Applications

From UFRC
(Redirected from Installed Software)
Jump to navigation Jump to search

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, 3.6.2, 4.0 [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 20.3.00, 2018_04_12 [14] biology,bioinformatics,neurology,imaging
AfterQC 0.9.7 [15] phylogenetics
AGAT 0.4.0 [16] phylogenetics
AGfusion 1.252 [17] phylogenetics
AGOUTI 0.3.3 [18] biology, genomics
Albacore 2.3.1, 2.3.3 [19] Biology, Phylogenetics
ALFA 1.1.1 [20] phylogenetics
AliStat 1.12 [21] phylogenetics
ALLMAPS 20180117 [22] biology, phylogenetics
ALLPATHS-LG 42316, 44837, 49232 [23] biology,bioinformatics,ngs
Alphaimpute 1.9.8.2 [24] phylogenetics
AltAnalyze 2.1.0 [25] Biology, genomics
AMAS 1.0 [26] phylogenetics
AMBER 16.0, 18, 20 [27] Computational Chemistry, Molecular Dynamics
AMICO 1.0.1 [28] library, imaging, optimization
AMOS 3.1.0 [29] biology,bioinformatics,genomics,assembly
AMP 0.6.1 [30] phylogenetics
Amphora2 20140305 [31] biology, phylogenetics
AMPtk 0.8.0, 0.8.5, 1.2.4 [32] biology, bioinformatics, ngs
AMRPlusPlus 20180508 [33] phylogenetics
AMUSE 10.0, 13.1.0 [34] Astrophysics
ANGEL 2.3 [35] biology,bioinformatics,sequence
Angsd 20150306, 20150909 [36] biology, ngs
Annocript 2.0 [37] phylogenetics
AnnoTALE 1.4.1 [38] phylogenetics
ANNOVAR 20121023, 20130221, 20150322 [39] biology, bioinformatics, genomics
Ansible 2.5.5, 2.8.1 [40] automation, deployment
Ansysem 17.0 [41] Electromechanics
AntiSMASH 4.1.0, 5.1.2 [42] phylogenetics
ANTs 2.2.0 [43] biology, phylogenetics
Anvio 5.5.0, 6.0, 6.1 [44] biology, microbial 'omics
APT 1.15.0, 1.18.0, 1.20.5 [45] biology, bioinformatics, genomics, microarray
ARC 1.1.4 [46] biology,bioinformatics,ngs
ArcGIS 1.5.1, 10.3.1 [47] geospatial
ARCS 1.0.0, 1.0.1, 1.0.5 [48] biology, genomics
Aria2 1.35.0 [49] Utility
ARKS 1.0.2 [50] phylogenetics
Armadillo 6.200.3, 7.900.0, 9.200.6 [51] library, C++, math
ARPACK 1.0 [52] Solve eigenvalue problems
ArrayFire 3.4.2 [53] Code Optimization
ART 20160417, 20160605 [54] phylogenetics
ASE-ANI 20180712 [55] biology, bioinformatics, genomics, ngs
ASHS 2.0 [56] biology, mri
Assembly-stats 1.0.1 [57] biology, sequencing, genomics
Assemblytics 1.2.1 [58] phylogenetics
Assexon 20190814 [59] phylogenetics
AStalavista 3.2, 4.0 [60] biology, bioinformatics, genomics
ASTRAL 5.0.3, 5.6.1, 5.6.2 [61] biology,bioinformatics,ngs,phylogenetics
ASTRID 2.2.1 [62] phylogenetics
Astropy 2.0.8 [63] biology, bioinformatics, phylogenetics
Atac 0.3.3 [64] biology, phylogenetics
ATAT 3.23, 3.34 [65] alloy theory
ATLAS 3.10.1, 3.10.2, 3.11.17 [66] library, data
AtomEye 3 [67] Material Science
AtomMan 1.3.3 [68] phylogenetics
ATRAM 2.1, 2.1.2, 2.2.0 [69] Math
Augustus 3.3, 3.3.2, 3.3.3 [70] biology,bioinformatics,genomics
Auto3DEM 4.05.2 [71] Image Reconstruction
AutoDock 4.2.6 [72] biology
Autometa 20190802 [73] phylogenetics
Badread 0.1.5 [74] phylogenetics
BALI-PHY 2.3.8, 3.4.1, 3.5.0 [75] Baesian Estimation
BAM-matcher 20161021 [76] phylogenetics
Bam-Readcount 20150616 [77] biology, genomics
Bamaddrg 20120326 [78] phylogenetics
BamBam 1.0 [79] biology, bioinformatics, genomics
BAMM 2.5.0 [80] bioinformatics, evolution
Bamstats 20140602 [81] biology,bioinformatics,ngs
Bamsurgeon 1.2 [82] phylogenetics
Bamtools 2.4.1, 2.5.0, 2.5.1 [83] biology,bioinformatics,ngs,sequencing
BamUtil 1.0.2 [84] biology, bioinformatics, genomics
BAPS 6.0 [85] biology, bioinformatics, genomics
Barrnap 0.7, 0.9 [86] biology, RNA-Seq
Basemount 0.1.2.464, 0.12.8.1516, 0.15.96 [87] biology,DNA Sequencing
Bashdb 4.4-0.94 [88] Debugger
BatVI 1.00 [89] biolgoy, phylogenetics
Bax2bam 0.0.9 [90] phylogenetics
BayArea 1.0.2 [91] biology
BAYENV 2.0 [92] biolgoy, phylogenetics
BayesAss 3.0.4, 3.0.4.2 [93] phylogenetics
BayeScan 2.1 [94] biology, SNP
BayeScEnv 1.1 [95] biology, phylogenetics
BayesR 20151016 [96] biology, phylogenetics
Baypass 2.1 [97] biology, phylogenetics
BBMap 37.09, 38.26, 38.44 [98] biology, alignment
Bcbio-nextgen 0.9.9 [99] biology, bioinformatics, ngs
Bcftools 1.6, 1.8, 1.9 [100] biology, bioinformatics, ngs
Bcl2fastq 2.17.1.14, 2.19.1.403, 2.20.0.422 [101] biology, ngs, illumina
BDG-SeQuila 0.5.5 [102] phylogenetics
BEAGLE 4.0, 4.1, 5.0 [103] biology, genetics, genotyping
BEAR 20170209 [104] biology, bioinformatics, metagenomics
BEAST 2.5.2, 2.6.0, 2.6.2 [105] biology,phylogeny
BEAST2-XML 1.0.9 [106] phylogenetics
BEDOPS 2.4.30 [107] biology,bioinformatics,sequence,ngs
BEDTools 2.29.0, 2.29.1, 2.29.2 [108] biology,bioinformatics,ngs
Bertini 1.6 [109] Mathemetics
BESST 2.2.4 [110] biology, NGS
BFAST 0.7.0 [111] biology,bioinformatics,ngs
Bifrost 0.2, 1.0.3, 20200225 [112] phylogenetics
BinPacker 1.0 [113] biology, RNA-seq, sequence assembly
BinSanity 0.2.6.4 [114] biology, genomics
Bioawk 1.0 [115] phylogenetics
BioBakery 0.13.2 [116] phylogenetics
Biodiverse 2.1 [117] phylogenetics
Biolite 0.3.5.1 [118] biology, bioinformatics, genomics, SNP
BIOM 2.1.5, 2.1.6 [119] biology, genomics
BIOMART 1.4 [120] biology,genomics
Bismark 0.22.3, 0.7.4, 0.7.7 [121] biology, bioinformatics, NGS
Blackfynn 0.2.7 [122] data mining
BLASR 20160518 (5.1), 20161215 (5.3), 5.3.2 [123] biology,bioinformatics,ngs
Blast2GO CLI 1.3.3, 2.5.0-20120705 [124] biology, bioinformatics, gene ontology
BLAT 20121105, 20140318 [125] Genomics, bioinformatics
Blender 2.63, 2.73, 2.77 [126] graphics
Blitz 0.10 [127] library
BlobTools 1.0, 2.2 [128] phylogenetics
Bloomfiltertrie 0.8.7 [129] phylogenetics
BloomTree 0.3.5 [130] data mining
BLUPF90 20160604, 20180301, 20190531 [131] biology, phylogenetics
BOLT-LMM 2.3.4 [132] phylogenetics
BoltzTraP 1.2.5 [133] physics
Boost 1.64.0, 1.67.0, 1.71.0 [134] programming,library,cpp
Booster 0.1.2 [135] phylogenetics
Bowtie 1.1.1, 1.2.0, 1.2.3 [136] biology,bioinformatics,ngs,sequencing
Bowtie2 2.3.5, 2.3.5.1, 2.4.2 [137] biology,bioinformatics,ngs,sequencing
BPGA 1.2 [138] biology, ngs
BPP 3.2, 3.4, 4.1.4 [139] biology, phylogenetics
Bracken 1.0.0, 2.5 [140] biology, phylogenetics
Braker 2.1.2, 2.1.5 [141] phylogenetics
BRANCH 1.8.1 [142] biology,bioinformatics,ngs,mapping
BRATNextGen 20150505 [143] biology, bioinformatics, genomics
BreakDancer 1.4.5 [144] biology, phylogenetics
Breakseq 2.2 [145] biology, phylogenetics
Brewery 20191205 [146] phylogenetics
Bridger 20141201 [147] NGS, Genomics, bioinformatics
BRIG 0.95 [148] biology, genomics
BRM 0.3 [149] phylogenetics
Bruker2nifti 1.0.4 [150] phylogenetics
Bsmap 2.87 [151] biology, bioinformatics, NGS
Bsoft 1.9.1 [152] biology, image analysis
BSseeker2 2.1.0, 2.1.8 [153] biology, phylogenetics
Bubbleparse 20140314 [154] biology, phylogenetics
BUCKy 1.4.4 [155] biology, phylogenetics
BUSCO 3.02, 4.0.6, 4.1.4 [156] biology, genomics
BWA 0.7.7, 0.7.8, 0.7.9a [157] biology,bioinformatics,ngs
BWA-PSSM 0.5.11 [158] phylogenetics
Bxh_xcede_tools 1.11.1 [159] biology, bioinformatics
BYOBU 5.92 [160] shell, screen, terminal
Bzip2 1.0.6 [161] archiver, library
CAFE 4.1 [162] biology, phylogenetics
Came 0.0.1 [163] phylogenetics
Camino 20140723 [164] biology,bioinformatics,neuroscience,imaging
Cantera 2.1.1 [165] kinetics, thermodynamics
Canu 1.9, 2.0, 2.1 [166] biology, sequencing
CANVAS 1.40.0.1613 [167] phylogenetics
CAP3 20120705 [168] biology,bioinformatics,assembly
Capnp 0.5.3 [169] C++
CASAVA 1.8.2 [170] biology,bioinformatics,ngs
CASM 0.2.0 [171] Statistical Mechanics
CasOFFinder 2.4 [172] phylogenetics
CAVIAR 20171218 [173] biology, phylogenetics
CBGpipe 20190702 [174] phylogenetics
CD-HIT 4.6, 4.6.4, 4.6.8 [175] biology, genomics
CDO 1.7.2rc3, 1.9.4 [176] Climate
CellProfiler 2.2.0 [177] biology, phylogenetics
Cell Ranger 3.1.0, 4.0.0, 5.0.0 [178] biology, bioinformatics, ngs, rna-seq
Cell Ranger ATAC 1.2.0 [179] biology, bioinformatics, ngs, rna-seq
CellRanger-DNA 1.0.0, 1.1.0 [180] biology, bioinformatics, ngs, rna-seq, 10xgenomics
Centrifuge 1.0.3 [181] biology, phylogenetics
CFITSIO 3.370 [182] library, C
CGAL 4.10, 4.9, 5.02 [183] library, math
CGATools 1.6.0.43 [184] biology, bioinformatics, ngs
Cgmaptools 0.1.1, 0.1.2 [185] phylogenetics
CHARMM 36a3, 43b2 [186] chemistry, simulation
CheckM 1.0.4, 1.0.7, 1.1.2 [187] biology, genomics
Chimera 1.12 [188] biology, bioinformatics, modeling
Chipyard 1.0 [189] hardware, design
ChromEvol 2.0 [190] Biology, NGS
CIMS 4.1.2 [191] biology,genomics
CIRCexplorer 1.1.10 [192] biology, bioinformatics, rna-seq
CIRCexplorer2 2.3.5 [193] phylogenetics
Circlator 1.5.5 [194] phylogenetics
