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 2.1.0, 2.2.5, 2.3.7 [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, 23.3.09 [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, 2.3.1, 2.3.2 [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 0.30.7, 2.0.0b1, 2.0.0b2 [34] protein, structure, machine_learning
AltAnalyze altanalyze 2.1.0 [35] biology, genomics
AMAS amas 1.0 [36] phylogenetics
AMBER amber 20, 22, 24 [37] chemistry, molecular_dynamics
ambertools ambertools 23 [38] chemistry, molecular_dynamics
AMICO amico 1.0.1, 2.0.1 [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 1.5.1, 1.5.4, 1.6 [45] biology, ngs
amptorch amptorch 20210313 [46] phylogenetics
amrfinderplus amrfinderplus 3.10.18, 3.12.8 [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
ANSYS ansys 2023R2 [58] modeling
ansysem ansysem 17.0, 2022r1, 2023r1 [59] physics
antiSMASH antismash 4.1.0, 6.0.1, 7.0.0 [60] phylogenetics
ANTs ants 2.2.0, 2.3.4 [61] biology, phylogenetics
anvio anvio 6.2, 7.1, 8.0 [62] biology
Appreci8 appreci8 20180530 [63] biology, genomics
apps clearmap 2.0 [64] biology, neurobiology
Apptainer apptainer 1.2.2, 1.3.1, 1.3.5 [65] workflow_automation
APT apt 1.18.0, 1.20.5, 2.11.8 [66] biology, genomics
aquamis aquamis 1.4.0 [67] biology, genomics
arb arb r19270 [68] phylogenetics
ARC arc 1.1.4 [69] biology, ngs
arcashla arcashla 0.5.0 [70] biology, genetics
Arcticporechop arcticporechop 0.3.2 [71] phylogenetics
Aria2 aria2 1.35.0 [72] utility
ARKS arks 1.0.2 [73] phylogenetics
Armadillo armadillo 7.900.0, 9.200.6, 9.900.4 [74] library, compiler, math
ARPACK arpack 1.0 [75] math
ArrayFire arrayfire 3.4.2 [76] math
arriba arriba 2.1.0 [77] phylogenetics
ART art 20160417, 20160605 [78] phylogenetics
artemis artemis 18.1.0 [79] biology
asap asap 2.0 [80] visualization, biology
asaq asaq 1.0 [81] alignment, sequencing, phylogenetics
ASDEC asdec 1.2 [82] bioinformatics
ASE-ANI ase-ani 20180712 [83] biology, genomics, ngs
ASHS ashs 2.0 [84] biology, imaging
ASPECT aspect 2.3.0, 2.5.0 [85] geodynamics
Assembly-stats assembly-stats 1.0.1 [86] biology, sequencing, genomics
Assemblytics assemblytics 1.2.1 [87] phylogenetics
asset asset 20210112 [88] sequencing, data_science
Assexon assexon 20190814 [89] phylogenetics
AStalavista astalavista 3.2, 4.0 [90] biology, genomics
aster aster 1.15, 1.16, 220718 [91] biology, data_science, sequencing
asteroid asteroid 1.0 [92] genomics
ASTRAL astral 5.6.1, 5.6.2, 5.7.7 [93] biology, ngs, phylogenetics
ASTRID astrid 2.2.1 [94] phylogenetics
Astropy astropy 2.0.8 [95] biology, phylogenetics
ATAT atat 3.23, 3.34 [96] material_science
ATLAS atlas 3.10.1, 3.10.2, 3.11.17 [97] library, data_science
Atom atom 1.57.0 [98] programming
AtomEye atomeye 3 [99] material_science
AtomMan atomman 1.3.3 [100] phylogenetics
aTRAM atram 2.2.0, 2.4.3 [101] math
Augustus augustus 3.3.3, 3.4.0, 3.5.0 [102] biology, genomics
Auto3DEM auto3dem 4.05.2 [103] image_processing
AutoDock autodock 4.2.6 [104] biology
AutoDock-GPU autodock-gpu 1.5.3 [105] chemistry
autodock-vina autodock-vina 1.2.3, 1.2.5 [106] biology
Autometa autometa 2.2.0, 20190802 [107] phylogenetics
automlsa2 automlsa2 0.8.1 [108] phylogenetics, biology, genomics
AWSCLI awscli 2.11.7, 2.2.30 [109] utility
azoo azoo 1.3.1 [110] phylogenetics
bactopia bactopia 2.2.0 [111] genomics
Badread badread 0.1.5 [112] phylogenetics
bakta bakta 1.3.3, 1.9.4 [113] genomics, biology
BALi-Phy bali-phy 3.4.1, 3.5.0 [114] phylogenetics
BAM-matcher bam-matcher 20161021 [115] phylogenetics
Bam-Readcount bam-readcount 20150616 [116] biology, genomics
bamaddrg bamaddrg 20120326 [117] phylogenetics
BamBam bambam 1.0, 1.4 [118] biology, genomics
bamm bamm 2.5.0 [119] phylogenetics
bamsnap bamsnap 0.2.19 [120] phylogenetics
Bamstats bamstats 20140602 [121] biology, ngs
Bamsurgeon bamsurgeon 1.2 [122] phylogenetics
bamtofastq bamtofastq 1.3.5 [123] phylogenetics
Bamtools bamtools 2.5.0, 2.5.1, 2.5.2 [124] biology, ngs, sequencing
bamUtil bamutil 1.0.2 [125] biology, genomics
BAPS baps 6.0 [126] biology, genomics
Barrnap barrnap 0.7, 0.9 [127] biology, rna-seq
Basemount basemount 0.15.96, 0.25.2 [128] biology, sequencing
BatMeth2 batmeth2 20210720 [129] biology, genomics, mapping
bax2bam bax2bam 0.0.9 [130] phylogenetics
BayArea bayarea 1.0.2 [131] biology
BAYENV bayenv 2.0 [132] biology, phylogenetics
BayesAss bayesass 3.0.4, 3.0.4.2 [133] phylogenetics
bayesass3-snps bayesass3-snps 1.1 [134] phylogenetics
BayeScan bayescan 2.1 [135] biology, variant_calling
BayesR bayesr 20151016 [136] biology, phylogenetics
BayesTraits bayestraits 3.0.2 [137] phylogenetics
baypass baypass 2.1 [138] biology, phylogenetics
BBMap bbmap 38.44, 38.90, 39.06 [139] biology, alignment
bcftools bcftools 1.13, 1.15, 1.19 [140] biology, ngs
bcl2fastq bcl2fastq 2.16.0.10, 2.20.0.422 [141] biology, ngs
BCLConvert bclconvert 4.2.7 [142] biology, ngs
BDG-SeQuila bdg-sequila 0.5.5 [143] phylogenetics
BEAGLE beagle 4.1, 5.0, 5.2 [144] biology, genomics
BEAR bear 20170209 [145] biology, genomics
BEAST beast 2.7.0, 2.7.3, 2.7.5 [146] biology, phylogenetics
BEAST2-XML beast2-xml 1.0.9 [147] phylogenetics
BEDOPS bedops 2.4.30, 2.4.41 [148] biology, sequencing, ngs
BEDTools bedtools 2.29.1, 2.29.2, 2.30.0 [149] biology, ngs
Bertini bertini 1.6 [150] math
BERTopic bertopic 0.14.0, 0.7, 0.8.1 [151] machine_learning
BESST besst 2.2.4 [152] biology, ngs
BFAST bfast 0.7.0 [153] biology, ngs
BFC bfc 1.0 [154] genome
bgenix bgenix 1.1.7 [155] data_science, genomics
BIDSCOIN bidscoin 3.7.4, 4.3.0 [156] neuroscience
Bifrost bifrost 0.2, 1.0.3, 20200225 [157] phylogenetics
BiG-SCAPE big-scape 1.1.2, 1.1.9 [158] biology, genomics, phylogenetics, pipeline
bigslice bigslice 1.1.1, 2.0.0 [159] biology, genomics
bindash bindash 1.0.1, 1.0.2 [160] genomics
BinPacker binpacker 1.0 [161] biology, rna-seq, assembly
BinSanity binsanity 0.2.6.4 [162] biology, genomics
Bioawk bioawk 1.0 [163] phylogenetics
bioBakery biobakery 1.8, 3.0.0, 3.1.0 [164] phylogenetics
Biodiverse biodiverse 2.1 [165] phylogenetics
Biolite biolite 0.3.5.1 [166] biology, genomics, variant_calling
BIOM biom 2.1.5, 2.1.6 [167] biology, genomics
BIOMART biomart 1.4 [168] biology, genomics
BioNeMo bionemo 0.3.1, 1.2, 1.3 [169] ai, machine_learning
Biopieces biopieces 2.0 [170] phylogenetics
BirdNET birdnet 0.1.2 [171] bioinformatics
BIRDS fiji-birds 1.0 [172] workflow_automation, utility, imaging
Bismark bismark 0.24.2, 0.7.4, 0.7.7 [173] biology, ngs
Blackfynn blackfynn 0.2.7 [174] data_mining
BLASR blasr 20130815, 20161215 (5.3), 5.3.2 [175] biology, ngs
Blast2GO blast2go 2.5.0-20120705 [176] biology, genomics
Blast2GO CLI blast2go 1.3.3 [177] biology, genomics
BLAT blat 20121105, 20140318 [178] genomics
blender blender 2.77, 3.0.1, 4.0.2 [179] graphics
blink blink 0.01 [180] genomics
Blitz blitz 0.10, 1.0.2 [181] library
BlobTools blobtools 1.0, 2.2, 4.3.5 [182] phylogenetics
bloomfiltertrie bloomfiltertrie 0.8.7 [183] phylogenetics
BloomTree bloomtree 0.3.5 [184] data_mining
BLUPF90 blupf90 20160604, 20180301, 20190531 [185] biology, phylogenetics
BMGE bmge 1.12 [186] biology, genomics, phylogenetics
bmtagger bmtagger 3.101 [187] genomics, biology
BOLT-LMM bolt-lmm 2.3.4 [188] phylogenetics
BoltzTraP boltztrap 1.2.5 [189] physics
Boost boost 1.75.0, 1.77.0, 1.82.0 [190] programming, library, compiler
booster booster 0.1.2 [191] phylogenetics
botorch botorch 0.7.1 [192] phylogenetics, biology
Bowtie bowtie 1.1.1, 1.2.0, 1.2.3 [193] biology, ngs, sequencing
Bowtie2 bowtie2 2.3.5.1, 2.4.2, 2.4.5 [194] biology, ngs, sequencing
BoxCLI boxcli 2.9.0 [195] file_management, web, programming
BPGA bpga 1.2 [196] biology, ngs
BPP bpp 4.1.4, 4.3.8, 4.4.1 [197] biology, phylogenetics
BppSuite bppsuite 2.3.2 [198] genomics
Bracken bracken 1.0.0, 2.5, 2.9 [199] biology, phylogenetics
BrainIAK brainiak 0.11 [200] imaging
braker braker 3.0.2, 3.0.3, 3.0.8 [201] biology, genomics, annotation
BRANCH branch 1.8.1 [202] biology, ngs, mapping
BRATNextGen bratnextgen 20150505 [203] biology, genomics
BreakDancer breakdancer 1.4.5 [204] biology, phylogenetics
breakseq breakseq 2.2 [205] biology, phylogenetics
Brewery brewery 20191205 [206] phylogenetics
Bridger bridger 20141201 [207] ngs, genomics, biology
BRIG brig 0.95 [208] biology, genomics
brkraw brkraw 0.3.5 [209] data_science, imaging
BRM brm 0.3 [210] phylogenetics
Bruker2nifti bruker2nifti 1.0.4 [211] phylogenetics
Bsmap bsmap 2.87 [212] biology, ngs
Bsoft bsoft 1.9.1 [213] biology, image_processing
BSseeker2 bsseeker2 2.1.0, 2.1.8 [214] biology, phylogenetics
bubbleparse bubbleparse 20140314 [215] biology, phylogenetics
BUCKy bucky 1.4.4 [216] biology, phylogenetics
BUSCO busco 4.1.4, 5.2.0 [217] biology, genomics
BWA bwa 0.7.7, 0.7.8, 0.7.9a [218] biology, ngs
bwa-mem2 bwa-mem2 2.2.1 [219] phylogenetics
bwa-meth bwameth 0.2.7 [220] genomics, biology
BWA-PSSM bwa-pssm 0.5.11 [221] phylogenetics
bxh_xcede_tools bxh_xcede_tools 1.11.1 [222] biology
BYOBU byobu 5.133, 5.92 [223] shell
bzip2 bzip2 1.0.6 [224] utility, library
c-wap c-wap 20220624 [225] sequencing, genomics, biology
Cactus cactus 2.0.3, 2.0.5, 2.8.0 [226] phylogenetics
CAFE cafe 4.1, 5.0.0 [227] phylogenetics
came came 0.0.1 [228] phylogenetics
Camino camino 20140723 [229] biology, neuroscience, imaging
cammiq cammiq 0.1.1 [230] genomics, biology
CAMP camp 1.0.0 [231] biology, sequencing
Cantera cantera 2.1.1 [232] physics
Canu canu 2.0, 2.1, 2.2 [233] biology, sequencing
CANVAS canvas 1.40.0.1613 [234] phylogenetics
CAP3 cap3 20120705 [235] biology, assembly
Capnp capnp 0.5.3 [236] compiler
captus captus 0.9.88, 0.9.91 [237] phylogenetics, biology
CARTA carta 2.0 [238] image_processing
CASAVA casava 1.8.2 [239] biology, ngs
CASM casm 0.2.0 [240] physics
CasOFFinder casoffinder 2.4 [241] phylogenetics
CAT cat 12 Standalone [242] biology
Catch catch 1.4.0 [243] biology, genomics, sequencing
CAVIAR caviar 20171218 [244] biology, phylogenetics
CBGpipe cbgpipe 20190702 [245] phylogenetics
CCMetagen ccmetagen 1.4.0 [246] phylogenetics
CD-HIT cdhit 4.6, 4.6.4, 4.6.8 [247] biology, genomics
CDBFasta cdbfasta 20181005 [248] phylogenetics
CDNA_Cupcake cupcake 20180629, 22.0.0, 9.0.1 [249] biology, ngs, sequencing
CDO cdo 1.7.2rc3, 1.9.4 [250] climate
CDRT cdrt 23.10 [] machine_learning
CellProfiler cellprofiler 3.1.9, 4.1.3, 4.2.6 [251] phylogenetics
CellRanger cellranger 7.0.1, 7.2.0, 8.0.0 [252] biology, ngs, rna-seq
CellRanger-ARC cellranger-arc 2.0.1 [253] biology, ngs, rna-seq
CellRanger-ATAC cellranger-atac 1.2.0 [254] biology, ngs, rna-seq
CellRanger-DNA cellranger-dna 1.0.0, 1.1.0 [255] biology, ngs, rna-seq, genomics
Centrifuge centrifuge 1.0.3, 1.0.4b [256] biology, phylogenetics
CFITSIO cfitsio 3.370 [257] library, compiler
CGAL cgal 5.02, 5.5.2, 5.6 [258] library, math
CGATools cgatools 1.6.0.43 [259] biology, ngs
cgmaptools cgmaptools 0.1.1, 0.1.2 [260] phylogenetics
cgmlst cgmlst 0.2 [261] phylogenetics
cgmlstfinder cgmlstfinder 1.0 [262] genetics
CGView cgview 1.0.2 [263] phylogenetics
CHARMM charmm 36a3, 43b2, c48b2 [264] chemistry, simulation
ChartDirector libchartdir 5.1.0 [265] library, data_science
CheckM checkm 1.0.4, 1.0.7, 1.1.2 [266] biology, genomics
checkv checkv 1.0.1 [267] biology, genomics
chewbbaca chewbbaca 3.3.0 [268] biology, genomics
chewiesnake chewiesnake 3.0.0 [269] biology, genomics
Chimera chimera 1.12 [270] biology, modeling
Chipyard chipyard 1.0 [271] simulation
Chopper chopper 0.8.0 [272] bioinformatics
Chromeister chromeister 1.5a [273] biology, genomics
ChromEvol chromevol 2.0, 3.0 [274] biology, ngs
CIALIGN cialign 1.1.4 [275] bioinformatics
CIMS cims 4.1.2 [276] biology, genomics
CIRCexplorer circexplorer 1.1.10 [277] biology, rna-seq
CIRCexplorer2 circexplorer2 2.3.5, 2.3.8 [278] phylogenetics
circexplorer3 circexplorer3 01172021 [279] RNA-Seq
Circlator circlator 1.5.5 [280] phylogenetics
Circleator circleator 1.0.2 [281] phylogenetics
circompara2 circompara2 0.1.2.1 [282] phylogenetics
Circos circos 0.63-pre11, 0.69-2, 0.69-9 [283] biology, genomics, ngs
circtools circtools 1.2.1 [284] biology
CIRI ciri 2.0.6 [285] phylogenetics
ciriquant ciriquant 1.1.2 [286] phylogenetics
CisGenome cisgenome 2.0 [287] biology, genomics
cisTEM cistem 1.0.0 [288] phylogenetics
Clairvoyante clairvoyante 1.02 [289] phylogenetics
Clann clann 3.2.3 [290] biology, phylogenetics
clara clara v4.0 [291] ai, machine_learning
CLARK clark 1.2.2-b, 1.2.3 [292] biology, genomics
clean clean 1.0.1 [293] protein, machine_learning
CLHEP clhep 2.2.0.1 [294] physics
CLIFinder clifinder 4.1 [295] biology, phylogenetics
ClinicaDL clinicadl 1.0.4, 1.2.0 [296] biology, imaging, machine_learning
clipkit clipkit 1.3.0 [297] genomics, biology
CLIPper clipper 2.1.0 [298] phylogenetics
CLIPSeqTools clipseqtools 0.1.7 [299] biology, sequencing
CliqueSNV cliquesnv 2.0.3 [300] biology, phylogenetics
ClonalFrame clonalframe 1.1, 1.2 [301] biology, ngs, phylogenetics
ClonalFrameML clonalframeml 1.0, 1.11 [302] biology, ngs, phylogenetics
CloudCompare cloudcompare 2.10.3 [303] visualization
Clover clover 2.0 [304] biology, genomics, assembly
CLUMPP clumpp 1.1.2 [305] biology
ClustalO clustalo 1.2.0 [306] biology, alignment
ClustalW clustalw 2.1 [307] biology, alignment
cluster3 cluster3 1.52a [308] biology, genomics
Clview clview 20130402 [309] biology
CMake cmake 3.21.3, 3.26.4, 3.30.5 [310] programming
CMS cms 20170518, 20240429 [311] biology
CMWP cmwp 140518 [312] biology, genomics
CNCI cnci 20180305 [313] phylogenetics
CNSpipeline cnspipeline 20170827 [314] phylogenetics
CNV-Seq cnvseq 20110715, 20140812 [315] biology, genomics
CNV-Sim cnv-sim 0.9.2 [316] biology, phylogenetics
CNVkit cnvkit 0.9.6 [317] phylogenetics
CNVnator cnvnator 0.3.2 [318] biology, genomics
cobra-tf cobra-tf 0.1 [319] fluid_dynamics
Cobretti cobretti 1.0 [320] GeneExpression
