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
AAFTF 0.2.5 [4] Biology, Pipeline, Assembly
ABRicate 1.0.1 [5] Phylogenetics
ABruijn 1.0 [6] Biology, assembly, ngs, pacbio, nanopore
ABySS 1.5.2, 2.1.0, 2.2.5 [7] Biology, de novo
AdapterRemoval 2.2.2 [8] Phylogenetics
ADFRsuite 1.0 [9] Sequencing, Bioinformatics
ADMB 11.5, 12.0 [10] Math, modeling, optimization
AdmixTools 20150311, 7.0.2 [11] Biology, bioinformatics, genomics, ngs
ADMIXTURE 1.23, 1.3.0 [12] Biology, bioinformatics, genomics, ngs
AEGeAn 0.14.0, 0.16.0 [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
Albacore 2.3.1, 2.3.3 [18] Biology, Phylogenetics
Albumentations 1.0.3 [19] AI, Vision, Imaging
Alder 1.03 [20] biology, genomics, genetics
ALFA 1.1.1 [21] Phylogenetics
alienhunter 1.7 [22] Biology, bioinformatics, wgs
AliStat 1.12 [23] Phylogenetics
allhic 0.9.8 [24] Phylogenomics, biology
ALLMAPS 20180117 [25] Biology, phylogenetics
ALLPATHS-LG 42316, 44837, 49232 [26] Biology,bioinformatics,ngs
AlphaFold 2.0.0, 2.1.2, 2.2.0 [27] Protein, structure, ml, dl
Alphaimpute 0.0.2, 1.9.8.2, 1.9.8.3 [28] Phylogenetics
AltAnalyze 2.1.0 [29] Biology, genomics
AMAS 1.0 [30] Phylogenetics
AMBER 16.0, 18, 20 [31] Computational Chemistry, Molecular Dynamics
AMICO 1.0.1 [32] Library, imaging, optimization
AMOS 3.1.0 [33] Biology,bioinformatics,genomics,assembly
AMP 0.6.1 [34] Phylogenetics
amPEPpy 1.0 [35] Phylogenetics
amphora2 20140305 [36] Biology, phylogenetics
AMPtk 1.2.4, 1.5.1 [37] Biology, bioinformatics, ngs
amptorch 20210313 [38] Phylogenetics
amrfinderplus 3.10.18 [39] Phylogenetics
AMRPlusPlus 20180508 [40] Phylogenetics
AMUSE 10.0, 13.1.0 [41] Astrophysics
ANGSD 0.933 [42] Biology, ngs
annocript 2.0 [43] Phylogenetics
AnnoTALE 1.4.1 [44] Phylogenetics
ANNOVAR 20130221, 20150322, 20191024 [45] Biology, bioinformatics, genomics
Ansible 2.5.5, 2.8.1 [46] Automation, deployment
ansysem 17.0, 2022r1 [47] Electromechanics
antiSMASH 4.1.0, 6.0.1 [48] Phylogenetics
ANTs 2.2.0, 2.3.4 [49] Biology, phylogenetics
anvio 6.1, 6.2, 7.1 [50] Biology, microbial 'omics
Appreci8 20180530 [51] Biology, Genomics
Apptainer 1.0.3 [52] Containers
APT 1.15.0, 1.18.0, 1.20.5 [53] Biology, bioinformatics, genomics, microarray
ARC 1.1.4 [54] Biology,bioinformatics,ngs
Aria2 1.35.0 [55] Utility
ARKS 1.0.2 [56] Phylogenetics
Armadillo 7.900.0, 9.200.6, 9.900.4 [57] Library, C++, math
ARPACK 1.0 [58] Solve eigenvalue problems
ArrayFire 3.4.2 [59] Code Optimization
arriba 2.1.0 [60] Phylogenetics
ART 20160417, 20160605 [61] Phylogenetics
artemis 18.1.0 [62] Bioinformatics, biology
asap 2.0 [63] Visualization, Biology
asaq 1.0 [64] Alignment, Sequencing, Phylogenetics
ASE-ANI 20180712 [65] Biology, bioinformatics, genomics, ngs
ASHS 2.0 [66] Biology, mri
ASPECT 2.3.0 [67] Library
Assembly-stats 1.0.1 [68] Biology, sequencing, genomics
Assemblytics 1.2.1 [69] Phylogenetics
Assexon 20190814 [70] Phylogenetics
AStalavista 3.2, 4.0 [71] Biology, bioinformatics, genomics
aster 220718 [72] Biology, data, sequencing
ASTRAL 5.6.1, 5.6.2, 5.7.7 [73] Biology, bioinformatics, ngs, phylogenetics
ASTRID 2.2.1 [74] Phylogenetics
Astropy 2.0.8 [75] Biology, bioinformatics, phylogenetics
ATAT 3.23, 3.34 [76] Alloy Theory
ATLAS 3.10.1, 3.10.2, 3.11.17 [77] Library, data
Atom 1.57.0 [78] IDE
AtomEye 3 [79] Material Science
AtomMan 1.3.3 [80] Phylogenetics
aTRAM 2.2.0, 2.4.3 [81] Math
Augustus 3.3.2, 3.3.3, 3.4.0 [82] Biology,bioinformatics,genomics
Auto3DEM 4.05.2 [83] Image Reconstruction
AutoDock 4.2.6 [84] Biology
AutoDock-GPU 1.5.3 [85] Molecular Docking
Autometa 20190802 [86] Phylogenetics
automlsa2 0.8.1 [87] Phylogenetics, biology, phylogenomics
AWSCLI 2.2.30 [88] Utilities
azoo 1.3.1 [89] Phylogenetics
Badread 0.1.5 [90] Phylogenetics
bakta 1.3.3 [91] Phylogenomics, biology
BALi-Phy 3.4.1, 3.5.0 [92] Phylogenetics
BAM-matcher 20161021 [93] Phylogenetics
Bam-Readcount 20150616 [94] Biology, genomics
bamaddrg 20120326 [95] Phylogenetics
BamBam 1.0 [96] Biology, bioinformatics, genomics
bamm 2.5.0 [97] Phylogenetics
bamsnap 0.2.19 [98] Phylogenetics
Bamstats 20140602 [99] Biology,bioinformatics,ngs
Bamsurgeon 1.2 [100] Phylogenetics
bamtofastq 1.3.5 [101] Phylogenetics
Bamtools 2.4.1, 2.5.0, 2.5.1 [102] Biology,bioinformatics,ngs,sequencing
bamUtil 1.0.2 [103] Biology, bioinformatics, genomics
BAPS 6.0 [104] Biology, bioinformatics, genomics
Barrnap 0.7, 0.9 [105] Biology, RNA-Seq
Basemount 0.15.96 [106] Biology, DNA Sequencing
BatMeth2 20210720 [107] Biology, Genomics, Mapping
bax2bam 0.0.9 [108] Phylogenetics
BayArea 1.0.2 [109] Biology
BAYENV 2.0 [110] Biology, phylogenetics
BayesAss 3.0.4, 3.0.4.2 [111] Phylogenetics
BayeScan 2.1 [112] Biology, SNP
BayesR 20151016 [113] Biology, phylogenetics
BayesTraits 3.0.2 [114] Phylogenetics
baypass 2.1 [115] Biology, phylogenetics
BBMap 38.26, 38.44, 38.90 [116] Biology, alignment
bcftools 1.15, 1.3.1, 1.9 [117] Biology, bioinformatics, ngs
bcl2fastq 2.16.0.10, 2.20.0.422 [118] Biology, ngs, illumina
BDG-SeQuila 0.5.5 [119] Phylogenetics
BEAGLE 4.1, 5.0, 5.2 [120] Biology, genetics, genotyping
BEAR 20170209 [121] Biology, bioinformatics, metagenomics
BEAST 2.6.2, 2.6.3, 2.6.7 [122] Biology,phylogeny
BEAST2-XML 1.0.9 [123] Phylogenetics
BEDOPS 2.4.30 [124] Biology,bioinformatics,sequence,ngs
BEDTools 2.29.1, 2.29.2, 2.30.0 [125] Biology,bioinformatics,ngs
Bertini 1.6 [126] Mathemetics
BERTopic 0.7, 0.8.1 [127] Machine Learning
BESST 2.2.4 [128] Biology, NGS
BFAST 0.7.0 [129] Biology,bioinformatics,ngs
bgenix 1.1.7 [130] Data, genomics
Bifrost 0.2, 1.0.3, 20200225 [131] Phylogenetics
BiG-SCAPE 1.1.2 [132] Biology, Genomics, Phylogenetics, Pipeline
BinPacker 1.0 [133] Biology, RNA-seq, sequence assembly
BinSanity 0.2.6.4 [134] Biology, genomics
Bioawk 1.0 [135] Phylogenetics
bioBakery 0.15.1, 1.8, 3.0.0 [136] Phylogenetics
Biodiverse 2.1 [137] Phylogenetics
Biolite 0.3.5.1 [138] Biology, bioinformatics, genomics, SNP
BIOM 2.1.5, 2.1.6 [139] Biology, genomics
BIOMART 1.4 [140] Biology,genomics
Biopieces 2.0 [141] Phylogenetics
BIRDS 1.0 [142] Fiji, plugin, imaging
Bismark 0.22.3, 0.7.4, 0.7.7 [143] Biology, bioinformatics, NGS
Blackfynn 0.2.7 [144] Data Mining
BLASR 20130815, 20161215 (5.3), 5.3.2 [145] Biology,bioinformatics,ngs
Blast2GO 2.5.0-20120705 [146] Biology,bioinformatics,gene ontology
Blast2GO CLI 1.3.3 [147] Biology, bioinformatics, gene ontology
BLAT 20121105, 20140318 [148] Genomics, bioinformatics
blender 2.73, 2.77, 3.0.1 [149] Graphics
blink 0.01 [150] Phylogenomics
Blitz 0.10 [151] Library
BlobTools 1.0, 2.2 [152] Phylogenetics
bloomfiltertrie 0.8.7 [153] Phylogenetics
BloomTree 0.3.5 [154] Data Mining
BLUPF90 20160604, 20180301, 20190531 [155] Biology, phylogenetics
BMGE 1.12 [156] Biology, genetics, phylogeny
bmtagger 3.101 [157] Phylogenomics, biology
BOLT-LMM 2.3.4 [158] Phylogenetics
BoltzTraP 1.2.5 [159] Physics
Boost 1.71.0, 1.75.0, 1.77.0 [160] Programming, library, cpp
booster 0.1.2 [161] Phylogenetics
Bowtie 1.1.1, 1.2.0, 1.2.3 [162] Biology,bioinformatics,ngs,sequencing
Bowtie2 2.3.5.1, 2.4.2, 2.4.5 [163] Biology,bioinformatics,ngs,sequencing
BoxCLI 2.9.0 [164] Storage, web, api
BPGA 1.2 [165] Biology, ngs
BPP 4.1.4, 4.3.8, 4.4.1 [166] Biology, phylogenetics
Bracken 1.0.0, 2.5 [167] Biology, phylogenetics
BrainIAK 0.11 [168] Imaging
braker 2.1.2, 2.1.5, 2.1.6 [169] Phylogenetics
BRANCH 1.8.1 [170] Biology,bioinformatics,ngs,mapping
BRATNextGen 20150505 [171] Biology, bioinformatics, genomics
BreakDancer 1.4.5 [172] Biology, phylogenetics
breakseq 2.2 [173] Biology, phylogenetics
Brewery 20191205 [174] Phylogenetics
Bridger 20141201 [175] NGS, Genomics, bioinformatics
BRIG 0.95 [176] Biology, genomics
BRM 0.3 [177] Phylogenetics
Bruker2nifti 1.0.4 [178] Phylogenetics
Bsmap 2.87 [179] Biology, bioinformatics, NGS
Bsoft 1.9.1 [180] Biology, image analysis
BSseeker2 2.1.0, 2.1.8 [181] Biology, phylogenetics
bubbleparse 20140314 [182] Biology, phylogenetics
BUCKy 1.4.4 [183] Biology, phylogenetics
BUSCO 4.0.6, 4.1.4, 5.2.0 [184] Biology, genomics
BWA 0.7.7, 0.7.8, 0.7.9a [185] Biology,bioinformatics,ngs
bwa-mem2 2.2.1 [186] Phylogenetics
BWA-PSSM 0.5.11 [187] Phylogenetics
bxh_xcede_tools 1.11.1 [188] Biology, bioinformatics
BYOBU 5.133, 5.92 [189] Shell, screen, terminal
bzip2 1.0.6 [190] Archiver, library
c-wap 20220624 [191] Sequencing, Genomics, Biology, SARS-CoV2
Cactus 2.0.3, 2.0.5 [192] Phylogenetics
CAFE 4.1, 5.0.0 [193] Phylogenetics
came 0.0.1 [194] Phylogenetics
Camino 20140723 [195] Biology,bioinformatics,neuroscience,imaging
CAMP 1.0.0 [196] Biology, Sequencing
Cantera 2.1.1 [197] Kinetics, thermodynamics
Canu 1.9, 2.0, 2.1 [198] Biology, sequencing
CANVAS 1.40.0.1613 [199] Phylogenetics
CAP3 20120705 [200] Biology,bioinformatics,assembly
Capnp 0.5.3 [201] C++
CARTA 2.0 [202] Image Processing
CASAVA 1.8.2 [203] Biology,bioinformatics,ngs
CASM 0.2.0 [204] Statistical Mechanics
CasOFFinder 2.4 [205] Phylogenetics
Catch 1.4.0 [206] Biology, Bioinformatics, Genomics, Sequencing
CAVIAR 20171218 [207] Biology, phylogenetics
CBGpipe 20190702 [208] Phylogenetics
CCMetagen 1.4.0 [209] Phylogenetics
CD-HIT 4.6, 4.6.4, 4.6.8 [210] Biology,genomics
CDBFasta 20181005 [211] Phylogenetics
CDNA_Cupcake 20180629, 22.0.0, 9.0.1 [212] Biology, bioinformatics, ngs, iso-seq
CDO 1.7.2rc3, 1.9.4 [213] Climate
CellProfiler 3.1.9, 4.1.3 [214] Phylogenetics
CellRanger 6.0.1, 6.1.2, 7.0.0 [215] Biology, bioinformatics, ngs, rna-seq
CellRanger-ARC 2.0.1 [216] Biology, bioinformatics, ngs, rna-seq
CellRanger-ATAC 1.2.0 [217] Biology, bioinformatics, ngs, rna-seq
CellRanger-DNA 1.0.0, 1.1.0 [218] Biology, bioinformatics, ngs, rna-seq, 10xgenomics
Centrifuge 1.0.3, 1.0.4b [219] Biology, phylogenetics
CFITSIO 3.370 [220] Library, C
CGAL 4.10, 4.9, 5.02 [221] Library, math
CGATools 1.6.0.43 [222] Biology, bioinformatics, ngs
cgmaptools 0.1.1, 0.1.2 [223] Phylogenetics
CGView 1.0.2 [224] Phylogenetics
CHARMM 36a3, 43b2 [225] Chemistry, simulation
ChartDirector 5.1.0 [226] Library, data
CheckM 1.0.4, 1.0.7, 1.1.2 [227] Biology, genomics
Chimera 1.12 [228] Biology, bioinformatics, modeling
Chipyard 1.0 [229] Hardware, design
Chromeister 1.5a [230] Biology, genomics
ChromEvol 2.0 [231] Biology, NGS
CIMS 4.1.2 [232] Biology,genomics
CIRCexplorer 1.1.10 [233] Biology, bioinformatics, rna-seq
CIRCexplorer2 2.3.5, 2.3.8 [234] Phylogenetics
Circlator 1.5.5 [235] Phylogenetics
Circleator 1.0.2 [236] Phylogenetics
circompara2 0.1.2.1 [237] Phylogenetics
Circos 0.63-pre11, 0.69-2, 0.69-9 [238] Biology,genomics,ngs
CIRI 2.0.6 [239] Phylogenetics
