Difference between revisions of "Applications"

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Revision as of 14:35, 18 July 2022

Note: Up to three latest versions are listed even though there could be more available. Run module spider keyword for a full list of provided versions. Use the Module value from the second column below as the keyword.
If it's a 'core' module you should be able to directly combine the Module name and a Version for a load command e.g. 'module load pylucene'.

Name Module Versions URL Categories

3d-dna 3d-dna 20170330 [1] biology, phylogenetics
3PCLR 3pclr 20150906 [2] biology, phylogenetics
4p 4p 1.0 [3] biology, variant_calling
AAFTF aaftf 0.2.5 [4] biology, pipeline, assembly
ABRicate abricate 1.0.1 [5] phylogenetics
ABruijn abruijn 1.0 [6] biology, assembly, ngs
ABySS abyss 1.5.2, 2.1.0, 2.2.5 [7] biology, de_novo
AdapterRemoval adapterremoval 2.2.2 [8] phylogenetics
ADFRsuite adfrsuite 1.0 [9] sequencing, biology
ADMB admb 11.5, 12.0 [10] math, modeling
AdmixTools admixtools 20150311, 7.0.2 [11] biology, genomics, ngs
ADMIXTURE admixture 1.23, 1.3.0 [12] biology, genomics, ngs
AEGeAn aegean 0.14.0, 0.16.0 [13] biology, genomics
AFNI afni 20.3.00, 2018_04_12 [14] biology, neuroscience, imaging
AfterQC afterqc 0.9.7 [15] phylogenetics
AGAT agat 0.4.0 [16] phylogenetics
AGfusion agfusion 1.252 [17] phylogenetics
Albacore albacore 2.3.1, 2.3.3 [18] biology, phylogenetics
Albumentations albumentations 1.0.3 [19] ai, image_processing, imaging
Alder alder 1.03 [20] biology, genomics
ALFA alfa 1.1.1 [21] phylogenetics
alienhunter alienhunter 1.7 [22] biology, sequencing
AliStat alistat 1.12 [23] phylogenetics
allhic allhic 0.9.8 [24] genomics, biology
ALLMAPS allmaps 20180117 [25] biology, phylogenetics
ALLPATHS-LG allpaths 42316, 44837, 49232 [26] biology, ngs
AlphaFold alphafold 2.0.0, 2.1.2, 2.2.0 [27] protein, structure, machine_learning
Alphaimpute alphaimpute 0.0.2, 1.9.8.2, 1.9.8.3 [28] phylogenetics
AltAnalyze altanalyze 2.1.0 [29] biology, genomics
AMAS amas 1.0 [30] phylogenetics
AMBER amber 16.0, 18, 20 [31] chemistry, molecular_dynamics
AMICO amico 1.0.1 [32] library, imaging, math
AMOS amos 3.1.0 [33] biology, genomics, assembly
AMP amp 0.6.1 [34] phylogenetics
amPEPpy ampeppy 1.0 [35] phylogenetics
amphora2 amphora2 20140305 [36] biology, phylogenetics
AMPtk amptk 1.2.4, 1.5.1 [37] biology, ngs
amptorch amptorch 20210313 [38] phylogenetics
amrfinderplus amrfinderplus 3.10.18 [39] phylogenetics
AMRPlusPlus amrplusplus 20180508 [40] phylogenetics
AMUSE amuse 10.0, 13.1.0 [41] astronomy
ANGSD angsd 0.933 [42] biology, ngs
annocript annocript 2.0 [43] phylogenetics
AnnoTALE annotale 1.4.1 [44] phylogenetics
ANNOVAR annovar 20130221, 20150322, 20191024 [45] biology, genomics
Ansible ansible 2.5.5, 2.8.1 [46] workflow_automation
ansysem ansysem 17.0, 2022r1 [47] physics
antiSMASH antismash 4.1.0, 6.0.1 [48] phylogenetics
ANTs ants 2.2.0, 2.3.4 [49] biology, phylogenetics
anvio anvio 6.1, 6.2, 7.1 [50] biology
Appreci8 appreci8 20180530 [51] biology, genomics
Apptainer apptainer 1.0.3 [52] workflow_automation
APT apt 1.15.0, 1.18.0, 1.20.5 [53] biology, genomics
ARC arc 1.1.4 [54] biology, ngs
Aria2 aria2 1.35.0 [55] utility
ARKS arks 1.0.2 [56] phylogenetics
Armadillo armadillo 7.900.0, 9.200.6, 9.900.4 [57] library, compiler, math
ARPACK arpack 1.0 [58] math
ArrayFire arrayfire 3.4.2 [59] math
arriba arriba 2.1.0 [60] phylogenetics
ART art 20160417, 20160605 [61] phylogenetics
artemis artemis 18.1.0 [62] biology
asap asap 2.0 [63] visualization, biology
asaq asaq 1.0 [64] alignment, sequencing, phylogenetics
ASE-ANI ase-ani 20180712 [65] biology, genomics, ngs
ASHS ashs 2.0 [66] biology, imaging
ASPECT aspect 2.3.0 [67] library
Assembly-stats assembly-stats 1.0.1 [68] biology, sequencing, genomics
Assemblytics assemblytics 1.2.1 [69] phylogenetics
Assexon assexon 20190814 [70] phylogenetics
AStalavista astalavista 3.2, 4.0 [71] biology, genomics
aster aster 220718 [72] biology, data_science, sequencing
ASTRAL astral 5.6.1, 5.6.2, 5.7.7 [73] biology, ngs, phylogenetics
ASTRID astrid 2.2.1 [74] phylogenetics
Astropy astropy 2.0.8 [75] biology, phylogenetics
ATAT atat 3.23, 3.34 [76] material_science
ATLAS atlas 3.10.1, 3.10.2, 3.11.17 [77] library, data_science
Atom atom 1.57.0 [78] programming
AtomEye atomeye 3 [79] material_science
AtomMan atomman 1.3.3 [80] phylogenetics
aTRAM atram 2.2.0, 2.4.3 [81] math
Augustus augustus 3.3.2, 3.3.3, 3.4.0 [82] biology, genomics
Auto3DEM auto3dem 4.05.2 [83] image_processing
AutoDock autodock 4.2.6 [84] biology
AutoDock-GPU autodock-gpu 1.5.3 [85] chemistry
Autometa autometa 20190802 [86] phylogenetics
automlsa2 automlsa2 0.8.1 [87] phylogenetics, biology, genomics
AWSCLI awscli 2.2.30 [88] utility
azoo azoo 1.3.1 [89] phylogenetics
Badread badread 0.1.5 [90] phylogenetics
bakta bakta 1.3.3 [91] genomics, biology
BALi-Phy bali-phy 3.4.1, 3.5.0 [92] phylogenetics
BAM-matcher bam-matcher 20161021 [93] phylogenetics
Bam-Readcount bam-readcount 20150616 [94] biology, genomics
bamaddrg bamaddrg 20120326 [95] phylogenetics
BamBam bambam 1.0 [96] biology, genomics
bamm bamm 2.5.0 [97] phylogenetics
bamsnap bamsnap 0.2.19 [98] phylogenetics
Bamstats bamstats 20140602 [99] biology, ngs
Bamsurgeon bamsurgeon 1.2 [100] phylogenetics
bamtofastq bamtofastq 1.3.5 [101] phylogenetics
Bamtools bamtools 2.4.1, 2.5.0, 2.5.1 [102] biology, ngs, sequencing
bamUtil bamutil 1.0.2 [103] biology, genomics
BAPS baps 6.0 [104] biology, genomics
Barrnap barrnap 0.7, 0.9 [105] biology, rna-seq
Basemount basemount 0.15.96 [106] biology, sequencing
BatMeth2 batmeth2 20210720 [107] biology, genomics, mapping
bax2bam bax2bam 0.0.9 [108] phylogenetics
BayArea bayarea 1.0.2 [109] biology
BAYENV bayenv 2.0 [110] biology, phylogenetics
BayesAss bayesass 3.0.4, 3.0.4.2 [111] phylogenetics
BayeScan bayescan 2.1 [112] biology, variant_calling
BayesR bayesr 20151016 [113] biology, phylogenetics
BayesTraits bayestraits 3.0.2 [114] phylogenetics
baypass baypass 2.1 [115] biology, phylogenetics
BBMap bbmap 38.26, 38.44, 38.90 [116] biology, alignment
bcftools bcftools 1.15, 1.3.1, 1.9 [117] biology, ngs
bcl2fastq bcl2fastq 2.16.0.10, 2.20.0.422 [118] biology, ngs
BDG-SeQuila bdg-sequila 0.5.5 [119] phylogenetics
BEAGLE beagle 4.1, 5.0, 5.2 [120] biology, genomics
BEAR bear 20170209 [121] biology, genomics
BEAST beast 2.6.2, 2.6.3, 2.6.7 [122] biology, phylogenetics
BEAST2-XML beast2-xml 1.0.9 [123] phylogenetics
BEDOPS bedops 2.4.30 [124] biology, sequencing, ngs
BEDTools bedtools 2.29.1, 2.29.2, 2.30.0 [125] biology, ngs
Bertini bertini 1.6 [126] math
BERTopic bertopic 0.7, 0.8.1 [127] machine_learning
BESST besst 2.2.4 [128] biology, ngs
BFAST bfast 0.7.0 [129] biology, ngs
bgenix bgenix 1.1.7 [130] data_science, genomics
Bifrost bifrost 0.2, 1.0.3, 20200225 [131] phylogenetics
BiG-SCAPE big-scape 1.1.2 [132] biology, genomics, phylogenetics, pipeline
BinPacker binpacker 1.0 [133] biology, rna-seq, assembly
BinSanity binsanity 0.2.6.4 [134] biology, genomics
Bioawk bioawk 1.0 [135] phylogenetics
bioBakery biobakery 0.15.1, 1.8, 3.0.0 [136] phylogenetics
Biodiverse biodiverse 2.1 [137] phylogenetics
Biolite biolite 0.3.5.1 [138] biology, genomics, variant_calling
BIOM biom 2.1.5, 2.1.6 [139] biology, genomics
BIOMART biomart 1.4 [140] biology, genomics
Biopieces biopieces 2.0 [141] phylogenetics
BIRDS fiji-birds 1.0 [142] workflow_automation, utility, imaging
Bismark bismark 0.22.3, 0.7.4, 0.7.7 [143] biology, ngs
Blackfynn blackfynn 0.2.7 [144] data_mining
BLASR blasr 20130815, 20161215 (5.3), 5.3.2 [145] biology, ngs
Blast2GO blast2go 2.5.0-20120705 [146] biology, genomics
Blast2GO CLI blast2go 1.3.3 [147] biology, genomics
BLAT blat 20121105, 20140318 [148] genomics
blender blender 2.73, 2.77, 3.0.1 [149] graphics
blink blink 0.01 [150] genomics
Blitz blitz 0.10 [151] library
BlobTools blobtools 1.0, 2.2 [152] phylogenetics
bloomfiltertrie bloomfiltertrie 0.8.7 [153] phylogenetics
BloomTree bloomtree 0.3.5 [154] data_mining
BLUPF90 blupf90 20160604, 20180301, 20190531 [155] biology, phylogenetics
BMGE bmge 1.12 [156] biology, genomics, phylogenetics
bmtagger bmtagger 3.101 [157] genomics, biology
BOLT-LMM bolt-lmm 2.3.4 [158] phylogenetics
BoltzTraP boltztrap 1.2.5 [159] physics
Boost boost 1.71.0, 1.75.0, 1.77.0 [160] programming,library,cpp
booster booster 0.1.2 [161] phylogenetics
Bowtie bowtie 1.1.1, 1.2.0, 1.2.3 [162] biology, ngs, sequencing
Bowtie2 bowtie2 2.3.5.1, 2.4.2, 2.4.5 [163] biology, ngs, sequencing
BoxCLI boxcli 2.9.0 [164] file_management, web, programming
BPGA bpga 1.2 [165] biology, ngs
BPP bpp 4.1.4, 4.3.8, 4.4.1 [166] biology, phylogenetics
Bracken bracken 1.0.0, 2.5 [167] biology, phylogenetics
BrainIAK brainiak 0.11 [168] imaging
braker braker 2.1.2, 2.1.5, 2.1.6 [169] phylogenetics
BRANCH branch 1.8.1 [170] biology, ngs, mapping
BRATNextGen bratnextgen 20150505 [171] biology, genomics
BreakDancer breakdancer 1.4.5 [172] biology, phylogenetics
breakseq breakseq 2.2 [173] biology, phylogenetics
Brewery brewery 20191205 [174] phylogenetics
Bridger bridger 20141201 [175] ngs, genomics, biology
BRIG brig 0.95 [176] biology, genomics
BRM brm 0.3 [177] phylogenetics
Bruker2nifti bruker2nifti 1.0.4 [178] phylogenetics
Bsmap bsmap 2.87 [179] biology, ngs
Bsoft bsoft 1.9.1 [180] biology, image_processing
BSseeker2 bsseeker2 2.1.0, 2.1.8 [181] biology, phylogenetics
bubbleparse bubbleparse 20140314 [182] biology, phylogenetics
BUCKy bucky 1.4.4 [183] biology, phylogenetics
BUSCO busco 4.0.6, 4.1.4, 5.2.0 [184] biology, genomics
BWA bwa 0.7.7, 0.7.8, 0.7.9a [185] biology, ngs
bwa-mem2 bwa-mem2 2.2.1 [186] phylogenetics
BWA-PSSM bwa-pssm 0.5.11 [187] phylogenetics
bxh_xcede_tools bxh_xcede_tools 1.11.1 [188] biology
BYOBU byobu 5.133, 5.92 [189] shell
bzip2 bzip2 1.0.6 [190] utility, library
c-wap c-wap 20220624 [191] sequencing, genomics, biology
Cactus cactus 2.0.3, 2.0.5 [192] phylogenetics
CAFE cafe 4.1, 5.0.0 [193] biology, phylogenetics
came came 0.0.1 [194] phylogenetics
Camino camino 20140723 [195] biology, neuroscience, imaging
CAMP camp 1.0.0 [196] biology, sequencing
Cantera cantera 2.1.1 [197] biology, physics
Canu canu 1.9, 2.0, 2.1 [198] biology, sequencing
CANVAS canvas 1.40.0.1613 [199] phylogenetics
CAP3 cap3 20120705 [200] biology, assembly
Capnp capnp 0.5.3 [201] compiler
CARTA carta 2.0 [202] image_processing
CASAVA casava 1.8.2 [203] biology, ngs
CASM casm 0.2.0 [204] physics
CasOFFinder casoffinder 2.4 [205] phylogenetics
Catch catch 1.4.0 [206] biology, genomics, sequencing
CAVIAR caviar 20171218 [207] biology, phylogenetics
CBGpipe cbgpipe 20190702 [208] phylogenetics
CCMetagen ccmetagen 1.4.0 [209] phylogenetics
CD-HIT cdhit 4.6, 4.6.4, 4.6.8 [210] biology, genomics
CDBFasta cdbfasta 20181005 [211] phylogenetics
CDNA_Cupcake cupcake 20180629, 22.0.0, 9.0.1 [212] biology, ngs, sequencing
CDO cdo 1.7.2rc3, 1.9.4 [213] climate
CellProfiler cellprofiler 3.1.9, 4.1.3 [214] phylogenetics
CellRanger cellranger 6.0.1, 6.1.2, 7.0.0 [215] biology, ngs, rna-seq
CellRanger-ARC cellranger-arc 2.0.1 [216] biology, ngs, rna-seq
CellRanger-ATAC cellranger-atac 1.2.0 [217] biology, ngs, rna-seq
CellRanger-DNA cellranger-dna 1.0.0, 1.1.0 [218] biology, ngs, rna-seq, genomics
Centrifuge centrifuge 1.0.3, 1.0.4b [219] biology, phylogenetics
CFITSIO cfitsio 3.370 [220] library, compiler
CGAL cgal 4.10, 4.9, 5.02 [221] library, math
CGATools cgatools 1.6.0.43 [222] biology, ngs
cgmaptools cgmaptools 0.1.1, 0.1.2 [223] phylogenetics
CGView cgview 1.0.2 [224] phylogenetics
CHARMM charmm 36a3, 43b2 [225] chemistry, simulation
ChartDirector libchartdir 5.1.0 [226] library, data_science
CheckM checkm 1.0.4, 1.0.7, 1.1.2 [227] biology, genomics
Chimera chimera 1.12 [228] biology, modeling
Chipyard chipyard 1.0 [229] design
Chromeister chromeister 1.5a [230] biology, genomics
ChromEvol chromevol 2.0 [231] biology, ngs
CIMS cims 4.1.2 [232] biology, genomics