CodonPhyML codonphyml 20150303 [321] phylogenetics
Coevol coevol 1.3c, 1.4b, 1.6 [322] biology, phylogenetics
Cogent cogent 2.1 [323] biology, phylogenetics
COLMAP colmap 3.6 [324] modeling
CoMap comap 1.4.1 [325] biology, genomics
Comp-D_MPI comp-d_mpi 1.0 [326] statistics
Compacta compacta 1.02 [327] biology, genomics
COMSOL comsol 6.1, 6.2, 6.2.04 [328] simulation
Concaterpillar concaterpillar 1.8a [329] phylogenetics
CONCOCT concoct 1.1.0 [330] biology, genomics
Conda conda 24.3.0, 24.7.1 [331] programming
Conefor conefor 2.7.3 [332] software
CONN conn 22a [333] imaging
CONNECT connect 20200614 [334] phylogenetics
connectomemapper3 connectomemapper3 3.0.0-rc1 [335] phylogenetics
ConPADE conpade 1.0 [336] phylogenetics
Conpair conpair 20161010, 20180624 [337] biology, phylogenetics
Consed consed 23.0, 25.0, 29.0 [338] biology, genomics
CONSEL consel 0.20 [339] biology, phylogenetics
ContaVect contavect 0.2 [340] biology, phylogenetics
Convert3D convert3d 1.1.0 [341] imaging, utility
Coot coot 0.9.5 [342] modeling
CoPTR coptr 1.1.6 [343] biology
Coreutils coreutils 8.23, 8.28 [344] utility
Corset corset 1.06 [345] biology, ngs
Counterr counterr 0.1, 20230501 [346] phylogenetics
Coverm coverm 0.6.1 [347] biology, genomics, ngs
covNMR covnmr 2014 [348] chemistry, biology
cp2k cp2k 2024.1, 7.0.0 [349] imaging
CPAT cpat 3.0.2 [350] phylogenetics
cpc cpc 2.0 [351] phylogenetics
CPLEX cplex 12.6.2, 12.7, 12.9 [352] climate
Crass crass 1.0.1 [353] biology, assembly
crest crest 12.2, 2.12, 3.0 [354] chemistry
crisflash crisflash 1.2.0 [355] phylogenetics
CRISP crisp 20181122, 20240419 [356] phylogenetics
CRISPRanalyzer crispranalyzer 1.50 [357] biology, genomics, ngs
CRISPRCasFinder crisprcasfinder 4.2.17 [358] phylogenetics
CRISPResso2 crispresso2 20220811 [359] genomics, sequencing, biology
CrossMap crossmap 0.3.9, 0.6.3 [360] biology, genomics
crossmapper crossmapper 1.1.1 [361] phylogenetics
Crux crux 1.40 [362] biology, spectroscopy
cryodrgn cryodrgn 2.3.0 [363] biology
CryptoMiniSat cryptominisat 5.0.1 [364] math
csubst csubst 1.3.0 [365] Biology, Phylogenetics
csvpad csvpad 1.2 [366] data science
csvtk csvtk 0.23.0, 0.30.0 [367] biology
ctk ctk 1.1.4 [368] biology, genomics
CUBE cube 4.4 [369] library, compiler, math
CUDA cuda 12.2.2, 12.3.2, 12.4.1 [370] programming, library, graphics
Cufflinks cufflinks 2.1.1, 2.2.1, 2.2.1.1 [371] biology, ngs, sequencing
cuOpt cuopt 22.12 [372] Accelerated AI Logistics and Route Optimization
cupy cupy 8.3.0 [373] phylogenetics
cutadapt cutadapt 1.18, 2.8, 3.4 [374] biology, ngs
CutRunTools cutruntools 20200104 [375] phylogenetics
cvbio cvbio 3.0.0 [376] phylogenetics
CViT cvit 1.3 [377] programming, library
CWLtool cwltool 1.0.20190906, 2.0.20200126, 3.0.20210124104916 [378] workflow_automation, scheduler
cx_oracle cxoracle 8.3.0 [379] database, utility
CycleGan cyclegan 20201015 [380] phylogenetics
Cytoscape cytoscape 3.10.2, 3.4.0 [381] biology, ngs, phylogenetics
cyvcf2 cyvcf2 20230728 [382] library
d2go d2go 20210702 [383] machine_learning, ai
dadi dadi 2.1.1 [384] phylogenetics
DAKOTA dakota 6.15, 6.8, 6.8-gui [385] math
DALIGNER daligner 1.0 [386] biology, phylogenetics
dammit dammit 1.0rc2 [387] biology, phylogenetics
dancemapper dancemapper 1.0.0 [388] machine learning
dapars dapars 1.0.0 [389] genomics, biology
darwin-gpu darwin-gpu 20190115 [390] genomics, alignment
DASTool dastool 1.1.0, 1.1.2 [391] biology, phylogenetics
datamash datamash 1.1.0 [392] math
DAWGPAWS dawgpaws 1.0 [393] biology, phylogenetics
dbcanlight dbcanlight 1.1.0 [394] biology, annotation
DCC dcc 0.4.4 [395] biology, ngs
Dcmstack dcmstack 0.6.2 [396] biology, imaging
DCMTK dcmtk 3.6.0 [397] biology, neuroscience, imaging
dDocent ddocent 2.7.8 [398] phylogenetics
ddprotocol ddprotocol 20230405 [399] biology, machine learning
DDSCAT ddscat 7.3.0 [400] astronomy
DDT ddt 20.0, 20.2, 23.0 [401] programming
DealII dealii 8.3.0, 9.3.1, 9.5.1 [402] library
DeconSeq deconseq 0.4.3 [403] biology, phylogenetics
decontaMiner decontaminer 1.4 [404] genomics, biology
DECX decx 20180205 [405] phylogenetics
DeepARG deeparg 1.0.1 [406] phylogenetics
deepbgc deepbgc 0.1.18 [407] phylogenetics
Deepcoil deepcoil 2.0.1 [408] sequencing, biology
deepfri deepfri 03312021 [409] machine learning, biology
DeepGS deepgs 1.2 [410] phylogenetics
DeepLabCut deeplabcut 2.0.7-gpu, 2.1.1, 2.2.1 [411] phylogenetics
deeplexicon deeplexicon 1.2.0 [412] RNAseq
DeePMD-kit deepmd-kit 2.1.11 [413] molecular dynamics, deep learning
DeepMD-LAMMPS deepmd-lammps 2.2.0-02Aug23 [414] molecular Dynamics
deepmicrobes deepmicrobes 20200219 [415] biology, genomics, machine_learning
DeepMReye deepmreye 01192022 [416] library, biology
DeepPicker deeppicker 20161102 [417] imaging
deepsig deepsig 1.2.5 [418] biology
deepTools deeptools 2.4.3, 3.1.1, 3.5.2 [419] biology, ngs
deepvariant deepvariant 1.4.0, 1.5.0, 1.6.1 [420] biology, genomics, sequencing, machine_learning
deFusion defusion 20200305 [421] phylogenetics
Delft3D delft3d 4.06.01, 7545 [422] physics
Delineate delineate 1.2.2 [423] biology, genomics
Delly delly 0.7.7, 0.7.8, 1.1.5 [424] biology, phylogenetics
delucs delucs 20220512 [425] sequencing, genomics, machine_learning
DeNoGAP denogap 1.0 [426] biology, phylogenetics, ngs
DERIVA deriva 1.5.0 [427] phylogenetics
deSALT desalt 1.5.6 [428] biology, genomics, sequencing
Desmond desmond 6.9 [429] biology
Detectron2 detectron2 0.4, 0.5, 0.6 [430] library
DeTiN detin 1.7.5.9 [431] imaging, ngs, genomics
DEXTRACTOR dextractor 1.0 [432] biology, sequencing
Diamond diamond 2.1.1, 2.1.3, 2.1.8 [433] biology, genomics
DIANN diann 1.8.1 [434] protein, structure
diCal2 dical2 2.2.0.1 [435] biology, phylogenetics
diffDomain diffdomain 1.0.0 [436] bioinformatics
diffReps diffreps 1.55.4 [437] biology
disbatch disbatch 2.5 [438] software
DISCOVAR de novo discovardenovo 52488 [439] biology, ngs, assembly
DiscoVista discovista 20180906 [440] phylogenetics
discvrseq discvrseq 1.3.10 [441] biology, phylogenetics
Distruct distruct 2.3 [442] phylogenetics
DIYABC diyabc 1.0.4.43b, 2.0.3, 2.1.0 [443] biology, phylogenetics
DL_POLY dlpoly 1.9 [444] molecular_dynamics
Dlib dlib 19.19 [445] phylogenetics
DNA Clust dnaclust 3.0 [446] biology, genomics
DOCK dock 6.7, 6.8, 6.9 [447] chemistry
DoGFinder dogfinder 20201103 [448] phylogenetics
dorado dorado 0.7.0, 0.7.2, 0.8.2 [449] genomics
DosageConvertor dosageconvertor 1.0.3 [450] biology
DOT dot 2.0 [451] biology, chemistry
Doxygen doxygen 1.12.0, 1.8.3.1, 1.9.7 [452] programming, documentation
dragmap dragmap 1.2.1 [453] phylogenetics, sequencing, biology
dragonflye dragonflye 1.0.12 [454] sequencing, genomics
dram dram 1.3 [455] biology, genomics, annotation
DRAP drap 1.91 [456] biology, phylogenetics
dRep drep 2.3.2, 3.4.2 [457] phylogenetics
dretools dretools 0.0.1.20 [458] rna-seq
drishti drishti 3.2 [459] visualization
Dropseq dropseq 2.4.0 [460] phylogenetics
DS9 saoimageds9 7.5, 8.0.1 [461] imaging
DScribe dscribe 1.2.0 [462] machine_learning
dsistudio dsistudio 20210123, 20220803, 20240311 [463] imaging
DSK dsk 2.1.0, 2.3.0 [464] biology, ngs
DSRC dsrc 2.0 [465] phylogenetics
DSSAT dssat 4.6 [466] simulation
DSSP dssp 2.2.1, 3.0.0 [467] molecular_dynamics
DSuite dsuite 0.4, 0.4-r41, 0.4-r49 [468] biology, genomics
DTI-TK dtitk 2.3.1 [469] imaging
dtiprep dtiprep 0.1.1 [470] phylogenetics
duchamp duchamp 1.6.2 [471] phylogenetics
DVGfinder dvgfinder 3.1 [472] genomics, search, sequencing
dx-toolkit dx-toolkit 0.347.0 [473] biology
dynamicDBG dynamicdbg 20181003 [474] phylogenetics
Dynare dynare 4.4.3 [475] math
dynasor dynasor 2.0 [] Molecular_Dynamics
ea-utils eautils 1.04.807.18, 1.1.2.537 [476] biology, genomics, ngs
EAGLE eagle 2.0 [477] phylogenetics
eagle-rc eagle-rc 1.1.1 [478] phylogenetics
Earlgrey earlgrey 4.2.4 [479] biology
ECE ece 1.2 [480] physics
ecopcr ecopcr 0.5.0 [481] Biology
eddy-squeeze eddy-squeeze 1.0.8 [482] data_science, visualization
EDirect edirect 10.7, 12.2 [483] biology, phylogenetics
EDTA edta 1.9.6, 2.1.0 [484] phylogenetics
Edyeet edyeet 0.1, 0.3 [485] phylogenetics
EEGLAB eeglab 12.0.2.1b, 13.2.2b, 13.4.4b [486] biology
effectorp effectorp 2.0.1, 3.0 [487] biology
eGene-MVN egene-mvn 0.1 [488] biology, genomics
eggNOG-mapper eggnog-mapper 2.0.1, 2.1.12, 2.1.6 [489] phylogenetics
Ego4D ego4d 1.3.2 [490] image processing
EGSnrc egsnrc 2019 [491] phylogenetics
EIGEN3 eigen3 3.4.0 [492] libraries, mathematics
EIGENSOFT eigensoft 5.0.1, 6.0.1, 6.1.4 [493] biology
Elastix elastix 4.9.0, 5.1.0 [494] phylogenetics
ELPA elpa 2019.11.001 [495] library, compiler, math
elPrep elprep 4.1.4 [496] phylogenetics
Emacs emacs 27.2, 28.2 [497] programming, language
Email Alert Service email_storage_alert 1.0.0 [498] file_management
EMAN2 eman2 2.22, 2.31 [499] image_processing
EMBOSS emboss 6.6.0 [500] biology
Embree embree 3.6.1 [501] graphics
EMC emc 9.4.3 [502] simulation
emerald emerald 0.1 [503] biology
EMMAX emmax 20100307, 20120210 [504] biology, ngs, mapping
emu emu 3.4.5 [505] phylogenetics
EnergyPlus energyplus 9.3.0 [506] simulation
enrichm enrichm 0.6.5 [507] biology
Ensembl Tools ensembl_tools 100, 80 [508] biology
enTAP entap 0.6.1.2, 20160416 [509] biology, phylogenetics
EPACTS epacts 3.2.6, 3.4.2, 3.4.2.hg38 [510] biology, genomics
EpiNano epinano 1.2.0 [511] biology, ngs
epiteome epiteome 1.0 [512] phylogenetics
epoch epoch 4.7.3 [513] astronomy
eQTLA eqtla 1.1 [514] biology, genomics
eQtlBma eqtlbma 1.2.2, 1.3.0r20140820 [515] biology, genomics
Erpin erpin 5.5.4 [516] biology, phylogenetics
esmf esmf 8.3.0), 8.7.0) [517] geospatial
ESOM esom 1.1 [518] biology, phylogenetics
ESPRESSO espresso 7.0, 7.1, 7.2 [519] chemistry, modeling
ESPRIT esprit 2009-nogap, 201102 [520] biology
ETE3 ete3 3.0.0, 3.1.1 [521] biology, phylogenetics
ETE4 ete 4.0.0 [522] biology, phylogenetics
EUKulele eukulele 2.0.7 [523] alignment, biology, genomics
EVidenceModeler evidencemodeler 1.1.1 [524] phylogenetics
Evigene evigene 20180730, 20200520 [525] phylogenetics
EvoLSTM evolstm 20220103 [526] biology
ExaBayes exabayes 1.5 [527] phylogenetics
Exonerate exonerate 2.2.0, 2.4.0 [528] biology, genomics
ExpansionHunter expansionhunter 4.0.2 [529] biology, genomics
ExpansionHunterDenovo expansionhunterdenovo 0.9.0 [530] biology, genomics
export2graphlan export2graphlan 0.22 [531] statistics, mapping, visualization
eXpress express 1.3.1, 1.5.1 [532] biology, ngs
ezaai ezaai 1.0 [533] biology, phylogenetics
face_morpher face_morpher 20190630 [534] phylogenetics
face_recognition face_recognition 1.2.2 [535] phylogenetics
fairseq fairseq 0.12.2 [536] modeling, ai
falco falco 1.2.1 [537] biology, sequencing
FALCON falcon 20161027, 20161222, 20190601 [538] biology, ngs, sequencing
FALCON_unzip falcon_unzip 20161222 [539] biology
fanc fanc 0.9.28 [540] biology, genomics, ngs
faqcs faqcs 2.10 [541] Genomics, biology
FAR far 2.15 [542] biology, genomics
FAST fast 1.06 [543] biology, phylogenetics
fast-gep fast-gep 1.0 [544] phylogenetics
Fast-Plast fast-plast 1.2.6 [545] biology, phylogenetics
fast5tools fast5tools 0.3.1 [546] phylogenetics, biology
FASTA fasta 34.26.5, 36.3.6d [547] biology, genomics
fastai fastai 2.1.5, 2.6.3, 2.7.10 [548] Machine_Learning
FastANI fastani 1.1, 1.34 [549] phylogenetics
fastchaos fastchaos 0.1.0 [550] sequencing
FastGEAR fastgear 20161216 [551] biology, genomics
Fastix fastix 0.1.0 [552] biology, ngs
FastML fastml 3.0 [553] biology, phylogenetics
Fastp fastp 0.20.0, 0.22.0, 0.23.4 [554] biology, ngs
FASTphase fastphase 1.4.8 [555] phylogenetics
FastPlast fastplast 1.2.8 [556] phylogenetics
fastq-pair fastq-pair 1.0 [557] phylogenetics
FastQ-Screen fastq-screen 0.14.0 [558] phylogenetics
Fastq-tools fastq-tools 0.8 [559] biology, ngs
FastQC fastqc 0.11.7, 0.12.1, 0.9.6 [560] biology, ngs
FastqPuri fastqpuri 1.0.7 [561] phylogenetics
FastQTL fastqtl 2.184 [562] phylogenetics
FASTRAL-constrained fastral-constrained 20211108 [563] phylogenetics
fastsimcoal fastsimcoal2 2.6.0.3, 2.7.0.2 [564] biology, phylogenetics
FastSpar fastspar 0.0.4 [565] biology, genomics
fastStructure faststructure 20150112, 20240221 [566] biology, genomics
FastTree fasttree 2.1.11 [567] biology, phylogenetics
FastUniq fastuniq 1.1 [568] biology, phylogenetics
fastv fastv 0.10.0 [569] bioinformatics, sequencing
Fastx Toolkit fastx_toolkit 0.0.13.2, 0.0.14 [570] biology, ngs
fcGENE fcgene 1.0.7, 1.0.7.1 [571] biology, genomics, variant_calling
FDSTools fdstools 1.2.0 [572] phylogenetics
fdupes fdupes 1.51 [573] file_management
febio febio 2.9.1 [574] biomechanics
FEELnc feelnc 0.1.1 [575] phylogenetics
FEniCS fenics 2018.1.0 [576] biology, phylogenetics
Ferret ferret 6.82 [577] visualization, geospatial, climate
FFmpeg ffmpeg 2.8.3, 4.3.1, n6.1 [578] audio, visualization
FFTW fftw 3.3.6, 3.3.7, 3.3.8 [579] library, compiler, math
fgbio fgbio 0.5.0, 0.7.0 [580] phylogenetics
FGMP fgmp 1.0.1 [581] phylogenetics
FGTPartitioner fgtpartitioner 1.0.1 [582] genomics
FIGARO figaro 1.1.2 [583] phylogenetics
Fiji fiji 2.0.0rc59 [584] image_processing
Filtlong filtlong 0.2.0 [585] biology, phylogenetics
Finder finder 20210503, 20210609 [586] biology, search
finemap finemap 1.4 [587] phylogenetics
fineRADstructure fineradstructure 0.3.2 [588] phylogenetics
finesse finesse 2.3.1 [589] simulation
Firefox firefox 1.0 [590] linux, web
fit-sne fit-sne 1.2.1 [591] phylogenetics
FLAIR flair 1.5, 2.0 [592] phylogenetics
flairNLP flairnlp 0.10 [593] visualization, language
flappie flappie 1.1.0, 2.1.3 [594] phylogenetics
FLASh flash 1.2.10, 1.2.11 [595] biology, genomics
FLEA flea 2.0.0 [596] phylogenetics
flex flex 2.6.4 [597] programming
Flexbar flexbar 2.3, 2.34, 3.5.0 [598] biology, genomics, ngs
FLEXLm flexlm 1.0 [599] utility
flopp flopp 0.2.0 [600] genomics
FlowCraft flowcraft 1.4.1 [601] phylogenetics
