Difference between revisions of "Applications"

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'''Note:''' Up to three latest versions are listed even though there could be more available. Run <code>module spider '''keyword'''</code>  for a full list of provided versions. Use the '''Module''' value from the second column below as the keyword. <br>
 
'''Note:''' Up to three latest versions are listed even though there could be more available. Run <code>module spider '''keyword'''</code>  for a full list of provided versions. Use the '''Module''' value from the second column below as the keyword. <br>
 
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'.
 
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'.
−
{{#get_web_data:url=https://data.rc.ufl.edu/pub/ufrc/data/ai_reference_data.csv
+
{{#get_web_data:url=https://data.rc.ufl.edu/pub/ufrc/data/installed_apps.csv
 
|format=CSV with header
 
|format=CSV with header
 
|delimiter=;
 
|delimiter=;

Latest revision as of 13:26, 27 September 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, 0.4.1 [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
ACTC actc 0.3.1 [8] biology
AdapterRemoval adapterremoval 2.2.2 [9] phylogenetics
ADFRsuite adfrsuite 1.0 [10] sequencing, biology
ADMB admb 11.5, 12.0 [11] math, modeling
AdmixTools admixtools 20150311, 7.0.2 [12] biology, genomics, ngs
ADMIXTURE admixture 1.23, 1.3.0 [13] biology, genomics, ngs
AEGeAn aegean 0.14.0, 0.16.0 [14] biology, genomics
AFNI afni 20.3.00, 2018_04_12 [15] biology, neuroscience, imaging
AfterQC afterqc 0.9.7 [16] phylogenetics
AGAT agat 0.4.0 [17] phylogenetics
AGFusion agfusion 1.252 [18] phylogenetics
Albacore albacore 2.3.1, 2.3.3 [19] biology, phylogenetics
Albumentations albumentations 1.0.3 [20] ai, image_processing, imaging
Alder alder 1.03 [21] biology, genomics
Alevin-fry alevin-fry 0.8.1 [22] sequencing, biology
ALFA alfa 1.1.1 [23] phylogenetics
alfred alfred 0.2.6 [24] web, math
alienhunter alienhunter 1.7 [25] biology, sequencing
AliStat alistat 1.12 [26] phylogenetics
alleleCount allelecount 20210713 [27] biology
allhic allhic 0.9.8 [28] genomics, biology
ALLMAPS allmaps 20180117 [29] biology, phylogenetics
ALLPATHS-LG allpaths 42316, 44837, 49232 [30] biology, ngs
AlphaFold alphafold 2.1.2, 2.2.0, 2.3.1 [31] protein, structure, machine_learning
Alphaimpute alphaimpute 0.0.2, 1.9.8.2, 1.9.8.3 [32] phylogenetics
AlphaMate alphamate 0.1.1 [33] biology
AlphaPulldown alphapulldown 0.30.5, 0.30.7 [34] protein, structure, machine_learning
AltAnalyze altanalyze 2.1.0 [35] biology, genomics
AMAS amas 1.0 [36] phylogenetics
AMBER amber 18, 20, 22 [37] chemistry, molecular_dynamics
ambertools ambertools 23 [38] chemistry, molecular_dynamics
AMICO amico 1.0.1 [39] library, imaging, math
AMOS amos 3.1.0 [40] biology, genomics, assembly
AMP amp 0.6.1 [41] phylogenetics
amPEPpy ampeppy 1.0 [42] phylogenetics
amphora2 amphora2 20140305 [43] biology, phylogenetics
Ampligraph ampligraph 2.0.0 [44] programming, library, math
AMPtk amptk 1.2.4, 1.5.1, 1.5.4 [45] biology, ngs
amptorch amptorch 20210313 [46] phylogenetics
amrfinderplus amrfinderplus 3.10.18 [47] phylogenetics
AMRPlusPlus amrplusplus 20180508 [48] phylogenetics
AMUSE amuse 10.0, 13.1.0 [49] astronomy
ancestryhmm ancestryhmm 1.0.2 [50] genomics, biology
anchorwave anchorwave 1.2.1 [51] biology, genomics
ANDI andi 0.15b [52] assembly
ANGSD angsd 0.933, 0.940 [53] biology, ngs
annocript annocript 2.0 [54] phylogenetics
AnnoTALE annotale 1.4.1 [55] phylogenetics
ANNOVAR annovar 20130221, 20150322, 20191024 [56] biology, genomics
Ansible ansible 2.5.5, 2.8.1 [57] workflow_automation
ansysem ansysem 17.0, 2022r1, 2023r1 [58] physics
antiSMASH antismash 4.1.0, 6.0.1, 7.0.0 [59] phylogenetics
ANTs ants 2.2.0, 2.3.4 [60] biology, phylogenetics
anvio anvio 6.1, 6.2, 7.1 [61] biology
Appreci8 appreci8 20180530 [62] biology, genomics
Apptainer apptainer 1.2.2 [63] workflow_automation
APT apt 1.15.0, 1.18.0, 1.20.5 [64] biology, genomics
ARC arc 1.1.4 [65] biology, ngs
arcashla arcashla 0.5.0 [66] biology, genetics
Aria2 aria2 1.35.0 [67] utility
ARKS arks 1.0.2 [68] phylogenetics
Armadillo armadillo 7.900.0, 9.200.6, 9.900.4 [69] library, compiler, math
ARPACK arpack 1.0 [70] math
ArrayFire arrayfire 3.4.2 [71] math
arriba arriba 2.1.0 [72] phylogenetics
ART art 20160417, 20160605 [73] phylogenetics
artemis artemis 18.1.0 [74] biology
asap asap 2.0 [75] visualization, biology
asaq asaq 1.0 [76] alignment, sequencing, phylogenetics
ASE-ANI ase-ani 20180712 [77] biology, genomics, ngs
ASHS ashs 2.0 [78] biology, imaging
ASPECT aspect 2.3.0 [79] library
Assembly-stats assembly-stats 1.0.1 [80] biology, sequencing, genomics
Assemblytics assemblytics 1.2.1 [81] phylogenetics
asset asset 20210112 [82] sequencing, data_science
Assexon assexon 20190814 [83] phylogenetics
AStalavista astalavista 3.2, 4.0 [84] biology, genomics
aster aster 1.15, 220718 [85] biology, data_science, sequencing
asteroid asteroid 1.0 [86] genomics
ASTRAL astral 5.6.1, 5.6.2, 5.7.7 [87] biology, ngs, phylogenetics
ASTRID astrid 2.2.1 [88] phylogenetics
Astropy astropy 2.0.8 [89] biology, phylogenetics
ATAT atat 3.23, 3.34 [90] material_science
ATLAS atlas 3.10.1, 3.10.2, 3.11.17 [91] library, data_science
Atom atom 1.57.0 [92] programming
AtomEye atomeye 3 [93] material_science
AtomMan atomman 1.3.3 [94] phylogenetics
aTRAM atram 2.2.0, 2.4.3 [95] math
Augustus augustus 3.3.2, 3.3.3, 3.4.0 [96] biology, genomics
Auto3DEM auto3dem 4.05.2 [97] image_processing
AutoDock autodock 4.2.6 [98] biology
AutoDock-GPU autodock-gpu 1.5.3 [99] chemistry
autodock-vina autodock-vina 1.2.3 [100] biology
Autometa autometa 2.2.0, 20190802 [101] phylogenetics
automlsa2 automlsa2 0.8.1 [102] phylogenetics, biology, genomics
AWSCLI awscli 2.11.7, 2.2.30 [103] utility
azoo azoo 1.3.1 [104] phylogenetics
bactopia bactopia 2.2.0 [105] genomics
Badread badread 0.1.5 [106] phylogenetics
bakta bakta 1.3.3 [107] genomics, biology
BALi-Phy bali-phy 3.4.1, 3.5.0 [108] phylogenetics
BAM-matcher bam-matcher 20161021 [109] phylogenetics
Bam-Readcount bam-readcount 20150616 [110] biology, genomics
bamaddrg bamaddrg 20120326 [111] phylogenetics
BamBam bambam 1.0, 1.4 [112] biology, genomics
bamm bamm 2.5.0 [113] phylogenetics
bamsnap bamsnap 0.2.19 [114] phylogenetics
Bamstats bamstats 20140602 [115] biology, ngs
Bamsurgeon bamsurgeon 1.2 [116] phylogenetics
bamtofastq bamtofastq 1.3.5 [117] phylogenetics
Bamtools bamtools 2.5.0, 2.5.1, 2.5.2 [118] biology, ngs, sequencing
bamUtil bamutil 1.0.2 [119] biology, genomics
BAPS baps 6.0 [120] biology, genomics
Barrnap barrnap 0.7, 0.9 [121] biology, rna-seq
Basemount basemount 0.15.96, 0.25.2 [122] biology, sequencing
BatMeth2 batmeth2 20210720 [123] biology, genomics, mapping
bax2bam bax2bam 0.0.9 [124] phylogenetics
BayArea bayarea 1.0.2 [125] biology
BAYENV bayenv 2.0 [126] biology, phylogenetics
BayesAss bayesass 3.0.4, 3.0.4.2 [127] phylogenetics
bayesass3-snps bayesass3-snps 1.1 [128] phylogenetics
BayeScan bayescan 2.1 [129] biology, variant_calling
BayesR bayesr 20151016 [130] biology, phylogenetics
BayesTraits bayestraits 3.0.2 [131] phylogenetics
baypass baypass 2.1 [132] biology, phylogenetics
BBMap bbmap 38.26, 38.44, 38.90 [133] biology, alignment
bcftools bcftools 1.15, 1.3.1, 1.9 [134] biology, ngs
bcl2fastq bcl2fastq 2.16.0.10, 2.20.0.422 [135] biology, ngs
BDG-SeQuila bdg-sequila 0.5.5 [136] phylogenetics
BEAGLE beagle 4.1, 5.0, 5.2 [137] biology, genomics
BEAR bear 20170209 [138] biology, genomics
BEAST beast 2.7.0, 2.7.3, 2.7.5 [139] biology, phylogenetics
BEAST2-XML beast2-xml 1.0.9 [140] phylogenetics
BEDOPS bedops 2.4.30 [141] biology, sequencing, ngs
BEDTools bedtools 2.29.1, 2.29.2, 2.30.0 [142] biology, ngs
Bertini bertini 1.6 [143] math
BERTopic bertopic 0.14.0, 0.7, 0.8.1 [144] machine_learning
BESST besst 2.2.4 [145] biology, ngs
BFAST bfast 0.7.0 [146] biology, ngs
bgenix bgenix 1.1.7 [147] data_science, genomics
BIDSCOIN bidscoin 3.7.4 [148] neuroscience
Bifrost bifrost 0.2, 1.0.3, 20200225 [149] phylogenetics
BiG-SCAPE big-scape 1.1.2 [150] biology, genomics, phylogenetics, pipeline
bigslice bigslice 1.1.1 [151] biology, genomics
bindash bindash 1.0.1, 1.0.2 [152] genomics
BinPacker binpacker 1.0 [153] biology, rna-seq, assembly
BinSanity binsanity 0.2.6.4 [154] biology, genomics
Bioawk bioawk 1.0 [155] phylogenetics
bioBakery biobakery 0.15.1, 1.8, 3.0.0 [156] phylogenetics
Biodiverse biodiverse 2.1 [157] phylogenetics
Biolite biolite 0.3.5.1 [158] biology, genomics, variant_calling
BIOM biom 2.1.5, 2.1.6 [159] biology, genomics
BIOMART biomart 1.4 [160] biology, genomics
Biopieces biopieces 2.0 [161] phylogenetics
BIRDS fiji-birds 1.0 [162] workflow_automation, utility, imaging
Bismark bismark 0.22.3, 0.7.4, 0.7.7 [163] biology, ngs
Blackfynn blackfynn 0.2.7 [164] data_mining
BLASR blasr 20130815, 20161215 (5.3), 5.3.2 [165] biology, ngs
Blast2GO blast2go 2.5.0-20120705 [166] biology, genomics
Blast2GO CLI blast2go 1.3.3 [167] biology, genomics
BLAT blat 20121105, 20140318 [168] genomics
blender blender 2.73, 2.77, 3.0.1 [169] graphics
blink blink 0.01 [170] genomics
Blitz blitz 0.10 [171] library
BlobTools blobtools 1.0, 2.2 [172] phylogenetics
bloomfiltertrie bloomfiltertrie 0.8.7 [173] phylogenetics
BloomTree bloomtree 0.3.5 [174] data_mining
BLUPF90 blupf90 20160604, 20180301, 20190531 [175] biology, phylogenetics
BMGE bmge 1.12 [176] biology, genomics, phylogenetics
bmtagger bmtagger 3.101 [177] genomics, biology
BOLT-LMM bolt-lmm 2.3.4 [178] phylogenetics
BoltzTraP boltztrap 1.2.5 [179] physics
Boost boost 1.75.0, 1.77.0, 1.82.0 [180] programming, library, compiler
booster booster 0.1.2 [181] phylogenetics
botorch botorch 0.7.1 [182] phylogenetics, biology
Bowtie bowtie 1.1.1, 1.2.0, 1.2.3 [183] biology, ngs, sequencing
Bowtie2 bowtie2 2.3.5.1, 2.4.2, 2.4.5 [184] biology, ngs, sequencing
BoxCLI boxcli 2.9.0 [185] file_management, web, programming
BPGA bpga 1.2 [186] biology, ngs
BPP bpp 4.1.4, 4.3.8, 4.4.1 [187] biology, phylogenetics
BppSuite bppsuite 2.3.2 [188] genomics
Bracken bracken 1.0.0, 2.5 [189] biology, phylogenetics
BrainIAK brainiak 0.11 [190] imaging
braker braker 2.1.6, 3.0.2, 3.0.3 [191] phylogenetics
BRANCH branch 1.8.1 [192] biology, ngs, mapping
BRATNextGen bratnextgen 20150505 [193] biology, genomics
BreakDancer breakdancer 1.4.5 [194] biology, phylogenetics
breakseq breakseq 2.2 [195] biology, phylogenetics
Brewery brewery 20191205 [196] phylogenetics
Bridger bridger 20141201 [197] ngs, genomics, biology
BRIG brig 0.95 [198] biology, genomics
brkraw brkraw 0.3.5 [199] data_science, imaging
BRM brm 0.3 [200] phylogenetics
Bruker2nifti bruker2nifti 1.0.4 [201] phylogenetics
Bsmap bsmap 2.87 [202] biology, ngs
Bsoft bsoft 1.9.1 [203] biology, image_processing
BSseeker2 bsseeker2 2.1.0, 2.1.8 [204] biology, phylogenetics
bubbleparse bubbleparse 20140314 [205] biology, phylogenetics
BUCKy bucky 1.4.4 [206] biology, phylogenetics
BUSCO busco 4.0.6, 4.1.4, 5.2.0 [207] biology, genomics
BWA bwa 0.7.7, 0.7.8, 0.7.9a [208] biology, ngs
bwa-mem2 bwa-mem2 2.2.1 [209] phylogenetics
bwa-meth bwameth 0.2.7 [210] genomics, biology
BWA-PSSM bwa-pssm 0.5.11 [211] phylogenetics
bxh_xcede_tools bxh_xcede_tools 1.11.1 [212] biology
BYOBU byobu 5.133, 5.92 [213] shell
bzip2 bzip2 1.0.6 [214] utility, library
c-wap c-wap 20220624 [215] sequencing, genomics, biology
Cactus cactus 2.0.3, 2.0.5 [216] phylogenetics
CAFE cafe 4.1, 5.0.0 [217] biology, phylogenetics
came came 0.0.1 [218] phylogenetics
Camino camino 20140723 [219] biology, neuroscience, imaging
cammiq cammiq 0.1.1 [220] genomics, biology
CAMP camp 1.0.0 [221] biology, sequencing
Cantera cantera 2.1.1 [222] physics
Canu canu 2.0, 2.1, 2.2 [223] biology, sequencing
CANVAS canvas 1.40.0.1613 [224] phylogenetics
CAP3 cap3 20120705 [225] biology, assembly
Capnp capnp 0.5.3 [226] compiler
captus captus 0.9.88, 0.9.91 [227] phylogenetics, biology
CARTA carta 2.0 [228] image_processing
CASAVA casava 1.8.2 [229] biology, ngs
CASM casm 0.2.0 [230] physics
CasOFFinder casoffinder 2.4 [231] phylogenetics
Catch catch 1.4.0 [232] biology, genomics, sequencing
CAVIAR caviar 20171218 [233] biology, phylogenetics
CBGpipe cbgpipe 20190702 [234] phylogenetics
CCMetagen ccmetagen 1.4.0 [235] phylogenetics
CD-HIT cdhit 4.6, 4.6.4, 4.6.8 [236] biology, genomics
CDBFasta cdbfasta 20181005 [237] phylogenetics
CDNA_Cupcake cupcake 20180629, 22.0.0, 9.0.1 [238] biology, ngs, sequencing
CDO cdo 1.7.2rc3, 1.9.4 [239] climate
CellProfiler cellprofiler 3.1.9, 4.1.3 [240] phylogenetics
CellRanger cellranger 6.1.2, 7.0.0, 7.0.1 [241] biology, ngs, rna-seq
CellRanger-ARC cellranger-arc 2.0.1 [242] biology, ngs, rna-seq
CellRanger-ATAC cellranger-atac 1.2.0 [243] biology, ngs, rna-seq
CellRanger-DNA cellranger-dna 1.0.0, 1.1.0 [244] biology, ngs, rna-seq, genomics
Centrifuge centrifuge 1.0.3, 1.0.4b [245] biology, phylogenetics