CIRCexplorer circexplorer 1.1.10 [233] biology, rna-seq
CIRCexplorer2 circexplorer2 2.3.5, 2.3.8 [234] phylogenetics
Circlator circlator 1.5.5 [235] phylogenetics
Circleator circleator 1.0.2 [236] phylogenetics
circompara2 circompara2 0.1.2.1 [237] phylogenetics
Circos circos 0.63-pre11, 0.69-2, 0.69-9 [238] biology, genomics, ngs
CIRI ciri 2.0.6 [239] phylogenetics
ciriquant ciriquant 1.1.2 [240] phylogenetics
CisGenome cisgenome 2.0 [241] biology, genomics
cisTEM cistem 1.0.0 [242] phylogenetics
Clairvoyante clairvoyante 1.02 [243] phylogenetics
Clann clann 3.2.3 [244] biology, phylogenetics
clara clara v4.0 [245] ai, machine_learning
CLARK clark 1.2.2-b, 1.2.3 [246] biology, genomics
CLHEP clhep 2.2.0.1 [247] physics
CLIFinder clifinder 4.1 [248] biology, phylogenetics
ClinicaDL clinicadl 1.0.4 [249] biology, imaging, machine_learning
clipkit clipkit 1.3.0 [250] genomics, biology
CLIPper clipper 2.1.0 [251] phylogenetics
CLIPSeqTools clipseqtools 0.1.7 [252] biology, sequencing
ClonalFrame clonalframe 1.1, 1.2 [253] biology, ngs, phylogenetics
ClonalFrameML clonalframeml 1.0, 1.11 [254] biology, ngs, phylogenetics
CloudCompare cloudcompare 2.10.3 [255] visualization
Clover clover 2.0 [256] biology, genomics, assembly
CLUMPP clumpp 1.1.2 [257] biology
ClustalO clustalo 1.2.0 [258] biology, alignment
ClustalW clustalw 2.1 [259] biology, alignment
cluster3 cluster3 1.52a [260] biology, genomics
Clview clview 20130402 [261] biology
CMake cmake 3.19.1, 3.21.3 [262] programming
CMS cms 20170518 [263] biology
CMWP cmwp 140518 [264] biology, genomics
CNCI cnci 20180305 [265] phylogenetics
CNSpipeline cnspipeline 20170827 [266] phylogenetics
CNV-Seq cnvseq 20110715, 20140812 [267] biology, genomics
CNV-Sim cnv-sim 0.9.2 [268] biology, phylogenetics
CNVkit cnvkit 0.9.6 [269] phylogenetics
CNVnator cnvnator 0.3.2 [270] biology, genomics
cobra-tf cobra-tf 0.1 [271] fluid_dynamics
CodonPhyML codonphyml 20150303 [272] phylogenetics
Coevol coevol 1.3c, 1.4b, 1.6 [273] biology, phylogenetics
Cogent cogent 2.1 [274] biology, phylogenetics
COLMAP colmap 3.6 [275] modeling
CoMap comap 1.4.1 [276] biology, genomics
Comp-D_MPI comp-D_MPI 1.0 [277] statistics
Compacta compacta 1.02 [278] biology, genomics
COMSOL comsol 5.4.0 [279] simulation
Concaterpillar concaterpillar 1.8a [280] phylogenetics
CONCOCT concoct 1.1.0 [281] biology, genomics
Conda conda 4.10.3, 4.12.0 [282] programming
CONN conn 18a [283] imaging
CONNECT connect 20200614 [284] phylogenetics
connectomemapper3 connectomemapper3 3.0.0-rc1 [285] phylogenetics
ConPADE conpade 1.0 [286] phylogenetics
Conpair conpair 20161010, 20180624 [287] biology, phylogenetics
Consed consed 23.0, 25.0, 29.0 [288] biology, genomics
CONSEL consel 0.20 [289] biology, phylogenetics
ContaVect contavect 0.2 [290] biology, phylogenetics
Convert3D convert3d 1.1.0 [291] imaging, utility
Coot coot 0.9.5 [292] modeling
Coreutils coreutils 8.23, 8.28 [293] utility
Corset corset 1.06 [294] biology, ngs
Counterr counterr 0.1 [295] phylogenetics
covNMR covnmr 2014 [296] biochemistry
cp2k cp2k 7.0.0 [297] chemistry
CPAT cpat 3.0.2 [298] phylogenetics
cpc cpc 2.0 [299] phylogenetics
CPLEX cplex 12.6.1, 12.6.2, 12.7 [300] climate
Crass crass 1.0.1 [301] biology, assembly
crisflash crisflash 1.2.0 [302] phylogenetics
CRISP crisp 20181122 [303] phylogenetics
CRISPRanalyzer crispranalyzer 1.50 [304] biology, genomics, ngs
CRISPRCasFinder crisprcasfinder 4.2.17 [305] phylogenetics
CRISPResso2 crispresso2 20220811 [306] genomics, sequencing, biology
CrossMap crossmap 0.3.9, 0.6.3 [307] biology, genomics
crossmapper crossmapper 1.1.1 [308] phylogenetics
Crux crux 1.40 [309] biology, spectroscopy
CryptoMiniSat cryptominisat 5.0.1 [310] math
csvtk csvtk 0.23.0 [311] biology
ctk ctk 1.1.4 [312] biology, genomics
CUBE cube 4.4 [313] library, compiler, math
CUDA cuda 11.0.207, 11.1.0, 11.4.3 [314] programming, library, graphics
Cufflinks cufflinks 2.1.1, 2.2.1, 2.2.1.1 [315] biology, ngs, sequencing
cupy cupy 8.3.0 [316] phylogenetics
cutadapt cutadapt 1.18, 2.8, 3.4 [317] biology, ngs
CutRunTools cutruntools 20200104 [318] phylogenetics
cvbio cvbio 3.0.0 [319] phylogenetics
CViT cvit 1.3 [320] programming, library
CWLtool cwltool 1.0.20190906, 2.0.20200126, 3.0.20210124104916 [321] workflow_automation, scheduler
cx_oracle cxoracle 8.3.0 [322] database, utility
CycleGan cyclegan 20201015 [323] phylogenetics
Cytoscape cytoscape 3.4.0 [324] biology, ngs, phylogenetics
d2go d2go 20210702 [325] machine_learning, ai
dadi dadi 2.1.1 [326] phylogenetics
DAKOTA dakota 6.15, 6.8, 6.8-gui [327] math
DALIGNER daligner 1.0 [328] biology, phylogenetics
dammit dammit 1.0rc2 [329] biology, phylogenetics
DASTool dastool 1.1.0, 1.1.2 [330] biology, phylogenetics
datamash datamash 1.1.0 [331] math
DAWGPAWS dawgpaws 1.0 [332] biology, phylogenetics
DCC dcc 0.4.4 [333] biology, ngs
Dcmstack dcmstack 0.6.2 [334] biology, imaging
DCMTK dcmtk 3.6.0 [335] biology, neuroscience, imaging
dDocent ddocent 2.7.8 [336] phylogenetics
DDSCAT ddscat 7.3.0 [337] astronomy
DDT ddt 18.2, 20.0, 20.2 [338] programming
DealII dealii 8.3.0, 9.3.1 [339] library
DeconSeq deconseq 0.4.3 [340] biology, phylogenetics
decontaMiner decontaminer 1.4 [341] genomics, biology
DECX decx 20180205 [342] phylogenetics
DeepARG deeparg 1.0.1 [343] phylogenetics
deepbgc deepbgc 0.1.18 [344] phylogenetics
Deepcoil deepcoil 2.0.1 [345] sequencing, biology
DeepGS deepgs 1.2 [346] phylogenetics
DeepLabCut deeplabcut 2.0.7-gpu, 2.1.1, 2.2.1 [347] phylogenetics
deepmicrobes deepmicrobes 20200219 [348] biology, genomics, machine_learning
DeepMReye deepmreye 01192022 [349] library, biology
DeepPicker deeppicker 20161102 [350] imaging
deepTools deeptools 2.4.3, 3.1.1 [351] biology, ngs
deepvariant deepvariant 1.4.0 [352] biology, genomics, sequencing, machine_learning
deFusion defusion 20200305 [353] phylogenetics
Delft3D delft3d 7545 [354] physics
Delineate delineate 1.2.2 [355] biology, genomics
Delly delly 0.7.5, 0.7.7, 0.7.8 [356] biology, phylogenetics
delucs delucs 20220512 [357] sequencing, genomics, machine_learning
DeNoGAP denogap 1.0 [358] biology, phylogenetics, ngs
DERIVA deriva 1.5.0 [359] phylogenetics
deSALT desalt 1.5.6 [360] biology, genomics, sequencing
Detectron2 detectron2 0.4, 0.5, 0.6 [361] library
DeTiN detin 1.7.5.9 [362] imaging, ngs, genomics
DEXTRACTOR dextractor 1.0 [363] biology, sequencing
Diamond diamond 0.9.15, 0.9.34, 2.0.9 [364] biology, genomics
diCal2 dical2 2.2.0.1 [365] biology, phylogenetics
diffReps diffreps 1.55.4 [366] biology
DISCOVAR de novo discovardenovo 52488 [367] biology, ngs, assembly
DiscoVista discovista 20180906 [368] phylogenetics
discvrseq discvrseq 1.3.10 [369] biology, phylogenetics
Distruct distruct 2.3 [370] phylogenetics
DIYABC diyabc 1.0.4.43b, 2.0.3, 2.1.0 [371] biology, phylogenetics
DL_POLY dlpoly 1.9 [372] molecular_dynamics
Dlib dlib 19.19 [373] phylogenetics
DNA Clust dnaclust 3.0 [374] biology, genomics
DOCK dock 6.7, 6.8, 6.9 [375] chemistry
DoGFinder dogfinder 20201103 [376] phylogenetics
DosageConvertor dosageconvertor 1.0.3 [377] biology
DOT dot 2.0 [378] biology, chemistry
Doxygen doxygen 1.8.3.1 [379] programming, documentation
dragmap dragmap 1.2.1 [380] phylogenetics, sequencing, biology
dragonflye dragonflye 1.0.12 [381] sequencing, genomics
DRAP drap 1.91 [382] biology, phylogenetics
dRep drep 2.3.2 [383] phylogenetics
Dropseq dropseq 2.4.0 [384] phylogenetics
DS9 saoimageds9 7.5, 8.0.1 [385] imaging
DScribe dscribe 1.2.0 [386] machine_learning
dsistudio dsistudio 20210123 [387] machine_learning
DSK dsk 2.1.0, 2.3.0 [388] biology, ngs
DSRC dsrc 2.0 [389] phylogenetics
DSSAT dssat 4.6 [390] simulation
DSSP dssp 2.2.1, 3.0.0 [391] molecular_dynamics
DSuite dsuite 0.4, 0.4-r41 [392] biology, genomics
dtiprep dtiprep 0.1.1 [393] phylogenetics
duchamp duchamp 1.6.2 [394] phylogenetics
dynamicDBG dynamicdbg 20181003 [395] phylogenetics
Dynare dynare 4.4.3 [396] math
ea-utils eautils 1.04.807.18, 1.1.2.537 [397] biology, genomics, ngs
EAGLE eagle 2.0 [398] phylogenetics
eagle-rc eagle-rc 1.1.1 [399] phylogenetics
ECE ece 1.2 [400] physics
EDirect edirect 10.7, 12.2 [401] biology, phylogenetics
EDTA edta 1.9.6 [402] phylogenetics
Edyeet edyeet 0.1, 0.3 [403] phylogenetics
EEGLAB eeglab 12.0.2.1b, 13.2.2b, 13.4.4b [404] biology,bioinformatics,matlab
eGene-MVN egene-mvn 0.1 [405] biology, genetics
eggNOG-mapper eggnog-mapper 2.0.1, 2.1.6 [406] phylogenetics
EGSnrc egsnrc 2019 [407] phylogenetics
EIGENSOFT eigensoft 4.2, 5.0.1, 6.0.1 [408] biology
Elastix elastix 4.9.0 [409] phylogenetics
ELPA elpa 2019.11.001 [410] library, compiler, math
elPrep elprep 4.1.4 [411] phylogenetics
Emacs emacs 27.2 [412] programming, scripting, language
EMAN2 eman2 2.22, 2.31 [413] image_processing
EMBOSS emboss 6.6.0 [414] biology,bioinformatics
Embree embree 3.6.1 [415] ray, tracing, kernels
EMC emc 9.4.3 [416] monte Carlo Simulations
EMMAX emmax 20100307, 20120210 [417] biology, ngs, mapping
EnergyPlus energyplus 9.3.0 [418] simulation
Ensembl Tools ensembl_tools 100, 80 [419] biology
enTAP entap 0.6.1.2, 20160416 [420] biology, phylogenetics
EPACTS epacts 3.2.6, 3.4.2, 3.4.2.hg38 [421] biology, genomics
EpiNano epinano 1.2.0 [422] biology, ngs
epiteome epiteome 1.0 [423] phylogenetics
epoch epoch 4.7.3 [424] astronomy,CCPP
eQTLA eqtla 1.1 [425] biology, genomics
eQtlBma eqtlbma 1.2.2, 1.3.0r20140820 [426] biology, genotyping
Erpin erpin 5.5.4 [427] biology, phylogenetics
ESOM esom 1.1 [428] biology, phylogenetics
ESPRESSO espresso 6.2.1, 6.4.1, 7.0 [429] quantum,modeling
ESPRIT esprit 2009-nogap, 201102 [430] biology,bioinformatics
ETE3 ete3 3.0.0, 3.1.1 [431] biology, phylogenetics
EVidenceModeler evidencemodeler 1.1.1 [432] phylogenetics
Evigene evigene 20180730, 20200520 [433] phylogenetics
EvoLSTM evolstm 20220103 [434] biology, Bioinformatics
ExaBayes exabayes 1.5 [435] phylogenetics
Exonerate exonerate 2.2.0 [436] biology, genomics
ExpansionHunter expansionhunter 4.0.2 [437] biology, genomics
ExpansionHunterDenovo expansionhunterdenovo 0.9.0 [438] biology, genomics
export2graphlan export2graphlan 0.22 [439] statistics, mapping, graphing
eXpress express 1.3.1, 1.5.1 [440] biology, ngs
ezaai ezaai 1.0 [441] biology, phylogenetics
face_morpher face_morpher 20190630 [442] phylogenetics
face_recognition face_recognition 1.2.2 [443] phylogenetics
fairseq fairseq 0.12.2 [444] modeling, ai
FALCON falcon 20161027, 20161222, 20190601 [445] biology, ngs, sequencing
FALCON_unzip falcon_unzip 20161222 [446] biology
FAR far 2.15 [447] biology, genomics
FAST fast 1.06 [448] biology phylogenetics
fast-gep fast-gep 1.0 [449] phylogenetics
Fast-Plast fast-plast 1.2.6 [450] biology, phylogenetics
fast5tools fast5tools 0.3.1 [451] phylogenetics, biology
FASTA fasta 34.26.5, 36.3.6d [452] biology, genomics
fastai fastai 2.1.5, 2.6.3 [453] phylogenetics
FastANI fastani 1.1 [454] phylogenetics
fastchaos fastchaos 0.1.0 [455] sequencing
FastGEAR fastgear 20161216 [456] biology, genomics
Fastix fastix 0.1.0 [457] biology, ngs
FastML fastml 3.0 [458] biology,bioinformatics,phylogenetics
Fastp fastp 0.20.0, 0.22.0 [459] biology, ngs
FASTphase fastphase 1.4.8 [460] phylogenetics
FastPlast fastplast 1.2.8 [461] phylogenetics
fastq-pair fastq-pair 1.0 [462] phylogenetics
FastQ-Screen fastq-screen 0.14.0 [463] phylogenetics
Fastq-tools fastq-tools 0.8 [464] biology, ngs,
FastQC fastqc 0.11.4, 0.11.7, 0.9.6 [465] biology, ngs
FastqPuri fastqpuri 1.0.7 [466] phylogenetics
FastQTL fastqtl 2.184 [467] phylogenetics
FASTRAL-constrained fastral-constrained 20211108 [468] phylogenetics
fastsimcoal fastsimcoal2 2.6.0.3, 2.7.0.2 [469] biology, phylogenetics
FastSpar fastspar 0.0.4 [470] biology, genomics
fastStructure faststructure 20150112 [471] biology, genomics
FastTree fasttree 2.1.11 [472] biology,bioinformatics,phylogenetics
FastUniq fastuniq 1.1 [473] biology, phylogenetics
Fastx Toolkit fastx_toolkit 0.0.13.2, 0.0.14 [474] biology,ngs