Fluent fluent 17.2, 19.1, 2020R1 [602] fluid_dynamics
Flye flye 2.9.1, 2.9.2, 2.9.3 [603] biology, ngs
fMRIPrep fmriprep 20.2.3, 23.1.3, 23.1.4 [604] data_mining
foldseek foldseek 9.427df8a [605] bioinformatics
forecasting forecasting 0.10.3 [606] Machine_Learning, Data_Science
ForeSeqs foreseqs 1.0.4 [607] phylogenetics
forwardgenomics forwardgenomics 1.0 [608] phylogenetics
fpocket fpocket 4.0.2 [609] sequencing, biology
fqtools fqtools 20160224 [610] biology, ngs, sequencing
FragGeneScan fraggenescan 1.16 [611] biology, genomics
FRAMA frama 20151019 [612] biology
FrameDP framedp 1.2.2 [613] biology, sequencing
FRAPOSA fraposa 20200421 [614] phylogenetics
FreeBayes freebayes 1.3.1, 1.3.2, 1.3.7 [615] biology, genomics
freecad freecad 0.20.2 [616] modeling
freesasa freesasa 2.1.2 [617] molecular_dynamics, biology
Freesurfer freesurfer 7.2.0, 7.3.2, 7.4.1 [618] biology, neuroscience, imaging
Freyja freyja 1.3.1, 1.3.4, 1.3.8 [619] biology, phylogenetics, sequencing
FSA fsa 1.15.9 [620] phylogenetics
FSL fsl 6.0.4, 6.0.5, 6.0.6 [621] biology, neuroscience, imaging
fslmrs fslmrs 1.1.10 [622] spectroscopy, metabolomics
funannotate funannotate 1.8.5, 1.8.7, 1.8.9 [623] phylogenetics
fusion_twas fusion_twas 20210218 [624] phylogenetics
GAL gal 20180906 [625] biology, genomics, annotation
Galaxy galaxytools 1.0 [626] biology
galaxyml galaxyml 0.10.0 [627] library, machine_learning
GAML gaml 20150610 [628] biology, genomics, assembly
GapCloser gapcloser 1.12r6 [629] biology, genomics, ngs
GapFiller gapfiller 1.10, 1.11 [630] biology, genomics
gapseq gapseq 1.2 [631] chemistry, biology
garfield garfield 2 [632] genomics
GARLI garli 2.0, 2.01 [633] biology, phylogenetics
GASVPro gasvpro 201310 [634] biology, ngs
GATE gate 7.0 [635] library
GATK gatk 4.1.9.0, 4.3.0.0, 4.4.0.0 [636] biology, ngs
Gaussian gaussian 09 D.01, 16, 16-c02 [637] chemistry
Gawk gawk 4.2.0 [638] utility
Gblocks gblocks 0.91b [639] biology, alignment
GCC gcc 7.3.0, 8.2.0, 9.3.0 [640] compiler
GCE gce 1.0.2 [641] biology, genomics
gcloud gcloud 471.0.0 [642] cloud, google, cli
gcnenv gcnenv 1.13 [643] library, math
GCT gct 6.2.1 [644] file_management, utility
GCTA gcta 1.26.0, 1.92.4beta, 1.93.2beta [645] biology, genomics, variant_calling
GDAL gdal 2.3.1, 3.7.0, 3.9.0 [646] geospatial, library
GDB gdb 8.3, 9.2 [647] programming
GDC-Client gdc-client 1.0.1, 1.5.0 [648] biology, sequencing, ngs
GDrive gdrive 2.1.0 [649] utility, file_management
GDSL gdsl 1.18 [650] library
Geant4 geant4 4.10, 4.10.03, 4.10.5 [651] physics
geant4 geant4 11.0.2, 4-11.0.3 [652] physics, simulation
GEM gem 20130406 [653] biology, ngs, sequencing
gem5 gem5 2.0 [654] simulation
GEMMA gemma 0.98.1, 0.98.5 [655] phylogenetics
gemma_llm gemma_llm 1 [656] library, math
genblastg genblastg 1.39 [657] biology, genomics
GeneMark-ES genemark_es 4.68, 4.69, 4.71 [658] biology, genomics
GeneMarkS genemark_s 2012.04 [659] biology, genomics
GeneMarkS-T genemark_s 3.10.001 [660] biology, genomics
GenePainter genepainter 2.0.4 [661] biology, phylogenetics
GeneRax generax 1.2.2 [662] phylogenetics
Generic Mapping Tools gmt 6.4.0 [663] physics, biology
GeneSeqer geneseqer 2014-02-26 [664] biology, genomics
genesis genesis 2.1.2, 2.1.2-cpu [665] Physics
genesum genesum 0.1.0 [666] biology, genomics
GeneTorrent genetorrent 3.8.7 [667] biology, file_management
genewalk genewalk 1.5.3 [668] phylogenetics
GenGen gengen 1.0.1 [669] biology, phylogenetics
genmap genmap v1.3.0 [670] Gene mapping, biology
geNomad genomad 1.5.1 [671] biology, genomics
Genome STRiP genomestrip 2.00.1602 [672] biology, genomics, ngs
Genome_Graph_Annotation genome_graph_annotation 20190131 [673] phylogenetics
GenomeScope2 genomescope2 2.0 [674] phylogenetics
GenomeThreader genomethreader 1.7.3 [675] phylogenetics
GenomeTools genometools 1.5.7, 1.5.9 [676] biology
genomic-fluidity genomic-fluidity 20151109 [677] phylogenetics
GenomicConsensus genomicconsensus 2.3.3 [678] biology, phylogenetics
GenomicNeuralnet genomic-neuralnet 20161030 [679] phylogenetics
GenomicTools genomictools 2.7.0 [680] biology, ngs, chip-seq, rna-seq
GenotypeHarmonizer genotypeharmonizer 1.4.18 [681] biology
Genrich genrich 0.5 [682] phylogenetics
GenSel gensel 4.90 [683] genomics
geomxngspipeline geomxngspipeline 3.1.1.5 [684] NGS
geopython geopython 1.0.0, 1.0.1, 1.0.2 [685] programming, geospatial
GEOS geos 3.3.8, 3.6.2 [686] library, data_science
GeP gep 2.1 [687] biology, phylogenetics
gepard gepard 1.40.0, 2.1.0 [688] phylogenetics
Gephi gephi 0.10.0 [689] visualization, image_processing
Gerbil gerbil 1.11 [690] phylogenetics
get_homologues get_homologues 3.3.3 [691] biology, genomics
GetOrganelle getorganelle 1.7.3.5, 1.7.5.0 [692] phylogenetics
GFam gfam 1.1 [693] biology, genomics, annotation
GFF-Ex gff-ex 2.3 [694] phylogenetics
GFF3toolkit gff3toolkit 2.0.3 [695] phylogenetics
gffcompare gffcompare 0.12.2 [696] phylogenetics
gffread gffread 0.11.8, 0.12.7, 0.9.8c [697] biology
Gflags gflags 2.2.1, 20150520 [698] web, library
GFOLD gfold 1.1.4 [699] biology, rna-seq
ggsashimi ggsashimi 0.5.0 [700] phylogenetics
GHOST-MP ghost-mp 1.3.4 [701] phylogenetics
Ghostscript ghostscript 9.22 [702] documentation
giggle giggle 20221212 [703] Genomics
Gimmemotifs gimmemotifs 0.18.0 [704] biology, genetics
Giotto giotto 0.1.0 [705] phylogenetics
giraf giraf 1.02 [706] sequencing, biology
Git git 2.14.1, 2.30.1 [707] revision_control
git-filter-repo git-filter-repo 2.33.0 [708] phylogenetics
Github Cli github-cli 2.40.1 [709] revision_control
Gkeyll gkeyll 2.0 [710] Plasma Physics
glactools glactools 1.0.8 [711] phylogenetics
Glimmer glimmer 3.02 [712] biology, annotation
GlimmerHMM glimmerhmm 3.0.4 [713] biology, annotation
GLMsingle glmsingle 1.0 [714] imaging
glnexus glnexus 1.4.1 [715] programming
Globus globus 2.1.3, 3.13.0, 3.18.0 [716] file_management
glog glog 0.3.5 [717] web, library
GLPK glpk 4.55, 4.65 [718] programming
Glueviz glueviz 0.15.2 [719] phylogenetics
GMAP gmap 20180212, 20180212_sse2, 20190610 [720] biology, genomics, ngs
GMcloser gmcloser 1.6 [721] biology, ngs
GMP gmp 6.1.2, 6.3.0 [722] library
gnuastro gnuastro 0.21 [723] astronomy
GnuPlot gnuplot 5.2.2, 5.2.3, 5.4.1 [724] graphics, math
Go go 1.15.4, 1.18.3, 1.21.0 [725] language
goatools goatools 1.2.3 [726] biology, ontology
GOMAP gomap 1.3, 1.4 [727] biology, ngs
GoPHY gophy 201030 [728] phylogenetics
Gosling gosling 0.2.2 [729] genomics, visualization
gotcloud gotcloud 1.17.5 [730] phylogenetics
GPA gpa 1.1 [731] phylogenetics
GPhoCS gphocs 1.2.3 [732] phylogenetics
gptl gptl 20140212 [733] utility
GPTL gptl 20140212 [734] utility
Gpufit gpufit 20201127 [735] phylogenetics
Grace grace 5.1.22 [736] graphics, statistics
GRACKLE grackle 3.1 [737] library, compiler, astronomy
Grackle grackle 3.2.1 [738] library, compiler, astronomy
GrADS grads 2.0.1 [739] geospatial, math
Graftm graftm 0.12.2 [740] phylogenetics
GramCluster gramcluster 1.3 [741] biology, sequencing
graph-tool graph-tool 2.32 [742] phylogenetics
Graph_annotation graph_annotation 0.1 [743] phylogenetics
graphaligner graphaligner 1.0.11, 1.0.16 [744] genomics
GraPhlAn graphlan 1.1.3 [745] phylogenetics
GraphMap2 graphmap2 0.6.5 [746] phylogenetics
GRAPHMB graphmb 0.2.5 [747] biology, genomics
GraphSplitting graphsplitting 2.4 [748] phylogenetics
graphtyper graphtyper 2.7.2 [749] phylogenetics
GraphViz graphviz 2.38.0, 2.46.1 [750] biology, neuroscience, imaging
GRASS grass 7.0, 7.4 [751] geospatial
grf grf 1.0.0 [752] genomics
Grib_api grib_api 1.10.1, 1.15.1, 1.26.1 [753] compiler, library
GRIDSS gridss 2.6.2 [754] phylogenetics
GROCSVs grocsvs 0.2.5 [755] phylogenetics
GROMACS gromacs 2021.4, 2022.3, 2023.2 [756] chemistry, molecular_dynamics
GroopM groopm 0.3.5 [757] biology, phylogenetics
Groovy groovy 2.4.15 [758] programming
Gscripts gscripts 1.1 [759] biology
GSEA gsea 4.2.2 [760] biology, genomics
GSL gsl 2.6, 2.7, 2.7.1 [761] library, data_science
GSNP gsnp 1.0 [762] biology, ngs
gsp gsp 05192017 [763] biology
GTAHunter gtahunter 20200106 [764] phylogenetics
GTDBTk gtdbtk 2.0.0, 2.1.0, 2.3.2 [765] phylogenetics
GTOOL gtool 0.7.5 [766] phylogenetics
GUAVA guava 1.0 [767] phylogenetics
Gubbins gubbins 2.4.1, 3.2.1, 3.3.0 [768] phylogenetics
guideseq guideseq 1.0.2 [769] sequencing, genomics, biology, data_science
guile guile 2.2.2 [770] programming
GULP gulp 4.4, 5.0 [771] material_science
guppy guppy 6.1.7, 6.4.2, 6.4.3 [772] phylogenetics
Gurobi gurobi 10.0.0, 11.0.1, 9.5.1 [773] math, programming
GWAMA gwama 2.2.2 [774] phylogenetics
Gzip gzip 1.10 [775] compression
hacdivsel hacdivsel 1.4.1 [776] genomics, biology
Hail hail 0.2.130, 0.2.77 [777] biology, genomics
hal hal 2.1 [778] phylogenetics
HALC halc 1.1 [779] biology, phylogenetics
halla halla 0.8.17 [780] phylogenetics
HaMStR hamstr 13.2.3, 13.2.4, v8b [781] biology, genomics
hapbin hapbin 1.3.0 [782] biology, genomics
HapCompass hapcompass 0.7.7 [783] imaging, ngs, genomics
HAPCUT hapcut 0.7 [784] biology, assembly
HapCUT2 hapcut2 1.3.3 [785] biology, genomics, sequencing
hapdup hapdup 0.6 [786] phylogenetics, biology
haphpipe haphpipe 1.0.3 [787] phylogenetics, biology
Haploflow haploflow 0.1 [788] biology, phylogenetics
Haplomerger2 haplomerger2 20180603 [789] biology, genomics
HAPLOSWEEP haplosweep 1.0 [790] biology, phylogenetics
happy happy 0.3.14 [791] phylogenetics, biology
hapQTL hapqtl 1.00 [792] biology
hapsembler hapsembler 2.21 [793] biology, assembly
harvesttools harvesttools 1.2 [794] phylogenetics, biology
HASLR haslr 0.8a1 [795] phylogenetics
hclust2 hclust2 1.0.0 [796] statistics, mapping
HDF4 hdf4 4.2.11 [797] library, data_science
HDF5 hdf5 1.8.19, 1.8.20, 1.8.9 [798] library, data_science
hecaton hecaton 0.5.1 [799] genomics, biology
HELEN helen 20200516 [800] phylogenetics
HelitronScanner helitronscanner 1.1 [801] phylogenetics
helixer helixer 0.3.3 [802] Genomics
herro herro 0.1.0 [803] Genomics
hgraph2graph hgraph2graph 20210428 [804] chemistry
hgtector hgtector 2.0 [805] biology, sequencing
hhsuite hhsuite 3.3.0 [806]
Hi-Corrector hi-corrector 1.2 [807] biology, ngs, sequencing
hic-lift hic-lift 06112023 [808] genomics
HiC-Pro hic-pro 3.0.0, 3.1.0 [809] biology, pipeline, genomics
Hifiasm hifiasm 0.19.9, 0.4, 0.8 [810] phylogenetics
Hificnv hificnv 0.1.7 [811] biology, genomics, ngs
hillerlab hillerlab 20240819 [812] phylogenetics
hiphase hiphase 1.4.0 [813] biology, ngs
HipSTR hipstr 0.7 [814] phylogenetics
HISAT2 hisat2 2.2.1, 2.2.1-3n, 20230203 [815] biology, alignment, ngs
hivtrace hivtrace 1.5.0 [816] biology,alignment
HLAminer hlaminer 1.3.1, 1.4 [817] biology, phylogenetics
HMM-FRAME hmm-frame 20140724 [818] phylogenetics
HmmCleaner hmmcleaner 0.180750 [819] phylogenetics
HMMER hmmer 3.2.1, 3.3.2, 3.4 [820] biology, genomics
hmmer2go hmmer2go 0.18.1 [821] phylogenetics, biology
HMMRATAC hmmratac 1.2.10 [822] phylogenetics
HoCoRT hocort 1.2.2 [823] RNA-Seq, QC
HOMER homer 4.10, 4.11, 4.8 [824] biology, sequencing, ngs
homopolish homopolish 0.3.3, 0.4.1 [825] genomics, biology
HOOMD hoomd 2.1.7 [826] library, math
HPL hpl 2.1 [827] programming, performance_analysis
hpsandbox hpsandbox 1.0.0 [828] Programming
HTMLDoc htmldoc 1.8.28, 1.9.3 [829] documentation, web
HTSeq htseq 0.11.2, 2.0.3 [830] biology, ngs
HUMAnN humann 2.8.1, 3.8 [831] sequencing, biology
humann2 humann2 0.11.2, 2.8.1 [832] phylogenetics
hxtorch hxtorch 0.8 [833] imaging
hyb hyb 20141126, 20200815 [834] biology, ngs, rna-seq
hybkit hybkit 0.3.4, 0.3.5, 0.3.6 [835] biology
HybPiper hybpiper 2.1.5, 2.1.6, 2.3.0 [836] biology, phylogenetics
HyDe hyde 0.4.3 [837] phylogenetics
hylite hylite 2.0.2 [838] genomics, biology
Hyper-Gen hypergen 0.1.0 [839] Programming
HyPhy hyphy 2.5.4, 2.5.7, 2.5.8 [840] biology, genomics
HYPRE hypre 2.15.1, 2.18.2, 2.19.0 [841] math
iAnnotateSV iannotatesv 1.0.6, 1.0.9 [842] biology, phylogenetics
iaps iaps 02012023 [843] programming
iAssembler iassembler 1.3.2 [844] biology, assembly
IBDmix ibdmix 1.0.1 [845] biology
ibdne ibdne 20150815 [846] biology, ngs
icommands icommands 3.3.1 [847] utility
IDBA-MT idba-mt 1.0 [848] biology, ngs
IDBA-UD idba-ud 1.1.1, 1.1.1-512, 1.1.1-512-mem [849] genomics, phylogenetics
IDL idl 8.3 [850] language, programming, data_science
IDR idr 2.0.3 [851] phylogenetics
IGB igb 8.4.1 [852] biology, genomics
igBLAST igblast 1.5.0, 1.7.0 [853] biology
IGoR igor 1.4.0 [854] phylogenetics
iGTP igtp 1.1 [855] biology, phylogenetics
IGV igv 2.3.91, 2.4.16, 2.8.6 [856] biology, ngs, phylogenetics
illumina-utils illumina-utils 2.11 [857] phylogenetics
Illumiprocessor illumiprocessor 2.0.9 [858] phylogenetics
IM and IMa ima 20091217 [859] biology, genomics
Ima2 ima2 20120827 [860] biology, genomics
IMa2p ima2p 20170712 [861] biology, phylogenetics
IMA3 ima3 22Aug18 [862] molecular_dynamics
ImageJ imagej 1.48 [863] imaging
imagej2 imagej2 09302022 [864] image processing, imaging
ImageMagick imagemagick 7.0.8-20 [865] imaging
Imaginaire imaginaire 20201229 [866] imaging, visualization, ai, machine_learning
IMOD imod 4.7.15, 4.9.10 [867] image_processing
imoka imoka 1.0 [868] biology, genomics
impg impg 0.1.0 [869] biology, alignment
IMPUTE2 impute2 2.3.2 [870] phylogenetics
IMPUTE5 impute5 1.1.5, 1.2.0 [871] biology, math
INDELible indelible 1.03 [872] phylogenetics
Infernal infernal 1.1.1, 1.1.4 [873] biology, alignment
INLA inla 20160718, 20170620 [874] statistics, modeling, programming
InParanoid inparanoid 4.1 [875] biology
Inspector inspector 1.0.2 [876] biology, genomics
InStruct instruct 20160723 [877] phylogenetics
Intel Compilers and Libraries intel 2023.0.0, 2023.2.0, 2024.1.0 [878] language, programming, library, math, compiler
Intel MPI impi 5.1.1 [879] programming, library
InterProScan iprscan 5.60, 5.68, 5.69 [880] biology
intervene intervene 0.6.2 [881] biology, phylogenetics
