Difference between revisions of "Applications"

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Revision as of 19:58, 6 July 2022

Note: Up to three latest versions are listed even though there could be more available. Run module spider name for a full list of provided versions.

Name Versions URL Description 3d-dna 20170330 [1] biology, phylogenetics 3PCLR 20150906 [2] biology, phylogenetics 4p 1.0 [3] biology, variant_calling AAFTF 0.2.5 [4] biology, pipeline, assembly ABRicate 1.0.1 [5] phylogenetics ABruijn 1.0 [6] biology, assembly, ngs ABySS 1.5.2, 2.1.0, 2.2.5 [7] biology, de_novo AdapterRemoval 2.2.2 [8] phylogenetics ADFRsuite 1.0 [9] sequencing, biology ADMB 11.5, 12.0 [10] math, modeling AdmixTools 20150311, 7.0.2 [11] biology, genomics, ngs ADMIXTURE 1.23, 1.3.0 [12] biology, genomics, ngs AEGeAn 0.14.0, 0.16.0 [13] biology, genomics AFNI 20.3.00, 2018_04_12 [14] biology, neuroscience, imaging AfterQC 0.9.7 [15] phylogenetics AGAT 0.4.0 [16] phylogenetics AGfusion 1.252 [17] phylogenetics Albacore 2.3.1, 2.3.3 [18] biology, phylogenetics Albumentations 1.0.3 [19] ai, image_processing, imaging Alder 1.03 [20] biology, genomics ALFA 1.1.1 [21] phylogenetics alienhunter 1.7 [22] biology, sequencing AliStat 1.12 [23] phylogenetics allhic 0.9.8 [24] genomics, biology ALLMAPS 20180117 [25] biology, phylogenetics ALLPATHS-LG 42316, 44837, 49232 [26] biology, ngs AlphaFold 2.0.0, 2.1.2, 2.2.0 [27] protein, structure, machine_learning Alphaimpute 0.0.2, 1.9.8.2, 1.9.8.3 [28] phylogenetics AltAnalyze 2.1.0 [29] biology, genomics AMAS 1.0 [30] phylogenetics AMBER 16.0, 18, 20 [31] chemistry, molecular_dynamics AMICO 1.0.1 [32] library, imaging, math AMOS 3.1.0 [33] biology, genomics, assembly AMP 0.6.1 [34] phylogenetics amPEPpy 1.0 [35] phylogenetics amphora2 20140305 [36] biology, phylogenetics AMPtk 1.2.4, 1.5.1 [37] biology, ngs amptorch 20210313 [38] phylogenetics amrfinderplus 3.10.18 [39] phylogenetics AMRPlusPlus 20180508 [40] phylogenetics AMUSE 10.0, 13.1.0 [41] astronomy ANGSD 0.933 [42] biology, ngs annocript 2.0 [43] phylogenetics AnnoTALE 1.4.1 [44] phylogenetics ANNOVAR 20130221, 20150322, 20191024 [45] biology, genomics Ansible 2.5.5, 2.8.1 [46] workflow_automation ansysem 17.0, 2022r1 [47] physics antiSMASH 4.1.0, 6.0.1 [48] phylogenetics ANTs 2.2.0, 2.3.4 [49] biology, phylogenetics anvio 6.1, 6.2, 7.1 [50] biology Appreci8 20180530 [51] biology, genomics Apptainer 1.0.3 [52] workflow_automation APT 1.15.0, 1.18.0, 1.20.5 [53] biology, genomics ARC 1.1.4 [54] biology, ngs Aria2 1.35.0 [55] utility ARKS 1.0.2 [56] phylogenetics Armadillo 7.900.0, 9.200.6, 9.900.4 [57] library, compiler, math ARPACK 1.0 [58] math ArrayFire 3.4.2 [59] math arriba 2.1.0 [60] phylogenetics ART 20160417, 20160605 [61] phylogenetics artemis 18.1.0 [62] biology asap 2.0 [63] visualization, biology asaq 1.0 [64] alignment, sequencing, phylogenetics ASE-ANI 20180712 [65] biology, genomics, ngs ASHS 2.0 [66] biology, imaging ASPECT 2.3.0 [67] library Assembly-stats 1.0.1 [68] biology, sequencing, genomics Assemblytics 1.2.1 [69] phylogenetics Assexon 20190814 [70] phylogenetics AStalavista 3.2, 4.0 [71] biology, genomics aster 220718 [72] biology, data_science, sequencing ASTRAL 5.6.1, 5.6.2, 5.7.7 [73] biology, ngs, phylogenetics ASTRID 2.2.1 [74] phylogenetics Astropy 2.0.8 [75] biology, phylogenetics ATAT 3.23, 3.34 [76] material_science ATLAS 3.10.1, 3.10.2, 3.11.17 [77] library, data_science Atom 1.57.0 [78] programming AtomEye 3 [79] material_science AtomMan 1.3.3 [80] phylogenetics aTRAM 2.2.0, 2.4.3 [81] math Augustus 3.3.2, 3.3.3, 3.4.0 [82] biology, genomics Auto3DEM 4.05.2 [83] image_processing AutoDock 4.2.6 [84] biology AutoDock-GPU 1.5.3 [85] chemistry Autometa 20190802 [86] phylogenetics automlsa2 0.8.1 [87] phylogenetics, biology, genomics AWSCLI 2.2.30 [88] utility azoo 1.3.1 [89] phylogenetics Badread 0.1.5 [90] phylogenetics bakta 1.3.3 [91] genomics, biology BALi-Phy 3.4.1, 3.5.0 [92] phylogenetics BAM-matcher 20161021 [93] phylogenetics Bam-Readcount 20150616 [94] biology, genomics bamaddrg 20120326 [95] phylogenetics BamBam 1.0 [96] biology, genomics bamm 2.5.0 [97] phylogenetics bamsnap 0.2.19 [98] phylogenetics Bamstats 20140602 [99] biology, ngs Bamsurgeon 1.2 [100] phylogenetics bamtofastq 1.3.5 [101] phylogenetics Bamtools 2.4.1, 2.5.0, 2.5.1 [102] biology, ngs, sequencing bamUtil 1.0.2 [103] biology, genomics BAPS 6.0 [104] biology, genomics Barrnap 0.7, 0.9 [105] biology, rna-seq Basemount 0.15.96 [106] biology, sequencing BatMeth2 20210720 [107] biology, genomics, mapping bax2bam 0.0.9 [108] phylogenetics BayArea 1.0.2 [109] biology BAYENV 2.0 [110] biology, phylogenetics BayesAss 3.0.4, 3.0.4.2 [111] phylogenetics BayeScan 2.1 [112] biology, variant_calling BayesR 20151016 [113] biology, phylogenetics BayesTraits 3.0.2 [114] phylogenetics baypass 2.1 [115] biology, phylogenetics BBMap 38.26, 38.44, 38.90 [116] biology, alignment bcftools 1.15, 1.3.1, 1.9 [117] biology, ngs bcl2fastq 2.16.0.10, 2.20.0.422 [118] biology, ngs BDG-SeQuila 0.5.5 [119] phylogenetics BEAGLE 4.1, 5.0, 5.2 [120] biology, genomics BEAR 20170209 [121] biology, genomics BEAST 2.6.2, 2.6.3, 2.6.7 [122] biology, phylogenetics BEAST2-XML 1.0.9 [123] phylogenetics BEDOPS 2.4.30 [124] biology, sequencing, ngs BEDTools 2.29.1, 2.29.2, 2.30.0 [125] biology, ngs Bertini 1.6 [126] math BERTopic 0.7, 0.8.1 [127] machine_learning BESST 2.2.4 [128] biology, ngs BFAST 0.7.0 [129] biology, ngs bgenix 1.1.7 [130] data_science, genomics Bifrost 0.2, 1.0.3, 20200225 [131] phylogenetics BiG-SCAPE 1.1.2 [132] biology, genomics, phylogenetics, pipeline BinPacker 1.0 [133] biology, rna-seq, assembly BinSanity 0.2.6.4 [134] biology, genomics Bioawk 1.0 [135] phylogenetics bioBakery 0.15.1, 1.8, 3.0.0 [136] phylogenetics Biodiverse 2.1 [137] phylogenetics Biolite 0.3.5.1 [138] biology, genomics, variant_calling BIOM 2.1.5, 2.1.6 [139] biology, genomics BIOMART 1.4 [140] biology, genomics Biopieces 2.0 [141] phylogenetics BIRDS 1.0 [142] workflow_automation, utility, imaging Bismark 0.22.3, 0.7.4, 0.7.7 [143] biology, ngs Blackfynn 0.2.7 [144] data_mining BLASR 20130815, 20161215 (5.3), 5.3.2 [145] biology, ngs Blast2GO 2.5.0-20120705 [146] biology, genomics Blast2GO CLI 1.3.3 [147] biology, genomics BLAT 20121105, 20140318 [148] genomics blender 2.73, 2.77, 3.0.1 [149] graphics blink 0.01 [150] genomics Blitz 0.10 [151] library BlobTools 1.0, 2.2 [152] phylogenetics bloomfiltertrie 0.8.7 [153] phylogenetics BloomTree 0.3.5 [154] data_mining BLUPF90 20160604, 20180301, 20190531 [155] biology, phylogenetics BMGE 1.12 [156] biology, genomics, phylogenetics bmtagger 3.101 [157] genomics, biology BOLT-LMM 2.3.4 [158] phylogenetics BoltzTraP 1.2.5 [159] physics Boost 1.71.0, 1.75.0, 1.77.0 [160] programming,library,cpp booster 0.1.2 [161] phylogenetics Bowtie 1.1.1, 1.2.0, 1.2.3 [162] biology, ngs, sequencing Bowtie2 2.3.5.1, 2.4.2, 2.4.5 [163] biology, ngs, sequencing BoxCLI 2.9.0 [164] file_management, web, programming BPGA 1.2 [165] biology, ngs BPP 4.1.4, 4.3.8, 4.4.1 [166] biology, phylogenetics Bracken 1.0.0, 2.5 [167] biology, phylogenetics