fcGENE fcgene 1.0.7, 1.0.7.1 [475] biology, genomics,snp
FDSTools fdstools 1.2.0 [476] phylogenetics
fdupes fdupes 1.51 [477] file Management
FEELnc feelnc 0.1.1 [478] phylogenetics
FEniCS fenics 2018.1.0 [479] biology, phylogenetics
Ferret ferret 6.82 [480] data Visualization and Analysis, Oceanography, Meteorology
FFmpeg ffmpeg 2.1.3, 2.8.3, 4.3.1 [481] audio, Video
FFTW fftw 3.3.6, 3.3.7, 3.3.8 [482] library, compiler, math
fgbio fgbio 0.5.0, 0.7.0 [483] phylogenetics
FGMP fgmp 1.0.1 [484] phylogenetics
FIGARO figaro 1.1.2 [485] phylogenetics
Fiji fiji 2.0.0rc59 [486] imageJ
Filtlong filtlong 0.2.0 [487] biology, phylogenetics
Finder finder 20210503, 20210609 [488] biology, finder
finemap finemap 1.4 [489] phylogenetics
fineRADstructure fineradstructure 0.3.2 [490] phylogenetics
finesse finesse 2.3.1 [491] simulation
fit-sne fit-sne 1.2.1 [492] phylogenetics
FLAIR flair 1.5 [493] phylogenetics
flairNLP flairnlp 0.10 [494] data Visualization, language
flappie flappie 1.1.0, 2.1.3 [495] phylogenetics
FLASh flash 1.2.10, 1.2.11 [496] biology, genomics
FLEA flea 2.0.0 [497] phylogenetics
flex flex 2.6.4 [498] programming
Flexbar flexbar 2.3, 2.34, 3.5.0 [499] biology, genomics, ngs
FLEXLm flexlm 1.0 [500] administration
FlowCraft flowcraft 1.4.1 [501] phylogenetics
Fluent fluent 17.2, 19.1, 2020R1 [502] cFD
Flye flye 2.7.1, 2.8.1, 2.9 [503] biology, ngs
fMRIPrep fmriprep 1.4.0a1, 1.5.4, 20.2.3 [504] data_mining
ForeSeqs foreseqs 1.0.4 [505] phylogenetics
fpocket fpocket 4.0.2 [506] sequencing, biology
fqtools fqtools 20160224 [507] biology, ngs, sequencing
FragGeneScan fraggenescan 1.16 [508] biology, genomics
FRAMA frama 20151019 [509] biology
FrameDP framedp 1.2.2 [510] biology, sequencing
FRAPOSA fraposa 20200421 [511] phylogenetics
FreeBayes freebayes 1.1.0-20170823, 1.3.1, 1.3.2 [512] biology, genomics
freesasa freesasa 2.1.2 [513] molecular dynamics, biology
Freesurfer freesurfer 7.1.0, 7.1.1, 7.2.0 [514] biology, neuroscience, imaging
Freyja freyja 1.3.1, 1.3.4, 1.3.8 [515] biology,phylogenetics,sequencing
FSA fsa 1.15.9 [516] phylogenetics
FSL fsl 6.0.3, 6.0.4, 6.0.5 [517] biology, neuroscience, imaging
fslmrs fslmrs 1.1.10 [518] mRS, metabolomics
funannotate funannotate 1.8.7, 1.8.9 [519] phylogenetics
fusion_twas fusion_twas 20210218 [520] phylogenetics
GAL gal 20180906 [521] phylogenetics
Galaxy galaxytools 1.0 [522] biology,bioinformatics
GAML gaml 20150610 [523] biology, genomics
GapCloser gapcloser 1.12r6 [524] biology, genomics, ngs
GapFiller gapfiller 1.10, 1.11 [525] biology, genomics
GARLI garli 2.0, 2.01 [526] biology,bioinformatics,phylogeny
GASVPro gasvpro 201310 [527] biology, ngs
GATE gate 7.0 [528] library
GATK gatk 4.1.4.0, 4.1.8.1, 4.1.9.0 [529] biology, ngs
Gaussian gaussian 09 D.01, 16, 16-c02 [530] computational Chemistry
Gawk gawk 4.2.0 [531] utility
Gblocks gblocks 0.91b [532] biology,bioinformatics
GCC gcc 7.3.0, 8.2.0, 9.3.0 [533] compilers
GCE gce 1.0.2, 4.0 [534] biology, genomics
GCT gct 6.2.1 [535] gridftp, globus, toolkit
GCTA gcta 1.26.0, 1.92.4beta, 1.93.2beta [536] biology, genomics, variant_calling,
GDAL gdal 2.2.1, 2.2.4, 2.3.1 [537] geospatial, Library
GDB gdb 8.3, 9.2 [538] programming
GDC-Client gdc-client 1.0.1, 1.5.0 [539] biology, sequencing, ngs
GDrive gdrive 2.1.0 [540] applications, Utilities, Data Transfer
GDSL gdsl 1.18 [541] library
Geant4 geant4 4.10, 4.10.03, 4.10.5 [542] physics
GEM gem 20130406 [543] biology, ngs, sequencing
gem5 gem5 2.0 [544] computer Simulator
GEMMA gemma 0.98.1 [545] phylogenetics
GeneMark-ES genemark_es 4.65, 4.68, 4.69 [546] biology, genomics
GeneMarkS genemark_s 2012.04 [547] biology, genomics
GeneMarkS-T genemark_s 3.10.001 [548] biology, genomics
GenePainter genepainter 2.0.4 [549] biology, phylogenetics
GeneRax generax 1.2.2 [550] phylogenetics
Generic Mapping Tools gmt 6.4.0 [551] physics, biology
GeneSeqer geneseqer 2014-02-26 [552] biology, genomics
genesum genesum 0.1.0 [553] biology, genomics
GeneTorrent genetorrent 3.8.7 [554] biology,bioinformatics,data download
GenGen gengen 1.0.1 [555] biology, phylogenetics
Genome STRiP genomestrip 2.00.1602 [556] biology, genomics, ngs
Genome_Graph_Annotation genome_graph_annotation 20190131 [557] phylogenetics
GenomeScope2 genomescope2 2.0 [558] phylogenetics
GenomeThreader genomethreader 1.7.3 [559] phylogenetics
GenomeTools genometools 1.5.7, 1.5.9 [560] biology
genomic-fluidity genomic-fluidity 20151109 [561] phylogenetics
GenomicConsensus genomicconsensus 2.3.3 [562] biology, phylogenetics
GenomicNeuralnet genomic-neuralnet 20161030 [563] phylogenetics
GenomicTools genomictools 2.7.0 [564] biology, ngs,chip-seq,rna-seq
GenotypeHarmonizer genotypeharmonizer 1.4.18 [565] biology
Genrich genrich 0.5 [566] phylogenetics
GenSel gensel 4.90 [567] population Genetics
geopython geopython 1.0.0, 1.0.1 [568] python, geospatial, cartography
GEOS geos 3.3.8, 3.6.2 [569] library, data_science
GeP gep 2.1 [570] biology, phylogenetics
gepard gepard 1.40.0 [571] phylogenetics
Gerbil gerbil 1.11 [572] phylogenetics
get_homologues get_homologues 3.3.3 [573] biology, genome
GetOrganelle getorganelle 1.7.3.5, 1.7.5.0 [574] phylogenetics
GFam gfam 1.1 [575] biology, genomics, annotation
GFF-Ex gff-ex 2.3 [576] phylogenetics
GFF3toolkit gff3toolkit 2.0.3 [577] phylogenetics
gffcompare gffcompare 0.12.2 [578] phylogenetics
gffread gffread 0.11.8, 0.12.7, 0.9.8c [579] biology
Gflags gflags 2.2.1, 20150520 [580] google,libraries
GFOLD gfold 1.1.4 [581] biology, RNA-seq
ggsashimi ggsashimi 0.5.0 [582] phylogenetics
GHOST-MP ghost-mp 1.3.4 [583] phylogenetics
Ghostscript ghostscript 9.22 [584] pDF
Giotto giotto 0.1.0 [585] phylogenetics
Git git 2.14.1, 2.30.1 [586] revision Control
git-filter-repo git-filter-repo 2.33.0 [587] phylogenetics
glactools glactools 1.0.8 [588] phylogenetics
Glimmer glimmer 3.02 [589] biology, microbial annotation
GlimmerHMM glimmerhmm 3.0.4 [590] biology, microbial annotation
GLMsingle glmsingle 1.0 [591] fMRI
Globus globus 1.10.1, 2.1.3 [592] data Transfer
glog glog 0.3.5 [593] google,libraries
GLPK glpk 4.55, 4.65 [594] programming
Glueviz glueviz 0.15.2 [595] phylogenetics
GMAP gmap 20180212, 20180212_sse2, 20190610 [596] biology, genomics, ngs
GMcloser gmcloser 1.6 [597] biology, ngs
GMP gmp 6.1.2 [598] library, crypto
GnuPlot gnuplot 5.2.2, 5.2.3, 5.4.1 [599] graphics,plotting,math
Go go 1.13.6, 1.15.4, 1.18.3 [600] language
GOMAP gomap 1.3 [601] biology, ngs
GoPHY gophy 201030 [602] phylogenetics
gotcloud gotcloud 1.17.5 [603] phylogenetics
GPA gpa 1.1 [604] phylogenetics
GPhoCS gphocs 1.2.3 [605] phylogenetics
Gpufit gpufit 20201127 [606] phylogenetics
Grace grace 5.1.22 [607] graphics, statistics, 2D
GRACKLE grackle 3.1 [608] library,c,astrophysics
GrADS grads 2.0.1 [609] environment, grid analysis
Graftm graftm 0.12.2 [610] phylogenetics
GramCluster gramcluster 1.3 [611] biology,sequencing,
graph-tool graph-tool 2.32 [612] phylogenetics
Graph_annotation graph_annotation 0.1 [613] phylogenetics
GraPhlAn graphlan 1.1.3 [614] phylogenetics
GraphMap2 graphmap2 0.6.5 [615] phylogenetics
GraphSplitting graphsplitting 2.4 [616] phylogenetics
graphtyper graphtyper 2.7.2 [617] phylogenetics
GraphViz graphviz 2.38.0, 2.46.1 [618] biology, neuroscience, imaging
GRASS grass 7.0, 7.4 [619] geography
grf grf 1.0.0 [620] genomics
Grib_api grib_api 1.10.1, 1.15.1, 1.26.1 [621] c, fortran, library
GRIDSS gridss 2.6.2 [622] phylogenetics
GROCSVs grocsvs 0.2.5 [623] phylogenetics
GROMACS gromacs 2021.2, 2021.3, 2021.4 [624] chemistry, molecular_dynamics
GroopM groopm 0.3.5 [625] biology, phylogenetics
Groovy groovy 2.4.15 [626] programming
Gscripts gscripts 1.1 [627] biology
GSEA gsea 3.0.0, 4.2.2 [628] biology, genomics
GSL gsl 2.4, 2.5, 2.6 [629] library, data_science
GSNP gsnp 1.0 [630] biology, ngs
GTAHunter gtahunter 20200106 [631] phylogenetics
GTDBTk gtdbtk 1.7.0, 2.0.0, 2.1.0 [632] phylogenetics
GTOOL gtool 0.7.5 [633] phylogenetics
GUAVA guava 1.0 [634] phylogenetics
Gubbins gubbins 2.4.1, 3.2.1 [635] phylogenetics
guideseq guideseq 1.0.2 [636] sequencing, genomics, bioinformatics, data
guile guile 2.2.2 [637] programming Language
GULP gulp 4.4, 5.0 [638] material_science
guppy guppy 4.4.1, 4.5.4, 6.1.7 [639] phylogenetics
Gurobi gurobi 9.5.1 [640] math, python
GWAMA gwama 2.2.2 [641] phylogenetics
Gzip gzip 1.10 [642] compression
Hail hail 0.2.77 [643] biology, genomics
hal hal 2.1 [644] phylogenetics
HALC halc 1.1 [645] biology, phylogenetics
halla halla 0.8.17 [646] phylogenetics
HaMStR hamstr 13.2.3, 13.2.4, v8b [647] biology, genome
hapbin hapbin 1.3.0 [648] biology, Genetics
HapCompass hapcompass 0.7.7 [649] imaging, ngs, genomics
HAPCUT hapcut 0.7 [650] biology, assembly
HapCUT2 hapcut2 1.3.3 [651] biology, genomics, sequencing
hapdup hapdup 0.6 [652] phylogenetics, biology
Haploflow haploflow 0.1 [653] biology, phylogenetics
Haplomerger2 haplomerger2 20180603 [654] biology, genomics
HAPLOSWEEP haplosweep 1.0 [655] biology, phylogenetics
happy happy 0.3.14 [656] phylogenetics, biology
hapQTL hapqtl 1.00 [657] biology
hapsembler hapsembler 2.21 [658] biology, assembly
HASLR haslr 0.8a1 [659] phylogenetics
hclust2 hclust2 1.0.0 [660] statistics, mapping
HDF4 hdf4 4.2.11 [661] library, data_science
HDF5 hdf5 1.8.19, 1.8.20, 1.8.9 [662] library, data_science
hecaton hecaton 0.5.1 [663] genomics, Biology
HELEN helen 20200516 [664] phylogenetics
HelitronScanner helitronscanner 1.1 [665] phylogenetics
hgraph2graph hgraph2graph 20210428 [666] chemistry
HiC-Pro hic-pro 3.0.0 [667] biology, Pipeline, Genomics
Hifiasm hifiasm 0.16.1, 0.4, 0.8 [668] phylogenetics
HipSTR hipstr 0.7 [669] phylogenetics
HISAT2 hisat2 2.2.0, 2.2.1, 2.2.1-3n [670] biology, Sequence Alignment, NGS
HLAminer hlaminer 1.3.1, 1.4 [671] biology, phylogenetics
HMM-FRAME hmm-frame 20140724 [672] phylogenetics
HmmCleaner hmmcleaner 0.180750 [673] phylogenetics
HMMER hmmer 3.1b1, 3.1b2, 3.2.1 [674] biology, genome
hmmer2go hmmer2go 0.18.1 [675] phylogenetics, biology
HMMRATAC hmmratac 1.2.10 [676] phylogenetics
HOMER homer 4.10, 4.11, 4.8 [677] biology, sequencing, ngs
homopolish homopolish 0.3.3 [678] genomics, Biology
HOOMD hoomd 2.1.7 [679] library, math
HPL hpl 2.1 [680] parallel Programming, benchmarks, MPI
HTMLDoc htmldoc 1.8.28, 1.9.3 [681] pdf, docs, html
HTSeq htseq 0.11.2 [682] biology, ngs
HUMAnN humann 2.8.1 [683] sequencing, microbial ecology
humann2 humann2 0.11.2, 2.8.1 [684] phylogenetics
hyb hyb 20141126, 20200815 [685] biology, ngs, RNA-Seq
HybPiper hybpiper 1.2, 1.3.1, 2.0.1 [686] biology, phylogenetics
HyDe hyde 0.4.3 [687] phylogenetics
HyPhy hyphy 2.5.4, 2.5.7, 2.5.8 [688] biology,bioinformatics,evolution
HYPRE hypre 2.15.1, 2.18.2, 2.19.0 [689] math, Numerical Solvers
iAnnotateSV iannotatesv 1.0.6, 1.0.9 [690] biology, phylogenetics
iAssembler iassembler 1.3.2 [691] biology, assembly
ibdne ibdne 20150815 [692] biology,ngs
icommands icommands 3.3.1 [693] iRods
IDBA-MT idba-mt 1.0 [694] biology,NGS
IDBA-UD idba-ud 1.1.1, 1.1.1-512, 1.1.1-512-mem [695] genomics, phylogenetics
IDL idl 8.3 [696] language, programming, science
IDR idr 2.0.3 [697] phylogenetics
IGB igb 8.4.1 [698] biology, genomics
igBLAST igblast 1.5.0, 1.7.0 [699] biology
IGoR igor 1.4.0 [700] phylogenetics
iGTP igtp 1.1 [701] biology, phylogenetics
IGV igv 2.3.91, 2.4.16, 2.8.6 [702] biology, ngs, phylogenetics
illumina-utils illumina-utils 2.11 [703] phylogenetics
Illumiprocessor illumiprocessor 2.0.9 [704] phylogenetics
IM and IMa ima 20091217 [705] biology,bioinformatics,population genetics
Ima2 ima2 20120827 [706] biology,bioinformatics,population genetics
IMa2p ima2p 20170712 [707] biology, phylogenetics
IMA3 ima3 22Aug18 [708] molecular_dynamics
ImageJ imagej 1.48 [709] imaging
ImageMagick imagemagick 7.0.8-20 [710] imaging
Imaginaire imaginaire 20201229 [711] imaging, Video, AI, synthesis
IMOD imod 4.7.15, 4.9.10 [712] image_processing
imoka imoka 1.0 [713] biology, genomics