ciriquant 1.1.2 [240] Phylogenetics
cirspresso2 20220811 [241] Genomics, sequencing, biology
CisGenome 2.0 [242] Biology, bioinformatics, genomics
cisTEM 1.0.0 [243] Phylogenetics
Clairvoyante 1.02 [244] Phylogenetics
Clann 3.2.3 [245] Biology,bioinformatics,phylogentics
clara v4.0 [246] AI, machine learning
CLARK 1.2.2-b, 1.2.3 [247] Biology, genomics
CLHEP 2.2.0.1 [248] High Energy Physics
CLIFinder 4.1 [249] Biology, phylogenetics
ClinicaDL 1.0.4 [250] Biology, bioinformatics, neuroimaging, deep learning
clipkit 1.3.0 [251] Phylogenomics, biology
CLIPper 2.1.0 [252] Phylogenetics
CLIPSeqTools 0.1.7 [253] Biology, sequencing
ClonalFrame 1.1, 1.2 [254] Biology,bioinformatics,ngs,phylogenetics
ClonalFrameML 1.0, 1.11 [255] Biology, bioinformatics, ngs, phylogenetics
CloudCompare 2.10.3 [256] Visualization
Clover 2.0 [257] Biology, genomics, assembly
CLUMPP 1.1.2 [258] Biology, bioinformatics
ClustalO 1.2.0 [259] Biology, bioinformatics, alignment
ClustalW 2.1 [260] Biology,bioinformatics,alignment
cluster3 1.52a [261] Biology, genomics
Clview 20130402 [262] Biology, bioinformatics
CMake 3.19.1, 3.21.3 [263] Software Development
CMS 20170518 [264] Biology
CMWP 140518 [265] Biology, genomics
CNCI 20180305 [266] Phylogenetics
CNSpipeline 20170827 [267] Phylogenetics
CNV-Seq 20110715, 20140812 [268] Biology,bioinformatics,genomics
CNV-Sim 0.9.2 [269] Biology, phylogenetics
CNVkit 0.9.6 [270] Phylogenetics
CNVnator 0.3.2 [271] Biology, genomics, CNV
cobra-tf 0.1 [272] Nuclear Engineering
CodonPhyML 20150303 [273] Phylogenetics
Coevol 1.3c, 1.4b, 1.6 [274] Bio,bioinformatics,phylogenetics
Cogent 2.1 [275] Biology, phylogenics
COLMAP 3.6 [276] Modeling
CoMap 1.4.1 [277] Bioinformatics, Genomics
Comp-D_MPI 1.0 [278] Statistics
Compacta 1.02 [279] Biology, Contig clustering
COMSOL 5.4.0 [280] General-purpose simulation software
Concaterpillar 1.8a [281] Phylogenetics
CONCOCT 1.1.0 [282] Biology, bioinformatics, genomics
Conda 4.10.3, 4.12.0 [283] Programming, development, packages
CONN 18a [284] MRI,fmri,matlab
CONNECT 20200614 [285] Phylogenetics
connectomemapper3 3.0.0-rc1 [286] Phylogenetics
ConPADE 1.0 [287] Phylogenetics
Conpair 20161010, 20180624 [288] Biology, phylogenetics
Consed 23.0, 25.0, 29.0 [289] Biology, bioinformatics, genomics
CONSEL 0.20 [290] Biology, phylogenetics
ContaVect 0.2 [291] Biology, phylogenetics
Convert3D 1.1.0 [292] Imaging, Data Conversion
Coot 0.9.5 [293] Modeling
Coreutils 8.23 [294] Software Tools
coreutils 8.28 [295] Software Tools
Corset 1.06 [296] Biology, NGS
Counterr 0.1 [297] Phylogenetics
covNMR 2014 [298] Biochemistry
cp2k 7.0.0 [299] Quantum Chemistry
CPAT 3.0.2 [300] Phylogenetics
cpc 2.0 [301] Phylogenetics
CPLEX 12.6.1, 12.6.2, 12.7 [302] Meteorology
Crass 1.0.1 [303] Biology, assembly
crisflash 1.2.0 [304] Phylogenetics
CRISP 20181122 [305] Phylogenetics
CRISPRanalyzer 1.50 [306] Biology,genomics,ngs
CRISPRCasFinder 4.2.17 [307] Phylogenetics
CrossMap 0.3.9, 0.6.3 [308] biology, genomics
crossmapper 1.1.1 [309] Phylogenetics
Crux 1.40 [310] Biology, mass-spectroscopy
CryptoMiniSat 5.0.1 [311] SAT
csvtk 0.23.0 [312] Bioinformatics
ctk 1.1.4 [313] Biology, genomics
CUBE 4.4 [314] Library,c,math
CUDA 11.0.207, 11.1.0, 11.4.3 [315] Programming, library, graphics, runtime
Cufflinks 2.1.1, 2.2.1, 2.2.1.1 [316] Biology,bioinformatics,ngs,sequencing
cupy 8.3.0 [317] Phylogenetics
cutadapt 1.18, 2.8, 3.4 [318] Biology,bioinformatics,ngs
CutRunTools 20200104 [319] Phylogenetics
cvbio 3.0.0 [320] Phylogenetics
CViT 1.3 [321] Perl, library
CWLtool 1.0.20190906, 2.0.20200126, 3.0.20210124104916 [322] Workflow, scheduler
cx_oracle 8.3.0 [323] Oracle, Database, Software Tools
CycleGan 20201015 [324] Phylogenetics
Cytoscape 3.4.0 [325] Biology, bioinformatics, ngs, phylogenetics
d2go 20210702 [326] Machine Learning, dl, ai
dadi 2.1.1 [327] Phylogenetics
DAKOTA 6.15, 6.8, 6.8-gui [328] Computational Science and Engineering
DALIGNER 1.0 [329] Biology, phylogenetics
dammit 1.0rc2 [330] Biology, phylogenetics
DASTool 1.1.0, 1.1.2 [331] Biology, phylogenetics
datamash 1.1.0 [332] Math
DAWGPAWS 1.0 [333] Biology, phylogenetics
DCC 0.4.4 [334] Biology, bioinformatics, ngs
Dcmstack 0.6.2 [335] Biology, imaging
DCMTK 3.6.0 [336] Biology,neuroscience,imaging
dDocent 2.7.8 [337] Phylogenetics
DDSCAT 7.3.0 [338] Astrophysics
DDT 18.2, 20.0, 20.2 [339] Software Development
DealII 8.3.0, 9.3.1 [340] Library
DeconSeq 0.4.3 [341] Biology, phylogenetics
decontaMiner 1.4 [342] Genomics, biology
DECX 20180205 [343] Phylogenetics
DeepARG 1.0.1 [344] Phylogenetics
deepbgc 0.1.18 [345] Phylogenetics
Deepcoil 2.0.1 [346] Sequencing, bioinformatics
DeepGS 1.2 [347] Phylogenetics
DeepLabCut 2.0.7-gpu, 2.1.1, 2.2.1 [348] Phylogenetics
deepmicrobes 20200219 [349] Biology, genomics, metagenomics, ML
DeepMReye 01192022 [350] Library, bioinformatics
DeepPicker 20161102 [351] Particle Picking
deepTools 2.4.3, 3.1.1 [352] Biology, bioinformatics, NGS
deepvariant 1.4.0 [353] bioinformatics, biology, genomics, sequencing, machine learning
deFusion 20200305 [354] Phylogenetics
Delft3D 7545 [355] Physics
Delineate 1.2.2 [356] Biology, genomics
Delly 0.7.5, 0.7.7, 0.7.8 [357] Biology, phylogenetics
delucs 20220512 [358] sequencing, genomics, taxonomy, machine learning
DeNoGAP 1.0 [359] Biology, phylogenetics, ngs
DERIVA 1.5.0 [360] Phylogenetics
deSALT 1.5.6 [361] Biology, Genomics, Sequencing
Detectron2 0.4, 0.5, 0.6 [362] Library
DeTiN 1.7.5.9 [363] Particle NGS, genomics
DEXTRACTOR 1.0 [364] Biology, sequencing
Diamond 0.9.15, 0.9.34, 2.0.9 [365] Computational Biology, genomics
diCal2 2.2.0.1 [366] Biology, phylogenetics
diffReps 1.55.4 [367] Bioinformatics
DISCOVAR de novo 52488 [368] Biology, ngs, assembler
DiscoVista 20180906 [369] Phylogenetics
discvrseq 1.3.10 [370] Biology, Phylogenetics
Distruct 2.3 [371] Phylogenetics
DIYABC 1.0.4.43b, 2.0.3, 2.1.0 [372] Biology, phylogenetics
DL_POLY 1.9 [373] Molecular Dynamics
Dlib 19.19 [374] Phylogenetics
DNA Clust 3.0 [375] Biology,bioinformatics,genomics
DOCK 6.7, 6.8, 6.9 [376] Chemistry
DoGFinder 20201103 [377] Phylogenetics
DosageConvertor 1.0.3 [378] Biology
DOT 2.0 [379] Biology,bioinformatics,docking
Doxygen 1.8.3.1 [380] Programming, documentation
dragmap 1.2.1 [381] Phylogenetics, sequencing, biology
dragonflye 1.0.12 [382] Sequencing, Genomics
DRAP 1.91 [383] Biology, phylogenetics
dRep 2.3.2 [384] Phylogenetics
Dropseq 2.4.0 [385] Phylogenetics
DS9 7.5, 8.0.1 [386] Imaging
DScribe 1.2.0 [387] Machine Learning
dsistudio 20210123 [388] Machine Learning
DSK 2.1.0, 2.3.0 [389] Biology, NGS
DSRC 2.0 [390] Phylogenetics
DSSAT 4.6 [391] Agriculture
DSSP 2.2.1, 3.0.0 [392] Molecular Dynamics
DSuite 0.4, 0.4-r41 [393] Biology, Genomics
dtiprep 0.1.1 [394] Phylogenetics
duchamp 1.6.2 [395] Phylogenetics
dynamicDBG 20181003 [396] Phylogenetics
Dynare 4.4.3 [397] Math
ea-utils 1.04.807.18, 1.1.2.537 [398] Biology,bioinformatics,genomics,ngs
EAGLE 2.0 [399] Phylogenetics
eagle-rc 1.1.1 [400] Phylogenetics
ECE 1.2 [401] ECE
EDirect 10.7, 12.2 [402] Biology, phylogenetics
EDTA 1.9.6 [403] Phylogenetics
Edyeet 0.1, 0.3 [404] Phylogenetics
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [405] Biology,bioinformatics,matlab
eGene-MVN 0.1 [406] Biology, genetics
eggNOG-mapper 2.0.1, 2.1.6 [407] Phylogenetics
EGSnrc 2019 [408] Phylogenetics
EIGENSOFT 4.2, 5.0.1, 6.0.1 [409] Biology, bioinformatics
Elastix 4.9.0 [410] Phylogenetics
ELPA 2019.11.001 [411] Library,c,math
elPrep 4.1.4 [412] Phylogenetics
Emacs 27.2 [413] Programming, scripting, language
EMAN2 2.22, 2.31 [414] Image Processing
EMBOSS 6.6.0 [415] Biology,bioinformatics
Embree 3.6.1 [416] Ray, tracing, kernels
EMC 9.4.3 [417] Monte Carlo Simulations
EMMAX 20100307, 20120210 [418] Biology, NGS, mapping
EnergyPlus 9.3.0 [419] Simulation
Ensembl Tools 100, 80 [420] Biology, bioinformatics
enTAP 0.6.1.2, 20160416 [421] Biology, phylogenetics
EPACTS 3.2.6, 3.4.2, 3.4.2.hg38 [422] Biology, bioinformatics, genomics
EpiNano 1.2.0 [423] biology, NGS
epiteome 1.0 [424] Phylogenetics
epoch 4.7.3 [425] Astronomy,CCPP
eQTLA 1.1 [426] Biology, bioinformatics, genomics
eQtlBma 1.2.2, 1.3.0r20140820 [427] Biology, genotyping
Erpin 5.5.4 [428] Biology, phylogenetics
ESOM 1.1 [429] Biology, phylogenetics
ESPRESSO 6.2.1, 6.4.1, 7.0 [430] Quantum,modeling
ESPRIT 2009-nogap, 201102 [431] Biology,bioinformatics
ETE3 3.0.0, 3.1.1 [432] Biology, phylogenetics
EVidenceModeler 1.1.1 [433] Phylogenetics
Evigene 20180730, 20200520 [434] Phylogenetics
EvoLSTM 20220103 [435] Biology, Bioinformatics
ExaBayes 1.5 [436] Phylogenetics
Exonerate 2.2.0 [437] Biology,bioinformatics,genomics
ExpansionHunter 4.0.2 [438] Biology, genomics
ExpansionHunterDenovo 0.9.0 [439] Biology, genomics
export2graphlan 0.22 [440] Statistics, mapping, graphing
eXpress 1.3.1, 1.5.1 [441] Biology,bioinformatics,ngs
ezaai 1.0 [442] Biology, phylogenetics
face_morpher 20190630 [443] Phylogenetics
face_recognition 1.2.2 [444] Phylogenetics
fairseq 0.12.2 [445] modeling, ai
FALCON 20161027, 20161222, 20190601 [446] Biology,bioinformatics,ngs,sequencing
FALCON_unzip 20161222 [447] Biology, bioinformatics
FAR 2.15 [448] Biology,bioinformatics,genomics
FAST 1.06 [449] Biology phylogenetics
fast-gep 1.0 [450] Phylogenetics
Fast-Plast 1.2.6 [451] Biology, phylogenetics
fast5tools 0.3.1 [452] Phylogenetics, biology
FASTA 34.26.5, 36.3.6d [453] Biology,bioinformatics,genomics
fastai 2.1.5, 2.6.3 [454] Phylogenetics
FastANI 1.1 [455] Phylogenetics
fastchaos 0.1.0 [456] Sequencing
FastGEAR 20161216 [457] Biology, bioinformatics, genomics
Fastix 0.1.0 [458] Biology, NGS
FastML 3.0 [459] Biology,bioinformatics,phylogenetics
Fastp 0.20.0, 0.22.0 [460] Biology,bioinformatics,ngs
FASTphase 1.4.8 [461] Phylogenetics
FastPlast 1.2.8 [462] Phylogenetics
fastq-pair 1.0 [463] Phylogenetics
FastQ-Screen 0.14.0 [464] Phylogenetics
Fastq-tools 0.8 [465] Biology, NGS,
FastQC 0.11.4, 0.11.7, 0.9.6 [466] Biology,bioinformatics,ngs
FastqPuri 1.0.7 [467] Phylogenetics
FastQTL 2.184 [468] Phylogenetics
FASTRAL-constrained 20211108 [469] Phylogenetics
fastsimcoal 2.6.0.3, 2.7.0.2 [470] Biology, phylogenetics
FastSpar 0.0.4 [471] Biology, genomics
fastStructure 20150112 [472] Biology, genomics
FastTree 2.1.11 [473] Biology,bioinformatics,phylogenetics
FastUniq 1.1 [474] Biology, phylogenetics
Fastx Toolkit 0.0.13.2, 0.0.14 [475] Biology,ngs
fcGENE 1.0.7, 1.0.7.1 [476] Biology,bioinformatics,genomics,snp
FDSTools 1.2.0 [477] Phylogenetics
fdupes 1.51 [478] File Management
FEELnc 0.1.1 [479] Phylogenetics
