Applications
Revision as of 19:58, 6 July 2022 by Moskalenko (talk | contribs)
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 |