Difference between revisions of "Applications"
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!Description {{#for_external_table:<nowiki/> | !Description {{#for_external_table:<nowiki/> | ||
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{{!}} [[{{{name}}}]] | {{!}} [[{{{name}}}]] | ||
{{!}} {{{versions}}} | {{!}} {{{versions}}} |
Revision as of 19:58, 6 July 2022
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, variant_calling | AAFTF | 0.2.5 | [4] | biology, pipeline, assembly | ABRicate | 1.0.1 | [5] | phylogenetics | ABruijn | 1.0 | [6] | biology, assembly, ngs | 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, biology | ADMB | 11.5, 12.0 | [10] | math, modeling | AdmixTools | 20150311, 7.0.2 | [11] | biology, genomics, ngs | ADMIXTURE | 1.23, 1.3.0 | [12] | biology, genomics, ngs | AEGeAn | 0.14.0, 0.16.0 | [13] | biology, genomics | AFNI | 20.3.00, 2018_04_12 | [14] | biology, neuroscience, 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, image_processing, imaging | Alder | 1.03 | [20] | biology, genomics | ALFA | 1.1.1 | [21] | phylogenetics | alienhunter | 1.7 | [22] | biology, sequencing | AliStat | 1.12 | [23] | phylogenetics | allhic | 0.9.8 | [24] | genomics, biology | ALLMAPS | 20180117 | [25] | biology, phylogenetics | ALLPATHS-LG | 42316, 44837, 49232 | [26] | biology, ngs | AlphaFold | 2.0.0, 2.1.2, 2.2.0 | [27] | protein, structure, machine_learning | 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] | chemistry, molecular_dynamics | AMICO | 1.0.1 | [32] | library, imaging, math | AMOS | 3.1.0 | [33] | biology, 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, ngs | amptorch | 20210313 | [38] | phylogenetics | amrfinderplus | 3.10.18 | [39] | phylogenetics | AMRPlusPlus | 20180508 | [40] | phylogenetics | AMUSE | 10.0, 13.1.0 | [41] | astronomy | ANGSD | 0.933 | [42] | biology, ngs | annocript | 2.0 | [43] | phylogenetics | AnnoTALE | 1.4.1 | [44] | phylogenetics | ANNOVAR | 20130221, 20150322, 20191024 | [45] | biology, genomics | Ansible | 2.5.5, 2.8.1 | [46] | workflow_automation | ansysem | 17.0, 2022r1 | [47] | physics | 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 | Appreci8 | 20180530 | [51] | biology, genomics | Apptainer | 1.0.3 | [52] | workflow_automation | APT | 1.15.0, 1.18.0, 1.20.5 | [53] | biology, genomics | ARC | 1.1.4 | [54] | biology, 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, compiler, math | ARPACK | 1.0 | [58] | math | ArrayFire | 3.4.2 | [59] | math | arriba | 2.1.0 | [60] | phylogenetics | ART | 20160417, 20160605 | [61] | phylogenetics | artemis | 18.1.0 | [62] | biology | asap | 2.0 | [63] | visualization, biology | asaq | 1.0 | [64] | alignment, sequencing, phylogenetics | ASE-ANI | 20180712 | [65] | biology, genomics, ngs | ASHS | 2.0 | [66] | biology, imaging | 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, genomics | aster | 220718 | [72] | biology, data_science, sequencing | ASTRAL | 5.6.1, 5.6.2, 5.7.7 | [73] | biology, ngs, phylogenetics | ASTRID | 2.2.1 | [74] | phylogenetics | Astropy | 2.0.8 | [75] | biology, phylogenetics | ATAT | 3.23, 3.34 | [76] | material_science | ATLAS | 3.10.1, 3.10.2, 3.11.17 | [77] | library, data_science | Atom | 1.57.0 | [78] | programming | 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, genomics | Auto3DEM | 4.05.2 | [83] | image_processing | AutoDock | 4.2.6 | [84] | biology | AutoDock-GPU | 1.5.3 | [85] | chemistry | Autometa | 20190802 | [86] | phylogenetics | automlsa2 | 0.8.1 | [87] | phylogenetics, biology, genomics | AWSCLI | 2.2.30 | [88] | utility | azoo | 1.3.1 | [89] | phylogenetics | Badread | 0.1.5 | [90] | phylogenetics | bakta | 1.3.3 | [91] | genomics, 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, genomics | bamm | 2.5.0 | [97] | phylogenetics | bamsnap | 0.2.19 | [98] | phylogenetics | Bamstats | 20140602 | [99] | biology, ngs | Bamsurgeon | 1.2 | [100] | phylogenetics | bamtofastq | 1.3.5 | [101] | phylogenetics | Bamtools | 2.4.1, 2.5.0, 2.5.1 | [102] | biology, ngs, sequencing | bamUtil | 1.0.2 | [103] | biology, genomics | BAPS | 6.0 | [104] | biology, genomics | Barrnap | 0.7, 0.9 | [105] | biology, rna-seq | Basemount | 0.15.96 | [106] | biology, 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, variant_calling | 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, ngs | bcl2fastq | 2.16.0.10, 2.20.0.422 | [118] | biology, ngs | BDG-SeQuila | 0.5.5 | [119] | phylogenetics | BEAGLE | 4.1, 5.0, 5.2 | [120] | biology, genomics | BEAR | 20170209 | [121] | biology, genomics | BEAST | 2.6.2, 2.6.3, 2.6.7 | [122] | biology, phylogenetics | BEAST2-XML | 1.0.9 | [123] | phylogenetics | BEDOPS | 2.4.30 | [124] | biology, sequencing, ngs | BEDTools | 2.29.1, 2.29.2, 2.30.0 | [125] | biology, ngs | Bertini | 1.6 | [126] | math | BERTopic | 0.7, 0.8.1 | [127] | machine_learning | BESST | 2.2.4 | [128] | biology, ngs | BFAST | 0.7.0 | [129] | biology, ngs | bgenix | 1.1.7 | [130] | data_science, 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, 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, genomics, variant_calling | 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] | workflow_automation, utility, imaging | Bismark | 0.22.3, 0.7.4, 0.7.7 | [143] | biology, ngs | Blackfynn | 0.2.7 | [144] | data_mining | BLASR | 20130815, 20161215 (5.3), 5.3.2 | [145] | biology, ngs | Blast2GO | 2.5.0-20120705 | [146] | biology, genomics | Blast2GO CLI | 1.3.3 | [147] | biology, genomics | BLAT | 20121105, 20140318 | [148] | genomics | blender | 2.73, 2.77, 3.0.1 | [149] | graphics | blink | 0.01 | [150] | genomics | 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, genomics, phylogenetics | bmtagger | 3.101 | [157] | genomics, 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, ngs, sequencing | Bowtie2 | 2.3.5.1, 2.4.2, 2.4.5 | [163] | biology, ngs, sequencing | BoxCLI | 2.9.0 | [164] | file_management, web, programming | 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, ngs, mapping | BRATNextGen | 20150505 | [171] | biology, genomics | BreakDancer | 1.4.5 | [172] | biology, phylogenetics | breakseq | 2.2 | [173] | biology, phylogenetics | Brewery | 20191205 | [174] | phylogenetics | Bridger | 20141201 | [175] | ngs, genomics, biology | BRIG | 0.95 | [176] | biology, genomics | BRM | 0.3 | [177] | phylogenetics | Bruker2nifti | 1.0.4 | [178] | phylogenetics | Bsmap | 2.87 | [179] | biology, ngs | Bsoft | 1.9.1 | [180] | biology, image_processing | 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, ngs | bwa-mem2 | 2.2.1 | [186] | phylogenetics | BWA-PSSM | 0.5.11 | [187] | phylogenetics | bxh_xcede_tools | 1.11.1 | [188] | biology | BYOBU | 5.133, 5.92 | [189] | shell | bzip2 | 1.0.6 | [190] | utility, library | c-wap | 20220624 | [191] | sequencing, genomics, biology | Cactus | 2.0.3, 2.0.5 | [192] | phylogenetics | CAFE | 4.1, 5.0.0 | [193] | biology, phylogenetics | came | 0.0.1 | [194] | phylogenetics | Camino | 20140723 | [195] | biology, neuroscience, imaging | CAMP | 1.0.0 | [196] | biology, sequencing | Cantera | 2.1.1 | [197] | biology, physics | Canu | 1.9, 2.0, 2.1 | [198] | biology, sequencing | CANVAS | 1.40.0.1613 | [199] | phylogenetics | CAP3 | 20120705 | [200] | biology, assembly | Capnp | 0.5.3 | [201] | compiler | CARTA | 2.0 | [202] | image_processing | CASAVA | 1.8.2 | [203] | biology, ngs | CASM | 0.2.0 | [204] | physics | CasOFFinder | 2.4 | [205] | phylogenetics | Catch | 1.4.0 | [206] | biology, 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, ngs, sequencing | 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, ngs, rna-seq | CellRanger-ARC | 2.0.1 | [216] | biology, ngs, rna-seq | CellRanger-ATAC | 1.2.0 | [217] | biology, ngs, rna-seq | CellRanger-DNA | 1.0.0, 1.1.0 | [218] | biology, ngs, rna-seq, genomics | Centrifuge | 1.0.3, 1.0.4b | [219] | biology, phylogenetics | CFITSIO | 3.370 | [220] | library, compiler | CGAL | 4.10, 4.9, 5.02 | [221] | library, math | CGATools | 1.6.0.43 | [222] | biology, 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_science | CheckM | 1.0.4, 1.0.7, 1.1.2 | [227] | biology, genomics | Chimera | 1.12 | [228] | biology, modeling | Chipyard | 1.0 | [229] | 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, 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 | CisGenome | 2.0 | [241] | biology, genomics | cisTEM | 1.0.0 | [242] | phylogenetics | Clairvoyante | 1.02 | [243] | phylogenetics | Clann | 3.2.3 | [244] | biology, phylogenetics | clara | v4.0 | [245] | ai, machine_learning | CLARK | 1.2.2-b, 1.2.3 | [246] | biology, genomics | CLHEP | 2.2.0.1 | [247] | physics | CLIFinder | 4.1 | [248] | biology, phylogenetics | ClinicaDL | 1.0.4 | [249] | biology, imaging, machine_learning | clipkit | 1.3.0 | [250] | genomics, biology | CLIPper | 2.1.0 | [251] | phylogenetics | CLIPSeqTools | 0.1.7 | [252] | biology, sequencing | ClonalFrame | 1.1, 1.2 | [253] | biology, ngs, phylogenetics | ClonalFrameML | 1.0, 1.11 | [254] | biology, ngs, phylogenetics | CloudCompare | 2.10.3 | [255] | visualization | Clover | 2.0 | [256] | biology, genomics, assembly | CLUMPP | 1.1.2 | [257] | biology | ClustalO | 1.2.0 | [258] | biology, alignment | ClustalW | 2.1 | [259] | biology, alignment | cluster3 | 1.52a | [260] | biology, genomics | Clview | 20130402 | [261] | biology | CMake | 3.19.1, 3.21.3 | [262] | programming | CMS | 20170518 | [263] | biology | CMWP | 140518 | [264] | biology, genomics | CNCI | 20180305 | [265] | phylogenetics | CNSpipeline | 20170827 | [266] | phylogenetics | CNV-Seq | 20110715, 20140812 | [267] | biology, genomics | CNV-Sim | 0.9.2 | [268] | biology, phylogenetics | CNVkit | 0.9.6 | [269] | phylogenetics | CNVnator | 0.3.2 | [270] | biology, genomics | cobra-tf | 0.1 | [271] | fluid_dynamics | CodonPhyML | 20150303 | [272] | phylogenetics | Coevol | 1.3c, 1.4b, 1.6 | [273] | biology, phylogenetics | Cogent | 2.1 | [274] | biology, phylogenetics | COLMAP | 3.6 | [275] | modeling | CoMap | 1.4.1 | [276] | biology, genomics | Comp-D_MPI | 1.0 | [277] | statistics | Compacta | 1.02 | [278] | biology, genomics | COMSOL | 5.4.0 | [279] | simulation | Concaterpillar | 1.8a | [280] | phylogenetics | CONCOCT | 1.1.0 | [281] | biology, genomics | Conda | 4.10.3, 4.12.0 | [282] | programming | CONN | 18a | [283] | imaging | CONNECT | 20200614 | [284] | phylogenetics | connectomemapper3 | 3.0.0-rc1 | [285] | phylogenetics | ConPADE | 1.0 | [286] | phylogenetics | Conpair | 20161010, 20180624 | [287] | biology, phylogenetics | Consed | 23.0, 25.0, 29.0 | [288] | biology, genomics | CONSEL | 0.20 | [289] | biology, phylogenetics | ContaVect | 0.2 | [290] | biology, phylogenetics | Convert3D | 1.1.0 | [291] | imaging, utility | Coot | 0.9.5 | [292] | modeling | Coreutils | 8.23, 8.28 | [293] | utility | Corset | 1.06 | [294] | biology, ngs | Counterr | 0.1 | [295] | phylogenetics | covNMR | 2014 | [296] | biochemistry | cp2k | 7.0.0 | [297] | chemistry | CPAT | 3.0.2 | [298] | phylogenetics | cpc | 2.0 | [299] | phylogenetics | CPLEX | 12.6.1, 12.6.2, 12.7 | [300] | climate | Crass | 1.0.1 | [301] | biology, assembly | crisflash | 1.2.0 | [302] | phylogenetics | CRISP | 20181122 | [303] | phylogenetics | CRISPRanalyzer | 1.50 | [304] | biology, genomics, ngs | CRISPRCasFinder | 4.2.17 | [305] | phylogenetics | CRISPResso2 | 20220811 | [306] | genomics, sequencing, biology | CrossMap | 0.3.9, 0.6.3 | [307] | biology, genomics | crossmapper | 1.1.1 | [308] | phylogenetics | Crux | 1.40 | [309] | biology, spectroscopy | CryptoMiniSat | 5.0.1 | [310] | math | csvtk | 0.23.0 | [311] | biology | ctk | 1.1.4 | [312] | biology, genomics | CUBE | 4.4 | [313] | library, compiler, math | CUDA | 11.0.207, 11.1.0, 11.4.3 | [314] | programming, library, graphics | Cufflinks | 2.1.1, 2.2.1, 2.2.1.1 | [315] | biology, ngs, sequencing | cupy | 8.3.0 | [316] | phylogenetics | cutadapt | 1.18, 2.8, 3.4 | [317] | biology, ngs | CutRunTools | 20200104 | [318] | phylogenetics | cvbio | 3.0.0 | [319] | phylogenetics | CViT | 1.3 | [320] | programming, library | CWLtool | 1.0.20190906, 2.0.20200126, 3.0.20210124104916 | [321] | workflow_automation, scheduler | cx_oracle | 8.3.0 | [322] | database, utility | CycleGan | 20201015 | [323] | phylogenetics | Cytoscape | 3.4.0 | [324] | biology, ngs, phylogenetics | d2go | 20210702 | [325] | machine_learning, ai | dadi | 2.1.1 | [326] | phylogenetics | DAKOTA | 6.15, 6.8, 6.8-gui | [327] | math | DALIGNER | 1.0 | [328] | biology, phylogenetics | dammit | 1.0rc2 | [329] | biology, phylogenetics | DASTool | 1.1.0, 1.1.2 | [330] | biology, phylogenetics | datamash | 1.1.0 | [331] | math | DAWGPAWS | 1.0 | [332] | biology, phylogenetics | DCC | 0.4.4 | [333] | biology, ngs | Dcmstack | 0.6.2 | [334] | biology, imaging | DCMTK | 3.6.0 | [335] | biology, neuroscience, imaging | dDocent | 2.7.8 | [336] | phylogenetics | DDSCAT | 7.3.0 | [337] | astronomy | DDT | 18.2, 20.0, 20.2 | [338] | programming | DealII | 8.3.0, 9.3.1 | [339] | library | DeconSeq | 0.4.3 | [340] | biology, phylogenetics | decontaMiner | 1.4 | [341] | genomics, biology | DECX | 20180205 | [342] | phylogenetics | DeepARG | 1.0.1 | [343] | phylogenetics | deepbgc | 0.1.18 | [344] | phylogenetics | Deepcoil | 2.0.1 | [345] | sequencing, biology | DeepGS | 1.2 | [346] | phylogenetics | DeepLabCut | 2.0.7-gpu, 2.1.1, 2.2.1 | [347] | phylogenetics | deepmicrobes | 20200219 | [348] | biology, genomics, machine_learning | DeepMReye | 01192022 | [349] | library, biology | DeepPicker | 20161102 | [350] | imaging | deepTools | 2.4.3, 3.1.1 | [351] | biology, ngs | deepvariant | 1.4.0 | [352] | biology, genomics, sequencing, machine_learning | deFusion | 20200305 | [353] | phylogenetics | Delft3D | 7545 | [354] | physics | Delineate | 1.2.2 | [355] | biology, genomics | Delly | 0.7.5, 0.7.7, 0.7.8 | [356] | biology, phylogenetics | delucs | 20220512 | [357] | sequencing, genomics, machine_learning | DeNoGAP | 1.0 | [358] | biology, phylogenetics, ngs | DERIVA | 1.5.0 | [359] | phylogenetics | deSALT | 1.5.6 | [360] | biology, genomics, sequencing | Detectron2 | 0.4, 0.5, 0.6 | [361] | library | DeTiN | 1.7.5.9 | [362] | imaging, ngs, genomics | DEXTRACTOR | 1.0 | [363] | biology, sequencing | Diamond | 0.9.15, 0.9.34, 2.0.9 | [364] | biology, genomics | diCal2 | 2.2.0.1 | [365] | biology, phylogenetics | diffReps | 1.55.4 | [366] | biology | DISCOVAR de novo | 52488 | [367] | biology, ngs, assembly | DiscoVista | 20180906 | [368] | phylogenetics | discvrseq | 1.3.10 | [369] | biology, phylogenetics | Distruct | 2.3 | [370] | phylogenetics | DIYABC | 1.0.4.43b, 2.0.3, 2.1.0 | [371] | biology, phylogenetics | DL_POLY | 1.9 | [372] | molecular_dynamics | Dlib | 19.19 | [373] | phylogenetics | DNA Clust | 3.0 | [374] | biology, genomics | DOCK | 6.7, 6.8, 6.9 | [375] | chemistry | DoGFinder | 20201103 | [376] | phylogenetics | DosageConvertor | 1.0.3 | [377] | biology | DOT | 2.0 | [378] | biology, chemistry | Doxygen | 1.8.3.1 | [379] | programming, documentation | dragmap | 1.2.1 | [380] | phylogenetics, sequencing, biology | dragonflye | 1.0.12 | [381] | sequencing, genomics | DRAP | 1.91 | [382] | biology, phylogenetics | dRep | 2.3.2 | [383] | phylogenetics | Dropseq | 2.4.0 | [384] | phylogenetics | DS9 | 7.5, 8.0.1 | [385] | imaging | DScribe | 1.2.0 | [386] | machine_learning | dsistudio | 20210123 | [387] | machine_learning | DSK | 2.1.0, 2.3.0 | [388] | biology, ngs | DSRC | 2.0 | [389] | phylogenetics | DSSAT | 4.6 | [390] | simulation | DSSP | 2.2.1, 3.0.0 | [391] | molecular_dynamics | DSuite | 0.4, 0.4-r41 | [392] | biology, genomics | dtiprep | 0.1.1 | [393] | phylogenetics | duchamp | 1.6.2 | [394] | phylogenetics | dynamicDBG | 20181003 | [395] | phylogenetics | Dynare | 4.4.3 | [396] | math | ea-utils | 1.04.807.18, 1.1.2.537 | [397] | biology, genomics, ngs | EAGLE | 2.0 | [398] | phylogenetics | eagle-rc | 1.1.1 | [399] | phylogenetics | ECE | 1.2 | [400] | physics | EDirect | 10.7, 12.2 | [401] | biology, phylogenetics | EDTA | 1.9.6 | [402] | phylogenetics | Edyeet | 0.1, 0.3 | [403] | phylogenetics | EEGLAB | 12.0.2.1b, 13.2.2b, 13.4.4b | [404] | biology,bioinformatics,matlab | eGene-MVN | 0.1 | [405] | biology, genetics | eggNOG-mapper | 2.0.1, 2.1.6 | [406] | phylogenetics | EGSnrc | 2019 | [407] | phylogenetics | EIGENSOFT | 4.2, 5.0.1, 6.0.1 | [408] | biology | Elastix | 4.9.0 | [409] | phylogenetics | ELPA | 2019.11.001 | [410] | library, compiler, math | elPrep | 4.1.4 | [411] | phylogenetics | Emacs | 27.2 | [412] | programming, scripting, language | EMAN2 | 2.22, 2.31 | [413] | image_processing | EMBOSS | 6.6.0 | [414] | biology,bioinformatics | Embree | 3.6.1 | [415] | ray, tracing, kernels | EMC | 9.4.3 | [416] | monte Carlo Simulations | EMMAX | 20100307, 20120210 | [417] | biology, ngs, mapping | EnergyPlus | 9.3.0 | [418] | simulation | Ensembl Tools | 100, 80 | [419] | biology | enTAP | 0.6.1.2, 20160416 | [420] | biology, phylogenetics | EPACTS | 3.2.6, 3.4.2, 3.4.2.hg38 | [421] | biology, genomics | EpiNano | 1.2.0 | [422] | biology, ngs | epiteome | 1.0 | [423] | phylogenetics | epoch | 4.7.3 | [424] | astronomy,CCPP | eQTLA | 1.1 | [425] | biology, genomics | eQtlBma | 1.2.2, 1.3.0r20140820 | [426] | biology, genotyping | Erpin | 5.5.4 | [427] | biology, phylogenetics | ESOM | 1.1 | [428] | biology, phylogenetics | ESPRESSO | 6.2.1, 6.4.1, 7.0 | [429] | quantum,modeling | ESPRIT | 2009-nogap, 201102 | [430] | biology,bioinformatics | ETE3 | 3.0.0, 3.1.1 | [431] | biology, phylogenetics | EVidenceModeler | 1.1.1 | [432] | phylogenetics | Evigene | 20180730, 20200520 | [433] | phylogenetics | EvoLSTM | 20220103 | [434] | biology, Bioinformatics | ExaBayes | 1.5 | [435] | phylogenetics | Exonerate | 2.2.0 | [436] | biology, genomics | ExpansionHunter | 4.0.2 | [437] | biology, genomics | ExpansionHunterDenovo | 0.9.0 | [438] | biology, genomics | export2graphlan | 0.22 | [439] | statistics, mapping, graphing | eXpress | 1.3.1, 1.5.1 | [440] | biology, ngs | ezaai | 1.0 | [441] | biology, phylogenetics | face_morpher | 20190630 | [442] | phylogenetics | face_recognition | 1.2.2 | [443] | phylogenetics | fairseq | 0.12.2 | [444] | modeling, ai | FALCON | 20161027, 20161222, 20190601 | [445] | biology, ngs, sequencing | FALCON_unzip | 20161222 | [446] | biology | FAR | 2.15 | [447] | biology, genomics | FAST | 1.06 | [448] | biology phylogenetics | fast-gep | 1.0 | [449] | phylogenetics | Fast-Plast | 1.2.6 | [450] | biology, phylogenetics | fast5tools | 0.3.1 | [451] | phylogenetics, biology | FASTA | 34.26.5, 36.3.6d | [452] | biology, genomics | fastai | 2.1.5, 2.6.3 | [453] | phylogenetics | FastANI | 1.1 | [454] | phylogenetics | fastchaos | 0.1.0 | [455] | sequencing | FastGEAR | 20161216 | [456] | biology, genomics | Fastix | 0.1.0 | [457] | biology, ngs | FastML | 3.0 | [458] | biology,bioinformatics,phylogenetics | Fastp | 0.20.0, 0.22.0 | [459] | biology, ngs | FASTphase | 1.4.8 | [460] | phylogenetics | FastPlast | 1.2.8 | [461] | phylogenetics | fastq-pair | 1.0 | [462] | phylogenetics | FastQ-Screen | 0.14.0 | [463] | phylogenetics | Fastq-tools | 0.8 | [464] | biology, ngs, | FastQC | 0.11.4, 0.11.7, 0.9.6 | [465] | biology, ngs | FastqPuri | 1.0.7 | [466] | phylogenetics | FastQTL | 2.184 | [467] | phylogenetics | FASTRAL-constrained | 20211108 | [468] | phylogenetics | fastsimcoal | 2.6.0.3, 2.7.0.2 | [469] | biology, phylogenetics | FastSpar | 0.0.4 | [470] | biology, genomics | fastStructure | 20150112 | [471] | biology, genomics | FastTree | 2.1.11 | [472] | biology,bioinformatics,phylogenetics | FastUniq | 1.1 | [473] | biology, phylogenetics | Fastx Toolkit | 0.0.13.2, 0.0.14 | [474] | biology,ngs | fcGENE | 1.0.7, 1.0.7.1 | [475] | biology, genomics,snp | FDSTools | 1.2.0 | [476] | phylogenetics | fdupes | 1.51 | [477] | file Management | FEELnc | 0.1.1 | [478] | phylogenetics | FEniCS | 2018.1.0 | [479] | biology, phylogenetics | Ferret | 6.82 | [480] | data Visualization and Analysis, Oceanography, Meteorology | FFmpeg | 2.1.3, 2.8.3, 4.3.1 | [481] | audio, Video | FFTW | 3.3.6, 3.3.7, 3.3.8 | [482] | library, compiler, math | fgbio | 0.5.0, 0.7.0 | [483] | phylogenetics | FGMP | 1.0.1 | [484] | phylogenetics | FIGARO | 1.1.2 | [485] | phylogenetics | Fiji | 2.0.0rc59 | [486] | imageJ | Filtlong | 0.2.0 | [487] | biology, phylogenetics | Finder | 20210503, 20210609 | [488] | biology, finder | finemap | 1.4 | [489] | phylogenetics | fineRADstructure | 0.3.2 | [490] | phylogenetics | finesse | 2.3.1 | [491] | simulation | fit-sne | 1.2.1 | [492] | phylogenetics | FLAIR | 1.5 | [493] | phylogenetics | flairNLP | 0.10 | [494] | data Visualization, language | flappie | 1.1.0, 2.1.3 | [495] | phylogenetics | FLASh | 1.2.10, 1.2.11 | [496] | biology, genomics | FLEA | 2.0.0 | [497] | phylogenetics | flex | 2.6.4 | [498] | programming | Flexbar | 2.3, 2.34, 3.5.0 | [499] | biology, genomics, ngs | FLEXLm | 1.0 | [500] | administration | FlowCraft | 1.4.1 | [501] | phylogenetics | Fluent | 17.2, 19.1, 2020R1 | [502] | cFD | Flye | 2.7.1, 2.8.1, 2.9 | [503] | biology, ngs | fMRIPrep | 1.4.0a1, 1.5.4, 20.2.3 | [504] | data_mining | ForeSeqs | 1.0.4 | [505] | phylogenetics | fpocket | 4.0.2 | [506] | sequencing, biology | fqtools | 20160224 | [507] | biology, ngs, sequencing | FragGeneScan | 1.16 | [508] | biology, genomics | FRAMA | 20151019 | [509] | biology | FrameDP | 1.2.2 | [510] | biology, sequencing | FRAPOSA | 20200421 | [511] | phylogenetics | FreeBayes | 1.1.0-20170823, 1.3.1, 1.3.2 | [512] | biology, genomics | freesasa | 2.1.2 | [513] | molecular dynamics, biology | Freesurfer | 7.1.0, 7.1.1, 7.2.0 | [514] | biology, neuroscience, imaging | Freyja | 1.3.1, 1.3.4, 1.3.8 | [515] | biology,phylogenetics,sequencing | FSA | 1.15.9 | [516] | phylogenetics | FSL | 6.0.3, 6.0.4, 6.0.5 | [517] | biology, neuroscience, imaging | fslmrs | 1.1.10 | [518] | mRS, metabolomics | funannotate | 1.8.7, 1.8.9 | [519] | phylogenetics | fusion_twas | 20210218 | [520] | phylogenetics | GAL | 20180906 | [521] | phylogenetics | Galaxy | 1.0 | [522] | biology,bioinformatics | GAML | 20150610 | [523] | biology, genomics | GapCloser | 1.12r6 | [524] | biology, genomics, ngs | GapFiller | 1.10, 1.11 | [525] | biology, genomics | GARLI | 2.0, 2.01 | [526] | biology,bioinformatics,phylogeny | GASVPro | 201310 | [527] | biology, ngs | GATE | 7.0 | [528] | library | GATK | 4.1.4.0, 4.1.8.1, 4.1.9.0 | [529] | biology, ngs | Gaussian | 09 D.01, 16, 16-c02 | [530] | computational Chemistry | Gawk | 4.2.0 | [531] | utility | Gblocks | 0.91b | [532] | biology,bioinformatics | GCC | 7.3.0, 8.2.0, 9.3.0 | [533] | compilers | GCE | 1.0.2, 4.0 | [534] | biology, genomics | GCT | 6.2.1 | [535] | gridftp, globus, toolkit | GCTA | 