Circleator 1.0.2 [195] phylogenetics
Circos 0.63-pre11, 0.69-2, 0.69-9 [196] biology,genomics,ngs
CIRI 2.0.6 [197] phylogenetics
CisGenome 2.0 [198] biology, bioinformatics, genomics
CisTEM 1.0.0 [199] phylogenetics
Clairvoyante 1.02 [200] phylogenetics
Clann 3.2.3 [201] biology,bioinformatics,phylogentics
CLARK 1.2.2-b, 1.2.3 [202] biology, genomics
CLHEP 2.2.0.1 [203] High Energy Physics
CLIFinder 4.1 [204] biology, phylogenetics
CLIPSeqTools 0.1.7 [205] biology, sequencing
ClonalFrame 1.1, 1.2 [206] biology,bioinformatics,ngs,phylogenetics
ClonalFrameML 1.0, 1.11 [207] biology, bioinformatics, ngs, phylogenetics
CloudCompare 2.10.3 [208] 3D visualization
CLUMPP 1.1.2 [209] biology, bioinformatics
ClustalO 1.2.0 [210] biology, bioinformatics, alignment
ClustalW 2.1 [211] biology,bioinformatics,alignment
Cluster3 1.52a [212] biology, genomics
ClusterFinder 313 [213] biology, bioinformatics, metabolomics
Clview 20130402 [214] biology, bioinformatics
CMake 3.14.5, 3.15.6, 3.6.3 [215] Software Development
CMS 20170518 [216] biology
CMWP 140518 [217] biology, genomics
CNSpipeline 20170827 [218] phylogenetics
CNV-Sim 0.9.2 [219] biology, phylogenetics
CNVkit 0.9.0, 0.9.6 [220] biology
CNVnator 0.3.2 [221] biology, genomics, CNV
CNV-Seq 20110715, 20140812 [222] biology,bioinformatics,genomics
Cobra-tf 0.1 [223] Nuclear Engineering
CodonPhyML 20150303 [224] phylogenetics
Coevol 1.3c, 1.4b [225] bio,bioinformatics,phylogenetics
Cogent 2.1 [226] biology, phylogenics
COLMAP 3.6 [227] modeling
CoMap 1.4.1 [228] Bioinformatics, Genomics
Comp-D_MPI 1.0 [229] Statistics
COMSOL 5.4.0 [230] General-purpose simulation software
Concaterpillar 1.8a [231] phylogenetics
CONCOCT 1.1.0 [232] biology, bioinformatics, genomics
Conda 4.8.3, 4.8.4 [233] programming, development, packages
CONN 18a [234] mri,fmri,matlab
CONNECT 20200614 [235] phylogenetics
Connectomemapper3 3.0.0-rc1 [236] phylogenetics
ConPADE 1.0 [237] phylogenetics
Conpair 20161010, 20180624 [238] biology, phylogenetics
Consed 23.0, 25.0, 29.0 [239] biology, bioinformatics, genomics
CONSEL 0.20 [240] biology, phylogenetics
ContaVect 0.2 [241] biology, phylogenetics
Coot 0.8.9 [242] Modeling
Coreutils 8.23, 8.28 [243] Software tools
Corset 1.06 [244] biology, NGS
Counterr 0.1 [245] phylogenetics
CovNMR 2014 [246] Biochemistry
Cp2k 7.0.0 [247] Quantum Chemistry
CPAT 1.2.2 [248] biology, phylogenetics
CPLEX 12.6.1, 12.6.2, 12.7 [249] Meteorology
Crass 1.0.1 [250] biology, assembly
Crisflash 1.2.0 [251] phylogenetics
CRISP 20181122 [252] phylogenetics
CRISPRanalyzer 1.50 [253] biology,genomics,ngs
CrossMap 0.3.9 [254] biology, genomics
Crux 1.40 [255] biology, mass-spectroscopy
CryptoMiniSat 5.0.1 [256] SAT
CryptSplice 20180111 [257] biology, phylogenetics
CUBE 4.3.4, 4.4 [258] library,c,math
Nvidia CUDA Toolkit 10.0.130, 11.0.207, 11.1.0 [259] programming, library, graphics, runtime
Cufflinks 2.1.1, 2.2.1, 2.2.1.1 [260] biology,bioinformatics,ngs,sequencing
CDNA_Cupcake 9.0.1 [261] biology, bioinformatics, ngs, iso-seq
Cutadapt 2.6, 2.7, 2.8 [262] biology,bioinformatics,ngs
CUTE 3.2.6 [263] astronomy
CutRunTools 20200104 [264] phylogenetics
Cvbio 3.0.0 [265] phylogenetics
CWLtool 1.0.20190228, 1.0.20190906, 2.0.20200126 [266] workflow, scheduler
Cytoscape 3.4.0 [267] biology, bioinformatics, ngs, phylogenetics
DAKOTA 6.10, 6.8, 6.8-gui [268] Computational Science and Engineering
DALIGNER 1.0 [269] biology, phylogenetics
Dammit 1.0rc2 [270] biology, phylogenetics
DASTool 1.1.0, 1.1.2 [271] biology, phylogenetics
Datamash 1.1.0 [272] math
DAWGPASW 1.0 [273] biology, phylogenetics
DCC 0.4.4 [274] biology, bioinformatics, ngs
Dcmstack 0.6.2 [275] biology, imaging
DCMTK 3.6.0 [276] biology,neuroscience,imaging
DDocent 2.7.8 [277] phylogenetics
DDSCAT 7.3.0 [278] Astrophysics
DDT 18.2, 20.0, 20.2 [279] Software Development
DealII 8.3.0 [280] Library
DeconSeq 0.4.3 [281] biology, phylogenetics
DeepARG 1.0.1 [282] phylogenetics
Deepbgc 0.1.18 [283] phylogenetics
DeepGS 1.2 [284] phylogenetics
DeepLabCut 2.0.7-cpu, 2.0.7-gpu, 2.1.1 [285] phylogenetics
DeepPicker 20161102 [286] particle picking
DeepTools 2.4.3, 3.1.1 [287] biology, bioinformatics, NGS
DeFusion 20200305 [288] phylogenetics
Delft3D 7545 [289] Physics
Delly 0.7.5, 0.7.7, 0.7.8 [290] biology, phylogenetics
DeNoGAP 1.0 [291] biology, phylogenetics, ngs
DeTiN 1.7.5.9 [292] ngs, genomics
DETONATE 1.11, 1.9 [293] biology, rna-seq
DEXTRACTOR 1.0 [294] biology, sequencing
Diamond 0.8.5, 0.9.15, 0.9.34 [295] computational biology, genomics
DiCal2 2.2.0.1 [296] biology, phylogenetics
DiffReps 1.55.4 [297] Bioinformatics
DiscoSnp 2.2.10 [298] biology, phylogenetics
DISCOVAR de novo 52488 [299] biology, ngs, assembler
DiscoVista 20180906 [300] phylogenetics
DIYABC 1.0.4.43b, 2.0.3, 2.1.0 [301] biology, phylogenetics
Dlib 19.19 [302] phylogenetics
DL_POLY 1.9 [303] Molecular Dynamics
DNA Clust 3.0 [304] biology,bioinformatics,genomics
DNA-ML 1.0 [305] Biology, NGS
DOCK 6.7, 6.8, 6.9 [306] chemistry
DoGFinder 20201103 [307] phylogenetics
DosageConvertor 1.0.3 [308] biology
DOT 2.0 [309] biology,bioinformatics,docking
Doxygen 1.8.3.1 [310] programming, documentation
DRAP 1.91 [311] biology, phylogenetics
DRep 2.3.2 [312] phylogenetics
Dropseq 2.4.0 [313] phylogenetics
DSK 2.1.0, 2.3.0 [314] biology, NGS
DSSAT 4.6 [315] Agriculture
DSSP 2.2.1, 3.0.0 [316] Molecular Dynamics
Dtiprep 0.1.1 [317] phylogenetics
PHYLDOG 20130116-dbg [318] biology,bioinformatics,phylogenetics
DynamicDBG 20181003 [319] phylogenetics
Dynare 4.4.3 [320] math
EAGLE 2.0 [321] phylogenetics
Eagle-rc 1.1.1 [322] phylogenetics
Ea-utils 1.04.807.18, 1.1.2.537 [323] biology,bioinformatics,genomics,ngs
ECE 1.2 [324] ECE
EDirect 10.7, 12.2 [325] biology, phylogenetics
EDTA 1.9.0, 1.9.4, 20190108 [326] phylogenetics
Edyeet 0.1 [327] phylogenetics
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [328] biology,bioinformatics,matlab
EGene-MVN 0.1 [329] biology, genetics
EggNOG-mapper 2.0.1 [330] phylogenetics
EGSnrc 2019 [331] phylogenetics
EIGENSOFT 4.2, 5.0.1, 6.0.1 [332] biology, bioinformatics
Elastix 4.9.0 [333] phylogenetics
ELPA 2019.11.001 [334] library,c,math
ElPrep 4.1.4 [335] phylogenetics
Emacs 25.3 [336] programming, scripting, language
EMAN2 2.22, 2.31 [337] image processing
EMBOSS 6.5.7 [338] biology,bioinformatics
Embree 3.6.1 [339] ray, tracing, kernels
EMC 9.4.3 [340] Monte Carlo Simulations
EMMAX 20100307, 20120210 [341] biology, NGS, mapping
EnergyPlus 9.3.0 [342] simulation
Ensembl Tools 100, 80 [343] biology, bioinformatics
EnTAP 0.6.1.2, 20160416 [344] biology, phylogenetics
EPACTS 3.2.6, 3.4.2, 3.4.2.hg38 [345] biology, bioinformatics, genomics
Epiteome 1.0 [346] phylogenetics
Epoch 4.7.3 [347] astronomy,CCPP
EQTLA 1.1 [348] biology, bioinformatics, genomics
EQtlBma 1.2.2, 1.3.0r20140820 [349] biology, genotyping
Erpin 5.5.4 [350] biology, phylogenetics
ESOM 1.1 [351] biology, phylogenetics
ESPRESSO 6.2.0, 6.2.1, 6.4.1 [352] Quantum,modeling
ESPRIT 2009-nogap, 201102 [353] biology,bioinformatics
ETE3 3.0.0, 3.1.1 [354] biology, phylogenetics
EVidenceModeler 1.1.1 [355] phylogenetics
Evigene 20180730 [356] phylogenetics
ExaBayes 1.5 [357] phylogenetics
Exonerate 2.2.0 [358] biology,bioinformatics,genomics
EXpress 1.3.1, 1.5.1 [359] biology,bioinformatics,ngs
Face_recognition 1.2.2 [360] phylogenetics
FALCON 20161027, 20161222, 20190601 [361] biology,bioinformatics,ngs,sequencing
FALCON_unzip 20161222 [362] biology, bioinformatics
FAR 2.15 [363] biology,bioinformatics,genomics
FAST 1.06 [364] biology phylogenetics
Fast-gep 1.0 [365] phylogenetics
Fast-Plast 1.2.6 [366] biology, phylogenetics
FASTA 34.26.5, 36.3.6d [367] biology,bioinformatics,genomics
Fastai 2.1.5 [368] phylogenetics
FastANI 1.1 [369] phylogenetics
FastGEAR 20161216 [370] biology, bioinformatics, genomics
R8s 1.8 [371] phylogenetics
FastML 3.0 [372] biology,bioinformatics,phylogenetics
Fastp 0.20.0 [373] biology,bioinformatics,ngs
FASTphase 1.4.8 [374] phylogenetics
Fastq-pair 1.0 [375] phylogenetics
FastQ-Screen 0.14.0 [376] phylogenetics
Fastq-tools 0.8 [377] biology, NGS,
FastQC 0.11.4, 0.11.7, 0.9.6 [378] biology,bioinformatics,ngs
FastQTL 2.184 [379] phylogenetics
Fastsimcoal 2.6.0.3 [380] biology, phylogenetics
FastSpar 0.0.4 [381] biology, genomics
FastStructure 20150112 [382] biology, genomics
FastTree 2.1.7 [383] biology,bioinformatics,phylogenetics
FastUniq 1.1 [384] biology, phylogenetics
Fastx Toolkit 0.0.13.2, 0.0.14 [385] biology,ngs