IMPUTE2 impute2 2.3.2 [714] phylogenetics
IMPUTE5 impute5 1.1.5 [715] biology, Imputation
INDELible indelible 1.03 [716] phylogenetics
Infernal infernal 1.1.1, 1.1.4 [717] biology, sequence alignment
INLA inla 20160718, 20170620 [718] statistics, modeling, R
InParanoid inparanoid 4.1 [719] biology
Inspector inspector 1.0.2 [720] biology, genomics
InStruct instruct 20160723 [721] phylogenetics
Intel Compilers and Libraries intel 2018.1.163, 2019.1.144, 2020.0.166 [722] language, development, library, math, intel
Intel MPI impi 5.1.1 [723] parallel Programming, development, MPI, library
InterProScan iprscan 5.54-87.0, 5.56-89.0, 5.57 [724] biology,bioinformatics
intervene intervene 0.6.2 [725] biology, phylogenetics
IOAPI ioapi 3.1, 3.2 [726] climate
IPOPT ipopt 3.12.10, 3.12.6 [727] library,c/c++,math
ipyrad ipyrad 0.7.24, 0.7.30, 0.9.53 [728] phylogenetics
IQ-TREE iq-tree 2.1.0, 2.1.2, 2.1.3 [729] biology, phylogenetics,
IRAP irap 0.8.1p7 [730] biology, ngs, pacbio
irep irep 1.10 [731] biology, genomics
IRFinder irfinder 1.2.0, 1.3.0, 1.3.1 [732] biology, rna-seq
isONclust isonclust 0.0.6 [733] phylogenetics
IsoSel isosel 1.0 [734] phylogenetics
IsoSeq3 isoseq3 3.2.2, 3.4.0, 3.7.0 [735] biology, ngs, pacbio
ISOWN isown 20180820 [736] phylogenetics
isPcr ispcr 3.3 [737] biology, phylogenetics
ITK itk 3.20.1, 4.10.1 [738] biology
ITK-SNAP itksnap 3.0.0, 3.8.0 [739] biology, neuroscience, imaging
ITSx itsx 1.1b [740] phylogenetics
IVA iva 1.0.11 [741] phylogenetics
iVar ivar 1.3.1 [742] biology
Jabba jabba 1.0 [743] biology, phylogenetics
JACUSA jacusa 1.2.0 [744] biology, ngs, phylogenetics
JAGS jags 3.3.0, 3.4.0, 4.2.0 [745] statistics
Jasmine jasmine 1.1.4 [746] phylogenetics
jasp jasp 0.14.3 [747] statistics
jbrowse2 jbrowse2 1.7.4 [748] web Browser
JCVI jcvi 0.8.12, 1.0.13, 1.2.10 [749] phylogenetics
JDK java 11.0.1, 14, 9.0.1 [750] programming,runtime
Je je 1.0 [751] biology, ngs
Jellyfish jellyfish 2.2.4, 2.2.6, 2.3.0 [752] biology,ngs
jModelTest jmodeltest 2.1.1 [753] biology, genomics, phylogenetics
jo jo 1.3 [754] software
jq jq 1.6 [755] software
juicer juicer 1.22.01 [756] phylogenetics
Julia julia 1.6.2, 1.7.1, 1.7.3 [757] programming, language, statistics
Jupyter jupyter 5.7.8, 6.0.3, 6.2.0 [758] python, R, jupyter
jutils jutils 1.0 [759] genomics, biology
JVARKIT jvarkit 20180405 [760] biology, phylogenetics
Kaiju kaiju 1.6.2, 1.7.2 [761] biology, phylogenetics
KaKs kaks 1.2, 2.0 [762] biology, evolution, phylogenetics
Kalign kalign 3.3.1 [763] biology, Bioinformatics, Sequencing, Alignment
kallisto kallisto 0.43.0, 0.44.0, 0.48.0 [764] biology,NGS,RNA-Seq
khmer khmer 2.0, 2.1 [765] biology, ngs
KIM kim 1.7.2, 1.8.2, 1.9.3 [766] simulation
KING king 2.1.2 [767] biology, genome, gwas
KisSplice kissplice 2.4.0-p1 [768] biology, RNA
KLayout klayout 0.26.7 [769] phylogenetics
KMC kmc 3.1.0, 3.1.1, 3.2.1 [770] phylogenetics
kmerdb kmerdb 1.9.2 [771] genomics, biology
KMOS kmos 0.3.21 [772] phylogenetics
kneaddata kneaddata 0.7.4, 0.9.0 [773] phylogenetics
Knitro knitro 12.2.0 [774] mathematical Optimization Problems
KofamScan kofamscan 1.3.0 [775] phylogenetics
kover kover 2.0.3 [776] phylogenetics
Kraken kraken 2.0.6b, 2.0.8b, 2.1.2 [777] biology, ngs
KrakenUniq krakenuniq 0.5.8, 0.7.3 [778] phylogenetics
Krona krona 20161019 [779] biology
ksnp ksnp 3.021 [780] biology, phylogenetics, SNP
Ksrates ksrates 1.1.1 [781] genomics, biology
LACHESIS lachesis 2.1 [782] phylogenetics
Lambda lambda 0.9.4, 1.0.3, 2.0.0 [783] biology, sequencing, phylogenetics
LAMMPS lammps 30Jul16, 7Aug19, 7Dec15 [784] molecular_dynamics
LAMP lamp 2.5 [785] biology, genomics
laneta laneta 20220517, 20220808, 20220812 [786] biology
langdetect langdetect 1.0.9 [787] nLP, utility
LAPACK lapack 3.8.0 [788] programming,library,fortran
Last last 916, 979 [789] biology,bioinformatics,sequence,alignment
LAStools lastools 20200114 [790] liDAR
LASTZ lastz 1.02.00, 1.03.02, 1.04.00 [791] biology, ngs
Lazypipe lazypipe 1.2 [792] genomics,taxonomy,binning
LazyPredict lazypredict 0.2.8 [793] phylogenetics
lbzip lbzip 2.5 [794] compression
LCModel lcmodel 6.3 [795] biology, NMR
ldak ldak 5.2 [796] phylogenetics, biology
LDhat ldhat 2.2a [797] biology, genomics
ldsc ldsc 1.0.1 [798] genomics, biology
leafaudio leafaudio 0.1.0 [799] tensorflow, audio, leafaudio
LEfSe lefse 20180219 [800] phylogenetics
LEMON liblemon 1.2.3 [801] library
LFMM lfmm 1.4, 1.5 [802] biology, phylogenetics
Libint libint 2.5.0, 2.5.0b [803] library
libMesh libmesh 1.5.0 [804] math, Numerical Solvers
libunistring libunistring 0.9.7 [805] library
libvips libvips 8.5.4 [806] image_processing
LIBXC libxc 4.2.3, 4.3.4 [807] library, density function
LIBXSMM libxsmm 1.13 [808] library, compiler, math
LIBZMQ libzmq 4.3.1 [809] library
Liftoff liftoff 1.4.2 [810] phylogenetics
LIGR ligr 2.05 [811] biology,assembly
lima lima 2.0.0, 2.2.0 [812] phylogenetics
lingua lingua 1.0.1 [813] nLP, utility
LINKS links 1.8.5, 1.8.6 [814] biology, genomics
Linksbrowser linksbrowser 2.14 [815] web browser
LIQA liqa 1.0.0 [816] phylogenetics
LMAP lmap 1.0.2 [817] biology, phylogenetics
lncScore lncscore 1.0.2 [818] biology, phylogenetics
lobSTR lobstr 4.0.6 [819] biology, phylogenetics
localbrainage localbrainage 20210415 [820] biology, ml
localizer localizer 1.0.4 [821] phylogenetics
LocusZoom locuszoom 1.4 [822] phylogenetics
LoFreq lofreq 2.1.3.1 [823] phylogenetics
LongQC longqc 1.2.0c [824] phylogenetics
LongRanger longranger 2.1.5, 2.2.2 [825] biology, phylogenetics
LongStitch longstitch 1.0.3 [826] genomics, biology
LoRDEC lordec 0.9 [827] phylogenetics
LoRMA lorma 0.3, 0.5 [828] biology, ngs, pacbio
LRBinner lrbinner 0.1 [829] biology, Bioinformatics, Metagenomics, Binning
lrgapcloser lrgapcloser 09042018 [830] biology
LS-DYNA ls-dyna 700, 711, 901 [831] physics
LSD2 lsd2 1.6.5 [832] phylogenetics
ltr_finder ltr_finder 1.07 [833] biology, phylogenetics
LTRRetriever ltrretriever 2.1, 2.5, 20170514 [834] biology, phylogenetics
Lua lua 3.5.2 [835] programming, scripting, language
Lucene pylucene 7.7.1, 9.1.0 [836] java,search,indexing
lumpy-sv lumpy 0.2.1, 0.2.13, 0.3.1 [837] biology, genotyping
LZO lzo 2.09 [838] library, compression
M5nr m5tools 20121126 [839] biology, genomics
Macaulay2 macaulay2 1.15 [840] phylogenetics
MACH mach 1.0.18 [841] biology, genomics, ngs
Mach2VCF mach2vcf 20150515 [842] biology
MACS macs 2.0.10, 2.1.2, 2.2.7.1 [843] biology, CHiP-Seq
MafFilter maffilter 1.3.0 [844] phylogenetics
MAFFT mafft 7.294, 7.397, 7.490 [845] bio,bioinformatics,sequence
MAGeCK mageck 0.5.9.4 [846] phylogenetics
MAGeCK-VISPR mageck-vispr 0.5.6 [847] phylogenetics
MAGeCKFlute mageckflute 1.14.0 [848] phylogenetics
Magenta magenta 2.1.2 [849] phylogenetics
MAGMA-GWAS magma-gwas 1.09 [850] phylogenetics
magus magus 20220121 [851] sequencing, alignment
MAJIQ majiq 2.2, 2.3 [852] phylogenetics
Maker maker 2.31.10, 2.31.6, 3.01.03 [853] biology,bioinformatics
MAnorm manorm 20120316 [854] biology, phylogenetics
MANTA manta 1.6.0 [855] phylogenetics
mantis mantis 1.0.4 [856] phylogenetics
mapclassify mapclassify 2.4.2 [857] statistics, mapping, geography
MapThin mapthin 1.11 [858] phylogenetics
Maq maq 0.7.1 [859] biology, ngs
MarginPolish marginpolish 1.0.0 [860] phylogenetics
MARK mark 2.0.1 [861] application, data, capture
MarkerMiner markerminer 20150710 [862] biology, genomics
Mash mash 1.1, 2.3 [863] biology, genomics
MasHmap mashmap 2.0 [864] phylogenetics
mashtree mashtree 1.2.0 [865] genomics, biology
MASS mass 1.1.1 [866] genomics, Biology
MASSMINE massmine 0.10.0, 0.11.0, 0.9.5 [867] data_mining
MaSuRCA masurca 4.0.8, 4.0.9, 4.1.0 [868] biology,bioinformatics,short read alignment
Mathematica mathematica 12.1.1.0 [869] math
MATLAB matlab 2020a, 2020b, 2022a [870] math,language
MATS mats 4.0.1, 4.0.2, 4.1.0 [871] biology, ngs,rna-seq
Mauve mauve 2.3.1 [872] biology,ngs,genomics
mawk mawk 1.3.4-20150503 [873] language
maxbin maxbin 2.1.1 [874] biology,NGS
Maxima maxima 5.41.0 [875] math
MC mc 4.6.1 [876] shell
mCarts mcarts 1.0.2 [877] biology, genomics, markov
mccortex mccortex 1.0 [878] phylogenetics
MCL mcl 12-135, 14-137 [879] biology, genomics
MCNP mcnp 6, 6.1 [880] physics
MCNPX mcnpx 2.7.0 [881] physics
MCR mcr 2019b, 2020a, 2020b [882] math, language
MCScanX mcscanx 20130328 [883] biology, phylogenetics
mdanalysis mdanalysis 1.1.1 [www.mdanalysis.org] physics, Bioinformatics
MECAT mecat 20180308 [884] phylogenetics
Medaka medaka 1.0.1, 1.2.1, 1.6.0 [885] biology, phylogenetics
Medusa medusa 1.6 [886] phylogenetics
MEGA mega 7.0.26 [887] biology, phylogenetics
Mega2 mega2 4.9.2, 6.0.0 [888] biology, phylogenetics
MEGAHIT megahit 1.1.1, 1.1.4 [889] biology, phylogenetics
Megalodon megalodon 2.0.0 [890] phylogenetics
MEGAN megan 5.10.3, 6.23.4, 6.4.15 [891] biology, ngs
MEGASAT megasat 1.0 [892] phylogenetics
Megraft megraft 1.0.2 [893] biology,sequencing,
MELD meld 0.4.14, 0.4.19, 0.5.9 [894] chemistry, molecular_dynamics
MELTING melting 4.3.1 [895] biology, genome, RNA, folding
MEME meme 5.0.2, 5.0.5, 5.4.1 [896] biology,bioinformatics,sequence
MentaLiST mentalist 0.1.3 [897] biology, phylogenetics
Meraculous meraculous 2.0.5 [898] biology,NGS
Mercurial mercurial 4.8.2 [899] revision Control
merge_peaks merge_peaks 0.1.0 [900] workflow_automation
Merlin merlin 1.1.2 [901] biology, variant_calling
Merqury merqury 1.1, 1.3 [902] phylogenetics
Meryl meryl 1.0 [903] phylogenetics
MeShClust meshclust 1.2.0 [904] biology
Meshroom meshroom 2019.2.0 [905] phylogenetics
MET met 10.0 [906] climate, Models, Verification
Meta-Marc meta-marc 1.0.0 [907] phylogenetics
Meta-Tissue meta-tissue 0.4 [908] biology, genetics
MetaBAT metabat 0.32.4, 2.13 [909] biology, genomics
MetaBCC-LR metabcc_lr 2.0.0 [910] biology, Metagenomics, Binning
Metabin metabin 1.0 [911] genomics, metagenomics
metabolic metabolic 4.0 [912] phylogenetics
MetaCherchant metacherchant 0.1.0 [913] biology, phylogenetics
MetaCluster metacluster 5.0b [914] biology, genomics
MetaCompare metacompare 20181016 [915] phylogenetics
metacrast metacrast 20200309 [916] phylogenetics
MetaGeneMark metagenemark 2.10, 3.26 [917] biology, genomics
METAL metal 20110325 [918] biology, ngs, genomics
MetaLAFFA metalaffa 1.0.0 [919] phylogenetics
MetaMaps metamaps 20201207 [920] phylogenetics
METANNOT metannot 20171129 [921] phylogenetics
Metaphlan metaphlan 3.0.3, 3.1.0, 4.0.1 [922] phylogenetics
MetaPhlAn2 metaphlan2 2.7.7 [923] biology, phylogenetics
MetaPhysicl metaphysicl 1.0.0 [924] math, Astronomy, Numerical Simulation
MetaSV metasv 0.5.4 [925] biology, phylogenetics, NGS
MetaVelvet metavelvet 1.2.06 [926] biology, genomics
metaWRAP metawrap 1.2 [927] phylogenetics
Metaxa2 metaxa2 2.1.1, 2.1.3 [928] biology, ngs, sequencing
MethylDackel methyldackel 0.5.0, 0.6.1 [929] phylogenetics
methylpy methylpy 1.2.9 [930] biology, phylogenetics
Metilene metilene 0.2.8 [931] biology, genomics, methylation
METIS metis 5.1.0 [932] software
Mfannot mfannot 20180405 [933] biology, phylogenetics
mfold mfold 3.6 [934] biology,structure,RNA
mg-rast mg-rast 20150919 [935] biology, genomics
MGEfinder mgefinder 1.0.5 [936] phylogenetics
MGERT mgert 1.0.1 [937] phylogenetics
MGEScan mgescan 20160416 [938] biology, genomics
MGLTools mgltools 1.5.7 [939] biology, Molecular Biology, Visualization
MHAP mhap 1.6 [940] biology, sequencing
MHCflurry mhcflurry 1.4.3 [941] phylogenetics
MIA mia 20130201 [942] biology, ngs
MicrobeAnnotator microbeannotator 2.0.5 [943] microbial annotation, biology
MIDAS midas 1.3.2, 20160830 [944] biology, phylogenetics
MIGRATE-N migraten 4.2.14, 4.4.4, 5.0.4 [945] biology,bioinformatics,population genetics
Mikado mikado 2.3.3 [946] biology, Genetics, Transcripts, Pipeline
MIKE mike 1.0 [947] environment,water,modeling
Minced minced 0.2.0 [948] biology, genomics
Minia minia 3.2.6 [949] genomics, biology
Miniasm miniasm 0.2-r168, 0.3-r179 [950] biology, phylogenetics
MiniCaller minicaller 20161201 [951] biology, ngs, phylogenetics