1.26.0, 1.92.4beta, 1.93.2beta | [536] | biology, genomics, variant_calling, | GDAL | 2.2.1, 2.2.4, 2.3.1 | [537] | geospatial, Library | GDB | 8.3, 9.2 | [538] | programming | GDC-Client | 1.0.1, 1.5.0 | [539] | biology, sequencing, ngs | GDrive | 2.1.0 | [540] | applications, Utilities, Data Transfer | GDSL | 1.18 | [541] | library | Geant4 | 4.10, 4.10.03, 4.10.5 | [542] | physics | GEM | 20130406 | [543] | biology, ngs, sequencing | gem5 | 2.0 | [544] | computer Simulator | GEMMA | 0.98.1 | [545] | phylogenetics | GeneMark-ES | 4.65, 4.68, 4.69 | [546] | biology, genomics | GeneMarkS | 2012.04 | [547] | biology, genomics | GeneMarkS-T | 3.10.001 | [548] | biology, genomics | GenePainter | 2.0.4 | [549] | biology, phylogenetics | GeneRax | 1.2.2 | [550] | phylogenetics | Generic Mapping Tools | 6.4.0 | [551] | physics, biology | GeneSeqer | 2014-02-26 | [552] | biology, genomics | genesum | 0.1.0 | [553] | biology, genomics | GeneTorrent | 3.8.7 | [554] | biology,bioinformatics,data download | GenGen | 1.0.1 | [555] | biology, phylogenetics | Genome STRiP | 2.00.1602 | [556] | biology, genomics, ngs | Genome_Graph_Annotation | 20190131 | [557] | phylogenetics | GenomeScope2 | 2.0 | [558] | phylogenetics | GenomeThreader | 1.7.3 | [559] | phylogenetics | GenomeTools | 1.5.7, 1.5.9 | [560] | biology | genomic-fluidity | 20151109 | [561] | phylogenetics | GenomicConsensus | 2.3.3 | [562] | biology, phylogenetics | GenomicNeuralnet | 20161030 | [563] | phylogenetics | GenomicTools | 2.7.0 | [564] | biology, ngs,chip-seq,rna-seq | GenotypeHarmonizer | 1.4.18 | [565] | biology | Genrich | 0.5 | [566] | phylogenetics | GenSel | 4.90 | [567] | population Genetics | geopython | 1.0.0, 1.0.1 | [568] | python, geospatial, cartography | GEOS | 3.3.8, 3.6.2 | [569] | library, data_science | GeP | 2.1 | [570] | biology, phylogenetics | gepard | 1.40.0 | [571] | phylogenetics | Gerbil | 1.11 | [572] | phylogenetics | get_homologues | 3.3.3 | [573] | biology, genome | GetOrganelle | 1.7.3.5, 1.7.5.0 | [574] | phylogenetics | GFam | 1.1 | [575] | biology, genomics, annotation | GFF-Ex | 2.3 | [576] | phylogenetics | GFF3toolkit | 2.0.3 | [577] | phylogenetics | gffcompare | 0.12.2 | [578] | phylogenetics | gffread | 0.11.8, 0.12.7, 0.9.8c | [579] | biology | Gflags | 2.2.1, 20150520 | [580] | google,libraries | GFOLD | 1.1.4 | [581] | biology, RNA-seq | ggsashimi | 0.5.0 | [582] | phylogenetics | GHOST-MP | 1.3.4 | [583] | phylogenetics | Ghostscript | 9.22 | [584] | Giotto | 0.1.0 | [585] | phylogenetics | Git | 2.14.1, 2.30.1 | [586] | revision Control | git-filter-repo | 2.33.0 | [587] | phylogenetics | glactools | 1.0.8 | [588] | phylogenetics | Glimmer | 3.02 | [589] | biology, microbial annotation | GlimmerHMM | 3.0.4 | [590] | biology, microbial annotation | GLMsingle | 1.0 | [591] | fMRI | Globus | 1.10.1, 2.1.3 | [592] | data Transfer | glog | 0.3.5 | [593] | google,libraries | GLPK | 4.55, 4.65 | [594] | programming | Glueviz | 0.15.2 | [595] | phylogenetics | GMAP | 20180212, 20180212_sse2, 20190610 | [596] | biology, genomics, ngs | GMcloser | 1.6 | [597] | biology, ngs | GMP | 6.1.2 | [598] | library, crypto | GnuPlot | 5.2.2, 5.2.3, 5.4.1 | [599] | graphics,plotting,math | Go | 1.13.6, 1.15.4, 1.18.3 | [600] | language | GOMAP | 1.3 | [601] | biology, ngs | GoPHY | 201030 | [602] | phylogenetics | gotcloud | 1.17.5 | [603] | phylogenetics | GPA | 1.1 | [604] | phylogenetics | GPhoCS | 1.2.3 | [605] | phylogenetics | Gpufit | 20201127 | [606] | phylogenetics | Grace | 5.1.22 | [607] | graphics, statistics, 2D | GRACKLE | 3.1 | [608] | library,c,astrophysics | GrADS | 2.0.1 | [609] | environment, grid analysis | Graftm | 0.12.2 | [610] | phylogenetics | GramCluster | 1.3 | [611] | biology,sequencing, | graph-tool | 2.32 | [612] | phylogenetics | Graph_annotation | 0.1 | [613] | phylogenetics | GraPhlAn | 1.1.3 | [614] | phylogenetics | GraphMap2 | 0.6.5 | [615] | phylogenetics | GraphSplitting | 2.4 | [616] | phylogenetics | graphtyper | 2.7.2 | [617] | phylogenetics | GraphViz | 2.38.0, 2.46.1 | [618] | biology, neuroscience, imaging | GRASS | 7.0, 7.4 | [619] | geography | grf | 1.0.0 | [620] | genomics | Grib_api | 1.10.1, 1.15.1, 1.26.1 | [621] | c, fortran, library | GRIDSS | 2.6.2 | [622] | phylogenetics | GROCSVs | 0.2.5 | [623] | phylogenetics | GROMACS | 2021.2, 2021.3, 2021.4 | [624] | chemistry, molecular_dynamics | GroopM | 0.3.5 | [625] | biology, phylogenetics | Groovy | 2.4.15 | [626] | programming | Gscripts | 1.1 | [627] | biology | GSEA | 3.0.0, 4.2.2 | [628] | biology, genomics | GSL | 2.4, 2.5, 2.6 | [629] | library, data_science | GSNP | 1.0 | [630] | biology, ngs | GTAHunter | 20200106 | [631] | phylogenetics | GTDBTk | 1.7.0, 2.0.0, 2.1.0 | [632] | phylogenetics | GTOOL | 0.7.5 | [633] | phylogenetics | GUAVA | 1.0 | [634] | phylogenetics | Gubbins | 2.4.1, 3.2.1 | [635] | phylogenetics | guideseq | 1.0.2 | [636] | sequencing, genomics, bioinformatics, data | guile | 2.2.2 | [637] | programming Language | GULP | 4.4, 5.0 | [638] | material_science | guppy | 4.4.1, 4.5.4, 6.1.7 | [639] | phylogenetics | Gurobi | 9.5.1 | [640] | math, python | GWAMA | 2.2.2 | [641] | phylogenetics | Gzip | 1.10 | [642] | compression | Hail | 0.2.77 | [643] | biology, genomics | hal | 2.1 | [644] | phylogenetics | HALC | 1.1 | [645] | biology, phylogenetics | halla | 0.8.17 | [646] | phylogenetics | HaMStR | 13.2.3, 13.2.4, v8b | [647] | biology, genome | hapbin | 1.3.0 | [648] | biology, Genetics | HapCompass | 0.7.7 | [649] | imaging, ngs, genomics | HAPCUT | 0.7 | [650] | biology, assembly | HapCUT2 | 1.3.3 | [651] | biology, genomics, sequencing | hapdup | 0.6 | [652] | phylogenetics, biology | Haploflow | 0.1 | [653] | biology, phylogenetics | Haplomerger2 | 20180603 | [654] | biology, genomics | HAPLOSWEEP | 1.0 | [655] | biology, phylogenetics | happy | 0.3.14 | [656] | phylogenetics, biology | hapQTL | 1.00 | [657] | biology | hapsembler | 2.21 | [658] | biology, assembly | HASLR | 0.8a1 | [659] | phylogenetics | hclust2 | 1.0.0 | [660] | statistics, mapping | HDF4 | 4.2.11 | [661] | library, data_science | HDF5 | 1.8.19, 1.8.20, 1.8.9 | [662] | library, data_science | hecaton | 0.5.1 | [663] | genomics, Biology | HELEN | 20200516 | [664] | phylogenetics | HelitronScanner | 1.1 | [665] | phylogenetics | hgraph2graph | 20210428 | [666] | chemistry | HiC-Pro | 3.0.0 | [667] | biology, Pipeline, Genomics | Hifiasm | 0.16.1, 0.4, 0.8 | [668] | phylogenetics | HipSTR | 0.7 | [669] | phylogenetics | HISAT2 | 2.2.0, 2.2.1, 2.2.1-3n | [670] | biology, Sequence Alignment, NGS | HLAminer | 1.3.1, 1.4 | [671] | biology, phylogenetics | HMM-FRAME | 20140724 | [672] | phylogenetics | HmmCleaner | 0.180750 | [673] | phylogenetics | HMMER | 3.1b1, 3.1b2, 3.2.1 | [674] | biology, genome | hmmer2go | 0.18.1 | [675] | phylogenetics, biology | HMMRATAC | 1.2.10 | [676] | phylogenetics | HOMER | 4.10, 4.11, 4.8 | [677] | biology, sequencing, ngs | homopolish | 0.3.3 | [678] | genomics, Biology | HOOMD | 2.1.7 | [679] | library, math | HPL | 2.1 | [680] | parallel Programming, benchmarks, MPI | HTMLDoc | 1.8.28, 1.9.3 | [681] | pdf, docs, html | HTSeq | 0.11.2 | [682] | biology, ngs | HUMAnN | 2.8.1 | [683] | sequencing, microbial ecology | humann2 | 0.11.2, 2.8.1 | [684] | phylogenetics | hyb | 20141126, 20200815 | [685] | biology, ngs, RNA-Seq | HybPiper | 1.2, 1.3.1, 2.0.1 | [686] | biology, phylogenetics | HyDe | 0.4.3 | [687] | phylogenetics | HyPhy | 2.5.4, 2.5.7, 2.5.8 | [688] | biology,bioinformatics,evolution | HYPRE | 2.15.1, 2.18.2, 2.19.0 | [689] | math, Numerical Solvers | iAnnotateSV | 1.0.6, 1.0.9 | [690] | biology, phylogenetics | iAssembler | 1.3.2 | [691] | biology, assembly | ibdne | 20150815 | [692] | biology,ngs | icommands | 3.3.1 | [693] | iRods | IDBA-MT | 1.0 | [694] | biology,NGS | IDBA-UD | 1.1.1, 1.1.1-512, 1.1.1-512-mem | [695] | genomics, phylogenetics | IDL | 8.3 | [696] | language, programming, science | IDR | 2.0.3 | [697] | phylogenetics | IGB | 8.4.1 | [698] | biology, genomics | igBLAST | 1.5.0, 1.7.0 | [699] | biology | IGoR | 1.4.0 | [700] | phylogenetics | iGTP | 1.1 | [701] | biology, phylogenetics | IGV | 2.3.91, 2.4.16, 2.8.6 | [702] | biology, ngs, phylogenetics | illumina-utils | 2.11 | [703] | phylogenetics | Illumiprocessor | 2.0.9 | [704] | phylogenetics | IM and IMa | 20091217 | [705] | biology,bioinformatics,population genetics | Ima2 | 20120827 | [706] | biology,bioinformatics,population genetics | IMa2p | 20170712 | [707] | biology, phylogenetics | IMA3 | 22Aug18 | [708] | molecular_dynamics | ImageJ | 1.48 | [709] | imaging | ImageMagick | 7.0.8-20 | [710] | imaging | Imaginaire | 20201229 | [711] | imaging, Video, AI, synthesis | IMOD | 4.7.15, 4.9.10 | [712] | image_processing | imoka | 1.0 | [713] | biology, genomics | IMPUTE2 | 2.3.2 | [714] | phylogenetics | IMPUTE5 | 1.1.5 | [715] | biology, Imputation | INDELible | 1.03 | [716] | phylogenetics | Infernal | 1.1.1, 1.1.4 | [717] | biology, sequence alignment | INLA | 20160718, 20170620 | [718] | statistics, modeling, R | InParanoid | 4.1 | [719] | biology | Inspector | 1.0.2 | [720] | biology, genomics | InStruct | 20160723 | [721] | phylogenetics | Intel Compilers and Libraries | 2018.1.163, 2019.1.144, 2020.0.166 | [722] | language, development, library, math, intel | Intel MPI | 5.1.1 | [723] | parallel Programming, development, MPI, library | InterProScan | 5.54-87.0, 5.56-89.0, 5.57 | [724] | biology,bioinformatics | intervene | 0.6.2 | [725] | biology, phylogenetics | IOAPI | 3.1, 3.2 | [726] | climate | IPOPT | 3.12.10, 3.12.6 | [727] | library,c/c++,math | ipyrad | 0.7.24, 0.7.30, 0.9.53 | [728] | phylogenetics | IQ-TREE | 2.1.0, 2.1.2, 2.1.3 | [729] | biology, phylogenetics, | IRAP | 0.8.1p7 | [730] | biology, ngs, pacbio | irep | 1.10 | [731] | biology, genomics | IRFinder | 1.2.0, 1.3.0, 1.3.1 | [732] | biology, rna-seq | isONclust | 0.0.6 | [733] | phylogenetics | IsoSel | 1.0 | [734] | phylogenetics | IsoSeq3 | 3.2.2, 3.4.0, 3.7.0 | [735] | biology, ngs, pacbio | ISOWN | 20180820 | [736] | phylogenetics | isPcr | 3.3 | [737] | biology, phylogenetics | ITK | 3.20.1, 4.10.1 | [738] | biology | ITK-SNAP | 3.0.0, 3.8.0 | [739] | biology, neuroscience, imaging | ITSx | 1.1b | [740] | phylogenetics | IVA | 1.0.11 | [741] | phylogenetics | iVar | 1.3.1 | [742] | biology | Jabba | 1.0 | [743] | biology, phylogenetics | JACUSA | 1.2.0 | [744] | biology, ngs, phylogenetics | JAGS | 3.3.0, 3.4.0, 4.2.0 | [745] | statistics | Jasmine | 1.1.4 | [746] | phylogenetics | jasp | 0.14.3 | [747] | statistics | jbrowse2 | 1.7.4 | [748] | web Browser | JCVI | 0.8.12, 1.0.13, 1.2.10 | [749] | phylogenetics | JDK | 11.0.1, 14, 9.0.1 | [750] | programming,runtime | Je | 1.0 | [751] | biology, ngs | Jellyfish | 2.2.4, 2.2.6, 2.3.0 | [752] | biology,ngs | jModelTest | 2.1.1 | [753] | biology, genomics, phylogenetics | jo | 1.3 | [754] | software | jq | 1.6 | [755] | software | juicer | 1.22.01 | [756] | phylogenetics | Julia | 1.6.2, 1.7.1, 1.7.3 | [757] | programming, language, statistics | Jupyter | 5.7.8, 6.0.3, 6.2.0 | [758] | python, R, jupyter | jutils | 1.0 | [759] | genomics, biology | JVARKIT | 20180405 | [760] | biology, phylogenetics | Kaiju | 1.6.2, 1.7.2 | [761] | biology, phylogenetics | KaKs | 1.2, 2.0 | [762] | biology, evolution, phylogenetics | Kalign | 