FcGENE 1.0.7, 1.0.7.1 [386] biology,bioinformatics,genomics,snp
FDSTools 1.2.0 [387] phylogenetics
Fdupes 1.51 [388] file management
FEELnc 0.1.1 [389] phylogenetics
FEniCS 2018.1.0 [390] biology, phylogenetics
Ferret 6.82 [391] Data Visualization and Analysis, Oceanography, Meteorology
FFmpeg 2.1.3, 2.8.3 [392] Audio, Video
FFTW 3.3.6, 3.3.7, 3.3.8 [393] library,c,math
Fgbio 0.5.0, 0.7.0 [394] phylogenetics
FGMP 1.0.1 [395] phylogenetics
Fiji 2.0.0rc59 [396] ImageJ
Filtlong 0.2.0 [397] biology, phylogenetics
Finemap 1.4 [398] phylogenetics
Finesse 2.3.1 [399] simulation
FineSTRUCTURE 1.8, 2.0.7, 2.1.3 [400] biology, population genetics
FLAIR 1.5 [401] phylogenetics
Flappie 1.1.0, 2.1.3 [402] phylogenetics
FLASh 1.2.10, 1.2.11 [403] biology, genomics
FLEA 2.0.0 [404] phylogenetics
Flex 2.6.4 [405] programming tool
Flexbar 2.3, 2.34 [406] biology, bioinformatics, genomics, ngs
FLEXLm 1.0 [407] Administration
FlowCraft 1.4.1 [408] phylogenetics
Fluent 17.2, 19.1, 2020R1 [409] CFD
Flye 2.6, 2.7.1, 2.8.1 [410] Biology, NGS
FMRIPrep 1.3.2, 1.4.0a1, 1.5.4 [411] data mining
ForeSeqs 1.0.4 [412] phylogenetics
Pascal 3.0.0 [413] Compiler, Programming
Fqtools 20160224 [414] biology,bioinformatics,ngs,sequencing
FragGeneScan 1.16 [415] biology,genomics
FRAMA 20151019 [416] biology
FrameDP 1.2.2 [417] biology, sequencing
FreeBayes 1.3.1, 1.3.2, v0.9.15-1-g076a2a2 [418] biology,genomics
FREEC 11.0, 9.6 [419] biology, sequencing
Freesurfer 5.3.0, 6.0.0, 7.1.0 [420] biology,bioinformatics,neuroscience,imaging
FSL 5.0.9, 6.0.1, 6.0.3 [421] biology,bioinformatics,neuroscience,imaging
FusionInspector 1.1.0 [422] biology, phylogenetics
GAL 20180906 [423] phylogenetics
Galaxy 1.0 [424] biology,bioinformatics
GAMBIT 15.1.0, 16.0.0 [425] Game theory Software
GAML 20150610 [426] biology, bioinformatics, genomics
GapCloser 1.12r6 [427] biology, genomics, ngs
GapFiller 1.10, 1.11 [428] biology, genomics
GARLI 2.0, 2.01 [429] biology,bioinformatics,phylogeny
GASVPro 201310 [430] biology, bioinformatics, ngs
GATE 7.0 [431] Date analysis and visualization
GATK 4.1.4.0, 4.1.8.1, 4.1.9.0 [432] biology,bioinformatics,ngs
Gaussian 09 A.02, 09 D.01, 16 [433] Computational Chemistry
Gawk 4.2.0 [434] Software tools
Gblocks 0.91b [435] biology,bioinformatics
GNU Compiler Collection 7.3.0, 8.2.0, 9.3.0 [436] compilers
GCT 6.2.1 [437] gridftp, globus, toolkit
GCTA 1.24.7, 1.26.0, 1.92.4beta [438] biology, genomics, SNP,
GDAL 2.2.1, 2.2.4, 2.3.1 [439] Geospatial library
GDB 8.3 [440] Software Development
GDC-Client 1.0.1, 1.5.0 [441] biology, bioinformatics, sequence, ngs
GDSL 1.18 [442] library
Geant4 4.10, 4.10.03, 4.10.5 [443] Physics
GEM 20130406 [444] biology,bioinformatics,ngs,sequencing
Gem5 2.0 [445] Computer Simulator
GEMMA 0.98.1 [446] phylogenetics
NCBI GenBank Tools 20140130 [447] Biology,bioinformatics,NCBI,GenBank
GeneMark-ES 4.33, 4.58 [448] biology, genomics
GeneMarkS 2012.04, 3.10.001 [449] biology,genomics
GenePainter 2.0.4 [450] biology, phylogenetics
GeneRax 1.2.2 [451] phylogenetics
GeneSeqer 2014-02-26 [452] biology, genomics
Genesum 0.1.0 [453] biology,genomics
GeneTorrent 3.8.7 [454] biology,bioinformatics,data download
GenGen 1.0.1 [455] biology, phylogenetics
Genome_Graph_Annotation 20190131 [456] phylogenetics
Genome STRiP 2.00.1602 [457] biology, genomics, ngs
GenomeTools 1.5.7, 1.5.9 [458] biology, bioinformatics
Genomic-fluidity 20151109 [459] phylogenetics
GenomicNeuralnet 20161030 [460] phylogenetics
GenomicConsensus 2.3.3 [461] biology, phylogenetics
GenomicTools 2.7.0 [462] biology,bioinformatics,ngs,chip-seq,rna-seq
GenotypeHarmonizer 1.4.18 [463] biology, bioinformatics
Genrich 0.5 [464] phylogenetics
GenSel 4.90 [465] population genetics
Geopython 1.0.0, 1.0.1 [466] python, geospatial, cartography
GEOS 3.3.8, 3.6.2 [467] library, data
GeP 2.1 [468] biology, phylogenetics
Gepard 1.40.0 [469] phylogenetics
Gerbil 1.11 [470] phylogenetics
Get_homologues 20150529 [471] biology, genome
GFF-Ex 2.3 [472] phylogenetics
Gffread 0.11.8, 0.9.8c [473] biology, bioinformatics
Gflags 2.2.1, 20150520 [474] google,libraries
GFOLD 1.1.4 [475] biology, RNA-seq
Ggsashimi 0.5.0 [476] phylogenetics
GHOST-MP 1.3.4 [477] phylogenetics
Ghostscript 9.21, 9.22 [478] PDF
Giotto 0.1.0 [479] phylogenetics
Git 2.14.1 [480] Revision Control
Glactools 1.0.8 [481] phylogenetics
Glimmer 3.02 [482] biology, microbial annotation
GlimmerHMM 3.0.4 [483] biology, microbial annotation
Globus 1.10.1, 2.1.3 [484] Data Transfer
Glog 0.3.5 [485] google,libraries
GLPK 4.55, 4.65 [486] Programming
Glueviz 0.15.2 [487] phylogenetics
GMAP 20180212, 20180212_sse2, 20190610 [488] biology, bioinformatics, genomics, ngs
GMcloser 1.6 [489] Biology, NGS
GMP 6.1.2 [490] library, crypto
GnuPlot 4.6.0, 5.2.2, 5.2.3 [491] graphics,plotting,math
Go 1.12.9, 1.13.6, 1.15.4 [492] programming language
GOMAP 1.3 [493] biology, bioinformatics, ngs
GoPHY 201030 [494] phylogenetics
Gotcloud 1.17.5 [495] phylogenetics
GPA 1.1 [496] phylogenetics
GPhoCS 1.2.3 [497] phylogenetics
Grace 5.1.22 [498] graphics, statistics, 2D
GRACKLE 3.1 [499] library,c,astrophysics
GrADS 2.0.1 [500] environment, grid analysis
Graftm 0.12.2 [501] phylogenetics
GramCluster 1.3 [502] biology,sequencing,
Graph-tool 2.32 [503] phylogenetics
Graph_annotation 0.1 [504] phylogenetics
GraPhlAn 0.9.7 [505] biology, phylogenetics
GraphMap 0.4.0 [506] biology, nanopore sequencing
GraphViz 2.38.0 [507] biology,bioinformatics,neuroscience,imaging
GRASS 7.0, 7.4 [508] Geography
Grf 1.0.0 [509] genomics, bioinformatics
Grib_api 1.10.1, 1.15.1, 1.26.1 [510] C, fortran, library
GRIDSS 2.6.2 [511] phylogenetics
GROCSVs 0.2.5 [512] phylogenetics
GROMACS 2018.0, 2019.2, 2020.3 [513] Computational Chemistry, Molecular Dynamics
GroopM 0.3.5 [514] biology, phylogenetics
Groovy 2.4.15 [515] Programming
Gscripts 1.1 [516] scripts
GSEA 3.0.0 [517] biology, bioinformatics, genomics
GSL 2.4, 2.5, 2.6 [518] library, data
GSNP 1.0 [519] biology,bioinformatics,ngs
GTDBTk 0.1.3 [520] phylogenetics
GTOOL 0.7.5 [521] phylogenetics
GUAVA 1.0 [522] phylogenetics
Gubbins 2.4.1 [523] phylogenetics
Guile 2.2.2 [524] Programming Language
GULP 4.4, 5.0 [525] Material Science
Guppy 3.6.1, 4.0.11, 4.0.15 [526] phylogenetics
GWAMA 2.2.2 [527] phylogenetics
HALC 1.1 [528] biology, phylogenetics
HaMStR 13.2.3, 13.2.4, v8b [529] biology, genome
HapCompass 0.7.7 [530] ngs, genomics
HAPCUT 0.7 [531] biology, assembly
HAPLOSWEEP 1.0 [532] biology, phylogenetics
HapQTL 1.00 [533] biology
Hapsembler 2.21 [534] biology, bioinformatics, assembly
HASLR 0.8a1 [535] phylogenetics
HDF4 4.2.11 [536] library, data
HDF5 1.8.19, 1.8.20, 1.8.9 [537] library, data
HELEN 20200516 [538] phylogenetics
HelitronScanner 1.1 [539] phylogenetics
HGTFinder 20160720 [540] biology, genomics
Hifiasm 0.12, 0.4, 0.8 [541] phylogenetics
HipSTR 0.7 [542] phylogenetics
HISAT2 2.1.0, 2.2.0, 2.2.1 [543] Biology, Sequence Alignment, NGS
HLAHD 1.1.1 [544] biology, phylogenetics
HLAminer 1.3.1 [545] biology, phylogenetics
HMM-FRAME 20140724 [546] phylogenetics
HmmCleaner 0.180750 [547] phylogenetics
HMMER 3.1b1, 3.1b2, 3.2.1 [548] biology, genome
HomBlocks 1.0 [549] biology, phylogenetics
HOMER 4.10, 4.11, 4.8 [550] biology,bioinformatics,sequence,ngs
HOOMD 2.1.7 [551] library, math
HPL 2.1 [552] parallel programming, benchmarks, MPI
HTMLDoc 1.8.28, 1.9.3 [553] pdf, docs, html
HTSeq 0.11.0, 0.11.2, 0.9.1 [554] biology, bioinformatics, ngs
Humann2 0.11.2, 2.8.1 [555] phylogenetics
HUPAN 20200429 [556] phylogenetics
Hyb 20141126 [557] biology, ngs, RNA-Seq
HybPhyloMaker 1.5 [558] biology, phylogenetics
HybPiper 1.2, 1.3.1 [559] biology, phylogenetics
HyDe 0.4.3 [560] phylogenetics
HyPhy 2.5.4, 2.5.7, 2.5.8 [561] biology,bioinformatics,evolution
HYPRE 2.15.1, 2.18.2, 2.19.0 [562] Math, Numerical Solvers
IAnnotateSV 1.0.6, 1.0.9 [563] Biology, Phylogenetics
IAssembler 1.3.2 [564] biology, assembly
Ibdne 20150815 [565] biology,ngs
ICallSV 0.0.6 [566] Biology, Phylogenetics
Icommands 3.3.1 [567] iRods
ICORN2 0.95 [568] biology, sequencing
IDBA-MT 1.0 [569] biology,NGS
IDBA-UD 1.1.1, 1.1.1-512, 1.1.1-512-mem [570] Genomics, bioinformatics, phylogenetics
IDL 8.3 [571] language, programming, science
IDR 2.0.3 [572] phylogenetics
IGB 8.4.1 [573] biology, bioinformatics, genomics
IgBLAST 1.5.0, 1.7.0 [574] biology, bioinformatics
IGoR 1.4.0 [575] phylogenetics
IGTP 1.1 [576] biology, bioinformatics, phylogenetics