CFITSIO cfitsio 3.370 [246] library, compiler
CGAL cgal 5.02, 5.5.2, 5.6 [247] library, math
CGATools cgatools 1.6.0.43 [248] biology, ngs
cgmaptools cgmaptools 0.1.1, 0.1.2 [249] phylogenetics
CGView cgview 1.0.2 [250] phylogenetics
CHARMM charmm 36a3, 43b2, c48b2 [251] chemistry, simulation
ChartDirector libchartdir 5.1.0 [252] library, data_science
CheckM checkm 1.0.4, 1.0.7, 1.1.2 [253] biology, genomics
checkv checkv 1.0.1 [254] biology, genomics
Chimera chimera 1.12 [255] biology, modeling
Chipyard chipyard 1.0 [256] simulation
Chromeister chromeister 1.5a [257] biology, genomics
ChromEvol chromevol 2.0 [258] biology, ngs
CIMS cims 4.1.2 [259] biology, genomics
CIRCexplorer circexplorer 1.1.10 [260] biology, rna-seq
CIRCexplorer2 circexplorer2 2.3.5, 2.3.8 [261] phylogenetics
circexplorer3 circexplorer3 01172021 [262] RNA-Seq
Circlator circlator 1.5.5 [263] phylogenetics
Circleator circleator 1.0.2 [264] phylogenetics
circompara2 circompara2 0.1.2.1 [265] phylogenetics
Circos circos 0.63-pre11, 0.69-2, 0.69-9 [266] biology, genomics, ngs
circtools circtools 1.2.1 [267] biology
CIRI ciri 2.0.6 [268] phylogenetics
ciriquant ciriquant 1.1.2 [269] phylogenetics
CisGenome cisgenome 2.0 [270] biology, genomics
cisTEM cistem 1.0.0 [271] phylogenetics
Clairvoyante clairvoyante 1.02 [272] phylogenetics
Clann clann 3.2.3 [273] biology, phylogenetics
clara clara v4.0 [274] ai, machine_learning
CLARK clark 1.2.2-b, 1.2.3 [275] biology, genomics
CLHEP clhep 2.2.0.1 [276] physics
CLIFinder clifinder 4.1 [277] biology, phylogenetics
ClinicaDL clinicadl 1.0.4, 1.2.0 [278] biology, imaging, machine_learning
clipkit clipkit 1.3.0 [279] genomics, biology
CLIPper clipper 2.1.0 [280] phylogenetics
CLIPSeqTools clipseqtools 0.1.7 [281] biology, sequencing
ClonalFrame clonalframe 1.1, 1.2 [282] biology, ngs, phylogenetics
ClonalFrameML clonalframeml 1.0, 1.11 [283] biology, ngs, phylogenetics
CloudCompare cloudcompare 2.10.3 [284] visualization
Clover clover 2.0 [285] biology, genomics, assembly
CLUMPP clumpp 1.1.2 [286] biology
ClustalO clustalo 1.2.0 [287] biology, alignment
ClustalW clustalw 2.1 [288] biology, alignment
cluster3 cluster3 1.52a [289] biology, genomics
Clview clview 20130402 [290] biology
CMake cmake 3.21.3, 3.26.4 [291] programming
CMS cms 20170518 [292] biology
CMWP cmwp 140518 [293] biology, genomics
CNCI cnci 20180305 [294] phylogenetics
CNSpipeline cnspipeline 20170827 [295] phylogenetics
CNV-Seq cnvseq 20110715, 20140812 [296] biology, genomics
CNV-Sim cnv-sim 0.9.2 [297] biology, phylogenetics
CNVkit cnvkit 0.9.6 [298] phylogenetics
CNVnator cnvnator 0.3.2 [299] biology, genomics
cobra-tf cobra-tf 0.1 [300] fluid_dynamics
CodonPhyML codonphyml 20150303 [301] phylogenetics
Coevol coevol 1.3c, 1.4b, 1.6 [302] biology, phylogenetics
Cogent cogent 2.1 [303] biology, phylogenetics
COLMAP colmap 3.6 [304] modeling
CoMap comap 1.4.1 [305] biology, genomics
Comp-D_MPI comp-D_MPI 1.0 [306] statistics
Compacta compacta 1.02 [307] biology, genomics
COMSOL comsol 5.4.0, 6.1.0 [308] simulation
Concaterpillar concaterpillar 1.8a [309] phylogenetics
CONCOCT concoct 1.1.0 [310] biology, genomics
Conda conda 23.3.1, 23.7.2, 4.12.0 [311] programming
Conefor conefor 2.7.3 [312] software
CONN conn 18a, 22a [313] imaging
CONNECT connect 20200614 [314] phylogenetics
connectomemapper3 connectomemapper3 3.0.0-rc1 [315] phylogenetics
ConPADE conpade 1.0 [316] phylogenetics
Conpair conpair 20161010, 20180624 [317] biology, phylogenetics
Consed consed 23.0, 25.0, 29.0 [318] biology, genomics
CONSEL consel 0.20 [319] biology, phylogenetics
ContaVect contavect 0.2 [320] biology, phylogenetics
Convert3D convert3d 1.1.0 [321] imaging, utility
Coot coot 0.9.5 [322] modeling
Coreutils coreutils 8.23, 8.28 [323] utility
Corset corset 1.06 [324] biology, ngs
Counterr counterr 0.1, 20230501 [325] phylogenetics
Coverm coverm 0.6.1 [326] biology, genomics, ngs
covNMR covnmr 2014 [327] chemistry, biology
cp2k cp2k 7.0.0 [328] chemistry
CPAT cpat 3.0.2 [329] phylogenetics
cpc cpc 2.0 [330] phylogenetics
CPLEX cplex 12.6.2, 12.7, 12.9 [331] climate
Crass crass 1.0.1 [332] biology, assembly
crest crest 2.12 [333] chemistry
crisflash crisflash 1.2.0 [334] phylogenetics
CRISP crisp 20181122 [335] phylogenetics
CRISPRanalyzer crispranalyzer 1.50 [336] biology, genomics, ngs
CRISPRCasFinder crisprcasfinder 4.2.17 [337] phylogenetics
CRISPResso2 crispresso2 20220811 [338] genomics, sequencing, biology
CrossMap crossmap 0.3.9, 0.6.3 [339] biology, genomics
crossmapper crossmapper 1.1.1 [340] phylogenetics
Crux crux 1.40 [341] biology, spectroscopy
cryodrgn cryodrgn 2.3.0 [342] biology
CryptoMiniSat cryptominisat 5.0.1 [343] math
csubst csubst 1.3.0 [344] Biology, Phylogenetics
csvpad csvpad 1.2 [345] data science
csvtk csvtk 0.23.0 [346] biology
ctk ctk 1.1.4 [347] biology, genomics
CUBE cube 4.4 [348] library, compiler, math
CUDA cuda 12.1.1, 12.2.0, 12.2.2 [349] programming, library, graphics
Cufflinks cufflinks 2.1.1, 2.2.1, 2.2.1.1 [350] biology, ngs, sequencing
cuOpt cuopt 22.12 [351] Accelerated AI Logistics and Route Optimization
cupy cupy 8.3.0 [352] phylogenetics
cutadapt cutadapt 1.18, 2.8, 3.4 [353] biology, ngs
CutRunTools cutruntools 20200104 [354] phylogenetics
cvbio cvbio 3.0.0 [355] phylogenetics
CViT cvit 1.3 [356] programming, library
CWLtool cwltool 1.0.20190906, 2.0.20200126, 3.0.20210124104916 [357] workflow_automation, scheduler
cx_oracle cxoracle 8.3.0 [358] database, utility
CycleGan cyclegan 20201015 [359] phylogenetics
Cytoscape cytoscape 3.4.0 [360] biology, ngs, phylogenetics
cyvcf2 cyvcf2 20230728 [361] library
d2go d2go 20210702 [362] machine_learning, ai
dadi dadi 2.1.1 [363] phylogenetics
DAKOTA dakota 6.15, 6.8, 6.8-gui [364] math
DALIGNER daligner 1.0 [365] biology, phylogenetics
dammit dammit 1.0rc2 [366] biology, phylogenetics
dancemapper dancemapper 1.0.0 [367] machine learning
dapars dapars 1.0.0 [368] genomics, biology
DASTool dastool 1.1.0, 1.1.2 [369] biology, phylogenetics
datamash datamash 1.1.0 [370] math
DAWGPAWS dawgpaws 1.0 [371] biology, phylogenetics
DCC dcc 0.4.4 [372] biology, ngs
Dcmstack dcmstack 0.6.2 [373] biology, imaging
DCMTK dcmtk 3.6.0 [374] biology, neuroscience, imaging
dDocent ddocent 2.7.8 [375] phylogenetics
ddprotocol ddprotocol 20230405 [376] biology, machine learning
DDSCAT ddscat 7.3.0 [377] astronomy
DDT ddt 20.0, 20.2, 23.0 [378] programming
DealII dealii 8.3.0, 9.3.1 [379] library
DeconSeq deconseq 0.4.3 [380] biology, phylogenetics
decontaMiner decontaminer 1.4 [381] genomics, biology
DECX decx 20180205 [382] phylogenetics
DeepARG deeparg 1.0.1 [383] phylogenetics
deepbgc deepbgc 0.1.18 [384] phylogenetics
Deepcoil deepcoil 2.0.1 [385] sequencing, biology
deepfri deepfri 03312021 [386] machine learning, biology
DeepGS deepgs 1.2 [387] phylogenetics
DeepLabCut deeplabcut 2.0.7-gpu, 2.1.1, 2.2.1 [388] phylogenetics
deepmicrobes deepmicrobes 20200219 [389] biology, genomics, machine_learning
DeepMReye deepmreye 01192022 [390] library, biology
DeepPicker deeppicker 20161102 [391] imaging
deepsig deepsig 1.2.5 [392] biology
deepTools deeptools 2.4.3, 3.1.1, 3.5.2 [393] biology, ngs
deepvariant deepvariant 1.4.0, 1.5.0 [394] biology, genomics, sequencing, machine_learning
deFusion defusion 20200305 [395] phylogenetics
Delft3D delft3d 7545 [396] physics
Delineate delineate 1.2.2 [397] biology, genomics
Delly delly 0.7.7, 0.7.8, 1.1.5 [398] biology, phylogenetics
delucs delucs 20220512 [399] sequencing, genomics, machine_learning
DeNoGAP denogap 1.0 [400] biology, phylogenetics, ngs
DERIVA deriva 1.5.0 [401] phylogenetics
deSALT desalt 1.5.6 [402] biology, genomics, sequencing
Desmond desmond 6.9 [403] biology
Detectron2 detectron2 0.4, 0.5, 0.6 [404] library
DeTiN detin 1.7.5.9 [405] imaging, ngs, genomics
DEXTRACTOR dextractor 1.0 [406] biology, sequencing
Diamond diamond 2.1.1, 2.1.3, 2.1.8 [407] biology, genomics
DIANN diann 1.8.1 [408] protein, structure
diCal2 dical2 2.2.0.1 [409] biology, phylogenetics
diffReps diffreps 1.55.4 [410] biology
disbatch disbatch 2.5 [411] software
DISCOVAR de novo discovardenovo 52488 [412] biology, ngs, assembly
DiscoVista discovista 20180906 [413] phylogenetics
discvrseq discvrseq 1.3.10 [414] biology, phylogenetics
Distruct distruct 2.3 [415] phylogenetics
DIYABC diyabc 1.0.4.43b, 2.0.3, 2.1.0 [416] biology, phylogenetics
DL_POLY dlpoly 1.9 [417] molecular_dynamics
Dlib dlib 19.19 [418] phylogenetics
DNA Clust dnaclust 3.0 [419] biology, genomics
DOCK dock 6.7, 6.8, 6.9 [420] chemistry
DoGFinder dogfinder 20201103 [421] phylogenetics
dorado dorado 0.1.1, 0.3.0, 0.3.3 [422] genomics
DosageConvertor dosageconvertor 1.0.3 [423] biology
DOT dot 2.0 [424] biology, chemistry
Doxygen doxygen 1.8.3.1, 1.9.7 [425] programming, documentation
dragmap dragmap 1.2.1 [426] phylogenetics, sequencing, biology
dragonflye dragonflye 1.0.12 [427] sequencing, genomics
dram dram 1.3 [428] biology, genomics, annotation
DRAP drap 1.91 [429] biology, phylogenetics
dRep drep 2.3.2 [430] phylogenetics
dretools dretools 0.0.1.20 [431] rna-seq
drishti drishti 3.1 [432] visualization
Dropseq dropseq 2.4.0 [433] phylogenetics
DS9 saoimageds9 7.5, 8.0.1 [434] imaging
DScribe dscribe 1.2.0 [435] machine_learning
dsistudio dsistudio 20210123, 20220803 [436] imaging
DSK dsk 2.1.0, 2.3.0 [437] biology, ngs
DSRC dsrc 2.0 [438] phylogenetics
DSSAT dssat 4.6 [439] simulation
DSSP dssp 2.2.1, 3.0.0 [440] molecular_dynamics
DSuite dsuite 0.4, 0.4-r41, 0.4-r49 [441] biology, genomics
DTI-TK dtitk 2.3.1 [442] imaging
dtiprep dtiprep 0.1.1 [443] phylogenetics
duchamp duchamp 1.6.2 [444] phylogenetics
DVGfinder dvgfinder 3.1 [445] genomics, search, sequencing
dx-toolkit dx-toolkit 0.347.0 [446] biology
dynamicDBG dynamicdbg 20181003 [447] phylogenetics
Dynare dynare 4.4.3 [448] math
ea-utils eautils 1.04.807.18, 1.1.2.537 [449] biology, genomics, ngs
EAGLE eagle 2.0 [450] phylogenetics
eagle-rc eagle-rc 1.1.1 [451] phylogenetics
ECE ece 1.2 [452] physics
eddy-squeeze eddy-squeeze 1.0.8 [453] data_science, visualization
EDirect edirect 10.7, 12.2 [454] biology, phylogenetics
EDTA edta 1.9.6, 2.1.0 [455] phylogenetics
Edyeet edyeet 0.1, 0.3 [456] phylogenetics
EEGLAB eeglab 12.0.2.1b, 13.2.2b, 13.4.4b [457] biology
eGene-MVN egene-mvn 0.1 [458] biology, genomics
eggNOG-mapper eggnog-mapper 2.0.1, 2.1.6 [459] phylogenetics
Ego4D ego4d 1.3.2 [460] image processing
EGSnrc egsnrc 2019 [461] phylogenetics
EIGENSOFT eigensoft 4.2, 5.0.1, 6.0.1 [462] biology
Elastix elastix 4.9.0 [463] phylogenetics
ELPA elpa 2019.11.001 [464] library, compiler, math
elPrep elprep 4.1.4 [465] phylogenetics
Emacs emacs 27.2, 28.2 [466] programming, language
Email Alert Service email_storage_alert 1.0.0 [467] file_management
EMAN2 eman2 2.22, 2.31 [468] image_processing
EMBOSS emboss 6.6.0 [469] biology
Embree embree 3.6.1 [470] graphics
EMC emc 9.4.3 [471] simulation
EMMAX emmax 20100307, 20120210 [472] biology, ngs, mapping
EnergyPlus energyplus 9.3.0 [473] simulation
Ensembl Tools ensembl_tools 100, 80 [474] biology
enTAP entap 0.6.1.2, 20160416 [475] biology, phylogenetics
EPACTS epacts 3.2.6, 3.4.2, 3.4.2.hg38 [476] biology, genomics
EpiNano epinano 1.2.0 [477] biology, ngs
epiteome epiteome 1.0 [478] phylogenetics
epoch epoch 4.7.3 [479] astronomy
eQTLA eqtla 1.1 [480] biology, genomics
eQtlBma eqtlbma 1.2.2, 1.3.0r20140820 [481] biology, genomics
Erpin erpin 5.5.4 [482] biology, phylogenetics
esmf esmf 8.3.0) [483] geospatial
ESOM esom 1.1 [484] biology, phylogenetics
ESPRESSO espresso 7.0, 7.1, 7.2 [485] chemistry, modeling
ESPRIT esprit 2009-nogap, 201102 [486] biology
ETE3 ete3 3.0.0, 3.1.1 [487] biology, phylogenetics
EVidenceModeler evidencemodeler 1.1.1 [488] phylogenetics
Evigene evigene 20180730, 20200520 [489] phylogenetics
EvoLSTM evolstm 20220103 [490] biology
ExaBayes exabayes 1.5 [491] phylogenetics
Exonerate exonerate 2.2.0, 2.4.0 [492] biology, genomics
ExpansionHunter expansionhunter 4.0.2 [493] biology, genomics
ExpansionHunterDenovo expansionhunterdenovo 0.9.0 [494] biology, genomics
export2graphlan export2graphlan 0.22 [495] statistics, mapping, visualization
eXpress express 1.3.1, 1.5.1 [496] biology, ngs
ezaai ezaai 1.0 [497] biology, phylogenetics
face_morpher face_morpher 20190630 [498] phylogenetics
face_recognition face_recognition 1.2.2 [499] phylogenetics
fairseq fairseq 0.12.2 [500] modeling, ai
falco falco 1.2.1 [501] biology, sequencing
FALCON falcon 20161027, 20161222, 20190601 [502] biology, ngs, sequencing
FALCON_unzip falcon_unzip 20161222 [503] biology
faqcs faqcs 2.10 [504] Genomics, biology
FAR far 2.15 [505] biology, genomics
FAST fast 1.06 [506] biology, phylogenetics
fast-gep fast-gep 1.0 [507] phylogenetics
Fast-Plast fast-plast 1.2.6 [508] biology, phylogenetics
fast5tools fast5tools 0.3.1 [509] phylogenetics, biology
FASTA fasta 34.26.5, 36.3.6d [510] biology, genomics
fastai fastai 2.1.5, 2.6.3, 2.7.10 [511] phylogenetics