3.3.1 | [763] | biology, Bioinformatics, Sequencing, Alignment | kallisto | 0.43.0, 0.44.0, 0.48.0 | [764] | biology,NGS,RNA-Seq | khmer | 2.0, 2.1 | [765] | biology, ngs | KIM | 1.7.2, 1.8.2, 1.9.3 | [766] | simulation | KING | 2.1.2 | [767] | biology, genome, gwas | KisSplice | 2.4.0-p1 | [768] | biology, RNA | KLayout | 0.26.7 | [769] | phylogenetics | KMC | 3.1.0, 3.1.1, 3.2.1 | [770] | phylogenetics | kmerdb | 1.9.2 | [771] | genomics, biology | KMOS | 0.3.21 | [772] | phylogenetics | kneaddata | 0.7.4, 0.9.0 | [773] | phylogenetics | Knitro | 12.2.0 | [774] | mathematical Optimization Problems | KofamScan | 1.3.0 | [775] | phylogenetics | kover | 2.0.3 | [776] | phylogenetics | Kraken | 2.0.6b, 2.0.8b, 2.1.2 | [777] | biology, ngs | KrakenUniq | 0.5.8, 0.7.3 | [778] | phylogenetics | Krona | 20161019 | [779] | biology | ksnp | 3.021 | [780] | biology, phylogenetics, SNP | Ksrates | 1.1.1 | [781] | genomics, biology | LACHESIS | 2.1 | [782] | phylogenetics | Lambda | 0.9.4, 1.0.3, 2.0.0 | [783] | biology, sequencing, phylogenetics | LAMMPS | 30Jul16, 7Aug19, 7Dec15 | [784] | molecular_dynamics | LAMP | 2.5 | [785] | biology, genomics | laneta | 20220517, 20220808, 20220812 | [786] | biology | langdetect | 1.0.9 | [787] | nLP, utility | LAPACK | 3.8.0 | [788] | programming,library,fortran | Last | 916, 979 | [789] | biology,bioinformatics,sequence,alignment | LAStools | 20200114 | [790] | liDAR | LASTZ | 1.02.00, 1.03.02, 1.04.00 | [791] | biology, ngs | Lazypipe | 1.2 | [792] | genomics,taxonomy,binning | LazyPredict | 0.2.8 | [793] | phylogenetics | lbzip | 2.5 | [794] | compression | LCModel | 6.3 | [795] | biology, NMR | ldak | 5.2 | [796] | phylogenetics, biology | LDhat | 2.2a | [797] | biology, genomics | ldsc | 1.0.1 | [798] | genomics, biology | leafaudio | 0.1.0 | [799] | tensorflow, audio, leafaudio | LEfSe | 20180219 | [800] | phylogenetics | LEMON | 1.2.3 | [801] | library | LFMM | 1.4, 1.5 | [802] | biology, phylogenetics | Libint | 2.5.0, 2.5.0b | [803] | library | libMesh | 1.5.0 | [804] | math, Numerical Solvers | libunistring | 0.9.7 | [805] | library | libvips | 8.5.4 | [806] | image_processing | LIBXC | 4.2.3, 4.3.4 | [807] | library, density function | LIBXSMM | 1.13 | [808] | library, compiler, math | LIBZMQ | 4.3.1 | [809] | library | Liftoff | 1.4.2 | [810] | phylogenetics | LIGR | 2.05 | [811] | biology,assembly | lima | 2.0.0, 2.2.0 | [812] | phylogenetics | lingua | 1.0.1 | [813] | nLP, utility | LINKS | 1.8.5, 1.8.6 | [814] | biology, genomics | Linksbrowser | 2.14 | [815] | web browser | LIQA | 1.0.0 | [816] | phylogenetics | LMAP | 1.0.2 | [817] | biology, phylogenetics | lncScore | 1.0.2 | [818] | biology, phylogenetics | lobSTR | 4.0.6 | [819] | biology, phylogenetics | localbrainage | 20210415 | [820] | biology, ml | localizer | 1.0.4 | [821] | phylogenetics | LocusZoom | 1.4 | [822] | phylogenetics | LoFreq | 2.1.3.1 | [823] | phylogenetics | LongQC | 1.2.0c | [824] | phylogenetics | LongRanger | 2.1.5, 2.2.2 | [825] | biology, phylogenetics | LongStitch | 1.0.3 | [826] | genomics, biology | LoRDEC | 0.9 | [827] | phylogenetics | LoRMA | 0.3, 0.5 | [828] | biology, ngs, pacbio | LRBinner | 0.1 | [829] | biology, Bioinformatics, Metagenomics, Binning | lrgapcloser | 09042018 | [830] | biology | LS-DYNA | 700, 711, 901 | [831] | physics | LSD2 | 1.6.5 | [832] | phylogenetics | ltr_finder | 1.07 | [833] | biology, phylogenetics | LTRRetriever | 2.1, 2.5, 20170514 | [834] | biology, phylogenetics | Lua | 3.5.2 | [835] | programming, scripting, language | Lucene | 7.7.1, 9.1.0 | [836] | java,search,indexing | lumpy-sv | 0.2.1, 0.2.13, 0.3.1 | [837] | biology, genotyping | LZO | 2.09 | [838] | library, compression | M5nr | 20121126 | [839] | biology, genomics | Macaulay2 | 1.15 | [840] | phylogenetics | MACH | 1.0.18 | [841] | biology, genomics, ngs | Mach2VCF | 20150515 | [842] | biology | MACS | 2.0.10, 2.1.2, 2.2.7.1 | [843] | biology, CHiP-Seq | MafFilter | 1.3.0 | [844] | phylogenetics | MAFFT | 7.294, 7.397, 7.490 | [845] | bio,bioinformatics,sequence | MAGeCK | 0.5.9.4 | [846] | phylogenetics | MAGeCK-VISPR | 0.5.6 | [847] | phylogenetics | MAGeCKFlute | 1.14.0 | [848] | phylogenetics | Magenta | 2.1.2 | [849] | phylogenetics | MAGMA-GWAS | 1.09 | [850] | phylogenetics | magus | 20220121 | [851] | sequencing, alignment | MAJIQ | 2.2, 2.3 | [852] | phylogenetics | Maker | 2.31.10, 2.31.6, 3.01.03 | [853] | biology,bioinformatics | MAnorm | 20120316 | [854] | biology, phylogenetics | MANTA | 1.6.0 | [855] | phylogenetics | mantis | 1.0.4 | [856] | phylogenetics | mapclassify | 2.4.2 | [857] | statistics, mapping, geography | MapThin | 1.11 | [858] | phylogenetics | Maq | 0.7.1 | [859] | biology, ngs | MarginPolish | 1.0.0 | [860] | phylogenetics | MARK | 2.0.1 | [861] | application, data, capture | MarkerMiner | 20150710 | [862] | biology, genomics | Mash | 1.1, 2.3 | [863] | biology, genomics | MasHmap | 2.0 | [864] | phylogenetics | mashtree | 1.2.0 | [865] | genomics, biology | MASS | 1.1.1 | [866] | genomics, Biology | MASSMINE | 0.10.0, 0.11.0, 0.9.5 | [867] | data_mining | MaSuRCA | 4.0.8, 4.0.9, 4.1.0 | [868] | biology,bioinformatics,short read alignment | Mathematica | 12.1.1.0 | [869] | math | MATLAB | 2020a, 2020b, 2022a | [870] | math,language | MATS | 4.0.1, 4.0.2, 4.1.0 | [871] | biology, ngs,rna-seq | Mauve | 2.3.1 | [872] | biology,ngs,genomics | mawk | 1.3.4-20150503 | [873] | language | maxbin | 2.1.1 | [874] | biology,NGS | Maxima | 5.41.0 | [875] | math | MC | 4.6.1 | [876] | shell | mCarts | 1.0.2 | [877] | biology, genomics, markov | mccortex | 1.0 | [878] | phylogenetics | MCL | 12-135, 14-137 | [879] | biology, genomics | MCNP | 6, 6.1 | [880] | physics | MCNPX | 2.7.0 | [881] | physics | MCR | 2019b, 2020a, 2020b | [882] | math, language | MCScanX | 20130328 | [883] | biology, phylogenetics | mdanalysis | 1.1.1 | [www.mdanalysis.org] | physics, Bioinformatics | MECAT | 20180308 | [884] | phylogenetics | Medaka | 1.0.1, 1.2.1, 1.6.0 | [885] | biology, phylogenetics | Medusa | 1.6 | [886] | phylogenetics | MEGA | 7.0.26 | [887] | biology, phylogenetics | Mega2 | 4.9.2, 6.0.0 | [888] | biology, phylogenetics | MEGAHIT | 1.1.1, 1.1.4 | [889] | biology, phylogenetics | Megalodon | 2.0.0 | [890] | phylogenetics | MEGAN | 5.10.3, 6.23.4, 6.4.15 | [891] | biology, ngs | MEGASAT | 1.0 | [892] | phylogenetics | Megraft | 1.0.2 | [893] | biology,sequencing, | MELD | 0.4.14, 0.4.19, 0.5.9 | [894] | chemistry, molecular_dynamics | MELTING | 4.3.1 | [895] | biology, genome, RNA, folding | MEME | 5.0.2, 5.0.5, 5.4.1 | [896] | biology,bioinformatics,sequence | MentaLiST | 0.1.3 | [897] | biology, phylogenetics | Meraculous | 2.0.5 | [898] | biology,NGS | Mercurial | 4.8.2 | [899] | revision Control | merge_peaks | 0.1.0 | [900] | workflow_automation | Merlin | 1.1.2 | [901] | biology, variant_calling | Merqury | 1.1, 1.3 | [902] | phylogenetics | Meryl | 1.0 | [903] | phylogenetics | MeShClust | 1.2.0 | [904] | biology | Meshroom | 2019.2.0 | [905] | phylogenetics | MET | 10.0 | [906] | climate, Models, Verification | Meta-Marc | 1.0.0 | [907] | phylogenetics | Meta-Tissue | 0.4 | [908] | biology, genetics | MetaBAT | 0.32.4, 2.13 | [909] | biology, genomics | MetaBCC-LR | 2.0.0 | [910] | biology, Metagenomics, Binning | Metabin | 1.0 | [911] | genomics, metagenomics | metabolic | 4.0 | [912] | phylogenetics | MetaCherchant | 0.1.0 | [913] | biology, phylogenetics | MetaCluster | 5.0b | [914] | biology, genomics | MetaCompare | 20181016 | [915] | phylogenetics | metacrast | 20200309 | [916] | phylogenetics | MetaGeneMark | 2.10, 3.26 | [917] | biology, genomics | METAL | 20110325 | [918] | biology, ngs, genomics | MetaLAFFA | 1.0.0 | [919] | phylogenetics | MetaMaps | 20201207 | [920] | phylogenetics | METANNOT | 20171129 | [921] | phylogenetics | Metaphlan | 3.0.3, 3.1.0, 4.0.1 | [922] | phylogenetics | MetaPhlAn2 | 2.7.7 | [923] | biology, phylogenetics | MetaPhysicl | 1.0.0 | [924] | math, Astronomy, Numerical Simulation | MetaSV | 0.5.4 | [925] | biology, phylogenetics, NGS | MetaVelvet | 1.2.06 | [926] | biology, genomics | metaWRAP | 1.2 | [927] | phylogenetics | Metaxa2 | 2.1.1, 2.1.3 | [928] | biology, ngs, sequencing | MethylDackel | 0.5.0, 0.6.1 | [929] | phylogenetics | methylpy | 1.2.9 | [930] | biology, phylogenetics | Metilene | 0.2.8 | [931] | biology, genomics, methylation | METIS | 5.1.0 | [932] | software | Mfannot | 20180405 | [933] | biology, phylogenetics | mfold | 3.6 | [934] | biology,structure,RNA | mg-rast | 20150919 | [935] | biology, genomics | MGEfinder | 1.0.5 | [936] | phylogenetics | MGERT | 1.0.1 | [937] | phylogenetics | MGEScan | 20160416 | [938] | biology, genomics | MGLTools | 1.5.7 | [939] | biology, Molecular Biology, Visualization | MHAP | 1.6 | [940] | biology, sequencing | MHCflurry | 1.4.3 | [941] | phylogenetics | MIA | 20130201 | [942] | biology, ngs | MicrobeAnnotator | 2.0.5 | [943] | microbial annotation, biology | MIDAS | 1.3.2, 20160830 | [944] | biology, phylogenetics | MIGRATE-N | 4.2.14, 4.4.4, 5.0.4 | [945] | biology,bioinformatics,population genetics | Mikado | 2.3.3 | [946] | biology, Genetics, Transcripts, Pipeline | MIKE | 1.0 | [947] | environment,water,modeling | Minced | 0.2.0 | [948] | biology, genomics | Minia | 3.2.6 | [949] | genomics, biology | Miniasm | 0.2-r168, 0.3-r179 | [950] | biology, phylogenetics | MiniCaller | 20161201 | [951] | biology, ngs, phylogenetics | minigraph | 0.15 | [952] | phylogenetics | minimac | 1-20130717, 3-20150727 | [953] | biology, genomics | minimac2 | 2-20140915 | [954] | biology, ngs, | minimap | 2.1t, 2.21, 2.9-r720 | [955] | biology, phylogenetics | minimap2 | 2.24 | [956] | genomics, biology | Minipolish | 0.1.3 | [957] | biology, genomics | MinkowskiEngine | 0.5.3 | [958] | machine_learning, Deep Learning | MinPath | 1.4 | [959] | biology, phylogenetics | MIRA | 4.0.rc1, 4.9.6, 5rc2 | [960] | biology, genomics, assembly | miRanda | 1.9 | [961] | phylogenetics | miRBShunter | 0.2 | [962] | phylogenetics | mirdeep | 0.1.0, 0.1.1, 2.0.1.3 | [963] | phylogenetics | miRDP2 | 1.1.4 | [964] | biology, genomics | Mireap | 0.20 | [965] | biology | miRge | 2.0 | [966] | phylogenetics | Misa | 1.0 | [967] | biology, genomics | MISO | 0.5.3 | [968] | biology, ngs, sequencing, rna-seq | MITE-Hunter | 20111101 | [969] | biology, phylogenetics | MITObim | 1.9.1 | [970] | phylogenetics | MitoFinder | 1.0.2, 1.1, 1.4 | [971] | phylogenetics | mitohifi | 2.2 | [972] | genomics, sequencing | MitoPhAST | 3.0 | [973] | phylogenetics | Mitsuba2 | 2.2.1 | [974] | rendering | MiXCR | 2.1.8, 3.0.13 | [975] | biology, phylogenetics | MixMHC2pred | 1.2 | [976] | phylogenetics | MixMHCpred | 2.0.2 | [977] | phylogenetics | mixmogam | 20190322 | [978] | phylogenetics | MKL | 2018.1.163, 2019.1.144, 2020.0.166 | [979] | programming, library, math, intel | mlcoalsim | 1.9916b | [980] | biology, phylogenetics | mlpack | 3.4.2 | [981] | library | mlst | 2.15.2 | [982] | phylogenetics | mlstcheck | 2.1 | [983] | phylogenetics | MMSEQ | 1.0.8 | [984] | biology, genomics | MMseqs2 | 11, 12 | [985] | phylogenetics | MMvec | 1.0.5, 1.0.6 | [986] | metabolomics | MNEtools | 0.22.0 | [987] | phylogenetics | MOABS | 1.2.9, 1.3.2, 1.3.4 | [988] | biology, ngs | mobsuite | 3.1.0 | [989] | sequencing, biology | MOCCASIN | 0.25 | [990] | phylogenetics | MODELLER | 9.14, 9.23 | [991] | biology,bioinformatics,modelling,structure | MODELTEST | 0.1.2, 0.1.7 | [992] | biology, phylogenetics | Modulus | 21.06, 22.03 | [993] | physics, AI, Neural Network | Molden | 5.0 | [994] | molecular, Electronic Structure | momi | 2.1.19 | [995] | phylogenetics, biology | monai | 0.8, 0.8.1, 0.9.0 | [996] | data Science in Healthcare | MONAI label | 0.3.2 | [997] | data Science in Healthcare | MongoDB | 4.0.3 | [998] | database | Moni | 0.2.0 | [999] | genomics, biology | mono | 5.18 | [1,000] | linux, runtime | Monolix | 4.3.2 | [1,001] | modeling, pharmacokinetics | MOOSE | 20200722, 20210726, 20220610 | [1,002] | physics, simulation | Mosaic | 1.7.4 | [1,003] | phylogenetics | MOSAIK | 2.1.33, 2.2.3, 2.2.30 | [1,004] | biology,bioinformatics,short read alignment | Mosdepth | 0.2.3, 0.3.1 | [1,005] | biology, phylogenetics | Mothur | 1.38.1, 1.41.3, 1.46.1 | [1,006] | biology, microbial ecology | MotionCor2 | 1.2.3, 1.3.1 | [1,007] | motion Correction | mOTU | 1.1 | [1,008] | biology, genomics | mOTUs | 2.5.1 | [1,009] | phylogenetics | MountainSort | 0.9.0 | [1,010] | library | MP-EST | 1.4 | [1,011] | biology, ngs, sequencing | MPACK | 0.8.0 | [1,012] | library | MPB | 1.5 | [1,013] | library, math | MPBoot | 1.1.0 | [1,014] | biology, phylogenetics | MPFR | 3.1.6 | [1,015] | library, math | mpinterfaces | 20170613 | [1,016] | dFT | MrBayes | 3.2.4, 3.2.5, 3.2.6 | [1,017] | application, biology, phylogenetics | MRIcroGL | 20201102, 20210327, 20211006 | [1,018] | biology, imaging | MRIcron | 201306, 20161012, 20190911 | [1,019] | biology, imaging | mriqc | 0.11.0, 0.16.1, 22.0.1 | [1,020] | imaging, biology | MRtrix | 3.0.1, 3.0.3, 3.0rc2 | [1,021] | biology, imaging | ms | 20171108 | [1,022] | phylogenetics | ms-dial | 4.4.8 | [1,023] | biology, metabolomics | msfinder | 3.52 | [1,024] | biology, Metabolomics | mSINGS | 20180810 | [1,025] | phylogenetics | MSMC-Tools | 20190614 | [1,026] | phylogenetics | msprime | 0.7.4 | [1,027] | phylogenetics | MstatX | 1.0 | [1,028] | biology, phylogenetics | MSTmap | 1.0 | [1,029] | phylogenetics | msvar | 1.3 | [1,030] | biology,bioinformatics,population genetics | MTG2 | 2.15 | [1,031] | phylogenetics | mTR | 20210526 | [1,032] | biology, genomics | Mugsy | 1.2.3 | [1,033] | biology, phylogenetics | MultiQC | 1.12, 1.7 | [1,034] | biology, CHiP-Seq | MUMmer | 3.23, 4.0.0beta2 | [1,035] | biology, genomics | MUSCLE | 3.8.31 | [1,036] | biology, alignment | MuSE | 1.0rc | [1,037] | phylogenetics | Musket | 1.1 | [1,038] | biology, genomics, ngs | MuTect | 1.1.4, 1.1.7 | [1,039] | biology, genomics | MutSig | 1.4, 1.41 | [1,040] | biology, genomics | mvftools | 20191124 | [1,041] | phylogenetics | mxnet | 22.08 | [1,042] | data Science in Healthcare | MZMine | 2.41, 2.52, 2.53 | [1,043] | biology, spectrometry, NMR | NAMD | 2.14, 2.14b2, 3.0 Alpha | [1,044] | molecular_dynamics | NANO | 2.8.2 | [1,045] | text Editor | nanocomp | 1.17.0 | [1,046] | programming, python, sequencing | NanoCount | 0.2.1 | [1,047] | phylogenetics | Nanodisco | 1.0.3 | [1,048] | phylogenetics | Nanofilt | 2.7.1 | [1,049] | phylogenetics | nanolyse | 1.2.0 | [1,050] | genomics, biology | NanoPlot | 1.30.1 | [1,051] | phylogenetics | Nanopolish | 0.11.1, 0.13.2, 20171006 | [1,052] | biology | nanostripper | 0.1 | [1,053] | phylogenetics, biology | NanoSV | 1.2.0, 1.2.3, 1.2.4 | [1,054] | biology, genomics | NanoVar | 1.3.9 | [1,055] | phylogenetics | Napari | 0.3.8, 0.4.7 | [1,056] | phylogenetics | NBODY | 6 | [1,057] | astronomy | NCBI BLAST+ | 2.7.1, 2.8.1, 2.9.0 | [1,058] | biology | NCBI C++ Toolkit | 12.0.0, 21.0.0, 7.0.0 | [1,059] | biology,bioinformatics,NCBI,programming,library,cpp | NCBI GenBank Tools | 20140130 | [1,060] | biology,bioinformatics,NCBI,GenBank | ncbi-vdb | 2.6.3, 2.8.2 | [1,061] | sRA toolkit library | nccl | 20.11 | [1,062] | development, library, communication, nvidia | ncftp | 3.2.5 | [1,063] | file transfer | NCL | 6.1.2, 6.3.0 | [1,064] | atmosphere Science | NCO | 4.2.1, 4.4.3 | [1,065] | data Analysis | ncview | 2.1.2, 2.1.7 | [1,066] | data Visualization | NECAT | 202001019 | [1,067] | phylogenetics | Necklace | 1.00 | [1,068] | biology, phylogenetics | NeEstimator | 2.1 | [1,069] | biology, Bioinformatics | nemo | 1.0.0rc1, 1.0.1, 1.2.0 | [1,070] | ai, machine_learning | neovim | 0.2.0 | [1,071] | editor, text, ide, vim | NetCDF | 4.3, 4.3.3, 4.4.3 | [1,072] | data_science, exchange | NetCDF-C | 4.7.4, 4.8.1, 4.9.0 | [1,073] | data_science, exchange | NetCDF-F | 4.4.4, 4.5.3, 4.5.4 | [1,074] | data_science, exchange | NetLogo | 5.3.64, 6.1.1, 6.2.0 | [1,075] | modeling | NEURON | 7.7.2, 8.0.0, 8.2.1 | [1,076] | biology, neuroscience | Newbler | 2.7, 2.8, 2.9 | [1,077] | biology, ngs,454,assembly,denovo | newick-utils | 1.6 | [1,078] | biology, genomics, phylogenetics | newick_utils | 1.6, 1.7 | [1,079] | biology, phylogenetics | NewTargets | 20210215 | [1,080] | biology | NextDenovo | 2.4.0 | [1,081] | phylogenetics | Nextflow | 21.04.0, 21.10.6, 22.04.5 | [1,082] | biology, workflow | NextGenMap | 0.5.5 | [1,083] | phylogenetics | NextPolish | 1.3.1 | [1,084] | phylogenetics | Nextstrain | 1.16.1 | [1,085] | phylogenetics | nf-core | 1.12.1, 2.1 | [1,086] | biology, workflow | NGC CLI | 2.10.1 | [1,087] | Command Line Interface | NGmerge | 0.3 | [1,088] | phylogenetics | ngmlr | 0.2.6, 0.2.7 | [1,089] | biology, phylogenetics | ngs-bits | 0.1 | [1,090] | biology, sequencing | NGS-SDK | 1.2.4, 1.3.0 | [1,091] | biology,bioinformatics,ncbi,sdk,library | ngscheckmate | 1.0 | [1,092] | phylogenetics | ngstools | 20150816 | [1,093] | biology, ngs | nilearn | 0.7.0, 0.9.0 | [1,094] | phylogenetics | nimare | 0.0.5 | [1,095] | neuroimaging | Nipype | 1.6.0, 1.7.0, 1.8.0 | [1,096] | biology, neuroscience, imaging | nlp | 1.1, 1.2 | [N/A] | machine_learning | nlr-annotator | 0.7 | [1,097] | phylogenetics | NLR-Parser | 1.0 | [1,098] | phylogenetics | NMRPipe | 7.9, 8.2 | [1,099] | biochemistry | NONMEM | 7.3.0, 7.4.4 | [1,100] | modeling | nonpareil | 3.3.4 | [1,101] | phylogenetics | Novoalign | 2.08.02, 3.00.02 | [1,102] | biology, ngs | NOVOPlasty | 3.7, 4.2, 4.3 | [1,103] | phylogenetics | nPhase | 1.1.3 | [1,104] | biology,pipeline,phasing,polyploid | npScarf | 1.7 | [1,105] | phylogenetics | nQuire | 20180405 | [1,106] | phylogenetics | Nsight | 2022.1 | [1,107] | gPU, profiler, tools | Nsightsys | 2022.2.1 | [1,108] | gPU, profiler, tools | nt | 20220404 | [1,109] | sequencing, neuroscience | ntEdit | 1.2.1 | [1,110] | phylogenetics | nubeamdedup | 20200907 | [1,111] | phylogenetics | NucDiff | 2.0.3 | [1,112] | phylogenetics | NucleoATAC | 0.3.1 | [1,113] | biology | Nullarbor | 1.41 | [1,114] | biology, phylogenetics | Numba | 0.36.2, 0.43.1, 0.48.0 | [1,115] | compiler | NUPACK | 3.2.2 | [1,116] | phylogenetics | nvhpc | 11.1, 21.7 | [1,117] | language, development, library, math, nvidia | nVidia HPC Compilers | 20.11 | [1,118] | compilers | NWChem | 6.8 | [1,119] | chemistry | NxTrim | 0.4.1 | [1,120] | biology, ngs | Oases | 0.2.08 | [1,121] | biology,ngs,assembler | OCaml | 4.02.3 | [1,122] | language, scripting, development | OCOCO | 0.1.2.6 | [1,123] | biology, phylogenetics | octave | 6.4.0, 7.2.0 | [1,124] | numerical Computation | odgi | 0.6 | [1,125] | phylogenetics | Olego | 1.1.2, 1.1.5, 1.1.6 | [1,126] | biology, ngs,rna-seq | OmicsBox | 1.1.78 | [1,127] | image_processing | OMindel | 20180129 | [1,128] | phylogenetics | omniCLIP | 0.1.0 | [1,129] | phylogenetics | OMNIVERSE | beta211004 | [1,130] | nVIDIA Omniverse | OMSV | 1.0.1 | [1,131] | phylogenetics | ONT-Bonito | 0.1.5, 0.5.3, 0.6.0 | [1,132] | phylogenetics | ont_fast5_api | 2.0.1, 4.0.2 | [1,133] | phylogenetics | ont_tutorial_cas9 | 20190705 | [1,134] | phylogenetics | open-cravat | 2.0.1 | [1,135] | biology, genomics | open3d | 0.13.0 | [1,136] | phylogenetics | OPENACC | 16.7 | [1,137] | programming, Accelerator toolkit | OpenBabel | 2.3.2, 2.4.1, 3.1.1 | [1,138] | biology | OpenBLAS | 0.2.20 | [1,139] | programming,library | OpenCL | 18.1.0.013 | [1,140] | phylogenetics | OpenCV | 4.5.2 | [1,141] | library | OpenFOAM | 4.1, 5.0, 8.0 | [1,142] | computational Fluid Dynamics | OpenMM | 7.5, 7.5.0, 7.6.0 | [1,143] | chemistry, molecular_dynamics | OpenMPI | 4.0.4, 4.0.5, 4.1.1 | [1,144] | parallel Programming, development, MPI, library | OpenNeuro | 3.17.4, 3.37.4 | [1,145] | biology, data | OpenPIV-python | 0.21.2 | [1,146] | python, imaging | OpenPIV-python-gpu | 20190506-gpu | [1,147] | python, imaging | OpenSim | 4.3 | [1,148] | phylogenetics | OpenSlide | 3.4.1 | [1,149] | imaging | OptiType | 1.3.1 | [1,150] | biology, phylogenetics | Orange3 | 3.3.6 | [1,151] | data_mining | ORCA | 4.0.1.2 | [1,152] | molecular, Electronic Structure | OrganellePBA | 20180904 | [1,153] | phylogenetics | OrthoFiller | 1.1.4 | [1,154] | phylogenetics | OrthoFinder | 1.1.10, 2.3.11, 2.5.2 | [1,155] | biology, ngs | Orthofisher | 0.1.2 | [1,156] | biology, Genetics | Orthograph | 0.6.3 | [1,157] | orthology | Orthologer | 2.2.0 | [1,158] | biology, | OrthoMCL | 2.0.3, 2.0.7 | [1,159] | biology, genomics | osprey | 1.1.0 | [1,160] | mRS,matlab,neuroscience | OTB | 5.8.0 | [1,161] | geospatial Data Modeling | p4est | 1.1, 2.8 | [1,162] | library | p4vasp | 0.3.29, 0.3.30 | [1,163] | molecular, Electronic Structure | p53MH | 20020901 | [1,164] | biology, DNA-sequencing | p7zip | 9.20.1 | [1,165] | archiver | PacBio | 10.2.0.133434, 11.0.0.146107, 7.0.1 | [1,166] | biology, ngs, pacbio, smrtlink | Package-GFE | 20150701 | [1,167] | biology, genomics | PALADIN | 1.3.1 | [1,168] | biology, phylogenetics | PALES | 122 | [1,169] | physics | PAML | 4.8a, 4.9a, 4.9h | [1,170] | biology, phylogenetics | Pandaseq | 20140808, 20150627 | [1,171] | biology, ngs, sequencing | Pandoc | 2.2.2.1 | [1,172] | converter | pangolin | 2 | [1,173] | phylogenetics | panseq | 3.2.1 | [1,174] | phylogenetics | panX | 1.6.0 | [1,175] | phylogenetics | PAPI | 5.5.1, 5.7.0 | [1,176] | programming interface, performance analysis | parabricks | 3.5.0, 3.7.0 | [1,177] | phylogenetics | parallel | 20150122, 20170322 | [1,178] | shell, process management | paralyzer | 1.5 | [1,179] | phylogenetics | ParaView | 5.4.1, 5.7.0, 5.9.1.1 | [1,180] | data Analysis | ParaView Server | 5.10.1 | [1,181] | data Analysis | ParGenes | 1.2.0 | [1,182] | phylogenetics | ParlAI | 1.3.0, 1.5.0 | [1,183] | phylogenetics | Parsnp | 1.2, 1.5.0, 1.6.2 | [1,184] | biology, phylogenetics | PartitionFinder | 2.0.0-pre-20160513, 2.1.1-20161205, 2.1.1.0 | [1,185] | biology,phylogenetics,evolution | PASA | 2.0.2-r20151207, 2.2.0-r20171013, 2.4.1 | [1,186] | biology, genomics, ngs | Pascal | 3.0.0 | [1,187] | compiler, Programming | PASTA | 0.2.0, 1.7.8, 20160616 | [1,188] | biology, sequence alignment | PATHd8 | 1.0 | [1,189] | biology, phylogenetics | pathoscope | 2.0.7 | [1,190] | sequencing, genomics, Biology | PATRIC | 1.034 | [1,191] | machine_learning | PAUDA | 1.0.1 | [1,192] | biology, ngs, phylogenetics | PAUP | 4.0a166, 4.0a168, 4.0b10 | [1,193] | biology, Phylogenetics | PB-Assembly | 0.0.6, 0.0.8 | [1,194] | biology, ngs, sequencing,pacbio | pbalign | 20160921, 20161221 | [1,195] | biology | PBCCS | 5.0.0 | [1,196] | phylogenetics | pbcore | 1.7.1 | [1,197] | biology,bioinformatics | PBGCpp | 1.9.0 | [1,198] | phylogenetics | pbipa | 1.8.0 | [1,199] | phylogenetics, biology | PBJelly | 15.8.24 | [1,200] | biology, ngs | pbmm2 | 1.3.0 | [1,201] | phylogenetics | pbrt | 20181017 | [1,202] | phylogenetics | pbsmrtpipe | 0.63.0 | [1,203] | biology,API | pbtranscript-tofu | 20150317, 20160119 | [1,204] | biology, ngs, pacbio | PCIT | 2014 | [1,205] | biology | PCRE | 8.38, 8.39 | [1,206] | programming, library | PDA | 1.0.3 | [1,207] | biology, phylogenetics | pdb2pqr | 2.1.0 | [1,208] | protein, modeling, pdb | PeakSplitter | 1.0 | [1,209] | biology, CHiP-Seq | PEAR | 0.9.2 | [1,210] | biology, genomics, ngs | peneasy | 20150530 | [1,211] | physics | PennCNV | 1.0.5 | [1,212] | phylogenetics | Perl | 5.16.0, 5.20.0, 5.24.1 | [1,213] | programming,scripting,language | PerM | 0.4.0 | [1,214] | biology, ngs, mapping | PETSc | 3.8.1, 3.8.3, 3.8.4 | [1,215] | math, Numerical Solvers | PfamScan | 1.3, 1.5 | [1,216] | biology, genomics | PGAP | 20220414 | [1,217] | biology, genomics, Annotation, Pipeline | PGDSpider | 2.0.9.0, 2.1.1.5 | [1,218] | biology, ngs | pggb | 0.4.1, 20201106, 20210121 | [1,219] | phylogenetics | PhaME | 1.0.3 | [1,220] | phylogenetics | pharmcat | 1.8.0 | [1,221] | biology, Bioinformatics, Phylogenetics | PHASE | 2.1.1 | [1,222] | phylogenetics | PHAST | 1.5 | [1,223] | biology,phylogeny | Phenix | 1.10.2155, 1.17.1, 1.8.1069 | [1,224] | crystallography | PHI | 3.1.1, 3.1.2b, 3.1.6 | [1,225] | calculations | PhiSpy | 3.2 | [1,226] | phylogenetics | PHITS | 2.76, 2.82, 2.84 | [1,227] | physics | PHLAWD | 20170427 | [1,228] | biology, phylogenetics | PhotoScan | 1.4.1, 1.4.5 | [1,229] | image_processing | Photutils | 0.5 | [1,230] | astronomy, photometry | PHYLDOG | 20130116-dbg | [1,231] | biology,bioinformatics,phylogenetics | PHYling | 1.0 | [1,232] | biology, phylogenetics, Markers, Genomics | PHYLIP | 3.696 | [1,233] | biology,phylogenetics | PhyloAcc | 1.0 | [1,234] | phylogenetics | PhyloBayes | 3.3f | [1,235] | biology,bioinformatics,phylogenetics | phyloFlash | 3.3b4 | [1,236] | phylogenetics | phylonet | 3.5.7, 3.8.2 | [1,237] | biology, phylogenetics | PhyloParser | 20180404 | [1,238] | phylogenetics | PhyloPhlAn2 | 0.41 | [1,239] | phylogenetics | phylopypruner | 1.2.3 | [1,240] | phylogenetics | PhyloSift | 1.1 | [1,241] | biology, genomics, phylogenetics, taxonomy | phyloTF2 | 20210726 | [1,242] | biology, genomics, alignment | Phyluce | 20180727, 20190308, 20191015 | [1,243] | biology, ngs, sequencing | PhyML | 3.0, 3.1 | [1,244] | biology,bioinformatics,phylogenetics | phynd | 20200409 | [1,245] | phylogenetics | Physher | 1.0.2 | [1,246] | phylogenetics | PHYUTILITY | 2.7.1 | [1,247] | biology | Phyx | 1.1 | [1,248] | phylogenetics | PIA2 | 20180305 | [1,249] | biology, phylogenetics | Picard-tools | 2.5.0, 2.9.0, 2.9.2 | [1,250] | biology, ngs | PICRUSt | 1.1.3, 1.1.4, 2.3.0b | [1,251] | biology, phylogenetics | PICSL | 1.3 | [1,252] | imaging, Atlas, Segmentation | Piggy | 20171220 | [1,253] | biology, ngs | Pigz | 2.4 | [1,254] | compression | PILON | 1.22, 1.24 | [1,255] | biology, ngs, phylogenetics | Pindel | 0.2.5b8 | [1,256] | biology, phylogenetics | pipe-clip | 1.1.0 | [1,257] | biology,NGS | pipits | 1.3.6, 1.4.0 | [1,258] | biology, sequencing | Piranha | 1.2.1 | [1,259] | biology,phylogenetics | PlantTribes | 1.0.4 | [1,260] | phylogenetics | plasflow | 1.1 | [1,261] | biology, phylogenetics | PLAST | 1.0, 2.3.2 | [1,262] | biology,bioinformatics | platanus | 1.2.4 | [1,263] | phylogenetics | Platon | 1.6 | [1,264] | biology, sequencing | Platypus | 0.8.1 | [1,265] | biology, ngs | PLEK | 1.2.2 | [1,266] | biology, phylogenetics | Plink | 1.90b3.39, 2.00a2, 2.00a3LM | [1,267] | biology, genomics,phylogenetics | plinkseq | 0.10 | [1,268] | biology, library | plotsr | 0.5.4 | [1,269] | genomics, biology | PLUMED | 2.7.3, 2021.2 | [1,270] | chemistry, molecular_dynamics | pod5 | 20220621 | [1,271] | sequencing | PolyGembler | 1.0 | [1,272] | phylogenetics | PolyPHen | 2.2.2.r405b | [1,273] | biology, genomics | polyply | 1.3.0 | [1,274] | phylogenetics, Biology | pomoxis | 0.1.11, 0.2.5, 0.3.2 | [1,275] | biology, phylogenetics | popcorn | 20211104 | [1,276] | phylogenetics, biology | PopLDdecay | 3.40 | [1,277] | phylogenetics | popoolation | 1.2.2 | [1,278] | biology, phylogenetics | Porechop | 0.2.4 | [1,279] | phylogenetics | Poretools | 0.6.1 | [1,280] | phylogenetics | portcullis | 1.2.3 | [1,281] | phylogenetics | PosiGene | 20171113 | [1,282] | biology, phylogenetics | POV-Ray | 3.7 | [1,283] | 3D Graphics | pplacer | 1.1.alpha19 | [1,284] | biology, phylogenetics, taxonomy | PRANK | 170427, 20150803 | [1,285] | biology, alignment | Predector | 20201110 | [1,286] | phylogenetics | preplot | 14.0.2 | [] | Preseq | 0.0.4 | [1,287] | biology, ngs | PRICE | 1.2 | [1,288] | biology, ngs | Primer3 | 2.3.4 | [1,289] | biology, genomics | primus | 1.8.0 | [1,290] | biology, phylogenetics | PRINSEQ | 0.20.4 | [1,291] | biology, sequencing | PRINSEQ++ | 1.2 | [1,292] | phylogenetics | ProbABEL | 0.4.2, 0.4.3, 0.4.5 | [1,293] | genomics, gwas | probalign | 1.4 | [1,294] | biology, ngs | Processing | 3.4 | [1,295] | java, language, programming, visual | Prodigal | 2.6.2, 2.6.3 | [1,296] | biology, genomics | ProDy | 2.0 | [1,297] | phylogenetics | Program Database Toolkit | 3.20, 3.22, 3.24 | [1,298] | language, development, performance analysis | PROJ | 4.9.3, 5.1.0, 8.0.1 | [1,299] | library, geospatial, cartography | Prokka | 1.12, 1.14.6 | [1,300] | biology, genomics, assembly | Proovread | 1.03rcl, 2.12, 2.13 | [1,301] | biology, genomics, ngs | ProSplign | 1.0.0 | [1,302] | phylogenetics | Protege | 5.1.0 | [1,303] | ontology | Proteinortho | 4.26, 5.11, 5.16 | [1,304] | biology, genomics | ProtExcluder | 1.2 | [1,305] | biology, phylogenetics | ProtHint | 2.6.0 | [1,306] | biology, genomics | protobuf | 2.5.0, 3.5.1 | [1,307] | google, libraries | PROVEAN | 1.1.5 | [1,308] | biology, genomics | PRSice | 2.3.3 | [1,309] | phylogenetics | Pseudofinder | 1.0 | [1,310] | phylogenetics | PsiCLASS | 1.0.1 | [1,311] | phylogenetics | PSMC | 0.6.5 | [1,312] | phylogenetics | psRobot | 1.2 | [1,313] | phylogenetics | Pufferfish | 20200417 | [1,314] | phylogenetics | PureCLIP | 1.1.1 | [1,315] | phylogenetics | Purge_Dups | 1.0.1 | [1,316] | phylogenetics | purge_haplotigs | 1.1.2 | [1,317] | sequencing, biology, biology | pyani | 0.2.10 | [1,318] | phylogenetics | Pybedtools | 0.8.2 | [1,319] | phylogenetics | PyBSASeq | 20200623 | [1,320] | phylogenetics | PyCharm | 2018.3 | [1,321] | editor, ide, programming, python | pychopper | 2.5.0, 2.7.1 | [1,322] | phylogenetics, sequencing | PyCogent | 1.9 | [1,323] | biology, genomics | pycoqc | 2.5.2 | [1,324] | Sequencing, data | PyDeface | 2.0.0 | [1,325] | imaging | pyEGA3 | 3.4.1 | [1,326] | biology, genomics, Utility | PyEXR | 0.3.10 | [1,327] | programming, python, openexr | Pyfaidx | 0.5.2 | [1,328] | biology, ngs, sequencing | pyfasta | 0.5.2 | [1,329] | phylogenetics | pygot | 20170518 | [1,330] | biology, phylogenetics | pyhdf | 0.9.0 | [1,331] | library, hdf4 | PyHIST | 1.0 | [1,332] | biology, Histology, Image segmentation | PyPHLAWD | 20180416, 20190414 | [1,333] | biology, phylogenetics | Pyroms | 1.0 | [1,334] | oceanography | PyRosetta | r56324 | [1,335] | biology,structure,modeling | pyrpipe | 0.0.3 | [1,336] | phylogenetics | Pysamstats | 1.1.2 | [1,337] | phylogenetics | PySLURM | 18.08.04 | [1,338] | sLURM | Python | 3.6.3, 3.6.5, 3.8 | [1,339] | language, scripting, development | Python-core | 3.6.5, 3.7, 3.8 | [1,340] | language, scripting, development | Python2 | 2.7.11 | [1,341] | language, scripting, development | PyTorch | 1.11.0, 1.9.0 | [1,342] | library, math | pytorch | 1.7.1, 1.8.1, 1.9.0 | [1,343] | library, math | PyVCF | 0.6.0, 0.6.8 | [1,344] | biology, phylogenetics | PyVista | 0.26.1 | [1,345] | phylogenetics | pyweka | 0.3.18 | [1,346] | phylogenetics | QAPA | 1.3.1 | [1,347] | phylogenetics | qcat | 1.1.0 | [1,348] | phylogenetics | qctool | 2.0.1 | [1,349] | phylogenetics | QD | 2.3.22 | [1,350] | library, compiler, math | QDD | 3.1.2 | [1,351] | biology, genomics, ngs | QGIS | 2.18.0, 3.14.0 | [1,352] | gIS | QIIME | 1.9.1 | [1,353] | biology, genomics | QIIME2 | 2021.11, 2021.4, 2022.8 | [1,354] | biology, genomics | QMCPACK | 3.4.0 | [1,355] | library | QRNA | 2.0.4 | [1,356] | phylogenetics | QT | 4.8.3, 5.12.9, 5.15.4 | [1,357] | uI Framework | QTL-seq | 2.2.2 | [1,358] | biology, sequencing, pipeline | QTLtools | 1.2, 1.3.1 | [1,359] | phylogenetics | Quake | 0.3 | [1,360] | biology, sequencing | QualiMap | 2.1.2 | [1,361] | biology,sequence alignment | Quantas | 1.0.4, 1.0.8, 1.0.9 | [1,362] | biology, ngs | quantisnp | 2 | [1,363] | bioinformatics, genomics | QuartetScores | 1.0.0 | [1,364] | phylogenetics | QUAST | 4.4, 5.0.0, 5.0.2 | [1,365] | biology, ngs, sequencing, rna-seq | quickmerge | 0.3 | [1,366] | phylogenetics | Quickquartet | 1.0.0 | [1,367] | biology, ngs | QUIP | 20201029, 20210626 | [1,368] | phylogenetics | QuorUM | 1.0.0 | [1,369] | biology | R | 4.0, 4.1, 4.2 | [1,370] | statistics | r-index | 20190711 | [1,371] | phylogenetics | r8s | 1.8, 1.81 | [1,372] | phylogenetics | RACA | 0.9.1.1 | [1,373] | biology, ngs | Racon | 1.3.3, 1.4.10, 1.4.13 | [1,374] | phylogenetics | RADICAL | 0.2 | [1,375] | biology, genomics | radorgminer | 0.9 | [1,376] | genomics, Biology, Sequencing | RaGOO | 1.11 | [1,377] | phylogenetics | Ragout | 2.3 | [1,378] | genomics | RagTag | 1.0.0, 2.0.1 | [1,379] | phylogenetics | rainbow | 2.0.4 | [1,380] | biology, sequencing | Rainbowfish | 0.1.0 | [1,381] | phylogenetics | RAiSD | 2.8 | [1,382] | phylogenetics | Randfold | 2.0.1 | [1,383] | biology, RNA | ranger | 1.9.3 | [1,384] | file Management | rapidsai | 21.10, 21.12, 22.04 | [1,385] | data Science | rapidtide | 1.9.0 | [1,386] | phylogenetics | RAPSearch | 2.24 | [1,387] | biology, phylogenetics | Rascaf | 1.0.2 | [1,388] | biology | RAVE | 2.1 | [1,389] | biology, phylogenetics | Raven | 1.8.1 | [1,390] | assembler | RAxML | 8.2.10, 8.2.12, 8.2.8 | [1,391] | application, biology, philogenetics | RAxML-NG | 0.9.0, 1.0.2, 1.1.0 | [1,392] | phylogenetics | razers3 | 3.5.7 | [1,393] | biology, phylogenetics | rbp-maps | 0.1.4 | [1,394] | phylogenetics | rclone | 1.57.0, 1.58.1 | [1,395] | cloud | Rcorrector | 1.0.4 | [1,396] | phylogenetics | RDKit | 2020092 | [1,397] | chemiformatics | rDnaTools | 0.1.3 | [1,398] | phylogenetics | READemption | 1.0.0 | [1,399] | phylogenetics | REAPR | 1.0.18 | [1,400] | biology, assembly | Rebaler | 0.2.0 | [1,401] | phylogenetics | reCOGnizer | 1.3.3 | [1,402] | phylogenetics | recon | 1.08 | [1,403] | biology,sequencing | Redis | 2.8.13, 2.8.19 | [1,404] | daemon, data, server | REDItools2 | 20200701 | [1,405] | phylogenetics | Redundans | 0.14a | [1,406] | biology, phylogenetics | ReFrame | 3.2 | [1,407] | hpc, internal | regtools | 0.5.2 | [1,408] | biology, RNA-seq, Genitics | release | 12082021 | [1,409] | molecular dynamics, deep learning | RELION | 3.0.2, 3.0b, 3.1.0 | [1,410] | biology, imaging | RelocaTE2 | 2.0.1 | [1,411] | phylogenetics | REMORA | 1.8.2, 1.8.3, 1.8.5 | [1,412] | system, profiler | REPdenovo | 20170222 | [1,413] | biology, phylogenetics | RepeatAnalysis | 0.10.0, 0.12.2 | [] | biology, phylogenetics | RepeatAnalysisTools | 20210506 | [1,414] | biology, genomics, sequencing, Utility | RepeatExplorer | 20150506, 