IGV 2.3.91, 2.4.16, 2.8.6 [577] biology, bioinformatics, ngs, phylogenetics
IM and IMa 20091217 [578] biology,bioinformatics,population genetics
Ima2 20120827 [579] biology,bioinformatics,population genetics
IMa2p 20170712 [580] biology, phylogenetics
IMA3 22Aug18 [581] Molecular Dynamics
ImageJ 1.48 [582] imaging
ImageMagick 7.0.8-20 [583] Imaging
IMOD 4.7.15, 4.9.10 [584] 3D modeling, image reconstruction
Intel MPI 5.1.1 [585] parallel programming, development, MPI, library
Infernal 1.1.1 [586] biology, sequence alignment
INLA 20160718, 20170620 [587] statistics, modeling, R
InParanoid 4.1 [588] biology, biology
InStruct 20160723 [589] phylogenetics
Intel Compilers and Libraries 2018.1.163, 2019.1.144, 2020.0.166 [590] programming languages, development, library, math, intel
Intervene 0.6.2 [591] biology, phylogenetics
IOAPI 3.1, 3.2 [592] Meteorology
IPOPT 3.12.10, 3.12.6 [593] library,c/c++,math
InterProScan 5.31-70.0, 5.34-73.0, 5.35-74.0 [594] biology,bioinformatics
Ipyrad 0.7.24, 0.7.30, 0.9.53 [595] phylogenetics
IQ-TREE 2.0.3, 2.0.6, 2.1.0 [596] biology, phylogenetics,
IRAP 0.8.1p7 [597] biology, ngs, pacbio
IRFinder 1.0.0, 1.2.0, 1.3.0 [598] biology, RNA-Seq
IsONclust 0.0.6 [599] phylogenetics
IsoSeq3 3.1.0, 3.2.2, 3.4.0 [600] biology, bioinformatics, ngs, pacbio
ISOWN 20180820 [601] phylogenetics
IsPcr 3.3 [602] biology, phylogenetics
ITK 3.20.1, 4.10.1 [603] Bioinformatics
ITK-SNAP 3.0.0, 3.8.0 [604] biology,bioinformatics,neuroscience,imaging
ITSx 1.1b [605] phylogenetics
Jabba 1.0 [606] biology, phylogenetics
JACUSA 1.2.0 [607] biology, bioinformatics, ngs, phylogenetics
JAGS 3.3.0, 3.4.0, 4.2.0 [608] Statistics
NpScarf 1.7 [609] phylogenetics
JDK 11.0.1, 14, 9.0.1 [610] programming,runtime
JCVI 0.8.12 [611] phylogenetics
Je 1.0 [612] biology, NGS
Jellyfish 2.2.4, 2.2.6, 2.3.0 [613] biology,ngs
JModelTest 2.1.1 [614] biology, bioinformatics, genomics, phylogenetics
Jo 1.3 [615] Software
Jq 1.6 [616] Software
Julia 0.6.4, 1.0.0, 1.5.0 [617] programming, language, statistics
Jupyter 5.7.0, 5.7.8, 6.0.3 [618] python, R, jupyter
JVARKIT 20180405 [619] biology, phylogenetics
Kaiju 1.6.2, 1.7.2 [620] biology, phylogenetics
KaKs 1.2, 2.0 [621] biology, bioinformatics, evolution, phylogenetics
Kallisto 0.42.4, 0.43.0, 0.44.0 [622] biology,NGS,RNA-Seq
Khmer 2.0, 2.1 [623] Biology, NGS
KIM 1.8.0, 1.8.2, 1.9.3 [624] Simulation
KINFIN 1.0.1 [625] biology, phylogenetics
KING 2.1.2 [626] biology, genome, gwas
KisSplice 2.4.0-p1 [627] biology, RNA
KLayout 0.26.7 [628] phylogenetics
KMC 3.1.0, 3.1.1 [629] phylogenetics
KMOS 0.3.21 [630] phylogenetics
Kneaddata 0.7.4 [631] phylogenetics
Knitro 12.2.0 [632] Mathematical Optimization Problems
Kover 2.0.3 [633] phylogenetics
Kraken 1.0, 2.0.6b, 2.0.8b [634] biology, ngs
KrakenUniq 0.5.8 [635] phylogenetics
Krona 20161019 [636] biology, bioinformatics
Ksnp 3.021 [637] biology, phylogenetics, SNP
LACHESIS 2.1 [638] phylogenetics
Lambda 0.9.4, 1.0.3, 2.0.0 [639] biology, sequencing, phylogenetics
LAMMPS 30Jul16, 7Aug19, 7Dec15 [640] Molecular Dynamics
LAMP 2.5 [641] biology, bioinformatics, genomics
LAPACK 3.8.0 [642] programming,library,fortran
Last 916, 979 [643] biology,bioinformatics,sequence,alignment
LAStools 20200114 [644] LiDAR
LASTZ 1.02.00, 1.03.02, 1.04.00 [645] biology, bioinformatics, ngs
Lbzip 2.5 [646] compression
LDhat 2.2a [647] biology,genomics
LEfSe 20180219 [648] phylogenetics
LFMM 1.4, 1.5 [649] biology, phylogenetics
ChartDirector 5.1.0 [650] library, data
Libint 2.5.0, 2.5.0b [651] library
LEMON 1.2.3 [652] library
LibMesh 1.5.0 [653] Math, Numerical Solvers
Libunistring 0.9.7 [654] library
Libvips 8.5.4 [655] image processing
LIBXC 4.2.3, 4.3.4 [656] library, density function
LIBXSMM 1.13 [657] library,c,math
LIBZMQ 4.3.1 [658] library
Liftoff 1.4.2 [659] phylogenetics
LIGR 2.05 [660] biology,assembly
Lima 2.0.0 [661] phylogenetics
LINKS 1.8.5, 1.8.6 [662] biology, genomics
Linksbrowser 2.14 [663] web browser
LMAP 1.0.2 [664] biology, phylogenetics
LncScore 1.0.2 [665] biolgoy, phylogenetics
LobSTR 4.0.6 [666] biology, phylogenetics
Localizer 1.0.4 [667] phylogenetics
LocusZoom 1.4 [668] phylogenetics
LoFreq 2.1.3.1 [669] phylogenetics
LongRanger 2.1.5, 2.2.2 [670] biology, phylogenetics
LoRMA 0.3, 0.5 [671] biology, ngs, pacbio
LS-DYNA 700, 711, 901 [672] Physics
LSD2 1.6.5 [673] phylogenetics
Ltr_finder 1.07 [674] biology, phylogenetics
LTRRetriever 2.1, 2.5, 20170514 [675] biology, phylogenetics
Lua 3.5.2 [676] programming, scripting, language
Lumpy-sv 0.2.1, 0.2.13 [677] biology, genotyping
LZO 2.09 [678] library, compression
M5nr 20121126 [679] biology, bioinformatics, genomics
Macaulay2 1.15 [680] phylogenetics
MACH 1.0.18 [681] biology,bioinformatics,genomics,ngs
Mach2VCF 20150515 [682] biology
MACS 2.0.10, 2.1.2, 2.2.7.1 [683] biology, bioinformatics, CHiP-Seq
MafFilter 1.3.0 [684] phylogenetics
MAFFT 7.245, 7.294, 7.397 [685] bio,bioinformatics,sequence
MAGeCK 0.5.7 [686] phylogenetics
Majiq 1.0.5, 2.1 [687] biology, phylogenetics
Maker 2.31.10, 2.31.6, 3.01.03 [688] biology,bioinformatics
Mamba 0.4.4, 0.5.3 [689] programming, development, packages, conda
MAnorm 20120316 [690] biology, phylogenetics
Mantis 1.0.4 [691] phylogenetics
MapThin 1.11 [692] phylogenetics
Maq 0.7.1 [693] biology,bioinformatics,ngs
MarginPolish 1.0.0 [694] phylogenetics
MARK 2.0.1 [695] application, data, capture
MarkerMiner 20150710 [696] biology, bioinformatics, genomics
Mash 1.1 [697] biology, genomics
MasHmap 2.0 [698] phylogenetics
MASSMINE 0.10.0, 0.11.0, 0.9.5 [699] data mining
MaSuRCA 3.3.0, 3.3.4, 3.4.2 [700] biology, bioinformatics, short read alignment
Mathematica 12.1.1.0 [701] Mathematica - a category of its own!
MATLAB 2019b, 2020a, 2020b [702] math,language
MATS 4.0.1, 4.0.2, 4.1.0 [703] biology,bioinformatics,ngs,rna-seq
Mauve 2.3.1 [704] biology,ngs,genomics
Mawk 1.3.4-20150503 [705] programming language
Maxbin 2.1.1 [706] biology,NGS
Maxima 5.41.0 [707] Math
MC 4.6.1 [708] shell
MCarts 1.0.2 [709] biology, genomics, markov
Mccortex 1.0 [710] phylogenetics
MCL 12-135, 14-137 [711] biology, genomics
MCNP 6, 6.1 [712] Physics
MCNPX 2.7.0 [713] Physics
MCR 2019b, 2020a, 2020b [714] math, language
MCScanX 20130328 [715] biology, phylogenetics
MECAT 20180308 [716] phylogenetics
Medaka 0.6.2, 0.7.1, 1.0.1 [717] biology, phylogenetics
Medusa 1.6 [718] phylogenetics
MEGA 7.0.26 [719] biology, phylogenetics
Mega2 4.9.2, 6.0.0 [720] biology, phylogenetics
MEGAHIT 1.1.1, 1.1.4 [721] biology, phylogenetics
Megalodon 2.0.0 [722] phylogenetics
MEGAN 5.10.3, 6.4.15 [723] biology, bioinformatics, ngs
MEGASAT 1.0 [724] phylogenetics
Megraft 1.0.2 [725] biology,sequencing,
MELD 0.4.14 [726] Computational Chemistry, Molecular Dynamics
MELTING 4.3.1 [727] biology, genome, RNA, folding
MEME 4.9.1, 5.0.2, 5.0.5 [728] biology,bioinformatics,sequence
MentaLiST 0.1.3 [729] biology, phylogenetics
Meraculous 2.0.5 [730] Biology,NGS
Mercurial 4.8.2 [731] Revision Control
Merlin 1.1.2 [732] biology,SNP
Merqury 1.1 [733] phylogenetics
Meryl 1.0 [734] phylogenetics
Meshroom 2019.2.0 [735] phylogenetics
Meta-Tissue 0.4 [736] biology, genetics
MetaBAT 0.32.4, 2.13 [737] biology, genomics
Metabin 1.0 [738] Genomics, bioinformatics, metagenomics
MetaCherchant 0.1.0 [739] biology, phylogenetics
MetaCluster 5.0b [740] biology,bioinformatics,genomics
MetaCompare 20181016 [741] phylogenetics
Metacrast 20200309 [742] phylogenetics
MetaCV 2.3.0 [743] Biology, NGS
MetaGeneMark 2.10, 3.26 [744] biology,genomics
METAL 20110325 [745] biology, ngs, genomics
METANNOT 20171129 [746] phylogenetics
Metaphinder 20161215 [747] biology, phylogenetics
MetaPhlAn2 2.7.7, 2.96.1, 3.0.3 [748] biology, phylogenetics
MetaPhysicl 1.0.0 [749] Math, Astronomy, Numerical Simulation
MetaSV 0.5.4 [750] biology, phylogenetics, NGS
MetaVelvet 1.2.06 [751] computational biology, genomics
MetaWRAP 1.2 [752] phylogenetics
Metaxa2 2.1.1, 2.1.3 [753] biology,bioinformatics,ngs,sequencing
MethylDackel 0.5.0 [754] phylogenetics
Methylpy 1.2.9 [755] Biology, Phylogenetics
Metilene 0.2.8 [756] biology, genomics, methylation
METIS 5.1.0 [757] software
Mfannot 20180405 [758] biology, phylogenetics
Mfold 3.6 [759] bioinformatics,structure,RNA
Mg-rast 20150919 [760] biolgoy, genomics
MGEfinder 1.0.5 [761] phylogenetics
MGERT 1.0.1 [762] phylogenetics
MGEScan 20160416 [763] biology, genomics
MHAP 1.6 [764] biology, sequencing
MHCflurry 1.4.3 [765] phylogenetics
MIA 20130201 [766] biology, ngs