FEniCS 2018.1.0 [480] Biology, phylogenetics
Ferret 6.82 [481] Data Visualization and Analysis, Oceanography, Meteorology
FFmpeg 2.1.3, 2.8.3, 4.3.1 [482] Audio, Video
FFTW 3.3.6, 3.3.7, 3.3.8 [483] Library,c,math
fgbio 0.5.0, 0.7.0 [484] Phylogenetics
FGMP 1.0.1 [485] Phylogenetics
FIGARO 1.1.2 [486] Phylogenetics
Fiji 2.0.0rc59 [487] ImageJ
Filtlong 0.2.0 [488] Biology, phylogenetics
Finder 20210503, 20210609 [489] Biology, bioinformatics, finder
finemap 1.4 [490] Phylogenetics
fineRADstructure 0.3.2 [491] Phylogenetics
finesse 2.3.1 [492] Simulation
fit-sne 1.2.1 [493] Phylogenetics
FLAIR 1.5 [494] Phylogenetics
flairNLP 0.10 [495] Data Visualization, language
flappie 1.1.0, 2.1.3 [496] Phylogenetics
FLASh 1.2.10, 1.2.11 [497] Biology, genomics
FLEA 2.0.0 [498] Phylogenetics
flex 2.6.4 [499] Programming
Flexbar 2.3, 2.34, 3.5.0 [500] Biology, bioinformatics, genomics, ngs
FLEXLm 1.0 [501] Administration
FlowCraft 1.4.1 [502] Phylogenetics
Fluent 17.2, 19.1, 2020R1 [503] CFD
Flye 2.7.1, 2.8.1, 2.9 [504] Biology, NGS
fMRIPrep 1.4.0a1, 1.5.4, 20.2.3 [505] Data Mining
ForeSeqs 1.0.4 [506] Phylogenetics
fpocket 4.0.2 [507] sequencing, biology
fqtools 20160224 [508] Biology,bioinformatics,ngs,sequencing
FragGeneScan 1.16 [509] Biology,genomics
FRAMA 20151019 [510] Biology
FrameDP 1.2.2 [511] Biology, sequencing
FRAPOSA 20200421 [512] Phylogenetics
FreeBayes 1.1.0-20170823, 1.3.1, 1.3.2 [513] Biology,genomics
freesasa 2.1.2 [514] molecular dynamics, biology
Freesurfer 7.1.0, 7.1.1, 7.2.0 [515] Biology,bioinformatics,neuroscience,imaging
Freyja 1.3.1, 1.3.4, 1.3.8 [516] Biology,phylogenetics,sequencing
FSA 1.15.9 [517] Phylogenetics
FSL 6.0.3, 6.0.4, 6.0.5 [518] Biology,bioinformatics,neuroscience,imaging
fslmrs 1.1.10 [519] MRS, metabolomics
funannotate 1.8.7, 1.8.9 [520] Phylogenetics
fusion_twas 20210218 [521] Phylogenetics
GAL 20180906 [522] Phylogenetics
Galaxy 1.0 [523] Biology,bioinformatics
GAML 20150610 [524] Biology, bioinformatics, genomics
GapCloser 1.12r6 [525] Biology, genomics, ngs
GapFiller 1.10, 1.11 [526] Biology, genomics
GARLI 2.0, 2.01 [527] Biology,bioinformatics,phylogeny
GASVPro 201310 [528] Biology, bioinformatics, ngs
GATE 7.0 [529] Library
GATK 4.1.4.0, 4.1.8.1, 4.1.9.0 [530] Biology,bioinformatics,ngs
Gaussian 09 D.01, 16, 16-c02 [531] Computational Chemistry
Gawk 4.2.0 [532] Software Tools
Gblocks 0.91b [533] Biology,bioinformatics
GCC 7.3.0, 8.2.0, 9.3.0 [534] Compilers
GCE 1.0.2, 4.0 [535] Biology, bioinformatics, genomics
GCT 6.2.1 [536] Gridftp, globus, toolkit
GCTA 1.26.0, 1.92.4beta, 1.93.2beta [537] Biology, genomics, SNP,
GDAL 2.2.1, 2.2.4, 2.3.1 [538] Geospatial, Library
GDB 8.3, 9.2 [539] Software Development
GDC-Client 1.0.1 [540] Biology, bioinformatics, sequence, ngs
gdc-client 1.5.0 [541] Phylogenetics
GDrive 2.1.0 [542] Applications, Utilities, Data Transfer
GDSL 1.18 [543] Library
Geant4 4.10, 4.10.03, 4.10.5 [544] Physics
GEM 20130406 [545] Biology,bioinformatics,ngs,sequencing
gem5 2.0 [546] Computer Simulator
GEMMA 0.98.1 [547] Phylogenetics
GeneMark-ES 4.58, 4.65, 4.68 [548] Biology, genomics
GeneMarkS 2012.04 [549] Biology,genomics
GeneMarkS-T 3.10.001 [550] Biology,genomics
GenePainter 2.0.4 [551] Biology, phylogenetics
GeneRax 1.2.2 [552] Phylogenetics
GeneSeqer 2014-02-26 [553] Biology, genomics
genesum 0.1.0 [554] Biology,genomics
GeneTorrent 3.8.7 [555] Biology,bioinformatics,data download
GenGen 1.0.1 [556] Biology, phylogenetics
Genome STRiP 2.00.1602 [557] Biology, genomics, ngs
Genome_Graph_Annotation 20190131 [558] Phylogenetics
GenomeScope2 2.0 [559] Phylogenetics
GenomeThreader 1.7.3 [560] Phylogenetics
GenomeTools 1.5.7, 1.5.9 [561] Biology, bioinformatics
genomic-fluidity 20151109 [562] Phylogenetics
GenomicConsensus 2.3.3 [563] Biology, phylogenetics
GenomicNeuralnet 20161030 [564] Phylogenetics
GenomicTools 2.7.0 [565] Biology,bioinformatics,ngs,chip-seq,rna-seq
GenotypeHarmonizer 1.4.18 [566] Biology, bioinformatics
Genrich 0.5 [567] Phylogenetics
GenSel 4.90 [568] Population Genetics
geopython 1.0.0, 1.0.1 [569] Python, geospatial, cartography
GEOS 3.3.8, 3.6.2 [570] Library, data
GeP 2.1 [571] Biology, phylogenetics
gepard 1.40.0 [572] Phylogenetics
Gerbil 1.11 [573] Phylogenetics
get_homologues 3.3.3 [574] Biology, genome
GetOrganelle 1.7.3.5, 1.7.5.0 [575] Phylogenetics
GFam 1.1 [576] Biology, genomics, annotation
GFF-Ex 2.3 [577] Phylogenetics
GFF3toolkit 2.0.3 [578] Phylogenetics
gffcompare 0.12.2 [579] Phylogenetics
gffread 0.11.8, 0.12.7, 0.9.8c [580] Biology, bioinformatics
Gflags 2.2.1, 20150520 [581] Google,libraries
GFOLD 1.1.4 [582] Biology, RNA-seq
ggsashimi 0.5.0 [583] Phylogenetics
GHOST-MP 1.3.4 [584] Phylogenetics
Ghostscript 9.22 [585] PDF
Giotto 0.1.0 [586] Phylogenetics
Git 2.14.1, 2.30.1 [587] Revision Control
git-filter-repo 2.33.0 [588] Phylogenetics
glactools 1.0.8 [589] Phylogenetics
Glimmer 3.02 [590] Biology, microbial annotation
GlimmerHMM 3.0.4 [591] Biology, microbial annotation
GLMsingle 1.0 [592] FMRI
Globus 1.10.1, 2.1.3 [593] Data Transfer
glog 0.3.5 [594] Google,libraries
GLPK 4.55, 4.65 [595] Programming
Glueviz 0.15.2 [596] Phylogenetics
GMAP 20180212, 20180212_sse2, 20190610 [597] Biology, bioinformatics, genomics, ngs
GMcloser 1.6 [598] Biology, NGS
GMP 6.1.2 [599] Library, crypto
GnuPlot 5.2.2, 5.2.3, 5.4.1 [600] Graphics,plotting,math
Go 1.13.6, 1.15.4, 1.18.3 [601] Language
GOMAP 1.3 [602] Biology, bioinformatics, ngs
GoPHY 201030 [603] Phylogenetics
gotcloud 1.17.5 [604] Phylogenetics
GPA 1.1 [605] Phylogenetics
GPhoCS 1.2.3 [606] Phylogenetics
Gpufit 20201127 [607] Phylogenetics
Grace 5.1.22 [608] Graphics, statistics, 2D
GRACKLE 3.1 [609] Library,c,astrophysics
GrADS 2.0.1 [610] Environment, grid analysis
Graftm 0.12.2 [611] Phylogenetics
GramCluster 1.3 [612] Biology,sequencing,
graph-tool 2.32 [613] Phylogenetics
Graph_annotation 0.1 [614] Phylogenetics
GraPhlAn 1.1.3 [615] Phylogenetics
GraphMap2 0.6.5 [616] Phylogenetics
GraphSplitting 2.4 [617] Phylogenetics
graphtyper 2.7.2 [618] Phylogenetics
GraphViz 2.38.0, 2.46.1 [619] Biology,bioinformatics,neuroscience,imaging
GRASS 7.0, 7.4 [620] Geography
grf 1.0.0 [621] Genomics, bioinformatics
Grib_api 1.10.1, 1.15.1, 1.26.1 [622] C, fortran, library
GRIDSS 2.6.2 [623] Phylogenetics
GROCSVs 0.2.5 [624] Phylogenetics
GROMACS 2021.2, 2021.3, 2021.4 [625] Computational Chemistry, Molecular Dynamics
GroopM 0.3.5 [626] Biology, phylogenetics
Groovy 2.4.15 [627] Programming
Gscripts 1.1 [628] Scripts
GSEA 3.0.0, 4.2.2 [629] Biology, bioinformatics, genomics
GSL 2.4, 2.5, 2.6 [630] Library, data
GSNP 1.0 [631] Biology,bioinformatics,ngs
GTAHunter 20200106 [632] Phylogenetics
GTDBTk 1.7.0, 2.0.0, 2.1.0 [633] Phylogenetics
GTOOL 0.7.5 [634] Phylogenetics
GUAVA 1.0 [635] Phylogenetics
Gubbins 2.4.1, 3.2.1 [636] Phylogenetics
guideseq 1.0.2 [637] sequencing, genomics, bioinformatics, data
guile 2.2.2 [638] Programming Language
GULP 4.4, 5.0 [639] Material Science
guppy 4.4.1, 4.5.4, 6.1.7 [640] Phylogenetics
Gurobi 9.5.1 [641] Math, python
GWAMA 2.2.2 [642] Phylogenetics
Gzip 1.10 [643] Compression
Hail 0.2.77 [644] Biology, Genomics
hal 2.1 [645] Phylogenetics
HALC 1.1 [646] Biology, phylogenetics
halla 0.8.17 [647] Phylogenetics
hamstr v8b [648] Biology, genome
HaMStR 13.2.2, 13.2.3, 13.2.4 [649] Biology, genome
hapbin 1.3.0 [650] Biology, Genetics
HapCompass 0.7.7 [651] Particle NGS, genomics
HAPCUT 0.7 [652] Biology, assembly
HapCUT2 1.3.3 [653] Biology, Genomics, Sequencing
hapdup 0.6 [654] Phylogenetics, biology
Haploflow 0.1 [655] Biology, Phylogenetics
Haplomerger2 20180603 [656] Biology, genomics
HAPLOSWEEP 1.0 [657] Biology, phylogenetics
happy 0.3.14 [658] Phylogenetics, biology
hapQTL 1.00 [659] Biology
hapsembler 2.21 [660] Biology, bioinformatics, assembly
HASLR 0.8a1 [661] Phylogenetics
hclust2 1.0.0 [662] Statistics, mapping
HDF4 4.2.11 [663] Library, data
HDF5 1.8.19, 1.8.20, 1.8.9 [664] Library, data
hecaton 0.5.1 [665] Genomics, Biology
HELEN 20200516 [666] Phylogenetics
HelitronScanner 1.1 [667] Phylogenetics
hgraph2graph 20210428 [668] Chemistry
HiC-Pro 3.0.0 [669] Biology, Pipeline, Genomics
Hifiasm 0.16.1, 0.4, 0.8 [670] Phylogenetics
HipSTR 0.7 [671] Phylogenetics
HISAT2 2.2.0, 2.2.1, 2.2.1-3n [672] Biology, Sequence Alignment, NGS
HLAminer 1.3.1, 1.4 [673] Biology, phylogenetics
HMM-FRAME 20140724 [674] Phylogenetics
HmmCleaner 0.180750 [675] Phylogenetics
HMMER 3.1b1, 3.1b2, 3.2.1 [676] Biology, genome
hmmer2go 0.18.1 [677] Phylogenetics, biology
HMMRATAC 1.2.10 [678] Phylogenetics
HOMER 4.10, 4.11, 4.8 [679] Biology,bioinformatics,sequence,ngs
homopolish 0.3.3 [680] Genomics, Biology
HOOMD 2.1.7 [681] Library, math
HPL 2.1 [682] Parallel Programming, benchmarks, MPI
HTMLDoc 1.8.28, 1.9.3 [683] Pdf, docs, html
HTSeq 0.11.2 [684] Biology,bioinformatics,ngs
humann2 0.11.2, 2.8.1 [685] Phylogenetics
hyb 20141126, 20200815 [686] Biology, ngs, RNA-Seq
HybPiper 1.2, 1.3.1, 2.0.1 [687] Biology, phylogenetics
HyDe 0.4.3 [688] Phylogenetics
HyPhy 2.5.4, 2.5.7, 2.5.8 [689] Biology,bioinformatics,evolution
HYPRE 2.15.1, 2.18.2, 2.19.0 [690] Math, Numerical Solvers
iAnnotateSV 1.0.6, 1.0.9 [691] Biology, Phylogenetics
iAssembler 1.3.2 [692] Biology, assembly
ibdne 20150815 [693] Biology,ngs
icommands 3.3.1 [694] IRods
IDBA-MT 1.0 [695] Biology,NGS
IDBA-UD 1.1.1, 1.1.1-512, 1.1.1-512-mem [696] Genomics, bioinformatics, phylogenetics
IDL 8.3 [697] Language, programming, science
IDR 2.0.3 [698] Phylogenetics
IGB 8.4.1 [699] Biology, bioinformatics, genomics
igBLAST 1.5.0, 1.7.0 [700] Biology, bioinformatics
IGoR 1.4.0 [701] Phylogenetics
iGTP 1.1 [702] Biology, bioinformatics, phylogenetics
IGV 2.3.91, 2.4.16, 2.8.6 [703] Biology, bioinformatics, ngs, phylogenetics
illumina-utils 2.11 [704] Phylogenetics
Illumiprocessor 2.0.9 [705] Phylogenetics
IM and IMa 20091217 [706] Biology,bioinformatics,population genetics
Ima2 20120827 [707] Biology,bioinformatics,population genetics
IMa2p 20170712 [708] Biology, phylogenetics
IMA3 22Aug18 [709] Molecular Dynamics
ImageJ 1.48 [710] Imaging
ImageMagick 7.0.8-20 [711] Imaging
Imaginaire 20201229 [712] Imaging, Video, AI, synthesis
IMOD 4.7.15, 4.9.10 [713] Image Processing
imoka 1.0 [714] Biology, genomics
IMPUTE2 2.3.2 [715] Phylogenetics
IMPUTE5 1.1.5 [716] Biology, Imputation
INDELible 1.03 [717] Phylogenetics
Infernal 1.1.1, 1.1.4 [718] Biology, sequence alignment
INLA 20160718, 20170620 [719] Statistics, modeling, R
InParanoid 4.1 [720] Biology, biology
Inspector 1.0.2 [721] Bioinformatics, genomics