BrainIAK 0.11 [168] imaging braker 2.1.2, 2.1.5, 2.1.6 [169] phylogenetics BRANCH 1.8.1 [170] biology, ngs, mapping BRATNextGen 20150505 [171] biology, genomics BreakDancer 1.4.5 [172] biology, phylogenetics breakseq 2.2 [173] biology, phylogenetics Brewery 20191205 [174] phylogenetics Bridger 20141201 [175] ngs, genomics, biology BRIG 0.95 [176] biology, genomics BRM 0.3 [177] phylogenetics Bruker2nifti 1.0.4 [178] phylogenetics Bsmap 2.87 [179] biology, ngs Bsoft 1.9.1 [180] biology, image_processing BSseeker2 2.1.0, 2.1.8 [181] biology, phylogenetics bubbleparse 20140314 [182] biology, phylogenetics BUCKy 1.4.4 [183] biology, phylogenetics BUSCO 4.0.6, 4.1.4, 5.2.0 [184] biology, genomics BWA 0.7.7, 0.7.8, 0.7.9a [185] biology, ngs bwa-mem2 2.2.1 [186] phylogenetics BWA-PSSM 0.5.11 [187] phylogenetics bxh_xcede_tools 1.11.1 [188] biology BYOBU 5.133, 5.92 [189] shell bzip2 1.0.6 [190] utility, library c-wap 20220624 [191] sequencing, genomics, biology Cactus 2.0.3, 2.0.5 [192] phylogenetics CAFE 4.1, 5.0.0 [193] biology, phylogenetics came 0.0.1 [194] phylogenetics Camino 20140723 [195] biology, neuroscience, imaging CAMP 1.0.0 [196] biology, sequencing Cantera 2.1.1 [197] biology, physics Canu 1.9, 2.0, 2.1 [198] biology, sequencing CANVAS 1.40.0.1613 [199] phylogenetics CAP3 20120705 [200] biology, assembly Capnp 0.5.3 [201] compiler CARTA 2.0 [202] image_processing CASAVA 1.8.2 [203] biology, ngs CASM 0.2.0 [204] physics CasOFFinder 2.4 [205] phylogenetics Catch 1.4.0 [206] biology, genomics, sequencing CAVIAR 20171218 [207] biology, phylogenetics CBGpipe 20190702 [208] phylogenetics CCMetagen 1.4.0 [209] phylogenetics CD-HIT 4.6, 4.6.4, 4.6.8 [210] biology, genomics CDBFasta 20181005 [211] phylogenetics CDNA_Cupcake 20180629, 22.0.0, 9.0.1 [212] biology, ngs, sequencing CDO 1.7.2rc3, 1.9.4 [213] climate CellProfiler 3.1.9, 4.1.3 [214] phylogenetics CellRanger 6.0.1, 6.1.2, 7.0.0 [215] biology, ngs, rna-seq CellRanger-ARC 2.0.1 [216] biology, ngs, rna-seq CellRanger-ATAC 1.2.0 [217] biology, ngs, rna-seq CellRanger-DNA 1.0.0, 1.1.0 [218] biology, ngs, rna-seq, genomics Centrifuge 1.0.3, 1.0.4b [219] biology, phylogenetics CFITSIO 3.370 [220] library, compiler CGAL 4.10, 4.9, 5.02 [221] library, math CGATools 1.6.0.43 [222] biology, ngs cgmaptools 0.1.1, 0.1.2 [223] phylogenetics CGView 1.0.2 [224] phylogenetics CHARMM 36a3, 43b2 [225] chemistry, simulation ChartDirector 5.1.0 [226] library, data_science CheckM 1.0.4, 1.0.7, 1.1.2 [227] biology, genomics Chimera 1.12 [228] biology, modeling Chipyard 1.0 [229] design Chromeister 1.5a [230] biology, genomics ChromEvol 2.0 [231] biology, ngs CIMS 4.1.2 [232] biology, genomics CIRCexplorer 1.1.10 [233] biology, rna-seq CIRCexplorer2 2.3.5, 2.3.8 [234] phylogenetics Circlator 1.5.5 [235] phylogenetics Circleator 1.0.2 [236] phylogenetics circompara2 0.1.2.1 [237] phylogenetics Circos 0.63-pre11, 0.69-2, 0.69-9 [238] biology, genomics, ngs CIRI 2.0.6 [239] phylogenetics ciriquant 1.1.2 [240] phylogenetics CisGenome 2.0 [241] biology, genomics cisTEM 1.0.0 [242] phylogenetics Clairvoyante 1.02 [243] phylogenetics Clann 3.2.3 [244] biology, phylogenetics clara v4.0 [245] ai, machine_learning CLARK 1.2.2-b, 1.2.3 [246] biology, genomics CLHEP 2.2.0.1 [247] physics CLIFinder 4.1 [248] biology, phylogenetics ClinicaDL 1.0.4 [249] biology, imaging, machine_learning clipkit 1.3.0 [250] genomics, biology CLIPper 2.1.0 [251] phylogenetics CLIPSeqTools 0.1.7 [252] biology, sequencing ClonalFrame 1.1, 1.2 [253] biology, ngs, phylogenetics ClonalFrameML 1.0, 1.11 [254] biology, ngs, phylogenetics CloudCompare 2.10.3 [255] visualization Clover 2.0 [256] biology, genomics, assembly CLUMPP 1.1.2 [257] biology ClustalO 1.2.0 [258] biology, alignment ClustalW 2.1 [259] biology, alignment cluster3 1.52a [260] biology, genomics Clview 20130402 [261] biology CMake 3.19.1, 3.21.3 [262] programming CMS 20170518 [263] biology CMWP 140518 [264] biology, genomics CNCI 20180305 [265] phylogenetics CNSpipeline 20170827 [266] phylogenetics CNV-Seq 20110715, 20140812 [267] biology, genomics CNV-Sim 0.9.2 [268] biology, phylogenetics CNVkit 0.9.6 [269] phylogenetics CNVnator 0.3.2 [270] biology, genomics cobra-tf 0.1 [271] fluid_dynamics CodonPhyML 20150303 [272] phylogenetics Coevol 1.3c, 1.4b, 1.6 [273] biology, phylogenetics Cogent 2.1 [274] biology, phylogenetics COLMAP 3.6 [275] modeling CoMap 1.4.1 [276] biology, genomics Comp-D_MPI 1.0 [277] statistics Compacta 1.02 [278] biology, genomics COMSOL 5.4.0 [279] simulation Concaterpillar 1.8a [280] phylogenetics CONCOCT 1.1.0 [281] biology, genomics Conda 4.10.3, 4.12.0 [282] programming CONN 18a [283] imaging CONNECT 20200614 [284] phylogenetics connectomemapper3 3.0.0-rc1 [285] phylogenetics ConPADE 1.0 [286] phylogenetics Conpair 20161010, 20180624 [287] biology, phylogenetics Consed 23.0, 25.0, 29.0 [288] biology, genomics CONSEL 0.20 [289] biology, phylogenetics ContaVect 0.2 [290] biology, phylogenetics Convert3D 1.1.0 [291] imaging, utility Coot 0.9.5 [292] modeling Coreutils 8.23, 8.28 [293] utility Corset 1.06 [294] biology, ngs Counterr 0.1 [295] phylogenetics covNMR 2014 [296] biochemistry cp2k 7.0.0 [297] chemistry CPAT 3.0.2 [298] phylogenetics cpc 2.0 [299] phylogenetics CPLEX 12.6.1, 12.6.2, 12.7 [300] climate Crass 1.0.1 [301] biology, assembly crisflash 1.2.0 [302] phylogenetics CRISP 20181122 [303] phylogenetics CRISPRanalyzer 1.50 [304] biology, genomics, ngs CRISPRCasFinder 4.2.17 [305] phylogenetics CRISPResso2 20220811 [306] genomics, sequencing, biology CrossMap 0.3.9, 0.6.3 [307] biology, genomics crossmapper 1.1.1 [308] phylogenetics Crux 1.40 [309] biology, spectroscopy CryptoMiniSat 5.0.1 [310] math csvtk 0.23.0 [311] biology ctk 1.1.4 [312] biology, genomics CUBE 4.4 [313] library, compiler, math CUDA 11.0.207, 11.1.0, 11.4.3 [314] programming, library, graphics Cufflinks 2.1.1, 2.2.1, 2.2.1.1 [315] biology, ngs, sequencing cupy 8.3.0 [316] phylogenetics cutadapt 1.18, 2.8, 3.4 [317] biology, ngs CutRunTools 20200104 [318] phylogenetics cvbio 3.0.0 [319] phylogenetics CViT 1.3 [320] programming, library CWLtool 1.0.20190906, 2.0.20200126, 3.0.20210124104916 [321] workflow_automation, scheduler cx_oracle 8.3.0 [322] database, utility CycleGan 20201015 [323] phylogenetics Cytoscape 3.4.0 [324] biology, ngs, phylogenetics d2go 20210702 [325] machine_learning, ai dadi 2.1.1 [326] phylogenetics DAKOTA 6.15, 6.8, 6.8-gui [327] math DALIGNER 1.0 [328] biology, phylogenetics dammit 1.0rc2 [329] biology, phylogenetics DASTool 1.1.0, 1.1.2 [330] biology, phylogenetics datamash 1.1.0 [331] math DAWGPAWS 1.0 [332] biology, phylogenetics DCC 0.4.4 [333] biology, ngs Dcmstack 0.6.2 [334] biology, imaging DCMTK 3.6.0 [335] biology, neuroscience, imaging dDocent 2.7.8 [336] phylogenetics DDSCAT 7.3.0 [337] astronomy DDT 18.2, 20.0, 20.2 [338] programming DealII 8.3.0, 9.3.1 [339] library DeconSeq 0.4.3 [340] biology, phylogenetics decontaMiner 1.4 [341] genomics, biology DECX 20180205 [342] phylogenetics DeepARG 1.0.1 [343] phylogenetics deepbgc 0.1.18 [344] phylogenetics Deepcoil 2.0.1 [345] sequencing, biology DeepGS 1.2 [346] phylogenetics