minigraph minigraph 0.15 [952] phylogenetics
minimac minimac 1-20130717, 3-20150727 [953] biology, genomics
minimac2 minimac 2-20140915 [954] biology, ngs,
minimap minimap 2.1t, 2.21, 2.9-r720 [955] biology, phylogenetics
minimap2 minimap2 2.24 [956] genomics, biology
Minipolish minipolish 0.1.3 [957] biology, genomics
MinkowskiEngine minkowskiengine 0.5.3 [958] machine_learning, Deep Learning
MinPath minpath 1.4 [959] biology, phylogenetics
MIRA mira 4.0.rc1, 4.9.6, 5rc2 [960] biology, genomics, assembly
miRanda miranda 1.9 [961] phylogenetics
miRBShunter mirbshunter 0.2 [962] phylogenetics
mirdeep mirdeep 0.1.0, 0.1.1, 2.0.1.3 [963] phylogenetics
miRDP2 mirdp2 1.1.4 [964] biology, genomics
Mireap mireap 0.20 [965] biology
miRge mirge 2.0 [966] phylogenetics
Misa misa 1.0 [967] biology, genomics
MISO miso 0.5.3 [968] biology, ngs, sequencing, rna-seq
MITE-Hunter mite-hunter 20111101 [969] biology, phylogenetics
MITObim mitobim 1.9.1 [970] phylogenetics
MitoFinder mitofinder 1.0.2, 1.1, 1.4 [971] phylogenetics
mitohifi mitohifi 2.2 [972] genomics, sequencing
MitoPhAST mitophast 3.0 [973] phylogenetics
Mitsuba2 mitsuba2 2.2.1 [974] rendering
MiXCR mixcr 2.1.8, 3.0.13 [975] biology, phylogenetics
MixMHC2pred mixmhc2pred 1.2 [976] phylogenetics
MixMHCpred mixmhcpred 2.0.2 [977] phylogenetics
mixmogam mixmogam 20190322 [978] phylogenetics
MKL mkl 2018.1.163, 2019.1.144, 2020.0.166 [979] programming, library, math, intel
mlcoalsim mlcoalsim 1.9916b [980] biology, phylogenetics
mlpack mlpack 3.4.2 [981] library
mlst mlst 2.15.2 [982] phylogenetics
mlstcheck mlst-check 2.1 [983] phylogenetics
MMSEQ mmseq 1.0.8 [984] biology, genomics
MMseqs2 mmseqs2 11, 12 [985] phylogenetics
MMvec mmvec 1.0.5, 1.0.6 [986] metabolomics
MNEtools mnetools 0.22.0 [987] phylogenetics
MOABS moabs 1.2.9, 1.3.2, 1.3.4 [988] biology, ngs
mobsuite mobsuite 3.1.0 [989] sequencing, biology
MOCCASIN moccasin 0.25 [990] phylogenetics
MODELLER modeller 9.14, 9.23 [991] biology,bioinformatics,modelling,structure
MODELTEST modeltest 0.1.2, 0.1.7 [992] biology, phylogenetics
Modulus modulus 21.06, 22.03 [993] physics, AI, Neural Network
Molden molden 5.0 [994] molecular, Electronic Structure
momi momi 2.1.19 [995] phylogenetics, biology
monai monai 0.8, 0.8.1, 0.9.0 [996] data Science in Healthcare
MONAI label ngc-monailabel 0.3.2 [997] data Science in Healthcare
MongoDB mongodb 4.0.3 [998] database
Moni moni 0.2.0 [999] genomics, biology
mono mono 5.18 [1,000] linux, runtime
Monolix monolix 4.3.2 [1,001] modeling, pharmacokinetics
MOOSE moose 20200722, 20210726, 20220610 [1,002] physics, simulation
Mosaic mosaic 1.7.4 [1,003] phylogenetics
MOSAIK mosaik 2.1.33, 2.2.3, 2.2.30 [1,004] biology,bioinformatics,short read alignment
Mosdepth mosdepth 0.2.3, 0.3.1 [1,005] biology, phylogenetics
Mothur mothur 1.38.1, 1.41.3, 1.46.1 [1,006] biology, microbial ecology
MotionCor2 motioncor2 1.2.3, 1.3.1 [1,007] motion Correction
mOTU motu 1.1 [1,008] biology, genomics
mOTUs motus 2.5.1 [1,009] phylogenetics
MountainSort mountainsort 0.9.0 [1,010] library
MP-EST mpest 1.4 [1,011] biology, ngs, sequencing
MPACK mpack 0.8.0 [1,012] library
MPB mpb 1.5 [1,013] library, math
MPBoot mpboot 1.1.0 [1,014] biology, phylogenetics
MPFR mpfr 3.1.6 [1,015] library, math
mpinterfaces mpinterfaces 20170613 [1,016] dFT
MrBayes mrbayes 3.2.4, 3.2.5, 3.2.6 [1,017] application, biology, phylogenetics
MRIcroGL mricrogl 20201102, 20210327, 20211006 [1,018] biology, imaging
MRIcron mricron 201306, 20161012, 20190911 [1,019] biology, imaging
mriqc mriqc 0.11.0, 0.16.1, 22.0.1 [1,020] imaging, biology
MRtrix mrtrix 3.0.1, 3.0.3, 3.0rc2 [1,021] biology, imaging
ms ms 20171108 [1,022] phylogenetics
ms-dial ms-dial 4.4.8 [1,023] biology, metabolomics
msfinder msfinder 3.52 [1,024] biology, Metabolomics
mSINGS msings 20180810 [1,025] phylogenetics
MSMC-Tools msmc-tools 20190614 [1,026] phylogenetics
msprime msprime 0.7.4 [1,027] phylogenetics
MstatX mstatx 1.0 [1,028] biology, phylogenetics
MSTmap mstmap 1.0 [1,029] phylogenetics
msvar msvar 1.3 [1,030] biology,bioinformatics,population genetics
MTG2 mtg2 2.15 [1,031] phylogenetics
mTR mtr 20210526 [1,032] biology, genomics
Mugsy mugsy 1.2.3 [1,033] biology, phylogenetics
MultiQC multiqc 1.12, 1.7 [1,034] biology, CHiP-Seq
MUMmer mummer 3.23, 4.0.0beta2 [1,035] biology, genomics
MUSCLE muscle 3.8.31 [1,036] biology, alignment
MuSE muse 1.0rc [1,037] phylogenetics
Musket musket 1.1 [1,038] biology, genomics, ngs
MuTect mutect 1.1.4, 1.1.7 [1,039] biology, genomics
MutSig mutsig 1.4, 1.41 [1,040] biology, genomics
mvftools mvftools 20191124 [1,041] phylogenetics
mxnet ngc-mxnet 22.08 [1,042] data Science in Healthcare
MZMine mzmine 2.41, 2.52, 2.53 [1,043] biology, spectrometry, NMR
NAMD namd 2.14, 2.14b2, 3.0 Alpha [1,044] molecular_dynamics
NANO nano 2.8.2 [1,045] text Editor
nanocomp nanocomp 1.17.0 [1,046] programming, python, sequencing
NanoCount nanocount 0.2.1 [1,047] phylogenetics
Nanodisco nanodisco 1.0.3 [1,048] phylogenetics
Nanofilt nanofilt 2.7.1 [1,049] phylogenetics
nanolyse nanolyse 1.2.0 [1,050] genomics, biology
NanoPlot nanoplot 1.30.1 [1,051] phylogenetics
Nanopolish nanopolish 0.11.1, 0.13.2, 20171006 [1,052] biology
nanostripper nanostripper 0.1 [1,053] phylogenetics, biology
NanoSV nanosv 1.2.0, 1.2.3, 1.2.4 [1,054] biology, genomics
NanoVar nanovar 1.3.9 [1,055] phylogenetics
Napari napari 0.3.8, 0.4.7 [1,056] phylogenetics
NBODY nbody 6 [1,057] astronomy
NCBI BLAST+ ncbi_blast 2.7.1, 2.8.1, 2.9.0 [1,058] biology
NCBI C++ Toolkit ncbi_toolkit 12.0.0, 21.0.0, 7.0.0 [1,059] biology,bioinformatics,NCBI,programming,library,cpp
NCBI GenBank Tools genbank_tools 20140130 [1,060] biology,bioinformatics,NCBI,GenBank
ncbi-vdb ncbi-vdb 2.6.3, 2.8.2 [1,061] sRA toolkit library
nccl nccl 20.11 [1,062] development, library, communication, nvidia
ncftp ncftp 3.2.5 [1,063] file transfer
NCL ncl 6.1.2, 6.3.0 [1,064] atmosphere Science
NCO nco 4.2.1, 4.4.3 [1,065] data Analysis
ncview ncview 2.1.2, 2.1.7 [1,066] data Visualization
NECAT necat 202001019 [1,067] phylogenetics
Necklace necklace 1.00 [1,068] biology, phylogenetics
NeEstimator neestimator 2.1 [1,069] biology, Bioinformatics
nemo nemo 1.0.0rc1, 1.0.1, 1.2.0 [1,070] ai, machine_learning
neovim neovim 0.2.0 [1,071] editor, text, ide, vim
NetCDF netcdf 4.3, 4.3.3, 4.4.3 [1,072] data_science, exchange
NetCDF-C netcdf-c 4.7.4, 4.8.1, 4.9.0 [1,073] data_science, exchange
NetCDF-F netcdf-f 4.4.4, 4.5.3, 4.5.4 [1,074] data_science, exchange
NetLogo netlogo 5.3.64, 6.1.1, 6.2.0 [1,075] modeling
NEURON neuron 7.7.2, 8.0.0, 8.2.1 [1,076] biology, neuroscience
Newbler newbler 2.7, 2.8, 2.9 [1,077] biology, ngs,454,assembly,denovo
newick-utils newickutils 1.6 [1,078] biology, genomics, phylogenetics
newick_utils newick_utils 1.6, 1.7 [1,079] biology, phylogenetics
NewTargets newtargets 20210215 [1,080] biology
NextDenovo nextdenovo 2.4.0 [1,081] phylogenetics
Nextflow nextflow 21.04.0, 21.10.6, 22.04.5 [1,082] biology, workflow
NextGenMap nextgenmap 0.5.5 [1,083] phylogenetics
NextPolish nextpolish 1.3.1 [1,084] phylogenetics
Nextstrain nextstrain 1.16.1 [1,085] phylogenetics
nf-core nf-core 1.12.1, 2.1 [1,086] biology, workflow
NGC CLI ngccli 2.10.1 [1,087] Command Line Interface
NGmerge ngmerge 0.3 [1,088] phylogenetics
ngmlr ngmlr 0.2.6, 0.2.7 [1,089] biology, phylogenetics
ngs-bits ngsbits 0.1 [1,090] biology, sequencing
NGS-SDK ngs-sdk 1.2.4, 1.3.0 [1,091] biology,bioinformatics,ncbi,sdk,library
ngscheckmate ngscheckmate 1.0 [1,092] phylogenetics
ngstools ngstools 20150816 [1,093] biology, ngs
nilearn nilearn 0.7.0, 0.9.0 [1,094] phylogenetics
nimare nimare 0.0.5 [1,095] neuroimaging
Nipype nipype 1.6.0, 1.7.0, 1.8.0 [1,096] biology, neuroscience, imaging
nlp nlp 1.1, 1.2 [N/A] machine_learning
nlr-annotator nlr-annotator 0.7 [1,097] phylogenetics
NLR-Parser nlr-parser 1.0 [1,098] phylogenetics
NMRPipe nmrpipe 7.9, 8.2 [1,099] biochemistry
NONMEM nonmem 7.3.0, 7.4.4 [1,100] modeling
nonpareil nonpareil 3.3.4 [1,101] phylogenetics
Novoalign novoalign 2.08.02, 3.00.02 [1,102] biology, ngs
NOVOPlasty novoplasty 3.7, 4.2, 4.3 [1,103] phylogenetics
nPhase nphase 1.1.3 [1,104] biology,pipeline,phasing,polyploid
npScarf japsa 1.7 [1,105] phylogenetics
nQuire nquire 20180405 [1,106] phylogenetics
Nsight nsight 2022.1 [1,107] gPU, profiler, tools
Nsightsys nsightsys 2022.2.1 [1,108] gPU, profiler, tools
nt nt 20220404 [1,109] sequencing, neuroscience
ntEdit ntedit 1.2.1 [1,110] phylogenetics
nubeamdedup nubeamdedup 20200907 [1,111] phylogenetics
NucDiff nucdiff 2.0.3 [1,112] phylogenetics
NucleoATAC nucleoatac 0.3.1 [1,113] biology
Nullarbor nullarbor 1.41 [1,114] biology, phylogenetics
Numba numba 0.36.2, 0.43.1, 0.48.0 [1,115] compiler
NUPACK nupack 3.2.2 [1,116] phylogenetics
nvhpc nvhpc 11.1, 21.7 [1,117] language, development, library, math, nvidia
nVidia HPC Compilers nvidia 20.11 [1,118] compilers
NWChem nwchem 6.8 [1,119] chemistry
NxTrim nxtrim 0.4.1 [1,120] biology, ngs
Oases oases 0.2.08 [1,121] biology,ngs,assembler
OCaml ocaml 4.02.3 [1,122] language, scripting, development
OCOCO ococo 0.1.2.6 [1,123] biology, phylogenetics
octave octave 6.4.0, 7.2.0 [1,124] numerical Computation
odgi odgi 0.6 [1,125] phylogenetics
Olego olego 1.1.2, 1.1.5, 1.1.6 [1,126] biology, ngs,rna-seq
OmicsBox omicsbox 1.1.78 [1,127] image_processing
OMindel omindel 20180129 [1,128] phylogenetics
omniCLIP omniclip 0.1.0 [1,129] phylogenetics
OMNIVERSE omniverse beta211004 [1,130] nVIDIA Omniverse
OMSV omsv 1.0.1 [1,131] phylogenetics
ONT-Bonito ont-bonito 0.1.5, 0.5.3, 0.6.0 [1,132] phylogenetics
ont_fast5_api ont-fast5-api 2.0.1, 4.0.2 [1,133] phylogenetics
ont_tutorial_cas9 ont_tutorial_cas9 20190705 [1,134] phylogenetics
open-cravat open-cravat 2.0.1 [1,135] biology, genomics
open3d open3d 0.13.0 [1,136] phylogenetics
OPENACC openacc 16.7 [1,137] programming, Accelerator toolkit
OpenBabel openbabel 2.3.2, 2.4.1, 3.1.1 [1,138] biology
OpenBLAS openblas 0.2.20 [1,139] programming,library
OpenCL opencl 18.1.0.013 [1,140] phylogenetics
OpenCV opencv 4.5.2 [1,141] library
OpenFOAM openfoam 4.1, 5.0, 8.0 [1,142] computational Fluid Dynamics
OpenMM openmm 7.5, 7.5.0, 7.6.0 [1,143] chemistry, molecular_dynamics
OpenMPI openmpi 4.0.4, 4.0.5, 4.1.1 [1,144] parallel Programming, development, MPI, library
OpenNeuro openneuro 3.17.4, 3.37.4 [1,145] biology, data
OpenPIV-python openpiv 0.21.2 [1,146] python, imaging
OpenPIV-python-gpu openpiv 20190506-gpu [1,147] python, imaging
OpenSim opensim 4.3 [1,148] phylogenetics
OpenSlide openslide 3.4.1 [1,149] imaging
OptiType optitype 1.3.1 [1,150] biology, phylogenetics
Orange3 orange3 3.3.6 [1,151] data_mining
ORCA orca 4.0.1.2 [1,152] molecular, Electronic Structure
OrganellePBA organellepba 20180904 [1,153] phylogenetics
OrthoFiller orthofiller 1.1.4 [1,154] phylogenetics
OrthoFinder orthofinder 1.1.10, 2.3.11, 2.5.2 [1,155] biology, ngs
Orthofisher orthofisher 0.1.2 [1,156] biology, Genetics
Orthograph orthograph 0.6.3 [1,157] orthology
Orthologer orthologer 2.2.0 [1,158] biology,
OrthoMCL orthomcl 2.0.3, 2.0.7 [1,159] biology, genomics
osprey osprey 1.1.0 [1,160] mRS,matlab,neuroscience
OTB otb 5.8.0 [1,161] geospatial Data Modeling
p4est p4est 1.1, 2.8 [1,162] library
p4vasp p4vasp 0.3.29, 0.3.30 [1,163] molecular, Electronic Structure
p53MH p53mh 20020901 [1,164] biology, DNA-sequencing
p7zip p7zip 9.20.1 [1,165] archiver
PacBio pacbio 10.2.0.133434, 11.0.0.146107, 7.0.1 [1,166] biology, ngs, pacbio, smrtlink
Package-GFE package-gfe 20150701 [1,167] biology, genomics
PALADIN paladin 1.3.1 [1,168] biology, phylogenetics
PALES pales 122 [1,169] physics
PAML paml 4.8a, 4.9a, 4.9h [1,170] biology, phylogenetics
Pandaseq pandaseq 20140808, 20150627 [1,171] biology, ngs, sequencing
Pandoc pandoc 2.2.2.1 [1,172] converter
pangolin pangolin 2 [1,173] phylogenetics
panseq panseq 3.2.1 [1,174] phylogenetics