InStruct 20160723 [722] Phylogenetics
Intel Compilers and Libraries 2018.1.163, 2019.1.144, 2020.0.166 [723] Language, development, library, math, intel
Intel MPI 5.1.1 [724] Parallel Programming, development, MPI, library
InterProScan 5.53-87.0, 5.54-87.0, 5.56-89.0 [725] Biology,bioinformatics
intervene 0.6.2 [726] Biology, phylogenetics
IOAPI 3.1, 3.2 [727] Meteorology
IPOPT 3.12.10, 3.12.6 [728] Library, c/c++,math, solver, optimization
ipyrad 0.7.24, 0.7.30, 0.9.53 [729] Phylogenetics
IQ-TREE 2.1.0, 2.1.2, 2.1.3 [730] Biology, phylogenetics,
IRAP 0.8.1p7 [731] Biology, ngs, pacbio
irep 1.10 [732] Biology,bioinformatics,genomics
IRFinder 1.2.0, 1.3.0, 1.3.1 [733] Biology, RNA-Seq
isONclust 0.0.6 [734] Phylogenetics
IsoSel 1.0 [735] Phylogenetics
IsoSeq3 3.1.0, 3.2.2, 3.4.0 [736] Biology, bioinformatics, ngs, pacbio
ISOWN 20180820 [737] Phylogenetics
isPcr 3.3 [738] Biology, phylogenetics
ITK 3.20.1, 4.10.1 [739] Bioinformatics
ITK-SNAP 3.0.0, 3.8.0 [740] Biology,bioinformatics,neuroscience,imaging
ITSx 1.1b [741] Phylogenetics
IVA 1.0.11 [742] Phylogenetics
iVar 1.3.1 [743] Biology
Jabba 1.0 [744] Biology, phylogenetics
JACUSA 1.2.0 [745] Biology, bioinformatics, ngs, phylogenetics
JAGS 3.3.0, 3.4.0, 4.2.0 [746] Statistics
Jasmine 1.1.4 [747] Phylogenetics
jasp 0.14.3 [748] Statistics
jbrowse2 1.7.4 [749] Web Browser
JCVI 0.8.12, 1.0.13 [750] Phylogenetics
JDK 11.0.1, 14, 9.0.1 [751] Programming,runtime
Je 1.0 [752] Biology, NGS
Jellyfish 2.2.4, 2.2.6, 2.3.0 [753] Biology,ngs
jModelTest 2.1.1 [754] Biology, bioinformatics, genomics, phylogenetics
jo 1.3 [755] Software
jq 1.6 [756] Software
juicer 1.22.01 [757] Phylogenetics
Julia 1.6.2, 1.7.1, 1.7.3 [758] Programming, language, statistics
Jupyter 5.7.8, 6.0.3, 6.2.0 [759] Python, R, jupyter
jutils 1.0 [760] Phylogenomics, biology
JVARKIT 20180405 [761] Biology, phylogenetics
Kaiju 1.6.2, 1.7.2 [762] Biology, phylogenetics
KaKs 1.2, 2.0 [763] Biology, bioinformatics, evolution, phylogenetics
Kalign 3.3.1 [764] Biology, Bioinformatics, Sequencing, Alignment
kallisto 0.43.0, 0.44.0, 0.48.0 [765] Biology,NGS,RNA-Seq
khmer 2.0, 2.1 [766] Biology, NGS
KIM 1.7.2, 1.8.2, 1.9.3 [767] Simulation
KING 2.1.2 [768] Biology, genome, gwas
KisSplice 2.4.0-p1 [769] Biology, RNA
KLayout 0.26.7 [770] Phylogenetics
KMC 3.1.0, 3.1.1, 3.2.1 [771] Phylogenetics
kmerdb 1.9.2 [772] Phylogenomics, biology
KMOS 0.3.21 [773] Phylogenetics
kneaddata 0.7.4, 0.9.0 [774] Phylogenetics
Knitro 12.2.0 [775] Mathematical Optimization Problems
KofamScan 1.3.0 [776] Phylogenetics
kover 2.0.3 [777] Phylogenetics
Kraken 2.0.6b, 2.0.8b, 2.1.2 [778] Biology, ngs
KrakenUniq 0.5.8, 0.7.3 [779] Phylogenetics
Krona 20161019 [780] Biology, bioinformatics
ksnp 3.021 [781] Biology, phylogenetics, SNP
Ksrates 1.1.1 [782] Phylogenomics, biology
LACHESIS 2.1 [783] Phylogenetics
Lambda 0.9.4, 1.0.3, 2.0.0 [784] Biology, sequencing, phylogenetics
LAMMPS 30Jul16, 7Aug19, 7Dec15 [785] Molecular Dynamics
LAMP 2.5 [786] Biology, bioinformatics, genomics
laneta 20220517, 20220808, 20220812 [787] Bioinformatics, biology
langdetect 1.0.9 [788] NLP, utility
LAPACK 3.8.0 [789] Programming,library,fortran
Last 916, 979 [790] Biology,bioinformatics,sequence,alignment
LAStools 20200114 [791] LiDAR
LASTZ 1.02.00, 1.03.02, 1.04.00 [792] Biology, bioinformatics, ngs
Lazypipe 1.2 [793] Genomics,taxonomy,binning
LazyPredict 0.2.8 [794] Phylogenetics
lbzip 2.5 [795] Compression
LCModel 6.3 [796] Biology, NMR
ldak 5.2 [797] Phylogenetics, biology
LDhat 2.2a [798] Biology,genomics
ldsc 1.0.1 [799] Phylogenomics, biology
leafaudio 0.1.0 [800] Tensorflow, audio, leafaudio
LEfSe 20180219 [801] Phylogenetics
LEMON 1.2.3 [802] Library
LFMM 1.4, 1.5 [803] Biology, phylogenetics
Libint 2.5.0b [804] Library
LIBINT 2.5.0 [805] Library,c,math
libMesh 1.5.0 [806] Math, Numerical Solvers
libunistring 0.9.7 [807] Library
libvips 8.5.4 [808] Image Processing
LIBXC 4.2.3, 4.3.4 [809] Library, density function
LIBXSMM 1.13 [810] Library,c,math
LIBZMQ 4.3.1 [811] Library
Liftoff 1.4.2 [812] Phylogenetics
LIGR 2.05 [813] Biology,assembly
lima 2.0.0, 2.2.0 [814] Phylogenetics
lingua 1.0.1 [815] NLP, utility
LINKS 1.8.5, 1.8.6 [816] Biology, genomics
Linksbrowser 2.14 [817] Web browser
LIQA 1.0.0 [818] Phylogenetics
LMAP 1.0.2 [819] Biology, phylogenetics
lncScore 1.0.2 [820] Biology, phylogenetics
lobSTR 4.0.6 [821] Biology, phylogenetics
localbrainage 20210415 [822] Bioinformatics, ml
localizer 1.0.4 [823] Phylogenetics
LocusZoom 1.4 [824] Phylogenetics
LoFreq 2.1.3.1 [825] Phylogenetics
LongQC 1.2.0c [826] Phylogenetics
LongRanger 2.1.5, 2.2.2 [827] Biology, phylogenetics
LongStitch 1.0.3 [828] genomics, biology
LoRDEC 0.9 [829] Phylogenetics
LoRMA 0.5 [830] Biology, ngs, pacbio
LORMA 0.3 [831] Biology, ngs, pacbio
LRBinner 0.1 [832] Biology, Bioinformatics, Metagenomics, Binning
lrgapcloser 09042018 [833] Biology, bioinformatics
LS-DYNA 700, 711, 901 [834] Physics
LSD2 1.6.5 [835] Phylogenetics
ltr_finder 1.07 [836] Biology, phylogenetics
LTRRetriever 2.1, 2.5, 20170514 [837] Biology, phylogenetics
Lua 3.5.2 [838] Programming, scripting, language
Lucene 7.7.1, 9.1.0 [839] Java,search,indexing
lumpy-sv 0.2.1, 0.2.13, 0.3.1 [840] Biology, genotyping
LZO 2.09 [841] Library, compression
M5nr 20121126 [842] Biology, bioinformatics, genomics
Macaulay2 1.15 [843] Phylogenetics
MACH 1.0.18 [844] Biology,bioinformatics,genomics,ngs
Mach2VCF 20150515 [845] Biology
MACS 2.0.10, 2.1.2, 2.2.7.1 [846] Biology, bioinformatics, CHiP-Seq
MafFilter 1.3.0 [847] Phylogenetics
MAFFT 7.294, 7.397, 7.490 [848] Bio,bioinformatics,sequence
MAGeCK 0.5.9.4 [849] Phylogenetics
MAGeCK-VISPR 0.5.6 [850] Phylogenetics
MAGeCKFlute 1.14.0 [851] Phylogenetics
Magenta 2.1.2 [852] Phylogenetics
MAGMA-GWAS 1.09 [853] Phylogenetics
magus 20220121 [854] Sequencing, alignment
MAJIQ 2.2, 2.3 [855] Phylogenetics
Maker 2.31.10, 2.31.6, 3.01.03 [856] Biology,bioinformatics
MAnorm 20120316 [857] Biology, phylogenetics
MANTA 1.6.0 [858] Phylogenetics
mantis 1.0.4 [859] Phylogenetics
mapclassify 2.4.2 [860] Statistics, mapping, geography
MapThin 1.11 [861] Phylogenetics
Maq 0.7.1 [862] Biology,bioinformatics,ngs
MarginPolish 1.0.0 [863] Phylogenetics
MARK 2.0.1 [864] Application, data, capture
MarkerMiner 20150710 [865] Biology, bioinformatics, genomics
mash 1.1 [866] Biology, genomics
Mash 2.3 [867] Phylogenetics
MasHmap 2.0 [868] Phylogenetics
mashtree 1.2.0 [869] Phylogenomics, biology
MASSMINE 0.10.0, 0.11.0, 0.9.5 [870] Data Mining
MaSuRCA 3.4.2, 4.0.8, 4.0.9 [871] Biology,bioinformatics,short read alignment
Mathematica 12.1.1.0 [872] Math
MATLAB 2020a, 2020b, 2022a [873] Math,language
MATS 4.0.1, 4.0.2, 4.1.0 [874] Biology,bioinformatics,ngs,rna-seq
Mauve 2.3.1 [875] Biology,ngs,genomics
mawk 1.3.4-20150503 [876] Language
maxbin 2.1.1 [877] Biology,NGS
Maxima 5.41.0 [878] Math
MC 4.6.1 [879] Shell
mCarts 1.0.2 [880] Biology, genomics, markov
mccortex 1.0 [881] Phylogenetics
MCL 12-135, 14-137 [882] Biology, genomics
MCNP 6, 6.1 [883] Physics
MCNPX 2.7.0 [884] Physics
MCR 2019b, 2020a, 2020b [885] Math, language
MCScanX 20130328 [886] Biology, phylogenetics
mdanalysis 1.1.1 [www.mdanalysis.org] Physics, Bioinformatics
MECAT 20180308 [887] Phylogenetics
Medaka 1.0.1, 1.2.1, 1.6.0 [888] Biology, phylogenetics
Medusa 1.6 [889] Phylogenetics
MEGA 7.0.26 [890] Biology, phylogenetics
Mega2 4.9.2, 6.0.0 [891] Biology, phylogenetics
MEGAHIT 1.1.1, 1.1.4 [892] Biology, phylogenetics
Megalodon 2.0.0 [893] Phylogenetics
MEGAN 5.10.3, 6.4.15 [894] Biology, bioinformatics, ngs
MEGASAT 1.0 [895] Phylogenetics
Megraft 1.0.2 [896] Biology,sequencing,
MELD 0.4.14, 0.4.19, 0.5.9 [897] Computational Chemistry, Molecular Dynamics
MELTING 4.3.1 [898] Biology, genome, RNA, folding
MEME 5.0.2, 5.0.5, 5.4.1 [899] Biology,bioinformatics,sequence
MentaLiST 0.1.3 [900] Biology, phylogenetics
Meraculous 2.0.5 [901] Biology,NGS
Mercurial 4.8.2 [902] Revision Control
merge_peaks 0.1.0 [903] Workflow
Merlin 1.1.2 [904] Biology,SNP
Merqury 1.1, 1.3 [905] Phylogenetics
Meryl 1.0 [906] Phylogenetics
MeShClust 1.2.0 [907] Biology
Meshroom 2019.2.0 [908] Phylogenetics
MET 10.0 [909] Meteorology, Models, Verification
Meta-Marc 1.0.0 [910] Phylogenetics
Meta-Tissue 0.4 [911] Biology, genetics
MetaBAT 0.32.4, 2.13 [912] Biology, genomics
MetaBCC-LR 2.0.0 [913] Biology, Metagenomics, Binning
Metabin 1.0 [914] Genomics, bioinformatics, metagenomics
metabolic 4.0 [915] Phylogenetics
MetaCherchant 0.1.0 [916] Biology, phylogenetics
MetaCluster 5.0b [917] Biology,bioinformatics,genomics
MetaCompare 20181016 [918] Phylogenetics
metacrast 20200309 [919] Phylogenetics
MetaGeneMark 2.10, 3.26 [920] Biology,genomics
METAL 20110325 [921] Biology, ngs, genomics
MetaLAFFA 1.0.0 [922] Phylogenetics
MetaMaps 20201207 [923] Phylogenetics
METANNOT 20171129 [924] Phylogenetics
Metaphlan 3.0.14, 3.0.3, 3.1.0 [925] Phylogenetics
MetaPhlAn2 2.7.7 [926] Biology, phylogenetics
MetaPhysicl 1.0.0 [927] Math, Astronomy, Numerical Simulation
MetaSV 0.5.4 [928] Biology, phylogenetics, NGS
MetaVelvet 1.2.06 [929] Computational Biology, genomics
metaWRAP 1.2 [930] Phylogenetics
Metaxa2 2.1.1, 2.1.3 [931] Biology,bioinformatics,ngs,sequencing
MethylDackel 0.5.0, 0.6.1 [932] Phylogenetics
methylpy 1.2.9 [933] Biology, Phylogenetics
Metilene 0.2.8 [934] Biology, genomics, methylation
METIS 5.1.0 [935] Software
Mfannot 20180405 [936] Biology, phylogenetics
mfold 3.6 [937] Bioinformatics,structure,RNA
mg-rast 20150919 [938] Biology, genomics
MGEfinder 1.0.5 [939] Phylogenetics
MGERT 1.0.1 [940] Phylogenetics
MGEScan 20160416 [941] Biology, genomics
MGLTools 1.5.7 [942] Biology, Molecular Biology, Visualization
MHAP 1.6 [943] Biology, sequencing
MHCflurry 1.4.3 [944] Phylogenetics
MIA 20130201 [945] Biology, ngs
MicrobeAnnotator 2.0.5 [946] microbial annotation, biology
MIDAS 1.3.2, 20160830 [947] Biology, phylogenetics
MIGRATE-N 4.2.14, 4.4.4, 5.0.4 [948] Biology,bioinformatics,population genetics
mIGRATE-N 4.2.14 [949] Biology, phylogenetics
Mikado 2.3.3 [950] Biology, Genetics, Transcripts, Pipeline
MIKE 1.0 [951] Environment,water,modeling
Minced 0.2.0 [952] Biology, genomics
Minia 3.2.6 [953] Phylogenomics, biology
Miniasm 0.2-r168, 0.3-r179 [954] Biology, phylogenetics
MiniCaller 20161201 [955] Biology,bioinformatics,ngs,phylogenetics
minigraph 0.15 [956] Phylogenetics
minimac 1-20130717, 3-20150727 [957] Biology, NGS,
minimac2 2-20140915 [958] Biology, NGS,
Minimap 2.17, 2.18, 2.21 [959] Biology, phylogenetics
minimap 2.12, 2.1t, 2.9-r720 [960] Biology, phylogenetics