DeepLabCut 2.0.7-gpu, 2.1.1, 2.2.1 [347] phylogenetics deepmicrobes 20200219 [348] biology, genomics, machine_learning DeepMReye 01192022 [349] library, biology DeepPicker 20161102 [350] imaging deepTools 2.4.3, 3.1.1 [351] biology, ngs deepvariant 1.4.0 [352] biology, genomics, sequencing, machine_learning deFusion 20200305 [353] phylogenetics Delft3D 7545 [354] physics Delineate 1.2.2 [355] biology, genomics Delly 0.7.5, 0.7.7, 0.7.8 [356] biology, phylogenetics delucs 20220512 [357] sequencing, genomics, machine_learning DeNoGAP 1.0 [358] biology, phylogenetics, ngs DERIVA 1.5.0 [359] phylogenetics deSALT 1.5.6 [360] biology, genomics, sequencing Detectron2 0.4, 0.5, 0.6 [361] library DeTiN 1.7.5.9 [362] imaging, ngs, genomics DEXTRACTOR 1.0 [363] biology, sequencing Diamond 0.9.15, 0.9.34, 2.0.9 [364] biology, genomics diCal2 2.2.0.1 [365] biology, phylogenetics diffReps 1.55.4 [366] biology DISCOVAR de novo 52488 [367] biology, ngs, assembly DiscoVista 20180906 [368] phylogenetics discvrseq 1.3.10 [369] biology, phylogenetics Distruct 2.3 [370] phylogenetics DIYABC 1.0.4.43b, 2.0.3, 2.1.0 [371] biology, phylogenetics DL_POLY 1.9 [372] molecular_dynamics Dlib 19.19 [373] phylogenetics DNA Clust 3.0 [374] biology, genomics DOCK 6.7, 6.8, 6.9 [375] chemistry DoGFinder 20201103 [376] phylogenetics DosageConvertor 1.0.3 [377] biology DOT 2.0 [378] biology, chemistry Doxygen 1.8.3.1 [379] programming, documentation dragmap 1.2.1 [380] phylogenetics, sequencing, biology dragonflye 1.0.12 [381] sequencing, genomics DRAP 1.91 [382] biology, phylogenetics dRep 2.3.2 [383] phylogenetics Dropseq 2.4.0 [384] phylogenetics DS9 7.5, 8.0.1 [385] imaging DScribe 1.2.0 [386] machine_learning dsistudio 20210123 [387] machine_learning DSK 2.1.0, 2.3.0 [388] biology, ngs DSRC 2.0 [389] phylogenetics DSSAT 4.6 [390] simulation DSSP 2.2.1, 3.0.0 [391] molecular_dynamics DSuite 0.4, 0.4-r41 [392] biology, genomics dtiprep 0.1.1 [393] phylogenetics duchamp 1.6.2 [394] phylogenetics dynamicDBG 20181003 [395] phylogenetics Dynare 4.4.3 [396] math ea-utils 1.04.807.18, 1.1.2.537 [397] biology, genomics, ngs EAGLE 2.0 [398] phylogenetics eagle-rc 1.1.1 [399] phylogenetics ECE 1.2 [400] physics EDirect 10.7, 12.2 [401] biology, phylogenetics EDTA 1.9.6 [402] phylogenetics Edyeet 0.1, 0.3 [403] phylogenetics EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [404] biology,bioinformatics,matlab eGene-MVN 0.1 [405] biology, genetics eggNOG-mapper 2.0.1, 2.1.6 [406] phylogenetics EGSnrc 2019 [407] phylogenetics EIGENSOFT 4.2, 5.0.1, 6.0.1 [408] biology Elastix 4.9.0 [409] phylogenetics ELPA 2019.11.001 [410] library, compiler, math elPrep 4.1.4 [411] phylogenetics Emacs 27.2 [412] programming, scripting, language EMAN2 2.22, 2.31 [413] image_processing EMBOSS 6.6.0 [414] biology,bioinformatics Embree 3.6.1 [415] ray, tracing, kernels EMC 9.4.3 [416] monte Carlo Simulations EMMAX 20100307, 20120210 [417] biology, ngs, mapping EnergyPlus 9.3.0 [418] simulation Ensembl Tools 100, 80 [419] biology enTAP 0.6.1.2, 20160416 [420] biology, phylogenetics EPACTS 3.2.6, 3.4.2, 3.4.2.hg38 [421] biology, genomics EpiNano 1.2.0 [422] biology, ngs epiteome 1.0 [423] phylogenetics epoch 4.7.3 [424] astronomy,CCPP eQTLA 1.1 [425] biology, genomics eQtlBma 1.2.2, 1.3.0r20140820 [426] biology, genotyping Erpin 5.5.4 [427] biology, phylogenetics ESOM 1.1 [428] biology, phylogenetics ESPRESSO 6.2.1, 6.4.1, 7.0 [429] quantum,modeling ESPRIT 2009-nogap, 201102 [430] biology,bioinformatics ETE3 3.0.0, 3.1.1 [431] biology, phylogenetics EVidenceModeler 1.1.1 [432] phylogenetics Evigene 20180730, 20200520 [433] phylogenetics EvoLSTM 20220103 [434] biology, Bioinformatics ExaBayes 1.5 [435] phylogenetics Exonerate 2.2.0 [436] biology, genomics ExpansionHunter 4.0.2 [437] biology, genomics ExpansionHunterDenovo 0.9.0 [438] biology, genomics export2graphlan 0.22 [439] statistics, mapping, graphing eXpress 1.3.1, 1.5.1 [440] biology, ngs ezaai 1.0 [441] biology, phylogenetics face_morpher 20190630 [442] phylogenetics face_recognition 1.2.2 [443] phylogenetics fairseq 0.12.2 [444] modeling, ai FALCON 20161027, 20161222, 20190601 [445] biology, ngs, sequencing FALCON_unzip 20161222 [446] biology FAR 2.15 [447] biology, genomics FAST 1.06 [448] biology phylogenetics fast-gep 1.0 [449] phylogenetics Fast-Plast 1.2.6 [450] biology, phylogenetics fast5tools 0.3.1 [451] phylogenetics, biology FASTA 34.26.5, 36.3.6d [452] biology, genomics fastai 2.1.5, 2.6.3 [453] phylogenetics FastANI 1.1 [454] phylogenetics fastchaos 0.1.0 [455] sequencing FastGEAR 20161216 [456] biology, genomics Fastix 0.1.0 [457] biology, ngs FastML 3.0 [458] biology,bioinformatics,phylogenetics Fastp 0.20.0, 0.22.0 [459] biology, ngs FASTphase 1.4.8 [460] phylogenetics FastPlast 1.2.8 [461] phylogenetics fastq-pair 1.0 [462] phylogenetics FastQ-Screen 0.14.0 [463] phylogenetics Fastq-tools 0.8 [464] biology, ngs, FastQC 0.11.4, 0.11.7, 0.9.6 [465] biology, ngs FastqPuri 1.0.7 [466] phylogenetics FastQTL 2.184 [467] phylogenetics FASTRAL-constrained 20211108 [468] phylogenetics fastsimcoal 2.6.0.3, 2.7.0.2 [469] biology, phylogenetics FastSpar 0.0.4 [470] biology, genomics fastStructure 20150112 [471] biology, genomics FastTree 2.1.11 [472] biology,bioinformatics,phylogenetics FastUniq 1.1 [473] biology, phylogenetics Fastx Toolkit 0.0.13.2, 0.0.14 [474] biology,ngs fcGENE 1.0.7, 1.0.7.1 [475] biology, genomics,snp FDSTools 1.2.0 [476] phylogenetics fdupes 1.51 [477] file Management FEELnc 0.1.1 [478] phylogenetics FEniCS 2018.1.0 [479] biology, phylogenetics Ferret 6.82 [480] data Visualization and Analysis, Oceanography, Meteorology FFmpeg 2.1.3, 2.8.3, 4.3.1 [481] audio, Video FFTW 3.3.6, 3.3.7, 3.3.8 [482] library, compiler, math fgbio 0.5.0, 0.7.0 [483] phylogenetics FGMP 1.0.1 [484] phylogenetics FIGARO 1.1.2 [485] phylogenetics Fiji 2.0.0rc59 [486] imageJ Filtlong 0.2.0 [487] biology, phylogenetics 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HTMLDoc 1.8.28, 1.9.3 [681] pdf, docs, html HTSeq 0.11.2 [682] biology, ngs HUMAnN 2.8.1 [683] sequencing, microbial ecology humann2 0.11.2, 2.8.1 [684] phylogenetics hyb 20141126, 20200815 [685] biology, ngs, RNA-Seq HybPiper 1.2, 1.3.1, 2.0.1 [686] biology, phylogenetics HyDe 0.4.3 [687] phylogenetics HyPhy 2.5.4, 2.5.7, 2.5.8 [688] biology,bioinformatics,evolution HYPRE 2.15.1, 2.18.2, 2.19.0 [689] math, Numerical Solvers iAnnotateSV 1.0.6, 1.0.9 [690] biology, phylogenetics iAssembler 1.3.2 [691] biology, assembly ibdne 20150815 [692] biology,ngs icommands 3.3.1 [693] iRods IDBA-MT 1.0 [694] biology,NGS IDBA-UD 1.1.1, 1.1.1-512, 1.1.1-512-mem [695] genomics, phylogenetics IDL 8.3 [696] language, programming, science IDR 2.0.3 [697] phylogenetics IGB 8.4.1 [698] biology, genomics igBLAST 1.5.0, 1.7.0 [699] biology IGoR 1.4.0 [700] phylogenetics iGTP 1.1 [701] biology, phylogenetics IGV 2.3.91, 2.4.16, 2.8.6 [702] biology, ngs, phylogenetics illumina-utils 2.11 [703] phylogenetics 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phylogenetics MMvec 1.0.5, 1.0.6 [986] metabolomics MNEtools 0.22.0 [987] phylogenetics MOABS 1.2.9, 1.3.2, 1.3.4 [988] biology, ngs