FastANI fastani 1.1 [512] phylogenetics
fastchaos fastchaos 0.1.0 [513] sequencing
FastGEAR fastgear 20161216 [514] biology, genomics
Fastix fastix 0.1.0 [515] biology, ngs
FastML fastml 3.0 [516] biology, phylogenetics
Fastp fastp 0.20.0, 0.22.0 [517] biology, ngs
FASTphase fastphase 1.4.8 [518] phylogenetics
FastPlast fastplast 1.2.8 [519] phylogenetics
fastq-pair fastq-pair 1.0 [520] phylogenetics
FastQ-Screen fastq-screen 0.14.0 [521] phylogenetics
Fastq-tools fastq-tools 0.8 [522] biology, ngs
FastQC fastqc 0.11.7, 0.12.1, 0.9.6 [523] biology, ngs
FastqPuri fastqpuri 1.0.7 [524] phylogenetics
FastQTL fastqtl 2.184 [525] phylogenetics
FASTRAL-constrained fastral-constrained 20211108 [526] phylogenetics
fastsimcoal fastsimcoal2 2.6.0.3, 2.7.0.2 [527] biology, phylogenetics
FastSpar fastspar 0.0.4 [528] biology, genomics
fastStructure faststructure 20150112 [529] biology, genomics
FastTree fasttree 2.1.11 [530] biology, phylogenetics
FastUniq fastuniq 1.1 [531] biology, phylogenetics
Fastx Toolkit fastx_toolkit 0.0.13.2, 0.0.14 [532] biology, ngs
fcGENE fcgene 1.0.7, 1.0.7.1 [533] biology, genomics, variant_calling
FDSTools fdstools 1.2.0 [534] phylogenetics
fdupes fdupes 1.51 [535] file_management
FEELnc feelnc 0.1.1 [536] phylogenetics
FEniCS fenics 2018.1.0 [537] biology, phylogenetics
Ferret ferret 6.82 [538] visualization, geospatial, climate
FFmpeg ffmpeg 2.1.3, 2.8.3, 4.3.1 [539] audio, visualization
FFTW fftw 3.3.6, 3.3.7, 3.3.8 [540] library, compiler, math
fgbio fgbio 0.5.0, 0.7.0 [541] phylogenetics
FGMP fgmp 1.0.1 [542] phylogenetics
FGTPartitioner fgtpartitioner 1.0.1 [543] genomics
FIGARO figaro 1.1.2 [544] phylogenetics
Fiji fiji 2.0.0rc59 [545] image_processing
Filtlong filtlong 0.2.0 [546] biology, phylogenetics
Finder finder 20210503, 20210609 [547] biology, search
finemap finemap 1.4 [548] phylogenetics
fineRADstructure fineradstructure 0.3.2 [549] phylogenetics
finesse finesse 2.3.1 [550] simulation
Firefox firefox 1.0 [551] linux, web
fit-sne fit-sne 1.2.1 [552] phylogenetics
FLAIR flair 1.5, 2.0 [553] genomics
flairNLP flairnlp 0.10 [554] visualization, language
flappie flappie 1.1.0, 2.1.3 [555] phylogenetics
FLASh flash 1.2.10, 1.2.11 [556] biology, genomics
FLEA flea 2.0.0 [557] phylogenetics
flex flex 2.6.4 [558] programming
Flexbar flexbar 2.3, 2.34, 3.5.0 [559] biology, genomics, ngs
FLEXLm flexlm 1.0 [560] utility
FlowCraft flowcraft 1.4.1 [561] phylogenetics
Fluent fluent 17.2, 19.1, 2020R1 [562] fluid_dynamics
Flye flye 2.9, 2.9.1, 2.9.2 [563] biology, ngs
fMRIPrep fmriprep 1.4.0a1, 1.5.4, 20.2.3 [564] data_mining
forecasting forecasting 0.10.3 [565] Machine_Learning, Data_Science
ForeSeqs foreseqs 1.0.4 [566] phylogenetics
fpocket fpocket 4.0.2 [567] sequencing, biology
fqtools fqtools 20160224 [568] biology, ngs, sequencing
FragGeneScan fraggenescan 1.16 [569] biology, genomics
FRAMA frama 20151019 [570] biology
FrameDP framedp 1.2.2 [571] biology, sequencing
FRAPOSA fraposa 20200421 [572] phylogenetics
FreeBayes freebayes 1.3.1, 1.3.2, 1.3.7 [573] biology, genomics
freecad freecad 0.20.2 [574] modeling
freesasa freesasa 2.1.2 [575] molecular_dynamics, biology
Freesurfer freesurfer 7.1.1, 7.2.0, 7.3.2 [576] biology, neuroscience, imaging
Freyja freyja 1.3.1, 1.3.4, 1.3.8 [577] biology, phylogenetics, sequencing
FSA fsa 1.15.9 [578] phylogenetics
FSL fsl 6.0.4, 6.0.5, 6.0.6 [579] biology, neuroscience, imaging
fslmrs fslmrs 1.1.10 [580] spectroscopy, metabolomics
funannotate funannotate 1.8.5, 1.8.7, 1.8.9 [581] phylogenetics
fusion_twas fusion_twas 20210218 [582] phylogenetics
GAL gal 20180906 [583] phylogenetics
Galaxy galaxytools 1.0 [584] biology
galaxyml galaxyml 0.10.0 [585] library, machine_learning
GAML gaml 20150610 [586] biology, genomics
GapCloser gapcloser 1.12r6 [587] biology, genomics, ngs
GapFiller gapfiller 1.10, 1.11 [588] biology, genomics
gapseq gapseq 1.2 [589] chemistry, biology
garfield garfield 2 [590] genomics
GARLI garli 2.0, 2.01 [591] biology, phylogenetics
GASVPro gasvpro 201310 [592] biology, ngs
GATE gate 7.0 [593] library
GATK gatk 4.1.8.1, 4.1.9.0, 4.3.0.0 [594] biology, ngs
Gaussian gaussian 09 D.01, 16, 16-c02 [595] chemistry
Gawk gawk 4.2.0 [596] utility
Gblocks gblocks 0.91b [597] biology
GCC gcc 7.3.0, 8.2.0, 9.3.0 [598] compiler
GCE gce 1.0.2 [599] biology, genomics
gcnenv gcnenv 1.13 [600] library, math
GCT gct 6.2.1 [601] file_management, utility
GCTA gcta 1.26.0, 1.92.4beta, 1.93.2beta [602] biology, genomics, variant_calling
GDAL gdal 2.2.4, 2.3.1, 3.7.0 [603] geospatial, library
GDB gdb 8.3, 9.2 [604] programming
GDC-Client gdc-client 1.0.1, 1.5.0 [605] biology, sequencing, ngs
GDrive gdrive 2.1.0 [606] utility, file_management
GDSL gdsl 1.18 [607] library
Geant4 geant4 4.10, 4.10.03, 4.10.5 [608] physics
geant4 geant4 11.0.2, 4-11.0.3 [609] physics, simulation
GEM gem 20130406 [610] biology, ngs, sequencing
gem5 gem5 2.0 [611] simulation
GEMMA gemma 0.98.1 [612] phylogenetics
GeneMark-ES genemark_es 4.65, 4.68, 4.69 [613] biology, genomics
GeneMarkS genemark_s 2012.04 [614] biology, genomics
GeneMarkS-T genemark_s 3.10.001 [615] biology, genomics
GenePainter genepainter 2.0.4 [616] biology, phylogenetics
GeneRax generax 1.2.2 [617] phylogenetics
Generic Mapping Tools gmt 6.4.0 [618] physics, biology
GeneSeqer geneseqer 2014-02-26 [619] biology, genomics
genesum genesum 0.1.0 [620] biology, genomics
GeneTorrent genetorrent 3.8.7 [621] biology, file_management
genewalk genewalk 1.5.3 [622] phylogenetics
GenGen gengen 1.0.1 [623] biology, phylogenetics
genmap genmap v1.3.0 [624] Gene mapping, biology
geNomad genomad 1.5.1 [625] biology, genomics
Genome STRiP genomestrip 2.00.1602 [626] biology, genomics, ngs
Genome_Graph_Annotation genome_graph_annotation 20190131 [627] phylogenetics
GenomeScope2 genomescope2 2.0 [628] phylogenetics
GenomeThreader genomethreader 1.7.3 [629] phylogenetics
GenomeTools genometools 1.5.7, 1.5.9 [630] biology
genomic-fluidity genomic-fluidity 20151109 [631] phylogenetics
GenomicConsensus genomicconsensus 2.3.3 [632] biology, phylogenetics
GenomicNeuralnet genomic-neuralnet 20161030 [633] phylogenetics
GenomicTools genomictools 2.7.0 [634] biology, ngs, chip-seq, rna-seq
GenotypeHarmonizer genotypeharmonizer 1.4.18 [635] biology
Genrich genrich 0.5 [636] phylogenetics
GenSel gensel 4.90 [637] genomics
geopython geopython 1.0.0, 1.0.1, 1.0.2 [638] programming, geospatial
GEOS geos 3.3.8, 3.6.2 [639] library, data_science
GeP gep 2.1 [640] biology, phylogenetics
gepard gepard 1.40.0 [641] phylogenetics
Gephi gephi 0.10.0 [642] visualization, image_processing
Gerbil gerbil 1.11 [643] phylogenetics
get_homologues get_homologues 3.3.3 [644] biology, genomics
GetOrganelle getorganelle 1.7.3.5, 1.7.5.0 [645] phylogenetics
GFam gfam 1.1 [646] biology, genomics, annotation
GFF-Ex gff-ex 2.3 [647] phylogenetics
GFF3toolkit gff3toolkit 2.0.3 [648] phylogenetics
gffcompare gffcompare 0.12.2 [649] phylogenetics
gffread gffread 0.11.8, 0.12.7, 0.9.8c [650] biology
Gflags gflags 2.2.1, 20150520 [651] web, library
GFOLD gfold 1.1.4 [652] biology, rna-seq
ggsashimi ggsashimi 0.5.0 [653] phylogenetics
GHOST-MP ghost-mp 1.3.4 [654] phylogenetics
Ghostscript ghostscript 9.22 [655] documentation
giggle giggle 20221212 [656] Genomics
Gimmemotifs gimmemotifs 0.18.0 [657] biology, genetics
Giotto giotto 0.1.0 [658] phylogenetics
giraf giraf 1.02 [659] sequencing, biology
Git git 2.14.1, 2.30.1 [660] revision_control
git-filter-repo git-filter-repo 2.33.0 [661] phylogenetics
glactools glactools 1.0.8 [662] phylogenetics
Glimmer glimmer 3.02 [663] biology, annotation
GlimmerHMM glimmerhmm 3.0.4 [664] biology, annotation
GLMsingle glmsingle 1.0 [665] imaging
Globus globus 2.1.3, 3.13.0 [666] file_management
glog glog 0.3.5 [667] web, library
GLPK glpk 4.55, 4.65 [668] programming
Glueviz glueviz 0.15.2 [669] phylogenetics
GMAP gmap 20180212, 20180212_sse2, 20190610 [670] biology, genomics, ngs
GMcloser gmcloser 1.6 [671] biology, ngs
GMP gmp 6.1.2, 6.3.0 [672] library
GnuPlot gnuplot 5.2.2, 5.2.3, 5.4.1 [673] graphics, math
Go go 1.15.4, 1.18.3, 1.21.0 [674] language
goatools goatools 1.2.3 [675] biology, ontology
GOMAP gomap 1.3 [676] biology, ngs
GoPHY gophy 201030 [677] phylogenetics
gotcloud gotcloud 1.17.5 [678] phylogenetics
GPA gpa 1.1 [679] phylogenetics
GPhoCS gphocs 1.2.3 [680] phylogenetics
Gpufit gpufit 20201127 [681] phylogenetics
Grace grace 5.1.22 [682] graphics, statistics
GRACKLE grackle 3.1 [683] library, compiler, astronomy
Grackle grackle 3.2.1 [/releases/tag/grackle-3.2.1] library, compiler, astronomy
GrADS grads 2.0.1 [684] geospatial, math
Graftm graftm 0.12.2 [685] phylogenetics
GramCluster gramcluster 1.3 [686] biology, sequencing
graph-tool graph-tool 2.32 [687] phylogenetics
Graph_annotation graph_annotation 0.1 [688] phylogenetics
graphaligner graphaligner 1.0.11, 1.0.16 [689] genomics
GraPhlAn graphlan 1.1.3 [690] phylogenetics
GraphMap2 graphmap2 0.6.5 [691] phylogenetics
GraphSplitting graphsplitting 2.4 [692] phylogenetics
graphtyper graphtyper 2.7.2 [693] phylogenetics
GraphViz graphviz 2.38.0, 2.46.1 [694] biology, neuroscience, imaging
GRASS grass 7.0, 7.4 [695] geospatial
grf grf 1.0.0 [696] genomics
Grib_api grib_api 1.10.1, 1.15.1, 1.26.1 [697] compiler, library
GRIDSS gridss 2.6.2 [698] phylogenetics
GROCSVs grocsvs 0.2.5 [699] phylogenetics
GROMACS gromacs 2021.4, 2022.3, 2023.2 [700] chemistry, molecular_dynamics
GroopM groopm 0.3.5 [701] biology, phylogenetics
Groovy groovy 2.4.15 [702] programming
Gscripts gscripts 1.1 [703] biology
GSEA gsea 3.0.0, 4.2.2 [704] biology, genomics
GSL gsl 2.5, 2.6, 2.7.1 [705] library, data_science
GSNP gsnp 1.0 [706] biology, ngs
GTAHunter gtahunter 20200106 [707] phylogenetics
GTDBTk gtdbtk 1.7.0, 2.0.0, 2.1.0 [708] phylogenetics
GTOOL gtool 0.7.5 [709] phylogenetics
GUAVA guava 1.0 [710] phylogenetics
Gubbins gubbins 2.4.1, 3.2.1, 3.3.0 [711] phylogenetics
guideseq guideseq 1.0.2 [712] sequencing, genomics, biology, data_science
guile guile 2.2.2 [713] programming
GULP gulp 4.4, 5.0 [714] material_science
guppy guppy 6.1.7, 6.4.2, 6.4.3 [715] phylogenetics
Gurobi gurobi 10.0.0, 9.5.1 [716] math, programming
GWAMA gwama 2.2.2 [717] phylogenetics
Gzip gzip 1.10 [718] compression
hacdivsel hacdivsel 1.4.1 [719] genomics, biology
Hail hail 0.2.77 [720] biology, genomics
hal hal 2.1 [721] phylogenetics
HALC halc 1.1 [722] biology, phylogenetics
halla halla 0.8.17 [723] phylogenetics
HaMStR hamstr 13.2.3, 13.2.4, v8b [724] biology, genomics
hapbin hapbin 1.3.0 [725] biology, genomics
HapCompass hapcompass 0.7.7 [726] imaging, ngs, genomics
HAPCUT hapcut 0.7 [727] biology, assembly
HapCUT2 hapcut2 1.3.3 [728] biology, genomics, sequencing
hapdup hapdup 0.6 [729] phylogenetics, biology
haphpipe haphpipe 1.0.3 [730] phylogenetics, biology
Haploflow haploflow 0.1 [731] biology, phylogenetics
Haplomerger2 haplomerger2 20180603 [732] biology, genomics
HAPLOSWEEP haplosweep 1.0 [733] biology, phylogenetics
happy happy 0.3.14 [734] phylogenetics, biology
hapQTL hapqtl 1.00 [735] biology
hapsembler hapsembler 2.21 [736] biology, assembly
harvesttools harvesttools 1.2 [737] phylogenetics, biology
HASLR haslr 0.8a1 [738] phylogenetics
hclust2 hclust2 1.0.0 [739] statistics, mapping
HDF4 hdf4 4.2.11 [740] library, data_science
HDF5 hdf5 1.8.19, 1.8.20, 1.8.9 [741] library, data_science
hecaton hecaton 0.5.1 [742] genomics, biology
HELEN helen 20200516 [743] phylogenetics
HelitronScanner helitronscanner 1.1 [744] phylogenetics
hgraph2graph hgraph2graph 20210428 [745] chemistry
hgtector hgtector 2.0 [746] biology, sequencing
hhsuite hhsuite 3.3.0 [747]
HiC-Pro hic-pro 3.0.0 [748] biology, pipeline, genomics
Hifiasm hifiasm 0.16.1, 0.4, 0.8 [749] phylogenetics
HipSTR hipstr 0.7 [750] phylogenetics
HISAT2 hisat2 2.2.1, 2.2.1-3n, 20230203 [751] biology, alignment, ngs
HLAminer hlaminer 1.3.1, 1.4 [752] biology, phylogenetics
HMM-FRAME hmm-frame 20140724 [753] phylogenetics
HmmCleaner hmmcleaner 0.180750 [754] phylogenetics
HMMER hmmer 3.1b2, 3.2.1, 3.3.2 [755] biology, genomics
hmmer2go hmmer2go 0.18.1 [756] phylogenetics, biology
HMMRATAC hmmratac 1.2.10 [757] phylogenetics
HOMER homer 4.10, 4.11, 4.8 [758] biology, sequencing, ngs
homopolish homopolish 0.3.3, 0.4.1 [759] genomics, biology
HOOMD hoomd 2.1.7 [760] library, math
HPL hpl 2.1 [761] programming, performance_analysis
hpsandbox hpsandbox 1.0.0 [762] Programming
HTMLDoc htmldoc 1.8.28, 1.9.3 [763] documentation, web
HTSeq htseq 0.11.2, 2.0.3 [764] biology, ngs
HUMAnN humann 2.8.1 [765] sequencing, biology
humann2 humann2 0.11.2, 2.8.1 [766] phylogenetics
hyb hyb 20141126, 20200815 [767] biology, ngs, rna-seq
hybkit hybkit 0.3.0 [768] biology
HybPiper hybpiper 2.1.3, 2.1.5, 2.1.6 [769] biology, phylogenetics
HyDe hyde 0.4.3 [770] phylogenetics
hylite hylite 2.0.2 [771] genomics, biology
HyPhy hyphy 2.5.4, 2.5.7, 2.5.8 [772] biology, genomics
HYPRE hypre 2.15.1, 2.18.2, 2.19.0 [773] math