MicrobeCensus 1.0.7 [767] biology, NGS
MIDAS 20160830 [768] biology, phylogenetics
MIGRATE-N 3.3.0, 3.6.6, 4.2.14 [769] biology,bioinformatics,population genetics
MIKE 1.0 [770] environment,water,modeling
Minced 0.2.0 [771] biology, genomics
Miniasm 0.2-r168, 0.3-r179 [772] biology, phylogenetics
MiniCaller 20161201 [773] biology,bioinformatics,ngs,phylogenetics
Minimac 1-20130717, 2-20140915, 3-20150727 [774] biology, NGS,
Minimap 2.17, 2.1t, 2.9-r720 [775] biology, phylogenetics
MinPath 1.4 [776] biology, phylogenetics
MIRA 4.0.rc1, 4.9.6, 5rc2 [777] biology,bioinformatics,genomics,assembly
MiRanda 1.9 [778] phylogenetics
MiRBShunter 0.2 [779] phylogenetics
Mirdeep 0.1.0, 0.1.1 [780] phylogenetics
Mireap 0.20 [781] biology
MIReNA 2.0 [782] biology, phylogenetics
MiRge 2.0 [783] phylogenetics
Misa 1.0 [784] biology, bioinformatics, genomics
MISO 0.5.3 [785] biology,bioinformatics,ngs,sequencing,rna-seq
MITE-Hunter 20111101 [786] biology, phylogenetics
MITObim 1.9.1 [787] phylogenetics
MitoFinder 1.0.2, 1.1 [788] phylogenetics
MitoPhAST 3.0 [789] phylogenetics
MiXCR 2.1.8, 3.0.13 [790] biolgoy, phylogenetics
MixMHC2pred 1.2 [791] phylogenetics
MixMHCpred 2.0.2 [792] phylogenetics
Mixmogam 20190322 [793] phylogenetics
MKL 2018.1.163, 2019.1.144, 2020.0.166 [794] programming, development, library, math, intel
Mlcoalsim 1.9916b [795] biology, phylogenetics
Mlst 2.15.2 [796] phylogenetics
Mlstcheck 2.1 [797] phylogenetics
MMSEQ 1.0.8 [798] biology,bioinformatics,genomics
MMseqs2 11, 12 [799] phylogenetics
MOABS 1.2.9, 1.3.2, 1.3.4 [800] biology, ngs
MODELLER 9.14, 9.23 [801] biology,bioinformatics,modelling,structure
MODELTEST 0.1.2 [802] biology, phylogenetics
Molden 5.0 [803] Molecular, Electronic Structure
MongoDB 4.0.3 [804] db, mongodb, mongo
Mono 5.18 [805] linux, runtime
Monolix 4.3.2 [806] modeling, pharmacokinetics
MOOSE 20180404, 20200316, 20200722 [807] physics, simulation
MOSAIK 2.1.33, 2.2.3, 2.2.30 [808] biology,bioinformatics,short read alignment
Mosdepth 0.2.3 [809] biology, phylogenetics
Mothur 1.37.0, 1.38.1, 1.41.3 [810] biology, microbial ecology
MotionCor2 1.2.3, 1.3.1 [811] Motion Correction
MOTU 1.1 [812] biology, bioinformatics, genomics
MOTUs 2.5.1 [813] phylogenetics
MountainSort 0.9.0 [814] library
MPACK 0.8.0 [815] library
MPB 1.5 [816] library, math
MPBoot 1.1.0 [817] biology, phylogenetics
MP-EST 1.4, 1.5 [818] biology,bioinformatics,ngs,sequencing
MPFR 3.1.6 [819] library, math
Mpinterfaces 20170613 [820] DFT
MrBayes 3.2.4, 3.2.5, 3.2.6 [821] application, biology, phylogenetics
MRIcroGL 20180623, 20200420 [822] biology, mri, imaging
MRIcron 201306, 20161012, 20190911 [823] biology, mri, imaging
Mriqc 0.11.0 [824] mri, imaging, biology
MRtrix 3.0.1, 3.0rc2 [825] biology, mri, imaging
Ms 20171108 [826] phylogenetics
MSINGS 20180810 [827] phylogenetics
MSMC-Tools 20190614 [828] phylogenetics
Msprime 0.7.4 [829] phylogenetics
MstatX 1.0 [830] biology, phylogenetics
MSTmap 1.0 [831] phylogenetics
Msvar 1.3 [832] biology,bioinformatics,population genetics
MTG2 2.15 [833] phylogenetics
Mugsy 1.2.3 [834] biology, phylogenetics
MultiQC 1.1, 1.5, 1.7 [835] biology, bioinformatics, CHiP-Seq
MUMmer 3.23, 4.0.0beta2 [836] biology,bioinformatics,genomics
MUSCLE 3.8.31 [837] biology, bioinformatics, alignment
Musket 1.1 [838] biology, genomics, ngs
MuTect 1.1.4, 1.1.7 [839] biology,genomics
MutSig 1.4, 1.41 [840] biology,genomics
Mvftools 20191124 [841] phylogenetics
MZMine 2.41, 2.52, 2.53 [842] biology, bioinformatics, spectrometry, NMR
NAMD 2.14, 2.14b2, 3.0 Alpha [843] Molecular Dynamics
NANO 2.8.2 [844] Text Editor
NanoCount 0.2.1 [845] phylogenetics
Nanofilt 2.7.1 [846] phylogenetics
NanoPlot 1.30.1 [847] phylogenetics
Nanopolish 0.11.1, 0.13.2, 20171006 [848] biology
NanoSV 1.2.0, 1.2.3, 1.2.4 [849] biology, genomics
NanoVar 1.0.1 [850] phylogenetics
NBODY 6 [851] Astronomy
Ncbi-vdb 2.6.3, 2.8.2 [852] SRA toolkit library
NCBI BLAST+ 2.7.1, 2.8.1, 2.9.0 [853] biology, bioinformatics
NCBI C++ Toolkit 12.0.0, 21.0.0, 7.0.0 [854] Biology,bioinformatics,NCBI,programming,library,cpp
Ncftp 3.2.5 [855] file transfer
NCL 6.1.2, 6.3.0 [856] Atmosphere Science
NCO 4.2.1, 4.4.3 [857] data tools
Ncview 2.1.2, 2.1.7 [858] data visualization
Neat-genreads 20171102, 20190331 [859] biology, bioinformatics, phylogenetics
NECAT 202001019 [860] phylogenetics
Necklace 1.00 [861] biology, phylogenetics
NeEstimator 2.01, 2.1 [862] Biology, Bioinformatics
Neovim 0.2.0 [863] editor, text, ide, vim
NetCDF 4.3.3, 4.4.3, 4.7.2 [864] data, exchange
NetCDF-C 4.4.1.1, 4.5.0, 4.6.1 [865] data, exchange
NetCDF-Fortran 4.4.3, 4.4.4 [866] data, exchange
NetLogo 5.3.64, 6.1.1 [867] modeling
NEURON 7.4, 7.6.2, 7.7.2 [868] biology, neuroscience
Newbler 2.7, 2.8, 2.9 [869] biology,bioinformatics,ngs,454,assembly,denovo
Newick_utils 1.6 [870] biology, phylogenetics
Newick-utils 1.6 [871] biology, bioinformatics, genomics, phylogenetics
Nextflow 20.01.0, 20.04.1, 20.07.1 [872] biology, bioinformatics, workflow
NextGenMap 0.5.3, 0.5.5 [873] biology, bioinformatics, ngs
Nextstrain 1.16.1 [874] phylogenetics
NGmerge 0.3 [875] phylogenetics
Ngmlr 0.2.6, 0.2.7 [876] biology, phylogenetics
NGS-SDK 1.2.4, 1.3.0 [877] biology,bioinformatics,ncbi,sdk,library
Ngs-bits 0.1 [878] biology, sequencing
Ngscheckmate 1.0 [879] phylogenetics
Ngstools 20150816 [880] biology, ngs
NGSUtils 20160507 [881] biology, ngs
Nipype 1.2.0, 1.4.1 [882] biology,bioinformatics,neuroscience,imaging
Nlr-annotator 0.7 [883] phylogenetics
NLR-Parser 1.0 [884] phylogenetics
NMRPipe 7.9, 8.2 [885] Biochemistry
NONMEM 7.2, 7.3.0 [886] Modeling
Nonpareil 3.3.4 [887] phylogenetics
Novoalign 2.08.02, 3.00.02 [888] biology,bioinformatics,ngs
NOVOPlasty 3.2, 3.7 [889] phylogenetics
NQuire 20180405 [890] phylogenetics
NtEdit 1.2.1 [891] phylogenetics
Nubeamdedup 20200907 [892] phylogenetics
NucleoATAC 0.3.1 [893] biology, bioinformatics
Nullarbor 1.41 [894] biology, phylogenetics
Numba 0.36.2, 0.43.1, 0.48.0 [895] Compiler
NUPACK 3.2.2 [896] phylogenetics
NWChem 6.8 [897] Chemistry
NxTrim 0.4.1 [898] biology, bioinformatics, ngs
Oases 0.2.08 [899] biology,ngs,assembler
Obitools 1.2.11 [900] biology, bioinformatics, phylogenetics
OCaml 4.02.3 [901] programming languages, scripting, development
OCOCO 0.1.2.6 [902] biology, phylogenetics
Octave 4.2.1 [903] numerical computation
Olego 1.1.2, 1.1.5, 1.1.6 [904] biology,bioinformatics,ngs,rna-seq
OmicsBox 1.1.78 [905] Image Processing
OMindel 20180129 [906] phylogenetics
OmniCLIP 0.1.0 [907] phylogenetics
OMSV 1.0.1 [908] phylogenetics
ONT-Bonito 0.0.5, 0.1.5 [909] phylogenetics
Ont_fast5_api 2.0.1 [910] phylogenetics
Ont_tutorial_cas9 20190705 [911] phylogenetics
OPENACC 16.7 [912] Programming, Accelerator toolkit
OpenBabel 2.3.2, 2.4.1 [913] biology, bioinformatics
OpenBLAS 0.2.20 [914] programming,library
OpenCL 18.1.0.013 [915] phylogenetics
OpenCV 2.4.13, 2.4.8 [916] Computervision
OpenFOAM 4.1, 5.0, 8.0 [917] Computational Fluid Dynamics
OPENMM 7.4.2, 7.5 [918] Computational Chemistry, Molecular Dynamics
OpenMPI 4.0.3, 4.0.4, 4.0.5 [919] parallel programming, development, MPI, library
OpenNeuro 3.17.4 [920] biology, data
OpenPIV-python-gpu 0.21.2, 20190506-gpu [921] python, imaging
OpenSlide 3.4.1 [922] imaging
Opera 2.0.6 [923] biology, phylogenetics
OptiType 1.3.1 [924] biology, phylogenetics
Orange3 3.3.6 [925] data mining
ORCA 4.0.1.2 [926] Molecular, Electronic Structure
OrganellePBA 20180904 [927] phylogenetics
OrthoFiller 1.1.4 [928] phylogenetics
OrthoFinder 1.0.2, 1.1.10, 2.3.11 [929] biology, ngs
Orthograph 0.6.3 [930] Orthology
OrthoMCL 2.0.3, 2.0.7 [931] biology,genomics
OTB 5.8.0 [932] Geospatial Data Modeling
P4est 1.1 [933] Library
P4vasp 0.3.29, 0.3.30 [934] Molecular, Electronic Structure
P53MH 20020901 [935] biology, DNA-sequencing
P7zip 9.20.1 [936] archiver
PacBio 7.0.1.66975, 8.0.0.79519, 9.0.0.92188 [937] biology, bioinformatics, ngs, pacbio, smrtlink
Package-GFE 20150701 [938] biology,genomics
PALADIN 1.3.1 [939] biology, phylogenetics
PALES 122 [940] physics
PAML 4.8a, 4.9a, 4.9h [941] biology, phylogenetics
Pandaseq 20140808, 20150627 [942] biology,bioinformatics,ngs,sequencing
Pandoc 2.2.2.1 [943] Converter
PanX 1.6.0 [944] phylogenetics
PAPI 5.5.1, 5.7.0 [945] programming interface, performance analysis
Parabricks 2.5.0, 3.0va, 3.1.1 [946] phylogenetics
Parallel 20150122, 20170322 [947] shell, process management
Paralyzer 1.5 [948] phylogenetics
ParaView 5.4.0, 5.4.1, 5.7.0 [949] Data Analysis