mobsuite 3.1.0 [989] sequencing, biology MOCCASIN 0.25 [990] phylogenetics MODELLER 9.14, 9.23 [991] biology,bioinformatics,modelling,structure MODELTEST 0.1.2, 0.1.7 [992] biology, phylogenetics Modulus 21.06, 22.03 [993] physics, AI, Neural Network Molden 5.0 [994] molecular, Electronic Structure momi 2.1.19 [995] phylogenetics, biology monai 0.8, 0.8.1, 0.9.0 [996] data Science in Healthcare MONAI label 0.3.2 [997] data Science in Healthcare MongoDB 4.0.3 [998] database Moni 0.2.0 [999] genomics, biology mono 5.18 [1,000] linux, runtime Monolix 4.3.2 [1,001] modeling, pharmacokinetics MOOSE 20200722, 20210726, 20220610 [1,002] physics, simulation Mosaic 1.7.4 [1,003] phylogenetics MOSAIK 2.1.33, 2.2.3, 2.2.30 [1,004] biology,bioinformatics,short read alignment Mosdepth 0.2.3, 0.3.1 [1,005] biology, phylogenetics Mothur 1.38.1, 1.41.3, 1.46.1 [1,006] biology, microbial ecology MotionCor2 1.2.3, 1.3.1 [1,007] motion Correction mOTU 1.1 [1,008] biology, genomics mOTUs 2.5.1 [1,009] phylogenetics MountainSort 0.9.0 [1,010] library MP-EST 1.4 [1,011] biology, ngs, sequencing MPACK 0.8.0 [1,012] library MPB 1.5 [1,013] library, math MPBoot 1.1.0 [1,014] biology, phylogenetics MPFR 3.1.6 [1,015] library, math mpinterfaces 20170613 [1,016] dFT MrBayes 3.2.4, 3.2.5, 3.2.6 [1,017] application, biology, phylogenetics MRIcroGL 20201102, 20210327, 20211006 [1,018] biology, imaging MRIcron 201306, 20161012, 20190911 [1,019] biology, imaging mriqc 0.11.0, 0.16.1, 22.0.1 [1,020] imaging, biology MRtrix 3.0.1, 3.0.3, 3.0rc2 [1,021] biology, imaging ms 20171108 [1,022] phylogenetics ms-dial 4.4.8 [1,023] biology, metabolomics msfinder 3.52 [1,024] biology, Metabolomics mSINGS 20180810 [1,025] phylogenetics MSMC-Tools 20190614 [1,026] phylogenetics msprime 0.7.4 [1,027] phylogenetics MstatX 1.0 [1,028] biology, phylogenetics MSTmap 1.0 [1,029] phylogenetics msvar 1.3 [1,030] biology,bioinformatics,population genetics MTG2 2.15 [1,031] phylogenetics mTR 20210526 [1,032] biology, genomics Mugsy 1.2.3 [1,033] biology, phylogenetics MultiQC 1.12, 1.7 [1,034] biology, CHiP-Seq MUMmer 3.23, 4.0.0beta2 [1,035] biology, genomics MUSCLE 3.8.31 [1,036] biology, alignment MuSE 1.0rc [1,037] phylogenetics Musket 1.1 [1,038] biology, genomics, ngs MuTect 1.1.4, 1.1.7 [1,039] biology, genomics MutSig 1.4, 1.41 [1,040] biology, genomics mvftools 20191124 [1,041] phylogenetics mxnet 22.08 [1,042] data Science in Healthcare MZMine 2.41, 2.52, 2.53 [1,043] biology, spectrometry, NMR NAMD 2.14, 2.14b2, 3.0 Alpha [1,044] molecular_dynamics NANO 2.8.2 [1,045] text Editor nanocomp 1.17.0 [1,046] programming, python, sequencing NanoCount 0.2.1 [1,047] phylogenetics Nanodisco 1.0.3 [1,048] phylogenetics Nanofilt 2.7.1 [1,049] phylogenetics nanolyse 1.2.0 [1,050] genomics, biology NanoPlot 1.30.1 [1,051] phylogenetics Nanopolish 0.11.1, 0.13.2, 20171006 [1,052] biology nanostripper 0.1 [1,053] phylogenetics, biology NanoSV 1.2.0, 1.2.3, 1.2.4 [1,054] biology, genomics NanoVar 1.3.9 [1,055] phylogenetics Napari 0.3.8, 0.4.7 [1,056] phylogenetics NBODY 6 [1,057] astronomy NCBI BLAST+ 2.7.1, 2.8.1, 2.9.0 [1,058] biology NCBI C++ Toolkit 12.0.0, 21.0.0, 7.0.0 [1,059] biology,bioinformatics,NCBI,programming,library,cpp NCBI GenBank Tools 20140130 [1,060] biology,bioinformatics,NCBI,GenBank ncbi-vdb 2.6.3, 2.8.2 [1,061] sRA toolkit library nccl 20.11 [1,062] development, library, communication, nvidia ncftp 3.2.5 [1,063] file transfer NCL 6.1.2, 6.3.0 [1,064] atmosphere Science NCO 4.2.1, 4.4.3 [1,065] data Analysis ncview 2.1.2, 2.1.7 [1,066] data Visualization NECAT 202001019 [1,067] phylogenetics Necklace 1.00 [1,068] biology, phylogenetics NeEstimator 2.1 [1,069] biology, Bioinformatics nemo 1.0.0rc1, 1.0.1, 1.2.0 [1,070] ai, machine_learning neovim 0.2.0 [1,071] editor, text, ide, vim NetCDF 4.3, 4.3.3, 4.4.3 [1,072] data_science, exchange NetCDF-C 4.7.4, 4.8.1, 4.9.0 [1,073] data_science, exchange NetCDF-F 4.4.4, 4.5.3, 4.5.4 [1,074] data_science, exchange NetLogo 5.3.64, 6.1.1, 6.2.0 [1,075] modeling NEURON 7.7.2, 8.0.0, 8.2.1 [1,076] biology, neuroscience Newbler 2.7, 2.8, 2.9 [1,077] biology, ngs,454,assembly,denovo newick-utils 1.6 [1,078] biology, genomics, phylogenetics newick_utils 1.6, 1.7 [1,079] biology, phylogenetics NewTargets 20210215 [1,080] biology NextDenovo 2.4.0 [1,081] phylogenetics Nextflow 21.04.0, 21.10.6, 22.04.5 [1,082] biology, workflow NextGenMap 0.5.5 [1,083] phylogenetics NextPolish 1.3.1 [1,084] phylogenetics Nextstrain 1.16.1 [1,085] phylogenetics nf-core 1.12.1, 2.1 [1,086] biology, workflow NGC CLI 2.10.1 [1,087] Command Line Interface NGmerge 0.3 [1,088] phylogenetics ngmlr 0.2.6, 0.2.7 [1,089] biology, phylogenetics ngs-bits 0.1 [1,090] biology, sequencing NGS-SDK 1.2.4, 1.3.0 [1,091] biology,bioinformatics,ncbi,sdk,library ngscheckmate 1.0 [1,092] phylogenetics ngstools 20150816 [1,093] biology, ngs nilearn 0.7.0, 0.9.0 [1,094] phylogenetics nimare 0.0.5 [1,095] neuroimaging Nipype 1.6.0, 1.7.0, 1.8.0 [1,096] biology, neuroscience, imaging nlp 1.1, 1.2 [N/A] machine_learning nlr-annotator 0.7 [1,097] phylogenetics NLR-Parser 1.0 [1,098] phylogenetics NMRPipe 7.9, 8.2 [1,099] biochemistry NONMEM 7.3.0, 7.4.4 [1,100] modeling nonpareil 3.3.4 [1,101] phylogenetics Novoalign 2.08.02, 3.00.02 [1,102] biology, ngs NOVOPlasty 3.7, 4.2, 4.3 [1,103] phylogenetics nPhase 1.1.3 [1,104] biology,pipeline,phasing,polyploid npScarf 1.7 [1,105] phylogenetics nQuire 20180405 [1,106] phylogenetics Nsight 2022.1 [1,107] gPU, profiler, tools Nsightsys 2022.2.1 [1,108] gPU, profiler, tools nt 20220404 [1,109] sequencing, neuroscience ntEdit 1.2.1 [1,110] phylogenetics nubeamdedup 20200907 [1,111] phylogenetics NucDiff 2.0.3 [1,112] phylogenetics NucleoATAC 0.3.1 [1,113] biology Nullarbor 1.41 [1,114] biology, phylogenetics Numba 0.36.2, 0.43.1, 0.48.0 [1,115] compiler NUPACK 3.2.2 [1,116] phylogenetics nvhpc 11.1, 21.7 [1,117] language, development, library, math, nvidia nVidia HPC Compilers 20.11 [1,118] compilers NWChem 6.8 [1,119] chemistry NxTrim 0.4.1 [1,120] biology, ngs Oases 0.2.08 [1,121] biology,ngs,assembler OCaml 4.02.3 [1,122] language, scripting, development OCOCO 0.1.2.6 [1,123] biology, phylogenetics octave 6.4.0, 7.2.0 [1,124] numerical Computation odgi 0.6 [1,125] phylogenetics Olego 1.1.2, 1.1.5, 1.1.6 [1,126] biology, ngs,rna-seq OmicsBox 1.1.78 [1,127] image_processing OMindel 20180129 [1,128] phylogenetics omniCLIP 0.1.0 [1,129] phylogenetics OMNIVERSE beta211004 [1,130] nVIDIA Omniverse OMSV 1.0.1 [1,131] phylogenetics ONT-Bonito 0.1.5, 0.5.3, 0.6.0 [1,132] phylogenetics ont_fast5_api 2.0.1, 4.0.2 [1,133] phylogenetics ont_tutorial_cas9 20190705 [1,134] phylogenetics open-cravat 2.0.1 [1,135] biology, genomics open3d 0.13.0 [1,136] phylogenetics OPENACC 16.7 [1,137] programming, Accelerator toolkit OpenBabel 2.3.2, 2.4.1, 3.1.1 [1,138] biology OpenBLAS 0.2.20 [1,139] programming,library OpenCL 18.1.0.013 [1,140] phylogenetics OpenCV 4.5.2 [1,141] library OpenFOAM 4.1, 5.0, 8.0 [1,142] computational Fluid Dynamics OpenMM 7.5, 7.5.0, 7.6.0 [1,143] chemistry, molecular_dynamics OpenMPI 4.0.4, 4.0.5, 4.1.1 [1,144] parallel