iAnnotateSV iannotatesv 1.0.6, 1.0.9 [774] biology, phylogenetics
iaps iaps 02012023 [775] programming
iAssembler iassembler 1.3.2 [776] biology, assembly
ibdne ibdne 20150815 [777] biology, ngs
icommands icommands 3.3.1 [778] utility
IDBA-MT idba-mt 1.0 [779] biology, ngs
IDBA-UD idba-ud 1.1.1, 1.1.1-512, 1.1.1-512-mem [780] genomics, phylogenetics
IDL idl 8.3 [781] language, programming, data_science
IDR idr 2.0.3 [782] phylogenetics
IGB igb 8.4.1 [783] biology, genomics
igBLAST igblast 1.5.0, 1.7.0 [784] biology
IGoR igor 1.4.0 [785] phylogenetics
iGTP igtp 1.1 [786] biology, phylogenetics
IGV igv 2.3.91, 2.4.16, 2.8.6 [787] biology, ngs, phylogenetics
illumina-utils illumina-utils 2.11 [788] phylogenetics
Illumiprocessor illumiprocessor 2.0.9 [789] phylogenetics
IM and IMa ima 20091217 [790] biology, genomics
Ima2 ima2 20120827 [791] biology, genomics
IMa2p ima2p 20170712 [792] biology, phylogenetics
IMA3 ima3 22Aug18 [793] molecular_dynamics
ImageJ imagej 1.48 [794] imaging
imagej2 imagej2 09302022 [795] image processing, imaging
ImageMagick imagemagick 7.0.8-20 [796] imaging
Imaginaire imaginaire 20201229 [797] imaging, visualization, ai, machine_learning
IMOD imod 4.7.15, 4.9.10 [798] image_processing
imoka imoka 1.0 [799] biology, genomics
IMPUTE2 impute2 2.3.2 [800] phylogenetics
IMPUTE5 impute5 1.1.5 [801] biology, math
INDELible indelible 1.03 [802] phylogenetics
Infernal infernal 1.1.1, 1.1.4 [803] biology, alignment
INLA inla 20160718, 20170620 [804] statistics, modeling, programming
InParanoid inparanoid 4.1 [805] biology
Inspector inspector 1.0.2 [806] biology, genomics
InStruct instruct 20160723 [807] phylogenetics
Intel Compilers and Libraries intel 2020.0.166, 2023.0.0, 2023.2.0 [808] language, programming, library, math, compiler
Intel MPI impi 5.1.1 [809] programming, library
InterProScan iprscan 5.57, 5.59, 5.60 [810] biology
intervene intervene 0.6.2 [811] biology, phylogenetics
IOAPI ioapi 3.1, 3.2 [812] climate
IPOPT ipopt 3.12.10, 3.12.6 [813] library, compiler, math
ipyrad ipyrad 0.7.24, 0.7.30, 0.9.53 [814] phylogenetics
IQ-TREE iq-tree 2.2.2, 2.2.2.6, 2.2.2.7 [815] biology, phylogenetics
IRAP irap 0.8.1p7 [816] biology, ngs
irep irep 1.10 [817] biology, genomics
IRFinder irfinder 1.2.0, 1.3.0, 1.3.1 [818] biology, rna-seq
isONclust isonclust 0.0.6 [819] phylogenetics
isonclust2 isonclust2 2.3 [820] rna-seq
IsoSel isosel 1.0 [821] phylogenetics
IsoSeq3 isoseq3 3.4.0, 3.7.0, 3.8.2 [822] biology, ngs
ISOWN isown 20180820 [823] phylogenetics
isPcr ispcr 3.3 [824] biology, phylogenetics
ITK itk 3.20.1, 4.10.1 [825] biology
ITK-SNAP itksnap 3.0.0, 3.8.0 [826] biology, neuroscience, imaging
ITSx itsx 1.1b [827] phylogenetics
IVA iva 1.0.11 [828] phylogenetics
iVar ivar 1.3.1 [829] biology
Jabba jabba 1.0 [830] biology, phylogenetics
JACUSA jacusa 1.2.0 [831] biology, ngs, phylogenetics
JAGS jags 3.3.0, 3.4.0, 4.2.0 [832] statistics
Jasmine jasmine 1.1.4 [833] phylogenetics
jasp jasp 0.14.3 [834] statistics
jbrowse2 jbrowse2 1.7.4 [835] web
JCVI jcvi 0.8.12, 1.0.13, 1.2.10 [836] phylogenetics
JDK java 14, 20, 9.0.1 [837] programming
Je je 1.0 [838] biology, ngs
Jellyfish jellyfish 2.2.4, 2.2.6, 2.3.0 [839] biology, ngs
jModelTest jmodeltest 2.1.1 [840] biology, genomics, phylogenetics
jo jo 1.3 [841] utility
jq jq 1.6 [842] utility
juicer juicer 1.22.01 [843] phylogenetics
Julia julia 1.7.3, 1.8.2, 1.9.2 [844] programming, language, statistics
Jupyter jupyter 6.2.0, 6.5.2, 6.5.4 [845] programming
jutils jutils 1.0 [846] genomics, biology
JVARKIT jvarkit 20180405 [847] biology, phylogenetics
Kaiju kaiju 1.6.2, 1.7.2 [848] biology, phylogenetics
KaKs kaks 1.2, 2.0 [849] biology, genomics, phylogenetics
Kalign kalign 3.3.1 [850] biology, sequencing, alignment
kallisto kallisto 0.46.2, 0.48.0, 0.50.0 [851] biology, ngs, rna-seq
khmer khmer 2.0, 2.1 [852] biology, ngs
KIM kim 1.7.2, 1.8.2, 1.9.3 [853] simulation
kimmingloci skimmingloc 1.0.0 [854] pipeline mapping, biology
KING king 2.1.2, 2.3.0 [855] biology, genomics
KisSplice kissplice 2.4.0-p1 [856] biology, RNA
KLayout klayout 0.26.7 [857] phylogenetics
kma kma 20230106 [858] alignment
KMC kmc 3.1.0, 3.1.1, 3.2.1 [859] phylogenetics
kmerdb kmerdb 1.9.2 [860] genomics, biology
kmerfreq kmerfreq 4.0 [861] biology, genomics
KMOS kmos 0.3.21 [862] phylogenetics
kneaddata kneaddata 0.7.4, 0.9.0 [863] phylogenetics
knime knime 4.7.3 [864] data science
Knitro knitro 12.2.0 [865] math
KofamScan kofamscan 1.3.0 [866] phylogenetics
kover kover 2.0.3 [867] phylogenetics
Kraken kraken 2.0.6b, 2.0.8b, 2.1.2 [868] biology, ngs
KrakenUniq krakenuniq 0.5.8, 0.7.3 [869] phylogenetics
Krona krona 2.8.1, 20161019 [870] biology
ksnp ksnp 3.021, 4.0 [871] biology, phylogenetics, variant_calling
Ksrates ksrates 1.1.1 [872] genomics, biology
kvarq kvarq 0.12.2 [873] biology
LACHESIS lachesis 2.1 [874] phylogenetics
Lambda lambda 0.9.4, 1.0.3, 2.0.0 [875] biology, sequencing, phylogenetics
LAMMPS lammps 3Nov2022, 7Aug19, 7Dec15 [876] molecular_dynamics
LAMMPS-PPA lammps-ppa 23Jun2022 [877] molecular Dynamics
LAMP lamp 2.5 [878] biology, genomics
laneta laneta 20220517, 20220808, 20220812 [879] biology
langdetect langdetect 1.0.9 [880] language, utility
LAPACK lapack 3.8.0 [881] programming, library, compiler
Last last 916, 979 [882] biology, sequencing, alignment
LAStools lastools 20200114 [883] image_processing
LASTZ lastz 1.02.00, 1.03.02, 1.04.00 [884] biology, ngs
Lazypipe lazypipe 1.2 [885] genomics
LazyPredict lazypredict 0.2.8 [886] phylogenetics
lbzip lbzip 2.5 [887] compression
LCModel lcmodel 6.3 [888] biology, spectroscopy
ldak ldak 5.2 [889] phylogenetics, biology
ldblockshow ldblockshow 1.40 [890] biology
LDhat ldhat 2.2a [891] biology, genomics
ldsc ldsc 1.0.1 [892] genomics, biology
leafaudio leafaudio 0.1.0 [893] machine_learning, audio
LEfSe lefse 20180219 [894] phylogenetics
LEMON liblemon 1.2.3 [895] library
LFMM lfmm 1.4, 1.5 [896] biology, phylogenetics
Libint libint 2.5.0, 2.5.0b [897] library
libMesh libmesh 1.5.0 [898] math
libunistring libunistring 0.9.7 [899] library
libvips libvips 8.5.4 [900] image_processing
LIBXC libxc 4.2.3, 4.3.4, 6.2.2 [901] library, math
LIBXSMM libxsmm 1.13 [902] library, compiler, math
LIBZMQ libzmq 4.3.1 [903] library
Liftoff liftoff 1.4.2, 1.6.2 [904] phylogenetics
LIGR ligr 2.05 [905] biology, assembly
LillyMol lillymol 6.1 [906]
lima lima 2.0.0, 2.2.0, 2.7.1 [907] phylogenetics
lingua lingua 1.0.1 [908] language, utility
LINKS links 1.8.5, 1.8.6 [909] biology, genomics
Linksbrowser linksbrowser 2.14 [910] web
LIQA liqa 1.0.0, 1.1.16 [911] phylogenetics
LMAP lmap 1.0.2 [912] biology, phylogenetics
lncScore lncscore 1.0.2 [913] biology, phylogenetics
lobSTR lobstr 4.0.6 [914] biology, phylogenetics
localbrainage localbrainage 20210415 [915] biology, machine_learning
localizer localizer 1.0.4 [916] phylogenetics
LocusZoom locuszoom 1.4 [917] phylogenetics
LoFreq lofreq 2.1.3.1 [918] phylogenetics
LongQC longqc 1.2.0c [919] phylogenetics
LongRanger longranger 2.1.5, 2.2.2 [920] biology, phylogenetics
longshot longshot 0.4.5 [921] genomics
LongStitch longstitch 1.0.3 [922] genomics, biology
LoRDEC lordec 0.9 [923] phylogenetics
LoRMA lorma 0.3, 0.5 [924] biology, ngs
loter loter 1.0 [925] genomics,
LRBinner lrbinner 0.1 [926] biology, genomics
lrgapcloser lrgapcloser 09042018 [927] biology
LS-DYNA ls-dyna 700, 711, 901 [928] physics
LSD2 lsd2 1.6.5 [929] phylogenetics
ltr_finder ltr_finder 1.07 [930] biology, phylogenetics
LTRRetriever ltrretriever 2.5, 2.9.0, 20170514 [931] biology, phylogenetics
Lua lua 5.3.2, 5.3.4, 5.4.6 [932] programming, language
Lucene pylucene 7.7.1, 9.1.0 [933] programming, search
lumpy-sv lumpy 0.2.1, 0.2.13, 0.3.1 [934] biology, genomics
LZO lzo 2.09 [935] library, compression
M5nr m5tools 20121126 [936] biology, genomics
Macaulay2 macaulay2 1.15 [937] phylogenetics
MACH mach 1.0.18 [938] biology, genomics, ngs
Mach2VCF mach2vcf 20150515 [939] biology
MACS macs 2.0.10, 2.1.2, 2.2.7.1 [940] biology, chip-seq
MafFilter maffilter 1.3.0 [941] phylogenetics
MAFFT mafft 7.490, 7.505, 7.520 [942] biology, sequencing
MAGeCK mageck 0.5.9.4 [943] phylogenetics
MAGeCK-VISPR mageck-vispr 0.5.6 [944] phylogenetics
MAGeCKFlute mageckflute 1.14.0 [945] phylogenetics
Magenta magenta 2.1.2 [946] phylogenetics
magicblast magicblast 1.6.0 [947] genomics, biology
MAGMA-GWAS magma-gwas 1.09 [948] phylogenetics
magpurify magpurify 2.1.2 [949] genomics
magus magus 20220121 [950] sequencing, alignment
MAJIQ majiq 2.2, 2.3 [951] phylogenetics
Maker maker 2.31.10, 2.31.6, 3.01.03 [952] biology
MAnorm manorm 20120316 [953] biology, phylogenetics
MANTA manta 1.6.0 [954] phylogenetics
mantis mantis 1.0.4 [955] phylogenetics
mapclassify mapclassify 2.4.2 [956] statistics, mapping, geospatial
mapdamage mapdamage 2.2.1 [957] ngs, sequencing, biology
MapThin mapthin 1.11 [958] phylogenetics
Maq maq 0.7.1 [959] biology, ngs
MarginPolish marginpolish 1.0.0 [960] phylogenetics
MARK mark 2.0.1 [961] data_science, math
MarkerMiner markerminer 20150710 [962] biology, genomics
Mash mash 1.1, 2.3 [963] biology, genomics
MasHmap mashmap 2.0 [964] phylogenetics
mashtree mashtree 1.2.0 [965] genomics, biology
maskrc-svg maskrc-svg 0.5 [966] genomics
MASS mass 1.1.1 [967] genomics, biology
MASSMINE massmine 0.10.0, 0.11.0, 0.9.5 [968] data_mining
MaSuRCA masurca 4.0.8, 4.0.9, 4.1.0 [969] biology, alignment
Mathematica mathematica 13.1 [970] math
MATLAB matlab 2022b, 2023a, 2023b [971] math, language
MATS mats 4.0.1, 4.0.2, 4.1.0 [972] biology, ngs, rna-seq
matt matt 1.3.1 [973]
Mauve mauve 2.3.1 [974] biology, ngs, genomics
mawk mawk 1.3.4-20150503 [975] language
maxbin maxbin 2.1.1 [976] biology, ngs
Maxima maxima 5.41.0 [977] math
MC mc 4.6.1 [978] shell
mCarts mcarts 1.0.2 [979] biology, genomics, math
mccortex mccortex 1.0 [980] phylogenetics
MCL mcl 12-135, 14-137 [981] biology, genomics
MCNP mcnp 6, 6.1 [982] physics
MCNPX mcnpx 2.7.0 [983] physics
MCR mcr 2019b, 2020a, 2020b [984] math, language
MCScanX mcscanx 20130328 [985] biology, phylogenetics
mdanalysis mdanalysis 1.1.1 [www.mdanalysis.org] physics, biology
MECAT mecat 20180308 [986] phylogenetics
Medaka medaka 1.6.0, 1.7.2, 1.8.0 [987] biology, phylogenetics
Medusa medusa 1.6 [988] phylogenetics
MEGA mega 7.0.26 [989] biology, phylogenetics
Mega2 mega2 4.9.2, 6.0.0 [990] biology, phylogenetics
MEGAHIT megahit 1.1.1, 1.1.4 [991] biology, phylogenetics
Megalodon megalodon 2.0.0, 2.4.1 [992] phylogenetics
MEGAN megan 5.10.3, 6.23.4, 6.4.15 [993] biology, ngs
MEGASAT megasat 1.0 [994] phylogenetics
Megraft megraft 1.0.2 [995] biology, sequencing
MELD meld 0.4.14, 0.4.19, 0.5.9 [996] chemistry, molecular_dynamics
MELTING melting 4.3.1 [997] biology, genomics, rna
MEME meme 5.0.2, 5.0.5, 5.4.1 [998] biology, sequencing
MentaLiST mentalist 0.1.3 [999] biology, phylogenetics
Meraculous meraculous 2.0.5 [1,000] biology, ngs
Mercurial mercurial 4.8.2 [1,001] revision_control
merge_peaks merge_peaks 0.1.0 [1,002] workflow_automation
Merlin merlin 1.1.2 [1,003] biology, variant_calling
Merqury merqury 1.1, 1.3 [1,004] phylogenetics
Meryl meryl 1.0 [1,005] phylogenetics
MeShClust meshclust 1.2.0 [1,006] biology
Meshroom meshroom 2019.2.0 [1,007] phylogenetics
MET met 10.0 [1,008] climate, modeling
Meta-Marc meta-marc 1.0.0 [1,009] phylogenetics
Meta-Tissue meta-tissue 0.4 [1,010] biology, genomics
MetaBAT metabat 0.32.4, 2.13 [1,011] biology, genomics
MetaBCC-LR metabcc_lr 2.0.0 [1,012] biology, genomics
Metabin metabin 1.0 [1,013] genomics
metabolic metabolic 4.0 [1,014] phylogenetics
MetaCherchant metacherchant 0.1.0 [1,015] biology, phylogenetics
MetaCluster metacluster 5.0b [1,016] biology, genomics
MetaCompare metacompare 20181016 [1,017] phylogenetics
metacrast metacrast 20200309 [1,018] phylogenetics
MetaGeneMark metagenemark 2.10, 3.26 [1,019] biology, genomics
METAL metal 20110325 [1,020] biology, ngs, genomics
MetaLAFFA metalaffa 1.0.0 [1,021] phylogenetics
MetaMaps metamaps 20201207 [1,022] phylogenetics
METANNOT metannot 20171129 [1,023] phylogenetics
Metaphlan metaphlan 3.0.3, 3.1.0, 4.0.1 [1,024] phylogenetics
MetaPhlAn2 metaphlan2 2.7.7 [1,025] biology, phylogenetics
MetaPhysicl metaphysicl 1.0.0 [1,026] math, astronomy, simulation
Metashape metashape 1.8.4 [1,027]
MetaSV metasv 0.5.4 [1,028] biology, phylogenetics, ngs
MetaVelvet metavelvet 1.2.06 [1,029] biology, genomics
metaWRAP metawrap 1.2 [1,030] phylogenetics
Metaxa2 metaxa2 2.1.1, 2.1.3, 2.2.3 [1,031] biology, ngs, sequencing
MethylDackel methyldackel 0.5.0, 0.6.1 [1,032] phylogenetics
methylpy methylpy 1.2.9 [1,033] biology, phylogenetics
Metilene metilene 0.2.8 [1,034] biology, genomics, methylation
METIS metis 5.1.0 [1,035] utility
Mfannot mfannot 20180405 [1,036] biology, phylogenetics
mfold mfold 3.6 [1,037] biology, structure, rna
mg-rast mg-rast 20150919 [1,038] biology, genomics
MGEfinder mgefinder 1.0.5 [1,039] phylogenetics
MGERT mgert 1.0.1 [1,040] phylogenetics