minimap2 2.24 [961] Phylogenomics, biology
Minipolish 0.1.3 [962] biology, genomics
MinkowskiEngine 0.5.3 [963] Machine Learning, Deep Learning
MinPath 1.4 [964] Biology, phylogenetics
MIRA 4.0.rc1, 4.9.6, 5rc2 [965] Biology,bioinformatics,genomics,assembly
miRanda 1.9 [966] Phylogenetics
miRBShunter 0.2 [967] Phylogenetics
mirdeep 0.1.0, 0.1.1, 2.0.1.3 [968] Phylogenetics
miRDP2 1.1.4 [969] Biology, Genomics
Mireap 0.20 [970] Biology
miRge 2.0 [971] Phylogenetics
Misa 1.0 [972] Biology, bioinformatics, genomics
MISO 0.5.3 [973] Biology,bioinformatics,ngs,sequencing,rna-seq
MITE-Hunter 20111101 [974] Biology, phylogenetics
MITObim 1.9.1 [975] Phylogenetics
MitoFinder 1.0.2, 1.1, 1.4 [976] Phylogenetics
mitohifi 2.2 [977] genomics, sequencing
MitoPhAST 3.0 [978] Phylogenetics
Mitsuba2 2.2.1 [979] Rendering
MiXCR 2.1.8, 3.0.13 [980] Biology, phylogenetics
MixMHC2pred 1.2 [981] Phylogenetics
MixMHCpred 2.0.2 [982] Phylogenetics
mixmogam 20190322 [983] Phylogenetics
MKL 2018.1.163, 2019.1.144, 2020.0.166 [984] Programming, development, library, math, intel
mlcoalsim 1.9916b [985] Biology, phylogenetics
Mlcoalsim 1.9916b [986] Biology, phylogenetics
mlpack 3.4.2 [987] Library
mlst 2.15.2 [988] Phylogenetics
mlstcheck 2.1 [989] Phylogenetics
MMSEQ 1.0.8 [990] Biology,bioinformatics,genomics
MMseqs2 11, 12 [991] Phylogenetics
MMvec 1.0.5, 1.0.6 [992] Metabolomics
MNEtools 0.22.0 [993] Phylogenetics
MOABS 1.2.9, 1.3.2, 1.3.4 [994] Biology, ngs
mobsuite 3.1.0 [995] Sequencing, biology
MOCCASIN 0.25 [996] Phylogenetics
MODELLER 9.14, 9.23 [997] Biology,bioinformatics,modelling,structure
MODELTEST 0.1.2, 0.1.7 [998] Biology, phylogenetics
Modulus 21.06, 22.03 [999] Physics, AI, Neural Network
Molden 5.0 [1,000] Molecular, Electronic Structure
momi 2.1.19 [1,001] Phylogenetics, biology
monai 0.8, 0.8.1, 0.9.0 [1,002] Data Science in Healthcare
MONAI label 0.3.2 [1,003] Data Science in Healthcare
MongoDB 4.0.3 [1,004] Database
Moni 0.2.0 [1,005] Phylogenomics, biology
mono 5.18 [1,006] Linux, runtime
Monolix 4.3.2 [1,007] Modeling, pharmacokinetics
MOOSE 20200316, 20200722, 20210726 [1,008] Physics, simulation
Mosaic 1.7.4 [1,009] Phylogenetics
MOSAIK 2.1.33, 2.2.3, 2.2.30 [1,010] Biology,bioinformatics,short read alignment
Mosdepth 0.2.3, 0.3.1 [1,011] Biology, phylogenetics
Mothur 1.38.1, 1.41.3, 1.46.1 [1,012] Biology, microbial ecology
MotionCor2 1.2.3, 1.3.1 [1,013] Motion Correction
mOTU 1.1 [1,014] Biology, bioinformatics, genomics
mOTUs 2.5.1 [1,015] Phylogenetics
MountainSort 0.9.0 [1,016] Library
MP-EST 1.4 [1,017] Biology,bioinformatics,ngs,sequencing
MPACK 0.8.0 [1,018] Library
MPB 1.5 [1,019] Library, math
MPBoot 1.1.0 [1,020] Biology, phylogenetics
MPFR 3.1.6 [1,021] Library, math
mpinterfaces 20170613 [1,022] DFT
MrBayes 3.2.4, 3.2.5, 3.2.6 [1,023] Application, biology, phylogenetics
MRIcroGL 20201102, 20210327, 20211006 [1,024] Biology, mri, imaging
MRIcron 201306, 20161012, 20190911 [1,025] Biology, mri, imaging
mriqc 0.11.0, 0.16.1, 22.0.1 [1,026] MRI, imaging, biology
MRtrix 3.0.1, 3.0.3, 3.0rc2 [1,027] Biology, mri, imaging
ms 20171108 [1,028] Phylogenetics
ms-dial 4.4.8 [1,029] Biology, bioinformatics, metabolomics
msfinder 3.52 [1,030] Biology, Metabolomics
mSINGS 20180810 [1,031] Phylogenetics
MSMC-Tools 20190614 [1,032] Phylogenetics
msprime 0.7.4 [1,033] Phylogenetics
MstatX 1.0 [1,034] Biology, phylogenetics
MSTmap 1.0 [1,035] Phylogenetics
msvar 1.3 [1,036] Biology,bioinformatics,population genetics
MTG2 2.15 [1,037] Phylogenetics
mTR 20210526 [1,038] Biology, Genomics
Mugsy 1.2.3 [1,039] Biology, phylogenetics
MultiQC 1.12, 1.7 [1,040] Biology, bioinformatics, CHiP-Seq
MUMmer 3.23, 4.0.0beta2 [1,041] Biology,bioinformatics,genomics
MUSCLE 3.8.31 [1,042] Biology, bioinformatics, alignment
MuSE 1.0rc [1,043] Phylogenetics
Musket 1.1 [1,044] Biology, genomics, ngs
MuTect 1.1.4, 1.1.7 [1,045] Biology,genomics
MutSig 1.4, 1.41 [1,046] Biology,genomics
mvftools 20191124 [1,047] Phylogenetics
MZMine 2.41, 2.52, 2.53 [1,048] Biology, bioinformatics, spectrometry, NMR
NAMD 2.14, 2.14b2, 3.0 Alpha [1,049] Molecular Dynamics
NANO 2.8.2 [1,050] Text Editor
nanocomp 1.17.0 [1,051] Programming, python, sequencing
NanoCount 0.2.1 [1,052] Phylogenetics
Nanodisco 1.0.3 [1,053] Phylogenetics
Nanofilt 2.7.1 [1,054] Phylogenetics
NanoPlot 1.30.1 [1,055] Phylogenetics
Nanopolish 0.11.1, 0.13.2, 20171006 [1,056] Biology
nanostripper 0.1 [1,057] Phylogenetics, biology
NanoSV 1.2.0, 1.2.3, 1.2.4 [1,058] Biology, genomics
NanoVar 1.3.9 [1,059] Phylogenetics
Napari 0.3.8, 0.4.7 [1,060] Phylogenetics
NBODY 6 [1,061] Astronomy
NCBI BLAST+ 2.7.1, 2.8.1, 2.9.0 [1,062] Biology, bioinformatics
NCBI C++ Toolkit 12.0.0, 21.0.0, 7.0.0 [1,063] Biology,bioinformatics,NCBI,programming,library,cpp
NCBI GenBank Tools 20140130 [1,064] Biology,bioinformatics,NCBI,GenBank
ncbi-vdb 2.6.3, 2.8.2 [1,065] SRA toolkit library
nccl 20.11 [1,066] Development, library, communication, nvidia
ncftp 3.2.5 [1,067] File transfer
NCL 6.1.2, 6.3.0 [1,068] Atmosphere Science
NCO 4.2.1, 4.4.3 [1,069] Data Analysis
ncview 2.1.2, 2.1.7 [1,070] Data Visualization
NECAT 202001019 [1,071] Phylogenetics
Necklace 1.00 [1,072] Biology, phylogenetics
NeEstimator 2.1 [1,073] Biology, Bioinformatics
nemo 1.0.0rc1, 1.0.1, 1.2.0 [1,074] AI, machine learning
neovim 0.2.0 [1,075] Editor, text, ide, vim
NetCDF 4.3, 4.3.3, 4.4.3 [1,076] Data, exchange
NetCDF-C 4.7.4, 4.8.1, 4.9.0 [1,077] Data, exchange
NetCDF-F 4.5.4 [1,078] Data, exchange
NetCDF-Fortran 4.4.3, 4.4.4 [1,079] Data, exchange
NetCDF-FORTRAN 4.5.3 [1,080] Data, exchange
NetLogo 5.3.64, 6.1.1, 6.2.0 [1,081] Modeling
NEURON 7.7.2, 8.0.0, 8.2.1 [1,082] Biology, neuroscience
Newbler 2.7, 2.8, 2.9 [1,083] Biology,bioinformatics,ngs,454,assembly,denovo
newick-utils 1.6 [1,084] Biology, bioinformatics, genomics, phylogenetics
newick_utils 1.6, 1.7 [1,085] Biology, phylogenetics
NewTargets 20210215 [1,086] Bioinformatics
NextDenovo 2.4.0 [1,087] Phylogenetics
Nextflow 21.04.0, 21.10.6, 22.04.5 [1,088] Biology, bioinformatics, workflow
NextGenMap 0.5.5 [1,089] Phylogenetics
NextPolish 1.3.1 [1,090] Phylogenetics
Nextstrain 1.16.1 [1,091] Phylogenetics
nf-core 1.12.1, 2.1 [1,092] Biology, bioinformatics, workflow
NGC CLI 2.10.1 [1,093] Command Line Interface
NGmerge 0.3 [1,094] Phylogenetics
ngmlr 0.2.6, 0.2.7 [1,095] Biology, phylogenetics
ngs-bits 0.1 [1,096] Biology, sequencing
NGS-SDK 1.2.4, 1.3.0 [1,097] Biology,bioinformatics,ncbi,sdk,library
ngscheckmate 1.0 [1,098] Phylogenetics
ngstools 20150816 [1,099] Biology, ngs
nilearn 0.7.0, 0.9.0 [1,100] Phylogenetics
nimare 0.0.5 [1,101] neuroimaging
Nipype 1.6.0, 1.7.0, 1.8.0 [1,102] Biology,bioinformatics,neuroscience,imaging
nlp 1.1, 1.2 [N/A] Machine Learning
nlr-annotator 0.7 [1,103] Phylogenetics
NLR-Parser 1.0 [1,104] Phylogenetics
NMRPipe 7.9, 8.2 [1,105] Biochemistry
NONMEM 7.3.0, 7.4.4 [1,106] Modeling
nonpareil 3.3.4 [1,107] Phylogenetics
Novoalign 2.08.02, 3.00.02 [1,108] Biology,bioinformatics,ngs
NOVOPlasty 3.7, 4.2, 4.3 [1,109] Phylogenetics
nPhase 1.1.3 [1,110] Bioinformatics,pipeline,phasing,polyploid
npScarf 1.7 [1,111] Phylogenetics
nQuire 20180405 [1,112] Phylogenetics
Nsight 2022.1 [1,113] GPU, profiler, tools
Nsightsys 2022.2.1 [1,114] GPU, profiler, tools
nt 20220404 [1,115] sequencing, neuroscience
ntEdit 1.2.1 [1,116] Phylogenetics
nubeamdedup 20200907 [1,117] Phylogenetics
NucDiff 2.0.3 [1,118] Phylogenetics
NucleoATAC 0.3.1 [1,119] Biology, bioinformatics
Nullarbor 1.41 [1,120] Biology, phylogenetics
Numba 0.36.2 [1,121] Compiler
NUMBA 0.43.1, 0.48.0 [1,122] Phylogenetics
NUPACK 3.2.2 [1,123] Phylogenetics
nvhpc 11.1, 21.7 [1,124] Language, development, library, math, nvidia
nVidia HPC Compilers 20.11 [1,125] Compilers
NWChem 6.8 [1,126] Chemistry
NxTrim 0.4.1 [1,127] Biology, bioinformatics, ngs
Oases 0.2.08 [1,128] Biology,ngs,assembler
OCaml 4.02.3 [1,129] Language, scripting, development
OCOCO 0.1.2.6 [1,130] Biology, phylogenetics
octave 6.4.0 [1,131] Numerical Computation
odgi 0.6 [1,132] Phylogenetics
Olego 1.1.2, 1.1.5, 1.1.6 [1,133] Biology,bioinformatics,ngs,rna-seq
OmicsBox 1.1.78 [1,134] Image Processing
OMindel 20180129 [1,135] Phylogenetics
omniCLIP 0.1.0 [1,136] Phylogenetics
OMNIVERSE beta211004 [1,137] NVIDIA Omniverse
OMSV 1.0.1 [1,138] Phylogenetics
ONT-Bonito 0.0.5, 0.1.5 [1,139] Phylogenetics
ont_fast5_api 2.0.1, 4.0.2 [1,140] phylogenetics
ont_tutorial_cas9 20190705 [1,141] Phylogenetics
open-cravat 2.0.1 [1,142] Bioinformatics, genomics
open3d 0.13.0 [1,143] Phylogenetics
OPENACC 16.7 [1,144] Programming, Accelerator toolkit
OpenBabel 2.3.2, 2.4.1, 3.1.1 [1,145] Biology, bioinformatics
OpenBLAS 0.2.20 [1,146] Programming,library
OpenCL 18.1.0.013 [1,147] Phylogenetics
OpenCV 4.5.2 [1,148] Library
OpenFOAM 4.1, 5.0, 8.0 [1,149] Computational Fluid Dynamics
OPENMM 7.4.2, 7.5 [1,150] Computational Chemistry, Molecular Dynamics
OpenMM 7.4.2, 7.5.0, 7.6.0 [1,151] Computational Chemistry, Molecular Dynamics
OpenMPI 4.0.4, 4.0.5, 4.1.1 [1,152] Parallel Programming, development, MPI, library
OpenNeuro 3.17.4, 3.37.4 [1,153] Biology, data
OpenPIV-python 0.21.2 [1,154] Python, imaging
OpenPIV-python-gpu 20190506-gpu [1,155] Python, imaging
OpenSim 4.3 [1,156] Phylogenetics
OpenSlide 3.4.1 [1,157] Imaging
OptiType 1.3.1 [1,158] Biology, phylogenetics
Orange3 3.3.6 [1,159] Data Mining
ORCA 4.0.1.2 [1,160] Molecular, Electronic Structure
OrganellePBA 20180904 [1,161] Phylogenetics
OrthoFiller 1.1.4 [1,162] Phylogenetics
OrthoFinder 1.1.10, 2.3.11, 2.5.2 [1,163] Biology, ngs
Orthofisher 0.1.2 [1,164] Biology, Genetics
Orthograph 0.6.3 [1,165] Orthology
Orthologer 2.2.0 [1,166] Biology,
OrthoMCL 2.0.3, 2.0.7 [1,167] Biology,genomics
osprey 1.1.0 [1,168] MRS,matlab,neuroscience
OTB 5.8.0 [1,169] Geospatial Data Modeling
p4est 1.1, 2.8 [1,170] Library
p4vasp 0.3.29, 0.3.30 [1,171] Molecular, Electronic Structure
p53MH 20020901 [1,172] Biology, DNA-sequencing
p7zip 9.20.1 [1,173] Archiver
PacBio 10.2.0.133434, 11.0.0.146107, 7.0.1 [1,174] Biology, bioinformatics, ngs, pacbio, smrtlink
Package-GFE 20150701 [1,175] Biology,genomics
PALADIN 1.3.1 [1,176] Biology, phylogenetics
PALES 122 [1,177] Physics
PAML 4.8a, 4.9a, 4.9h [1,178] Biology, phylogenetics
Pandaseq 20140808, 20150627 [1,179] Biology,bioinformatics,ngs,sequencing
Pandoc 2.2.2.1 [1,180] Converter
pangolin 2 [1,181] Phylogenetics
panseq 3.2.1 [1,182] Phylogenetics
panX 1.6.0 [1,183] Phylogenetics
PAPI 5.5.1, 5.7.0 [1,184] Programming interface, performance analysis