Programming, development, MPI, library OpenNeuro 3.17.4, 3.37.4 [1,145] biology, data OpenPIV-python 0.21.2 [1,146] python, imaging OpenPIV-python-gpu 20190506-gpu [1,147] python, imaging OpenSim 4.3 [1,148] phylogenetics OpenSlide 3.4.1 [1,149] imaging OptiType 1.3.1 [1,150] biology, phylogenetics Orange3 3.3.6 [1,151] data_mining ORCA 4.0.1.2 [1,152] molecular, Electronic Structure OrganellePBA 20180904 [1,153] phylogenetics OrthoFiller 1.1.4 [1,154] phylogenetics OrthoFinder 1.1.10, 2.3.11, 2.5.2 [1,155] biology, ngs Orthofisher 0.1.2 [1,156] biology, Genetics Orthograph 0.6.3 [1,157] orthology Orthologer 2.2.0 [1,158] biology, OrthoMCL 2.0.3, 2.0.7 [1,159] biology, genomics osprey 1.1.0 [1,160] mRS,matlab,neuroscience OTB 5.8.0 [1,161] geospatial Data Modeling p4est 1.1, 2.8 [1,162] library p4vasp 0.3.29, 0.3.30 [1,163] molecular, Electronic Structure p53MH 20020901 [1,164] biology, DNA-sequencing p7zip 9.20.1 [1,165] archiver PacBio 10.2.0.133434, 11.0.0.146107, 7.0.1 [1,166] biology, ngs, pacbio, smrtlink Package-GFE 20150701 [1,167] biology, genomics PALADIN 1.3.1 [1,168] biology, phylogenetics PALES 122 [1,169] physics PAML 4.8a, 4.9a, 4.9h [1,170] biology, phylogenetics Pandaseq 20140808, 20150627 [1,171] biology, ngs, sequencing Pandoc 2.2.2.1 [1,172] converter pangolin 2 [1,173] phylogenetics panseq 3.2.1 [1,174] phylogenetics panX 1.6.0 [1,175] phylogenetics PAPI 5.5.1, 5.7.0 [1,176] programming interface, performance analysis parabricks 3.5.0, 3.7.0 [1,177] phylogenetics parallel 20150122, 20170322 [1,178] shell, process management paralyzer 1.5 [1,179] phylogenetics ParaView 5.4.1, 5.7.0, 5.9.1.1 [1,180] data Analysis ParaView Server 5.10.1 [1,181] data Analysis ParGenes 1.2.0 [1,182] phylogenetics ParlAI 1.3.0, 1.5.0 [1,183] phylogenetics Parsnp 1.2, 1.5.0, 1.6.2 [1,184] biology, phylogenetics PartitionFinder 2.0.0-pre-20160513, 2.1.1-20161205, 2.1.1.0 [1,185] biology,phylogenetics,evolution PASA 2.0.2-r20151207, 2.2.0-r20171013, 2.4.1 [1,186] biology, genomics, ngs Pascal 3.0.0 [1,187] compiler, Programming PASTA 0.2.0, 1.7.8, 20160616 [1,188] biology, sequence alignment PATHd8 1.0 [1,189] biology, phylogenetics pathoscope 2.0.7 [1,190] sequencing, genomics, Biology PATRIC 1.034 [1,191] machine_learning PAUDA 1.0.1 [1,192] biology, ngs, phylogenetics PAUP 4.0a166, 4.0a168, 4.0b10 [1,193] biology, Phylogenetics PB-Assembly 0.0.6, 0.0.8 [1,194] biology, ngs, sequencing,pacbio pbalign 20160921, 20161221 [1,195] biology PBCCS 5.0.0 [1,196] phylogenetics pbcore 1.7.1 [1,197] biology,bioinformatics PBGCpp 1.9.0 [1,198] phylogenetics pbipa 1.8.0 [1,199] phylogenetics, biology PBJelly 15.8.24 [1,200] biology, ngs pbmm2 1.3.0 [1,201] phylogenetics pbrt 20181017 [1,202] phylogenetics pbsmrtpipe 0.63.0 [1,203] biology,API pbtranscript-tofu 20150317, 20160119 [1,204] biology, ngs, pacbio PCIT 2014 [1,205] biology PCRE 8.38, 8.39 [1,206] programming, library PDA 1.0.3 [1,207] biology, phylogenetics pdb2pqr 2.1.0 [1,208] protein, modeling, pdb PeakSplitter 1.0 [1,209] biology, CHiP-Seq PEAR 0.9.2 [1,210] biology, genomics, ngs peneasy 20150530 [1,211] physics PennCNV 1.0.5 [1,212] phylogenetics Perl 5.16.0, 5.20.0, 5.24.1 [1,213] programming,scripting,language PerM 0.4.0 [1,214] biology, ngs, mapping PETSc 3.8.1, 3.8.3, 3.8.4 [1,215] math, Numerical Solvers PfamScan 1.3, 1.5 [1,216] biology, genomics PGAP 20220414 [1,217] biology, genomics, Annotation, Pipeline PGDSpider 2.0.9.0, 2.1.1.5 [1,218] biology, ngs pggb 0.4.1, 20201106, 20210121 [1,219] phylogenetics PhaME 1.0.3 [1,220] phylogenetics pharmcat 1.8.0 [1,221] biology, Bioinformatics, Phylogenetics PHASE 2.1.1 [1,222] phylogenetics PHAST 1.5 [1,223] biology,phylogeny Phenix 1.10.2155, 1.17.1, 1.8.1069 [1,224] crystallography PHI 3.1.1, 3.1.2b, 3.1.6 [1,225] calculations PhiSpy 3.2 [1,226] phylogenetics PHITS 2.76, 2.82, 2.84 [1,227] physics PHLAWD 20170427 [1,228] biology, phylogenetics PhotoScan 1.4.1, 1.4.5 [1,229] image_processing Photutils 0.5 [1,230] astronomy, photometry PHYLDOG 20130116-dbg [1,231] biology,bioinformatics,phylogenetics PHYling 1.0 [1,232] biology, phylogenetics, Markers, Genomics PHYLIP 3.696 [1,233] biology,phylogenetics PhyloAcc 1.0 [1,234] phylogenetics PhyloBayes 3.3f [1,235] biology,bioinformatics,phylogenetics phyloFlash 3.3b4 [1,236] phylogenetics phylonet 3.5.7, 3.8.2 [1,237] biology, phylogenetics PhyloParser 20180404 [1,238] phylogenetics PhyloPhlAn2 0.41 [1,239] phylogenetics phylopypruner 1.2.3 [1,240] phylogenetics PhyloSift 1.1 [1,241] biology, genomics, phylogenetics, taxonomy phyloTF2 20210726 [1,242] biology, genomics, alignment Phyluce 20180727, 20190308, 20191015 [1,243] biology, ngs, sequencing PhyML 3.0, 3.1 [1,244] biology,bioinformatics,phylogenetics phynd 20200409 [1,245] phylogenetics Physher 1.0.2 [1,246] phylogenetics PHYUTILITY 2.7.1 [1,247] biology Phyx 1.1 [1,248] phylogenetics PIA2 20180305 [1,249] biology, phylogenetics Picard-tools 2.5.0, 2.9.0, 2.9.2 [1,250] biology, ngs PICRUSt 1.1.3, 1.1.4, 2.3.0b [1,251] biology, phylogenetics PICSL 1.3 [1,252] imaging, Atlas, Segmentation Piggy 20171220 [1,253] biology, ngs Pigz 2.4 [1,254] compression PILON 1.22, 1.24 [1,255] biology, ngs, phylogenetics Pindel 0.2.5b8 [1,256] biology, phylogenetics pipe-clip 1.1.0 [1,257] biology,NGS pipits 1.3.6, 1.4.0 [1,258] biology, sequencing Piranha 1.2.1 [1,259] biology,phylogenetics PlantTribes 1.0.4 [1,260] phylogenetics plasflow 1.1 [1,261] biology, phylogenetics PLAST 1.0, 2.3.2 [1,262] biology,bioinformatics platanus 1.2.4 [1,263] phylogenetics Platon 1.6 [1,264] biology, sequencing Platypus 0.8.1 [1,265] biology, ngs PLEK 1.2.2 [1,266] biology, phylogenetics Plink 1.90b3.39, 2.00a2, 2.00a3LM [1,267] biology, genomics,phylogenetics plinkseq 0.10 [1,268] biology, library plotsr 0.5.4 [1,269] genomics, biology PLUMED 2.7.3, 2021.2 [1,270] chemistry, molecular_dynamics pod5 20220621 [1,271] sequencing PolyGembler 1.0 [1,272] phylogenetics PolyPHen 2.2.2.r405b [1,273] biology, genomics polyply 1.3.0 [1,274] phylogenetics, Biology pomoxis 0.1.11, 0.2.5, 0.3.2 [1,275] biology, phylogenetics popcorn 20211104 [1,276] phylogenetics, biology PopLDdecay 3.40 [1,277] phylogenetics popoolation 1.2.2 [1,278] biology, phylogenetics Porechop 0.2.4 [1,279] phylogenetics Poretools 0.6.1 [1,280] phylogenetics portcullis 1.2.3 [1,281] phylogenetics PosiGene 20171113 [1,282] biology, phylogenetics POV-Ray 3.7 [1,283] 3D Graphics pplacer 1.1.alpha19 [1,284] biology, phylogenetics, taxonomy PRANK 170427, 20150803 [1,285] biology, alignment Predector 20201110 [1,286] phylogenetics preplot 14.0.2 [] Preseq 0.0.4 [1,287] biology, ngs PRICE 1.2 [1,288] biology, ngs Primer3 2.3.4 [1,289] biology, genomics primus 1.8.0 [1,290] biology, phylogenetics PRINSEQ 0.20.4 [1,291] biology, sequencing PRINSEQ++ 1.2 [1,292] phylogenetics ProbABEL 0.4.2, 0.4.3, 0.4.5 [1,293] genomics, gwas probalign 1.4 [1,294] biology, ngs Processing 3.4 [1,295] java, language, programming, visual Prodigal 2.6.2, 2.6.3 [1,296] biology, genomics ProDy 2.0 [1,297] phylogenetics Program Database Toolkit 3.20, 3.22, 3.24 [1,298] language, development, performance analysis PROJ 4.9.3, 