MGEScan mgescan 20160416 [1,041] biology, genomics
MGLTools mgltools 1.5.7 [1,042] biology, visualization
MHAP mhap 1.6 [1,043] biology, sequencing
MHCflurry mhcflurry 1.4.3 [1,044] phylogenetics
MIA mia 20130201 [1,045] biology, ngs
micop micop 03312022 [1,046] genomics
MicrobeAnnotator microbeannotator 2.0.5 [1,047] annotation, biology
MIDAS midas 1.3.2, 20160830 [1,048] biology, phylogenetics
MIGRATE-N migraten 4.2.14, 4.4.4, 5.0.4 [1,049] biology, genomics
Mikado mikado 2.3.3 [1,050] biology, genomics, sequencing, pipeline
MIKE mike 1.0 [1,051] geospatial, fluid_dynamics, modeling
Minced minced 0.2.0 [1,052] biology, genomics
Minia minia 3.2.6 [1,053] genomics, biology
Miniasm miniasm 0.2-r168, 0.3-r179 [1,054] biology, phylogenetics
MiniCaller minicaller 20161201 [1,055] biology, ngs, phylogenetics
minigraph minigraph 0.15 [1,056] phylogenetics
minimac minimac 1-20130717, 3-20150727 [1,057] biology, genomics
minimac2 minimac 2-20140915 [1,058] biology, ngs
minimap minimap 2.1t, 2.21, 2.9-r720 [1,059] biology, phylogenetics
minimap2 minimap2 2.24 [1,060] genomics, biology
Minipolish minipolish 0.1.3 [1,061] biology, genomics
Miniprot miniprot 0.12 [1,062] biology, genomics
MinkowskiEngine minkowskiengine 0.5.3, 0.5.4a [1,063] machine_learning
MinPath minpath 1.4 [1,064] biology, phylogenetics
MIRA mira 4.0.rc1, 4.9.6, 5rc2 [1,065] biology, genomics, assembly
miRanda miranda 1.9 [1,066] phylogenetics
miRBShunter mirbshunter 0.2 [1,067] phylogenetics
mirdeep mirdeep 0.1.0, 0.1.1, 2.0.1.3 [1,068] phylogenetics
miRDP2 mirdp2 1.1.4 [1,069] biology, genomics
Mireap mireap 0.20 [1,070] biology
miRge mirge 2.0 [1,071] phylogenetics
Misa misa 1.0 [1,072] biology, genomics
MISO miso 0.5.3 [1,073] biology, ngs, sequencing, rna-seq
MITE-Hunter mite-hunter 20111101 [1,074] biology, phylogenetics
MITObim mitobim 1.9.1 [1,075] phylogenetics
MitoFinder mitofinder 1.0.2, 1.1, 1.4 [1,076] phylogenetics
mitohifi mitohifi 2.2, 3.2 [1,077] genomics, sequencing
MitoPhAST mitophast 3.0 [1,078] phylogenetics
Mitsuba2 mitsuba2 2.2.1 [1,079] graphics
MiXCR mixcr 2.1.8, 3.0.13 [1,080] biology, phylogenetics
MixMHC2pred mixmhc2pred 1.2 [1,081] phylogenetics
MixMHCpred mixmhcpred 2.0.2 [1,082] phylogenetics
mixmogam mixmogam 20190322 [1,083] phylogenetics
MKL mkl 2019.1.144, 2020.0.166, 2020.2.0 [1,084] programming, library, math, compiler
mlcoalsim mlcoalsim 1.9916b [1,085] biology, phylogenetics
mlpack mlpack 3.4.2 [1,086] library
mlst mlst 2.15.2 [1,087] phylogenetics
mlstcheck mlst-check 2.1 [1,088] phylogenetics
mmaction2 mmaction2 1.0.0 [1,089] Machine_Learning, Visualization
MMSEQ mmseq 1.0.8 [1,090] biology, genomics
MMseqs2 mmseqs2 11, 12, 14 [1,091] phylogenetics
MMvec mmvec 1.0.5, 1.0.6 [1,092] metabolomics
MNEtools mnetools 0.22.0, 1.3.1, 1.4.0 [1,093] phylogenetics
MOABS moabs 1.2.9, 1.3.2, 1.3.4 [1,094] biology, ngs
mobsuite mobsuite 3.1.0 [1,095] sequencing, biology
MOCCASIN moccasin 0.25 [1,096] phylogenetics
moco moco 0.4.0 [1,097] Imagina
Model Card Toolkit model_card_toolkit 2.0.0 [1,098] Machine_Learning, Utility, Workflow_automation
MODELLER modeller 9.14, 9.23 [1,099] biology, modeling, structure
MODELTEST modeltest 0.1.2, 0.1.7 [1,100] biology, phylogenetics
Modulus modulus 21.06, 22.03 [1,101] physics, ai, neural_network
Molden molden 5.0 [1,102] chemistry, structure
MolProbity molprobity 20221216 [1,103] biology
momi momi 2.1.19 [1,104] phylogenetics, biology
monai monai 0.8.1, 0.9.0, 1.0.1 [1,105] healthcare
MONAI label ngc-monailabel 0.3.2, 0.6.0 [1,106] healthcare
MongoDB mongodb 4.0.3 [1,107] database
Moni moni 0.2.0 [1,108] genomics, biology
mono mono 5.18 [1,109] linux, programming
Monolix monolix 2023R1, 4.3.2 [1,110] modeling, biology
MOOSE moose 20220610, 20230320, 20230711 [1,111] physics, simulation
MORPHEUS morpheus 23.01 [1,112] machine_learning
Mosaic mosaic 1.7.4 [1,113] phylogenetics
MOSAIK mosaik 2.1.33, 2.2.3, 2.2.30 [1,114] biology, alignment
Mosdepth mosdepth 0.2.3, 0.3.1 [1,115] biology, phylogenetics
moses moses 0.3.1 [1,116] machine learning, data science
Mothur mothur 1.41.3, 1.46.1, 1.48.0 [1,117] biology
MotionCor2 motioncor2 1.2.3, 1.3.1, 1.6.4 [1,118] imaging
mOTU motu 1.1 [1,119] biology, genomics
mOTUs motus 2.5.1 [1,120] phylogenetics
MountainSort mountainsort 0.9.0 [1,121] library
MP-EST mpest 1.4 [1,122] biology, ngs, sequencing
MPACK mpack 0.8.0 [1,123] library
MPB mpb 1.5 [1,124] library, math
MPBoot mpboot 1.1.0 [1,125] biology, phylogenetics
MPFR mpfr 3.1.6, 4.2.1 [1,126] library, math
mpinterfaces mpinterfaces 20170613 [1,127] math
MrBayes mrbayes 3.2.4, 3.2.5, 3.2.6 [1,128] biology, phylogenetics
MRIcroGL mricrogl 20201102, 20210327, 20211006 [1,129] biology, imaging
MRIcron mricron 201306, 20161012, 20190911 [1,130] biology, imaging
mriqc mriqc 0.11.0, 0.16.1, 22.0.1 [1,131] mri, imaging, biology
MRtrix mrtrix 3.0.1, 3.0.3, 3.0rc2 [1,132] biology, imaging
mrtrix3tissue mrtrix3tissue 5.2.9 [1,133] phylogenetics
ms ms 20171108 [1,134] phylogenetics
ms-dial ms-dial 4.4.8 [1,135] biology, metabolomics
msfinder msfinder 3.52 [1,136] biology, metabolomics
mSINGS msings 20180810 [1,137] phylogenetics
MSMC-Tools msmc-tools 20190614 [1,138] phylogenetics
msprime msprime 0.7.4 [1,139] phylogenetics
MstatX mstatx 1.0 [1,140] biology, phylogenetics
MSTmap mstmap 1.0 [1,141] phylogenetics
msvar msvar 1.3 [1,142] biology, genomics
MTG2 mtg2 2.15 [1,143] phylogenetics
mTR mtr 20210526 [1,144] biology, genomics
Mugsy mugsy 1.2.3 [1,145] biology, phylogenetics
Multimatch-gaze multimatchgaze 0.1.3 [1,146] math, data_science
MultiQC multiqc 1.12, 1.7 [1,147] biology, chip-seq
MUMmer mummer 3.23, 4.0.0beta2 [1,148] biology, genomics
MUSCLE muscle 3.8.31, 5.1 [1,149] biology, alignment
MuSE muse 1.0rc [1,150] phylogenetics
Musket musket 1.1 [1,151] biology, genomics, ngs
MuTect mutect 1.1.4, 1.1.7 [1,152] biology, genomics
mutmap mutmap 2.3.3 [1,153] biology
MutSig mutsig 1.4, 1.41 [1,154] biology, genomics
mvftools mvftools 20191124 [1,155] phylogenetics
mvrsion mvrsion 07302018 [1,156] sequencing
mxnet ngc-mxnet 22.08 [1,157] healthcare
mykrobe mykrobe 0.12.2 [1,158] biology
MZMine mzmine 2.52, 2.53, 3.3.0 [1,159] biology, spectroscopy
NAMD namd 2.14b2, 3.0 Alpha, 3.0b2 [1,160] molecular_dynamics
NANO nano 2.8.2 [1,161] programming
nanocaller nanocaller 3.1.0 [1,162] sequencing
nanocomp nanocomp 1.17.0 [1,163] programming, sequencing
NanoCount nanocount 0.2.1 [1,164] phylogenetics
Nanodisco nanodisco 1.0.3 [1,165] phylogenetics
Nanofilt nanofilt 2.7.1 [1,166] phylogenetics
nanolyse nanolyse 1.2.0 [1,167] genomics, biology
NanoPlot nanoplot 1.30.1 [1,168] phylogenetics
Nanopolish nanopolish 0.11.1, 0.13.2, 20171006 [1,169] biology
nanostripper nanostripper 0.1 [1,170] phylogenetics, biology
NanoSV nanosv 1.2.0, 1.2.3, 1.2.4 [1,171] biology, genomics
NanoVar nanovar 1.3.9 [1,172] phylogenetics
Napari napari 0.3.8, 0.4.7 [1,173] phylogenetics
NBODY nbody 6 [1,174] astronomy
NCBI BLAST+ ncbi_blast 2.7.1, 2.8.1, 2.9.0 [1,175] biology
NCBI C++ Toolkit ncbi_toolkit 12.0.0, 21.0.0, 7.0.0 [1,176] biology, programming, library, compiler
NCBI GenBank Tools genbank_tools 20140130 [1,177] biology
ncbi-vdb ncbi-vdb 2.6.3, 2.8.2 [1,178] ngs
ncbi_cli ncbi_cli 15.3.1 [1,179] biology, sequencing, library
nccl nccl 20.11 [1,180] programming, library, gpu
ncftp ncftp 3.2.5 [1,181] file_management
NCL ncl 6.1.2, 6.3.0, 6.6.2 [1,182] climate
NCO nco 4.2.1, 4.4.3 [1,183] data_science
ncview ncview 2.1.2, 2.1.7 [1,184] visualization
NECAT necat 202001019, 20200803 [1,185] genomics
Necklace necklace 1.00 [1,186] biology, phylogenetics
NeEstimator neestimator 2.1 [1,187] biology
nemo nemo 1.0.0rc1, 1.0.1, 1.2.0 [1,188] ai, machine_learning
neovim neovim 0.2.0, 0.8.1, 0.8.3 [1,189] programming, shell
NetCDF netcdf 4.3, 4.3.3, 4.4.3 [1,190] data_science
NetCDF-C netcdf-c 4.8.1, 4.9.0, 4.9.2 [1,191] data_science
NetCDF-F netcdf-f 4.5.3, 4.5.4, 4.6.1 [1,192] data_science
NetLogo netlogo 5.3.64, 6.1.1, 6.2.0 [1,193] modeling
NEURON neuron 7.7.2, 8.0.0, 8.2.1 [1,194] biology, neuroscience
Newbler newbler 2.7, 2.8, 2.9 [1,195] biology, ngs, assembly, de_novo
newick-utils newickutils 1.6 [1,196] biology, genomics, phylogenetics
newick_utils newick_utils 1.6, 1.7 [1,197] biology, phylogenetics
NewTargets newtargets 20210215 [1,198] biology
nextclade nextclade 2.9.1 [1,199] phylogenetics, genomics
NextDenovo nextdenovo 2.4.0 [1,200] phylogenetics
Nextflow nextflow 22.04.5, 22.10.6, 22.11.0 [1,201] biology, workflow_automation
NextGenMap nextgenmap 0.5.5 [1,202] phylogenetics
NextPolish nextpolish 1.3.1 [1,203] phylogenetics
Nextstrain nextstrain 1.16.1 [1,204] phylogenetics
nf-core nf-core 1.12.1, 2.1, 2.7.2 [1,205] biology, workflow_automation
NGC CLI ngccli 2.10.1 [1,206] shell
NGmerge ngmerge 0.3 [1,207] phylogenetics
ngmlr ngmlr 0.2.6, 0.2.7 [1,208] biology, phylogenetics
ngs-bits ngsbits 0.1 [1,209] biology, sequencing
NGS-SDK ngs-sdk 1.2.4, 1.3.0 [1,210] biology, healthcare, programming, library
ngscheckmate ngscheckmate 1.0 [1,211] phylogenetics
ngsremix ngsremix 20221117 [1,212] genomics
ngstools ngstools 20150816 [1,213] biology, ngs
nilearn nilearn 0.7.0, 0.9.0 [1,214] phylogenetics
nimare nimare 0.0.5 [1,215] neuroscience
Nipype nipype 1.6.0, 1.7.0, 1.8.0 [1,216] biology, neuroscience, imaging
nlp nlp 1.1, 1.2 [N/A] machine_learning
nlr-annotator nlr-annotator 0.7 [1,217] phylogenetics
NLR-Parser nlr-parser 1.0 [1,218] phylogenetics
NMRPipe nmrpipe 7.9, 8.2 [1,219] chemistry, biology
NONMEM nonmem 7.3.0, 7.4.4 [1,220] modeling
nonpareil nonpareil 3.3.4 [1,221] phylogenetics
Novoalign novoalign 2.08.02, 3.00.02 [1,222] biology, ngs
NOVOPlasty novoplasty 3.7, 4.2, 4.3 [1,223] phylogenetics
nPhase nphase 1.1.3 [1,224] biology, pipeline
npScarf japsa 1.7 [1,225] phylogenetics
nQuire nquire 20180405 [1,226] phylogenetics
Nsight nsight 2022.1 [1,227] gpu, performance_analysis, utility
Nsightsys nsightsys 2022.2.1 [1,228] gpu, performance_analysis, utility
nt nt 20220404 [1,229] sequencing, neuroscience
ntEdit ntedit 1.2.1 [1,230] phylogenetics
nubeamdedup nubeamdedup 20200907 [1,231] phylogenetics
NucDiff nucdiff 2.0.3 [1,232] phylogenetics
NucleoATAC nucleoatac 0.3.1 [1,233] biology
Nuke nuke 14.0v5 [1,234] Graphics, Utility, Visualization
Nullarbor nullarbor 1.41 [1,235] biology, phylogenetics
Numba numba 0.36.2, 0.43.1, 0.48.0 [1,236] compiler
NUPACK nupack 3.2.2 [1,237] phylogenetics
nvhpc nvhpc 21.7, 23.5, 23.7 [1,238] language, programming, library, math, gpu
nVidia HPC Compilers nvidia 20.11 [1,239] compiler
NWChem nwchem 6.8 [1,240] chemistry
NxTrim nxtrim 0.4.1 [1,241] biology, ngs
Oases oases 0.2.08 [1,242] biology, ngs, assembly
OCaml ocaml 4.02.3 [1,243] language, programming
OCOCO ococo 0.1.2.6 [1,244] biology, phylogenetics
octave octave 6.4.0, 7.2.0, 7.3.0 [1,245] math
odgi odgi 0.6 [1,246] phylogenetics
Olego olego 1.1.2, 1.1.5, 1.1.6 [1,247] biology, ngs, rna-seq
OMindel omindel 20180129 [1,248] phylogenetics
omniCLIP omniclip 0.1.0 [1,249] phylogenetics
OMNIVERSE omniverse beta211004 [1,250] gpu
OMSV omsv 1.0.1 [1,251] phylogenetics
OneFormer oneformer 1.0 [1,252] ai, image_processing, imaging
ONT-Bonito ont-bonito 0.1.5, 0.5.3, 0.6.0 [1,253] phylogenetics
ont_fast5_api ont-fast5-api 2.0.1, 4.0.2 [1,254] phylogenetics
ont_tutorial_cas9 ont_tutorial_cas9 20190705 [1,255] phylogenetics
open-cravat open-cravat 2.0.1 [1,256] biology, genomics
open3d open3d 0.13.0, 0.17.0 [1,257] phylogenetics
OPENACC openacc 16.7 [1,258] programming
OpenBabel openbabel 2.3.2, 2.4.1, 3.1.1 [1,259] biology
OpenBLAS openblas 0.2.20 [1,260] programming, library
OpenCL opencl 18.1.0.013 [1,261] phylogenetics
OpenCV opencv 4.5.2, 4.7.0 [1,262] library
OpenFOAM openfoam 4.1, 5.0, 8.0 [1,263] fluid_dynamics
OpenMM openmm 7.5, 7.5.0, 7.6.0 [1,264] chemistry, molecular_dynamics
OpenMPI openmpi 4.1.1, 4.1.4, 4.1.5 [1,265] programming, library
OpenNeuro openneuro 3.17.4, 3.37.4, 4.19.2 [1,266] biology, data_science
opennmt-py opennmt-py 3.1.0 [1,267] language, machine_learning
OpenPIV-python openpiv 0.21.2 [1,268] programming, imaging
OpenPIV-python-gpu openpiv 20190506-gpu [1,269] programming, imaging
OpenPose openpose 20230106 [1,270] image_processing
OpenSim opensim 4.3 [1,271] phylogenetics
OpenSlide openslide 3.4.1 [1,272] imaging
openstructure openstructure 2.3.1 [1,273] biology
OptiType optitype 1.3.1 [1,274] biology, phylogenetics
Orange3 orange3 3.3.6 [1,275] data_mining
ORCA orca 4.0.1.2 [1,276] chemistry, structure
OrganellePBA organellepba 20180904 [1,277] phylogenetics
OrthoFiller orthofiller 1.1.4 [1,278] phylogenetics
OrthoFinder orthofinder 1.1.10, 2.3.11, 2.5.2 [1,279] biology, ngs
Orthofisher orthofisher 0.1.2 [1,280] biology, genomics
Orthograph orthograph 0.6.3 [1,281] orthology
Orthologer orthologer 2.2.0 [1,282] biology
OrthoMCL orthomcl 2.0.3, 2.0.7, 2.0.9 [1,283] biology, genomics
osprey osprey 1.1.0 [1,284] spectroscopy, neuroscience
OTB otb 5.8.0 [1,285] geospatial