panX panx 1.6.0 [1,175] phylogenetics
PAPI papi 5.5.1, 5.7.0 [1,176] programming interface, performance analysis
parabricks parabricks 3.5.0, 3.7.0 [1,177] phylogenetics
parallel parallel 20150122, 20170322 [1,178] shell, process management
paralyzer paralyzer 1.5 [1,179] phylogenetics
ParaView paraview 5.4.1, 5.7.0, 5.9.1.1 [1,180] data Analysis
ParaView Server paraview_server 5.10.1 [1,181] data Analysis
ParGenes pargenes 1.2.0 [1,182] phylogenetics
ParlAI parlai 1.3.0, 1.5.0 [1,183] phylogenetics
Parsnp parsnp 1.2, 1.5.0, 1.6.2 [1,184] biology, phylogenetics
PartitionFinder partitionfinder 2.0.0-pre-20160513, 2.1.1-20161205, 2.1.1.0 [1,185] biology,phylogenetics,evolution
PASA pasa 2.0.2-r20151207, 2.2.0-r20171013, 2.4.1 [1,186] biology, genomics, ngs
Pascal fpc 3.0.0 [1,187] compiler, Programming
PASTA pasta 0.2.0, 1.7.8, 20160616 [1,188] biology, sequence alignment
PATHd8 pathd8 1.0 [1,189] biology, phylogenetics
pathoscope pathoscope 2.0.7 [1,190] sequencing, genomics, Biology
PATRIC patric 1.034 [1,191] machine_learning
PAUDA pauda 1.0.1 [1,192] biology, ngs, phylogenetics
PAUP paup 4.0a166, 4.0a168, 4.0b10 [1,193] biology, Phylogenetics
PB-Assembly pb-assembly 0.0.6, 0.0.8 [1,194] biology, ngs, sequencing,pacbio
pbalign pbalign 20160921, 20161221 [1,195] biology
PBCCS pbccs 5.0.0 [1,196] phylogenetics
pbcore pbcore 1.7.1 [1,197] biology,bioinformatics
PBGCpp pbgcpp 1.9.0 [1,198] phylogenetics
pbipa pbipa 1.8.0 [1,199] phylogenetics, biology
PBJelly pbjelly 15.8.24 [1,200] biology, ngs
pbmm2 pbmm2 1.3.0 [1,201] phylogenetics
pbrt pbrt 20181017 [1,202] phylogenetics
pbsmrtpipe pbsmrtpipe 0.63.0 [1,203] biology,API
pbtranscript-tofu pbtranscript-tofu 20150317, 20160119 [1,204] biology, ngs, pacbio
PCIT pcit 2014 [1,205] biology
PCRE pcre 8.38, 8.39 [1,206] programming, library
PDA pda 1.0.3 [1,207] biology, phylogenetics
pdb2pqr pdb2pqr 2.1.0 [1,208] protein, modeling, pdb
PeakSplitter peaksplitter 1.0 [1,209] biology, CHiP-Seq
PEAR pear 0.9.2 [1,210] biology, genomics, ngs
peneasy peneasy 20150530 [1,211] physics
PennCNV penncnv 1.0.5 [1,212] phylogenetics
Perl perl 5.16.0, 5.20.0, 5.24.1 [1,213] programming,scripting,language
PerM perm 0.4.0 [1,214] biology, ngs, mapping
PETSc petsc 3.8.1, 3.8.3, 3.8.4 [1,215] math, Numerical Solvers
PfamScan pfamscan 1.3, 1.5 [1,216] biology, genomics
PGAP pgap 20220414 [1,217] biology, genomics, Annotation, Pipeline
PGDSpider pgdspider 2.0.9.0, 2.1.1.5 [1,218] biology, ngs
pggb pggb 0.4.1, 20201106, 20210121 [1,219] phylogenetics
PhaME phame 1.0.3 [1,220] phylogenetics
pharmcat pharmcat 1.8.0 [1,221] biology, Bioinformatics, Phylogenetics
PHASE phase 2.1.1 [1,222] phylogenetics
PHAST phast 1.5 [1,223] biology,phylogeny
Phenix phenix 1.10.2155, 1.17.1, 1.8.1069 [1,224] crystallography
PHI phi 3.1.1, 3.1.2b, 3.1.6 [1,225] calculations
PhiSpy phispy 3.2 [1,226] phylogenetics
PHITS phits 2.76, 2.82, 2.84 [1,227] physics
PHLAWD phlawd 20170427 [1,228] biology, phylogenetics
PhotoScan photoscan-pro 1.4.1, 1.4.5 [1,229] image_processing
Photutils photutils 0.5 [1,230] astronomy, photometry
PHYLDOG dtitk 20130116-dbg [1,231] biology,bioinformatics,phylogenetics
PHYling phyling 1.0 [1,232] biology, phylogenetics, Markers, Genomics
PHYLIP phylip 3.696 [1,233] biology,phylogenetics
PhyloAcc phyloacc 1.0 [1,234] phylogenetics
PhyloBayes phylobayes 3.3f [1,235] biology,bioinformatics,phylogenetics
phyloFlash phyloflash 3.3b4 [1,236] phylogenetics
phylonet phylonet 3.5.7, 3.8.2 [1,237] biology, phylogenetics
PhyloParser phyloparser 20180404 [1,238] phylogenetics
PhyloPhlAn2 phylophlan2 0.41 [1,239] phylogenetics
phylopypruner phylopypruner 1.2.3 [1,240] phylogenetics
PhyloSift phylosift 1.1 [1,241] biology, genomics, phylogenetics, taxonomy
phyloTF2 phylotf2 20210726 [1,242] biology, genomics, alignment
Phyluce phyluce 20180727, 20190308, 20191015 [1,243] biology, ngs, sequencing
PhyML phyml 3.0, 3.1 [1,244] biology,bioinformatics,phylogenetics
phynd phynd 20200409 [1,245] phylogenetics
Physher physher 1.0.2 [1,246] phylogenetics
PHYUTILITY phyutility 2.7.1 [1,247] biology
Phyx phyx 1.1 [1,248] phylogenetics
PIA2 pia2 20180305 [1,249] biology, phylogenetics
Picard-tools picard 2.5.0, 2.9.0, 2.9.2 [1,250] biology, ngs
PICRUSt picrust 1.1.3, 1.1.4, 2.3.0b [1,251] biology, phylogenetics
PICSL picsl 1.3 [1,252] imaging, Atlas, Segmentation
Piggy piggy 20171220 [1,253] biology, ngs
Pigz pigz 2.4 [1,254] compression
PILON pilon 1.22, 1.24 [1,255] biology, ngs, phylogenetics
Pindel pindel 0.2.5b8 [1,256] biology, phylogenetics
pipe-clip pipe-clip 1.1.0 [1,257] biology,NGS
pipits pipits 1.3.6, 1.4.0 [1,258] biology, sequencing
Piranha piranha 1.2.1 [1,259] biology,phylogenetics
PlantTribes planttribes 1.0.4 [1,260] phylogenetics
plasflow plasflow 1.1 [1,261] biology, phylogenetics
PLAST plast 1.0, 2.3.2 [1,262] biology,bioinformatics
platanus platanus 1.2.4 [1,263] phylogenetics
Platon platon 1.6 [1,264] biology, sequencing
Platypus platypus 0.8.1 [1,265] biology, ngs
PLEK plek 1.2.2 [1,266] biology, phylogenetics
Plink plink 1.90b3.39, 2.00a2, 2.00a3LM [1,267] biology, genomics,phylogenetics
plinkseq plinkseq 0.10 [1,268] biology, library
plotsr plotsr 0.5.4 [1,269] genomics, biology
PLUMED plumed 2.7.3, 2021.2 [1,270] chemistry, molecular_dynamics
pod5 pod5 20220621 [1,271] sequencing
PolyGembler polygembler 1.0 [1,272] phylogenetics
PolyPHen polyphen 2.2.2.r405b [1,273] biology, genomics
polyply polyply 1.3.0 [1,274] phylogenetics, Biology
pomoxis pomoxis 0.1.11, 0.2.5, 0.3.2 [1,275] biology, phylogenetics
popcorn popcorn 20211104 [1,276] phylogenetics, biology
PopLDdecay poplddecay 3.40 [1,277] phylogenetics
popoolation popoolation 1.2.2 [1,278] biology, phylogenetics
Porechop porechop 0.2.4 [1,279] phylogenetics
Poretools poretools 0.6.1 [1,280] phylogenetics
portcullis portcullis 1.2.3 [1,281] phylogenetics
PosiGene posigene 20171113 [1,282] biology, phylogenetics
POV-Ray povray 3.7 [1,283] 3D Graphics
pplacer pplacer 1.1.alpha19 [1,284] biology, phylogenetics, taxonomy
PRANK prank 170427, 20150803 [1,285] biology, alignment
Predector predector 20201110 [1,286] phylogenetics
preplot preplot 14.0.2 []
Preseq preseq 0.0.4 [1,287] biology, ngs
PRICE price 1.2 [1,288] biology, ngs
Primer3 primer3 2.3.4 [1,289] biology, genomics
primus primus 1.8.0 [1,290] biology, phylogenetics
PRINSEQ prinseq 0.20.4 [1,291] biology, sequencing
PRINSEQ++ prinseq++ 1.2 [1,292] phylogenetics
ProbABEL probabel 0.4.2, 0.4.3, 0.4.5 [1,293] genomics, gwas
probalign probalign 1.4 [1,294] biology, ngs
Processing processing 3.4 [1,295] java, language, programming, visual
Prodigal prodigal 2.6.2, 2.6.3 [1,296] biology, genomics
ProDy prody 2.0 [1,297] phylogenetics
Program Database Toolkit pdt 3.20, 3.22, 3.24 [1,298] language, development, performance analysis
PROJ proj 4.9.3, 5.1.0, 8.0.1 [1,299] library, geospatial, cartography
Prokka prokka 1.12, 1.14.6 [1,300] biology, genomics, assembly
Proovread proovread 1.03rcl, 2.12, 2.13 [1,301] biology, genomics, ngs
ProSplign prosplign 1.0.0 [1,302] phylogenetics
Protege protege 5.1.0 [1,303] ontology
Proteinortho proteinortho 4.26, 5.11, 5.16 [1,304] biology, genomics
ProtExcluder protexcluder 1.2 [1,305] biology, phylogenetics
ProtHint prothint 2.6.0 [1,306] biology, genomics
protobuf protobuf 2.5.0, 3.5.1 [1,307] google, libraries
PROVEAN provean 1.1.5 [1,308] biology, genomics
PRSice prsice 2.3.3 [1,309] phylogenetics
Pseudofinder pseudofinder 1.0 [1,310] phylogenetics
PsiCLASS psiclass 1.0.1 [1,311] phylogenetics
PSMC psmc 0.6.5 [1,312] phylogenetics
psRobot psrobot 1.2 [1,313] phylogenetics
Pufferfish pufferfish 20200417 [1,314] phylogenetics
PureCLIP pureclip 1.1.1 [1,315] phylogenetics
Purge_Dups purge_dups 1.0.1 [1,316] phylogenetics
purge_haplotigs purge_haplotigs 1.1.2 [1,317] sequencing, biology, biology
pyani pyani 0.2.10 [1,318] phylogenetics
Pybedtools pybedtools 0.8.2 [1,319] phylogenetics
PyBSASeq pybsaseq 20200623 [1,320] phylogenetics
PyCharm pycharm 2018.3 [1,321] editor, ide, programming, python
pychopper pychopper 2.5.0, 2.7.1 [1,322] phylogenetics, sequencing
PyCogent pycogent 1.9 [1,323] biology, genomics
pycoqc pycoqc 2.5.2 [1,324] Sequencing, data
PyDeface pydeface 2.0.0 [1,325] imaging
pyEGA3 pyega3 3.4.1 [1,326] biology, genomics, Utility
PyEXR pyexr 0.3.10 [1,327] programming, python, openexr
Pyfaidx pyfaidx 0.5.2 [1,328] biology, ngs, sequencing
pyfasta pyfasta 0.5.2 [1,329] phylogenetics
pygot pygot 20170518 [1,330] biology, phylogenetics
pyhdf pyhdf 0.9.0 [1,331] library, hdf4
PyHIST pyhist 1.0 [1,332] biology, Histology, Image segmentation
PyPHLAWD pyphlawd 20180416, 20190414 [1,333] biology, phylogenetics
Pyroms pyroms 1.0 [1,334] oceanography
PyRosetta pyrosetta r56324 [1,335] biology,structure,modeling
pyrpipe pyrpipe 0.0.3 [1,336] phylogenetics
Pysamstats pysamstats 1.1.2 [1,337] phylogenetics
PySLURM pyslurm 18.08.04 [1,338] sLURM
Python python 3.6.3, 3.6.5, 3.8 [1,339] language, scripting, development
Python-core python-core 3.6.5, 3.7, 3.8 [1,340] language, scripting, development
Python2 python 2.7.11 [1,341] language, scripting, development
PyTorch ngc-pytorch 1.11.0, 1.9.0 [1,342] library, math
pytorch pytorch 1.7.1, 1.8.1, 1.9.0 [1,343] library, math
PyVCF pyvcf 0.6.0, 0.6.8 [1,344] biology, phylogenetics
PyVista pyvista 0.26.1 [1,345] phylogenetics
pyweka pyweka 0.3.18 [1,346] phylogenetics
QAPA qapa 1.3.1 [1,347] phylogenetics
qcat qcat 1.1.0 [1,348] phylogenetics
qctool qctool 2.0.1 [1,349] phylogenetics
QD qd 2.3.22 [1,350] library, compiler, math
QDD qdd 3.1.2 [1,351] biology, genomics, ngs
QGIS qgis 2.18.0, 3.14.0 [1,352] gIS
QIIME qiime 1.9.1 [1,353] biology, genomics
QIIME2 qiime2 2021.11, 2021.4, 2022.8 [1,354] biology, genomics
QMCPACK qmcpack 3.4.0 [1,355] library
QRNA qrna 2.0.4 [1,356] phylogenetics
QT qt 4.8.3, 5.12.9, 5.15.4 [1,357] uI Framework
QTL-seq qtl-seq 2.2.2 [1,358] biology, sequencing, pipeline
QTLtools qtltools 1.2, 1.3.1 [1,359] phylogenetics
Quake quake 0.3 [1,360] biology, sequencing
QualiMap qualimap 2.1.2 [1,361] biology,sequence alignment
Quantas quantas 1.0.4, 1.0.8, 1.0.9 [1,362] biology, ngs
quantisnp quantisnp 2 [1,363] bioinformatics, genomics
QuartetScores quartetscores 1.0.0 [1,364] phylogenetics
QUAST quast 4.4, 5.0.0, 5.0.2 [1,365] biology, ngs, sequencing, rna-seq
quickmerge quickmerge 0.3 [1,366] phylogenetics
Quickquartet quickquartet 1.0.0 [1,367] biology, ngs
QUIP quip 20201029, 20210626 [1,368] phylogenetics
QuorUM quorum 1.0.0 [1,369] biology
R R 4.0, 4.1, 4.2 [1,370] statistics
r-index r-index 20190711 [1,371] phylogenetics
r8s r8s 1.8, 1.81 [1,372] phylogenetics
RACA raca 0.9.1.1 [1,373] biology, ngs
Racon racon 1.3.3, 1.4.10, 1.4.13 [1,374] phylogenetics
RADICAL radical 0.2 [1,375] biology, genomics
radorgminer radorgminer 0.9 [1,376] genomics, Biology, Sequencing
RaGOO ragoo 1.11 [1,377] phylogenetics
Ragout ragout 2.3 [1,378] genomics
RagTag ragtag 1.0.0, 2.0.1 [1,379] phylogenetics
rainbow rainbow 2.0.4 [1,380] biology, sequencing
Rainbowfish rainbowfish 0.1.0 [1,381] phylogenetics
RAiSD raisd 2.8 [1,382] phylogenetics
Randfold randfold 2.0.1 [1,383] biology, RNA
ranger ranger 1.9.3 [1,384] file Management
rapidsai rapidsai 21.10, 21.12, 22.04 [1,385] data Science
rapidtide rapidtide 1.9.0 [1,386] phylogenetics
RAPSearch rapsearch 2.24 [1,387] biology, phylogenetics
Rascaf rascaf 1.0.2 [1,388] biology
RAVE rave 2.1 [1,389] biology, phylogenetics
Raven raven 1.8.1 [1,390] assembler
RAxML raxml 8.2.10, 8.2.12, 8.2.8 [1,391] application, biology, philogenetics
RAxML-NG raxml-ng 0.9.0, 1.0.2, 1.1.0 [1,392] phylogenetics
razers3 razers3 3.5.7 [1,393] biology, phylogenetics
rbp-maps rbp-maps 0.1.4 [1,394] phylogenetics
rclone rclone 1.57.0, 1.58.1 [1,395] cloud
Rcorrector rcorrector 1.0.4 [1,396] phylogenetics
RDKit rdkit 2020092 [1,397] chemiformatics
rDnaTools rdnatools 0.1.3 [1,398] phylogenetics
READemption reademption 1.0.0 [1,399] phylogenetics