parabricks 3.5.0, 3.7.0 [1,185] Phylogenetics
parallel 20150122, 20170322 [1,186] Shell, process management
paralyzer 1.5 [1,187] Phylogenetics
ParaView 5.4.1, 5.7.0, 5.9.1.1 [1,188] Data Analysis
ParaView Server 5.10.1 [1,189] Data Analysis
ParGenes 1.2.0 [1,190] Phylogenetics
ParlAI 1.3.0, 1.5.0 [1,191] Phylogenetics
Parsnp 1.2, 1.5.0, 1.6.2 [1,192] Biology, phylogenetics
PartitionFinder 2.0.0-pre-20160513, 2.1.1-20161205, 2.1.1.0 [1,193] Biology,phylogenetics,evolution
PASA 2.0.2-r20151207, 2.2.0-r20171013, 2.4.1 [1,194] Biology, bioinformatics, genomics, ngs
Pascal 3.0.0 [1,195] Compiler, Programming
PASTA 0.2.0, 1.7.8, 20160616 [1,196] Biology, sequence alignment
PATHd8 1.0 [1,197] Biology, phylogenetics
pathoscope 2.0.7 [1,198] Sequencing, Genomics, Biology
PATRIC 1.034 [1,199] Machine Learning
PAUDA 1.0.1 [1,200] Biology,bioinformatics,ngs,phylogenetics
PAUP 4.0a166, 4.0a168, 4.0b10 [1,201] Bioinformatics, Phylogenetics
PB-Assembly 0.0.6, 0.0.8 [1,202] Biology,bioinformatics,ngs,sequencing,pacbio
pbalign 20160921, 20161221 [1,203] Biology, bioinformatics
PBCCS 5.0.0 [1,204] Phylogenetics
pbcore 1.7.1 [1,205] Biology,bioinformatics
PBGCpp 1.9.0 [1,206] Phylogenetics
pbipa 1.8.0 [1,207] Phylogenetics, biology
PBJelly 15.8.24 [1,208] Biology,bioinformatics,ngs
pbmm2 1.3.0 [1,209] Phylogenetics
pbrt 20181017 [1,210] Phylogenetics
pbsmrtpipe 0.63.0 [1,211] Biology,API
pbtranscript-tofu 20150317, 20160119 [1,212] Biology, bioinformatics, ngs, pacbio
PCIT 2014 [1,213] Bioinformatics
PCRE 8.38, 8.39 [1,214] Perl, library
PDA 1.0.3 [1,215] Biology, phylogenetics
pdb2pqr 2.1.0 [1,216] Protein, modeling, pdb
PeakSplitter 1.0 [1,217] Biology, bioinformatics, CHiP-Seq
PEAR 0.9.2 [1,218] Biology, genomics, ngs
peneasy 20150530 [1,219] Physics
PennCNV 1.0.5 [1,220] Phylogenetics
Perl 5.16.0, 5.20.0, 5.24.1 [1,221] Programming,scripting,language
PerM 0.4.0 [1,222] Biology,bioinformatics,ngs,mapping
PETSc 3.8.1, 3.8.3, 3.8.4 [1,223] Math, Numerical Solvers
PfamScan 1.3, 1.5 [1,224] Biology, genomics
PGAP 20220414 [1,225] Biology, Genomics, Annotation, Pipeline
PGDSpider 2.0.9.0, 2.1.1.5 [1,226] Biology, NGS
pggb 0.2.0, 20201106, 20210121 [1,227] Phylogenetics
PhaME 1.0.3 [1,228] Phylogenetics
pharmcat 1.8.0 [1,229] Biology, Bioinformatics, Phylogenetics
PHASE 2.1.1 [1,230] Phylogenetics
PHAST 1.5 [1,231] Biology,phylogeny
Phenix 1.10.2155, 1.17.1, 1.8.1069 [1,232] Crystallography
PHI 3.1.1, 3.1.2b, 3.1.6 [1,233] Calculations
PhiSpy 3.2 [1,234] Phylogenetics
PHITS 2.76, 2.82, 2.84 [1,235] Physics
PHLAWD 20170427 [1,236] Biology, phylogenetics
PhotoScan 1.4.1, 1.4.5 [1,237] Image Processing
Photutils 0.5 [1,238] Astronomy, photometry
PHYLDOG 20130116-dbg [1,239] Biology,bioinformatics,phylogenetics
PHYling 1.0 [1,240] Biology, Phylogenetics, Markers, Genomics
PHYLIP 3.696 [1,241] Biology,phylogenetics
PhyloAcc 1.0 [1,242] Phylogenetics
PhyloBayes 3.3f [1,243] Biology,bioinformatics,phylogenetics
phyloFlash 3.3b4 [1,244] Phylogenetics
phylonet 3.5.7, 3.8.2 [1,245] Biology, phylogenetics
PhyloParser 20180404 [1,246] Phylogenetics
PhyloPhlAn2 0.41 [1,247] Phylogenetics
phylopypruner 1.2.3 [1,248] Phylogenetics
PhyloSift 1.1 [1,249] Biology, genomics, phylogenetics, taxonomy
phyloTF2 20210726 [1,250] Bioinformatics, genomics, alignment
Phyluce 20180727, 20190308, 20191015 [1,251] Biology,bioinformatics,ngs,sequencing
PhyML 3.0, 3.1 [1,252] Biology,bioinformatics,phylogenetics
phynd 20200409 [1,253] Phylogenetics
Physher 1.0.2 [1,254] Phylogenetics
PHYUTILITY 2.7.1 [1,255] Biology, bioinformatics
Phyx 1.1 [1,256] Phylogenetics
PIA2 20180305 [1,257] Biology, phylogenetics
Picard-tools 2.5.0, 2.9.0, 2.9.2 [1,258] Biology,bioinformatics,ngs
PICRUSt 1.1.3, 1.1.4, 2.3.0b [1,259] Biology, phylogenics
PICSL 1.3 [1,260] Imaging, Atlas, Segmentation
Piggy 20171220 [1,261] Biology, bioinformatics, ngs
Pigz 2.4 [1,262] Compression
PILON 1.22, 1.24 [1,263] Biology, bioinformatics, ngs, phylogenetics
Pindel 0.2.5b8 [1,264] Biology, phylogenetics
pipe-clip 1.1.0 [1,265] Biology,NGS
pipits 1.3.6, 1.4.0 [1,266] Biology, sequencing
Piranha 1.2.1 [1,267] Biology,phylogenetics
PlantTribes 1.0.4 [1,268] Phylogenetics
plasflow 1.1 [1,269] Biology, phylogenetics
PLAST 1.0, 2.3.2 [1,270] Biology,bioinformatics
platanus 1.2.4 [1,271] Phylogenetics
Platypus 0.8.1 [1,272] Biology,bioinformatics,ngs
PLEK 1.2.2 [1,273] Biology, phylogenetics
Plink 1.90b3.39, 2.00a2, 2.00a3LM [1,274] Biology,bioinformatics,genomics,phylogenetics
plinkseq 0.10 [1,275] Biology, bioinformatics, library
plotsr 0.5.4 [1,276] genomics, biology
PLUMED 2.7.3, 2021.2 [1,277] Computational Chemistry, Molecular Dynamics
pod5 20220621 [1,278] sequencing
PolyGembler 1.0 [1,279] Phylogenetics
PolyPHen 2.2.2.r405b [1,280] Biology, genomics
polyply 1.3.0 [1,281] Phylogenetics, Biology
pomoxis 0.1.11, 0.2.5, 0.3.2 [1,282] Biology, phylogenetics
popcorn 20211104 [1,283] Phylogenetics, biology
PopLDdecay 3.40 [1,284] Phylogenetics
popoolation 1.2.2 [1,285] Biology, phylogenetics
Porechop 0.2.4 [1,286] Phylogenetics
Poretools 0.6.1 [1,287] Phylogenetics
portcullis 1.2.3 [1,288] Phylogenetics
PosiGene 20171113 [1,289] Biology, phylogenetics
POV-Ray 3.7 [1,290] 3D Graphics
pplacer 1.1.alpha19 [1,291] Biology, bioinformatics, phylogenics, taxonomy
PRANK 170427, 20150803 [1,292] Biology, bioinformatics, alignment
Predector 20201110 [1,293] Phylogenetics
preplot 14.0.2 []
Preseq 0.0.4 [1,294] Biology, bioinformatics, ngs
PRICE 1.2 [1,295] Biology, bioinformatics, ngs
Primer3 2.3.4 [1,296] Biology,bioinformatics,genomics
primus 1.8.0 [1,297] Biology, phylogenetics
PRINSEQ 0.20.4 [1,298] Biology, sequencing
PRINSEQ++ 1.2 [1,299] Phylogenetics
ProbABEL 0.4.2, 0.4.3, 0.4.5 [1,300] Genomics, bioinformatics, gwas
probalign 1.4 [1,301] Biology, bioinformatics, ngs
Processing 3.4 [1,302] Java, language, programming, visual
Prodigal 2.6.2, 2.6.3 [1,303] Biology, genomics
ProDy 2.0 [1,304] Phylogenetics
Program Database Toolkit 3.20, 3.22, 3.24 [1,305] Language, development, performance analysis
PROJ 4.9.3, 5.1.0, 8.0.1 [1,306] Library, geospatial, cartography
Prokka 1.12, 1.14.6 [1,307] Biology, bioinformatics, genomics, assembly
Proovread 1.03rcl, 2.12, 2.13 [1,308] Biology, genomics, ngs
ProSplign 1.0.0 [1,309] Phylogenetics
Protege 5.1.0 [1,310] Ontology
Proteinortho 4.26, 5.11, 5.16 [1,311] Biology, genomics
ProtExcluder 1.2 [1,312] Biology, phylogenetics
ProtHint 2.6.0 [1,313] Biology, bioinformatics, genomics
protobuf 2.5.0, 3.5.1 [1,314] Google, libraries
PROVEAN 1.1.5 [1,315] Biology, genomics
PRSice 2.3.3 [1,316] Phylogenetics
Pseudofinder 1.0 [1,317] Phylogenetics
PsiCLASS 1.0.1 [1,318] Phylogenetics
PSMC 0.6.5 [1,319] Phylogenetics
psRobot 1.2 [1,320] Phylogenetics
Pufferfish 20200417 [1,321] Phylogenetics
PureCLIP 1.1.1 [1,322] Phylogenetics
Purge_Dups 1.0.1 [1,323] Phylogenetics
purge_haplotigs 1.1.2 [1,324] Sequencing, bioinformatics, biology
pyani 0.2.10 [1,325] Phylogenetics
Pybedtools 0.8.2 [1,326] Phylogenetics
PyBSASeq 20200623 [1,327] Phylogenetics
PyCharm 2018.3 [1,328] Editor, ide, programming, python
pychopper 2.5.0, 2.7.1 [1,329] Phylogenetics, sequencing
PyCogent 1.9 [1,330] Biology, genomics
PyDeface 2.0.0 [1,331] MRI, imaging
pyEGA3 3.4.1 [1,332] Biology, Genomics, Utility
PyEXR 0.3.10 [1,333] Programming, python, openexr
Pyfaidx 0.5.2 [1,334] Biology, bioinformatics, ngs, sequencing
pyfasta 0.5.2 [1,335] Phylogenetics
pygot 20170518 [1,336] Biology, phylogenetics
pyhdf 0.9.0 [1,337] Library, hdf4
PyHIST 1.0 [1,338] Biology, Histology, Image segmentation
PyPHLAWD 20180416, 20190414 [1,339] Biology, phylogenetics
Pyroms 1.0 [1,340] Oceanography
PyRosetta r56324 [1,341] Biology,structure,modeling
pyrpipe 0.0.3 [1,342] Phylogenetics
Pysamstats 1.1.2 [1,343] Phylogenetics
PySLURM 18.08.04 [1,344] SLURM
Python 3.6.3, 3.6.5, 3.8 [1,345] Language, scripting, development
Python-core 3.6.5, 3.7, 3.8 [1,346] Language, scripting, development
Python2 2.7.11 [1,347] Language, scripting, development
PyTorch 1.11.0, 1.9.0 [1,348] Library, math
pytorch 1.7.1, 1.8.1, 1.9.0 [1,349] Library, math
PyVCF 0.6.0, 0.6.8 [1,350] Biology, phylogenetics
PyVista 0.26.1 [1,351] Phylogenetics
pyweka 0.3.18 [1,352] Phylogenetics
QAPA 1.3.1 [1,353] Phylogenetics
qcat 1.1.0 [1,354] Phylogenetics
qctool 2.0.1 [1,355] Phylogenetics
QD 2.3.22 [1,356] Library,c,math
QDD 3.1.2 [1,357] Biology, genomics, ngs
QGIS 2.18.0, 3.14.0 [1,358] GIS
QIIME 1.9.1 [1,359] Biology, bioinformatics, metagenomics
QIIME2 2020.8, 2021.11, 2021.4 [1,360] Biology, bioinformatics, metagenomics
QMCPACK 3.4.0 [1,361] Library
QRNA 2.0.4 [1,362] Phylogenetics
QT 4.8.3, 5.12.9, 5.15.4 [1,363] UI Framework
QTL-seq 2.2.2 [1,364] Biology, Sequencing, Pipeline
QTLtools 1.2, 1.3.1 [1,365] Phylogenetics
Quake 0.3 [1,366] Biology, sequencing
QualiMap 2.1.2 [1,367] Biology,sequence alignment
Quantas 1.0.4, 1.0.8, 1.0.9 [1,368] Biology,bioinformatics,ngs
quantisnp 2 [1,369] bioinformatics, genomics
QuartetScores 1.0.0 [1,370] Phylogenetics
QUAST 4.4, 5.0.0, 5.0.2 [1,371] Biology, bioinformatics, ngs, sequencing, rna-seq
quickmerge 0.3 [1,372] Phylogenetics
Quickquartet 1.0.0 [1,373] Biology,bioinformatics,ngs
QUIP 20201029, 20210626 [1,374] Phylogenetics
QuorUM 1.0.0 [1,375] Biology
R 4.0, 4.1, 4.2 [1,376] Statistics
r-index 20190711 [1,377] Phylogenetics
r8s 1.8, 1.81 [1,378] Phylogenetics
RACA 0.9.1.1 [1,379] Biology, ngs
Racon 1.3.3, 1.4.10, 1.4.13 [1,380] Phylogenetics
RADICAL 0.2 [1,381] Biology, bioinformatics, genomics
radorgminer 0.9 [1,382] Genomics, Biology, Sequencing
RaGOO 1.11 [1,383] Phylogenetics
Ragout 2.3 [1,384] Genomics
RagTag 1.0.0, 2.0.1 [1,385] Phylogenetics
rainbow 2.0.4 [1,386] Biology, sequencing
Rainbowfish 0.1.0 [1,387] Phylogenetics
RAiSD 2.8 [1,388] Phylogenetics
Randfold 2.0.1 [1,389] Biology, RNA
ranger 1.9.3 [1,390] File Management
rapidsai 21.10, 21.12, 22.04 [1,391] Data Science
rapidtide 1.9.0 [1,392] Phylogenetics
RAPSearch 2.24 [1,393] Biology, phylogenetics
Rascaf 1.0.2 [1,394] Biology, bioinformatics
RAVE 2.1 [1,395] Biology, phylogenetics
Raven 1.8.1 [1,396] assembler
RAxML 8.2.10, 8.2.12, 8.2.8 [1,397] Application, biology, philogenetics
RAxML-NG 0.9.0, 1.0.2, 1.1.0 [1,398] Phylogenetics
razers3 3.5.7 [1,399] Biology, phylogenetics
rbp-maps 0.1.4 [1,400] Phylogenetics
rclone 1.57.0, 1.58.1 [1,401] Cloud
Rcorrector 1.0.4 [1,402] Phylogenetics
RDKit 2020092 [1,403] Chemiformatics
rDnaTools 0.1.3 [1,404] Phylogenetics
READemption 1.0.0 [1,405] Phylogenetics
REAPR 1.0.18 [1,406] Biology,bioinformatics,assembly