5.1.0, 8.0.1 [1,299] library, geospatial, cartography Prokka 1.12, 1.14.6 [1,300] biology, genomics, assembly Proovread 1.03rcl, 2.12, 2.13 [1,301] biology, genomics, ngs ProSplign 1.0.0 [1,302] phylogenetics Protege 5.1.0 [1,303] ontology Proteinortho 4.26, 5.11, 5.16 [1,304] biology, genomics ProtExcluder 1.2 [1,305] biology, phylogenetics ProtHint 2.6.0 [1,306] biology, genomics protobuf 2.5.0, 3.5.1 [1,307] google, libraries PROVEAN 1.1.5 [1,308] biology, genomics PRSice 2.3.3 [1,309] phylogenetics Pseudofinder 1.0 [1,310] phylogenetics PsiCLASS 1.0.1 [1,311] phylogenetics PSMC 0.6.5 [1,312] phylogenetics psRobot 1.2 [1,313] phylogenetics Pufferfish 20200417 [1,314] phylogenetics PureCLIP 1.1.1 [1,315] phylogenetics Purge_Dups 1.0.1 [1,316] phylogenetics purge_haplotigs 1.1.2 [1,317] sequencing, biology, biology pyani 0.2.10 [1,318] phylogenetics Pybedtools 0.8.2 [1,319] phylogenetics PyBSASeq 20200623 [1,320] phylogenetics PyCharm 2018.3 [1,321] editor, ide, programming, python pychopper 2.5.0, 2.7.1 [1,322] phylogenetics, sequencing PyCogent 1.9 [1,323] biology, genomics pycoqc 2.5.2 [1,324] Sequencing, data PyDeface 2.0.0 [1,325] imaging pyEGA3 3.4.1 [1,326] biology, genomics, Utility PyEXR 0.3.10 [1,327] programming, python, openexr Pyfaidx 0.5.2 [1,328] biology, ngs, sequencing pyfasta 0.5.2 [1,329] phylogenetics pygot 20170518 [1,330] biology, phylogenetics pyhdf 0.9.0 [1,331] library, hdf4 PyHIST 1.0 [1,332] biology, Histology, Image segmentation PyPHLAWD 20180416, 20190414 [1,333] biology, phylogenetics Pyroms 1.0 [1,334] oceanography PyRosetta r56324 [1,335] biology,structure,modeling pyrpipe 0.0.3 [1,336] phylogenetics Pysamstats 1.1.2 [1,337] phylogenetics PySLURM 18.08.04 [1,338] sLURM Python 3.6.3, 3.6.5, 3.8 [1,339] language, scripting, development Python-core 3.6.5, 3.7, 3.8 [1,340] language, scripting, development Python2 2.7.11 [1,341] language, scripting, development PyTorch 1.11.0, 1.9.0 [1,342] library, math pytorch 1.7.1, 1.8.1, 1.9.0 [1,343] library, math PyVCF 0.6.0, 0.6.8 [1,344] biology, phylogenetics PyVista 0.26.1 [1,345] phylogenetics pyweka 0.3.18 [1,346] phylogenetics QAPA 1.3.1 [1,347] phylogenetics qcat 1.1.0 [1,348] phylogenetics qctool 2.0.1 [1,349] phylogenetics QD 2.3.22 [1,350] library, compiler, math QDD 3.1.2 [1,351] biology, genomics, ngs QGIS 2.18.0, 3.14.0 [1,352] gIS QIIME 1.9.1 [1,353] biology, genomics QIIME2 2021.11, 2021.4, 2022.8 [1,354] biology, genomics QMCPACK 3.4.0 [1,355] library QRNA 2.0.4 [1,356] phylogenetics QT 4.8.3, 5.12.9, 5.15.4 [1,357] uI Framework QTL-seq 2.2.2 [1,358] biology, sequencing, pipeline QTLtools 1.2, 1.3.1 [1,359] phylogenetics Quake 0.3 [1,360] biology, sequencing QualiMap 2.1.2 [1,361] biology,sequence alignment Quantas 1.0.4, 1.0.8, 1.0.9 [1,362] biology, ngs quantisnp 2 [1,363] bioinformatics, genomics QuartetScores 1.0.0 [1,364] phylogenetics QUAST 4.4, 5.0.0, 5.0.2 [1,365] biology, ngs, sequencing, rna-seq quickmerge 0.3 [1,366] phylogenetics Quickquartet 1.0.0 [1,367] biology, ngs QUIP 20201029, 20210626 [1,368] phylogenetics QuorUM 1.0.0 [1,369] biology R 4.0, 4.1, 4.2 [1,370] statistics r-index 20190711 [1,371] phylogenetics r8s 1.8, 1.81 [1,372] phylogenetics RACA 0.9.1.1 [1,373] biology, ngs Racon 1.3.3, 1.4.10, 1.4.13 [1,374] phylogenetics RADICAL 0.2 [1,375] biology, genomics radorgminer 0.9 [1,376] genomics, Biology, Sequencing RaGOO 1.11 [1,377] phylogenetics Ragout 2.3 [1,378] genomics RagTag 1.0.0, 2.0.1 [1,379] phylogenetics rainbow 2.0.4 [1,380] biology, sequencing Rainbowfish 0.1.0 [1,381] phylogenetics RAiSD 2.8 [1,382] phylogenetics Randfold 2.0.1 [1,383] biology, RNA ranger 1.9.3 [1,384] file Management rapidsai 21.10, 21.12, 22.04 [1,385] data Science rapidtide 1.9.0 [1,386] phylogenetics RAPSearch 2.24 [1,387] biology, phylogenetics Rascaf 1.0.2 [1,388] biology RAVE 2.1 [1,389] biology, phylogenetics Raven 1.8.1 [1,390] assembler RAxML 8.2.10, 8.2.12, 8.2.8 [1,391] application, biology, philogenetics RAxML-NG 0.9.0, 1.0.2, 1.1.0 [1,392] phylogenetics razers3 3.5.7 [1,393] biology, phylogenetics rbp-maps 0.1.4 [1,394] phylogenetics rclone 1.57.0, 1.58.1 [1,395] cloud Rcorrector 1.0.4 [1,396] phylogenetics RDKit 2020092 [1,397] chemiformatics rDnaTools 0.1.3 [1,398] phylogenetics READemption 1.0.0 [1,399] phylogenetics REAPR 1.0.18 [1,400] biology, assembly Rebaler 0.2.0 [1,401] phylogenetics reCOGnizer 1.3.3 [1,402] phylogenetics recon 1.08 [1,403] biology,sequencing Redis 2.8.13, 2.8.19 [1,404] daemon, data, server REDItools2 20200701 [1,405] phylogenetics Redundans 0.14a [1,406] biology, phylogenetics ReFrame 3.2 [1,407] hpc, internal regtools 0.5.2 [1,408] biology, RNA-seq, Genitics release 12082021 [1,409] molecular dynamics, deep learning RELION 3.0.2, 3.0b, 3.1.0 [1,410] biology, imaging RelocaTE2 2.0.1 [1,411] phylogenetics REMORA 1.8.2, 1.8.3, 1.8.5 [1,412] system, profiler REPdenovo 20170222 [1,413] biology, phylogenetics RepeatAnalysis 0.10.0, 0.12.2 [] biology, phylogenetics RepeatAnalysisTools 20210506 [1,414] biology, genomics, sequencing, Utility RepeatExplorer 20150506, 20180517 [1,415] biology, ngs RepeatMasker 4.0.5, 4.0.9, 4.1.1 [1,416] biology,bioinformatics RepeatModeler 1.0.8, 2.0 [1,417] biology,bioinformatics repeatscout 1.0.5 [1,418] biology RepeatSeq 0.8.2 [1,419] phylogenetics reptile 1.1 [1,420] biology,NGS,error correction ResFinder 4.0 [1,421] biology, genomics Resistome 20170111 [1,422] phylogenetics RevBayes 1.0.7, 1.0.9, 1.1.1 [1,423] biology, phylogenetics RFMIX 2.03 [1,424] phylogenetics RGAugury 20220107 [1,425] sequencing, biology RGI 4.2.2, 5.1.1 [1,426] phylogenetics RGIS 20180211, 20180814 [1,427] riverGIS RHash 1.3.3 [1,428] gNU RiboCode 1.2.11 [1,429] phylogenetics riboPicker 0.4.3 [1,430] biology,sequence RiboTaper 1.3.1a [1,431] phylogenetics RIGERJ 2.0.2 [1,432] phylogenetics rMATS turbo 4.1.2 [1,433] biology, sequencing, genomics rmats2sashimiplot 2.0.3, 2.0.4 [1,434] phylogenetics Rmpi 0.6.9 [1,435] statistics, R, mpi RNAFramework 2.7.2 [1,436] biology, RNA, Sequencing RNAhybrid 2.1.1 [1,437] biology, genomics RNAmmer 1.2 [1,438] biology, RNA-seq rnaQUAST 1.5.1 [1,439] biology, ngs, sequencing, rna-seq RNAsalsa 0.8.1 [1,440] biology, phylogenetics rnaseqlib 20150721 [1,441] biology, phylogenetics, RNA-seq RNAstructure 6.3 [1,442] biology, sequencing Roary 3.12.0, 3.4.1 [1,443] biology, genomics ROOT 5.34.17, 6.0, 6.06.02 [1,444] data Analysis ROOTPy 20160323 [1,445] data Analysis Rosetta 2014wk4, 2019.35.60890 [1,446] biology,structure,modeling RoseTTAFold 1.0.0 [1,447] phylogenetics rrnaselector 1.0 [1,448] biology, sequencing RSEG 0.4.8 [1,449] biology, genomics RSEM 1.2.31, 1.2.7, 1.3.3 [1,450] biology, ngs, sequencing RSeQC 2.6.4, 3.0.0 [1,451] biology,ngs,rna-seq RStudio 1.4, 2021.09.0, 2022.02.3 [1,452] statistics RTGTools 3.7.1 [1,453] biology, ngs Ruby 2.5.1 [1,454] programming,scripting,language Rust 1.48.0, 1.52.1, 1.62.1 [1,455] programming rvtests 2.1.0 [1,456] genomics, Biology, Sequencing S.A.G.E 6.4.2 [1,457] phylogenetics Sabre 1.0 [1,458] phylogenetics saffrontree 0.1.2 [1,459] phylogenetics Sailfish 0.6.3 [1,460] biology, genomics, ngs, rna-seq Salmon 1.1.0, 