REAPR reapr 1.0.18 [1,400] biology, assembly
Rebaler rebaler 0.2.0 [1,401] phylogenetics
reCOGnizer recognizer 1.3.3 [1,402] phylogenetics
recon recon 1.08 [1,403] biology,sequencing
Redis redis 2.8.13, 2.8.19 [1,404] daemon, data, server
REDItools2 reditools2 20200701 [1,405] phylogenetics
Redundans redundans 0.14a [1,406] biology, phylogenetics
ReFrame reframe 3.2 [1,407] hpc, internal
regtools regtools 0.5.2 [1,408] biology, RNA-seq, Genitics
release release 12082021 [1,409] molecular dynamics, deep learning
RELION relion 3.0.2, 3.0b, 3.1.0 [1,410] biology, imaging
RelocaTE2 relocate2 2.0.1 [1,411] phylogenetics
REMORA remora 1.8.2, 1.8.3, 1.8.5 [1,412] system, profiler
REPdenovo repdenovo 20170222 [1,413] biology, phylogenetics
RepeatAnalysis repeatanalysis 0.10.0, 0.12.2 [] biology, phylogenetics
RepeatAnalysisTools repeatanalysistools 20210506 [1,414] biology, genomics, sequencing, Utility
RepeatExplorer repeatexplorer 20150506, 20180517 [1,415] biology, ngs
RepeatMasker repeatmasker 4.0.5, 4.0.9, 4.1.1 [1,416] biology,bioinformatics
RepeatModeler repeatmodeler 1.0.8, 2.0 [1,417] biology,bioinformatics
repeatscout repeatscout 1.0.5 [1,418] biology
RepeatSeq repeatseq 0.8.2 [1,419] phylogenetics
reptile reptile 1.1 [1,420] biology,NGS,error correction
ResFinder resfinder 4.0 [1,421] biology, genomics
Resistome resistome 20170111 [1,422] phylogenetics
RevBayes revbayes 1.0.7, 1.0.9, 1.1.1 [1,423] biology, phylogenetics
RFMIX rfmix 2.03 [1,424] phylogenetics
RGAugury rgaugury 20220107 [1,425] sequencing, biology
RGI rgi 4.2.2, 5.1.1 [1,426] phylogenetics
RGIS rgis 20180211, 20180814 [1,427] riverGIS
RHash rhash 1.3.3 [1,428] gNU
RiboCode ribocode 1.2.11 [1,429] phylogenetics
riboPicker ribopicker 0.4.3 [1,430] biology,sequence
RiboTaper ribotaper 1.3.1a [1,431] phylogenetics
RIGERJ rigerj 2.0.2 [1,432] phylogenetics
rMATS turbo rmats-turbo 4.1.2 [1,433] biology, sequencing, genomics
rmats2sashimiplot rmats2sashimiplot 2.0.3, 2.0.4 [1,434] phylogenetics
Rmpi Rmpi 0.6.9 [1,435] statistics, R, mpi
RNAFramework rnaframework 2.7.2 [1,436] biology, RNA, Sequencing
RNAhybrid rnahybrid 2.1.1 [1,437] biology, genomics
RNAmmer rnammer 1.2 [1,438] biology, RNA-seq
rnaQUAST rnaquast 1.5.1 [1,439] biology, ngs, sequencing, rna-seq
RNAsalsa rnasalsa 0.8.1 [1,440] biology, phylogenetics
rnaseqlib rnaseqlib 20150721 [1,441] biology, phylogenetics, RNA-seq
RNAstructure rnastructure 6.3 [1,442] biology, sequencing
Roary roary 3.12.0, 3.4.1 [1,443] biology, genomics
ROOT root 5.34.17, 6.0, 6.06.02 [1,444] data Analysis
ROOTPy rootpy 20160323 [1,445] data Analysis
Rosetta rosetta 2014wk4, 2019.35.60890 [1,446] biology,structure,modeling
RoseTTAFold rosettafold 1.0.0 [1,447] phylogenetics
rrnaselector rrnaselector 1.0 [1,448] biology, sequencing
RSEG rseg 0.4.8 [1,449] biology, genomics
RSEM rsem 1.2.31, 1.2.7, 1.3.3 [1,450] biology, ngs, sequencing
RSeQC rseqc 2.6.4, 3.0.0 [1,451] biology,ngs,rna-seq
RStudio rstudio 1.4, 2021.09.0, 2022.02.3 [1,452] statistics
RTGTools rtgtools 3.7.1 [1,453] biology, ngs
Ruby ruby 2.5.1 [1,454] programming,scripting,language
Rust rust 1.48.0, 1.52.1, 1.62.1 [1,455] programming
rvtests rvtests 2.1.0 [1,456] genomics, Biology, Sequencing
S.A.G.E s.a.g.e 6.4.2 [1,457] phylogenetics
Sabre sabre 1.0 [1,458] phylogenetics
saffrontree saffrontree 0.1.2 [1,459] phylogenetics
Sailfish sailfish 0.6.3 [1,460] biology, genomics, ngs, rna-seq
Salmon salmon 1.1.0, 1.5.2, 1.8.0 [1,461] biology, RNA-seq
SALSA salsa 20171009, 20191001 [1,462] biology, ngs, pacbio
Sambamba sambamba 0.6.3, 0.6.6, 0.6.9 [1,463] biology, ngs
samblaster samblaster 0.1.14, 0.1.24 [1,464] biology, ngs, sequencing
sampledock sampledock 0.5.1 [1,465] molecular dynamics, AI
SAMStat samstat 1.08 [1,466] biology, ngs, sequencing
Samtools samtools 1.7, 1.8, 1.9 [1,467] biology, ngs, sequencing
SAS sas 9.3, 9.4 [1,468] statistics, data analysis
Sate sate 2.2.7 [1,469] biology, phylogenetics
Satsuma satsuma 3.0 [1,470] phylogenetics
Satsuma2 satsuma2 20161123, 3.1 [1,471] phylogenetics
sc-im scim 0.8.2 [1,472] software, data visualization
Scala scala 2.11.5, 3.0.1 [1,473] programming, language, java
Scalablast scalablast 2.4.53 [1,474] application, biology, genomics
ScaLAPACK scalapack 2.0.2, 2.1.0 [1,475] programming,library
scallop scallop 0.10.5 [1,476] phylogenetics
Scalpel scalpel 0.1.1, 0.5.3 [1,477] biology, ngs
Schrodinger Suite schrodinger 2019-3, 2020-4, 2021-2 [1,478] chemistry, molecular_dynamics
Scipion scipion 1.2 [1,479] image_processing
SCIrun scirun 5.0.Z [1,480] phylogenetics
Scoary scoary 1.6.16 [1,481] phylogenetics
Scons scons 2.5.1, 3.1.2 [1,482] programming
SCOP scop 20180311 [1,483] biology, Scaffolding, Assembly
Scrappie scrappie 1.4.2 [1,484] biology, genomics
SCRATCH-1D scratch1d 1.0, 2.0 [1,485] biology, ngs
Screen screen 4.8.0 [1,486] gNU, Terminal Multiplexer
SCRIPTURE scripture 20101211 [1,487] biology, genomics
Scythe scythe 0.991 [1,488] biology, ngs
sdsl sdsl 2.1.1 [1,489] library, c++
SE-MEI se-mei 0.1.0 [1,490] phylogenetics
SeCaPr secapr 1.1.12, 2.0.2, 2.1.1 [1,491] phylogenetics
Segemehl segemehl 0.1.9, 0.3.4 [1,492] biology, ngs, sequencing
segment-liftover segment-liftover 20211021 [1,493] biology, genomics
SEPP sepp 20160614 [1,494] biology, phylogenetics
Seq-Gen seq-gen 1.3.3 [1,495] biology,phylogenetics
seq_crumbs seq_crumbs 20150120 [1,496] biology, sequence, genomics, utilities
SeqKit seqkit 0.10.2, 0.8.0, 2.0.0 [1,497] biology, phylogenetics
seqmagick seqmagick 0.8.4 [1,498] biology
SeqMap seqmap 1.0.13 [1,499] biology, sequencing, ngs
SEQPower seqpower 1.1.1 [1,500] genomics, phylogenetics
SeqPrep seqprep 0.5, 1.1 [1,501] biology, ngs, sequencing
seqscreen seqscreen 3.3 [1,502] sequencing, biology
seqtk seqtk 1.3, 20140729 [1,503] biology, genomics, ngs
SEQuel sequel 1.0.1 [1,504] biology, ngs
SequelQC sequelqc 1.1.0 [1,505] phylogenetics
seqwish seqwish 0.7, 20190509 [1,506] phylogenetics
SeqyClean seqyclean 1.8.10 [1,507] biology, ngs, sequencing
SeSiMCMC sesimcmc 4.36 [1,508] biology, sequencing
SExtractor sextractor 2.19.5 [1,509] astronomy
SHAPE-MaP shapemap 1.2 [1,510] biology, phylogenetics
SHAPEIT shapeit 2.12, 2.5 [1,511] biology, variant_calling
SHAPEIT4 shapeit4 4.2.2 [1,512] biology, sequencing, phasing
ShapeMapper shapemapper 2.1.3, 2.1.5 [1,513] biology, phylogenetics
SHARCGS sharcgs 1.2.11 [1,514] biology, ngs, de novo assembly
Shasta shasta 0.1.0 [1,515] phylogenetics
SHEsisPlus shesisplus 1.0, 1.01 [1,516] biology, genetics
shogun shogun 6.1.3 [1,517] phylogenetics
Shortbred shortbred 0.9.4 [1,518] phylogenetics
shovill shovill 1.1.0 [1,519] genomics, sequencing, biology
SHRiMP shrimp 2.2.3 [1,520] biology, genomics, ngs
shustring shustring 2.6 [1,521] biology, sequencing
SibeliaZ sibeliaz 1.2.2, 1.2.3, 1.2.4 [1,522] biology, genomics, alignment
SICER sicer 1.1 [1,523] biology, ChIP-Seq
Sickle sickle 1.200, 1.33 [1,524] biology, ngs
Siesta siesta 3.2, 4.1b2, 4.1b3 [1,525] chemistry
SIFT sift 4.0.3b [1,526] biology, genomics
SIGffRid sigffrid 1.1 [1,527] phylogenetics
SignalP signalp 4.1c, 5.0b [1,528] biology, phylogenetics
SiLiX silix 1.2.11, 1.3.0 [1,529] phylogenetics
silo silo 4.7 [1,530] iO,library
sim4 sim4 20121010 [1,531] biology, genomics
Sim4Life sim4life 7.0.1 [1,532] biology,simulation
Simka simka 1.5.3 [1,533] phylogenetics
SimNIBS simnibs 3.2.1 [1,534] phylogenetics
SimSeq simseq 4.12.2011 [1,535] biology, ngs, phylogenetics
Simulia simulia 2019 [1,536] simulation, visualization
SInC sinc 20140120 [1,537] biology, phylogenetics
sine_scan sine_scan 1.1.1 [1,538] phylogenetics
Singularity singularity 3.7.4 [1,539] workflow_automation
SIPeS sipes 2.0 [1,540] biology, ChIP-Seq
sisl sisl 0.8.3 [1,541] physics, Tight-binding
skmer skmer 3.2.1 [1,542] genomics, biology
Slamdunk slamdunk 0.4.1, 0.4.2 [1,543] phylogenetics
SLAW slaw 20211217 [1,544] chromatography, Spectrometry
Slicer slicer 4.13.0, 4.3.1, 5.0.3 [1,545] biology, neuroscience, imaging
slow5tools slow5tools 0.5.1 [1,546] biology, sequencing
slurm-drmaa slurm-drmaa 1.1.2, 1.1.3 [1,547] libraries, slurm, api, drmaa
smalt smalt 0.7.6 [1,548] application, biology, phylogenetics
SMARTdenovo smartdenovo 20180219 [1,549] biology, phylogenetics
smartie-sv smartie-sv 20180308 [1,550] phylogenetics
SMC++ smcpp 1.15.4 [1,551] biology, genomics, sequencing
Smetana smetana 1.1.0 [1,552] phylogenetics
SMR smr 1.03 [1,553] biology, genomics
SMRT-SV smrtsv2 2.0.0 [1,554] biology, ngs
SMS sms 1.7 [1,555] biology
Smudgeplot smudgeplot 0.2.4 [1,556] phylogenetics
Snakemake snakemake 6.4.1, 7.5.0 [1,557] biology, workflow
SNAP snap 0.15.4, 2.0.0, 20100728 [1,558] biology,bioinformatics,sequencing
SNAPE-pooled snape-pooled 20130407 [1,559] biology, variant_calling
SNeP snep 1.1 [1,560] biology,phylogenetics
Sniffles sniffles 1.0.11, 1.0.6, 1.0.8 [1,561] phylogenetics
Sniffles2 sniffles2 2.0.6 [1,562] biology, Bioinformatics
Snippy snippy 20160419, 4.6.0 [1,563] biology, phylogenetics
SNP-Pipeline snp-pipeline 1.0.1 [1,564] biology, phylogenetics
SNP-sites snp-sites 2.0.3 [1,565] biology, variant_calling
snp2hla snp2hla 1.0.3 [1,566] biology, Bioinformatics, Genomics
SnpEff snpeff 4.3r, 4.3t, 5.0 [1,567] biology,bioinformatics,variant annotation
snpflip snpflip 20190515 [1,568] biology, phylogenetics
SNPGenie snpgenie 20190620 [1,569] phylogenetics
SNPhylo snphylo 20140701 [1,570] biology,phylogenetics
SNPsplit snpsplit 0.5.0 [1,571] biology,bioinformatics,sequencing
SNPTEST snptest 2.5.2 [1,572] phylogenetics
SOAPaligner soapaligner 2.21 [1,573] phylogenetics
SOAPdenovo soapdenovo 1.05, 2.04 [1,574] biology,ngs
SOAPdenovo-Trans soapdenovo-trans 1.01, 1.03 [1,575] biology,ngs
SOAPec soapec 2.03 [1,576] biology, phylogenetics
SOAPnuke soapnuke 2.1.0 [1,577] phylogenetics
SOAPsplice soapsplice 1.10 [1,578] biology,ngs
SODA soda 20200930 [1,579] biology
SOLAR solar 8.4.2 [1,580] phylogenetics
SomaticSeq somaticseq 3.6.2 [1,581] phylogenetics
SortaDate sortadate 20190705 [1,582] phylogenetics
SortMeRNA sortmerna 2.1, 4.0 [1,583] biology, sequencing, NGS
SourceTracker2 sourcetracker2 2.0.1 [1,584] phylogenetics
Sourmash sourmash 2.0.1 [1,585] phylogenetics
SoX sox 14.4.2 [1,586] phylogenetics
SpaceRanger spaceranger 1.3.1 [1,587] phylogenetics
SPAdes spades 3.15.3, 3.7.1, 3.8.0 [1,588] biology, ngs
SparCC sparcc 201608 [1,589] microbial Ecology
Spark spark 2.2.0, 3.1.1 [1,590] spark, hadoop
sparsehash sparsehash 2.0.3 [1,591] google, API
SPARTA+ sparta+ 2.60 [1,592] chemistry
Spec2nii spec2nii 0.3.4 [1,593] phylogenetics
SpeedSeq speedseq 0.1.2 [1,594] phylogenetics
Spidey spidey 20150922 [1,595] biology, genomics, bioinformatics
SpinalCordToolbox spinalcordtoolbox 5.4 [1,596] phylogenetics
SplAdder spladder 2.4.2 [1,597] phylogenetics
SpliceGrapher splicegrapher 0.2.5 [1,598] biology, sequencing
SpliceTrap splicetrap 0.90.5 [1,599] biology, genomics, ngs
SPM spm 12b, 8, 8r5236 [1,600] biology,bioinformatics,matlab
spruceup spruceup 2019.2.3 [1,601] phylogenetics
Sputnik sputnik 1.0 [1,602] biology,bioinformatics,repeats
spyder spyder 4.1.4, 5.1.1, 5.3.2 [1,603] iDE, editor, programming, scripting
SQANTI sqanti 1.2 [1,604] phylogenetics
SQANTI2 sqanti2 5.0 [1,605] phylogenetics
SQANTI3 sqanti3 0.1, 1.6, 4.2 [1,606] phylogenetics
SQL Developer sqldeveloper 4.1.2 [1,607] programming, oracle, sql
SQLite sqlite 3.33.0, 3.8.8.2 [1,608] database
SqueezeMeta squeezemeta 1.4.0, 1.5.2 [1,609] phylogenetics
squigglekit squigglekit 1.0.0 [1,610] data Visualization and Analysis, biology
squigglenet squigglenet 1.0 [1,611] sequencing, biology
SRA sra 2.10.9, 3.0.0 [1,612] biology,bioinformatics,sra
sra-human-scrubber sra_human_scrubber 1.1 [1,613] cSV_categories
SRAssembler srassembler 1.0.0 [1,614] phylogenetics
SSM ssm 20210511 [1,615] phylogenetics
SSPACE sspace 2.0, 3.0 [1,616] biology, ngs
ssr_pipeline ssr_pipeline 0.951 [1,617] biology, DNA sequencing,
Stacks stacks 2.53, 2.55, 20190403 [1,618] biology, genomics, ngs