Intrasom intrasom 1.0 [882] python
IOAPI ioapi 3.1, 3.2 [883] climate
IPOPT ipopt 3.12.10, 3.12.6 [884] library, compiler, math
ipyrad ipyrad 0.9.102, 0.9.53, 0.9.94 [885] phylogenetics
IQ-TREE iq-tree 2.2.2.7, 2.3.2, 2.3.6 [886] biology, phylogenetics
IRAP irap 0.8.1p7 [887] biology, ngs
irep irep 1.10 [888] biology, genomics
IRFinder irfinder 1.2.0, 1.3.0, 1.3.1 [889] biology, rna-seq
isce2 isce2 2.6.3 [890] library
ISCE3 isce3 0.23.0 [891] library
isONclust isonclust 0.0.6 [892] phylogenetics
isonclust2 isonclust2 2.3 [893] rna-seq
IsoSel isosel 1.0 [894] phylogenetics
IsoSeq3 isoseq3 3.7.0, 3.8.2, 4.0.0 [895] biology, ngs
ISOWN isown 20180820 [896] phylogenetics
isPcr ispcr 3.3 [897] biology, phylogenetics
ITK itk 3.20.1, 4.10.1 [898] biology
ITK-SNAP itksnap 3.0.0, 3.8.0 [899] biology, neuroscience, imaging
ITSx itsx 1.1b [900] phylogenetics
iupred2a iupred2a 1.0 [901] biology
IVA iva 1.0.11 [902] phylogenetics
iVar ivar 1.3.1, 1.4.2 [903] biology
Jabba jabba 1.0 [904] biology, phylogenetics
JACUSA jacusa 1.2.0 [905] biology, ngs, phylogenetics
JAGS jags 3.3.0, 3.4.0, 4.2.0 [906] statistics
janus janus 20240412 [907] biology
Jasmine jasmine 1.1.4 [908] phylogenetics
jasp jasp 0.14.3 [909] statistics
jasper jasper 1.0.4 [910] biology
jbrowse2 jbrowse2 1.7.4 [911] web
JCVI jcvi 0.8.12, 1.0.13, 1.2.10 [912] phylogenetics
JDK java 20, 23, 9.0.1 [913] programming
Je je 1.0 [914] biology, ngs
Jellyfish jellyfish 2.2.4, 2.2.6, 2.3.0 [915] biology, ngs
jModelTest jmodeltest 2.1.1 [916] biology, genomics, phylogenetics
jo jo 1.3 [917] utility
jq jq 1.6 [918] utility
juicer juicer 1.22.01, 2.0 [919] phylogenetics
Julia julia 1.7.3, 1.8.2, 1.9.2 [920] programming, language, statistics
Jupyter jupyter 6.2.0, 6.5.2, 6.5.4 [921] programming
jutils jutils 1.0 [922] genomics, biology
JVARKIT jvarkit 20180405 [923] biology, phylogenetics
Kaiju kaiju 1.6.2, 1.7.2 [924] biology, phylogenetics
KaKs kaks 1.2, 2.0 [925] biology, genomics, phylogenetics
Kalign kalign 3.3.1 [926] biology, sequencing, alignment
kallisto kallisto 0.46.2, 0.48.0, 0.50.1 [927] biology, ngs, rna-seq
khmer khmer 2.0, 2.1 [928] biology, ngs
KIM kim 1.7.2, 1.8.2, 1.9.3 [929] simulation
kimmingloci skimmingloc 1.0.0 [930] pipeline mapping, biology
KING king 2.1.2, 2.3.0 [931] biology, genomics
KisSplice kissplice 2.4.0-p1 [932] biology, RNA
KLayout klayout 0.26.7 [933] phylogenetics
kma kma 20230106 [934] alignment
KMC kmc 3.1.0, 3.1.1, 3.2.1 [935] phylogenetics
kmerdb kmerdb 1.9.2 [936] genomics, biology
kmerfreq kmerfreq 4.0 [937] biology, genomics
KMOS kmos 0.3.21 [938] phylogenetics
kneaddata kneaddata 0.12.0, 0.7.4, 0.9.0 [https:https://github.com/biobakery/kneaddata] biology, genomics
knime knime 4.7.3 [939] data science
Knitro knitro 12.2.0 [940] math
KofamScan kofamscan 1.3.0 [941] phylogenetics
kover kover 2.0.3 [942] phylogenetics
Kraken kraken 2.0.8b, 2.1.2, 2.1.3 [943] biology, ngs
KrakenTools krakentools 1.2 [944] biology, ngs
KrakenUniq krakenuniq 0.5.8, 0.7.3, 1.0.4 [945] phylogenetics
Krona krona 2.8.1, 20161019 [946] biology
ksnp ksnp 3.021, 4.0 [947] biology, phylogenetics, variant_calling
Ksrates ksrates 1.1.1 [948] genomics, biology
kvarq kvarq 0.12.2 [949] biology
LACHESIS lachesis 2.1 [950] phylogenetics
Lambda lambda 0.9.4, 1.0.3, 2.0.0 [951] biology, sequencing, phylogenetics
LAMMPS lammps 3Nov2022, 7Aug19, 7Dec15 [952] molecular_dynamics
LAMMPS-PPA lammps-ppa 23Jun2022 [953] molecular Dynamics
LAMP lamp 2.5 [954] biology, genomics
laneta laneta 20220517, 20220808, 20220812 [955] biology
langdetect langdetect 1.0.9 [956] language, utility
LAPACK lapack 3.11.0, 3.8.0 [957] programming, library, compiler
Last last 916, 979 [958] biology, sequencing, alignment
LAStools lastools 20200114 [959] image_processing
LASTZ lastz 1.02.00, 1.03.02, 1.04.00 [960] biology, ngs
Lazypipe lazypipe 1.2 [961] genomics
LazyPredict lazypredict 0.2.8 [962] phylogenetics
lbzip lbzip 2.5 [963] compression
LCModel lcmodel 6.3 [964] biology, spectroscopy
ldak ldak 5.2 [965] phylogenetics, biology
ldblockshow ldblockshow 1.40 [966] biology
LDhat ldhat 2.2a [967] biology, genomics
ldsc ldsc 1.0.1 [968] genomics, biology
leafaudio leafaudio 0.1.0 [969] machine_learning, audio
LEfSe lefse 20180219 [970] phylogenetics
LEMON liblemon 1.2.3 [971] library
LFMM lfmm 1.4, 1.5 [972] biology, phylogenetics
libgfortran libgfortran 3.0.0 [973] programming
Libint libint 2.5.0, 2.5.0b [974] library
libMesh libmesh 1.5.0 [975] math
libunistring libunistring 0.9.7 [976] library
libvips libvips 8.5.4 [977] image_processing
LIBXC libxc 4.3.4, 6.2.2, 7.0.0 [978] library, math
LIBXSMM libxsmm 1.13 [979] library, compiler, math
LIBZMQ libzmq 4.3.1 [980] library
Liftoff liftoff 1.4.2, 1.6.2 [981] phylogenetics
Lighter lighter 1.1.3 [982] genome
LIGR ligr 2.05 [983] biology, assembly
LillyMol lillymol 6.1 [984]
lima lima 2.0.0, 2.2.0, 2.7.1 [985] phylogenetics
lingua lingua 1.0.1 [986] language, utility
LINKS links 1.8.5, 1.8.6 [987] biology, genomics
Linksbrowser linksbrowser 2.14 [988] web
LIQA liqa 1.0.0, 1.1.16 [989] phylogenetics
llama llama 2, 3 [990] library, math
llama-alex llama alex [991] library, math
llava llava 1.6 [992] Machine Learning
LMAP lmap 1.0.2 [993] biology, phylogenetics
lncScore lncscore 1.0.2 [994] biology, phylogenetics
lobSTR lobstr 4.0.6 [995] biology, phylogenetics
localbrainage localbrainage 20210415 [996] biology, machine_learning
localizer localizer 1.0.4, 1.0.5 [997] phylogenetics
LocusZoom locuszoom 1.4 [998] phylogenetics
LoFreq lofreq 2.1.3.1 [999] phylogenetics
LongQC longqc 1.2.0c [1,000] phylogenetics
LongRanger longranger 2.1.5, 2.2.2 [1,001] biology, phylogenetics
longshot longshot 0.4.5 [1,002] genomics
LongStitch longstitch 1.0.3 [1,003] genomics, biology
LoRDEC lordec 0.9 [1,004] phylogenetics
LoRMA lorma 0.3, 0.5 [1,005] biology, ngs
loter loter 1.0 [1,006] genomics,
LRBinner lrbinner 0.1 [1,007] biology, genomics
lrgapcloser lrgapcloser 09042018 [1,008] biology
LS-DYNA ls-dyna 700, 711, 901 [1,009] physics
LSD2 lsd2 1.6.5 [1,010] phylogenetics
ltr_finder ltr_finder 1.07 [1,011] biology, phylogenetics
LTRRetriever ltrretriever 2.1, 2.5, 2.9.0 [1,012] biology, phylogenetics
Lua lua 5.3.2, 5.3.4, 5.4.6 [1,013] programming, language
Lucene pylucene 7.7.1, 9.1.0 [1,014] programming, search
lumpy-sv lumpy 0.2.1, 0.2.13, 0.3.1 [1,015] biology, genomics
LZO lzo 2.09 [1,016] library, compression
M5nr m5tools 20121126 [1,017] biology, genomics
Macaulay2 macaulay2 1.15 [1,018] phylogenetics
MACH mach 1.0.18 [1,019] biology, genomics, ngs
Mach2VCF mach2vcf 20150515 [1,020] biology
Macrel macrel 1.3.0 [1,021] biology, genomics
MACS macs 2.0.10, 2.1.2, 2.2.7.1 [1,022] biology, chip-seq
MafFilter maffilter 1.3.0 [1,023] phylogenetics
MAFFT mafft 7.490, 7.505, 7.520 [1,024] biology, sequencing
MAGeCK mageck 0.5.9.4 [1,025] phylogenetics
MAGeCK-VISPR mageck-vispr 0.5.6 [1,026] phylogenetics
MAGeCKFlute mageckflute 1.14.0 [1,027] phylogenetics
Magenta magenta 2.1.2 [1,028] phylogenetics
magicblast magicblast 1.6.0 [1,029] genomics, biology
MAGMA-GWAS magma-gwas 1.09 [1,030] phylogenetics
magpurify magpurify 2.1.2 [1,031] genomics
magus magus 20220121 [1,032] sequencing, alignment
MAJIQ majiq 2.2, 2.3, 2.5.7 [1,033] phylogenetics
Maker maker 2.31.10, 2.31.6, 3.01.03 [1,034] biology
MAnorm manorm 20120316 [1,035] biology, phylogenetics
MANTA manta 1.6.0 [1,036] phylogenetics
mantis mantis 1.0.4 [1,037] phylogenetics
mapclassify mapclassify 2.4.2 [1,038] statistics, mapping, geospatial
mapdamage mapdamage 2.2.1 [1,039] ngs, sequencing, biology
MapThin mapthin 1.11 [1,040] phylogenetics
Maq maq 0.7.1 [1,041] biology, ngs
MarginPolish marginpolish 1.0.0 [1,042] phylogenetics
MARK mark 2.0.1 [1,043] data_science, math
MarkerMiner markerminer 20150710 [1,044] biology, genomics
Mash mash 1.1, 2.3 [1,045] biology, genomics
MasHmap mashmap 2.0 [1,046] phylogenetics
mashtree mashtree 1.2.0 [1,047] genomics, biology
maskrc-svg maskrc-svg 0.5 [1,048] genomics
MASS mass 1.1.1 [1,049] genomics, biology
MASSMINE massmine 0.10.0, 0.11.0, 0.9.5 [1,050] data_mining
MaSuRCA masurca 4.0.8, 4.0.9, 4.1.0 [1,051] biology, alignment
Mathematica mathematica 13.1, 14.0 [1,052] math
MATLAB matlab 2023b, 2024a, 2024b [1,053] math, language
MATS mats 4.0.2, 4.1.0, 4.2.0 [1,054] biology, ngs, rna-seq
matt matt 1.3.1 [1,055]
Mauve mauve 2.3.1 [1,056] biology, ngs, genomics
mawk mawk 1.3.4-20150503 [1,057] language
maxbin maxbin 2.1.1 [1,058] biology, ngs
Maxima maxima 5.41.0 [1,059] math
MC mc 4.6.1 [1,060] shell
mCarts mcarts 1.0.2 [1,061] biology, genomics, math
mccortex mccortex 1.0 [1,062] phylogenetics
mcfost mcfost 4.1.07 [1,063] astronomy
MCL mcl 12-135, 14-137 [1,064] biology, genomics
MCNP mcnp 6, 6.1, 6.3.0 [1,065] physics
MCNPX mcnpx 2.7.0 [1,066] physics
MCR mcr 2020a, 2020b, 2023b [1,067] math, language
MCScanX mcscanx 20130328 [1,068] biology, phylogenetics
mdanalysis mdanalysis 1.1.1 [1,069] physics, biology
MECAT mecat 20180308 [1,070] phylogenetics
Medaka medaka 1.7.2, 1.8.0, 2.0 [1,071] biology, phylogenetics
Medusa medusa 1.6 [1,072] phylogenetics
MEGA mega 11.0.13, 7.0.26 [1,073] biology, phylogenetics
Mega2 mega2 4.9.2, 6.0.0 [1,074] biology, phylogenetics
MEGAHIT megahit 1.1.1, 1.1.4, 1.2.9 [1,075] biology, phylogenetics
Megalodon megalodon 2.0.0, 2.4.1 [1,076] phylogenetics
MEGAN megan 6.23.4, 6.25.9, 6.4.15 [1,077] biology, ngs
MEGASAT megasat 1.0 [1,078] phylogenetics
Megraft megraft 1.0.2 [1,079] biology, sequencing
MELD meld 0.4.14, 0.4.19, 0.5.9 [1,080] chemistry, molecular_dynamics
MELTING melting 4.3.1 [1,081] biology, genomics, rna
MEME meme 5.0.2, 5.0.5, 5.4.1 [1,082] biology, sequencing
MentaLiST mentalist 0.1.3 [1,083] biology, phylogenetics
Meraculous meraculous 2.0.5 [1,084] biology, ngs
Mercurial mercurial 4.8.2 [1,085] revision_control
merge_peaks merge_peaks 0.1.0 [1,086] workflow_automation
Merlin merlin 1.1.2 [1,087] biology, variant_calling
Merqury merqury 1.1, 1.3 [1,088] phylogenetics
Meryl meryl 1.0 [1,089] phylogenetics
MeShClust meshclust 1.2.0 [1,090] biology
Meshroom meshroom 2019.2.0 [1,091] phylogenetics
Meson meson 1.2.3 [1,092] biology, ngs, sequencing
MET met 10.0 [1,093] climate, modeling
Meta-Marc meta-marc 1.0.0 [1,094] phylogenetics
Meta-Tissue meta-tissue 0.4 [1,095] biology, genomics
MetaBAT metabat 0.32.4, 2.13 [1,096] biology, genomics
MetaBCC-LR metabcc_lr 2.0.0 [1,097] biology, genomics
Metabin metabin 1.0 [1,098] genomics
metabolic metabolic 4.0 [1,099] phylogenetics
MetaCherchant metacherchant 0.1.0 [1,100] biology, phylogenetics
MetaCluster metacluster 5.0b [1,101] biology, genomics
MetaCompare metacompare 20181016 [1,102] phylogenetics
metacrast metacrast 20200309 [1,103] phylogenetics
Metaeuk metaeuk 6.0 [1,104] phylogenetics
MetaGeneMark metagenemark 2.10, 3.26 [1,105] biology, genomics
METAL metal 20110325 [1,106] biology, ngs, genomics
MetaLAFFA metalaffa 1.0.0 [1,107] phylogenetics
MetaMaps metamaps 20201207 [1,108] phylogenetics
METANNOT metannot 20171129 [1,109] phylogenetics
Metaphlan metaphlan 4.0.6, 4.1.0, 4.1.1 [1,110] phylogenetics
MetaPhlAn2 metaphlan2 2.7.7 [1,111] biology, phylogenetics
MetaPhysicl metaphysicl 1.0.0 [1,112] math, astronomy, simulation
Metashape metashape 1.8.4, 2.1.1 [1,113]
MetaSV metasv 0.5.4 [1,114] biology, phylogenetics, ngs
MetaVelvet metavelvet 1.2.06 [1,115] biology, genomics
metaWRAP metawrap 1.2 [1,116] phylogenetics
Metaxa2 metaxa2 2.1.1, 2.1.3, 2.2.3 [1,117] biology, ngs, sequencing
methylartist methylartist 1.3.0 [1,118] biology
MethylDackel methyldackel 0.5.0, 0.6.1 [1,119] phylogenetics
methylpy methylpy 1.2.9 [1,120] biology, phylogenetics
Metilene metilene 0.2.8 [1,121] biology, genomics, methylation
METIS metis 5.1.0, 5.2.1 [1,122] utility
Mfannot mfannot 20180405 [1,123] biology, phylogenetics
mfold mfold 3.6 [1,124] biology, structure, rna
mg-rast mg-rast 20150919 [1,125] biology, genomics
MGEfinder mgefinder 1.0.5 [1,126] phylogenetics
MGERT mgert 1.0.1 [1,127] phylogenetics
MGEScan mgescan 20160416 [1,128] biology, genomics
MGLTools mgltools 1.5.7 [1,129] biology, visualization
Mgs2amr mgs2amr 2.0.1 [1,130] genomics
MHAP mhap 1.6 [1,131] biology, sequencing
MHCflurry mhcflurry 1.4.3 [1,132] phylogenetics
MIA mia 20130201 [1,133] biology, ngs
micop micop 03312022 [1,134] genomics
MicrobeAnnotator microbeannotator 2.0.5 [1,135] annotation, biology
MIDAS midas 1.3.2, 20160830 [1,136] biology, phylogenetics
MIGRATE-N migraten 4.2.14, 4.4.4, 5.0.4 [1,137] biology, genomics
Mikado mikado 2.3.3 [1,138] biology, genomics, sequencing, pipeline
MIKE mike 1.0 [1,139] geospatial, fluid_dynamics, modeling
milvus milvus 2.4.15 [1,140] database, llm, container
Minced minced 0.2.0 [1,141] biology, genomics
Minia minia 3.2.6 [1,142] genomics, biology
Miniasm miniasm 0.2-r168, 0.3-r179 [1,143] biology, phylogenetics
MiniCaller minicaller 20161201 [1,144] biology, ngs, phylogenetics
minigraph minigraph 0.15, 0.20 [1,145] phylogenetics
minimac minimac 1-20130717, 3-20150727 [1,146] biology, ngs
minimac2 minimac 2-20140915 [1,147] biology, ngs
minimap minimap 2.21, 2.9-r720, 2.ax [1,148] biology, phylogenetics
minimap2 minimap2 2.24, 2.28 [1,149] genomics, biology
Minipolish minipolish 0.1.3 [1,150] biology, genomics
Miniprot miniprot 0.12 [1,151] biology, genomics
miniwdl miniwdl 1.11.1 [1,152] bioinfomatics
MinkowskiEngine minkowskiengine 0.5.3, 0.5.4a [1,153] machine_learning
MinPath minpath 1.4 [1,154] biology, phylogenetics
MIRA mira 4.0.rc1, 4.9.6, 5rc2 [1,155] biology, genomics, assembly
miRanda miranda 1.9 [1,156] phylogenetics
miRBShunter mirbshunter 0.2 [1,157] phylogenetics
mirdeep mirdeep 0.1.0, 0.1.1, 2.0.1.3 [1,158] phylogenetics
miRDP2 mirdp2 1.1.4 [1,159] biology, genomics
Mireap mireap 0.20 [1,160] biology
miRge mirge 2.0 [1,161] phylogenetics