Rebaler 0.2.0 [1,407] Phylogenetics
reCOGnizer 1.3.3 [1,408] Phylogenetics
recon 1.08 [1,409] Biology,sequencing
Redis 2.8.13, 2.8.19 [1,410] Daemon, data, server
REDItools2 20200701 [1,411] Phylogenetics
Redundans 0.14a [1,412] Biology, phylogenetics
ReFrame 3.2 [1,413] Hpc, internal
regtools 0.5.2 [1,414] Biology, RNA-seq, Genitics
RELION 3.0.2, 3.0b, 3.1.0 [1,415] Biology, imaging
RelocaTE2 2.0.1 [1,416] Phylogenetics
REMORA 1.8.2, 1.8.3, 1.8.5 [1,417] System, profiler
REPdenovo 20170222 [1,418] Biology, phylogenetics
RepeatAnalysis 0.10.0, 0.12.2 [] Biology, phylogenetics
RepeatAnalysisTools 20210506 [1,419] Biology, Genomics, Sequencing, Utility
RepeatExplorer 20150506, 20180517 [1,420] Biology, bioinformatics, ngs
RepeatMasker 4.0.5, 4.0.9, 4.1.1 [1,421] Biology, bioinformatics
RepeatModeler 1.0.8, 2.0 [1,422] Biology,bioinformatics
repeatscout 1.0.5 [1,423] Biology
RepeatSeq 0.8.2 [1,424] Phylogenetics
reptile 1.1 [1,425] Biology,NGS,error correction
ResFinder 4.0 [1,426] Biology, genomics
Resistome 20170111 [1,427] Phylogenetics
RevBayes 1.0.7, 1.0.9, 1.1.1 [1,428] Biology, phylogenetics
RFMIX 2.03 [1,429] Phylogenetics
RGAugury 20220107 [1,430] Sequencing, biology
RGI 4.2.2, 5.1.1 [1,431] Phylogenetics
RGIS 20180211, 20180814 [1,432] RiverGIS
RHash 1.3.3 [1,433] GNU
RiboCode 1.2.11 [1,434] Phylogenetics
riboPicker 0.4.3 [1,435] Biology,sequence
RiboTaper 1.3.1a [1,436] Phylogenetics
RIGERJ 2.0.2 [1,437] Phylogenetics
rMATS turbo 4.1.2 [1,438] Biology, Sequencing, Genomics
rmats2sashimiplot 2.0.3 [1,439] Phylogenetics
Rmpi 0.6.9 [1,440] Statistics, R, mpi
RNAFramework 2.7.2 [1,441] Biology, RNA, Sequencing
RNAhybrid 2.1.1 [1,442] Biology, bioinformatics, genomics
RNAmmer 1.2 [1,443] Biology, RNA-seq
rnaQUAST 1.5.1 [1,444] Biology,bioinformatics,ngs,sequencing,rna-seq
RNAsalsa 0.8.1 [1,445] Biology, phylogenetics
rnaseqlib 20150721 [1,446] Biology, phylogenetics, RNA-seq
RNAstructure 6.3 [1,447] Biology, sequencing
Roary 3.12.0, 3.4.1 [1,448] Biology,genomics
ROOT 5.34.17, 6.0, 6.06.02 [1,449] Data Analysis
ROOTPy 20160323 [1,450] Data Analysis
Rosetta 2014wk4, 2019.35.60890 [1,451] Biology,structure,modeling
RoseTTAFold 1.0.0 [1,452] Phylogenetics
rrnaselector 1.0 [1,453] Biology, sequencing
RSEG 0.4.8 [1,454] Biology, bioinformatics, genomics
RSEM 1.2.31, 1.2.7, 1.3.3 [1,455] Biology,bioinformatics,ngs,sequencing
RSeQC 2.6.4, 3.0.0 [1,456] Biology,ngs,rna-seq
RStudio 1.4, 2021.09.0, 2022.02.3 [1,457] Statistics
RTGTools 3.7.1 [1,458] Biology, NGS
Ruby 2.5.1 [1,459] Programming,scripting,language
Rust 1.48.0, 1.52.1, 1.62.1 [1,460] Programming
rvtests 2.1.0 [1,461] Genomics, Biology, Sequencing
S.A.G.E 6.4.2 [1,462] Phylogenetics
Sabre 1.0 [1,463] Phylogenetics
saffrontree 0.1.2 [1,464] Phylogenetics
Sailfish 0.6.3 [1,465] Biology,genomics,ngs,rna-seq
Salmon 1.1.0, 1.5.2, 1.8.0 [1,466] Biology, RNA-seq
SALSA 20171009, 20191001 [1,467] Biology, ngs, pacbio
Sambamba 0.6.3, 0.6.6, 0.6.9 [1,468] Biology, NGS
samblaster 0.1.14, 0.1.24 [1,469] Biology,bioinformatics,ngs,sequencing
sampledock 0.5.1 [1,470] molecular dynamics, AI
SAMStat 1.08 [1,471] Biology,bioinformatics,ngs,sequencing
Samtools 1.7, 1.8, 1.9 [1,472] Biology,bioinformatics,ngs,sequencing
SAS 9.3, 9.4 [1,473] Statistics, data analysis
Sate 2.2.7 [1,474] Biology, bioinformatics, phylogenetics
Satsuma 3.0 [1,475] Phylogenetics
Satsuma2 3.1 [1,476] Phylogenetics
satsuma2 20161123 [1,477] Phylogenetics
sc-im 0.8.2 [1,478] Software, data visualization
Scala 2.11.5, 3.0.1 [1,479] Programming, language, java
Scalablast 2.4.53 [1,480] Application, biology, genomics
ScaLAPACK 2.0.2, 2.1.0 [1,481] Programming,library
scallop 0.10.5 [1,482] Phylogenetics
Scalpel 0.1.1, 0.5.3 [1,483] Biology, NGS
Schrodinger Suite 2019-3, 2020-4, 2021-2 [1,484] Computational Chemistry, Molecular Dynamics
Scipion 1.2 [1,485] Image Processing
SCIrun 5.0.Z [1,486] Phylogenetics
Scoary 1.6.16 [1,487] Phylogenetics
Scons 2.5.1, 3.1.2 [1,488] Programming
SCOP 20180311 [1,489] Biology, Scaffolding, Assembly
Scrappie 1.4.2 [1,490] Biology, Genomics
SCRATCH-1D 1.0, 2.0 [1,491] Biology, bioinformatics, ngs
Screen 4.8.0 [1,492] GNU, Terminal Multiplexer
SCRIPTURE 20101211 [1,493] Biology, bioinformatics, genomics
Scythe 0.991 [1,494] Biology, NGS
sdsl 2.1.1 [1,495] Library, c++
SE-MEI 0.1.0 [1,496] Phylogenetics
SeCaPr 1.1.12, 2.0.2, 2.1.1 [1,497] Phylogenetics
Segemehl 0.1.9, 0.3.4 [1,498] Biology,bioinformatics,ngs,sequencing
segment-liftover 20211021 [1,499] bioinformatics, biology, genome
SEPP 20160614 [1,500] Biology, phylogenetics
Seq-Gen 1.3.3 [1,501] Biology,phylogenetics
seq_crumbs 20150120 [1,502] Biology, sequence, genomics, utilities
SeqKit 0.10.2, 0.8.0, 2.0.0 [1,503] Biology, phylogenetics
seqmagick 0.8.4 [1,504] Biology, bioinformatics
SeqMap 1.0.13 [1,505] Biology,bioinformatics,sequence,ngs
SEQPower 1.1.1 [1,506] Genomics, bioinformatics, phylogenetics
SeqPrep 0.5, 1.1 [1,507] Biology,bioinformatics,ngs,sequencing
seqscreen 3.3 [1,508] Sequencing, biology
seqtk 1.3, 20140729 [1,509] Bioinformatics, Genomics, NGS
SEQuel 1.0.1 [1,510] Biology,bioinformatics,ngs
SequelQC 1.1.0 [1,511] Phylogenetics
seqwish 0.7, 20190509 [1,512] Phylogenetics
SeqyClean 1.8.10 [1,513] Biology,bioinformatics,ngs,sequencing
SeSiMCMC 4.36 [1,514] Biology, Sequencing
SExtractor 2.19.5 [1,515] Astronomy
SHAPE-MaP 1.2 [1,516] Biology, phylogenetics
SHAPEIT 2.12, 2.5 [1,517] Biology,SNP
SHAPEIT4 4.2.2 [1,518] Biology, Sequencing, Phasing
ShapeMapper 2.1.3, 2.1.5 [1,519] Biology, phylogenetics
SHARCGS 1.2.11 [1,520] Biology, NGS, de novo assembly
Shasta 0.1.0 [1,521] Phylogenetics
SHEsisPlus 1.0, 1.01 [1,522] Biology, genetics
shogun 6.1.3 [1,523] Phylogenetics
Shortbred 0.9.4 [1,524] Phylogenetics
SHRiMP 2.2.3 [1,525] Biology, genomics, ngs
shustring 2.6 [1,526] Biology, sequencing
SibeliaZ 1.2.2, 1.2.3, 1.2.4 [1,527] Bioinformatics, genomics, alignment
SICER 1.1 [1,528] Biology, ChIP-Seq
Sickle 1.200, 1.33 [1,529] Biology, bioinformatics, ngs
Siesta 3.2, 4.1b2, 4.1b3 [1,530] Chemistry
SIFT 4.0.3b [1,531] Biology,bioinformatics,genomics
SIGffRid 1.1 [1,532] Phylogenetics
SignalP 4.1c, 5.0b [1,533] Biology, phylogenetics
SiLiX 1.2.11, 1.3.0 [1,534] Phylogenetics
silo 4.7 [1,535] IO,library
sim4 20121010 [1,536] Biology, bioinformatics, genomics
Sim4Life 7.0.1 [1,537] Biology,simulation
Simka 1.5.3 [1,538] Phylogenetics
SimNIBS 3.2.1 [1,539] Phylogenetics
SimSeq 4.12.2011 [1,540] Biology, bioinformatics, ngs, phylogenetics
Simulia 2019 [1,541] Simulation, visualization
SInC 20140120 [1,542] Biology, phylogenetics
sine_scan 1.1.1 [1,543] Phylogenetics
Singularity 3.7.4 [1,544] Containers
SIPeS 2.0 [1,545] Biology, bioinformatics, ChIP-Seq
sisl 0.8.3 [1,546] Physics, Tight-binding
skmer 3.2.1 [1,547] Phylogenomics, biology
Slamdunk 0.4.1, 0.4.2 [1,548] Phylogenetics
SLAW 20211217 [1,549] Chromatography, Spectrometry
Slicer 4.13.0, 4.3.1, 5.0.3 [1,550] biology,bioinformatics,neuroscience,imaging
slow5tools 0.5.1 [1,551] biology, sequencing
slurm-drmaa 1.1.2, 1.1.3 [1,552] Libraries, slurm, api, drmaa
smalt 0.7.6 [1,553] Application, biology, phylogenetics
SMARTdenovo 20180219 [1,554] Biology, phylogenetics
smartie-sv 20180308 [1,555] Phylogenetics
SMC++ 1.15.4 [1,556] Biology, Genomics, Sequencing
Smetana 1.1.0 [1,557] Phylogenetics
SMR 1.03 [1,558] Biology, Genomics
SMRT-SV 2.0.0 [1,559] Biology, bioinformatics, ngs
SMS 1.7 [1,560] Biology, bioinformatics
Smudgeplot 0.2.4 [1,561] Phylogenetics
Snakemake 6.4.1, 7.5.0 [1,562] Biology, bioinformatics, workflow
SNAP 0.15.4, 2.0.0, 20100728 [1,563] Biology,bioinformatics,sequencing
SNAPE-pooled 20130407 [1,564] Biology, SNP
SNeP 1.1 [1,565] Biology,phylogenetics
Sniffles 1.0.11, 1.0.6, 1.0.8 [1,566] Phylogenetics
Sniffles2 2.0.6 [1,567] Biology, Bioinformatics
Snippy 20160419, 4.6.0 [1,568] Biology, phylogenetics
SNP-Pipeline 1.0.1 [1,569] Biology, phylogenics
SNP-sites 2.0.3 [1,570] Biology, SNP
snp2hla 1.0.3 [1,571] Biology, Bioinformatics, Genomics
SnpEff 4.3r, 4.3t, 5.0 [1,572] Biology,bioinformatics,variant annotation
snpflip 20190515 [1,573] Biology, Phylogenetics
SNPGenie 20190620 [1,574] Phylogenetics
SNPhylo 20140701 [1,575] Biology,phylogenetics
SNPsplit 0.5.0 [1,576] Biology,bioinformatics,sequencing
SNPTEST 2.5.2 [1,577] Phylogenetics
SOAPaligner 2.21 [1,578] Phylogenetics
SOAPdenovo 1.05, 2.04 [1,579] Biology,ngs
SOAPdenovo-Trans 1.01, 1.03 [1,580] Biology,ngs
SOAPec 2.03 [1,581] Biology, phylogenetics
SOAPnuke 2.1.0 [1,582] Phylogenetics
SOAPsplice 1.10 [1,583] Biology,ngs
SODA 20200930 [1,584] Biology
SOLAR 8.4.2 [1,585] Phylogenetics
SomaticSeq 3.6.2 [1,586] Phylogenetics
SortaDate 20190705 [1,587] Phylogenetics
SortMeRNA 2.1, 4.0 [1,588] Biology, sequencing, NGS
SourceTracker2 2.0.1 [1,589] Phylogenetics
Sourmash 2.0.1 [1,590] Phylogenetics
SoX 14.4.2 [1,591] Phylogenetics
SpaceRanger 1.3.1 [1,592] Phylogenetics
SPAdes 3.15.3, 3.7.1, 3.8.0 [1,593] Biology,bioinformatics,ngs
SparCC 201608 [1,594] Microbial Ecology
Spark 2.2.0, 3.1.1 [1,595] Spark, hadoop
sparsehash 2.0.3 [1,596] Google, API
SPARTA+ 2.60 [1,597] Chemistry
Spec2nii 0.3.4 [1,598] Phylogenetics
SpeedSeq 0.1.2 [1,599] Phylogenetics
Spidey 20150922 [1,600] Biology, genomics, bioinformatics
SpinalCordToolbox 5.4 [1,601] Phylogenetics
SplAdder 2.4.2 [1,602] Phylogenetics
SpliceGrapher 0.2.5 [1,603] Biology, sequencing
SpliceTrap 0.90.5 [1,604] Biology, bioinformatics, genomics, NGS
SPM 12b, 8, 8r5236 [1,605] Biology,bioinformatics,matlab
spruceup 2019.2.3 [1,606] Phylogenetics
Sputnik 1.0 [1,607] Biology,bioinformatics,repeats
spyder 4.1.4, 5.1.1 [1,608] IDE, editor, programming, scripting
SQANTI 1.2 [1,609] Phylogenetics
SQANTI2 5.0 [1,610] Phylogenetics
SQANTI3 0.1, 1.6, 4.2 [1,611] Phylogenetics
SQL Developer 4.1.2 [1,612] Programming, oracle, sql
SQLite 3.33.0, 3.8.8.2 [1,613] Database
SqueezeMeta 1.4.0, 1.5.2 [1,614] Phylogenetics
squigglekit 1.0.0 [1,615] Data Visualization and Analysis, biology
squigglenet 1.0 [1,616] Sequencing, biology
SRA 2.10.9, 3.0.0 [1,617] Biology,bioinformatics,sra
sra-human-scrubber 1.1 [1,618] CSV_categories
SRAssembler 1.0.0 [1,619] Phylogenetics
SSM 20210511 [1,620] Phylogenetics
SSPACE 2.0, 3.0 [1,621] Biology,bioinformatics,ngs
ssr_pipeline 0.951 [1,622] Biology, DNA sequencing,
Stacks 2.53, 2.55, 20190403 [1,623] Biology, bioinformatics, genomics, ngs
Staden 1.14.6 [1,624] Biology, phylogenetics
Stampy 1.0.31 [1,625] Biology, bioinformatics, sequencing
staphb-toolkit 1.2.0, 1.3.10 [1,626] Biology