1.5.2, 1.8.0 [1,461] biology, RNA-seq SALSA 20171009, 20191001 [1,462] biology, ngs, pacbio Sambamba 0.6.3, 0.6.6, 0.6.9 [1,463] biology, ngs samblaster 0.1.14, 0.1.24 [1,464] biology, ngs, sequencing sampledock 0.5.1 [1,465] molecular dynamics, AI SAMStat 1.08 [1,466] biology, ngs, sequencing Samtools 1.7, 1.8, 1.9 [1,467] biology, ngs, sequencing SAS 9.3, 9.4 [1,468] statistics, data analysis Sate 2.2.7 [1,469] biology, phylogenetics Satsuma 3.0 [1,470] phylogenetics Satsuma2 20161123, 3.1 [1,471] phylogenetics sc-im 0.8.2 [1,472] software, data visualization Scala 2.11.5, 3.0.1 [1,473] programming, language, java Scalablast 2.4.53 [1,474] application, biology, genomics ScaLAPACK 2.0.2, 2.1.0 [1,475] programming,library scallop 0.10.5 [1,476] phylogenetics Scalpel 0.1.1, 0.5.3 [1,477] biology, ngs Schrodinger Suite 2019-3, 2020-4, 2021-2 [1,478] chemistry, molecular_dynamics Scipion 1.2 [1,479] image_processing SCIrun 5.0.Z [1,480] phylogenetics Scoary 1.6.16 [1,481] phylogenetics Scons 2.5.1, 3.1.2 [1,482] programming SCOP 20180311 [1,483] biology, Scaffolding, Assembly Scrappie 1.4.2 [1,484] biology, genomics SCRATCH-1D 1.0, 2.0 [1,485] biology, ngs Screen 4.8.0 [1,486] gNU, Terminal Multiplexer SCRIPTURE 20101211 [1,487] biology, genomics Scythe 0.991 [1,488] biology, ngs sdsl 2.1.1 [1,489] library, c++ SE-MEI 0.1.0 [1,490] phylogenetics SeCaPr 1.1.12, 2.0.2, 2.1.1 [1,491] phylogenetics Segemehl 0.1.9, 0.3.4 [1,492] biology, ngs, sequencing segment-liftover 20211021 [1,493] biology, genomics SEPP 20160614 [1,494] biology, phylogenetics Seq-Gen 1.3.3 [1,495] biology,phylogenetics seq_crumbs 20150120 [1,496] biology, sequence, genomics, utilities SeqKit 0.10.2, 0.8.0, 2.0.0 [1,497] biology, phylogenetics seqmagick 0.8.4 [1,498] biology SeqMap 1.0.13 [1,499] biology, sequencing, ngs SEQPower 1.1.1 [1,500] genomics, phylogenetics SeqPrep 0.5, 1.1 [1,501] biology, ngs, sequencing seqscreen 3.3 [1,502] sequencing, biology seqtk 1.3, 20140729 [1,503] biology, genomics, ngs SEQuel 1.0.1 [1,504] biology, ngs SequelQC 1.1.0 [1,505] phylogenetics seqwish 0.7, 20190509 [1,506] phylogenetics SeqyClean 1.8.10 [1,507] biology, ngs, sequencing SeSiMCMC 4.36 [1,508] biology, sequencing SExtractor 2.19.5 [1,509] astronomy SHAPE-MaP 1.2 [1,510] biology, phylogenetics SHAPEIT 2.12, 2.5 [1,511] biology, variant_calling SHAPEIT4 4.2.2 [1,512] biology, sequencing, phasing ShapeMapper 2.1.3, 2.1.5 [1,513] biology, phylogenetics SHARCGS 1.2.11 [1,514] biology, ngs, de novo assembly Shasta 0.1.0 [1,515] phylogenetics SHEsisPlus 1.0, 1.01 [1,516] biology, genetics shogun 6.1.3 [1,517] phylogenetics Shortbred 0.9.4 [1,518] phylogenetics shovill 1.1.0 [1,519] genomics, sequencing, biology SHRiMP 2.2.3 [1,520] biology, genomics, ngs shustring 2.6 [1,521] biology, sequencing SibeliaZ 1.2.2, 1.2.3, 1.2.4 [1,522] biology, genomics, alignment SICER 1.1 [1,523] biology, ChIP-Seq Sickle 1.200, 1.33 [1,524] biology, ngs Siesta 3.2, 4.1b2, 4.1b3 [1,525] chemistry SIFT 4.0.3b [1,526] biology, genomics SIGffRid 1.1 [1,527] phylogenetics SignalP 4.1c, 5.0b [1,528] biology, phylogenetics SiLiX 1.2.11, 1.3.0 [1,529] phylogenetics silo 4.7 [1,530] iO,library sim4 20121010 [1,531] biology, genomics Sim4Life 7.0.1 [1,532] biology,simulation Simka 1.5.3 [1,533] phylogenetics SimNIBS 3.2.1 [1,534] phylogenetics SimSeq 4.12.2011 [1,535] biology, ngs, phylogenetics Simulia 2019 [1,536] simulation, visualization SInC 20140120 [1,537] biology, phylogenetics sine_scan 1.1.1 [1,538] phylogenetics Singularity 3.7.4 [1,539] workflow_automation SIPeS 2.0 [1,540] biology, ChIP-Seq sisl 0.8.3 [1,541] physics, Tight-binding skmer 3.2.1 [1,542] genomics, biology Slamdunk 0.4.1, 0.4.2 [1,543] phylogenetics SLAW 20211217 [1,544] chromatography, Spectrometry Slicer 4.13.0, 4.3.1, 5.0.3 [1,545] biology, neuroscience, imaging slow5tools 0.5.1 [1,546] biology, sequencing slurm-drmaa 1.1.2, 1.1.3 [1,547] libraries, slurm, api, drmaa smalt 0.7.6 [1,548] application, biology, phylogenetics SMARTdenovo 20180219 [1,549] biology, phylogenetics smartie-sv 20180308 [1,550] phylogenetics SMC++ 1.15.4 [1,551] biology, genomics, sequencing Smetana 1.1.0 [1,552] phylogenetics SMR 1.03 [1,553] biology, genomics SMRT-SV 2.0.0 [1,554] biology, ngs SMS 1.7 [1,555] biology Smudgeplot 0.2.4 [1,556] phylogenetics Snakemake 6.4.1, 7.5.0 [1,557] biology, workflow SNAP 0.15.4, 2.0.0, 20100728 [1,558] biology,bioinformatics,sequencing SNAPE-pooled 20130407 [1,559] biology, variant_calling SNeP 1.1 [1,560] biology,phylogenetics Sniffles 1.0.11, 1.0.6, 1.0.8 [1,561] phylogenetics Sniffles2 2.0.6 [1,562] biology, Bioinformatics Snippy 20160419, 4.6.0 [1,563] biology, phylogenetics SNP-Pipeline 1.0.1 [1,564] biology, phylogenetics SNP-sites 2.0.3 [1,565] biology, variant_calling snp2hla 1.0.3 [1,566] biology, Bioinformatics, Genomics SnpEff 4.3r, 4.3t, 5.0 [1,567] biology,bioinformatics,variant annotation snpflip 20190515 [1,568] biology, phylogenetics SNPGenie 20190620 [1,569] phylogenetics SNPhylo 20140701 [1,570] biology,phylogenetics SNPsplit 0.5.0 [1,571] biology,bioinformatics,sequencing SNPTEST 2.5.2 [1,572] phylogenetics SOAPaligner 2.21 [1,573] phylogenetics SOAPdenovo 1.05, 2.04 [1,574] biology,ngs SOAPdenovo-Trans 1.01, 1.03 [1,575] biology,ngs SOAPec 2.03 [1,576] biology, phylogenetics SOAPnuke 2.1.0 [1,577] phylogenetics SOAPsplice 1.10 [1,578] biology,ngs SODA 20200930 [1,579] biology SOLAR 8.4.2 [1,580] phylogenetics SomaticSeq 3.6.2 [1,581] phylogenetics SortaDate 20190705 [1,582] phylogenetics SortMeRNA 2.1, 4.0 [1,583] biology, sequencing, NGS SourceTracker2 2.0.1 [1,584] phylogenetics Sourmash 2.0.1 [1,585] phylogenetics SoX 14.4.2 [1,586] phylogenetics SpaceRanger 1.3.1 [1,587] phylogenetics SPAdes 3.15.3, 3.7.1, 3.8.0 [1,588] biology, ngs SparCC 201608 [1,589] microbial Ecology Spark 2.2.0, 3.1.1 [1,590] spark, hadoop sparsehash 2.0.3 [1,591] google, API SPARTA+ 2.60 [1,592] chemistry Spec2nii 0.3.4 [1,593] phylogenetics SpeedSeq 0.1.2 [1,594] phylogenetics Spidey 20150922 [1,595] biology, genomics, bioinformatics SpinalCordToolbox 5.4 [1,596] phylogenetics SplAdder 2.4.2 [1,597] phylogenetics SpliceGrapher 0.2.5 [1,598] biology, sequencing SpliceTrap 0.90.5 [1,599] biology, genomics, ngs SPM 12b, 8, 8r5236 [1,600] biology,bioinformatics,matlab spruceup 2019.2.3 [1,601] phylogenetics Sputnik 1.0 [1,602] biology,bioinformatics,repeats spyder 4.1.4, 5.1.1, 5.3.2 [1,603] iDE, editor, programming, scripting SQANTI 1.2 [1,604] phylogenetics SQANTI2 5.0 [1,605] phylogenetics SQANTI3 0.1, 1.6, 4.2 [1,606] phylogenetics SQL Developer 4.1.2 [1,607] programming, oracle, sql SQLite 3.33.0, 3.8.8.2 [1,608] database SqueezeMeta 1.4.0, 1.5.2 [1,609] phylogenetics squigglekit 1.0.0 [1,610] data Visualization and Analysis, biology squigglenet 1.0 [1,611] sequencing, biology SRA 2.10.9, 3.0.0 [1,612] biology,bioinformatics,sra sra-human-scrubber 1.1 [1,613] cSV_categories SRAssembler 1.0.0 [1,614] phylogenetics SSM 20210511 [1,615] phylogenetics SSPACE 2.0, 3.0 [1,616] biology, ngs ssr_pipeline 0.951 [1,617] biology, DNA sequencing, Stacks 2.53, 2.55, 20190403 [1,618] biology, genomics, ngs Staden 1.14.6 [1,619] biology, phylogenetics Stampy 1.0.31 [1,620] biology, sequencing staphb-toolkit 1.2.0, 1.3.10 [1,621] biology STAR 2.7.5c, 2.7.6a, 2.7.9a [1,622] biology, ngs, rna-seq STAR-CCM+ 14.04.011, 15.02.009, 8.06 [1,623] mechanical Engineering STAR-Fusion 1.1.0, 1.3.1, 1.9.1 [1,624] biology, transcriptome starseqr 0.6.7 [1,625] phylogenetics Stata 10.1, 13 [1,626] statistics stringMLST 0.4 [1,627] biology, CHiP-Seq Stringtie 1.3.4d, 2.0.4, 2.1.3b [1,628] biology, ngs, sequencing,alignment Structure 2.3.3, 2.3.4 [1,629] biology,bioinformatics,population genetics Structure_threader 1.3.10 [1,630] utility, Wrapper, Structure stylegan3 20211028 [1,631] aI, Image Processing SU2 7.0.6 [1,632] phylogenetics Subread 1.6.2, 2.0.0, 2.0.3 [1,633] biology, sequencing, SNP Subversion 1.9.7 [1,634] revision Control SUMO 1.13.0, 1.2.0, 1.9.2 [1,635] phylogenetics SUNDIALS 2.3.0, 2.5.0, 3.0.0 [1,636] math, Numerical Solvers supercell 20170602 [1,637] biology, ngs SuperCRUNCH 1.2.1 [1,638] phylogenetics Supernova 1.2.1, 2.0.0, 2.1.1 [1,639] biology, phylogenetics, ngs SUPPA 2.3 [1,640] phylogenetics Survival_Kit 6.12 [1,641] clinical Biometrics SURVIVOR 1.0.6 [1,642] phylogenetics SVDetect 0.8b [1,643] biology,ngs,genomics svim 1.4.2 [1,644] biology svim-asm 1.0.2 [1,645] biology swarm 1.2.11 [1,646] data Analysis Sweed 3.3.2 [1,647] biology, phylogenetics SWIG 2.0.9, 3.0.12, 3.0.8 [1,648] library, development, C++, python SWSC-EN 1.0.0 [1,649] phylogenetics Synima 20210908 [1,650] phylogenetics syri 1.5.4 [1,651] genomics, biology TACO 0.7.3 [1,652] phylogenetics Taiyaki 5.0.1 [1,653] phylogenetics talesf 20160814 [1,654] phylogenetics Tandem-Genotypes 1.4.0 [1,655] phylogenetics Tantan 13 [1,656] imaging, ngs, genomics Tapestri 2.0.1 [1,657] phylogenetics tapir 20160825 [1,658] biology, phylogenetics TAPIS 1.2.1 [1,659] biology, sequencing TASSEL 5.0, 5.2.20, 5.2.29 [1,660] biology, genomics,wga TAU 2.23, 2.26, 2.26.3 [1,661] library, profiling and optimization Tax4Fun 0.3.1 [1,662] phylogenetics taxMaps 0.1 [1,663] biology, phylogenetics, taxonomy TaxonKit 0.9.0 [1,664] phylogenetics Taxtastic 0.5.7, 0.9.1 [1,665] biology, taxonomy tbb 2017_20161128 [1,666] library tcllib 1.18 [1,667] library tcoffee 10.00.r1613, 9.03.r1318 [1,668] biology TDNAscan 20210304 [1,669] phylogenetics Tecplot 360 EX 2015R1 [1,670] plotting, animation, cfd, simulations tellseq 1.0.0 [1,671] sequencing, Phylogenetics TEMP 20170731 [1,672] phylogenetics TEMP2 0.1.4 [1,673] phylogenetics TensorFlow 2.6.0, 2.7.0, 2.8.0 [1,674] library, math TESS 2.3.1 [1,675] biology, genomics, markov Test 1.0 [1,676] shell TetGen 1.5.0 [1,677] tetrahedral meshes TEToolkit 1.5.1 [1,678] biology, sequencing TEtools 20180213 [1,679] biology, phylogenetics Texlive 20191127, 2020 [1,680] formatting, typesetting, document preparataion TGICL 2.1 [1,681] biology, ngs, sequencing TGSGapCloser 1.0.3 [1,682] phylogenetics the_silver_searcher 2.2.0 [1,683] search Theano 1.0.4 [1,684] library, math, gpu Themisto 0.2.0, 1.1.0 [1,685] genomics, Alignment Tiara 1.0.2 [1,686] phylogenetics tiff 3.8.0, 4.0.10 [1,687] imaging Tigmint 1.1.2 [1,688] phylogenetics Tmux 2.9, 3.1 [1,689] gNU TNTBLAST 2.04 [1,690] biology ToFU2 v17 [1,691] biology, ngs, sequencing toil 3.3.0, 3.3.3 [1,692] biology Tombo 1.4, 1.5, 1.5.1 [1,693] biology, genomics, ngs Tophat 2.1.0, 2.1.1, 2.1.2 [1,694] biology, ngs, sequencing torch-geometric 1.3.2 [1,695] phylogenetics TotalView 8.12 [1,696] parallel Computing TPMcalculator 0.0.3 [1,697] phylogenetics TPP 4.7.0, 4.7.1, 5.0.0 [1,698] biology, chemistry, nmr TraCeR 20160519 [1,699] biology, phylogenetics TrackTools 2011 [1,700] software TrackVis/DTK 0.5.2.2, 0.6.0.1 [1,701] biology, neuroscience, imaging Tracula 5.3.2014_05_26 [1,702] biology, neuroscience, imaging traitRate 1.1 [1,703] biology, evolution Trans-ABySS 2.0.1 [1,704] biology, phylogenetics TransDecoder 5.3.0, 5.4.0, 5.5.0 [1,705] biology, ngs TRANSIT 2.5.2, 3.2.3 [1,706] phylogenetics Transrate 1.0.1 [1,707] biology,assembly TransVar 2.3.3 [1,708] biology, phylogenetics TreeBreaker 20160621 [1,709] biology, phylogenetics TreeMix 1.12 [1,710] biology, phylogenetics treePL 20150305 [1,711] biology, phylogenetics TREEPUZZLE 5.3 [1,712] biology, phylogenetics TreeShrink 1.3.1, 1.3.2 [1,713] phylogenetics TreeTime 0.7.5, 0.8.1 [1,714] phylogenetics trelis 16.3 [1,715] geometry TRF 4.04, 4.09.1 [1,716] biology, genomics Trilinos 12.12.1, 12.18.1, 12.6.4 [1,717] mathematical Algorithms Trim Galore 0.4.4, 0.5.0, 0.6.5 [1,718] biology, ngs trim_isoseq_polya 0.0.3 [1,719] biology, Genetics, Sequencing trimAl 1.2 [1,720] biology, genomics,sequence alignment TriMetAss 1.1 [1,721] biology, ngs Trimmomatic 0.33, 0.36, 0.39 [1,722] biology, ngs Trinity r20130225, r20131110, r20140413 [1,723] biology, ngs, sequencing, rna-seq Trinotate 3.0.1, 3.2.0 [1,724] biology triobinning 0.2.3 [1,725] genomics, biology TRIPLEC 1.0 [1,726] biology TRITONSERVER 21.08 [1,727] machine_learning Inference Server tRNAscan-Se 1.23 [1,728] biology, ngs TRUST4 1.0.2b [1,729] phylogenetics Trycycler 0.4.2 [1,730] phylogenetics TURBOMOLE 7.4.1 [1,731] chemistry TWINSCAN 4.1.2 [1,732] biology, genomics Ubuntu 20.04, 22.04 [1,733] ubuntu Linux UCSC 20200320, 20210803 [1,734] genomics ucsc-fafiltern 377 [1,735] phylogenetics ucsc-maskoutfa 377 [1,736] phylogenetics UCX 1.11.2, 1.9.0 [1,737] parallel Programming, development, library UDUNITS 2.2.17 [1,738] library, data_science, units ufraw 0.22 [1,739] data_mining ugtm 1.1.6 [1,740] statistics, modeling UKFractography 20200127 [1,741] phylogenetics umi-tools 0.5.5 [1,742] phylogenetics UNAFold 3.8 [1,743] biology, genome, RNA, folding Unanimity 20171108, 3.4.1 [1,744] programming,library,cpp UNCALLED 2.2 [1,745] biology, genomics Unicycler 0.4.8 [1,746] phylogenetics Unrar 0.0.1, 4.20 [1,747] unarchiver, utility uproc 1.2.0 [1,748] biology, genome uropa 4.0.2 [1,749] genomics, sequencing, biology USEARCH 9.0.2132, 9.1.13, 9.2.64 [1,750] biology, alignment, sequencing UShER 0.1.4, 0.4.1, 0.5.2 [1,751] phylogenetics V-Phaser 02112013 [1,752] biology, phylogenetics v-pipe 2.0.0 [1,753] biology, genomics, 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phylogenetics WU BLAST 2.0 [1,818] biology Wub 0.2.0, 0.4.0 [1,819] biology, genomics, ngs xander 20151222 [1,820] biology, phylogenetics Xapian 1.4.4 [1,821] library XCrySDen 1.5.60 [1,822] computational Material Science Xerces 3.1.4 [1,823] phylogenetics xesmf 0.6.2 [1,824] grid Analysis, Climate xpclr 1.0, 1.1.1 [1,825] phylogenetics Xterm 1.1 [1,826] utility XWAS 3.0 [1,827] phylogenetics XY-Meta 20200413 [1,828] phylogenetics XZ 5.2.2 [1,829] compression, library YAGO 4 [1,830] data YAHA 0.1.82 [1,831] biology, ngs YAK 0.1 [1,832] phylogenetics YASM 1.3.0 [1,833] computer Programming YASRA 2.33 [1,834] biology, ngs, sequencing yolov4_darknet 4-pre [1,835] machine_learning yolov5 4.0 [1,836] machine_learning Zagros 1.0.0 [1,837] biology,phylogenetics ZEO++ 0.2.2 [1,838] chemistry zorro 2.2 [1,839] biology, sequencing Zstd 1.5.0 [1,840] phylogenetics ZUMIS 2.6.0 [1,841] biology, ngs, sequencing
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