Misa misa 1.0 [1,162] biology, genomics
MISO miso 0.5.3 [1,163] biology, ngs, sequencing, rna-seq
mistral mistral 0.1.5 [1,164] library, math
MITE-Hunter mite-hunter 20111101 [1,165] biology, phylogenetics
MITObim mitobim 1.9.1 [1,166] phylogenetics
MitoFinder mitofinder 1.4.1 [1,167] phylogenetics
mitohifi mitohifi 2.2, 3.2 [1,168] genomics, sequencing
MitoPhAST mitophast 3.0 [1,169] phylogenetics
Mitos mitos 2.1.9 [1,170] biology, phylogenetics
Mitsuba2 mitsuba2 2.2.1 [1,171] graphics
MiXCR mixcr 2.1.8, 3.0.13 [1,172] biology, phylogenetics
MixMHC2pred mixmhc2pred 1.2 [1,173] phylogenetics
MixMHCpred mixmhcpred 2.0.2 [1,174] phylogenetics
mixmogam mixmogam 20190322 [1,175] phylogenetics
MKL mkl 2019.1.144, 2020.0.166, 2020.2.0 [1,176] programming, library, math, compiler
mlcoalsim mlcoalsim 1.9916b [1,177] biology, phylogenetics
mlpack mlpack 3.4.2 [1,178] library
mlst mlst 2.15.2, 2.23.0 [1,179] phylogenetics
mlstcheck mlst-check 2.1 [1,180] phylogenetics
mmaction2 mmaction2 1.0.0 [1,181] Machine_Learning, Visualization
MMSEQ mmseq 1.0.8 [1,182] biology, genomics
MMseqs2 mmseqs2 11, 12, 14 [1,183] phylogenetics
MMvec mmvec 1.0.5, 1.0.6 [1,184] metabolomics
MNEtools mnetools 0.22.0, 1.3.1, 1.4.0 [1,185] phylogenetics
MOABS moabs 1.2.9, 1.3.2, 1.3.4 [1,186] biology, ngs
mobsuite mobsuite 3.1.0, 3.1.9 [1,187] sequencing, biology
MOCCASIN moccasin 0.25 [1,188] phylogenetics
moco moco 0.4.0 [1,189] modeling, tools
Model Card Toolkit model_card_toolkit 2.0.0 [1,190] Machine_Learning, Utility, Workflow_automation
MODELLER modeller 9.14, 9.23 [1,191] biology, modeling, structure
MODELTEST modeltest 0.1.2, 0.1.7 [1,192] biology, phylogenetics
ModernCSV moderncsv 2.0.2 [1,193] editor, viewer
Modkit modkit 0.4.1 [1,194] genomics, bioinformatics
Modulus modulus 23.11, 24.01, 24.07 [1,195] physics, ai, neural_network
Molden molden 5.0, 7.3 [1,196] chemistry, structure
MolPro molpro 0.1 [1,197] biology
MolProbity molprobity 20221216 [1,198] biology
momi momi 2.1.19 [1,199] phylogenetics, biology
monai monai 0.8.1, 0.9.0, 1.0.1 [1,200] healthcare
MONAI label ngc-monailabel 0.3.2, 0.6.0 [1,201] healthcare
MongoDB mongodb 4.0.3 [1,202] database
Moni moni 0.2.0 [1,203] genomics, biology
mono mono 5.18 [1,204] linux, programming
Monolix monolix 2023R1, 4.3.2 [1,205] modeling, biology
MOOSE moose 20220610, 20230320, 20230711 [1,206] physics, simulation
mopac mopac 22.1.1 [1,207] chemistry
MORPHEUS morpheus 23.01 [1,208] machine_learning
Mosaic mosaic 1.7.4 [1,209] phylogenetics
MOSAIK mosaik 2.1.33, 2.2.3, 2.2.30 [1,210] biology, alignment
Mosdepth mosdepth 0.2.3, 0.3.1 [1,211] biology, phylogenetics
moses moses 0.3.1 [1,212] machine learning, data science
Mothur mothur 1.41.3, 1.46.1, 1.48.0 [1,213] biology
MotionCor2 motioncor2 1.2.3, 1.3.1, 1.6.4 [1,214] imaging
mOTU motu 1.1 [1,215] biology, genomics
mOTUs motus 2.5.1 [1,216] phylogenetics
MountainSort mountainsort 0.9.0 [1,217] library
MP-EST mpest 1.4 [1,218] biology, ngs, sequencing
MPACK mpack 0.8.0 [1,219] library
MPB mpb 1.5 [1,220] library, math
MPBoot mpboot 1.1.0 [1,221] biology, phylogenetics
MPFR mpfr 3.1.6, 4.2.1 [1,222] library, math
mpi-test-suite mpi-test-suite 1.1.1 [1,223] utility
mpinterfaces mpinterfaces 20170613 [1,224] math
MrBayes mrbayes 3.2.4, 3.2.5, 3.2.6 [1,225] biology, phylogenetics
MRIcroGL mricrogl 20201102, 20210327, 20211006 [1,226] biology, imaging
MRIcron mricron 201306, 20161012, 20190911 [1,227] biology, imaging
mriqc mriqc 0.11.0, 0.16.1, 22.0.1 [1,228] imaging, biology
MRtrix mrtrix 3.0.1, 3.0.3, 3.0rc2 [1,229] statistics
mrtrix3tissue mrtrix3tissue 5.2.9 [1,230] phylogenetics
ms ms 20171108 [1,231] phylogenetics
ms-dial ms-dial 4.4.8 [1,232] biology, metabolomics
msfinder msfinder 3.52 [1,233] biology, metabolomics
mSINGS msings 20180810 [1,234] phylogenetics
MSMC-Tools msmc-tools 20190614 [1,235] phylogenetics
msprime msprime 0.7.4, 1.2.0 [1,236] phylogenetics
MstatX mstatx 1.0 [1,237] biology, phylogenetics
MSTmap mstmap 1.0 [1,238] phylogenetics
msvar msvar 1.3 [1,239] biology, genomics
MTG2 mtg2 2.15 [1,240] phylogenetics
mTR mtr 20210526, 20240801 [1,241] biology, genomics
Mugsy mugsy 1.2.3 [1,242] biology, phylogenetics
Multimatch-gaze multimatchgaze 0.1.3 [1,243] math, data_science
MultiQC multiqc 1.21, 1.24, 1.7 [1,244] biology, ngs, sequencing
MUMmer mummer 3.23, 4.0.0beta2 [1,245] biology, genomics
MUSCLE muscle 3.8.31, 5.1 [1,246] biology, alignment
MuSE muse 1.0rc [1,247] phylogenetics
Musket musket 1.1 [1,248] biology, genomics, ngs
MuTect mutect 1.1.4, 1.1.7 [1,249] biology, genomics
mutmap mutmap 2.3.3 [1,250] biology
MutSig mutsig 1.4, 1.41 [1,251] biology, genomics
mvftools mvftools 20191124 [1,252] phylogenetics
mvrsion mvrsion 07302018 [1,253] sequencing
mxnet ngc-mxnet 22.08 [1,254] healthcare
mykrobe mykrobe 0.12.2 [1,255] biology
MZMine mzmine 2.53, 3.3.0 [1,256] biology, spectroscopy
NAMD namd 2.14b2, 3.0 Alpha, 3.0b2 [1,257] molecular_dynamics
NANO nano 2.8.2 [1,258] programming
nanocaller nanocaller 3.1.0 [1,259] sequencing
nanocomp nanocomp 1.17.0 [1,260] programming, sequencing
Nanocompore nanocompore 1.3.0 [1,261] biology, genomics
NanoCount nanocount 0.2.1 [1,262] phylogenetics
Nanodisco nanodisco 1.0.3 [1,263] phylogenetics
Nanofilt nanofilt 2.7.1 [1,264] phylogenetics
nanolyse nanolyse 1.2.0 [1,265] genomics, biology
NanoPlot nanoplot 1.30.1, 1.42.0 [1,266] phylogenetics
Nanopolish nanopolish 0.11.1, 0.13.2, 20171006 [1,267] biology
nanoq nanoq 0.10.0 [1,268] biology, ngs, nanopore
nanostripper nanostripper 0.1 [1,269] phylogenetics, biology
NanoSV nanosv 1.2.0, 1.2.3, 1.2.4 [1,270] biology, genomics
NanoVar nanovar 1.3.9 [1,271] phylogenetics
Napari napari 0.3.8, 0.4.7 [1,272] phylogenetics
NBODY nbody 6 [1,273] astronomy
NCBI BLAST+ ncbi_blast 2.7.1, 2.8.1, 2.9.0 [1,274] biology
NCBI C++ Toolkit ncbi_toolkit 12.0.0, 21.0.0, 7.0.0 [1,275] biology, programming, library, compiler
NCBI GenBank Tools genbank_tools 20140130 [1,276] biology
ncbi-fcs ncbi-fcs 0.4.0, 0.5.0, 0.5.4 [1,277] genomics
ncbi-genome-download ncbi-genome-download 0.3.3 [1,278] biology, genomics
ncbi-vdb ncbi-vdb 2.6.3, 2.8.2 [1,279] ngs
ncbi_cli ncbi_cli 15.3.1 [1,280] biology, sequencing, library
nccl nccl 20.11 [1,281] programming, library, gpu
ncftp ncftp 3.2.5 [1,282] file_management
NCL ncl 6.1.2, 6.3.0, 6.6.2 [1,283] climate
NCO nco 4.2.1, 4.4.3 [1,284] data_science
ncview ncview 2.1.2, 2.1.7 [1,285] visualization
NECAT necat 202001019, 20200803 [1,286] phylogenetics
Necklace necklace 1.00 [1,287] biology, phylogenetics
NeEstimator neestimator 2.1 [1,288] biology
nemo nemo 1.2.0, 1.22.0, 1.23.0 [1,289] ai, machine_learning
neovim neovim 0.8.1, 0.8.3, 0.9.5 [1,290] programming, shell
nerfstudio nerfstudio 1.1.3 [1,291] Machine Learning
NetCDF netcdf 4.3, 4.3.3, 4.4.3 [1,292] data_science
NetCDF-C netcdf-c 4.8.1, 4.9.0, 4.9.2 [1,293] data_science
NetCDF-F netcdf-f 4.5.3, 4.5.4, 4.6.1 [1,294] data_science
NetLogo netlogo 5.3.64, 6.1.1, 6.2.0 [1,295] modeling
NEURON neuron 7.7.2, 8.0.0, 8.2.1 [1,296] biology, neuroscience
Newbler newbler 2.7, 2.8, 2.9 [1,297] biology, ngs, assembly, de_novo
newick-utils newickutils 1.6 [1,298] biology, genomics, phylogenetics
newick_utils newick_utils 1.6, 1.7 [1,299] biology, phylogenetics
NewTargets newtargets 20210215 [1,300] biology
nextclade nextclade 2.9.1, 3.2.0, 3.8.2 [1,301] phylogenetics, genomics
NextDenovo nextdenovo 2.4.0 [1,302] phylogenetics
Nextflow nextflow 23.10.0, 23.10.1, 24.04.2 [1,303] biology, workflow_automation
NextGenMap nextgenmap 0.5.5 [1,304] phylogenetics
NextPolish nextpolish 1.3.1 [1,305] phylogenetics
Nextstrain nextstrain 1.16.1 [1,306] phylogenetics
nf-core nf-core 2.11.1, 2.14.1, 2.7.2 [1,307] biology, workflow_automation
NGC CLI ngccli 2.10.1 [1,308] shell
NGmerge ngmerge 0.3 [1,309] phylogenetics
ngmlr ngmlr 0.2.6, 0.2.7 [1,310] biology, phylogenetics
ngs-bits ngsbits 0.1 [1,311] biology, sequencing
NGS-SDK ngs-sdk 1.2.4, 1.3.0 [1,312] biology, healthcare, programming, library
ngsremix ngsremix 20221117 [1,313] genomics
ngstools ngstools 20150816 [1,314] biology, ngs
nilearn nilearn 0.7.0, 0.9.0 [1,315] phylogenetics
nimare nimare 0.0.5 [1,316] neuroscience
Nipype nipype 1.6.0, 1.7.0, 1.8.0 [1,317] biology, neuroscience, imaging
nlp nlp 1.1, 1.2, 1.3 [1,318] machine_learning
nlr-annotator nlr-annotator 0.7 [1,319] phylogenetics
NLR-Parser nlr-parser 1.0 [1,320] phylogenetics
nlrtracker nlrtracker 20240306 [1,321] biology
NMRPipe nmrpipe 7.9, 8.2 [1,322] chemistry, biology
NONMEM nonmem 7.3.0, 7.4.4 [1,323] modeling
nonpareil nonpareil 3.3.4 [1,324] phylogenetics
Novoalign novoalign 2.08.02, 3.00.02 [1,325] biology, ngs
NOVOPlasty novoplasty 3.7, 4.2, 4.3 [1,326] phylogenetics
nPhase nphase 1.1.3 [1,327] biology, pipeline
npScarf japsa 1.7 [1,328] phylogenetics
nQuire nquire 20180405 [1,329] phylogenetics
Nsight nsight 2022.1, 2024.3.2.0 [1,330] gpu, performance_analysis, utility
Nsightsys nsightsys 2022.2.1, 2024.5.1 [1,331] gpu, performance_analysis, utility
nt nt 20220404 [1,332] sequencing, neuroscience
ntEdit ntedit 1.2.1 [1,333] phylogenetics
ntJoin ntjoin 1.1.4 [1,334] biology, genomics
nubeamdedup nubeamdedup 20200907 [1,335] phylogenetics
NucDiff nucdiff 2.0.3 [1,336] phylogenetics
NucleoATAC nucleoatac 0.3.1 [1,337] biology
Nuke nuke 14.0v5 [1,338] Graphics, Utility, Visualization
Nullarbor nullarbor 1.41 [1,339] biology, phylogenetics
Numba numba 0.36.2, 0.43.1, 0.48.0 [1,340] compiler
NUPACK nupack 3.2.2 [1,341] phylogenetics
nvhpc nvhpc 23.7, 24.3, 24.5 [1,342] language, programming, library, math, gpu
nVidia HPC Compilers nvidia 20.11 [1,343] compiler
NWChem nwchem 6.8, 7.2 [1,344] chemistry
NxTrim nxtrim 0.4.1 [1,345] biology, ngs
Oases oases 0.2.08 [1,346] biology, ngs, assembly
Oatk oatk 1.0 [1,347] genomics
Obitools obitools 1.2.13, 3.0 [1,348] biology, ngs, sequencing
OCaml ocaml 4.02.3 [1,349] language, programming
OCOCO ococo 0.1.2.6 [1,350] biology, phylogenetics
octave octave 6.4.0, 7.2.0, 7.3.0 [1,351] math
odgi odgi 0.6, 0.8.4 [1,352] phylogenetics
Olego olego 1.1.2, 1.1.5, 1.1.6 [1,353] biology, ngs, rna-seq
ollama ollama 0.3.8 [1,354] LLM
OMindel omindel 20180129 [1,355] phylogenetics
OMNI-C omnic 1.0 [1,356] genomics
omniCLIP omniclip 0.1.0 [1,357] phylogenetics
OMNIVERSE omniverse beta211004 [1,358] gpu
OMSV omsv 1.0.1 [1,359] phylogenetics
OneFormer oneformer 1.0 [1,360] ai, image_processing, imaging
ONT-Bonito ont-bonito 0.1.5, 0.5.3, 0.6.0 [1,361] phylogenetics
ont_fast5_api ont-fast5-api 2.0.1, 4.0.2 [1,362] phylogenetics
ont_tutorial_cas9 ont_tutorial_cas9 20190705 [1,363] phylogenetics
open-cravat open-cravat 2.0.1 [1,364] biology, genomics
open3d open3d 0.13.0, 0.17.0 [1,365] graphics
OPENACC openacc 16.7 [1,366] programming
OpenBabel openbabel 2.3.2, 2.4.1, 3.1.1 [1,367] biology
OpenBLAS openblas 0.2.20, 0.3.24 [1,368] programming, library
OpenCL opencl 18.1.0.013 [1,369] phylogenetics
OpenCV opencv 4.5.2, 4.7.0 [1,370] library
OpenFOAM openfoam 4.1, 5.0, 8.0 [1,371] fluid_dynamics
openmc openmc 0.14.0, 0.15.0 [1,372] physics
OpenMM openmm 7.6.0, 8.0.0, 8.1.2 [1,373] chemistry, molecular_dynamics
OpenMPI openmpi 4.1.4, 4.1.5, 4.1.6 [1,374] programming, library
OpenNeuro openneuro 3.17.4, 3.37.4, 4.19.2 [1,375] biology, data_science
opennmt-py opennmt-py 3.1.0 [1,376] language, machine_learning
OpenPIV-python openpiv 0.21.2 [1,377] programming, imaging
OpenPIV-python-gpu openpiv 20190506-gpu [1,378] programming, imaging
OpenPose openpose 20230106 [1,379] image_processing
openrdp openrdp 0.1.0-rc2 [1,380] biology
OpenSim opensim 4.3 [1,381] phylogenetics
OpenSlide openslide 3.4.1 [1,382] imaging
Openssl openssl 3.3.0 [1,383] libray
openstructure openstructure 2.3.1 [1,384] biology
OpenUSD openusd 23.08 [1,385] digital twin, simulation
OptiType optitype 1.3.1 [1,386] biology, phylogenetics
Orange3 orange3 3.3.6 [1,387] data_mining
Orca orca 5.0.1, 5.0.4 [1,388] chemistry
ORCA orca 4.0.1.2 [1,389] chemistry, structure
OrganellePBA organellepba 20180904 [1,390] phylogenetics
OrthoFiller orthofiller 1.1.4 [1,391] phylogenetics
OrthoFinder orthofinder 2.3.11, 2.5.2, 2.5.5 [1,392] biology, ngs
Orthofisher orthofisher 0.1.2 [1,393] biology, genomics
Orthograph orthograph 0.6.3 [1,394] orthology
Orthologer orthologer 2.2.0 [1,395] biology
OrthoMCL orthomcl 2.0.9 [1,396] biology, genomics
OSL osl 1.1.0 [1,397] biology, neuroscience, imaging
oslom oslom 0.3.0 [1,398] plotting
osprey osprey 1.1.0, 2.5.0 [1,399] spectroscopy, neuroscience
OTB otb 5.8.0 [1,400] geospatial
ovito ovito 3.8.5, 3.9.4 [1,401] programming
owitools owitools 1.0 [1,402] metabarcoding, bioinformatics, ecology
p4est p4est 1.1, 2.8 [1,403] library
p4vasp p4vasp 0.3.29, 0.3.30 [1,404] chemistry, structure
p53MH p53mh 20020901 [1,405] biology, sequencing
p7zip p7zip 9.20.1 [1,406] utility
PacBio pacbio 10.2.0.133434, 11.0.0.146107, 7.0.1 [1,407] biology, ngs
Package-GFE package-gfe 20150701 [1,408] biology, genomics
PacMAP pacmap 0.7.0 [1,409] genomics
PALADIN paladin 1.3.1 [1,410] biology, phylogenetics
PALES pales 122 [1,411] physics
PAML paml 4.8a, 4.9a, 4.9h [1,412] biology, phylogenetics
panaroo panaroo 1.3.3 [1,413] biology, genomics
Pandaseq pandaseq 20140808, 20150627 [1,414] biology, ngs, sequencing
Pandoc pandoc 2.2.2.1 [1,415] utility
pangolin pangolin 2, 4.3 [1,416] phylogenetics
panseq panseq 3.2.1 [1,417] phylogenetics
pantools pantools 4.3.1 [1,418] biology, genomics
panX panx 1.6.0 [1,419] phylogenetics
PAPI papi 5.5.1, 5.7.0 [1,420] programming, performance_analysis
parabricks parabricks 4.2.1, 4.3.0, 4.3.1 [1,421] phylogenetics
parallel parallel 20150122, 20170322 [1,422] shell, workflow_automation
paralyzer paralyzer 1.5 [1,423] phylogenetics
ParaView paraview 5.4.1, 5.7.0, 5.9.1.1 [1,424] data_science
ParaView Server paraview_server 5.10.1 [1,425] data_science