p4est p4est 1.1, 2.8 [1,286] library
p4vasp p4vasp 0.3.29, 0.3.30 [1,287] chemistry, structure
p53MH p53mh 20020901 [1,288] biology, sequencing
p7zip p7zip 9.20.1 [1,289] utility
PacBio pacbio 10.2.0.133434, 11.0.0.146107, 7.0.1 [1,290] biology, ngs, workflow_automation
Package-GFE package-gfe 20150701 [1,291] biology, genomics
PacMAP pacmap 0.7.0 [1,292] genomics
PALADIN paladin 1.3.1 [1,293] biology, phylogenetics
PALES pales 122 [1,294] physics
PAML paml 4.8a, 4.9a, 4.9h [1,295] biology, phylogenetics
panaroo panaroo 1.3.3 [1,296] biology, genomics
Pandaseq pandaseq 20140808, 20150627 [1,297] biology, ngs, sequencing
Pandoc pandoc 2.2.2.1 [1,298] utility
pangolin pangolin 2 [1,299] phylogenetics
panseq panseq 3.2.1 [1,300] phylogenetics
panX panx 1.6.0 [1,301] phylogenetics
PAPI papi 5.5.1, 5.7.0 [1,302] programming, performance_analysis
parabricks parabricks 3.5.0, 3.7.0, 4.0.1 [1,303] phylogenetics
parallel parallel 20150122, 20170322 [1,304] shell, workflow_automation
paralyzer paralyzer 1.5 [1,305] phylogenetics
ParaView paraview 5.4.1, 5.7.0, 5.9.1.1 [1,306] data_science
ParaView Server paraview_server 5.10.1 [1,307] data_science
ParGenes pargenes 1.2.0 [1,308] phylogenetics
ParlAI parlai 1.3.0, 1.5.0 [1,309] phylogenetics
Parsnp parsnp 1.2, 1.5.0, 1.6.2 [1,310] biology, phylogenetics
PartitionFinder partitionfinder 2.0.0-pre-20160513, 2.1.1-20161205, 2.1.1.0 [1,311] biology, phylogenetics, genomics
PASA pasa 2.0.2-r20151207, 2.2.0-r20171013, 2.4.1 [1,312] biology, genomics, ngs
Pascal fpc 3.0.0 [1,313] compiler, programming
PASTA pasta 0.2.0, 1.7.8, 20160616 [1,314] biology, alignment
PATHd8 pathd8 1.0 [1,315] biology, phylogenetics
pathoscope pathoscope 2.0.7 [1,316] sequencing, genomics, biology
PATRIC patric 1.034 [1,317] machine_learning
PAUDA pauda 1.0.1 [1,318] biology, ngs, phylogenetics
PAUP paup 4.0a166, 4.0a168, 4.0b10 [1,319] biology, phylogenetics
PB-Assembly pb-assembly 0.0.6, 0.0.8 [1,320] biology, ngs, sequencing
pbalign pbalign 20160921, 20161221 [1,321] biology
PBCCS pbccs 5.0.0, 6.4.0 [1,322] phylogenetics
pbcore pbcore 1.7.1 [1,323] biology
PBGCpp pbgcpp 1.9.0 [1,324] phylogenetics
pbipa pbipa 1.8.0 [1,325] phylogenetics, biology
PBJelly pbjelly 15.8.24 [1,326] biology, ngs
pbmm2 pbmm2 1.3.0 [1,327] phylogenetics
pbrt pbrt 20181017 [1,328] phylogenetics
pbsmrtpipe pbsmrtpipe 0.63.0 [1,329] biology, programming
pbtk pbtk 3.1.0 [1,330] biology
pbtranscript-tofu pbtranscript-tofu 20150317, 20160119 [1,331] biology, ngs
PCIT pcit 2014 [1,332] biology
PCRE pcre 8.38, 8.39 [1,333] programming, library
PDA pda 1.0.3 [1,334] biology, phylogenetics
pdb2pqr pdb2pqr 2.1.0 [1,335] protein, modeling, biology
PeakSplitter peaksplitter 1.0 [1,336] biology, chip-seq
PEAR pear 0.9.2 [1,337] biology, genomics, ngs
peneasy peneasy 20150530 [1,338] physics
PennCNV penncnv 1.0.5 [1,339] phylogenetics
Perl perl 5.16.0, 5.20.0, 5.24.1 [1,340] programming, language
PerM perm 0.4.0 [1,341] biology, ngs, mapping
PETSc petsc 3.8.1, 3.8.3, 3.8.4 [1,342] math
PfamScan pfamscan 1.3, 1.5 [1,343] biology, genomics
PGAP pgap 20220414, 20230306 [1,344] biology, genomics, annotation, pipeline
PGDSpider pgdspider 2.0.9.0, 2.1.1.5 [1,345] biology, ngs
pggb pggb 0.4.1, 20201106, 20210121 [1,346] phylogenetics
PhaME phame 1.0.3 [1,347] phylogenetics
phanotate phanotate 1.5.0 [1,348] genomics
pharmcat pharmcat 1.8.0 [1,349] biology, phylogenetics
PHASE phase 2.1.1 [1,350] phylogenetics
PHAST phast 1.5 [1,351] biology, phylogenetics
Phenix phenix 1.10.2155, 1.17.1, 1.8.1069 [1,352] material_science
PHI phi 3.1.1, 3.1.2b, 3.1.6 [1,353] math
PhiSpy phispy 3.2 [1,354] phylogenetics
PHLAWD phlawd 20170427 [1,355] biology, phylogenetics
PhotoScan photoscan-pro 1.4.1, 1.4.5 [1,356] image_processing
Photutils photutils 0.5 [1,357] astronomy
PHYling phyling 1.0 [1,358] biology, phylogenetics, genomics
PHYLIP phylip 3.696 [1,359] biology, phylogenetics
PhyloAcc phyloacc 1.0 [1,360] phylogenetics
PhyloBayes phylobayes 3.3f [1,361] biology, phylogenetics
phyloFlash phyloflash 3.3b4 [1,362] phylogenetics
phylonet phylonet 3.5.7, 3.8.2 [1,363] biology, phylogenetics
PhyloParser phyloparser 20180404 [1,364] phylogenetics
PhyloPhlAn2 phylophlan2 0.41 [1,365] phylogenetics
phylopypruner phylopypruner 1.2.3 [1,366] phylogenetics
PhyloSift phylosift 1.1 [1,367] biology, genomics, phylogenetics
phyloTF2 phylotf2 20210726 [1,368] biology, genomics, alignment
Phyluce phyluce 20180727, 20190308, 20191015 [1,369] biology, ngs, sequencing
PhyML phyml 3.0, 3.1, 3.3.20220408 [1,370] biology, phylogenetics
phynd phynd 20200409 [1,371] phylogenetics
Physher physher 1.0.2 [1,372] phylogenetics
PHYUTILITY phyutility 2.7.1 [1,373] biology
Phyx phyx 1.1 [1,374] phylogenetics
PIA2 pia2 20180305 [1,375] biology, phylogenetics
Picard-tools picard 2.5.0, 2.9.0, 2.9.2 [1,376] biology, ngs
PICRUSt picrust 1.1.3, 1.1.4, 2.3.0b [1,377] biology, phylogenetics
PICSL picsl 1.3 [1,378] imaging
Piggy piggy 20171220 [1,379] biology, ngs
Pigz pigz 2.4 [1,380] compression
PILON pilon 1.22, 1.24 [1,381] biology, ngs, phylogenetics
Pindel pindel 0.2.5b8 [1,382] biology, phylogenetics
pipe-clip pipe-clip 1.1.0 [1,383] biology, ngs
pipits pipits 1.3.6, 1.4.0 [1,384] biology, sequencing
Piranha piranha 1.2.1 [1,385] biology, phylogenetics
PlantTribes planttribes 1.0.4 [1,386] phylogenetics
PLAST plast 1.0, 2.3.2 [1,387] biology
platanus platanus 1.2.4 [1,388] phylogenetics
Platon platon 1.6 [1,389] biology, sequencing
Platypus platypus 0.8.1 [1,390] biology, ngs
PLEK plek 1.2.2 [1,391] biology, phylogenetics
Plink plink 2.00a2, 2.00a3LM, 2.00a5LM [1,392] biology, genomics, phylogenetics
plinkseq plinkseq 0.10 [1,393] biology, library
plotsr plotsr 0.5.4 [1,394] genomics, biology
PLUMED plumed 2.7.3, 2.9.0, 2021.2 [1,395] chemistry, molecular_dynamics
pm4py pm4py 2.7.4 [1,396] Data_Mining, Machine_Learning
pod5 pod5 0.1.5, 20220621 [1,397] sequencing
PolyGembler polygembler 1.0 [1,398] phylogenetics
PolyPHen polyphen 2.2.2.r405b [1,399] biology, genomics
polyply polyply 1.3.0 [1,400] phylogenetics, biology
Polypolish polypolish 0.5.0 [1,401] biology, genomics
pomoxis pomoxis 0.1.11, 0.2.5, 0.3.2 [1,402] biology, phylogenetics
popcorn popcorn 20211104 [1,403] phylogenetics, biology
PopLDdecay poplddecay 3.40 [1,404] phylogenetics
popoolation popoolation 1.2.2 [1,405] biology, phylogenetics
Porechop porechop 0.2.4 [1,406] phylogenetics
Poretools poretools 0.6.1 [1,407] phylogenetics
portcullis portcullis 1.2.3 [1,408] phylogenetics
PosiGene posigene 20171113 [1,409] biology, phylogenetics
POV-Ray povray 3.7 [1,410] graphics
powerfit powerfit 2.0.0 [1,411] Physics
pplacer pplacer 1.1.alpha19 [1,412] biology, phylogenetics, genomics
PRANK prank 170427, 20150803 [1,413] biology, alignment
Predector predector 20201110 [1,414] phylogenetics
preplot preplot 14.0.2 []
Preseq preseq 0.0.4 [1,415] biology, ngs
PRICE price 1.2 [1,416] biology, ngs
Primer3 primer3 2.3.4 [1,417] biology, genomics
primus primus 1.8.0 [1,418] biology, phylogenetics
PRINSEQ prinseq 0.20.4 [1,419] biology, sequencing
PRINSEQ++ prinseq++ 1.2 [1,420] phylogenetics
ProbABEL probabel 0.4.2, 0.4.3, 0.4.5 [1,421] genomics
probalign probalign 1.4 [1,422] biology, ngs
Processing processing 3.4 [1,423] programming, language, visualization
Prodigal prodigal 2.6.2, 2.6.3 [1,424] biology, genomics
ProDy prody 2.0 [1,425] phylogenetics
Program Database Toolkit pdt 3.20, 3.22, 3.24 [1,426] language, programming, performance_analysis
PROJ proj 4.9.3, 5.1.0, 8.0.1 [1,427] library, geospatial
Prokka prokka 1.12, 1.14.6 [1,428] biology, genomics, assembly
Proovread proovread 1.03rcl, 2.12, 2.13 [1,429] biology, genomics, ngs
ProSplign prosplign 1.0.0 [1,430] phylogenetics
Protege protege 5.1.0 [1,431] genomics
Proteinortho proteinortho 4.26, 5.11, 5.16 [1,432] biology, genomics
ProtExcluder protexcluder 1.2 [1,433] biology, phylogenetics
ProtHint prothint 2.6.0 [1,434] biology, genomics
protobuf protobuf 2.5.0, 3.5.1 [1,435] web, library
prottest3 prottest3 3.4.2 [1,436] biology
PROVEAN provean 1.1.5 [1,437] biology, genomics
PRSice prsice 2.3.3 [1,438] phylogenetics
Pseudofinder pseudofinder 1.0 [1,439] phylogenetics
PsiCLASS psiclass 1.0.1 [1,440] phylogenetics
PSMC psmc 0.6.5 [1,441] phylogenetics
psRobot psrobot 1.2 [1,442] phylogenetics
Pufferfish pufferfish 20200417, 20230223 [1,443] phylogenetics
PureCLIP pureclip 1.1.1 [1,444] phylogenetics
Purge_Dups purge_dups 1.0.1 [1,445] phylogenetics
purge_haplotigs purge_haplotigs 1.1.2 [1,446] sequencing, biology
pvconv pvconv 10152018 [1,447] imaging
pyani pyani 0.2.10, 0.2.12 [1,448] phylogenetics
Pybedtools pybedtools 0.8.2, 0.9.0 [1,449] phylogenetics
PyBSASeq pybsaseq 20200623 [1,450] phylogenetics
PyCharm pycharm 2018.3, 2023.1.2 [1,451] programming
Pycharm Pro pycharm-pro 23.1.3 [1,452] software
pychopper pychopper 2.5.0, 2.7.1 [1,453] phylogenetics, sequencing
PyCogent pycogent 1.9 [1,454] biology, genomics
pycoqc pycoqc 2.5.2 [1,455] sequencing
PyDeface pydeface 2.0.0 [1,456] imaging
pyEGA3 pyega3 3.4.1, 5.0.2 [1,457] biology, genomics, utility
PyEXR pyexr 0.3.10 [1,458] programming
Pyfaidx pyfaidx 0.5.2 [1,459] biology, ngs, sequencing
pyfasta pyfasta 0.5.2 [1,460] phylogenetics
pygenometracks pygenometracks 3.8 [1,461] genomics, biology
pygot pygot 20170518 [1,462] biology, phylogenetics
pyhdf pyhdf 0.9.0 [1,463] library
PyHIST pyhist 1.0 [1,464] biology, imaging, image_processing
pymesh pymesh 0.3.0 [1,465] math, graphics
PyPHLAWD pyphlawd 20180416, 20190414 [1,466] biology, phylogenetics
Pyroms pyroms 1.0 [1,467] geospatial
PyRosetta pyrosetta r56324 [1,468] biology, structure, modeling
pyrpipe pyrpipe 0.0.3 [1,469] phylogenetics
Pysamstats pysamstats 1.1.2 [1,470] phylogenetics
PySLURM pyslurm 18.08.04 [1,471] scheduler
Python python 3.6.3, 3.6.5, 3.8 [1,472] language, programming
Python-core python-core 3.6.5, 3.7, 3.8 [1,473] language, programming
Python2 python 2.7.11 [1,474] language, programming
PyTorch ngc-pytorch 1.11.0, 1.9.0 [1,475] library, math
pytorch pytorch 1.8.1, 1.9.0, 2.0.1 [1,476] library, math
PyVCF pyvcf 0.6.0, 0.6.8 [1,477] biology, phylogenetics
PyVista pyvista 0.26.1 [1,478] phylogenetics
pyweka pyweka 0.3.18 [1,479] phylogenetics
QAPA qapa 1.3.1, 1.3.3 [1,480] phylogenetics
qcat qcat 1.1.0 [1,481] phylogenetics
qctool qctool 2.0.1 [1,482] phylogenetics
QD qd 2.3.22 [1,483] library, compiler, math
QDD qdd 3.1.2 [1,484] biology, genomics, ngs
QGIS qgis 2.18.0, 3.14.0 [1,485] geospatial
QIIME2 qiime2 2022.8, 2023.5, 2023.7 [1,486] biology, genomics
QMCPACK qmcpack 3.4.0 [1,487] library
QRNA qrna 2.0.4 [1,488] phylogenetics
QT qt 5.12.9, 5.15.2, 5.15.4 [1,489] library
QTL-seq qtl-seq 2.2.2 [1,490] biology, sequencing, pipeline
QTLtools qtltools 1.2, 1.3.1 [1,491] phylogenetics
Quake quake 0.3 [1,492] biology, sequencing
QualiMap qualimap 2.1.2 [1,493] biology, sequencing, alignment
Quantas quantas 1.0.4, 1.0.8, 1.0.9 [1,494] biology, ngs
quantisnp quantisnp 2 [1,495] biology, genomics
QuartetScores quartetscores 1.0.0 [1,496] phylogenetics
QUAST quast 4.4, 5.0.0, 5.0.2 [1,497] biology, ngs, sequencing, rna-seq
quickmerge quickmerge 0.3 [1,498] phylogenetics
Quickquartet quickquartet 1.0.0 [1,499] biology, ngs
QUIP quip 20201029, 20210626 [1,500] phylogenetics
QuorUM quorum 1.0.0 [1,501] biology
qupath qupath 0.4.3 [1,502] biology, Imaging
R R 4.1, 4.2, 4.3 [1,503] statistics
r-index r-index 20190711 [1,504] phylogenetics
r8s r8s 1.8, 1.81 [1,505] phylogenetics
RACA raca 0.9.1.1 [1,506] biology, ngs
Racon racon 1.4.10, 1.4.13, 1.5.0 [1,507] phylogenetics
RADICAL radical 0.2 [1,508] biology, genomics
radorgminer radorgminer 0.9 [1,509] genomics, biology, sequencing
RaGOO ragoo 1.11 [1,510] phylogenetics
Ragout ragout 2.3 [1,511] genomics
RagTag ragtag 1.0.0, 2.0.1 [1,512] phylogenetics
rainbow rainbow 2.0.4 [1,513] biology, sequencing
Rainbowfish rainbowfish 0.1.0 [1,514] phylogenetics
RAiSD raisd 2.8 [1,515] phylogenetics
Randfold randfold 2.0.1 [1,516] biology, RNA
ranger ranger 1.9.3 [1,517] file_management
rapidsai rapidsai 21.12, 22.04, 23.02 [1,518] data_science
rapidtide rapidtide 1.9.0 [1,519] phylogenetics
RAPSearch rapsearch 2.24 [1,520] biology, phylogenetics
Rascaf rascaf 1.0.2 [1,521] biology
RATTLE rattle 1.0 [1,522] Sequencing
RAVE rave 2.1 [1,523] biology, phylogenetics
Raven raven 1.8.1 [1,524] assembly
RAxML raxml 8.2.10, 8.2.12, 8.2.8 [1,525] biology, phylogenetics
RAxML-NG raxml-ng 0.9.0, 1.0.2, 1.1.0 [1,526] phylogenetics
razers3 razers3 3.5.7 [1,527] biology, phylogenetics
rbp-maps rbp-maps 0.1.4 [1,528] phylogenetics
rclone rclone 1.57.0, 1.58.1 [1,529] web
Rcorrector rcorrector 1.0.4 [1,530] phylogenetics
RDKit rdkit 2020092 [1,531] chemistry
rDnaTools rdnatools 0.1.3 [1,532] phylogenetics
read2tree read2tree 0.1.5 [1,533] alignment, biology, genomics, phylogenetics
READemption reademption 1.0.0 [1,534] phylogenetics
REAPR reapr 1.0.18 [1,535] biology, assembly