20180517 | [1,415] | biology, ngs | RepeatMasker | 4.0.5, 4.0.9, 4.1.1 | [1,416] | biology,bioinformatics | RepeatModeler | 1.0.8, 2.0 | [1,417] | biology,bioinformatics | repeatscout | 1.0.5 | [1,418] | biology | RepeatSeq | 0.8.2 | [1,419] | phylogenetics | reptile | 1.1 | [1,420] | biology,NGS,error correction | ResFinder | 4.0 | [1,421] | biology, genomics | Resistome | 20170111 | [1,422] | phylogenetics | RevBayes | 1.0.7, 1.0.9, 1.1.1 | [1,423] | biology, phylogenetics | RFMIX | 2.03 | [1,424] | phylogenetics | RGAugury | 20220107 | [1,425] | sequencing, biology | RGI | 4.2.2, 5.1.1 | [1,426] | phylogenetics | RGIS | 20180211, 20180814 | [1,427] | riverGIS | RHash | 1.3.3 | [1,428] | gNU | RiboCode | 1.2.11 | [1,429] | phylogenetics | riboPicker | 0.4.3 | [1,430] | biology,sequence | RiboTaper | 1.3.1a | [1,431] | phylogenetics | RIGERJ | 2.0.2 | [1,432] | phylogenetics | rMATS turbo | 4.1.2 | [1,433] | biology, sequencing, genomics | rmats2sashimiplot | 2.0.3, 2.0.4 | [1,434] | phylogenetics | Rmpi | 0.6.9 | [1,435] | statistics, R, mpi | RNAFramework | 2.7.2 | [1,436] | biology, RNA, Sequencing | RNAhybrid | 2.1.1 | [1,437] | biology, genomics | RNAmmer | 1.2 | [1,438] | biology, RNA-seq | rnaQUAST | 1.5.1 | [1,439] | biology, ngs, sequencing, rna-seq | RNAsalsa | 0.8.1 | [1,440] | biology, phylogenetics | rnaseqlib | 20150721 | [1,441] | biology, phylogenetics, RNA-seq | RNAstructure | 6.3 | [1,442] | biology, sequencing | Roary | 3.12.0, 3.4.1 | [1,443] | biology, genomics | ROOT | 5.34.17, 6.0, 6.06.02 | [1,444] | data Analysis | ROOTPy | 20160323 | [1,445] | data Analysis | Rosetta | 2014wk4, 2019.35.60890 | [1,446] | biology,structure,modeling | RoseTTAFold | 1.0.0 | [1,447] | phylogenetics | rrnaselector | 1.0 | [1,448] | biology, sequencing | RSEG | 0.4.8 | [1,449] | biology, genomics | RSEM | 1.2.31, 1.2.7, 1.3.3 | [1,450] | biology, ngs, sequencing | RSeQC | 2.6.4, 3.0.0 | [1,451] | biology,ngs,rna-seq | RStudio | 1.4, 2021.09.0, 2022.02.3 | [1,452] | statistics | RTGTools | 3.7.1 | [1,453] | biology, ngs | Ruby | 2.5.1 | [1,454] | programming,scripting,language | Rust | 1.48.0, 1.52.1, 1.62.1 | [1,455] | programming | rvtests | 2.1.0 | [1,456] | genomics, Biology, Sequencing | S.A.G.E | 6.4.2 | [1,457] | phylogenetics | Sabre | 1.0 | [1,458] | phylogenetics | saffrontree | 0.1.2 | [1,459] | phylogenetics | Sailfish | 0.6.3 | [1,460] | biology, genomics, ngs, rna-seq | Salmon | 1.1.0, 1.5.2, 1.8.0 | [1,461] | biology, RNA-seq | SALSA | 20171009, 20191001 | [1,462] | biology, ngs, pacbio | Sambamba | 0.6.3, 0.6.6, 0.6.9 | [1,463] | biology, ngs | samblaster | 0.1.14, 0.1.24 | [1,464] | biology, ngs, sequencing | sampledock | 0.5.1 | [1,465] | molecular dynamics, AI | SAMStat | 1.08 | [1,466] | biology, ngs, sequencing | Samtools | 1.7, 1.8, 1.9 | [1,467] | biology, ngs, sequencing | SAS | 9.3, 9.4 | [1,468] | statistics, data analysis | Sate | 2.2.7 | [1,469] | biology, phylogenetics | Satsuma | 3.0 | [1,470] | phylogenetics | Satsuma2 | 20161123, 3.1 | [1,471] | phylogenetics | sc-im | 0.8.2 | [1,472] | software, data visualization | Scala | 2.11.5, 3.0.1 | [1,473] | programming, language, java | Scalablast | 2.4.53 | [1,474] | application, biology, genomics | ScaLAPACK | 2.0.2, 2.1.0 | [1,475] | programming,library | scallop | 0.10.5 | [1,476] | phylogenetics | Scalpel | 0.1.1, 0.5.3 | [1,477] | biology, ngs | Schrodinger Suite | 2019-3, 2020-4, 2021-2 | [1,478] | chemistry, molecular_dynamics | Scipion | 1.2 | [1,479] | image_processing | SCIrun | 5.0.Z | [1,480] | phylogenetics | Scoary | 1.6.16 | [1,481] | phylogenetics | Scons | 2.5.1, 3.1.2 | [1,482] | programming | SCOP | 20180311 | [1,483] | biology, Scaffolding, Assembly | Scrappie | 1.4.2 | [1,484] | biology, genomics | SCRATCH-1D | 1.0, 2.0 | [1,485] | biology, ngs | Screen | 4.8.0 | [1,486] | gNU, Terminal Multiplexer | SCRIPTURE | 20101211 | [1,487] | biology, genomics | Scythe | 0.991 | [1,488] | biology, ngs | sdsl | 2.1.1 | [1,489] | library, c++ | SE-MEI | 0.1.0 | [1,490] | phylogenetics | SeCaPr | 1.1.12, 2.0.2, 2.1.1 | [1,491] | phylogenetics | Segemehl | 0.1.9, 0.3.4 | [1,492] | biology, ngs, sequencing | segment-liftover | 20211021 | [1,493] | biology, genomics | SEPP | 20160614 | [1,494] | biology, phylogenetics | Seq-Gen | 1.3.3 | [1,495] | biology,phylogenetics | seq_crumbs | 20150120 | [1,496] | biology, sequence, genomics, utilities | SeqKit | 0.10.2, 0.8.0, 2.0.0 | [1,497] | biology, phylogenetics | seqmagick | 0.8.4 | [1,498] | biology | SeqMap | 1.0.13 | [1,499] | biology, sequencing, ngs | SEQPower | 1.1.1 | [1,500] | genomics, phylogenetics | SeqPrep | 0.5, 1.1 | [1,501] | biology, ngs, sequencing | seqscreen | 3.3 | [1,502] | sequencing, biology | seqtk | 1.3, 20140729 | [1,503] | biology, genomics, ngs | SEQuel | 1.0.1 | [1,504] | biology, ngs | SequelQC | 1.1.0 | [1,505] | phylogenetics | seqwish | 0.7, 20190509 | [1,506] | phylogenetics | SeqyClean | 1.8.10 | [1,507] | biology, ngs, sequencing | SeSiMCMC | 4.36 | [1,508] | biology, sequencing | SExtractor | 2.19.5 | [1,509] | astronomy | SHAPE-MaP | 1.2 | [1,510] | biology, phylogenetics | SHAPEIT | 2.12, 2.5 | [1,511] | biology, variant_calling | SHAPEIT4 | 4.2.2 | [1,512] | biology, sequencing, phasing | ShapeMapper | 2.1.3, 2.1.5 | [1,513] | biology, phylogenetics | SHARCGS | 1.2.11 | [1,514] | biology, ngs, de novo assembly | Shasta | 0.1.0 | [1,515] | phylogenetics | SHEsisPlus | 1.0, 1.01 | [1,516] | biology, genetics | shogun | 6.1.3 | [1,517] | phylogenetics | Shortbred | 0.9.4 | [1,518] | phylogenetics | shovill | 1.1.0 | [1,519] | genomics, sequencing, biology | SHRiMP | 2.2.3 | [1,520] | biology, genomics, ngs | shustring | 2.6 | [1,521] | biology, sequencing | SibeliaZ | 1.2.2, 1.2.3, 1.2.4 | [1,522] | biology, genomics, alignment | SICER | 1.1 | [1,523] | biology, ChIP-Seq | Sickle | 1.200, 1.33 | [1,524] | biology, ngs | Siesta | 3.2, 4.1b2, 4.1b3 | [1,525] | chemistry | SIFT | 4.0.3b | [1,526] | biology, genomics | SIGffRid | 1.1 | [1,527] | phylogenetics | SignalP | 4.1c, 5.0b | [1,528] | biology, phylogenetics | SiLiX | 1.2.11, 1.3.0 | [1,529] | phylogenetics | silo | 4.7 | [1,530] | iO,library | sim4 | 20121010 | [1,531] | biology, genomics | Sim4Life | 7.0.1 | [1,532] | biology,simulation | Simka | 1.5.3 | [1,533] | phylogenetics | SimNIBS | 3.2.1 | [1,534] | phylogenetics | SimSeq | 4.12.2011 | [1,535] | biology, ngs, phylogenetics | Simulia | 2019 | [1,536] | simulation, visualization | SInC | 20140120 | [1,537] | biology, phylogenetics | sine_scan | 1.1.1 | [1,538] | phylogenetics | Singularity | 3.7.4 | [1,539] | workflow_automation | SIPeS | 2.0 | [1,540] | biology, ChIP-Seq | sisl | 0.8.3 | [1,541] | physics, Tight-binding | skmer | 3.2.1 | [1,542] | genomics, biology | Slamdunk | 0.4.1, 0.4.2 | [1,543] | phylogenetics | SLAW | 20211217 | [1,544] | chromatography, Spectrometry | Slicer | 4.13.0, 4.3.1, 5.0.3 | [1,545] | biology, neuroscience, imaging | slow5tools | 0.5.1 | [1,546] | biology, sequencing | slurm-drmaa | 1.1.2, 1.1.3 | [1,547] | libraries, slurm, api, drmaa | smalt | 0.7.6 | [1,548] | application, biology, phylogenetics | SMARTdenovo | 20180219 | [1,549] | biology, phylogenetics | smartie-sv | 20180308 | [1,550] | phylogenetics | SMC++ | 1.15.4 | [1,551] | biology, genomics, sequencing | Smetana | 1.1.0 | [1,552] | phylogenetics | SMR | 1.03 | [1,553] | biology, genomics | SMRT-SV | 2.0.0 | [1,554] | biology, ngs | SMS | 1.7 | [1,555] | biology | Smudgeplot | 0.2.4 | [1,556] | phylogenetics | Snakemake | 6.4.1, 7.5.0 | [1,557] | biology, workflow | SNAP | 0.15.4, 2.0.0, 20100728 | [1,558] | biology,bioinformatics,sequencing | SNAPE-pooled | 20130407 | [1,559] | biology, variant_calling | SNeP | 1.1 | [1,560] | biology,phylogenetics | Sniffles | 1.0.11, 1.0.6, 1.0.8 | [1,561] | phylogenetics | Sniffles2 | 2.0.6 | [1,562] | biology, Bioinformatics | Snippy | 20160419, 4.6.0 | [1,563] | biology, phylogenetics | SNP-Pipeline | 1.0.1 | [1,564] | biology, phylogenetics | SNP-sites | 2.0.3 | [1,565] | biology, variant_calling | snp2hla | 1.0.3 | [1,566] | biology, Bioinformatics, Genomics | SnpEff | 4.3r, 4.3t, 5.0 | [1,567] | biology,bioinformatics,variant annotation | snpflip | 20190515 | [1,568] | biology, phylogenetics | SNPGenie | 20190620 | [1,569] | phylogenetics | SNPhylo | 20140701 | [1,570] | biology,phylogenetics | SNPsplit | 0.5.0 | [1,571] | biology,bioinformatics,sequencing | SNPTEST | 2.5.2 | [1,572] | phylogenetics | SOAPaligner | 2.21 | [1,573] | phylogenetics | SOAPdenovo | 1.05, 2.04 | [1,574] | biology,ngs | SOAPdenovo-Trans | 1.01, 1.03 | [1,575] | biology,ngs | SOAPec | 2.03 | [1,576] | biology, phylogenetics | SOAPnuke | 2.1.0 | [1,577] | phylogenetics | SOAPsplice | 1.10 | [1,578] | biology,ngs | SODA | 20200930 | [1,579] | biology | SOLAR | 8.4.2 | [1,580] | phylogenetics | SomaticSeq | 3.6.2 | [1,581] | phylogenetics | SortaDate | 20190705 | [1,582] | phylogenetics | SortMeRNA | 2.1, 4.0 | [1,583] | biology, sequencing, NGS | SourceTracker2 | 2.0.1 | [1,584] | phylogenetics | Sourmash | 2.0.1 | [1,585] | phylogenetics | SoX | 14.4.2 | [1,586] | phylogenetics | SpaceRanger | 1.3.1 | [1,587] | phylogenetics | SPAdes | 3.15.3, 3.7.1, 3.8.0 | [1,588] | biology, ngs | SparCC | 201608 | [1,589] | microbial Ecology | Spark | 2.2.0, 3.1.1 | [1,590] | spark, hadoop | sparsehash | 2.0.3 | [1,591] | google, API | SPARTA+ | 2.60 | [1,592] | chemistry | Spec2nii | 0.3.4 | [1,593] | phylogenetics | SpeedSeq | 0.1.2 | [1,594] | phylogenetics | Spidey | 20150922 | [1,595] | biology, genomics, bioinformatics | SpinalCordToolbox | 5.4 | [1,596] | phylogenetics | SplAdder | 2.4.2 | [1,597] | phylogenetics | SpliceGrapher | 0.2.5 | [1,598] | biology, sequencing | SpliceTrap | 0.90.5 | [1,599] | biology, genomics, ngs | SPM | 12b, 8, 8r5236 | [1,600] | biology,bioinformatics,matlab | spruceup | 2019.2.3 | [1,601] | phylogenetics | Sputnik | 1.0 | [1,602] | biology,bioinformatics,repeats | spyder | 4.1.4, 5.1.1, 5.3.2 | [1,603] | iDE, editor, programming, scripting | SQANTI | 1.2 | [1,604] | phylogenetics | SQANTI2 | 5.0 | [1,605] | phylogenetics | SQANTI3 | 0.1, 1.6, 4.2 | [1,606] | phylogenetics | SQL Developer | 4.1.2 | [1,607] | programming, oracle, sql | SQLite | 3.33.0, 3.8.8.2 | [1,608] | database | SqueezeMeta | 1.4.0, 1.5.2 | [1,609] | phylogenetics | squigglekit | 1.0.0 | [1,610] | data Visualization and Analysis, biology | squigglenet | 1.0 | [1,611] | sequencing, biology | SRA | 2.10.9, 3.0.0 | [1,612] | biology,bioinformatics,sra | sra-human-scrubber | 1.1 | [1,613] | cSV_categories | SRAssembler | 1.0.0 | [1,614] | phylogenetics | SSM | 20210511 | [1,615] | phylogenetics | SSPACE | 2.0, 3.0 | [1,616] | biology, ngs | ssr_pipeline | 0.951 | [1,617] | biology, DNA sequencing, | Stacks | 2.53, 2.55, 20190403 | [1,618] | biology, genomics, ngs | Staden | 1.14.6 | [1,619] | biology, phylogenetics | Stampy | 1.0.31 | [1,620] | biology, sequencing | staphb-toolkit | 1.2.0, 1.3.10 | [1,621] | biology | STAR | 2.7.5c, 2.7.6a, 2.7.9a | [1,622] | biology, ngs, rna-seq | STAR-CCM+ | 14.04.011, 15.02.009, 8.06 | [1,623] | mechanical Engineering | STAR-Fusion | 1.1.0, 1.3.1, 1.9.1 | [1,624] | biology, transcriptome | starseqr | 0.6.7 | [1,625] | phylogenetics | Stata | 10.1, 13 | [1,626] | statistics | stringMLST | 0.4 | [1,627] | biology, CHiP-Seq | Stringtie | 