ParGenes pargenes 1.2.0 [1,426] phylogenetics
ParlAI parlai 1.3.0, 1.5.0 [1,427] phylogenetics
PARMETIS parmetis 4.0.3 [1,428] utility
Parsnp parsnp 1.2, 1.5.0, 1.6.2 [1,429] biology, phylogenetics
PartitionFinder partitionfinder 2.0.0-pre-20160513, 2.1.1-20161205, 2.1.1.0 [1,430] biology, phylogenetics, genomics
PASA pasa 2.2.0-r20171013, 2.4.1, 2.5.3 [1,431] biology, genomics, ngs
Pascal fpc 3.0.0 [1,432] compiler, programming
PASTA pasta 0.2.0, 1.7.8, 20160616 [1,433] biology, alignment
PATHd8 pathd8 1.0 [1,434] biology, phylogenetics
pathoscope pathoscope 2.0.7 [1,435] sequencing, genomics, biology
PATRIC patric 1.034 [1,436] machine_learning
PAUDA pauda 1.0.1 [1,437] biology, ngs, phylogenetics
PAUP paup 4.0a166, 4.0a168, 4.0b10 [1,438] biology, phylogenetics
PB-Assembly pb-assembly 0.0.6, 0.0.8 [1,439] biology, ngs, sequencing
pbalign pbalign 20160921, 20161221 [1,440] biology
PBCCS pbccs 5.0.0, 6.4.0 [1,441] phylogenetics
pbcore pbcore 1.7.1 [1,442] biology
PBGCpp pbgcpp 1.9.0 [1,443] phylogenetics
pbipa pbipa 1.8.0 [1,444] phylogenetics, biology
PBJelly pbjelly 15.8.24 [1,445] biology, ngs
pbmm2 pbmm2 1.13.1, 1.3.0 [1,446] phylogenetics
pbpigeon pbpigeon 1.2.0 [1,447] biology, ngs
pbrt pbrt 20181017 [1,448] phylogenetics
pbsmrtpipe pbsmrtpipe 0.63.0 [1,449] biology, programming
pbtk pbtk 3.1.0 [1,450] biology
pbtranscript-tofu pbtranscript-tofu 20150317, 20160119 [1,451] biology, ngs
pcangsd pcangsd 1.2 [1,452] biology
PCIT pcit 2014 [1,453] biology
PCRE pcre 8.38, 8.39 [1,454] programming, library
PDA pda 1.0.3 [1,455] biology, phylogenetics
pdb2pqr pdb2pqr 2.1.0 [1,456] protein, modeling, biology
PeakSplitter peaksplitter 1.0 [1,457] biology, chip-seq
PEAR pear 0.9.2 [1,458] biology, genomics, ngs
peneasy peneasy 20150530 [1,459] physics
PennCNV penncnv 1.0.5 [1,460] phylogenetics
Perl perl 5.16.0, 5.20.0, 5.24.1 [1,461] programming, language
PerM perm 0.4.0 [1,462] biology, ngs, mapping
PETSc petsc 3.8.1, 3.8.3, 3.8.4 [1,463] math
PfamScan pfamscan 1.3, 1.5 [1,464] biology, genomics
PGAP pgap 20230306, 20231003, 20240703 [1,465] biology, genomics, annotation, pipeline
PGDSpider pgdspider 2.0.9.0, 2.1.1.5 [1,466] biology, ngs
pggb pggb 0.6.0, 20201106, 20210121 [1,467] phylogenetics
PhaME phame 1.0.3 [1,468] phylogenetics
phanotate phanotate 1.5.0 [1,469] genomics
pharmcat pharmcat 1.8.0 [1,470] biology, phylogenetics
PHASE phase 2.1.1 [1,471] phylogenetics
PHAST phast 1.5 [1,472] biology, phylogenetics
Phenix phenix 1.10.2155, 1.17.1, 1.8.1069 [1,473] material_science
PHI phi 3.1.1, 3.1.2b, 3.1.6 [1,474] math
PhiSpy phispy 3.2 [1,475] phylogenetics
PHLAWD phlawd 20170427 [1,476] biology, phylogenetics
PhotoScan photoscan-pro 1.4.1, 1.4.5 [1,477] image_processing
Photutils photutils 0.5 [1,478] astronomy
PHYling phyling 1.0 [1,479] biology, phylogenetics, genomics
PHYLIP phylip 3.696 [1,480] biology, phylogenetics
PhyloAcc phyloacc 1.0 [1,481] phylogenetics
PhyloBayes phylobayes 3.3f [1,482] biology, phylogenetics
phyloFlash phyloflash 3.3b4 [1,483] phylogenetics
phylonet phylonet 3.5.7, 3.8.2 [1,484] biology, phylogenetics
PhyloParser phyloparser 20180404 [1,485] phylogenetics
PhyloPhlAn2 phylophlan2 0.41 [1,486] phylogenetics
phylopypruner phylopypruner 1.2.3 [1,487] phylogenetics
PhyloSift phylosift 1.1 [1,488] biology, genomics, phylogenetics
phyloTF2 phylotf2 20210726 [1,489] biology, genomics, alignment
Phyluce phyluce 20180727, 20190308, 20191015 [1,490] biology, ngs, sequencing
PhyML phyml 3.0, 3.1, 3.3.20220408 [1,491] biology, phylogenetics
phynd phynd 20200409 [1,492] phylogenetics
Physher physher 1.0.2 [1,493] phylogenetics
PHYUTILITY phyutility 2.7.1 [1,494] biology
Phyx phyx 1.1 [1,495] phylogenetics
PIA2 pia2 20180305 [1,496] biology, phylogenetics
Picard-tools picard 2.9.2, 3.1.1, 3.2.0 [1,497] biology, ngs
PICRUSt picrust 1.1.3, 1.1.4, 2.3.0b [1,498] biology, phylogenetics
PICSL picsl 1.3 [1,499] imaging
Piggy piggy 20171220 [1,500] biology, ngs
Pigz pigz 2.4 [1,501] compression
PILON pilon 1.22, 1.24 [1,502] biology, ngs, phylogenetics
Pindel pindel 0.2.5b8 [1,503] biology, phylogenetics
pipe-clip pipe-clip 1.1.0 [1,504] biology, ngs
pipits pipits 1.3.6, 1.4.0 [1,505] biology, sequencing
Piranha piranha 1.2.1 [1,506] biology, phylogenetics
PLantismash plantismash 1.0 [1,507] biology, genomics
PlantTribes planttribes 1.0.4 [1,508] phylogenetics
plasme plasme 1.1 [1,509] Genomics
PLAST plast 1.0, 2.3.2 [1,510] biology
platanus platanus 1.2.4 [1,511] phylogenetics
Platon platon 1.6 [1,512] biology, sequencing
Platypus platypus 0.8.1 [1,513] biology, ngs
PLEK plek 1.2.2 [1,514] biology, phylogenetics
Plink plink 2.00a2, 2.00a3LM, 2.00a5LM [1,515] biology, genomics, phylogenetics
plinkseq plinkseq 0.10 [1,516] biology, library
plip plip 2.3.0 [1,517] Protein-structure
plotsr plotsr 0.5.4 [1,518] genomics, biology
PLUMED plumed 2.7.3, 2.9.0, 2021.2 [1,519] chemistry, molecular_dynamics
pm4py pm4py 2.7.4 [1,520] Data_Mining, Machine_Learning
pod5 pod5 0.1.5, 0.3.6, 20220621 [1,521] sequencing
PolyGembler polygembler 1.0 [1,522] phylogenetics
PolyPHen polyphen 2.2.2.r405b [1,523] biology, genomics
polyply polyply 1.3.0 [1,524] phylogenetics, biology
Polypolish polypolish 0.5.0 [1,525] biology, genomics
pomdp pomdp 1.3.4 [1,526] software
pomoxis pomoxis 0.1.11, 0.2.5, 0.3.2 [1,527] biology, phylogenetics
popcorn popcorn 20211104 [1,528] phylogenetics, biology
PopLDdecay poplddecay 3.40 [1,529] phylogenetics
popoolation popoolation 1.2.2 [1,530] biology, phylogenetics
popoolation2 popoolation2 1.201 [1,531] biology, phylogenetics
Porechop porechop 0.2.4 [1,532] phylogenetics
Poretools poretools 0.6.1 [1,533] phylogenetics
portcullis portcullis 1.2.3 [1,534] phylogenetics
PosiGene posigene 20171113 [1,535] biology, phylogenetics
POV-Ray povray 3.7, 3.7.0.8 [1,536] graphics
powerfit powerfit 2.0.0 [1,537] Physics
pplacer pplacer 1.1.alpha19 [1,538] biology, phylogenetics, genomics
PRANK prank 170427, 20150803 [1,539] biology, alignment
Predector predector 20201110 [1,540] phylogenetics
predectorutils predectorutils 0.9.1 [1,541] biology, genomics
preplot preplot 14.0.2 []
Preseq preseq 0.0.4 [1,542] biology, ngs
PRICE price 1.2 [1,543] biology, ngs
Primer3 primer3 2.3.4 [1,544] biology, genomics
primus primus 1.8.0 [1,545] biology, phylogenetics
PRINSEQ prinseq 0.20.4 [1,546] biology, sequencing
PRINSEQ++ prinseq++ 1.2 [1,547] phylogenetics
ProbABEL probabel 0.4.2, 0.4.3, 0.4.5 [1,548] genomics
probalign probalign 1.4 [1,549] biology, ngs
Processing processing 3.4 [1,550] programming, language, visualization
Prodigal prodigal 2.6.2, 2.6.3 [1,551] biology, genomics
ProDy prody 2.0 [1,552] phylogenetics
Program Database Toolkit pdt 3.20, 3.22, 3.24 [1,553] language, programming, performance_analysis
PROJ proj 5.1.0, 8.0.1, 9.4.0 [1,554] library, Cartographic Projections and Coordinate Transformations
Prokka prokka 1.12, 1.14.6 [1,555] biology, genomics, assembly
Proovread proovread 1.03rcl, 2.12, 2.13 [1,556] biology, genomics, ngs
ProSplign prosplign 1.0.0 [1,557] phylogenetics
Protege protege 5.1.0 [1,558] genomics
Proteinortho proteinortho 4.26, 5.11, 5.16 [1,559] biology, genomics
ProtExcluder protexcluder 1.2 [1,560] biology, phylogenetics
ProtHint prothint 2.6.0 [1,561] biology, genomics
protobuf protobuf 2.5.0, 3.5.1 [1,562] web, library
prottest3 prottest3 3.4.2 [1,563] biology
PROVEAN provean 1.1.5 [1,564] biology, genomics
PRSice prsice 2.3.3 [1,565] phylogenetics
Pseudofinder pseudofinder 1.0 [1,566] phylogenetics
PsiCLASS psiclass 1.0.1 [1,567] phylogenetics
PSMC psmc 0.6.5 [1,568] phylogenetics
psRobot psrobot 1.2 [1,569] phylogenetics
Pufferfish pufferfish 20200417, 20230223 [1,570] phylogenetics
PureCLIP pureclip 1.1.1 [1,571] phylogenetics
Purge_Dups purge_dups 1.0.1 [1,572] phylogenetics
purge_haplotigs purge_haplotigs 1.1.2, 1.1.3 [1,573] sequencing, biology
pvconv pvconv 10152018 [1,574] imaging
pyani pyani 0.2.10, 0.2.12 [1,575] phylogenetics
Pybedtools pybedtools 0.8.2, 0.9.0 [1,576] phylogenetics
Pybind11 pybind11 2.13.5 [1,577] programming
PyBSASeq pybsaseq 20200623 [1,578] phylogenetics
PyCharm pycharm 2018.3, 2023.1.2 [1,579] programming
Pycharm Pro pycharm-pro 23.1.3 [1,580] software
pychopper pychopper 2.5.0, 2.7.1 [1,581] phylogenetics, sequencing
PyCogent pycogent 1.9 [1,582] biology, genomics
pycoqc pycoqc 2.5.2 [1,583] sequencing
PyCUDA pycuda 2024.1 [1,584] GPU programming
pydarwin pydarwin 3.0.0 [1,585] machine_learning
PyDeface pydeface 2.0.0 [1,586] imaging
pydock3 pydock3 20240513 [1,587] biology
pyEGA3 pyega3 3.4.1, 5.0.2 [1,588] biology, genomics, utility
PyEXR pyexr 0.3.10 [1,589] programming
Pyfaidx pyfaidx 0.5.2 [1,590] biology, ngs, sequencing
pyfasta pyfasta 0.5.2 [1,591] phylogenetics
pyfastx pyfastx 2.1.0 [1,592] bioinformatics
pygenometracks pygenometracks 3.8 [1,593] genomics, biology
pygot pygot 20170518 [1,594] biology, phylogenetics
pyhdf pyhdf 0.9.0 [1,595] library
PyHIST pyhist 1.0 [1,596] biology, imaging, image_processing
pymesh pymesh 0.3.0 [1,597] math, graphics
pypaftol pypaftol 1.0 [1,598] biology, ngs, phylogenetics
PyPHLAWD pyphlawd 20180416, 20190414 [1,599] biology, phylogenetics
Pyroms pyroms 1.0 [1,600] geospatial
PyRosetta pyrosetta r56324 [1,601] biology, structure, modeling
pyrpipe pyrpipe 0.0.3 [1,602] phylogenetics
Pysamstats pysamstats 1.1.2 [1,603] phylogenetics
PySLURM pyslurm 18.08.04 [1,604] scheduler
Python python 3.6.3, 3.6.5, 3.8 [1,605] programming, language
Python-core python-core 3.6.5, 3.7, 3.8 [1,606] language, programming
Python2 python 2.7.11 [1,607] language, programming
PyTorch ngc-pytorch 1.9.0, 2.3.0, 2.5.0 [1,608] library, math
pytorch pytorch 1.9.0, 2.0.1, 2.2.0 [1,609] library, math
Pytorch Lightning pytorch_lightning 2.2.0 [1,610] library, math
PyVCF pyvcf 0.6.0, 0.6.8 [1,611] biology, phylogenetics
PyVista pyvista 0.26.1 [1,612] phylogenetics
pyweka pyweka 0.3.18 [1,613] phylogenetics
QAPA qapa 1.3.1, 1.3.3 [1,614] phylogenetics
qcat qcat 1.1.0 [1,615] phylogenetics
qctool qctool 2.0.1 [1,616] phylogenetics
qcustomplot-pyqt5 qcustomplot-pyqt5 2.1.1.2 [1,617] plotting, visualization
QD qd 2.3.22 [1,618] library, compiler, math
QDD qdd 3.1.2 [1,619] biology, genomics, ngs
QGIS qgis 2.18.0, 3.14.0 [1,620] geospatial
QIIME2 qiime2 2024.10, 2024.2, 2024.5 [1,621] biology, genomics
QMCPACK qmcpack 3.4.0 [1,622] library
QRNA qrna 2.0.4 [1,623] phylogenetics
qsirep qsiprep 0.19.1 [1,624] data_mining
QT qt 5.15.4, 5.15.9, 6.7.3 [1,625] library
QTL-seq qtl-seq 2.2.2 [1,626] biology, sequencing, pipeline
QTLtools qtltools 1.2, 1.3.1 [1,627] phylogenetics
Quake quake 0.3 [1,628] biology, sequencing
QualiMap qualimap 2.1.2, 2.3 [1,629] biology, sequencing, alignment
Quantas quantas 1.0.4, 1.0.8, 1.0.9 [1,630] biology, ngs
quantisnp quantisnp 2 [1,631] biology, genomics
QuantLib quantlib 1.34 [1,632] financial, quantitative analysis
quarTeT quartet 1.1.6 [1,633] phylogenetics
QuartetScores quartetscores 1.0.0 [1,634] phylogenetics
QUARTO quarto 1.4.550 [1,635] desktop publishing
QUAST quast 5.0.0, 5.0.2, 5.2.0 [1,636] biology, ngs, sequencing, rna-seq
quickmerge quickmerge 0.3 [1,637] phylogenetics
Quickquartet quickquartet 1.0.0 [1,638] biology, ngs
QUIP quip 20201029, 20210626 [1,639] phylogenetics
QuorUM quorum 1.0.0 [1,640] biology
qupath qupath 0.4.3 [1,641] biology, Imaging
R R 4.2, 4.3, 4.4 [1,642] statistics
r-index r-index 20190711 [1,643] phylogenetics
r8s r8s 1.8, 1.81 [1,644] phylogenetics
RACA raca 0.9.1.1 [1,645] biology, ngs
Racon racon 1.4.10, 1.4.13, 1.5.0 [1,646] phylogenetics
RADICAL radical 0.2 [1,647] biology, genomics
radinitio radinitio 1.2.3 [1,648] biology
radorgminer radorgminer 0.9 [1,649] genomics, biology, sequencing
RaGOO ragoo 1.11 [1,650] phylogenetics
Ragout ragout 2.3 [1,651] genomics
RagTag ragtag 1.0.0, 2.0.1 [1,652] phylogenetics
rainbow rainbow 2.0.4 [1,653] biology, sequencing
Rainbowfish rainbowfish 0.1.0 [1,654] phylogenetics
RAiSD raisd 2.8, 3.1 [1,655] phylogenetics
Randfold randfold 2.0.1 [1,656] biology, RNA
ranger ranger 1.9.3 [1,657] file_management
Rapidnj rapidnj 2.3.3 [1,658] biology, phylogenetics
Rapids Base rapidsai 24.02, 24.08 [1,659] data_science
rapidsai rapidsai 23.02, 23.06, 24.04 [1,660] data_science
rapidtide rapidtide 1.9.0 [1,661] phylogenetics
RAPSearch rapsearch 2.24 [1,662] biology, phylogenetics
RAPT rapt 0.5.5 [1,663] biology,assembly
Rascaf rascaf 1.0.2 [1,664] biology
Rasterio rasterio 1.3.10 [1,665] geospatial
RATTLE rattle 1.0 [1,666] Sequencing
RAVE rave 2.1 [1,667] biology, phylogenetics
Raven raven 1.8.1 [1,668] assembly
RAxML raxml 8.2.10, 8.2.12, 8.2.8 [1,669] biology, phylogenetics
RAxML-NG raxml-ng 0.9.0, 1.0.2, 1.1.0 [1,670] phylogenetics
razers3 razers3 3.5.7 [1,671] biology, phylogenetics
rbp-maps rbp-maps 0.1.4 [1,672] phylogenetics
rcapptests rcapptests 1.0 [1,673] software
rclone rclone 1.57.0, 1.58.1, 1.65.2 [1,674] web
Rcorrector rcorrector 1.0.4 [1,675] phylogenetics
RDKit rdkit 2020092 [1,676] chemistry
rDnaTools rdnatools 0.1.3 [1,677] phylogenetics
read2tree read2tree 0.1.5 [1,678] alignment, biology, genomics, phylogenetics
READemption reademption 1.0.0 [1,679] phylogenetics
REAPR reapr 1.0.18 [1,680] biology, assembly
Rebaler rebaler 0.2.0 [1,681] phylogenetics
reCOGnizer recognizer 1.3.3 [1,682] phylogenetics
recon recon 1.08 [1,683] biology, sequencing
recycler recycler 0.7 [1,684] biology, sequencing
Redis redis 2.8.13, 2.8.19 [1,685] database, data_science
REDItools2 reditools2 20200701 [1,686] phylogenetics
Redundans redundans 0.14a [1,687] biology, phylogenetics
refmaker refmaker 1.0 [1,688] biology, phylogenomics
ReFrame reframe 3.2 [1,689] performance_analysis, utility
regtools regtools 0.5.2 [1,690] biology, rna-seq, genomics
release release 12082021 [1,691] molecular_dynamics, machine_learning
ReLERNN relernn 1.0.0 [1,692] biology/AI
