreeBreaker 20160621 [1,492] biology, phylogenetics
TreeMix 1.12 [1,493] biology, phylogenetics
TreePL 20150305 [1,494] biology, bioinformatics, phylogenetics
TREEPUZZLE 5.3 [1,495] biology, phylogenetics
TreeShrink 1.3.1, 1.3.2 [1,496] phylogenetics
TreeTime 0.7.5, 0.8.1 [1,497] phylogenetics
Trelis 16.3 [1,498] Geometry
TRF 4.04, 4.09.1 [1,499] biology,bioinformatics,genomics
Trilinos 12.12.1, 12.18.1, 12.6.4 [1,500] Mathematical Algorithms
Trim Galore 0.4.4, 0.5.0, 0.6.5 [1,501] biology,bioinformatics,ngs
Trim_isoseq_polya 0.0.3 [1,502] Biology, Genetics, Sequencing
TrimAl 1.2 [1,503] biology,genomics,sequence alignment
TriMetAss 1.1 [1,504] biology,bioinformatics,ngs
Trimmomatic 0.33, 0.36, 0.39 [1,505] biology,bioinformatics,ngs
Trinity r20130225, r20131110, r20140413 [1,506] biology,bioinformatics,ngs,sequencing,rna-seq
Trinotate 3.0.1, 3.2.0 [1,507] biology
TRIPLEC 1.0 [1,508] biology, bioinformatics
TRITONSERVER 21.08 [1,509] Machine Learning Inference Server
TRNAscan-Se 1.23 [1,510] biology,bioinformatics,ngs
TRUST4 1.0.2b [1,511] phylogenetics
Trycycler 0.4.2 [1,512] phylogenetics
TURBOMOLE 7.4.1 [1,513] Quantum Chemistry
TWINSCAN 4.1.2 [1,514] biology,genomics
Ubuntu 20.04 [1,515] Ubuntu Linux
UCSC 20200320, 20210803 [1,516] Genomics, bioinformatics
Ucsc-fafiltern 377 [1,517] phylogenetics
Ucsc-maskoutfa 377 [1,518] phylogenetics
UCX 1.9.0 [1,519] parallel programming, development, library
UDUNITS 2.2.17 [1,520] library, data, units
Ufraw 0.22 [1,521] data mining
Ugtm 1.1.6 [1,522] statistics, modeling
UKFractography 20200127 [1,523] phylogenetics
Umi-tools 0.5.5 [1,524] phylogenetics
UNAFold 3.8 [1,525] biology, genome, RNA, folding
Unanimity 20171108, 3.4.1 [1,526] programming,library,cpp
UNCALLED 2.2 [1,527] biology, bioinformatics, genomics
Unicycler 0.4.8 [1,528] phylogenetics
Uproc 1.2.0 [1,529] biology, genome
USEARCH 9.0.2132, 9.1.13, 9.2.64 [1,530] biology,bioinformatics,alignment,sequence analysis
UShER 0.1.4, 0.4.1 [1,531] phylogenetics
V-pipe 2.0.0 [1,532] biology, bioinformatics, genomics, sequencing, virus
Valgrind 3.11.0, 3.15.0, 3.8.1 [1,533] Computer Programming
Valouev 20160325 [1,534] Biology, Phylogenetics
Vamb 3.0.2 [1,535] biology
VAMPIR 9.1 [1,536] High Performance Computing
VarDictJava 1.6.0, 20160521, 20170531 [1,537] biology, phylogenetics
VAIR 0.7.0 [1,538] Geospatial Data Modeling
Varnorm 0.21 [1,539] biology, bioinformatics
VarScan 2.3.6 [1,540] biology,bioinformatics,ngs
VarSim 0.8.4, 0.8.6 [1,541] phylogenetics
VarSimLab 20180220, 20180921 [1,542] biology, simulation, genomics
Vasp 5.4.4, 6.1.0, 6.2.0 [1,543] Quantum Chemistry
Vaspkit 1.2.5 [1,544] phylogenetics
VAST-TOOLS 20150506 [1,545] biology, rna-seq, ngs, splicing
VCF-kit 0.2.6 [1,546] phylogenetics
Vcfanno 0.2.8 [1,547] biology, phylogenetics
Vcflib 1.0.1 [1,548] biology,bioinformatics,genomics
Vcftools 0.1.15, 0.1.16, 0.1.9 [1,549] biology,bioinformatics,genomics
Vcf-validator 0.6 [1,550] biology, phylogenetics