1.3.4d, 2.0.4, 2.1.3b | [1,628] | biology, ngs, sequencing,alignment | Structure | 2.3.3, 2.3.4 | [1,629] | biology,bioinformatics,population genetics | Structure_threader | 1.3.10 | [1,630] | utility, Wrapper, Structure | stylegan3 | 20211028 | [1,631] | aI, Image Processing | SU2 | 7.0.6 | [1,632] | phylogenetics | Subread | 1.6.2, 2.0.0, 2.0.3 | [1,633] | biology, sequencing, SNP | Subversion | 1.9.7 | [1,634] | revision Control | SUMO | 1.13.0, 1.2.0, 1.9.2 | [1,635] | phylogenetics | SUNDIALS | 2.3.0, 2.5.0, 3.0.0 | [1,636] | math, Numerical Solvers | supercell | 20170602 | [1,637] | biology, ngs | SuperCRUNCH | 1.2.1 | [1,638] | phylogenetics | Supernova | 1.2.1, 2.0.0, 2.1.1 | [1,639] | biology, phylogenetics, ngs | SUPPA | 2.3 | [1,640] | phylogenetics | Survival_Kit | 6.12 | [1,641] | clinical Biometrics | SURVIVOR | 1.0.6 | [1,642] | phylogenetics | SVDetect | 0.8b | [1,643] | biology,ngs,genomics | svim | 1.4.2 | [1,644] | biology | svim-asm | 1.0.2 | [1,645] | biology | swarm | 1.2.11 | [1,646] | data Analysis | Sweed | 3.3.2 | [1,647] | biology, phylogenetics | SWIG | 2.0.9, 3.0.12, 3.0.8 | [1,648] | library, development, C++, python | SWSC-EN | 1.0.0 | [1,649] | phylogenetics | Synima | 20210908 | [1,650] | phylogenetics | syri | 1.5.4 | [1,651] | genomics, biology | TACO | 0.7.3 | [1,652] | phylogenetics | Taiyaki | 5.0.1 | [1,653] | phylogenetics | talesf | 20160814 | [1,654] | phylogenetics | Tandem-Genotypes | 1.4.0 | [1,655] | phylogenetics | Tantan | 13 | [1,656] | imaging, ngs, genomics | Tapestri | 2.0.1 | [1,657] | phylogenetics | tapir | 20160825 | [1,658] | biology, phylogenetics | TAPIS | 1.2.1 | [1,659] | biology, sequencing | TASSEL | 5.0, 5.2.20, 5.2.29 | [1,660] | biology, genomics,wga | TAU | 2.23, 2.26, 2.26.3 | [1,661] | library, profiling and optimization | Tax4Fun | 0.3.1 | [1,662] | phylogenetics | taxMaps | 0.1 | [1,663] | biology, phylogenetics, taxonomy | TaxonKit | 0.9.0 | [1,664] | phylogenetics | Taxtastic | 0.5.7, 0.9.1 | [1,665] | biology, taxonomy | tbb | 2017_20161128 | [1,666] | library | tcllib | 1.18 | [1,667] | library | tcoffee | 10.00.r1613, 9.03.r1318 | [1,668] | biology | TDNAscan | 20210304 | [1,669] | phylogenetics | Tecplot 360 EX | 2015R1 | [1,670] | plotting, animation, cfd, simulations | tellseq | 1.0.0 | [1,671] | sequencing, Phylogenetics | TEMP | 20170731 | [1,672] | phylogenetics | TEMP2 | 0.1.4 | [1,673] | phylogenetics | TensorFlow | 2.6.0, 2.7.0, 2.8.0 | [1,674] | library, math | TESS | 2.3.1 | [1,675] | biology, genomics, markov | Test | 1.0 | [1,676] | shell | TetGen | 1.5.0 | [1,677] | tetrahedral meshes | TEToolkit | 1.5.1 | [1,678] | biology, sequencing | TEtools | 20180213 | [1,679] | biology, phylogenetics | Texlive | 20191127, 2020 | [1,680] | formatting, typesetting, document preparataion | TGICL | 2.1 | [1,681] | biology, ngs, sequencing | TGSGapCloser | 1.0.3 | [1,682] | phylogenetics | the_silver_searcher | 2.2.0 | [1,683] | search | Theano | 1.0.4 | [1,684] | library, math, gpu | Themisto | 0.2.0, 1.1.0 | [1,685] | genomics, Alignment | Tiara | 1.0.2 | [1,686] | phylogenetics | tiff | 3.8.0, 4.0.10 | [1,687] | imaging | Tigmint | 1.1.2 | [1,688] | phylogenetics | Tmux | 2.9, 3.1 | [1,689] | gNU | TNTBLAST | 2.04 | [1,690] | biology | ToFU2 | v17 | [1,691] | biology, ngs, sequencing | toil | 3.3.0, 3.3.3 | [1,692] | biology | Tombo | 1.4, 1.5, 1.5.1 | [1,693] | biology, genomics, ngs | Tophat | 2.1.0, 2.1.1, 2.1.2 | [1,694] | biology, ngs, sequencing | torch-geometric | 1.3.2 | [1,695] | phylogenetics | TotalView | 8.12 | [1,696] | parallel Computing | TPMcalculator | 0.0.3 | [1,697] | phylogenetics | TPP | 4.7.0, 4.7.1, 5.0.0 | [1,698] | biology, chemistry, nmr | TraCeR | 20160519 | [1,699] | biology, phylogenetics | TrackTools | 2011 | [1,700] | software | TrackVis/DTK | 0.5.2.2, 0.6.0.1 | [1,701] | biology, neuroscience, imaging | Tracula | 5.3.2014_05_26 | [1,702] | biology, neuroscience, imaging | traitRate | 1.1 | [1,703] | biology, evolution | Trans-ABySS | 2.0.1 | [1,704] | biology, phylogenetics | TransDecoder | 5.3.0, 5.4.0, 5.5.0 | [1,705] | biology, ngs | TRANSIT | 2.5.2, 3.2.3 | [1,706] | phylogenetics | Transrate | 1.0.1 | [1,707] | biology,assembly | TransVar | 2.3.3 | [1,708] | biology, phylogenetics | TreeBreaker | 20160621 | [1,709] | biology, phylogenetics | TreeMix | 1.12 | [1,710] | biology, phylogenetics | treePL | 20150305 | [1,711] | biology, phylogenetics | TREEPUZZLE | 5.3 | [1,712] | biology, phylogenetics | TreeShrink | 1.3.1, 1.3.2 | [1,713] | phylogenetics | TreeTime | 0.7.5, 0.8.1 | [1,714] | phylogenetics | trelis | 16.3 | [1,715] | geometry | TRF | 4.04, 4.09.1 | [1,716] | biology, genomics | Trilinos | 12.12.1, 12.18.1, 12.6.4 | [1,717] | mathematical Algorithms | Trim Galore | 0.4.4, 0.5.0, 0.6.5 | [1,718] | biology, ngs | trim_isoseq_polya | 0.0.3 | [1,719] | biology, Genetics, Sequencing | trimAl | 1.2 | [1,720] | biology, genomics,sequence alignment | TriMetAss | 1.1 | [1,721] | biology, ngs | Trimmomatic | 0.33, 0.36, 0.39 | [1,722] | biology, ngs | Trinity | r20130225, r20131110, r20140413 | [1,723] | biology, ngs, sequencing, rna-seq | Trinotate | 3.0.1, 3.2.0 | [1,724] | biology | triobinning | 0.2.3 | [1,725] | genomics, biology | TRIPLEC | 1.0 | [1,726] | biology | TRITONSERVER | 21.08 | [1,727] | machine_learning Inference Server | tRNAscan-Se | 1.23 | [1,728] | biology, ngs | TRUST4 | 1.0.2b | [1,729] | phylogenetics | Trycycler | 0.4.2 | [1,730] | phylogenetics | TURBOMOLE | 7.4.1 | [1,731] | chemistry | TWINSCAN | 4.1.2 | [1,732] | biology, genomics | Ubuntu | 20.04, 22.04 | [1,733] | ubuntu Linux | UCSC | 20200320, 20210803 | [1,734] | genomics | ucsc-fafiltern | 377 | [1,735] | phylogenetics | ucsc-maskoutfa | 377 | [1,736] | phylogenetics | UCX | 1.11.2, 1.9.0 | [1,737] | parallel Programming, development, library | UDUNITS | 2.2.17 | [1,738] | library, data_science, units | ufraw | 0.22 | [1,739] | data_mining | ugtm | 1.1.6 | [1,740] | statistics, modeling | UKFractography | 20200127 | [1,741] | phylogenetics | umi-tools | 0.5.5 | [1,742] | phylogenetics | UNAFold | 3.8 | [1,743] | biology, genome, RNA, folding | Unanimity | 20171108, 3.4.1 | [1,744] | programming,library,cpp | UNCALLED | 2.2 | [1,745] | biology, genomics | Unicycler | 0.4.8 | [1,746] | phylogenetics | Unrar | 0.0.1, 4.20 | [1,747] | unarchiver, utility | uproc | 1.2.0 | [1,748] | biology, genome | uropa | 4.0.2 | [1,749] | genomics, sequencing, biology | USEARCH | 9.0.2132, 9.1.13, 9.2.64 | [1,750] | biology, alignment, sequencing | UShER | 0.1.4, 0.4.1, 0.5.2 | [1,751] | phylogenetics | V-Phaser | 02112013 | [1,752] | biology, phylogenetics | v-pipe | 2.0.0 | [1,753] | biology, genomics, sequencing, virus | VAIR | 0.7.0 | [1,754] | geospatial Data Modeling | Valgrind | 3.11.0, 3.15.0, 3.8.1 | [1,755] | computer Programming | Valouev | 20160325 | [1,756] | biology, phylogenetics | vamb | 3.0.2 | [1,757] | biology | VAMPIR | 9.1 | [1,758] | high Performance Computing | VarDictJava | 1.6.0, 20160521, 20170531 | [1,759] | biology, phylogenetics | varnorm | 0.21 | [1,760] | biology | VarScan | 2.3.6 | [1,761] | biology, ngs | VarSim | 0.8.4, 0.8.6 | [1,762] | phylogenetics | VarSimLab | 20180220, 20180921 | [1,763] | biology, simulation, genomics | vasp | 5.4.4, 6.1.0, 6.2.0 | [1,764] | chemistry | vaspkit | 1.2.5 | [1,765] | phylogenetics | VAST-TOOLS | 2.5.1, 20150506 | [1,766] | biology, rna-seq, ngs, splicing | VCF-kit | 0.2.6 | [1,767] | phylogenetics | vcf-validator | 0.6 | [1,768] | biology, phylogenetics | vcfanno | 0.2.8, 0.3.3 | [1,769] | biology, phylogenetics | vcflib | 1.0.1 | [1,770] | biology, genomics | vcftools | 0.1.15, 0.1.16, 0.1.9 | [1,771] | biology, genomics | vcontact | 20190512 | [1,772] | phylogenetics | VDJtools | 1.1.7, 1.2.1 | [1,773] | biology, phylogenetics | Velvet | 1.2.10, 1.2.10-long | [1,774] | biology, genomics | VEP | 83, 88.8, 92 | [1,775] | biology, genomics, ngs | Vermouth-martinize | 0.7.2 | [1,776] | phylogenetics | VeryFastTree | 3.0.1 | [1,777] | phylogenetics | vg | 1.33.0, 1.38.0, 1.39.0 | [1,778] | phylogenetics | vibrant | 1.2.0 | [1,779] | genomics, virus | ViennaRNA | 2.2.6, 2.4.18 | [1,780] | biology, RNA-seq | ViewBS | 0.1.10, 0.1.9 | [1,781] | phylogenetics | Vim | 8.1.1566, 8.2.2465 | [1,782] | programming,scripting,language | viralmsa | 1.1.10, 1.1.12 | [1,783] | phylogenetics | VirSIeve | 20210406 | [1,784] | biology, Pipeline | VirtualCell | 7.1 | [1,785] | phylogenetics | VIRULIGN | 1.0.2 | [1,786] | phylogenetics | VirusDetect | 1.7 | [1,787] | phylogenetics | VirusFinder | 2.0 | [1,788] | biology, phylogenetics | visit | 2.13.3, 3.0.1, 3.1.4 | [1,789] | visualization, Animation and Analysis | VISPR | 0.4.14 | [1,790] | phylogenetics | VMD | 1.9.1, 1.9.3 | [1,791] | visualization, animation, 3d | vscode | 1.38.1, 1.65.2 | [1,792] | programming | VSearch | 20151022, 20161209-2.3.4 | [1,793] | biology,NGS | vt | 0.57721, 20140903, 20160129 | [1,794] | biology, genomics | VTC | 0.9.3 | [1,795] | biology, VCF | VTK | 8.2.0, 9.0.3, 9.1.0 | [1,796] | biology, neuroscience, imaging | w2rap-contigger | 20161124 | [1,797] | biology, genomics | Wannier90 | 1.2, 2.1.0 | [1,798] | computational Physics | WarpedLMM | 0.21 | [1,799] | modeling | WaveGAN | 20190829 | [1,800] | machine_learning, Audio, GAN, Synthesis | WDSSII | 5 | [1,801] | weather, Meteorology | WebLogo | 2.8.2, 3.3, 3.5.0 | [1,802] | biology,bioinformatics,sequence,graphics | Weka | 3.8, 3.8.5 | [1,803] | statistics,machine learning | Wengan | 0.2 | [1,804] | biology, genomics | wgd | 1.1.1 | [1,805] | phylogenetics | WGS Assembler | 8.3rc1.r4638, 8.3rc2 | [1,806] | biology, genomics | Wgsim | 0.3.1-r13 | [1,807] | biology, phylogenetics | WHAMM | 0.14a | [1,808] | biology, phylogenetics | WhatsHap | 1.1 | [1,809] | biology, phylogenetics | whiteboxtools | 1.5.0 | [1,810] | phylogenetics | Wine | 4.0.0, 7.0.0 | [1,811] | windows, emulator | Wise | 2.2.0, 2.4.1 | [1,812] | biology, genome | WIsH | 1.0 | [1,813] | phylogenetics | WoLFPSort | 0.2 | [1,814] | phylogenetics | WOMBAT | 20180118 | [1,815] | biology, phylogenetics | workbench | 4.1.1 | [1,816] | modeling, simulation | wtdbg | 2.1, 2.4, 2.5 | [1,817] | phylogenetics | WU BLAST | 2.0 | [1,818] | biology | Wub | 0.2.0, 0.4.0 | [1,819] | biology, genomics, ngs | xander | 20151222 | [1,820] | biology, phylogenetics | Xapian | 1.4.4 | [1,821] | library | XCrySDen | 1.5.60 | [1,822] | computational Material Science | Xerces | 3.1.4 | [1,823] | phylogenetics | xesmf | 0.6.2 | [1,824] | grid Analysis, Climate | xpclr | 1.0, 1.1.1 | [1,825] | phylogenetics | Xterm | 1.1 | [1,826] | utility | XWAS | 3.0 | [1,827] | phylogenetics | XY-Meta | 20200413 | [1,828] | phylogenetics | XZ | 5.2.2 | [1,829] | compression, library | YAGO | 4 | [1,830] | data | YAHA | 0.1.82 | [1,831] | biology, ngs | YAK | 0.1 | [1,832] | phylogenetics | YASM | 1.3.0 | [1,833] | computer Programming | YASRA | 2.33 | [1,834] | biology, ngs, sequencing | yolov4_darknet | 4-pre | [1,835] | machine_learning | yolov5 | 4.0 | [1,836] | machine_learning | Zagros | 1.0.0 | [1,837] | biology,phylogenetics | ZEO++ | 0.2.2 | [1,838] | chemistry | zorro | 2.2 | [1,839] | biology, sequencing | Zstd | 1.5.0 | [1,840] | phylogenetics | ZUMIS | 2.6.0 | [1,841] | biology, ngs, sequencing |
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