RELION relion 3.0.2, 3.1.0, 4.0.1 [1,693] biology, imaging
RelocaTE2 relocate2 2.0.1 [1,694] phylogenetics
REMORA remora 1.8.3, 1.8.5, 2.0.0 [1,695] performance_analysis
REPdenovo repdenovo 20170222 [1,696] biology, phylogenetics
RepeatAnalysis repeatanalysis 0.10.0, 0.12.2 [] biology, phylogenetics
RepeatAnalysisTools repeatanalysistools 20210506 [1,697] biology, genomics, sequencing, utility
RepeatExplorer repeatexplorer 20150506, 20180517 [1,698] biology, ngs
RepeatMasker repeatmasker 4.0.9, 4.1.1, 4.1.7 [1,699] biology
RepeatModeler repeatmodeler 1.0.8, 2.0 [1,700] biology
repeatscout repeatscout 1.0.5 [1,701] biology
RepeatSeq repeatseq 0.8.2 [1,702] phylogenetics
reptile reptile 1.1 [1,703] biology, ngs, math
ResFinder resfinder 4.0 [1,704] biology, genomics
resistify resistify 0.1.0 [1,705] biology, molecular
Resistome resistome 20170111 [1,706] phylogenetics
Resolve resolve 18.1.4 [1,707] Graphics, Utility, Visualization
RevBayes revbayes 1.0.9, 1.1.1, 1.2.3 [1,708] biology, phylogenetics
RFAA rfaa 20240323 [1,709] biology, genomics
RFMIX rfmix 2.03 [1,710] phylogenetics
RGAugury rgaugury 2.2 [1,711] sequencing, biology
RGI rgi 4.2.2, 5.1.1, 6.0.2 [1,712] phylogenetics
RGIS rgis 20180211, 20180814 [1,713] geospatial
RHash rhash 1.3.3 [1,714] programming
RiboCode ribocode 1.2.11 [1,715] phylogenetics
ribodetector ribodetector 0.3.1 [1,716] biology
riboPicker ribopicker 0.4.3 [1,717] biology, sequencing
RiboTaper ribotaper 1.3.1a [1,718] phylogenetics
Ribotricer ribotricer 1.3.3 [1,719] phylogenetics
RIGERJ rigerj 2.0.2 [1,720] phylogenetics
rMATS turbo rmats-turbo 4.1.2 [1,721] biology, sequencing, genomics
rmats2sashimiplot rmats2sashimiplot 2.0.3, 2.0.4 [1,722] phylogenetics
Rmpi Rmpi 3.5.1, 4.0.3 [1,723] statistics, programming
rnabloom rnabloom 2.0.1 [1,724] biology, ngs, sequencing, rna-seq
rnaeditingindexer rnaeditingindexer 12152022 [1,725] data_mining
RNAFramework rnaframework 2.7.2 [1,726] biology, RNA, sequencing
RNAhybrid rnahybrid 2.1.1 [1,727] biology, genomics
rnalysis rnalysis 3.7.0 [1,728] sequencing, biology
RNAmmer rnammer 1.2 [1,729] biology, rna-seq
rnaQUAST rnaquast 1.5.1 [1,730] biology, ngs, sequencing, rna-seq
RNAsalsa rnasalsa 0.8.1 [1,731] biology, phylogenetics
rnaseqlib rnaseqlib 20150721 [1,732] biology, phylogenetics, rna-seq
RNAstructure rnastructure 6.3 [1,733] biology, sequencing
Roary roary 3.12.0, 3.13.0, 3.4.1 [1,734] biology, genomics
roguenarok roguenarok 20230418 [1,735] phylogenetics
ROOT root 5.34.17, 6.0, 6.06.02 [1,736] data_science
ROOTPy rootpy 20160323 [1,737] data_science
Rosetta rosetta 2019.35.60890, 2021.16.61629, 2023.11.30 [1,738] biology, structure, modeling
RoseTTAFold rosettafold 1.0.0 [1,739] phylogenetics
rrnaselector rrnaselector 1.0 [1,740] biology, sequencing
RSEG rseg 0.4.8 [1,741] biology, genomics
RSEM rsem 1.2.31, 1.2.7, 1.3.3 [1,742] biology, ngs, sequencing
RSeQC rseqc 2.6.4, 3.0.0, 5.0.3 [1,743] biology, ngs, rna-seq
RStudio rstudio 1.4, 2021.09.0, 2022.02.3 [1,744] statistics
rsync rsync 3.2.7 [1,745] software, utility
RTGTools rtgtools 3.7.1 [1,746] biology, ngs
Ruby ruby 2.5.1 [1,747] programming, language
run_dbcan run_dbcan 4.0.0, 4.1.4 [1,748] biology
Rust rust 1.62.1, 1.70.0, 1.76.0 [1,749] programming
rvtests rvtests 2.1.0 [1,750] genomics, biology, sequencing
S.A.G.E s.a.g.e 6.4.2 [1,751] phylogenetics
Sabre sabre 1.0 [1,752] phylogenetics
saffrontree saffrontree 0.1.2 [1,753] phylogenetics
saige saige 0.45.0 [1,754] genomics
Sailfish sailfish 0.6.3 [1,755] biology, genomics, ngs, rna-seq
Salmon salmon 1.5.2, 1.8.0, 1.9.0 [1,756] biology, rna-seq
SALSA salsa 20171009, 20191001, 20220408 [1,757] biology, ngs
samapi samapi 0.4.0 [1,758] Imaging
Sambamba sambamba 0.6.3, 0.6.6, 0.6.9 [1,759] biology, ngs
samblaster samblaster 0.1.14, 0.1.24 [1,760] biology, ngs, sequencing
sampledock sampledock 0.5.1 [1,761] molecular_dynamics, AI
SAMStat samstat 1.08 [1,762] biology, ngs, sequencing
Samtools samtools 1.7, 1.8, 1.9 [1,763] biology, ngs, sequencing
SAS sas 9.4.8 [1,764] statistics, data_science
Sate sate 2.2.7 [1,765] biology, phylogenetics
Satsuma satsuma 3.0 [1,766] phylogenetics
Satsuma2 satsuma2 20161123, 3.1 [1,767] phylogenetics
sc-im scim 0.8.2 [1,768] utility, visualization
Scala scala 2.11.5, 3.0.1 [1,769] programming, language
Scalablast scalablast 2.4.53 [1,770] biology, genomics
ScaLAPACK scalapack 2.1.0, 2.2.0, 2.2.1.5 [1,771] programming, library
scallop scallop 0.10.5 [1,772] phylogenetics
Scalpel scalpel 0.1.1, 0.5.3 [1,773] biology, ngs
scanpy scanpy 1.8.2 [1,774] biology
scapp scapp 0.1.4 [1,775] genomics, assembly
scGPT scgpt 0.1.2 [1,776] Biology, Data_Science, Genomics
Schrodinger Maestro maestro 2024-1 [1,777] chemistry, molecular_dynamics
Schrodinger Suite schrodinger 2023-2, 2023-3, 2024-2 [1,778] chemistry, molecular_dynamics
sciann sciann 0.7.0.1 [1,779] machine_learning
scikit-learn scikit-learn 1.4.1.post1 [1,780] Data_Science
scipion scipion 3.0.0, 3.1.0 [1,781] image_processing
Scipion scipion 1.2 [1,782] image_processing
SCIrun scirun 5.0.Z [1,783] phylogenetics
scnic scnic 1.0 [1,784] library
Scoary scoary 1.6.16 [1,785] phylogenetics
Scons scons 2.5.1, 3.1.2 [1,786] programming
SCOP scop 20180311 [1,787] biology, assembly
score-sde score-sde 20221110 [1,788] Machine_Learning
Scrappie scrappie 1.4.2 [1,789] biology, genomics
SCRATCH-1D scratch1d 1.0, 1.2, 2.0 [1,790] biology, ngs
Screen screen 4.8.0, 4.9.1 [1,791] programming, shell
SCRIPTURE scripture 20101211 [1,792] biology, genomics
scVelo scvelo 0.2.5 [1,793] biology
Scythe scythe 0.991 [1,794] biology, ngs
sdsl sdsl 2.1.1 [1,795] library, compiler
SE-MEI se-mei 0.1.0 [1,796] phylogenetics
SeCaPr secapr 1.1.12, 2.0.2, 2.1.1 [1,797] phylogenetics
seekdeep seekdeep 3.0.1 [1,798] biology, sequencing
Segemehl segemehl 0.1.9, 0.3.4 [1,799] biology, ngs, sequencing
segment-liftover segment-liftover 20211021 [1,800] biology, genomics
seismometer seismometer 0.2.1 [1,801] AI, utility
SemiBin semibin 2.1.0 [1,802] bioinformatics
SEPP sepp 20160614 [1,803] biology, phylogenetics
Seq-Gen seq-gen 1.3.3 [1,804] biology, phylogenetics
seq_crumbs seq_crumbs 20150120 [1,805] biology, sequencing, genomics, utility
SeqKit seqkit 0.8.0, 2.0.0, 2.4.0 [1,806] biology, phylogenetics
seqmagick seqmagick 0.8.4 [1,807] biology
SeqMap seqmap 1.0.13 [1,808] biology, sequencing, ngs
seqmule seqmule 1.2.6 [1,809] biology, sequencing
SEQPower seqpower 1.1.1 [1,810] genomics, phylogenetics
SeqPrep seqprep 0.5, 1.1 [1,811] biology, ngs, sequencing
seqscreen seqscreen 3.3 [1,812] sequencing, biology
seqtk seqtk 1.3, 20140729 [1,813] biology, genomics, ngs
SEQuel sequel 1.0.1 [1,814] biology, ngs
SequelQC sequelqc 1.1.0 [1,815] phylogenetics
seqwish seqwish 0.7, 20190509 [1,816] phylogenetics
SeqyClean seqyclean 1.8.10 [1,817] biology, ngs, sequencing
SeSiMCMC sesimcmc 4.36 [1,818] biology, sequencing
SExtractor sextractor 2.19.5 [1,819] astronomy
SHAPE-MaP shapemap 1.2 [1,820] biology, phylogenetics
SHAPEIT shapeit 2.12, 2.5 [1,821] biology, variant_calling
SHAPEIT4 shapeit4 4.2.2 [1,822] biology, sequencing
ShapeMapper shapemapper 2.1.3, 2.1.5, 2.2.2 [1,823] biology, phylogenetics
SHARCGS sharcgs 1.2.11 [1,824] biology, ngs, de_novo
Shasta shasta 0.1.0 [1,825] phylogenetics
SHEsisPlus shesisplus 1.0, 1.01 [1,826] biology, genomics
shogun shogun 6.1.3 [1,827] phylogenetics
Shortbred shortbred 0.9.4 [1,828] phylogenetics
shortstack shortstack 4.0.3 [1,829] biology
shovill shovill 1.1.0 [1,830] genomics, sequencing, biology
SHRiMP shrimp 2.2.3 [1,831] biology, genomics, ngs
shustring shustring 2.6 [1,832] biology, sequencing
SibeliaZ sibeliaz 1.2.2, 1.2.3, 1.2.4 [1,833] biology, genomics, alignment
SICER sicer 1.1 [1,834] biology, chip-seq
Sickle sickle 1.200, 1.33 [1,835] biology, ngs
Siesta siesta 3.2, 4.1b2, 4.1b3 [1,836] chemistry
SIFT sift 4.0.3b [1,837] biology, genomics
SIGffRid sigffrid 1.1 [1,838] phylogenetics
SignalP signalp 4.1c, 5.0b, 6.0h [1,839] biology, phylogenetics
SiLiX silix 1.2.11, 1.3.0 [1,840] phylogenetics
silo silo 4.7 [1,841] library
sim4 sim4 20121010 [1,842] biology, genomics
Sim4Life sim4life 7.0.1, 7.2.3 [1,843] biology, simulation
Simka simka 1.5.3 [1,844] phylogenetics
SimNIBS simnibs 3.2.1, 4.0.0, 4.1.0 [1,845] phylogenetics
SimSeq simseq 4.12.2011 [1,846] biology, ngs, phylogenetics
Simulia simulia 2019 [1,847] simulation, visualization
SInC sinc 20140120 [1,848] biology, phylogenetics
sine_scan sine_scan 1.1.1 [1,849] phylogenetics
Singularity singularity 3.10.4 [1,850] workflow_automation
SIPeS sipes 2.0 [1,851] biology, chip-seq
SIRIL siril 1.2.0 [1,852] image processing
sisl sisl 0.8.3 [1,853] physics, structure
Ska2 ska2 0.3.0 [1,854] alignment, biology, genomics
skmer skmer 3.2.1 [1,855] genomics, biology
Slamdunk slamdunk 0.4.1, 0.4.2 [1,856] phylogenetics
SLAW slaw 20211217 [1,857] chemistry, spectroscopy
Sleap sleap 1.3.3 [1,858] machine learning
Slicer slicer 4.3.1, 5.0.3, 5.2.1 [1,859] biology, neuroscience, imaging
slicer slicer 5.6.2 [1,860] biology, neuroscience, medicine, imaging
slivar slivar 0.3.0 [1,861] biology
slow5tools slow5tools 0.5.1, 1.1.0 [1,862] biology, sequencing
SLR slr 1.0.0 [1,863] genomics
slurm-drmaa slurm-drmaa 1.1.3, 1.1.4, 1.1.4.1 [1,864] library, scheduler, programming
smalt smalt 0.7.6 [1,865] biology, phylogenetics
SMARTdenovo smartdenovo 20180219 [1,866] biology, phylogenetics
smartie-sv smartie-sv 20180308 [1,867] phylogenetics
SMC++ smcpp 1.15.4 [1,868] biology, genomics, sequencing
Smetana smetana 1.1.0 [1,869] phylogenetics
SMR smr 1.03 [1,870] biology, genomics
SMRT-SV smrtsv2 2.0.0 [1,871] biology, ngs
SMS sms 1.7 [1,872] biology
Smudgeplot smudgeplot 0.2.4 [1,873] phylogenetics
Snakemake snakemake 7.5.0, 8.10.8, 8.4.0 [1,874] biology, workflow_automation
SNAP snap 2.0.0, 2.0.3, 20100728 [1,875] biology, sequencing
SNAPE-pooled snape-pooled 20130407 [1,876] biology, variant_calling
SNeP snep 1.1 [1,877] biology, phylogenetics
Sniffles sniffles 1.0.11, 1.0.6, 1.0.8 [1,878] phylogenetics
Sniffles2 sniffles2 2.0.6 [1,879] biology
Snippy snippy 20160419, 4.6.0 [1,880] biology, phylogenetics
SNP-Pipeline snp-pipeline 1.0.1 [1,881] biology, phylogenetics
SNP-sites snp-sites 2.0.3 [1,882] biology, variant_calling
snp2hla snp2hla 1.0.3 [1,883] biology, genomics
SnpEff snpeff 5.0, 5.1d, 5.2e [1,884] biology, annotation
snpflip snpflip 20190515 [1,885] biology, phylogenetics
SNPGenie snpgenie 20190620 [1,886] phylogenetics
SNPhylo snphylo 20140701, 3.0 [1,887] biology, phylogenetics
SNPsplit snpsplit 0.5.0 [1,888] biology, sequencing
SNPTEST snptest 2.5.2 [1,889] phylogenetics
SOAPaligner soapaligner 2.21 [1,890] phylogenetics
SOAPdenovo soapdenovo 1.05, 2.04 [1,891] biology, ngs
SOAPdenovo-Trans soapdenovo-trans 1.01, 1.03 [1,892] biology, ngs
SOAPec soapec 2.03 [1,893] biology, phylogenetics
SOAPnuke soapnuke 2.1.0 [1,894] phylogenetics
SOAPsplice soapsplice 1.10 [1,895] biology, ngs
SODA soda 20200930 [1,896] biology
SOLAR solar 8.4.2 [1,897] phylogenetics
SomaticSeq somaticseq 3.6.2 [1,898] phylogenetics
SortaDate sortadate 20190705 [1,899] phylogenetics
SortMeRNA sortmerna 2.1, 4.0, 4.3.6 [1,900] biology, sequencing, ngs
SourceTracker2 sourcetracker2 2.0.1 [1,901] phylogenetics
Sourmash sourmash 2.0.1, 4.5.0 [1,902] genomics
SoX sox 14.4.2 [1,903] phylogenetics
spacemake spacemake 0.5.5 [1,904] sequencing
SpaceRanger spaceranger 2.1.0, 3.0.1, 3.1.1 [1,905] phylogenetics
SPAdes spades 3.7.1, 3.8.0, 4.0.0 [1,906] biology, ngs
SparCC sparcc 201608 [1,907] biology
Spark spark 2.2.0, 3.1.1 [1,908] utility
sparsehash sparsehash 2.0.3 [1,909] web, programming
SPARTA+ sparta+ 2.60 [1,910] chemistry
Spec2nii spec2nii 0.3.4 [1,911] phylogenetics
SpeedSeq speedseq 0.1.2 [1,912] phylogenetics
Spidey spidey 20150922 [1,913] biology, genomics
SpinalCordToolbox spinalcordtoolbox 5.4 [1,914] phylogenetics
SplAdder spladder 2.4.2 [1,915] phylogenetics
SpliceGrapher splicegrapher 0.2.5 [1,916] biology, sequencing
SpliceTrap splicetrap 0.90.5 [1,917] biology, genomics, ngs
SPM spm 12b, 8, 8r5236 [1,918] biology
spruceup spruceup 2019.2.3 [1,919] phylogenetics
Sputnik sputnik 1.0 [1,920] biology
spyder spyder 4.1.4, 5.1.1, 5.3.2 [1,921] programming
SQANTI sqanti 1.2 [1,922] phylogenetics
SQANTI2 sqanti2 5.0 [1,923] phylogenetics
SQANTI3 sqanti3 1.6, 4.2, 5.1.1 [1,924] phylogenetics
SQL Developer sqldeveloper 4.1.2 [1,925] programming, database
SQLite sqlite3 3.33.0, 3.45.3, 3.8.8.2 [1,926] database
squashfuse squashfuse 0.5.2 [1,927] containers, library
SqueezeMeta squeezemeta 1.4.0, 1.5.2, 1.6.0 [1,928] phylogenetics
squigglekit squigglekit 1.0.0 [1,929] visualization, biology
squigglenet squigglenet 1.0 [1,930] sequencing, biology
SRA sra 3.0.2, 3.0.5, 3.0.8 [1,931] biology, ngs
sra-human-scrubber sra_human_scrubber 1.1 [1,932] genomics
SRAssembler srassembler 1.0.0 [1,933] phylogenetics
srst2 srst2 0.2.0 [1,934] sequencing, genomics, biology
SSM ssm 20210511 [1,935] phylogenetics
SSPACE sspace 2.0, 3.0 [1,936] biology, ngs
ssr_pipeline ssr_pipeline 0.951 [1,937] biology, sequencing
SSU-ALIGN ssu-align 0.1.1 [1,938] phylogenetics
stable-diffusion stable-diffusion 20221116 [1,939] machine_learning
Stacks stacks 2.53, 2.55, 20190403 [1,940] biology, genomics, ngs
stacks stacks 2.61, 2.64 [1,941] biology, genomics, ngs
Staden staden 1.14.6 [1,942] biology, phylogenetics
Stampy stampy 1.0.31 [1,943] biology, sequencing
staphb-toolkit staphb-toolkit 1.2.0, 1.3.10, 2.0.1 [1,944] biology
STAR star 2.7.5c, 2.7.6a, 2.7.9a [1,945] biology, ngs, rna-seq
STAR-CCM+ starccm+ 14.04.011, 15.02.009, 8.06 [1,946] fluid_dynamics
STAR-Fusion star-fusion 1.13.0, 1.3.1, 1.9.1 [1,947] biology, sequencing
starseqr starseqr 0.6.7 [1,948] phylogenetics
Stata stata 10.1, 13, 18 [1,949] statistics
Strainline strainline 1.0 [1,950] biology