Staden staden 1.14.6 [1,619] biology, phylogenetics
Stampy stampy 1.0.31 [1,620] biology, sequencing
staphb-toolkit staphb-toolkit 1.2.0, 1.3.10 [1,621] biology
STAR star 2.7.5c, 2.7.6a, 2.7.9a [1,622] biology, ngs, rna-seq
STAR-CCM+ starccm+ 14.04.011, 15.02.009, 8.06 [1,623] mechanical Engineering
STAR-Fusion star-fusion 1.1.0, 1.3.1, 1.9.1 [1,624] biology, transcriptome
starseqr starseqr 0.6.7 [1,625] phylogenetics
Stata stata 10.1, 13 [1,626] statistics
stringMLST stringmlst 0.4 [1,627] biology, CHiP-Seq
Stringtie stringtie 1.3.4d, 2.0.4, 2.1.3b [1,628] biology, ngs, sequencing,alignment
Structure structure 2.3.3, 2.3.4 [1,629] biology,bioinformatics,population genetics
Structure_threader structure_threader 1.3.10 [1,630] utility, Wrapper, Structure
stylegan3 stylegan3 20211028 [1,631] aI, Image Processing
SU2 su2 7.0.6 [1,632] phylogenetics
Subread subread 1.6.2, 2.0.0, 2.0.3 [1,633] biology, sequencing, SNP
Subversion subversion 1.9.7 [1,634] revision Control
SUMO sumo 1.13.0, 1.2.0, 1.9.2 [1,635] phylogenetics
SUNDIALS sundials 2.3.0, 2.5.0, 3.0.0 [1,636] math, Numerical Solvers
supercell supercell 20170602 [1,637] biology, ngs
SuperCRUNCH supercrunch 1.2.1 [1,638] phylogenetics
Supernova supernova 1.2.1, 2.0.0, 2.1.1 [1,639] biology, phylogenetics, ngs
SUPPA suppa 2.3 [1,640] phylogenetics
Survival_Kit survival_kit 6.12 [1,641] clinical Biometrics
SURVIVOR survivor 1.0.6 [1,642] phylogenetics
SVDetect svdetect 0.8b [1,643] biology,ngs,genomics
svim svim 1.4.2 [1,644] biology
svim-asm svim-asm 1.0.2 [1,645] biology
swarm swarm 1.2.11 [1,646] data Analysis
Sweed sweed 3.3.2 [1,647] biology, phylogenetics
SWIG swig 2.0.9, 3.0.12, 3.0.8 [1,648] library, development, C++, python
SWSC-EN swsc-en 1.0.0 [1,649] phylogenetics
Synima synima 20210908 [1,650] phylogenetics
syri syri 1.5.4 [1,651] genomics, biology
TACO taco 0.7.3 [1,652] phylogenetics
Taiyaki taiyaki 5.0.1 [1,653] phylogenetics
talesf talesf 20160814 [1,654] phylogenetics
Tandem-Genotypes tandem-genotypes 1.4.0 [1,655] phylogenetics
Tantan tantan 13 [1,656] imaging, ngs, genomics
Tapestri tapestri 2.0.1 [1,657] phylogenetics
tapir tapir 20160825 [1,658] biology, phylogenetics
TAPIS tapis 1.2.1 [1,659] biology, sequencing
TASSEL tassel 5.0, 5.2.20, 5.2.29 [1,660] biology, genomics,wga
TAU tau 2.23, 2.26, 2.26.3 [1,661] library, profiling and optimization
Tax4Fun tax4fun 0.3.1 [1,662] phylogenetics
taxMaps taxmaps 0.1 [1,663] biology, phylogenetics, taxonomy
TaxonKit taxonkit 0.9.0 [1,664] phylogenetics
Taxtastic taxtastic 0.5.7, 0.9.1 [1,665] biology, taxonomy
tbb tbb 2017_20161128 [1,666] library
tcllib tcllib 1.18 [1,667] library
tcoffee tcoffee 10.00.r1613, 9.03.r1318 [1,668] biology
TDNAscan tdnascan 20210304 [1,669] phylogenetics
Tecplot 360 EX tecplot 2015R1 [1,670] plotting, animation, cfd, simulations
tellseq tellseq 1.0.0 [1,671] sequencing, Phylogenetics
TEMP temp 20170731 [1,672] phylogenetics
TEMP2 temp2 0.1.4 [1,673] phylogenetics
TensorFlow ngc-tensorflow 2.6.0, 2.7.0, 2.8.0 [1,674] library, math
TESS tess 2.3.1 [1,675] biology, genomics, markov
Test test 1.0 [1,676] shell
TetGen tetgen 1.5.0 [1,677] tetrahedral meshes
TEToolkit tetoolkit 1.5.1 [1,678] biology, sequencing
TEtools tetools 20180213 [1,679] biology, phylogenetics
Texlive texlive 20191127, 2020 [1,680] formatting, typesetting, document preparataion
TGICL tgicl 2.1 [1,681] biology, ngs, sequencing
TGSGapCloser tgsgapcloser 1.0.3 [1,682] phylogenetics
the_silver_searcher the_silver_searcher 2.2.0 [1,683] search
Theano theano 1.0.4 [1,684] library, math, gpu
Themisto themisto 0.2.0, 1.1.0 [1,685] genomics, Alignment
Tiara tiara 1.0.2 [1,686] phylogenetics
tiff tiff 3.8.0, 4.0.10 [1,687] imaging
Tigmint tigmint 1.1.2 [1,688] phylogenetics
Tmux tmux 2.9, 3.1 [1,689] gNU
TNTBLAST tntblast 2.04 [1,690] biology
ToFU2 tofu2 v17 [1,691] biology, ngs, sequencing
toil toil 3.3.0, 3.3.3 [1,692] biology
Tombo tombo 1.4, 1.5, 1.5.1 [1,693] biology, genomics, ngs
Tophat tophat 2.1.0, 2.1.1, 2.1.2 [1,694] biology, ngs, sequencing
torch-geometric torch-geometric 1.3.2 [1,695] phylogenetics
TotalView totalview 8.12 [1,696] parallel Computing
TPMcalculator tpmcalculator 0.0.3 [1,697] phylogenetics
TPP tpp 4.7.0, 4.7.1, 5.0.0 [1,698] biology, chemistry, nmr
TraCeR tracer 20160519 [1,699] biology, phylogenetics
TrackTools tracktools 2011 [1,700] software
TrackVis/DTK trackvis 0.5.2.2, 0.6.0.1 [1,701] biology, neuroscience, imaging
Tracula tracula 5.3.2014_05_26 [1,702] biology, neuroscience, imaging
traitRate traitrate 1.1 [1,703] biology, evolution
Trans-ABySS transabyss 2.0.1 [1,704] biology, phylogenetics
TransDecoder transdecoder 5.3.0, 5.4.0, 5.5.0 [1,705] biology, ngs
TRANSIT transit 2.5.2, 3.2.3 [1,706] phylogenetics
Transrate transrate 1.0.1 [1,707] biology,assembly
TransVar transvar 2.3.3 [1,708] biology, phylogenetics
TreeBreaker treebreaker 20160621 [1,709] biology, phylogenetics
TreeMix treemix 1.12 [1,710] biology, phylogenetics
treePL treepl 20150305 [1,711] biology, phylogenetics
TREEPUZZLE treepuzzle 5.3 [1,712] biology, phylogenetics
TreeShrink treeshrink 1.3.1, 1.3.2 [1,713] phylogenetics
TreeTime treetime 0.7.5, 0.8.1 [1,714] phylogenetics
trelis trelis 16.3 [1,715] geometry
TRF trf 4.04, 4.09.1 [1,716] biology, genomics
Trilinos trilinos 12.12.1, 12.18.1, 12.6.4 [1,717] mathematical Algorithms
Trim Galore trim_galore 0.4.4, 0.5.0, 0.6.5 [1,718] biology, ngs
trim_isoseq_polya trim_isoseq_polya 0.0.3 [1,719] biology, Genetics, Sequencing
trimAl trimal 1.2 [1,720] biology, genomics,sequence alignment
TriMetAss trimetass 1.1 [1,721] biology, ngs
Trimmomatic trimmomatic 0.33, 0.36, 0.39 [1,722] biology, ngs
Trinity trinity r20130225, r20131110, r20140413 [1,723] biology, ngs, sequencing, rna-seq
Trinotate trinotate 3.0.1, 3.2.0 [1,724] biology
triobinning triobinning 0.2.3 [1,725] genomics, biology
TRIPLEC triplec 1.0 [1,726] biology
TRITONSERVER tritonserver 21.08 [1,727] machine_learning Inference Server
tRNAscan-Se trnascan-se 1.23 [1,728] biology, ngs
TRUST4 trust4 1.0.2b [1,729] phylogenetics
Trycycler trycycler 0.4.2 [1,730] phylogenetics
TURBOMOLE turbomole 7.4.1 [1,731] chemistry
TWINSCAN twinscan 4.1.2 [1,732] biology, genomics
Ubuntu ubuntu 20.04, 22.04 [1,733] ubuntu Linux
UCSC ucsc 20200320, 20210803 [1,734] genomics
ucsc-fafiltern ucsc-fafiltern 377 [1,735] phylogenetics
ucsc-maskoutfa ucsc-maskoutfa 377 [1,736] phylogenetics
UCX ucx 1.11.2, 1.9.0 [1,737] parallel Programming, development, library
UDUNITS udunits 2.2.17 [1,738] library, data_science, units
ufraw ufraw 0.22 [1,739] data_mining
ugtm ugtm 1.1.6 [1,740] statistics, modeling
UKFractography ukfractography 20200127 [1,741] phylogenetics
umi-tools umi-tools 0.5.5 [1,742] phylogenetics
UNAFold unafold 3.8 [1,743] biology, genome, RNA, folding
Unanimity unanimity 20171108, 3.4.1 [1,744] programming,library,cpp
UNCALLED uncalled 2.2 [1,745] biology, genomics
Unicycler unicycler 0.4.8 [1,746] phylogenetics
Unrar rar 0.0.1, 4.20 [1,747] unarchiver, utility
uproc uproc 1.2.0 [1,748] biology, genome
uropa uropa 4.0.2 [1,749] genomics, sequencing, biology
USEARCH usearch 9.0.2132, 9.1.13, 9.2.64 [1,750] biology, alignment, sequencing
UShER usher 0.1.4, 0.4.1, 0.5.2 [1,751] phylogenetics
V-Phaser vphaser2 02112013 [1,752] biology, phylogenetics
v-pipe v-pipe 2.0.0 [1,753] biology, genomics, sequencing, virus
VAIR vari 0.7.0 [1,754] geospatial Data Modeling
Valgrind valgrind 3.11.0, 3.15.0, 3.8.1 [1,755] computer Programming
Valouev valouev 20160325 [1,756] biology, phylogenetics
vamb vamb 3.0.2 [1,757] biology
VAMPIR vampir 9.1 [1,758] high Performance Computing
VarDictJava vardictjava 1.6.0, 20160521, 20170531 [1,759] biology, phylogenetics
varnorm varnorm 0.21 [1,760] biology
VarScan varscan 2.3.6 [1,761] biology, ngs
VarSim varsim 0.8.4, 0.8.6 [1,762] phylogenetics
VarSimLab varsimlab 20180220, 20180921 [1,763] biology, simulation, genomics
vasp vasp 5.4.4, 6.1.0, 6.2.0 [1,764] chemistry
vaspkit vaspkit 1.2.5 [1,765] phylogenetics
VAST-TOOLS vast-tools 2.5.1, 20150506 [1,766] biology, rna-seq, ngs, splicing
VCF-kit vcf-kit 0.2.6 [1,767] phylogenetics
vcf-validator vcfvalidator 0.6 [1,768] biology, phylogenetics
vcfanno vcfanno 0.2.8, 0.3.3 [1,769] biology, phylogenetics
vcflib vcflib 1.0.1 [1,770] biology, genomics
vcftools vcftools 0.1.15, 0.1.16, 0.1.9 [1,771] biology, genomics
vcontact vcontact 20190512 [1,772] phylogenetics
VDJtools vdjtools 1.1.7, 1.2.1 [1,773] biology, phylogenetics
Velvet velvet 1.2.10, 1.2.10-long [1,774] biology, genomics
VEP vep 83, 88.8, 92 [1,775] biology, genomics, ngs
Vermouth-martinize vermouth-martinize 0.7.2 [1,776] phylogenetics
VeryFastTree veryfasttree 3.0.1 [1,777] phylogenetics
vg vg 1.33.0, 1.38.0, 1.39.0 [1,778] phylogenetics
vibrant vibrant 1.2.0 [1,779] genomics, virus
ViennaRNA viennarna 2.2.6, 2.4.18 [1,780] biology, RNA-seq
ViewBS viewbs 0.1.10, 0.1.9 [1,781] phylogenetics
Vim vim 8.1.1566, 8.2.2465 [1,782] programming,scripting,language
viralmsa viralmsa 1.1.10, 1.1.12 [1,783] phylogenetics
VirSIeve virsieve 20210406 [1,784] biology, Pipeline
VirtualCell virtualcell 7.1 [1,785] phylogenetics
VIRULIGN virulign 1.0.2 [1,786] phylogenetics
VirusDetect virusdetect 1.7 [1,787] phylogenetics
VirusFinder virusfinder 2.0 [1,788] biology, phylogenetics
visit visit 2.13.3, 3.0.1, 3.1.4 [1,789] visualization, Animation and Analysis
VISPR vispr 0.4.14 [1,790] phylogenetics
VMD vmd 1.9.1, 1.9.3 [1,791] visualization, animation, 3d
vscode vscode 1.38.1, 1.65.2 [1,792] programming
VSearch vsearch 20151022, 20161209-2.3.4 [1,793] biology,NGS
vt vt 0.57721, 20140903, 20160129 [1,794] biology, genomics
VTC vtc 0.9.3 [1,795] biology, VCF
VTK vtk 8.2.0, 9.0.3, 9.1.0 [1,796] biology, neuroscience, imaging
w2rap-contigger w2rap-contigger 20161124 [1,797] biology, genomics
Wannier90 wannier90 1.2, 2.1.0 [1,798] computational Physics
WarpedLMM warpedlmm 0.21 [1,799] modeling
WaveGAN wavegan 20190829 [1,800] machine_learning, Audio, GAN, Synthesis
WDSSII wdss2 5 [1,801] weather, Meteorology
WebLogo weblogo 2.8.2, 3.3, 3.5.0 [1,802] biology,bioinformatics,sequence,graphics
Weka weka 3.8, 3.8.5 [1,803] statistics,machine learning
Wengan wengan 0.2 [1,804] biology, genomics
wgd wgd 1.1.1 [1,805] phylogenetics
WGS Assembler wgs 8.3rc1.r4638, 8.3rc2 [1,806] biology, genomics
Wgsim wgsim 0.3.1-r13 [1,807] biology, phylogenetics
WHAMM whamm 0.14a [1,808] biology, phylogenetics
WhatsHap whatshap 1.1 [1,809] biology, phylogenetics
whiteboxtools whiteboxtools 1.5.0 [1,810] phylogenetics
Wine wine 4.0.0, 7.0.0 [1,811] windows, emulator
Wise wise 2.2.0, 2.4.1 [1,812] biology, genome
WIsH wish 1.0 [1,813] phylogenetics
WoLFPSort wolfpsort 0.2 [1,814] phylogenetics
WOMBAT wombat 20180118 [1,815] biology, phylogenetics
workbench workbench 4.1.1 [1,816] modeling, simulation
wtdbg wtdbg 2.1, 2.4, 2.5 [1,817] phylogenetics
WU BLAST wublast 2.0 [1,818] biology
Wub wub 0.2.0, 0.4.0 [1,819] biology, genomics, ngs
xander xander 20151222 [1,820] biology, phylogenetics
Xapian xapian 1.4.4 [1,821] library
XCrySDen xcrysden 1.5.60 [1,822] computational Material Science
Xerces xerces 3.1.4 [1,823] phylogenetics
xesmf xesmf 0.6.2 [1,824] grid Analysis, Climate
xpclr xpclr 1.0, 1.1.1 [1,825] phylogenetics
Xterm xterm 1.1 [1,826] utility
XWAS xwas 3.0 [1,827] phylogenetics
XY-Meta xy-meta 20200413 [1,828] phylogenetics
XZ xz 5.2.2 [1,829] compression, library
YAGO yago 4 [1,830] data
YAHA yaha 0.1.82 [1,831] biology, ngs
YAK yak 0.1 [1,832] phylogenetics
YASM yasm 1.3.0 [1,833] computer Programming
YASRA yasra 2.33 [1,834] biology, ngs, sequencing
yolov4_darknet yolov4_darknet 4-pre [1,835] machine_learning
yolov5 yolov5 4.0 [1,836] machine_learning
Zagros zagros 1.0.0 [1,837] biology,phylogenetics
ZEO++ zeo++ 0.2.2 [1,838] chemistry
zorro zorro 2.2 [1,839] biology, sequencing
Zstd zstd 1.5.0 [1,840] phylogenetics
ZUMIS zumis 2.6.0 [1,841] biology, ngs, sequencing
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