STAR 2.7.5c, 2.7.6a, 2.7.9a [1,627] Biology, ngs, rna-seq
STAR-CCM+ 14.04.011, 15.02.009, 8.06 [1,628] Mechanical Engineering
STAR-Fusion 1.1.0, 1.3.1, 1.9.1 [1,629] Biology, transcriptome
starseqr 0.6.7 [1,630] Phylogenetics
Stata 10.1, 13 [1,631] Statistics
stringMLST 0.4 [1,632] Biology, bioinformatics, CHiP-Seq
Stringtie 1.3.4d, 2.0.4, 2.1.3b [1,633] Biology,bioinformatics,ngs,sequencing,alignment
Structure 2.3.3, 2.3.4 [1,634] Biology,bioinformatics,population genetics
Structure_threader 1.3.10 [1,635] Utility, Wrapper, Structure
stylegan3 20211028 [1,636] AI, Image Processing
SU2 7.0.6 [1,637] Phylogenetics
Subread 1.6.2, 2.0.0, 2.0.3 [1,638] Biology, sequencing, SNP
Subversion 1.9.7 [1,639] Revision Control
SUMO 1.13.0, 1.2.0, 1.9.2 [1,640] Simulation, traffic, engineering
SUNDIALS 2.3.0, 2.5.0, 3.0.0 [1,641] Math, Numerical Solvers
supercell 20170602 [1,642] Biology, NGS
SuperCRUNCH 1.2.1 [1,643] Phylogenetics
Supernova 1.2.1, 2.0.0, 2.1.1 [1,644] Biology, phylogenetics, ngs
SUPPA 2.3 [1,645] Phylogenetics
Survival_Kit 6.12 [1,646] Clinical Biometrics
SURVIVOR 1.0.6 [1,647] Phylogenetics
SVDetect 0.8b [1,648] Biology,ngs,genomics
svim 1.4.2 [1,649] Biology
svim-asm 1.0.2 [1,650] Biology
swarm 1.2.11 [1,651] Data Analysis
Sweed 3.3.2 [1,652] Biology, phylogenetics
SWIG 2.0.9, 3.0.12, 3.0.8 [1,653] Library, development, C++, python
SWSC-EN 1.0.0 [1,654] Phylogenetics
Synima 20210908 [1,655] Phylogenetics
syri 1.5.4 [1,656] Phylogenomics, biology
TACO 0.7.3 [1,657] Phylogenetics
Taiyaki 5.0.1 [1,658] Phylogenetics
talesf 20160814 [1,659] Phylogenetics
Tandem-Genotypes 1.4.0 [1,660] Phylogenetics
Tantan 13 [1,661] Particle NGS, genomics
Tapestri 2.0.1 [1,662] Phylogenetics
tapir 20160825 [1,663] Biology, phylogenetics
TAPIS 1.2.1 [1,664] Biology, sequencing
TASSEL 5.0, 5.2.20, 5.2.29 [1,665] Biology,bioinformatics,genomics,wga
TAU 2.23, 2.26, 2.26.3 [1,666] Library, profiling and optimization
Tax4Fun 0.3.1 [1,667] Phylogenetics
taxMaps 0.1 [1,668] Biology, phylogenetics, taxonomy
TaxonKit 0.9.0 [1,669] Phylogenetics
Taxtastic 0.5.7 [1,670] Biology, taxonomy
taxtastic 0.9.1 [1,671] Biology, bioinformatics, phylogenics, taxonomy
tbb 2017_20161128 [1,672] Library
tcllib 1.18 [1,673] Library
tcoffee 10.00.r1613, 9.03.r1318 [1,674] Bioinformatics
TDNAscan 20210304 [1,675] Phylogenetics
Tecplot 360 EX 2015R1 [1,676] Plotting, animation, cfd, simulations
tellseq 1.0.0 [1,677] Sequencing, Phylogenetics
TEMP 20170731 [1,678] Phylogenetics
TEMP2 0.1.4 [1,679] Phylogenetics
TensorFlow 2.6.0, 2.7.0, 2.8.0 [1,680] Library, math
TESS 2.3.1 [1,681] Biology, bioinformatics, genomics, markov
Test 1.0 [1,682] Shell
TetGen 1.5.0 [1,683] Tetrahedral meshes
TEToolkit 1.5.1 [1,684] Biology, bioinformatics, sequencing
TEtools 20180213 [1,685] Biology, phylogenetics
Texlive 20191127, 2020 [1,686] Formatting, typesetting, document preparataion
TGICL 2.1 [1,687] Biology,bioinformatics,ngs,sequencing
TGSGapCloser 1.0.3 [1,688] Phylogenetics
the_silver_searcher 2.2.0 [1,689] Search
Theano 1.0.4 [1,690] Library, math, gpu
Themisto 0.2.0, 1.1.0 [1,691] Genomics, Alignment
Tiara 1.0.2 [1,692] Phylogenetics
tiff 3.8.0, 4.0.10 [1,693] Imaging
Tigmint 1.1.2 [1,694] Phylogenetics
Tmux 2.9, 3.1 [1,695] GNU
TNTBLAST 2.04 [1,696] Biology
ToFU2 v17 [1,697] Biology, bioinformatics, ngs, iso-seq
toil 3.3.0, 3.3.3 [1,698] Biology, bioinformatics
Tombo 1.4, 1.5, 1.5.1 [1,699] Biology, genomics, ngs
Tophat 2.1.0, 2.1.1, 2.1.2 [1,700] Biology,bioinformatics,ngs,sequencing
torch-geometric 1.3.2 [1,701] Phylogenetics
TotalView 8.12 [1,702] Parallel Computing
TPMcalculator 0.0.3 [1,703] Phylogenetics
TPP 4.7.0, 4.7.1, 5.0.0 [1,704] Biology, chemistry, nmr
TraCeR 20160519 [1,705] Biology, phylogenetics
TrackTools 2011 [1,706] Software
TrackVis/DTK 0.5.2.2, 0.6.0.1 [1,707] Biology,bioinformatics,neuroscience,imaging
Tracula 5.3.2014_05_26 [1,708] Biology,bioinformatics,neuroscience,imaging
traitRate 1.1 [1,709] Biology, evolution
Trans-ABySS 2.0.1 [1,710] Biology, phylogenetics
TransDecoder 5.3.0, 5.4.0, 5.5.0 [1,711] Biology, ngs
TRANSIT 2.5.2, 3.2.3 [1,712] Phylogenetics
Transrate 1.0.1 [1,713] Biology,assembly
TransVar 2.3.3 [1,714] Biology, bioinformatics, phylogenetics
TreeBreaker 20160621 [1,715] Biology, phylogenetics
TreeMix 1.12 [1,716] Biology, phylogenetics
treePL 20150305 [1,717] Biology, bioinformatics, phylogenetics
TREEPUZZLE 5.3 [1,718] Biology, phylogenetics
TreeShrink 1.3.1, 1.3.2 [1,719] Phylogenetics
TreeTime 0.7.5, 0.8.1 [1,720] Phylogenetics
trelis 16.3 [1,721] Geometry
TRF 4.04, 4.09.1 [1,722] Biology,bioinformatics,genomics
Trilinos 12.12.1, 12.18.1, 12.6.4 [1,723] Mathematical Algorithms
Trim Galore 0.4.4, 0.5.0, 0.6.5 [1,724] Biology,bioinformatics,ngs
trim_isoseq_polya 0.0.3 [1,725] Biology, Genetics, Sequencing
trimAl 1.2 [1,726] Biology,genomics,sequence alignment
TriMetAss 1.1 [1,727] Biology,bioinformatics,ngs
Trimmomatic 0.33, 0.36, 0.39 [1,728] Biology,bioinformatics,ngs
Trinity r20130225, r20131110, r20140413 [1,729] Biology,bioinformatics,ngs,sequencing,rna-seq
Trinotate 3.0.1, 3.2.0 [1,730] Biology
triobinning 0.2.3 [1,731] Phylogenomics, biology
TRIPLEC 1.0 [1,732] Biology, bioinformatics
TRITONSERVER 21.08 [1,733] Machine Learning Inference Server
tRNAscan-Se 1.23 [1,734] Biology,bioinformatics,ngs
TRUST4 1.0.2b [1,735] Phylogenetics
Trycycler 0.4.2 [1,736] Phylogenetics
TURBOMOLE 7.4.1 [1,737] Quantum Chemistry
TWINSCAN 4.1.2 [1,738] Biology,genomics
Ubuntu 20.04 [1,739] Ubuntu Linux
UCSC 20200320, 20210803 [1,740] Genomics, bioinformatics
ucsc-fafiltern 377 [1,741] Phylogenetics
ucsc-maskoutfa 377 [1,742] Phylogenetics
UCX 1.11.2, 1.9.0 [1,743] Parallel Programming, development, library
UDUNITS 2.2.17 [1,744] Library, data, units
ufraw 0.22 [1,745] Data Mining
ugtm 1.1.6 [1,746] Statistics, modeling
UKFractography 20200127 [1,747] Phylogenetics
umi-tools 0.5.5 [1,748] Phylogenetics
UNAFold 3.8 [1,749] Biology, genome, RNA, folding
Unanimity 20171108, 3.4.1 [1,750] Programming,library,cpp
UNCALLED 2.2 [1,751] Biology, bioinformatics, genomics
Unicycler 0.4.8 [1,752] Phylogenetics
Unrar 0.0.1, 4.20 [1,753] Unarchiver, utility
uproc 1.2.0 [1,754] Biology, genome
USEARCH 9.0.2132, 9.1.13, 9.2.64 [1,755] Biology,bioinformatics,alignment,sequence analysis
UShER 0.1.4, 0.4.1, 0.5.2 [1,756] Phylogenetics
V-Phaser 02112013 [1,757] Biology, phylogenetics
v-pipe 2.0.0 [1,758] Biology, bioinformatics, genomics, sequencing, virus
VAIR 0.7.0 [1,759] Geospatial Data Modeling
Valgrind 3.11.0, 3.15.0, 3.8.1 [1,760] Computer Programming
Valouev 20160325 [1,761] Biology, Phylogenetics
vamb 3.0.2 [1,762] Biology
VAMPIR 9.1 [1,763] High Performance Computing
VarDictJava 1.6.0, 20160521, 20170531 [1,764] Biology, phylogenetics
varnorm 0.21 [1,765] Biology, bioinformatics
VarScan 2.3.6 [1,766] Biology,bioinformatics,ngs
VarSim 0.8.4, 0.8.6 [1,767] Phylogenetics
VarSimLab 20180220, 20180921 [1,768] Biology, simulation, genomics
vasp 5.4.4, 6.1.0, 6.2.0 [1,769] Quantum Chemistry
vaspkit 1.2.5 [1,770] Phylogenetics
VAST-TOOLS 2.5.1, 20150506 [1,771] Biology, rna-seq, ngs, splicing
VCF-kit 0.2.6 [1,772] Phylogenetics
vcf-validator 0.6 [1,773] Biology, phylogenetics
vcfanno 0.2.8, 0.3.3 [1,774] Biology, phylogenetics
vcflib 1.0.1 [1,775] Biology,bioinformatics,genomics
vcftools 0.1.15, 0.1.16, 0.1.9 [1,776] Biology,bioinformatics,genomics
vcontact 20190512 [1,777] Phylogenetics
VDJtools 1.1.7, 1.2.1 [1,778] Biology, phylogenetics
Velvet 1.2.10, 1.2.10-long [1,779] Computational Biology, genomics
VEP 83, 88.8, 92 [1,780] Biology, genomics, ngs
Vermouth-martinize 0.7.2 [1,781] Phylogenetics
VeryFastTree 3.0.1 [1,782] Phylogenetics
vg 1.33.0, 1.38.0, 1.39.0 [1,783] Phylogenetics
vibrant 1.2.0 [1,784] genomics, virus
ViennaRNA 2.2.6, 2.4.18 [1,785] Biology, RNA-seq
ViewBS 0.1.10, 0.1.9 [1,786] Phylogenetics
Vim 8.1.1566, 8.2.2465 [1,787] Programming,scripting,language
viralmsa 1.1.10, 1.1.12 [1,788] Phylogenetics
VirSIeve 20210406 [1,789] Biology, Pipeline
VirtualCell 7.1 [1,790] Phylogenetics
VIRULIGN 1.0.2 [1,791] Phylogenetics
VirusDetect 1.7 [1,792] Phylogenetics
VirusFinder 2.0 [1,793] Biology, phylogenetics
visit 2.13.3, 3.0.1, 3.1.4 [1,794] Visualization, Animation and Analysis
VISPR 0.4.14 [1,795] Phylogenetics
VMD 1.9.1, 1.9.3 [1,796] Visualization, animation, 3d
vscode 1.38.1, 1.65.2 [1,797] IDE, editor, programming, scripting
VSearch 20151022, 20161209-2.3.4 [1,798] Biology,NGS
vt 0.57721, 20140903, 20160129 [1,799] Biology, genomics
VTC 0.9.3 [1,800] Biology, bioinformatics, VCF
VTK 8.2.0, 9.0.3, 9.1.0 [1,801] Biology,bioinformatics,neuroscience,imaging
w2rap-contigger 20161124 [1,802] Biology, genomics
Wannier90 1.2, 2.1.0 [1,803] Computational Physics
WarpedLMM 0.21 [1,804] Modeling
WaveGAN 20190829 [1,805] Machine Learning, Audio, GAN, Synthesis
WDSSII 5 [1,806] Weather, Meteorology
WebLogo 2.8.2, 3.3, 3.5.0 [1,807] Biology,bioinformatics,sequence,graphics
Weka 3.8, 3.8.5 [1,808] Statistics,machine learning
Wengan 0.2 [1,809] Biology,bioinformatics,genomics
wgd 1.1.1 [1,810] Phylogenetics
WGS Assembler 8.3rc1.r4638, 8.3rc2 [1,811] Biology, bioinformatics, genomics
Wgsim 0.3.1-r13 [1,812] Biology, phylogenetics
WHAMM 0.14a [1,813] Biology, phylogenetics
WhatsHap 1.1 [1,814] Biology, phylogenetics
whiteboxtools 1.5.0 [1,815] Phylogenetics
Wine 4.0.0, 7.0.0 [1,816] Windows, emulator
Wise 2.2.0, 2.4.1 [1,817] Biology, genome
WIsH 1.0 [1,818] Phylogenetics
WoLFPSort 0.2 [1,819] Phylogenetics
WOMBAT 20180118 [1,820] Biology, phylogenetics
workbench 4.1.1 [1,821] Nuclear Engineering
wtdbg 2.1, 2.4, 2.5 [1,822] Phylogenetics
WU BLAST 2.0 [1,823] Biology, bioinformatics
Wub 0.2.0, 0.4.0 [1,824] Biology, genomics, ngs
xander 20151222 [1,825] Biology, phylogenetics
Xapian 1.4.4 [1,826] Library
XCrySDen 1.5.60 [1,827] Computational Material Science
Xerces 3.1.4 [1,828] Phylogenetics
xesmf 0.6.2 [1,829] Grid Analysis, Climate
xpclr 1.0, 1.1.1 [1,830] Phylogenetics
Xterm 1.1 [1,831] Shell
XWAS 3.0 [1,832] Phylogenetics
XY-Meta 20200413 [1,833] Phylogenetics
XZ 5.2.2 [1,834] Compression, library
YAGO 4 [1,835] Data
YAHA 0.1.82 [1,836] Biology, ngs
YAK 0.1 [1,837] Phylogenetics
YASM 1.3.0 [1,838] Computer Programming
YASRA 2.33 [1,839] Biology,bioinformatics,ngs,sequencing
yolov4_darknet 4-pre [1,840] Machine Learning
yolov5 4.0 [1,841] Machine Learning
Zagros 1.0.0 [1,842] Biology,phylogenetics
ZEO++ 0.2.2 [1,843] Chemistry
zorro 2.2 [1,844] Biology, sequencing
Zstd 1.5.0 [1,845] Phylogenetics
ZUMIS 2.6.0 [1,846] Biology, bioinformatics, ngs, sequencing