Strelka strelka 2.9.2 [1,951] biology, genomics
stringMLST stringmlst 0.4 [1,952] biology, chip-seq
Stringtie stringtie 2.0.4, 2.1.3b, 2.2.3 [1,953] biology, ngs, sequencing, alignment
Structure structure 2.3.3, 2.3.4 [1,954] biology, genomics
Structure_threader structure_threader 1.3.10 [1,955] utility, structure
stumpy stumpy 1.11.1 [1,956] library, math
stylegan3 stylegan3 20211028 [1,957] ai, image_processing
SU2 su2 7.0.6 [1,958] phylogenetics
subphaser subphaser 1.2.6 [1,959] sequencing, biology
Subread subread 2.0.0, 2.0.3, 2.0.6 [1,960] biology, sequencing, variant_calling
Subversion subversion 1.14.2, 1.9.7 [1,961] revision_control
SUMO sumo 1.2.0, 1.20.0, 1.9.2 [1,962] phylogenetics
SUNDIALS sundials 2.5.0, 3.0.0, 6.1.1 [1,963] math
supercell supercell 20170602 [1,964] biology, ngs
SuperCRUNCH supercrunch 1.2.1 [1,965] phylogenetics
SUperLU-DIST superlu_dist 6.0.1, 8.2.1 [1,966] linear algebra
Supernova supernova 1.2.1, 2.0.0, 2.1.1 [1,967] biology, phylogenetics, ngs
SUPPA suppa 2.3 [1,968] phylogenetics
support support 24.03.20 [1,969] ufrc, admin, tools
SurrealDB surrealdb 1.3.1, 1.5.0, 2.0.1 [1,970] database
Survival_Kit survival_kit 6.12 [1,971] healthcare
SURVIVOR survivor 1.0.6 [1,972] phylogenetics
SVDetect svdetect 0.8b [1,973] biology, ngs, genomics
svim svim 1.4.2 [1,974] biology
svim-asm svim-asm 1.0.2 [1,975] biology
svtyper svtyper 0.7.1 [1,976] biology, genomics, sequencing
swarm swarm 1.2.11 [1,977] data_science
Sweed sweed 3.3.2 [1,978] biology, phylogenetics
SWIG swig 3.0.8, 4.1.1, 4.2.1 [1,979] library, programming, compiler
SWSC-EN swsc-en 1.0.0 [1,980] phylogenetics
Synima synima 20210908 [1,981] phylogenetics
syri syri 1.5.4 [1,982] genomics, biology
TACO taco 0.7.3 [1,983] phylogenetics
Taiyaki taiyaki 5.0.1 [1,984] phylogenetics
talesf talesf 20160814 [1,985] phylogenetics
talon talon 5.0 [1,986] biology, sequencing
Tandem-Genotypes tandem-genotypes 1.4.0 [1,987] phylogenetics
Tantan tantan 13 [1,988] imaging, ngs, genomics
Tapestri tapestri 2.0.1 [1,989] phylogenetics
tapir tapir 20160825 [1,990] biology, phylogenetics
TAPIS tapis 1.2.1 [1,991] biology, sequencing
TASSEL tassel 5.2.20, 5.2.29, 5.2.82 [1,992] biology, genomics, sequencing
TAU tau 2.23, 2.26, 2.26.3 [1,993] library, performance_analysis
Tax4Fun tax4fun 0.3.1 [1,994] phylogenetics
taxMaps taxmaps 0.1 [1,995] biology, phylogenetics, genomics
TaxonKit taxonkit 0.13.0, 0.9.0 [1,996] phylogenetics
Taxtastic taxtastic 0.5.7, 0.9.1 [1,997] biology, genomics
tbb tbb 2017_20161128 [1,998] library
tbprofiler tbprofiler 4.4.1 [1,999] genomics, biology
tcllib tcllib 1.18 [2,000] library
tcoffee tcoffee 10.00.r1613, 9.03.r1318 [2,001] biology
TDNAscan tdnascan 20210304 [2,002] phylogenetics
Tecplot 360 EX tecplot 2015R1 [2,003] math, animation, fluid_dynamics, simulation
tellseq tellseq 1.0.0 [2,004] sequencing, phylogenetics
TEMP temp 20170731 [2,005] phylogenetics
TEMP2 temp2 0.1.4 [2,006] phylogenetics
TensorFlow ngc-tensorflow 2.6.0, 2.7.0, 2.8.0 [2,007] library, math
TESS tess 2.3.1 [2,008] biology, genomics, math
tesseract tesseract 5.3.4 [2,009] OCR
Test test 1.0 [2,010] shell
TetGen tetgen 1.5.0 [2,011] modeling
TEToolkit tetoolkit 1.5.1 [2,012] biology, sequencing
TEtools tetools 20180213 [2,013] biology, phylogenetics
Texlive texlive 20191127, 2020, 2023 [2,014] documentation
textract textract 1.6.1 [2,015] data_science, file_management
TGICL tgicl 2.1 [2,016] biology, ngs, sequencing
TGSGapCloser tgsgapcloser 1.0.3 [2,017] phylogenetics
the_silver_searcher the_silver_searcher 2.2.0 [2,018] search
Themisto themisto 0.2.0, 1.1.0 [2,019] genomics, alignment
Tiara tiara 1.0.2 [2,020] phylogenetics
tidk tidk 0.2.41 [2,021] bioinformatics
tiff tiff 3.8.0, 4.0.10, 4.6.0 [2,022] imaging
tighe-r tighe-r 4.2, studio [2,023] statistics
Tigmint tigmint 1.1.2 [2,024] phylogenetics
TMHMM tmhmm 2.0 [2,025] biology
Tmux tmux 2.9, 3.1, 3.4 [2,026] programming
TNTBLAST tntblast 2.04 [2,027] biology
ToFU2 tofu2 v17 [2,028] biology, ngs, sequencing
toil toil 3.3.0, 3.3.3 [2,029] biology
Tombo tombo 1.4, 1.5, 1.5.1 [2,030] biology, genomics, ngs
topd topd 4.6 [2,031] phylogenetics
Tophat tophat 2.1.0, 2.1.1, 2.1.2 [2,032] biology, ngs, sequencing
torch-geometric torch-geometric 1.3.2, 2.0.4 [2,033] math, machine_learning
TotalView totalview 8.12 [2,034] programming
TPMcalculator tpmcalculator 0.0.3 [2,035] phylogenetics
TPP tpp 4.7.0, 4.7.1, 5.0.0 [2,036] biology, chemistry, spectroscopy
TraCeR tracer 20160519 [2,037] biology, phylogenetics
TrackTools tracktools 2011 [2,038] utility
TrackVis/DTK trackvis 0.5.2.2, 0.6.0.1 [2,039] biology, neuroscience, imaging
Tracula tracula 5.3.2014_05_26 [2,040] biology, neuroscience, imaging
traitRate traitrate 1.1 [2,041] biology, genomics
Trans-ABySS transabyss 2.0.1 [2,042] biology, phylogenetics
TransDecoder transdecoder 5.3.0, 5.4.0, 5.5.0 [2,043] biology, ngs
TRANSIT transit 2.5.2, 3.2.3 [2,044] phylogenetics
Transrate transrate 1.0.1, 1.0.3 [2,045] biology, assembly
TransVar transvar 2.3.3 [2,046] biology, phylogenetics
TreeBreaker treebreaker 20160621 [2,047] biology, phylogenetics
TreeMix treemix 1.12 [2,048] biology, phylogenetics
treePL treepl 20150305 [2,049] biology, phylogenetics
TREEPUZZLE treepuzzle 5.3 [2,050] biology, phylogenetics
TreeShrink treeshrink 1.3.1, 1.3.2, 1.3.9 [2,051] phylogenetics
TreeTime treetime 0.10.1, 0.7.5, 0.8.1 [2,052] phylogenetics
trelis trelis 16.3 [2,053] math
TRF trf 4.04, 4.09.1 [2,054] biology, genomics
trgt trgt 0.4.0 [2,055] genetics, biology
Trilinos trilinos 12.6.4, 14.4.0, 16.6.0 [2,056] math
Trim Galore trim_galore 0.5.0, 0.6.10, 0.6.5 [2,057] biology, ngs
trim_isoseq_polya trim_isoseq_polya 0.0.3 [2,058] biology, genomics, sequencing
trimAl trimal 1.2, 1.4.1 [2,059] biology, genomics, alignment
trimesh trimesh 3.20.2 [2,060] graphics, math
TriMetAss trimetass 1.1 [2,061] biology, ngs
Trimmomatic trimmomatic 0.33, 0.36, 0.39 [2,062] biology, ngs
Trinity trinity r20130225, r20131110, r20140413 [2,063] biology, ngs, sequencing, rna-seq
Trinotate trinotate 3.0.1, 3.2.0, 4.0.0 [2,064] biology
triobinning triobinning 0.2.3 [2,065] genomics, biology
TRIPLEC triplec 1.0 [2,066] biology
TRITONSERVER tritonserver 21.08, 23.01 [2,067] machine_learning
tRNAscan-Se trnascan-se 1.23, 2.0.12 [2,068] biology, ngs
TRUST4 trust4 1.0.2b [2,069] phylogenetics
trvz trvz 0.4.0 [2,070] genetics, biology
Trycycler trycycler 0.4.2 [2,071] phylogenetics
TURBOMOLE turbomole 7.4.1 [2,072] chemistry
TWINSCAN twinscan 4.1.2 [2,073] biology, genomics
Ubuntu ubuntu 20.04, 22.04, 24.04 [2,074] linux
UCSC ucsc 20200320, 20210803 [2,075] genomics
ucsc-fafiltern ucsc-fafiltern 377 [2,076] phylogenetics
ucsc-maskoutfa ucsc-maskoutfa 377 [2,077] phylogenetics
UCX ucx 1.11.2, 1.15.0, 1.9.0 [2,078] programming, library
UDUNITS udunits 2.2.17 [2,079] library, data_science, math
UFCG ufcg 1.0.3, 1.0.5 [2,080] biology, genomics
ufraw ufraw 0.22 [2,081] data_mining
ugtm ugtm 1.1.6 [2,082] statistics, modeling
UKFractography ukfractography 20200127 [2,083] phylogenetics
umi-tools umi-tools 0.5.5, 1.1.4, 1.1.5 [2,084] phylogenetics
UMICollapse umicollapse 02072021 [2,085] chemestry
UNAFold unafold 3.8 [2,086] biology, genomics, rna
Unanimity unanimity 20171108, 3.4.1 [2,087] programming, library, compiler
UNCALLED uncalled 2.2 [2,088] biology, genomics
Unicycler unicycler 0.4.8 [2,089] phylogenetics
Unrar rar 0.0.1, 4.20 [2,090] utility
unrealengine editor unrealengine 5.2.1 [2,091] programming, design, digitaltwin
uproc uproc 1.2.0 [2,092] biology, genomics
UPSCAYL upscayl 2.5.5, 2.8.1, 2.9.1 [2,093] image processing
uropa uropa 4.0.2 [2,094] genomics, sequencing, biology
USEARCH usearch 9.0.2132, 9.1.13, 9.2.64 [2,095] biology, alignment, sequencing
UShER usher 0.1.4, 0.4.1, 0.5.2 [2,096] phylogenetics
V-Phaser vphaser2 02112013 [2,097] biology, phylogenetics
v-pipe v-pipe 2.0.0, 2.99.3 [2,098] biology, genomics, sequencing
Valgrind valgrind 3.11.0, 3.15.0, 3.8.1 [2,099] programming
Valouev valouev 20160325 [2,100] biology, phylogenetics
vamb vamb 3.0.2 [2,101] biology
VAMPIR vampir 9.1 [2,102] performance_analysis
VarDictJava vardictjava 1.6.0, 20160521, 20170531 [2,103] biology, phylogenetics
VARI vari 0.7.0 [2,104] math, visualization
varnorm varnorm 0.21 [2,105] biology
varpipe-wgs varpipe-wgs 20230222 [2,106] sequencing, biology
VarScan varscan 2.3.6 [2,107] biology, ngs
VarSim varsim 0.8.4, 0.8.6 [2,108] phylogenetics
VarSimLab varsimlab 20180220, 20180921 [2,109] biology, simulation, genomics
vasp vasp 5.4.4, 6.1.0, 6.2.0 [2,110] chemistry
VASP vasp 5.4.4, 6.4.1, 6.4.3 [2,111] chemistry
vaspkit vaspkit 1.2.5, 1.4.1 [2,112] phylogenetics
VAST-TOOLS vast-tools 2.5.1, 20150506 [2,113] biology, rna-seq, ngs
VCF-kit vcf-kit 0.2.6 [2,114] phylogenetics
vcf-validator vcfvalidator 0.6 [2,115] biology, phylogenetics
vcfanno vcfanno 0.2.8, 0.3.3 [2,116] biology, phylogenetics
vcflib vcflib 1.0.1 [2,117] biology, genomics
vcftools vcftools 0.1.15, 0.1.16, 0.1.9 [2,118] biology, genomics
vcontact vcontact 20190512 [2,119] phylogenetics
VDJtools vdjtools 1.1.7, 1.2.1 [2,120] biology, phylogenetics
Velocyto velocyto 0.17 [2,121] biology, RNA seq
Velvet velvet 1.2.10, 1.2.10-long [2,122] biology, genomics
VEP vep 83, 88.8, 92 [2,123] biology, genomics, ngs
Verkko verkko 1.3.1 [2,124] genomics
vermouth-martinize vermouth-martinize 0.11.0 [2,125] biology, molecular
Vermouth-martinize vermouth-martinize 0.7.2 [2,126] phylogenetics
VeryFastTree veryfasttree 3.0.1 [2,127] phylogenetics
VFUparr vfuparr 20240320 [2,128] sequencing, biology
vg vg 1.45.0, 1.49.0, 1.55.0 [2,129] phylogenetics
vibrant vibrant 1.2.0 [2,130] genomics
ViennaRNA viennarna 2.2.6, 2.4.18 [2,131] biology, rna-seq
ViewBS viewbs 0.1.10, 0.1.9 [2,132] phylogenetics
vigor4 vigor4 20200702 [2,133] biology, annotation
Vim vim 8.1.1566, 8.2.2465, 9.0.1946i [2,134] programming, language
vina-gpu vina-gpu 20230530 [2,135] biology
viralmsa viralmsa 1.1.10, 1.1.12, 1.1.14 [2,136] phylogenetics
VIRCLUST virclust 2.0 [2,137] biology, annotation
viromescan viromescan 2015 [2,138] genomics, biology
VirSieve virsieve 20210406 [2,139] biology, pipeline
virsorter virsorter 2.2.3 [2,140] genomics
VirtualCell virtualcell 7.1 [2,141] phylogenetics
VIRULIGN virulign 1.0.2 [2,142] phylogenetics
VirusDetect virusdetect 1.7 [2,143] phylogenetics
VirusFinder virusfinder 2.0 [2,144] biology, phylogenetics
visit visit 3.3.3, 3.3.3-mpi, 3.3.3_mpi [2,145] visualization, animation
VISPR vispr 0.4.14 [2,146] phylogenetics
vmamba vmamba 2.0 [2,147] machine_learning
VMD vmd 1.9.1, 1.9.3, 1.9.4 [2,148] visualization, animation, graphics
vray vray 6.10.04 [2,149] graphics
vscode vscode 1.86.2, 1.87, 1.92 [2,150] programming
VSearch vsearch 2.22.1, 20151022, 20161209-2.3.4 [2,151] biology, ngs
vt vt 0.57721, 20140903, 20160129 [2,152] biology, genomics
VTC vtc 0.9.3 [2,153] biology
VTK vtk 9.1.0, 9.2.6, 9.3.0 [2,154] biology, neuroscience, imaging
w2rap-contigger w2rap-contigger 20161124 [2,155] biology, genomics
Wannier90 wannier90 1.2, 2.1.0, 3.1.0 [2,156] computational Physics
WarpedLMM warpedlmm 0.21 [2,157] modeling
WaveGAN wavegan 20190829 [2,158] machine_learning, audio, GAN
WDSSII wdss2 5, 6 [2,159] climate
WebLogo weblogo 3.3, 3.5.0, 3.7 [2,160] biology, sequencing, graphics
webodm webodm 20240718 [2,161] graphics
Weka weka 3.8, 3.8.5 [2,162] statistics, machine_learning
Wengan wengan 0.2 [2,163] biology, genomics
wfmash wfmash 0.13.0 [2,164] phylogenetics
wgd wgd 1.1.1 [2,165] phylogenetics
WGS Assembler wgs 8.3rc1.r4638, 8.3rc2 [2,166] biology, genomics
Wgsim wgsim 0.3.1-r13 [2,167] biology, phylogenetics
WHAMM whamm 0.14a [2,168] biology, phylogenetics
WhatsHap whatshap 1.1, 2.1 [2,169] biology, phylogenetics
whiteboxtools whiteboxtools 1.5.0 [2,170] phylogenetics
widis-lstm-tools widis-lstm-tools 0.4 [2,171] ML
Wine wine 4.0.0, 7.0.0 [2,172] linux, utility
Wise wise 2.2.0, 2.4.1 [2,173] biology, genomics
WIsH wish 1.0 [2,174] phylogenetics
WoLFPSort wolfpsort 0.2 [2,175] phylogenetics
WOMBAT wombat 20180118 [2,176] biology, phylogenetics
workbench workbench 4.1.1 [2,177] modeling, simulation
wtdbg wtdbg 2.1, 2.4, 2.5 [2,178] phylogenetics
WU BLAST wublast 2.0 [2,179] biology
Wub wub 0.2.0, 0.4.0 [2,180] biology, genomics, ngs
xander xander 20151222 [2,181] biology, phylogenetics
Xapian xapian 1.4.4 [2,182] library
XCrySDen xcrysden 1.5.60 [2,183] material_science
Xerces xerces 3.1.4 [2,184] phylogenetics
xesmf xesmf 0.6.2 [2,185] math, climate
xlsx2csv xlsx2csv 0.8.0 [2,186] utility
xpclr xpclr 1.0, 1.1.1 [2,187] phylogenetics
xppaut xppaut 8.0 [2,188] math
xroms xroms v0.5.4 [2,189] geospatial
Xterm xterm 1.1 [2,190] utility
xwalk xwalk 0.6 [2,191] biology
XWAS xwas 3.0 [2,192] phylogenetics
XY-Meta xy-meta 20200413 [2,193] phylogenetics
XZ xz 5.2.2 [2,194] compression, library
yagcloser yagcloser 1.0.0 [2,195] biology, genomics, assembly
YAGO yago 4 [2,196] data_science
YAHA yaha 0.1.82 [2,197] biology, ngs
Yaha yahs 1.1 [2,198] biology
YAK yak 0.1 [2,199] phylogenetics
YASM yasm 1.3.0 [2,200] programming
YASRA yasra 2.33 [2,201] biology, ngs, sequencing
ydata-profiling ydata-profiling 4.6.1 [2,202] biology, ai, machine learning
yolo yolo 10.0, 8.2 [2,203] machine_learning
yolo-nas yolo NAS [2,204] machine_learning
yolov4_darknet yolov4_darknet 4-pre [2,205] machine_learning
yolov5 yolo 7.0, 8, 8.1 [2,206] machine_learning
Z1Plus z1plus 1.0 [2,207] molecular_dynamics
Zagros zagros 1.0.0 [2,208] biology, phylogenetics
Zbar zbar 0.23.90 [2,209] ai, image_processing, imaging
ZEO++ zeo++ 0.2.2 [2,210] chemistry
ZeroSum zerosum 20231113 [2,211] programming
zorro zorro 2.2 [2,212] biology, sequencing
Zstd zstd 1.5.0 [2,213] phylogenetics
ZUMIS zumis 2.6.0 [2,214] biology, ngs, sequencing
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