Rebaler rebaler 0.2.0 [1,536] phylogenetics
reCOGnizer recognizer 1.3.3 [1,537] phylogenetics
recon recon 1.08 [1,538] biology, sequencing
recycler recycler 0.7 [1,539] biology, sequencing
Redis redis 2.8.13, 2.8.19 [1,540] database, data_science
REDItools2 reditools2 20200701 [1,541] phylogenetics
Redundans redundans 0.14a [1,542] biology, phylogenetics
ReFrame reframe 3.2 [1,543] performance_analysis, utility
regtools regtools 0.5.2 [1,544] biology, rna-seq, genomics
release release 12082021 [1,545] molecular_dynamics, machine_learning
RELION relion 3.0b, 3.1.0, 4.0.1 [1,546] biology, imaging
RelocaTE2 relocate2 2.0.1 [1,547] phylogenetics
REMORA remora 1.8.2, 1.8.3, 1.8.5 [1,548] performance_analysis
REPdenovo repdenovo 20170222 [1,549] biology, phylogenetics
RepeatAnalysis repeatanalysis 0.10.0, 0.12.2 [] biology, phylogenetics
RepeatAnalysisTools repeatanalysistools 20210506 [1,550] biology, genomics, sequencing, utility
RepeatExplorer repeatexplorer 20150506, 20180517 [1,551] biology, ngs
RepeatMasker repeatmasker 4.0.5, 4.0.9, 4.1.1 [1,552] biology
RepeatModeler repeatmodeler 1.0.8, 2.0 [1,553] biology
repeatscout repeatscout 1.0.5 [1,554] biology
RepeatSeq repeatseq 0.8.2 [1,555] phylogenetics
reptile reptile 1.1 [1,556] biology, ngs, math
ResFinder resfinder 4.0 [1,557] biology, genomics
Resistome resistome 20170111 [1,558] phylogenetics
Resolve resolve 18.1.4 [1,559] Graphics, Utility, Visualization
RevBayes revbayes 1.0.7, 1.0.9, 1.1.1 [1,560] biology, phylogenetics
RFMIX rfmix 2.03 [1,561] phylogenetics
RGAugury rgaugury 20220107 [1,562] sequencing, biology
RGI rgi 4.2.2, 5.1.1, 6.0.2 [1,563] phylogenetics
RGIS rgis 20180211, 20180814 [1,564] geospatial
RHash rhash 1.3.3 [1,565] programming
RiboCode ribocode 1.2.11 [1,566] phylogenetics
riboPicker ribopicker 0.4.3 [1,567] biology, sequencing
RiboTaper ribotaper 1.3.1a [1,568] phylogenetics
RIGERJ rigerj 2.0.2 [1,569] phylogenetics
rMATS turbo rmats-turbo 4.1.2 [1,570] biology, sequencing, genomics
rmats2sashimiplot rmats2sashimiplot 2.0.3, 2.0.4 [1,571] phylogenetics
Rmpi Rmpi 3.5.1, 4.0.3 [1,572] statistics, programming
RNAFramework rnaframework 2.7.2 [1,573] biology, RNA, sequencing
RNAhybrid rnahybrid 2.1.1 [1,574] biology, genomics
rnalysis rnalysis 3.7.0 [1,575] sequencing, biology
RNAmmer rnammer 1.2 [1,576] biology, rna-seq
rnaQUAST rnaquast 1.5.1 [1,577] biology, ngs, sequencing, rna-seq
RNAsalsa rnasalsa 0.8.1 [1,578] biology, phylogenetics
rnaseqlib rnaseqlib 20150721 [1,579] biology, phylogenetics, rna-seq
RNAstructure rnastructure 6.3 [1,580] biology, sequencing
Roary roary 3.12.0, 3.13.0, 3.4.1 [1,581] biology, genomics
roguenarok roguenarok 20230418 [1,582] phylogenetics
ROOT root 5.34.17, 6.0, 6.06.02 [1,583] data_science
ROOTPy rootpy 20160323 [1,584] data_science
Rosetta rosetta 2014wk4, 2019.35.60890, 2021.16.61629 [1,585] biology, structure, modeling
RoseTTAFold rosettafold 1.0.0 [1,586] phylogenetics
rrnaselector rrnaselector 1.0 [1,587] biology, sequencing
RSEG rseg 0.4.8 [1,588] biology, genomics
RSEM rsem 1.2.31, 1.2.7, 1.3.3 [1,589] biology, ngs, sequencing
RSeQC rseqc 2.6.4, 3.0.0 [1,590] biology, ngs, rna-seq
RStudio rstudio 1.4, 2021.09.0, 2022.02.3 [1,591] statistics
rsync rsync 3.2.7 [1,592] software, utility
RTGTools rtgtools 3.7.1 [1,593] biology, ngs
Ruby ruby 2.5.1 [1,594] programming, language
run_dbcan run_dbcan 4.0.0 [1,595] biology
Rust rust 1.52.1, 1.62.1, 1.70.0 [1,596] programming
rvtests rvtests 2.1.0 [1,597] genomics, biology, sequencing
S.A.G.E s.a.g.e 6.4.2 [1,598] phylogenetics
Sabre sabre 1.0 [1,599] phylogenetics
saffrontree saffrontree 0.1.2 [1,600] phylogenetics
saige saige 0.45.0 [1,601] genomics
Sailfish sailfish 0.6.3 [1,602] biology, genomics, ngs, rna-seq
Salmon salmon 1.5.2, 1.8.0, 1.9.0 [1,603] biology, rna-seq
SALSA salsa 20171009, 20191001, 20220408 [1,604] biology, ngs
Sambamba sambamba 0.6.3, 0.6.6, 0.6.9 [1,605] biology, ngs
samblaster samblaster 0.1.14, 0.1.24 [1,606] biology, ngs, sequencing
sampledock sampledock 0.5.1 [1,607] molecular_dynamics, AI
SAMStat samstat 1.08 [1,608] biology, ngs, sequencing
Samtools samtools 1.7, 1.8, 1.9 [1,609] biology, ngs, sequencing
SAS sas 9.4, 9.4.TS1M8 [1,610] statistics, data_science
Sate sate 2.2.7 [1,611] biology, phylogenetics
Satsuma satsuma 3.0 [1,612] phylogenetics
Satsuma2 satsuma2 20161123, 3.1 [1,613] phylogenetics
sc-im scim 0.8.2 [1,614] utility, visualization
Scala scala 2.11.5, 3.0.1 [1,615] programming, language
Scalablast scalablast 2.4.53 [1,616] biology, genomics
ScaLAPACK scalapack 2.0.2, 2.1.0, 2.2.1.5 [1,617] programming, library
scallop scallop 0.10.5 [1,618] phylogenetics
Scalpel scalpel 0.1.1, 0.5.3 [1,619] biology, ngs
scapp scapp 0.1.4 [1,620] genomics, assembly
scGPT scgpt 0.1.2 [1,621] Biology, Data_Science, Genomics
Schrodinger Suite schrodinger 2019-3, 2020-4, 2021-2 [1,622] chemistry, molecular_dynamics
sciann sciann 0.7.0.1 [1,623] machine_learning
scipion scipion 3.0.0, 3.1.0 [1,624] image_processing
Scipion scipion 1.2 [1,625] image_processing
SCIrun scirun 5.0.Z [1,626] phylogenetics
Scoary scoary 1.6.16 [1,627] phylogenetics
Scons scons 2.5.1, 3.1.2 [1,628] programming
SCOP scop 20180311 [1,629] biology, assembly
score-sde score-sde 20221110 [1,630] Machine_Learning
Scrappie scrappie 1.4.2 [1,631] biology, genomics
SCRATCH-1D scratch1d 1.0, 2.0 [1,632] biology, ngs
Screen screen 4.8.0 [1,633] programming, shell
SCRIPTURE scripture 20101211 [1,634] biology, genomics
Scythe scythe 0.991 [1,635] biology, ngs
sdsl sdsl 2.1.1 [1,636] library, compiler
SE-MEI se-mei 0.1.0 [1,637] phylogenetics
SeCaPr secapr 1.1.12, 2.0.2, 2.1.1 [1,638] phylogenetics
seekdeep seekdeep 3.0.1, 3.0.1.0 [1,639] biology, sequencing
Segemehl segemehl 0.1.9, 0.3.4 [1,640] biology, ngs, sequencing
segment-liftover segment-liftover 20211021 [1,641] biology, genomics
SEPP sepp 20160614 [1,642] biology, phylogenetics
Seq-Gen seq-gen 1.3.3 [1,643] biology, phylogenetics
seq_crumbs seq_crumbs 20150120 [1,644] biology, sequencing, genomics, utility
SeqKit seqkit 0.8.0, 2.0.0, 2.4.0 [1,645] biology, phylogenetics
seqmagick seqmagick 0.8.4 [1,646] biology
SeqMap seqmap 1.0.13 [1,647] biology, sequencing, ngs
seqmule seqmule 1.2.6 [1,648] biology, sequencing
SEQPower seqpower 1.1.1 [1,649] genomics, phylogenetics
SeqPrep seqprep 0.5, 1.1 [1,650] biology, ngs, sequencing
seqscreen seqscreen 3.3 [1,651] sequencing, biology
seqtk seqtk 1.3, 20140729 [1,652] biology, genomics, ngs
SEQuel sequel 1.0.1 [1,653] biology, ngs
SequelQC sequelqc 1.1.0 [1,654] phylogenetics
seqwish seqwish 0.7, 20190509 [1,655] phylogenetics
SeqyClean seqyclean 1.8.10 [1,656] biology, ngs, sequencing
SeSiMCMC sesimcmc 4.36 [1,657] biology, sequencing
SExtractor sextractor 2.19.5 [1,658] astronomy
SHAPE-MaP shapemap 1.2 [1,659] biology, phylogenetics
SHAPEIT shapeit 2.12, 2.5 [1,660] biology, variant_calling
SHAPEIT4 shapeit4 4.2.2 [1,661] biology, sequencing
ShapeMapper shapemapper 2.1.3, 2.1.5 [1,662] biology, phylogenetics
SHARCGS sharcgs 1.2.11 [1,663] biology, ngs, de_novo
Shasta shasta 0.1.0 [1,664] phylogenetics
SHEsisPlus shesisplus 1.0, 1.01 [1,665] biology, genomics
shogun shogun 6.1.3 [1,666] phylogenetics
Shortbred shortbred 0.9.4 [1,667] phylogenetics
shovill shovill 1.1.0 [1,668] genomics, sequencing, biology
SHRiMP shrimp 2.2.3 [1,669] biology, genomics, ngs
shustring shustring 2.6 [1,670] biology, sequencing
SibeliaZ sibeliaz 1.2.2, 1.2.3, 1.2.4 [1,671] biology, genomics, alignment
SICER sicer 1.1 [1,672] biology, chip-seq
Sickle sickle 1.200, 1.33 [1,673] biology, ngs
Siesta siesta 3.2, 4.1b2, 4.1b3 [1,674] chemistry
SIFT sift 4.0.3b [1,675] biology, genomics
SIGffRid sigffrid 1.1 [1,676] phylogenetics
SignalP signalp 4.1c, 5.0b [1,677] biology, phylogenetics
SiLiX silix 1.2.11, 1.3.0 [1,678] phylogenetics
silo silo 4.7 [1,679] library
sim4 sim4 20121010 [1,680] biology, genomics
Sim4Life sim4life 7.0.1, 7.2.3 [1,681] biology, simulation
Simka simka 1.5.3 [1,682] phylogenetics
SimNIBS simnibs 3.2.1, 4.0.0 [1,683] phylogenetics
SimSeq simseq 4.12.2011 [1,684] biology, ngs, phylogenetics
Simulia simulia 2019 [1,685] simulation, visualization
SInC sinc 20140120 [1,686] biology, phylogenetics
sine_scan sine_scan 1.1.1 [1,687] phylogenetics
Singularity singularity 3.10.4 [1,688] workflow_automation
SIPeS sipes 2.0 [1,689] biology, chip-seq
SIRIL siril 1.2.0 [1,690] image processing
sisl sisl 0.8.3 [1,691] physics, structure
Ska2 ska2 0.3.0 [1,692] alignment, biology, genomics
skmer skmer 3.2.1 [1,693] genomics, biology
Slamdunk slamdunk 0.4.1, 0.4.2 [1,694] phylogenetics
SLAW slaw 20211217 [1,695] chemistry, spectroscopy
Slicer slicer 4.3.1, 5.0.3, 5.2.1 [1,696] biology, neuroscience, imaging
slow5tools slow5tools 0.5.1, 1.1.0 [1,697] biology, sequencing
slurm-drmaa slurm-drmaa 1.1.2, 1.1.3 [1,698] library, scheduler, programming
smalt smalt 0.7.6 [1,699] biology, phylogenetics
SMARTdenovo smartdenovo 20180219 [1,700] biology, phylogenetics
smartie-sv smartie-sv 20180308 [1,701] phylogenetics
SMC++ smcpp 1.15.4 [1,702] biology, genomics, sequencing
Smetana smetana 1.1.0 [1,703] phylogenetics
SMR smr 1.03 [1,704] biology, genomics
SMRT-SV smrtsv2 2.0.0 [1,705] biology, ngs
SMS sms 1.7 [1,706] biology
Smudgeplot smudgeplot 0.2.4 [1,707] phylogenetics
Snakemake snakemake 6.4.1, 7.16, 7.5.0 [1,708] biology, workflow_automation
SNAP snap 2.0.0, 2.0.3, 20100728 [1,709] biology, sequencing
SNAPE-pooled snape-pooled 20130407 [1,710] biology, variant_calling
SNeP snep 1.1 [1,711] biology, phylogenetics
Sniffles sniffles 1.0.11, 1.0.6, 1.0.8 [1,712] phylogenetics
Sniffles2 sniffles2 2.0.6 [1,713] biology
Snippy snippy 20160419, 4.6.0 [1,714] biology, phylogenetics
SNP-Pipeline snp-pipeline 1.0.1 [1,715] biology, phylogenetics
SNP-sites snp-sites 2.0.3 [1,716] biology, variant_calling
snp2hla snp2hla 1.0.3 [1,717] biology, genomics
SnpEff snpeff 4.3t, 5.0, 5.1d [1,718] biology, annotation
snpflip snpflip 20190515 [1,719] biology, phylogenetics
SNPGenie snpgenie 20190620 [1,720] phylogenetics
SNPhylo snphylo 20140701 [1,721] biology, phylogenetics
SNPsplit snpsplit 0.5.0 [1,722] biology, sequencing
SNPTEST snptest 2.5.2 [1,723] phylogenetics
SOAPaligner soapaligner 2.21 [1,724] phylogenetics
SOAPdenovo soapdenovo 1.05, 2.04 [1,725] biology, ngs
SOAPdenovo-Trans soapdenovo-trans 1.01, 1.03 [1,726] biology, ngs
SOAPec soapec 2.03 [1,727] biology, phylogenetics
SOAPnuke soapnuke 2.1.0 [1,728] phylogenetics
SOAPsplice soapsplice 1.10 [1,729] biology, ngs
SODA soda 20200930 [1,730] biology
SOLAR solar 8.4.2 [1,731] phylogenetics
SomaticSeq somaticseq 3.6.2 [1,732] phylogenetics
SortaDate sortadate 20190705 [1,733] phylogenetics
SortMeRNA sortmerna 2.1, 4.0, 4.3.6 [1,734] biology, sequencing, ngs
SourceTracker2 sourcetracker2 2.0.1 [1,735] phylogenetics
Sourmash sourmash 2.0.1, 4.5.0 [1,736] phylogenetics
SoX sox 14.4.2 [1,737] phylogenetics
spacemake spacemake 0.5.5 [1,738] sequencing
SpaceRanger spaceranger 1.3.1, 2.1.0 [1,739] phylogenetics
SPAdes spades 3.15.3, 3.7.1, 3.8.0 [1,740] biology, ngs
SparCC sparcc 201608 [1,741] biology
Spark spark 2.2.0, 3.1.1 [1,742] utility
sparsehash sparsehash 2.0.3 [1,743] web, programming
SPARTA+ sparta+ 2.60 [1,744] chemistry
Spec2nii spec2nii 0.3.4 [1,745] phylogenetics
SpeedSeq speedseq 0.1.2 [1,746] phylogenetics
Spidey spidey 20150922 [1,747] biology, genomics
SpinalCordToolbox spinalcordtoolbox 5.4 [1,748] phylogenetics
SplAdder spladder 2.4.2 [1,749] phylogenetics
SpliceGrapher splicegrapher 0.2.5 [1,750] biology, sequencing
SpliceTrap splicetrap 0.90.5 [1,751] biology, genomics, ngs
SPM spm 12b, 8, 8r5236 [1,752] biology
spruceup spruceup 2019.2.3 [1,753] phylogenetics
Sputnik sputnik 1.0 [1,754] biology
spyder spyder 4.1.4, 5.1.1, 5.3.2 [1,755] programming
SQANTI sqanti 1.2 [1,756] phylogenetics
SQANTI2 sqanti2 5.0 [1,757] phylogenetics
SQANTI3 sqanti3 1.6, 4.2, 5.1.1 [1,758] phylogenetics
SQL Developer sqldeveloper 4.1.2 [1,759] programming, database
SQLite sqlite 3.33.0, 3.8.8.2 [1,760] database
SqueezeMeta squeezemeta 1.4.0, 1.5.2, 1.6.0 [1,761] phylogenetics
squigglekit squigglekit 1.0.0 [1,762] visualization, biology
squigglenet squigglenet 1.0 [1,763] sequencing, biology
SRA sra 3.0.0, 3.0.2, 3.0.5 [1,764] biology, ngs
sra-human-scrubber sra_human_scrubber 1.1 [1,765] genomics
SRAssembler srassembler 1.0.0 [1,766] phylogenetics
srst2 srst2 0.2.0 [1,767] sequencing, genomics, biology
SSM ssm 20210511 [1,768] phylogenetics
SSPACE sspace 2.0, 3.0 [1,769] biology, ngs
ssr_pipeline ssr_pipeline 0.951 [1,770] biology, sequencing
stable-diffusion stable-diffusion 20221116 [1,771] machine_learning
Stacks stacks 2.53, 2.55, 20190403 [1,772] biology, genomics, ngs
stacks stacks 2.61, 2.64 [1,773] biology, genomics, ngs
Staden staden 1.14.6 [1,774] biology, phylogenetics
Stampy stampy 1.0.31 [1,775] biology, sequencing
staphb-toolkit staphb-toolkit 1.2.0, 1.3.10 [1,776] biology