PARSIMONATOR 1.0.2 [950] biology, bioinformatics
Parsnp 1.2, 1.5.0 [951] biology, phylogenetics
PartitionFinder 2.1.1, 2.1.1-20161205, 2.1.1.0 [952] biology,phylogenetics,evolution
PASA 2.0.2-r20150209, 2.0.2-r20151207, 2.2.0-r20171013 [953] biology, bioinformatics, genomics, ngs
PASTA 0.2.0, 20160616 [954] biology, sequence alignment
PATHd8 1.0 [955] biology, phylogenetics
PAUDA 1.0.1 [956] biology,bioinformatics,ngs,phylogenetics
PAUP 4.0a165, 4.0a166, 4.0b10 [957] inferring and interpreting phylogenetic trees
Pauvre 0.1.86 [958] biology, phylogenetics
PB-Assembly 0.0.6 [959] biology,bioinformatics,ngs,sequencing,pacbio
Pbalign 20160921, 20161221 [960] biology, bioinformatics
PBCCS 5.0.0 [961] phylogenetics
Pbcore 1.7.1 [962] biology,bioinformatics
PBGCpp 1.9.0 [963] phylogenetics
PBJelly 15.8.24 [964] biology,bioinformatics,ngs
Pbmm2 1.3.0 [965] phylogenetics
Pbrt 20181017 [966] phylogenetics
Pbsmrtpipe 0.63.0 [967] biology,API
Pbtranscript-tofu 20150317, 20160119 [968] biology, bioinformatics, ngs, pacbio
PCIT 2014 [969] Bioinformatics
PCRE 8.38, 8.39 [970] perl, library
PDA 1.0.3 [971] biology, phylogenetics
Pdb2pqr 2.1.0 [972] protein, modeling, pdb
Program Database Toolkit 3.20, 3.22, 3.24 [973] programming languages, development, performance analysis
PeakSplitter 1.0 [974] biology, bioinformatics, CHiP-Seq
PEAR 0.9.2 [975] biology, genomics, ngs
PECaller 1.0.0 [976] biology, NGS
PennCNV 1.0.5 [977] phylogenetics
Perl 5.16.0, 5.20.0, 5.24.1 [978] programming,scripting,language
PerM 0.4.0 [979] biology,bioinformatics,ngs,mapping
PETSc 3.8.1, 3.8.3, 3.8.4 [980] Math, Numerical Solvers
PfamScan 1.3, 1.5 [981] biology, genome
PGDSpider 2.0.9.0 [982] biology, NGS
Pggb 20201106 [983] phylogenetics
PhaME 1.0.3 [984] phylogenetics
PHASE 2.1.1 [985] phylogenetics
PHAST 1.4, 1.5 [986] biology,phylogeny
Phenix 1.10.2155, 1.17.1, 1.8.1069 [987] crystallography
PHI 3.1.1, 3.1.2b [988] Calculations
PhiSpy 3.2 [989] phylogenetics
PHITS 2.76, 2.82, 2.84 [990] Physics
PHLAWD 20170427 [991] biology, phylogenetics
PhotoScan 1.4.1, 1.4.5 [992] Image Processing
Photutils 0.5 [993] astronomy, photometry
PHYLIP 3.696 [994] biology,phylogenetics
PhyloBayes 3.3f [995] biology,bioinformatics,phylogenetics
PhyloFlash 3.3b4 [996] phylogenetics
Phylonet 3.5.7 [997] biology, phylogenetics
PhyloParser 20180404 [998] phylogenetics
PhyloPhlAn2 0.41 [999] phylogenetics
PhyloSift 1.1 [1,000] biology, genomics, phylogenetics, taxonomy
Phyluce 20180727, 20190308, 20191015 [1,001] biology,bioinformatics,ngs,sequencing
PhyML 3.0, 3.1 [1,002] biology,bioinformatics,phylogenetics
Phynd 20200409 [1,003] phylogenetics
PHYUTILITY 2.7.1 [1,004] biology, bioinformatics
Phyx 20190403 [1,005] phylogenetics
PIA2 20180305 [1,006] biology, phylogenetics
Picard-tools 2.5.0, 2.9.0, 2.9.2 [1,007] biology, bioinformatics, ngs
PICRUSt 1.1.0, 1.1.3, 1.1.4 [1,008] biology, phylogenics
PICRUSt 2.3.0b [1,009] biology,phylogenics
Piggy 20171220 [1,010] biology, bioinformatics, ngs
Pigz 2.4 [1,011] Compression
PILON 1.22 [1,012] biology, bioinformatics, ngs, phylogenetics
Pindel 0.2.5b8 [1,013] biology, phylogenetics
Pipe-clip 1.1.0 [1,014] biology,NGS
PiPipes 1.5.0 [1,015] phylogenetics
Pipits 1.3.6, 1.4.0 [1,016] biology, sequencing
Piranha 1.2.1 [1,017] biology,phylogenetics
PIRS 2.0.2 [1,018] biolgoy, phylogenetics
Plasflow 1.1 [1,019] biology, phylogenetics
PLAST 1.0, 2.3.2 [1,020] biology,bioinformatics
Platanus 1.2.4 [1,021] phylogenetics
Platypus 0.8.1 [1,022] biology,bioinformatics,ngs
PLEK 1.2.2 [1,023] biology, phylogenetics
Plink 1.90b3, 1.90b3.39, 2.00a2 [1,024] biology,bioinformatics,genomics,phylogenetics
Plinkseq 0.10 [1,025] biology, bioinformatics, library
PolyGembler 1.0 [1,026] phylogenetics
PolyPHen 2.2.2.r405b [1,027] biology, genomics
Pomoxis 0.1.11, 0.2.5, 0.3.2 [1,028] biology, phylogenetics
PopLDdecay 3.40 [1,029] phylogenetics
Popoolation 1.2.2 [1,030] biology, phylogenetics
Porechop 0.2.4 [1,031] phylogenetics
PosiGene 20171113 [1,032] biology, phylogenetics
POTION 1.1.2 [1,033] phylogenetics
POV-Ray 3.7 [1,034] 3D Graphics
PRANK 170427, 20150803 [1,035] biology, bioinformatics, alignment
Predector 20201110 [1,036] phylogenetics
Preplot 14.0.2 []
Preseq 0.0.4 [1,037] biology, bioinformatics, ngs
PRICE 1.2 [1,038] biology, bioinformatics, ngs
Primer3 2.3.4 [1,039] biology,bioinformatics,genomics
Primus 1.8.0 [1,040] biology, phylogenetics
PRINSEQ 0.20.4 [1,041] biology, sequencing
PRINSEQ++ 1.2 [1,042] phylogenetics
ProbABEL 0.4.2, 0.4.3, 0.4.5 [1,043] Genomics, bioinformatics, gwas
Probalign 1.4 [1,044] biology, bioinformatics, ngs
Processing 3.4 [1,045] java, language, programming, visual
Prodigal 2.6.2, 2.6.3 [1,046] biology, genomics
Libproj4 4.9.2, 4.9.3, 5.1.0 [1,047] library, geospatial, cartography
Prokka 1.10, 1.12, 1.14.6 [1,048] biology, bioinformatics, genomics, assembly
Proovread 1.03rcl, 2.12, 2.13 [1,049] biology, genomics, ngs
ProSplign 1.0.0 [1,050] phylogenetics
Protege 5.1.0 [1,051] Ontology
Proteinortho 4.26, 5.11, 5.16 [1,052] biology, genomics
ProtExcluder 1.2 [1,053] biology, phylogenetics
Protobuf 2.5.0, 3.5.1 [1,054] google, libraries
PROVEAN 1.1.5 [1,055] biology, genomics
PsiCLASS 1.0.1 [1,056] phylogenetics
PSMC 0.6.5 [1,057] phylogenetics
PsRobot 1.2 [1,058] phylogenetics
Pufferfish 20200417 [1,059] phylogenetics
PureCLIP 1.1.1 [1,060] phylogenetics
PurgeDups 1.0.1 [1,061] phylogenetics
Pyani 0.2.10 [1,062] phylogenetics
PyBSASeq 20200623 [1,063] phylogenetics
PyCharm 2018.3 [1,064] editor, ide, programming, python
PyCogent 1.9 [1,065] biology, genomics
PyDeface 2.0.0 [1,066] mri, imaging
Pyfaidx 0.5.2 [1,067] biology, bioinformatics, ngs, sequencing
Pyfasta 0.5.2 [1,068] biology, phylogenetics
Pygot 20170518 [1,069] biology, phylogenetics
Pyhdf 0.9.0 [1,070] library, hdf4
PyPHLAWD 20180416, 20190414 [1,071] biology, phylogenetics
PyRosetta r56324 [1,072] biology,structure,modeling
Pyrpipe 0.0.3 [1,073] phylogenetics
Pysamstats 1.1.2 [1,074] phylogenetics
PyScaf 0.12a [1,075] Biology, NGS
PySLURM 18.08.04 [1,076] SLURM
Python 3.6.5, 3.7, 3.8 [1,077] programming languages, scripting, development
Python-core 3.6.5, 3.7, 3.8 [1,078] programming languages, scripting, development
Pytorch 1.3.0, 1.6.0 [1,079] library, math
PyVCF 0.6.0 [1,080] biology, phylogenetics
PyVista 0.26.1 [1,081] phylogenetics
Pyweka 0.3.18 [1,082] phylogenetics
Qcat 1.1.0 [1,083] phylogenetics
Qctool 2.0.1 [1,084] phylogenetics
QDD 3.1.2 [1,085] biology, genomics, ngs
QGIS 2.18.0, 3.14.0 [1,086] GIS
QIIME 1.9.1 [1,087] biology, bioinformatics, metagenomics
QIIME2 2019.6, 2019.7, 2019.8 [1,088] biology, bioinformatics, metagenomics
QMCPACK 3.4.0 [1,089] Library
QRNA 2.0.4 [1,090] phylogenetics
QT 4.8.3 [1,091] UI Framework
QTLtools 1.2 [1,092] phylogenetics
Quake 0.3 [1,093] biology, sequencing
QualiMap 2.1.2 [1,094] biology,sequence alignment
Quantas 1.0.4, 1.0.8, 1.0.9 [1,095] biology,bioinformatics,ngs
QuartetScores 1.0.0 [1,096] phylogenetics
QUAST 4.4, 5.0.0, 5.0.2 [1,097] biology, bioinformatics, ngs, sequencing, rna-seq
Quickmerge 0.3 [1,098] phylogenetics
Quickquartet 1.0.0 [1,099] biology,bioinformatics,ngs
QuorUM 1.0.0 [1,100] biology
Quota-alignment 20170905 [1,101] biology, phylogenetics
R-index 20190711 [1,102] phylogenetics
R2R 1.0.4 [1,103] biology, RNA
R8s 1.8, 1.81 [1,104] phylogenetics
RACA 0.9.1.1 [1,105] biology, ngs
Racon 1.4.10, 1.4.13, 20161013 [1,106] biolgoy, sequencing
RADICAL 0.2 [1,107] biology, bioinformatics, genomics
RaGOO 1.11 [1,108] phylogenetics
RagTag 1.0.0 [1,109] phylogenetics
Rainbow 2.0.4 [1,110] biology, sequencing
Rainbowfish 0.1.0 [1,111] phylogenetics
RAiSD 2.8 [1,112] phylogenetics
Randfold 2.0.1 [1,113] biology, RNA
RAPIDS.ai 0.14, 0.14.1 [1,114] Data Science
Rapidtide 1.9.0 [1,115] phylogenetics
RAPSearch 2.24 [1,116] biology, phylogenetics
Unrar 0.0.1, 4.20 [1,117] unarchiver, utility
Rascaf 1.0.2 [1,118] biology, bioinformatics
RAVE 2.1 [1,119] biology, phylogenetics
RAxML 8.2.10, 8.2.12, 8.2.8 [1,120] application, biology, philogenetics
RAxML-NG 0.7.0b, 0.8.0b, 0.9.0 [1,121] phylogenetics
Razers3 3.5.7 [1,122] biology, phylogenetics
Rcorrector 1.0.2 [1,123] biology, phylogenetics
RDnaTools 0.1.3 [1,124] phylogenetics
READemption 1.0.0 [1,125] phylogenetics
REAPR 1.0.18 [1,126] biology,bioinformatics,assembly
Rebaler 0.2.0 [1,127] phylogenetics
Recon 1.08 [1,128] biology,sequencing
Recycler 0.62 [1,129] biology, bioinformatics