Vcontact 20190512 [1,551] phylogenetics
VDJtools 1.1.7, 1.2.1 [1,552] biolgoy, phylogenetics
Velvet 1.2.10, 1.2.10-long [1,553] computational biology, genomics
VEP 83, 88.8, 92 [1,554] biology, genomics, ngs
VeryFastTree 3.0.1 [1,555] phylogenetics
Vg 1.20.0, 1.32.0, 1.33.0 [1,556] phylogenetics
ViennaRNA 2.2.6, 2.4.18 [1,557] biology, RNA-seq
ViewBS 0.1.10, 0.1.9 [1,558] phylogenetics
Vim 8.1.1566, 8.2.2465 [1,559] programming,scripting,language
Viralmsa 1.1.10, 1.1.12 [1,560] phylogenetics
VirtualCell 7.1 [1,561] phylogenetics
VIRULIGN 1.0.2 [1,562] phylogenetics
VirusDetect 1.7 [1,563] phylogenetics
VirusFinder 2.0 [1,564] biology, phylogenetics
Visit 2.12.2, 2.13.3, 3.0.1 [1,565] Visualization, Animation and Analysis
VISPR 0.4.14 [1,566] phylogenetics
VMD 1.9.1, 1.9.3 [1,567] visualization, animation, 3d
V-Phaser 02112013 [1,568] biology, phylogenetics
Vscode 1.38.1 [1,569] ide, editor, programming, scripting
VSearch 20151022, 20161209-2.3.4 [1,570] biology,NGS
Vt 0.57721, 20140903, 20160129 [1,571] biology,genomics
VTC 0.9.3 [1,572] biology, bioinformatics, VCF
VTK 7.1.1, 8.2.0, 9.0.3 [1,573] biology,bioinformatics,neuroscience,imaging
VULCAN 6.3.1 [1,574] Fluid Dynamics
W2rap-contigger 20161124 [1,575] biology, genomics
Wannier90 1.2, 2.1.0 [1,576] Computational Physics
WarpedLMM 0.21 [1,577] modeling
WDSSII 5 [1,578] Weather, Meteorology
WebLogo 2.8.2, 3.3, 3.5.0 [1,579] biology,bioinformatics,sequence,graphics
Weka 3.8, 3.8.5 [1,580] statistics,machine learning
Wengan 0.2 [1,581] biology,bioinformatics,genomics
Wgd 1.1.1 [1,582] phylogenetics
WGS Assembler 8.3rc1.r4638, 8.3rc2 [1,583] biology, bioinformatics, genomics
Wgsim 0.3.1-r13 [1,584] biology, phylogenetics
WHAMM 0.14a [1,585] biology, phylogenetics
WhatsHap 1.1 [1,586] biology, phylogenetics
Whiteboxtools 1.5.0 [1,587] phylogenetics
Wine 1.6.2, 1.9.6, 4.0.0 [1,588] windows, emulator
Wise 2.2.0, 2.4.1 [1,589] biology, genome
WIsH 1.0 [1,590] phylogenetics
WoLFPSort 0.2 [1,591] phylogenetics
WOMBAT 20180118 [1,592] biology, phylogenetics
Wtdbg 2.1, 2.4, 2.5 [1,593] phylogenetics
Wub 0.2.0, 0.4.0 [1,594] biology, genomics, ngs
WU BLAST 2.0 [1,595] biology, bioinformatics
Xander 20151222 [1,596] biology, phylogenetics
Xapian 1.4.4 [1,597] library
XCrySDen 1.5.60 [1,598] Computational Material Science
Xerces 3.1.4 [1,599] phylogenetics
Xpclr 1.1.1 [1,600] phylogenetics
Xterm 1.1 [1,601] terminal emulator
XWAS 3.0 [1,602] phylogenetics
XY-Meta 20200413 [1,603] phylogenetics
XZ 5.2.2 [1,604] compression, library
YAHA 0.1.82 [1,605] biology, ngs
YAK 0.1 [1,606] phylogenetics
YASM 1.3.0 [1,607] Computer Programming
YASRA 2.33 [1,608] biology,bioinformatics,ngs,sequencing
Yolov4_darknet 4-pre [1,609] Machine Learning
Yolov5 4.0 [1,610] Machine Learning
Zagros 1.0.0 [1,611] biology,phylogenetics
ZEO++ 0.2.2 [1,612] chemistry
Zorro 2.2 [1,613] biology, sequencing
Zstd 1.5.0 [1,614] phylogenetics
ZUMIS 2.6.0 [1,615] biology, bioinformatics, ngs, sequencing