STAR star 2.7.5c, 2.7.6a, 2.7.9a [1,777] biology, ngs, rna-seq
STAR-CCM+ starccm+ 14.04.011, 15.02.009, 8.06 [1,778] fluid_dynamics
STAR-Fusion star-fusion 1.1.0, 1.3.1, 1.9.1 [1,779] biology, sequencing
starseqr starseqr 0.6.7 [1,780] phylogenetics
Stata stata 10.1, 13 [1,781] statistics
Strainline strainline 1.0 [1,782] biology
stringMLST stringmlst 0.4 [1,783] biology, chip-seq
Stringtie stringtie 1.3.4d, 2.0.4, 2.1.3b [1,784] biology, ngs, sequencing, alignment
Structure structure 2.3.3, 2.3.4 [1,785] biology, genomics
Structure_threader structure_threader 1.3.10 [1,786] utility, structure
stumpy stumpy 1.11.1 [1,787] library, math
stylegan3 stylegan3 20211028 [1,788] ai, image_processing
SU2 su2 7.0.6 [1,789] phylogenetics
subphaser subphaser 1.2.6 [1,790] sequencing, biology
Subread subread 1.6.2, 2.0.0, 2.0.3 [1,791] biology, sequencing, variant_calling
Subversion subversion 1.14.2, 1.9.7 [1,792] revision_control
SUMO sumo 1.18.0, 1.2.0, 1.9.2 [1,793] simulation, mapping
SUNDIALS sundials 2.5.0, 3.0.0, 6.1.1 [1,794] math
supercell supercell 20170602 [1,795] biology, ngs
SuperCRUNCH supercrunch 1.2.1 [1,796] phylogenetics
Supernova supernova 1.2.1, 2.0.0, 2.1.1 [1,797] biology, phylogenetics, ngs
SUPPA suppa 2.3 [1,798] phylogenetics
Survival_Kit survival_kit 6.12 [1,799] healthcare
SURVIVOR survivor 1.0.6 [1,800] phylogenetics
SVDetect svdetect 0.8b [1,801] biology, ngs, genomics
svim svim 1.4.2 [1,802] biology
svim-asm svim-asm 1.0.2 [1,803] biology
svtyper svtyper 0.7.1 [1,804] biology, genomics, sequencing
swarm swarm 1.2.11 [1,805] data_science
Sweed sweed 3.3.2 [1,806] biology, phylogenetics
SWIG swig 2.0.9, 3.0.12, 3.0.8 [1,807] library, programming, compiler
SWSC-EN swsc-en 1.0.0 [1,808] phylogenetics
Synima synima 20210908 [1,809] phylogenetics
syri syri 1.5.4 [1,810] genomics, biology
TACO taco 0.7.3 [1,811] phylogenetics
Taiyaki taiyaki 5.0.1 [1,812] phylogenetics
talesf talesf 20160814 [1,813] phylogenetics
talon talon 5.0 [1,814] biology, sequencing
Tandem-Genotypes tandem-genotypes 1.4.0 [1,815] phylogenetics
Tantan tantan 13 [1,816] imaging, ngs, genomics
Tapestri tapestri 2.0.1 [1,817] phylogenetics
tapir tapir 20160825 [1,818] biology, phylogenetics
TAPIS tapis 1.2.1 [1,819] biology, sequencing
TASSEL tassel 5.0, 5.2.20, 5.2.29 [1,820] biology, genomics, sequencing
TAU tau 2.23, 2.26, 2.26.3 [1,821] library, performance_analysis
Tax4Fun tax4fun 0.3.1 [1,822] phylogenetics
taxMaps taxmaps 0.1 [1,823] biology, phylogenetics, genomics
TaxonKit taxonkit 0.13.0, 0.9.0 [1,824] phylogenetics
Taxtastic taxtastic 0.5.7, 0.9.1 [1,825] biology, genomics
tbb tbb 2017_20161128 [1,826] library
tbprofiler tbprofiler 4.4.1 [1,827] genomics, biology
tcllib tcllib 1.18 [1,828] library
tcoffee tcoffee 10.00.r1613, 9.03.r1318 [1,829] biology
TDNAscan tdnascan 20210304 [1,830] phylogenetics
Tecplot 360 EX tecplot 2015R1 [1,831] math, animation, fluid_dynamics, simulation
tellseq tellseq 1.0.0 [1,832] sequencing, phylogenetics
TEMP temp 20170731 [1,833] phylogenetics
TEMP2 temp2 0.1.4 [1,834] phylogenetics
TensorFlow ngc-tensorflow 2.6.0, 2.7.0, 2.8.0 [1,835] library, math
TESS tess 2.3.1 [1,836] biology, genomics, math
Test test 1.0 [1,837] shell
TetGen tetgen 1.5.0 [1,838] modeling
TEToolkit tetoolkit 1.5.1 [1,839] biology, sequencing
TEtools tetools 20180213 [1,840] biology, phylogenetics
Texlive texlive 20191127, 2020 [1,841] documentation
textract textract 1.6.1 [1,842] data_science, file_management
TGICL tgicl 2.1 [1,843] biology, ngs, sequencing
TGSGapCloser tgsgapcloser 1.0.3 [1,844] phylogenetics
the_silver_searcher the_silver_searcher 2.2.0 [1,845] search
Theano theano 1.0.4 [1,846] library, math, gpu
Themisto themisto 0.2.0, 1.1.0 [1,847] genomics, alignment
Tiara tiara 1.0.2 [1,848] phylogenetics
tiff tiff 3.8.0, 4.0.10 [1,849] imaging
tighe-r tighe-r 4.2, studio [1,850] statistics
Tigmint tigmint 1.1.2 [1,851] phylogenetics
Tmux tmux 2.9, 3.1 [1,852] programming
TNTBLAST tntblast 2.04 [1,853] biology
ToFU2 tofu2 v17 [1,854] biology, ngs, sequencing
toil toil 3.3.0, 3.3.3 [1,855] biology
Tombo tombo 1.4, 1.5, 1.5.1 [1,856] biology, genomics, ngs
topd topd 4.6 [1,857] phylogenetics
Tophat tophat 2.1.0, 2.1.1, 2.1.2 [1,858] biology, ngs, sequencing
torch-geometric torch-geometric 1.3.2, 2.0.4 [1,859] math, machine_learning
TotalView totalview 8.12 [1,860] programming
TPMcalculator tpmcalculator 0.0.3 [1,861] phylogenetics
TPP tpp 4.7.0, 4.7.1, 5.0.0 [1,862] biology, chemistry, spectroscopy
TraCeR tracer 20160519 [1,863] biology, phylogenetics
TrackTools tracktools 2011 [1,864] utility
TrackVis/DTK trackvis 0.5.2.2, 0.6.0.1 [1,865] biology, neuroscience, imaging
Tracula tracula 5.3.2014_05_26 [1,866] biology, neuroscience, imaging
traitRate traitrate 1.1 [1,867] biology, genomics
Trans-ABySS transabyss 2.0.1 [1,868] biology, phylogenetics
TransDecoder transdecoder 5.3.0, 5.4.0, 5.5.0 [1,869] biology, ngs
TRANSIT transit 2.5.2, 3.2.3 [1,870] phylogenetics
Transrate transrate 1.0.1 [1,871] biology, assembly
TransVar transvar 2.3.3 [1,872] biology, phylogenetics
TreeBreaker treebreaker 20160621 [1,873] biology, phylogenetics
TreeMix treemix 1.12 [1,874] biology, phylogenetics
treePL treepl 20150305 [1,875] biology, phylogenetics
TREEPUZZLE treepuzzle 5.3 [1,876] biology, phylogenetics
TreeShrink treeshrink 1.3.1, 1.3.2, 1.3.9 [1,877] phylogenetics
TreeTime treetime 0.10.1, 0.7.5, 0.8.1 [1,878] phylogenetics
trelis trelis 16.3 [1,879] math
TRF trf 4.04, 4.09.1 [1,880] biology, genomics
trgt trgt 0.4.0 [1,881] genetics, biology
Trilinos trilinos 12.18.1, 12.6.4, 14.4.0 [1,882] math
Trim Galore trim_galore 0.5.0, 0.6.10, 0.6.5 [1,883] biology, ngs
trim_isoseq_polya trim_isoseq_polya 0.0.3 [1,884] biology, genomics, sequencing
trimAl trimal 1.2, 1.4.1 [1,885] biology, genomics, alignment
trimesh trimesh 3.20.2 [1,886] graphics, math
TriMetAss trimetass 1.1 [1,887] biology, ngs
Trimmomatic trimmomatic 0.33, 0.36, 0.39 [1,888] biology, ngs
Trinity trinity r20130225, r20131110, r20140413 [1,889] biology, ngs, sequencing, rna-seq
Trinotate trinotate 3.0.1, 3.2.0, 4.0.0 [1,890] biology
triobinning triobinning 0.2.3 [1,891] genomics, biology
TRIPLEC triplec 1.0 [1,892] biology
TRITONSERVER tritonserver 21.08, 23.01 [1,893] machine_learning
tRNAscan-Se trnascan-se 1.23 [1,894] biology, ngs
TRUST4 trust4 1.0.2b [1,895] phylogenetics
trvz trvz 0.4.0 [1,896] genetics, biology
Trycycler trycycler 0.4.2 [1,897] phylogenetics
TURBOMOLE turbomole 7.4.1 [1,898] chemistry
TWINSCAN twinscan 4.1.2 [1,899] biology, genomics
Ubuntu ubuntu 20.04, 22.04 [1,900] linux
UCSC ucsc 20200320, 20210803 [1,901] genomics
ucsc-fafiltern ucsc-fafiltern 377 [1,902] phylogenetics
ucsc-maskoutfa ucsc-maskoutfa 377 [1,903] phylogenetics
UCX ucx 1.11.2, 1.15.0, 1.9.0 [1,904] programming, library
UDUNITS udunits 2.2.17 [1,905] library, data_science, math
UFCG ufcg 1.0.3, 1.0.5 [1,906] biology, genomics
ufraw ufraw 0.22 [1,907] data_mining
ugtm ugtm 1.1.6 [1,908] statistics, modeling
UKFractography ukfractography 20200127 [1,909] phylogenetics
umi-tools umi-tools 0.5.5 [1,910] phylogenetics
UMICollapse umicollapse 02072021 [1,911] chemestry
UNAFold unafold 3.8 [1,912] biology, genomics, rna
Unanimity unanimity 20171108, 3.4.1 [1,913] programming, library, compiler
UNCALLED uncalled 2.2 [1,914] biology, genomics
Unicycler unicycler 0.4.8 [1,915] phylogenetics
Unrar rar 0.0.1, 4.20 [1,916] utility
unrealengine editor unrealengine 5.2.1 [www.unrealengine.com] programming, design, digitaltwin
uproc uproc 1.2.0 [1,917] biology, genomics
UPSCAYL upscayl 2.5.5, 2.8.1 [1,918] image processing
uropa uropa 4.0.2 [1,919] genomics, sequencing, biology
USEARCH usearch 9.0.2132, 9.1.13, 9.2.64 [1,920] biology, alignment, sequencing
UShER usher 0.1.4, 0.4.1, 0.5.2 [1,921] phylogenetics
V-Phaser vphaser2 02112013 [1,922] biology, phylogenetics
v-pipe v-pipe 2.0.0, 2.99.3 [1,923] biology, genomics, sequencing
Valgrind valgrind 3.11.0, 3.15.0, 3.8.1 [1,924] programming
Valouev valouev 20160325 [1,925] biology, phylogenetics
vamb vamb 3.0.2 [1,926] biology
VAMPIR vampir 9.1 [1,927] performance_analysis
VarDictJava vardictjava 1.6.0, 20160521, 20170531 [1,928] biology, phylogenetics
VARI vari 0.7.0 [1,929] math, visualization
varnorm varnorm 0.21 [1,930] biology
varpipe-wgs varpipe-wgs 20230222 [1,931] sequencing, biology
VarScan varscan 2.3.6 [1,932] biology, ngs
VarSim varsim 0.8.4, 0.8.6 [1,933] phylogenetics
VarSimLab varsimlab 20180220, 20180921 [1,934] biology, simulation, genomics
vasp vasp 5.4.4, 6.1.0, 6.2.0 [1,935] chemistry
VASP vasp 6.4.1 [1,936] chemistry
vaspkit vaspkit 1.2.5, 1.4.1 [1,937] phylogenetics
VAST-TOOLS vast-tools 2.5.1, 20150506 [1,938] biology, rna-seq, ngs
VCF-kit vcf-kit 0.2.6 [1,939] phylogenetics
vcf-validator vcfvalidator 0.6 [1,940] biology, phylogenetics
vcfanno vcfanno 0.2.8, 0.3.3 [1,941] biology, phylogenetics
vcflib vcflib 1.0.1 [1,942] biology, genomics
vcftools vcftools 0.1.15, 0.1.16, 0.1.9 [1,943] biology, genomics
vcontact vcontact 20190512 [1,944] phylogenetics
VDJtools vdjtools 1.1.7, 1.2.1 [1,945] biology, phylogenetics
Velocyto velocyto 0.17 [1,946] biology, RNA seq
Velvet velvet 1.2.10, 1.2.10-long [1,947] biology, genomics
VEP vep 83, 88.8, 92 [1,948] biology, genomics, ngs
Verkko verkko 1.3.1 [1,949] genomics
Vermouth-martinize vermouth-martinize 0.7.2 [1,950] phylogenetics
VeryFastTree veryfasttree 3.0.1 [1,951] phylogenetics
vg vg 1.43.0, 1.45.0, 1.49.0 [1,952] phylogenetics
vibrant vibrant 1.2.0 [1,953] genomics
ViennaRNA viennarna 2.2.6, 2.4.18 [1,954] biology, rna-seq
ViewBS viewbs 0.1.10, 0.1.9 [1,955] phylogenetics
Vim vim 8.1.1566, 8.2.2465 [1,956] programming, language
vina-gpu vina-gpu 20230530 [1,957] biology
viralmsa viralmsa 1.1.10, 1.1.12 [1,958] phylogenetics
viromescan viromescan 2015 [1,959] genomics, biology
VirSieve virsieve 20210406 [1,960] biology, pipeline
virsorter virsorter 2.2.3 [1,961] genomics
VirtualCell virtualcell 7.1 [1,962] phylogenetics
VIRULIGN virulign 1.0.2 [1,963] phylogenetics
VirusDetect virusdetect 1.7 [1,964] phylogenetics
VirusFinder virusfinder 2.0 [1,965] biology, phylogenetics
visit visit 3.0.1, 3.1.4, 3.3.3 [1,966] visualization, animation
VISPR vispr 0.4.14 [1,967] phylogenetics
VMD vmd 1.9.1, 1.9.3, 1.9.4 [1,968] visualization, animation, graphics
vray vray 6.10.04 [1,969] graphics
vscode vscode 1.72.2, 1.74.3 [1,970] programming
VSearch vsearch 2.22.1, 20151022, 20161209-2.3.4 [1,971] biology, ngs
vt vt 0.57721, 20140903, 20160129 [1,972] biology, genomics
VTC vtc 0.9.3 [1,973] biology
VTK vtk 9.1.0, 9.2.6, 9.3.0 [1,974] biology, neuroscience, imaging
w2rap-contigger w2rap-contigger 20161124 [1,975] biology, genomics
Wannier90 wannier90 1.2, 2.1.0, 3.1.0 [1,976] computational Physics
WarpedLMM warpedlmm 0.21 [1,977] modeling
WaveGAN wavegan 20190829 [1,978] machine_learning, audio, GAN
WDSSII wdss2 5, 6 [1,979] climate
WebLogo weblogo 3.3, 3.5.0, 3.7 [1,980] biology, sequencing, graphics
Weka weka 3.8, 3.8.5 [1,981] statistics, machine_learning
Wengan wengan 0.2 [1,982] biology, genomics
wgd wgd 1.1.1 [1,983] phylogenetics
WGS Assembler wgs 8.3rc1.r4638, 8.3rc2 [1,984] biology, genomics
Wgsim wgsim 0.3.1-r13 [1,985] biology, phylogenetics
WHAMM whamm 0.14a [1,986] biology, phylogenetics
WhatsHap whatshap 1.1 [1,987] biology, phylogenetics
whiteboxtools whiteboxtools 1.5.0 [1,988] phylogenetics
Wine wine 4.0.0, 7.0.0 [1,989] linux, utility
Wise wise 2.2.0, 2.4.1 [1,990] biology, genomics
WIsH wish 1.0 [1,991] phylogenetics
WoLFPSort wolfpsort 0.2 [1,992] phylogenetics
WOMBAT wombat 20180118 [1,993] biology, phylogenetics
workbench workbench 4.1.1 [1,994] modeling, simulation
wtdbg wtdbg 2.1, 2.4, 2.5 [1,995] phylogenetics
WU BLAST wublast 2.0 [1,996] biology
Wub wub 0.2.0, 0.4.0 [1,997] biology, genomics, ngs
xander xander 20151222 [1,998] biology, phylogenetics
Xapian xapian 1.4.4 [1,999] library
XCrySDen xcrysden 1.5.60 [2,000] material_science
Xerces xerces 3.1.4 [2,001] phylogenetics
xesmf xesmf 0.6.2 [2,002] math, climate
xlsx2csv xlsx2csv 0.8.0 [2,003] utility
xpclr xpclr 1.0, 1.1.1 [2,004] phylogenetics
Xterm xterm 1.1 [2,005] utility
xwalk xwalk 0.6 [2,006] biology
XWAS xwas 3.0 [2,007] phylogenetics
XY-Meta xy-meta 20200413 [2,008] phylogenetics
XZ xz 5.2.2 [2,009] compression, library
YAGO yago 4 [2,010] data_science
YAHA yaha 0.1.82 [2,011] biology, ngs
YAK yak 0.1 [2,012] phylogenetics
YASM yasm 1.3.0 [2,013] programming
YASRA yasra 2.33 [2,014] biology, ngs, sequencing
yolov4_darknet yolov4_darknet 4-pre [2,015] machine_learning
yolov5 yolo 4.0, 8 [2,016] machine_learning
Z1Plus Z1Plus 1.0 [2,017] molecular_dynamics
Zagros zagros 1.0.0 [2,018] biology, phylogenetics
Zbar zbar 0.23.90 [2,019] ai, image_processing, imaging
ZEO++ zeo++ 0.2.2 [2,020] chemistry
zorro zorro 2.2 [2,021] biology, sequencing
Zstd zstd 1.5.0 [2,022] phylogenetics
ZUMIS zumis 2.6.0 [2,023] biology, ngs, sequencing
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