Redis 2.8.13, 2.8.19 [1,130] daemon, data, server
Redundans 0.14a [1,131] biology, phylogenetics
ReFrame 3.2 [1,132] hpc, internal
Regtools 0.4.0 [1,133] biolgoy, RNA-seq
RELION 3.0.2, 3.0b, 3.1.0 [1,134] biology, imaging
RelocaTE2 2.0.1 [1,135] phylogenetics
REMORA 1.8.2, 1.8.3 [1,136] System, profiler
REPdenovo 20170222 [1,137] biology, phylogenetics
RepeatAnalysis 0.10.0, 0.12.2 [] biology, phylogenetics
RepeatExplorer 20150506, 20180517 [1,138] biology, bioinformatics, ngs
RepeatMasker 4.0.3, 4.0.5, 4.0.9 [1,139] biology,bioinformatics
RepeatModeler 1.0.8, 2.0 [1,140] biology,bioinformatics
Repeatscout 1.0.5 [1,141] biology
RepeatSeq 0.8.2 [1,142] phylogenetics
Reptile 1.1 [1,143] biology,NGS,error correction
Resistome 20170111 [1,144] phylogenetics
RevBayes 1.0.3, 1.0.7, 1.0.9 [1,145] biology, phylogenetics
RFMIX 2.03 [1,146] phylogenetics
RGI 4.2.2 [1,147] phylogenetics
RGIS 20180211, 20180814 [1,148] RiverGIS
RHash 1.3.3 [1,149] GNU
RiboCode 1.2.11 [1,150] phylogenetics
RiboPicker 0.4.3 [1,151] biology,sequence
RiboTaper 1.3.1a [1,152] phylogenetics
RIGERJ 2.0.2 [1,153] phylogenetics
Rmats2sashimiplot 2.0.3 [1,154] phylogenetics
Rmpi 0.6.9 [1,155] statistics, R, mpi
RNAhybrid 2.1.1 [1,156] biology, bioinformatics, genomics
RNAmmer 1.2 [1,157] biology, RNA-seq
RnaQUAST 1.5.1 [1,158] biology,bioinformatics,ngs,sequencing,rna-seq
RNAsalsa 0.8.1 [1,159] biology, phylogenetics
Rnaseqlib 20150721 [1,160] biology, phylogenetics, RNA-seq
RDnaTools 0.1.3 [1,161] phylogenetics
Roary 3.12.0, 3.4.1 [1,162] biology,genomics
ROOT 5.34.17, 6.0, 6.06.02 [1,163] Data Analysis
ROOTPy 20160323 [1,164] Data Analysis
Rosetta 2014wk4, 2019.35.60890 [1,165] biology,structure,modeling
Rrnaselector 1.0 [1,166] biology, sequencing
RSEG 0.4.8 [1,167] biology, bioinformatics, genomics
RSEM 1.2.31, 1.2.7, 1.3.3 [1,168] biology,bioinformatics,ngs,sequencing
RSeQC 2.6.4, 3.0.0 [1,169] biology,ngs,rna-seq
RStudio 1.1.453, 1.2.1335, 1.3.959 [1,170] statistics
RTGTools 3.7.1 [1,171] biology, NGS
Ruby 2.5.1 [1,172] programming,scripting,language
Rust 1.31.0 [1,173] programming
Sabre 1.0 [1,174] phylogenetics
Saffrontree 0.1.2 [1,175] phylogenetics
Sailfish 0.6.3 [1,176] biology,genomics,ngs,rna-seq
Salmon 0.6.0, 0.7.2, 1.1.0 [1,177] biology, RNA-seq
SALSA 20171009, 20191001 [1,178] biology, ngs, pacbio
Sambamba 0.6.3, 0.6.6, 0.6.9 [1,179] Biology, NGS
Samblaster 0.1.14, 0.1.24 [1,180] biology,bioinformatics,ngs,sequencing
SAMStat 1.08 [1,181] biology,bioinformatics,ngs,sequencing
Samtools 1.7, 1.8, 1.9 [1,182] biology,bioinformatics,ngs,sequencing
DS9 7.5, 8.0.1 [1,183] Imaging
SAS 9.3, 9.4 [1,184] statistics, data analysis
Sate 2.2.7 [1,185] biology, bioinformatics, phylogenetics
Satsuma 3.0 [1,186] phylogenetics
Satsuma2 20161123, 3.1 [1,187] phylogenetics
Scala 2.11.5 [1,188] programming, language, java
Scalablast 2.4.53 [1,189] application, biology, genomics
ScaLAPACK 2.0.2 [1,190] programming,library
Scalpel 0.1.1, 0.5.3 [1,191] Biology, NGS
Schrodinger Suite 2017, 2017-2, 2019-3 [1,192] Computational Chemistry, Molecular Dynamics
Scipion 1.2 [1,193] Image Processing
Scoary 1.6.10 [1,194] biology, bioinformatics, genomics
Scons 2.5.1, 3.1.2 [1,195] Programming
SCRATCH-1D 1.0 [1,196] biology, bioinformatics, ngs
Screen 4.7.0, 4.8.0 [1,197] GNU, Terminal Multiplerxer
SCRIPTURE 20101211 [1,198] biology, bioinformatics, genomics
Scythe 0.991 [1,199] Biology, NGS
Sdsl 2.1.1 [1,200] library, c++
SeCaPr 1.1.12 [1,201] phylogenetics
Segemehl 0.1.9, 0.3.4 [1,202] biology,bioinformatics,ngs,sequencing
SEPP 20160614 [1,203] biology, phylogenetics
Seq-Gen 1.3.3 [1,204] biology,phylogenetics
Seq_crumbs 20150120 [1,205] biology, sequence, genomics, utilities
SeqKit 0.10.2, 0.8.0 [1,206] biology, phylogenetics
SeqMap 1.0.13 [1,207] biology,bioinformatics,sequence,ngs
SEQPower 1.1.1 [1,208] Genomics, bioinformatics, phylogenetics
SeqPrep 0.5, 1.1 [1,209] biology,bioinformatics,ngs,sequencing
Seqtk 1.3, 20140729 [1,210] Bioinformatics, Genomics, NGS
SEQuel 1.0.1 [1,211] biology,bioinformatics,ngs
SequelQC 1.1.0 [1,212] phylogenetics
Seqwish 20190509 [1,213] phylogenetics
SeqyClean 1.8.10 [1,214] biology,bioinformatics,ngs,sequencing
SEXCMD 20170823 [1,215] biology, phylogenetics
SExtractor 2.19.5 [1,216] Astronomy
SHAPEIT 2.12, 2.5 [1,217] biology,SNP
SHAPE-MaP 1.2 [1,218] biology, phylogenetics
ShapeMapper 2.1.3, 2.1.5 [1,219] biology, phylogenetics
SHARCGS 1.2.11 [1,220] biology, NGS, de novo assembly
Shasta 0.1.0 [1,221] phylogenetics
SHEsisPlus 1.0, 1.01 [1,222] biology, genetics
Shogun 6.1.3 [1,223] phylogenetics
Shortbred 0.9.4 [1,224] phylogenetics
SHRiMP 2.2.3 [1,225] biology, genomics, ngs
Shustring 2.6 [1,226] biology, sequencing
SICER 1.1 [1,227] biology, ChIP-Seq
Sickle 1.200, 1.33 [1,228] biology, bioinformatics, ngs
Siesta 3.2, 4.1b2, 4.1b3 [1,229] Chemistry
SIFT 4.0.3b [1,230] biology,bioinformatics,genomics
SignalP 4.1c, 5.0b [1,231] biology, phylogenetics
SiLiX 1.2.11 [1,232] phylogenetics
Silo 4.7 [1,233] io,library
Sim4 20121010 [1,234] biology, bioinformatics, genomics
SimNIBS 3.2.1 [1,235] phylogenetics
SimSeq 4.12.2011 [1,236] biology, bioinformatics, ngs, phylogenetics
SInC 20140120 [1,237] biology, phylogenetics
Sine_scan 1.1.1 [1,238] phylogenetics
Singularity 3.5.2, 3.6.1 [1,239] Containers
SIPeS 2.0 [1,240] biology, bioinformatics, ChIP-Seq
Sisl 0.8.3 [1,241] Physics, Tight-binding
SKESA 2.3.0 [1,242] phylogenetics
Slamdunk 0.4.1, 0.4.2 [1,243] phylogenetics
Slicer 4.10.2, 4.3.1 [1,244] biology,bioinformatics,neuroscience,imaging
Slurm-drmaa 1.1.1.20, 1.2.1.19, 1.2.1.20 [1,245] libraries, slurm, api, drmaa
Smalt 0.7.6 [1,246] application, biology, phylogenetics
SMARTdenovo 20180219 [1,247] biology, phylogenetics
Smartie-sv 20180308 [1,248] phylogenetics
Smetana 1.1.0 [1,249] phylogenetics
SMRT-SV 2.0.0 [1,250] biology, bioinformatics, ngs
SMS 1.7 [1,251] biology, bioinformatics
Snakemake 5.17.0 [1,252] biology, bioinformatics, workflow
SNAP 0.15.4, 20100728 [1,253] biology,bioinformatics,sequencing
SPANE-pooled 20130407 [1,254] biology,SNP
Snappy 1.1.7 [1,255] library
SNeP 1.1 [1,256] biology,phylogenetics
Sniffles 1.0.11, 1.0.6, 1.0.8 [1,257] phylogenetics
Snippy 20160419 [1,258] biology, phylogenetics
SNP-Pipeline 1.0.1 [1,259] biology, phylogenics
SNP-sites 2.0.3 [1,260] biology, SNP
SnpEff 4.3r, 4.3t, 5.0 [1,261] biology,bioinformatics,variant annotation
SNPGenie 20190620 [1,262] phylogenetics
SNPhylo 20140701 [1,263] biology,phylogenetics
SNPTEST 2.5.2 [1,264] phylogenetics
SOAPaligner 2.21 [1,265] phylogenetics
SOAPdenovo 1.05, 2.04 [1,266] biology,ngs
SOAPdenovo-Trans 1.01, 1.03 [1,267] biology,ngs
SOAPec 2.03 [1,268] biology, phylogenetics
SOAPnuke 2.1.0 [1,269] phylogenetics
SOAPsplice 1.10 [1,270] biology,ngs
SOLAR 8.4.2 [1,271] phylogenetics
SortaDate 20190705 [1,272] phylogenetics
SortMeRNA 2.1, 4.0 [1,273] biology, sequencing, NGS
SourceTracker2 2.0.1 [1,274] phylogenetics
Sourmash 2.0.1 [1,275] phylogenetics
SoX 14.4.2 [1,276] phylogenetics
SPAdes 3.14.1, 3.7.1, 3.8.0 [1,277] biology,bioinformatics,ngs
SparCC 201608 [1,278] Microbial Ecology
Spark 2.2.0 [1,279] spark, hadoop
Sparsehash 2.0.3 [1,280] Google, API
SPARTA+ 2.60 [1,281] Chemistry
Spidey 20150922 [1,282] biology, genomics, bioinformatics
SplAdder 2.4.2 [1,283] phylogenetics
SpliceGrapher 0.2.5 [1,284] biology, sequencing
SpliceTrap 0.90.5 [1,285] biology, bioinformatics, genomics, NGS
SPM 12b, 8, 8r5236 [1,286] biology,bioinformatics,matlab
Spruceup 2019.2.3 [1,287] phylogenetics
Sputnik 1.0 [1,288] biology,bioinformatics,repeats
Spyder 4.1.0, 4.1.4 [1,289] ide, editor, programming, scripting
SQANTI 1.2 [1,290] phylogenetics
SQANTI2 5.0 [1,291] phylogenetics
SQANTI3 0.1 [1,292] phylogenetics
SQL Developer 4.1.2 [1,293] programming, oracle, sql
SQLite 3.33.0, 3.8.8.2 [1,294] database
SRA 2.10.3, 2.10.4, 2.10.8 [1,295] biology,bioinformatics,sra
SSPACE 2.0, 3.0 [1,296] biology,bioinformatics,ngs
Ssr_pipeline 0.951 [1,297] biology, DNA sequencing,
Stacks 2.41, 2.53, 20190403 [1,298] biology, bioinformatics, genomics, ngs
Staden 1.14.6 [1,299] biology, phylogenetics
Stampy 1.0.31 [1,300] biology, bioinformatics, sequencing
Staphb-toolkit 1.2.0 [1,301] biology
Rnastar 2.7.3a, 2.7.5c, 2.7.6a [1,302] biology, ngs, rna-seq
STAR-Fusion 1.1.0, 1.3.1 [1,303] biology, transcriptome
STAR-CCM+ 14.04.011, 15.02.009, 8.06 [1,304] Mechanical Engineering
Starseqr 0.6.7 [1,305] phylogenetics
Stata 10.1, 13 [1,306] Statistics
Statsmodels 0.8.0 [1,307] biology, library, math
StringMLST 0.4 [1,308] biology, bioinformatics, CHiP-Seq
Stringtie 1.3.4d, 2.0.4, 2.1.3b [1,309] biology,bioinformatics,ngs,sequencing,alignment
Structure 2.3.3, 2.3.4 [1,310] biology,bioinformatics,population genetics
SU2 7.0.6 [1,311] phylogenetics
Subread 1.5.3, 1.6.2, 2.0.0 [1,312] biology, sequencing, SNP
Subversion 1.9.7 [1,313] Revision Control
SUMO 1.2.0 [1,314] phylogenetics
SUNDIALS 2.3.0, 2.5.0, 3.0.0 [1,315] Math, Numerical Solvers
Supercell 20170602 [1,316] biology, NGS
SuperCRUNCH 1.2.1 [1,317] phylogenetics
Supernova 1.2.1, 2.0.0, 2.1.1 [1,318] biology, phylogenetics, ngs
SUPPA 2.3 [1,319] phylogenetics
SURVIVOR 1.0.6 [1,320] phylogenetics
SVDetect 0.8b [1,321] biology,ngs,genomics
Swarm 1.2.11 [1,322] Data Analysis
Sweed 3.3.2 [1,323] biology, phylogenetics
SWIG 2.0.9, 3.0.12, 3.0.8 [1,324] library, development, C++, python
SwitchSeq 20140907 [1,325] biology,bioinformatics,genomics
SWSC-EN 1.0.0 [1,326] phylogenetics
TACO 0.7.3 [1,327] phylogenetics
Taiyaki 5.0.1 [1,328] phylogenetics
Talesf 20160814 [1,329] phylogenetics
Tandem-Genotypes 1.4.0 [1,330] phylogenetics
Tantan 13 [1,331] ngs, genomics
Tapir 20160825 [1,332] biology, phylogenetics
TAPIS 1.2.1 [1,333] biology, sequencing
TASSEL 5.0, 5.2.20, 5.2.29 [1,334] biology,bioinformatics,genomics,wga
Tuning Analysis Utilities 2.23, 2.26, 2.26.3 [1,335] library, profiling and optimization
Tax4Fun 0.3.1 [1,336] phylogenetics
TaxMaps 0.1 [1,337] biology, phylogenetics, taxonomy
Taxtastic 0.5.7 [1,338] biology, taxonomy
Tbb 2017_20161128 [1,339] library
Tcllib 1.18 [1,340] library
Tcoffee 10.00.r1613, 9.03.r1318 [1,341] Bioinformatics
Tecplot 360 EX 2015R1 [1,342] plotting, animation, cfd, simulations
TEMP 20170731 [1,343] phylogenetics
TensorFlow 2.0, 2.1.0, 2.3.1 [1,344] library, math
TESS 2.3.1 [1,345] biology, bioinformatics, genomics, markov
Test 1.0 [1,346] shell
TetGen 1.5.0 [1,347] tetrahedral meshes
TEToolkit 1.5.1 [1,348] biology, bioinformatics, sequencing
TEtools 20180213 [1,349] biology, phylogenetics
Texlive 20191127, 2020 [1,350] formatting, typesetting, document preparataion
TGICL 2.1 [1,351] biology,bioinformatics,ngs,sequencing
Theano 1.0.4 [1,352] library, math, gpu
Tiff 3.8.0, 4.0.10 [1,353] imaging
Tigmint 1.1.2 [1,354] phylogenetics
Tmux 2.4, 2.9 [1,355] GNU
TNTBLAST 2.04 [1,356] Biology
ToFU2 20180629, v17 [1,357] biology, bioinformatics, ngs, iso-seq
Toil 3.3.0, 3.3.3 [1,358] biology, bioinformatics
Tombo 1.4, 1.5 [1,359] biology, genomics, ngs
Tophat 2.1.0, 2.1.1, 2.1.2 [1,360] biology,bioinformatics,ngs,sequencing
Torch-geometric 1.3.2 [1,361] phylogenetics
TotalView 8.12 [1,362] Parallel Computing
TPMcalculator 0.0.3 [1,363] phylogenetics
TPP 4.7.0, 4.7.1, 5.0.0 [1,364] biology, chemistry, nmr
TraCeR 0.5.1, 20160519 [1,365] Biology, Phylogenetics
TrackTools 2011 [1,366] Software
TrackVis/DTK 0.5.2.2, 0.6.0.1 [1,367] biology,bioinformatics,neuroscience,imaging
Tracula 5.3.2014_05_26 [1,368] biology,bioinformatics,neuroscience,imaging
TraitRate 1.1 [1,369] biology, evolution
Trans-ABySS 2.0.1 [1,370] biology, phylogenetics
TransDecoder 5.3.0, 5.4.0, 5.5.0 [1,371] biology, ngs
TRANSIT 2.5.2 [1,372] phylogenetics
Transrate 1.0.1 [1,373] biology,assembly
TransVar 2.3.3 [1,374] biology, bioinformatics, phylogenetics
TreeBreaker 20160621 [1,375] biology, phylogenetics
TreeMix 1.12 [1,376] biology, phylogenetics
TreePL 20150305 [1,377] biology, bioinformatics, phylogenetics
TREEPUZZLE 5.3 [1,378] biology, phylogenetics
TreeShrink 1.3.1, 1.3.2 [1,379] phylogenetics
TreeTime 0.7.5 [1,380] phylogenetics
Trelis 16.3 [1,381] Geometry
TRF 4.04 [1,382] biology,bioinformatics,genomics
Trilinos 12.12.1, 12.18.1, 12.6.4 [1,383] Mathematical Algorithms
Trim Galore 0.4.4, 0.5.0, 0.6.5 [1,384] biology,bioinformatics,ngs
TrimAl 1.2 [1,385] biology,genomics,sequence alignment
TriMetAss 1.1 [1,386] biology,bioinformatics,ngs
Trimmomatic 0.33, 0.36, 0.39 [1,387] biology,bioinformatics,ngs
Trinity r20130225, r20131110, r20140413 [1,388] biology,bioinformatics,ngs,sequencing,rna-seq
Trinotate 3.0.1, 3.2.0 [1,389] biology
TRIPLEC 1.0 [1,390] biology, bioinformatics
TRNAscan-Se 1.23 [1,391] biology,bioinformatics,ngs
TURBOMOLE 7.4.1 [1,392] Quantum Chemistry
TWINSCAN 4.1.2 [1,393] biology,genomics
Ubuntu 20.04 [1,394] Ubuntu Linux
Kent 20141111, 20180816, 20200320 [1,395] Genomics, bioinformatics
Ucsc-maskoutfa 377 [1,396] phylogenetics
UCX 1.9.0 [1,397] parallel programming, development, library
UDUNITS 2.2.17 [1,398] library, data, units
UFITS 0.7.2 [1,399] biology,bioinformatics,ngs
Ufraw 0.22 [1,400] data mining
Ugtm 1.1.6 [1,401] statistics, modeling
Umi-tools 0.5.5 [1,402] phylogenetics
UNAFold 3.8 [1,403] biology, genome, RNA, folding
Unanimity 20171108, 3.4.1 [1,404] programming,library,cpp
Unicycler 0.4.8 [1,405] phylogenetics
Uproc 1.2.0 [1,406] biology, genome
USEARCH 9.0.2132, 9.1.13, 9.2.64 [1,407] biology,bioinformatics,alignment,sequence analysis
Valgrind 3.11.0, 3.15.0, 3.8.1 [1,408] Computer Programming
Valouev 20160325 [1,409] Biology, Phylogenetics
VAMPIR 9.1 [1,410] High Performance Computing
VarDictJava 1.6.0, 20160521, 20170531 [1,411] biology, phylogenetics
VAIR 0.7.0 [1,412] Geospatial Data Modeling
Varnorm 0.21 [1,413] biology, bioinformatics
VarScan 2.3.6 [1,414] biology,bioinformatics,ngs
VarSim 0.8.4, 0.8.6 [1,415] phylogenetics
VarSimLab 20180220, 20180921 [1,416] biology, simulation, genomics
Vasp 5.4.1, 5.4.4 [1,417] Quantum Chemistry
VAST-TOOLS 20150506 [1,418] biology, rna-seq, ngs, splicing
VCF-kit 0.2.6 [1,419] phylogenetics
Vcfanno 0.2.8 [1,420] biology, phylogenetics
Vcflib 1.0.1, 20150313 [1,421] biology,bioinformatics,genomics
Vcftools 0.1.15, 0.1.16, 0.1.9 [1,422] biology,bioinformatics,genomics
Vcf-validator 0.6 [1,423] biology, phylogenetics
Vcontact 20190512 [1,424] phylogenetics
VDJtools 1.1.7, 1.2.1 [1,425] biolgoy, phylogenetics
Velvet 1.2.10, 1.2.10-long [1,426] computational biology, genomics
VEP 83, 88.8, 92 [1,427] biology, genomics, ngs
Vg 1.20.0 [1,428] phylogenetics
Vidjil 201703 [1,429] biology, genomics
ViennaRNA 2.2.6 [1,430] biology, RNA-seq
ViewBS 0.1.9 [1,431] phylogenetics
Vim 8.1.1566 [1,432] programming,scripting,language
VirSorter 1.0.3 [1,433] biology, phylogenetics
VirtualCell 7.1 [1,434] phylogenetics
VIRULIGN 1.0.2 [1,435] phylogenetics
VirusDetect 1.7 [1,436] phylogenetics
VirusFinder 2.0 [1,437] biology, phylogenetics
Visit 2.12.2, 2.13.3, 3.0.1 [1,438] Visualization, Animation and Analysis
VISPR 0.4.14 [1,439] phylogenetics
VMD 1.9.1, 1.9.3 [1,440] visualization, animation, 3d
V-Phaser 02112013 [1,441] biology, phylogenetics
Vscode 1.38.1 [1,442] ide, editor, programming, scripting
VSearch 20151022, 20161209-2.3.4 [1,443] biology,NGS
Vt 0.57721, 20140903, 20160129 [1,444] biology, genomics
VTC 0.9.3 [1,445] biology, bioinformatics, VCF
VTK 7.1.0, 7.1.1, 8.2.0 [1,446] biology,bioinformatics,neuroscience,imaging
VULCAN 6.3.1 [1,447] Fluid Dynamics
W2rap-contigger 20161124 [1,448] biology, genomics
Wannier90 1.2, 2.1.0 [1,449] Computational Physics
WDSSII 5 [1,450] Weather, Meteorology
WebLogo 2.8.2, 3.3, 3.5.0 [1,451] biology,bioinformatics,sequence,graphics
Weka 3.8 [1,452] statistics,machine learning
WEVOTE 1.5.0, 1.8.0 [1,453] biology, phylogenetics
WGS Assembler 8.3rc1.r4638, 8.3rc2 [1,454] biology, bioinformatics, genomics
Wgsim 0.3.1-r13 [1,455] biology, phylogenetics
WHAMM 0.14a [1,456] biology, phylogenetics
Wine 1.6.2, 1.9.6, 4.0.0 [1,457] windows, emulator
Wise 2.2.0, 2.4.1 [1,458] biology, genome
WIsH 1.0 [1,459] phylogenetics
WoLFPSort 0.2 [1,460] phylogenetics
WOMBAT 20180118 [1,461] biology, phylogenetics
Wtdbg 2.1, 2.4 [1,462] phylogenetics
Wub 0.2.0, 0.4.0 [1,463] biology, genomics, ngs
WU BLAST 2.0 [1,464] biology, bioinformatics
Xander 20151222 [1,465] biology, phylogenetics
Xapian 1.4.4 [1,466] library
XCrySDen 1.5.60 [1,467] Computational Material Science
Xerces 3.1.4 [1,468] phylogenetics
Xpclr 1.1.1 [1,469] phylogenetics
Xterm 1.1 [1,470] terminal emulator
XWAS 3.0 [1,471] phylogenetics
XY-Meta 20200413 [1,472] phylogenetics
XZ 5.2.2 [1,473] compression, library
YAHA 0.1.82 [1,474] biology, ngs
YASM 1.3.0 [1,475] Computer Programming
YASRA 2.33 [1,476] biology,bioinformatics,ngs,sequencing
Zagros 1.0.0 [1,477] biology,phylogenetics
ZEO++ 0.2.2 [1,478] chemistry
Zorro 2.2 [1,479] biology, sequencing
ZUMIS 2.6.0 [1,480] biology, bioinformatics, ngs, sequencing