Applications

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

Name	Versions	URL	Description
3d-dna	20170330	[1]	Biology, phylogenetics
3PCLR	20150906	[2]	Biology, phylogenetics
4p	1.0	[3]	Biology,SNP
AAFTF	0.2.5	[4]	Biology, Pipeline, Assembly
ABRicate	1.0.1	[5]	Phylogenetics
ABruijn	1.0	[6]	Biology, assembly, ngs, pacbio, nanopore
ABySS	1.5.2, 2.1.0, 2.2.5	[7]	Biology, de novo
AdapterRemoval	2.2.2	[8]	Phylogenetics
ADFRsuite	1.0	[9]	Sequencing, Bioinformatics
ADMB	11.5, 12.0	[10]	Math, modeling, optimization
AdmixTools	20150311, 7.0.2	[11]	Biology, bioinformatics, genomics, ngs
ADMIXTURE	1.23, 1.3.0	[12]	Biology, bioinformatics, genomics, ngs
AEGeAn	0.14.0, 0.16.0	[13]	Biology,genomics
AFNI	20.3.00, 2018_04_12	[14]	Biology,bioinformatics,neurology,imaging
AfterQC	0.9.7	[15]	Phylogenetics
AGAT	0.4.0	[16]	Phylogenetics
AGfusion	1.252	[17]	Phylogenetics
Albacore	2.3.1, 2.3.3	[18]	Biology, Phylogenetics
Albumentations	1.0.3	[19]	AI, Vision, Imaging
Alder	1.03	[20]	biology, genomics, genetics
ALFA	1.1.1	[21]	Phylogenetics
alienhunter	1.7	[22]	Biology, bioinformatics, wgs
AliStat	1.12	[23]	Phylogenetics
allhic	0.9.8	[24]	Phylogenomics, biology
ALLMAPS	20180117	[25]	Biology, phylogenetics
ALLPATHS-LG	42316, 44837, 49232	[26]	Biology,bioinformatics,ngs
AlphaFold	2.0.0, 2.1.2, 2.2.0	[27]	Protein, structure, ml, dl
Alphaimpute	0.0.2, 1.9.8.2, 1.9.8.3	[28]	Phylogenetics
AltAnalyze	2.1.0	[29]	Biology, genomics
AMAS	1.0	[30]	Phylogenetics
AMBER	16.0, 18, 20	[31]	Computational Chemistry, Molecular Dynamics
AMICO	1.0.1	[32]	Library, imaging, optimization
AMOS	3.1.0	[33]	Biology,bioinformatics,genomics,assembly
AMP	0.6.1	[34]	Phylogenetics
amPEPpy	1.0	[35]	Phylogenetics
amphora2	20140305	[36]	Biology, phylogenetics
AMPtk	1.2.4, 1.5.1	[37]	Biology, bioinformatics, ngs
amptorch	20210313	[38]	Phylogenetics
amrfinderplus	3.10.18	[39]	Phylogenetics
AMRPlusPlus	20180508	[40]	Phylogenetics
AMUSE	10.0, 13.1.0	[41]	Astrophysics
ANGSD	0.933	[42]	Biology, ngs
annocript	2.0	[43]	Phylogenetics
AnnoTALE	1.4.1	[44]	Phylogenetics
ANNOVAR	20130221, 20150322, 20191024	[45]	Biology, bioinformatics, genomics
Ansible	2.5.5, 2.8.1	[46]	Automation, deployment
ansysem	17.0, 2022r1	[47]	Electromechanics
antiSMASH	4.1.0, 6.0.1	[48]	Phylogenetics
ANTs	2.2.0, 2.3.4	[49]	Biology, phylogenetics
anvio	6.1, 6.2, 7.1	[50]	Biology, microbial 'omics
Appreci8	20180530	[51]	Biology, Genomics
Apptainer	1.0.3	[52]	Containers
APT	1.15.0, 1.18.0, 1.20.5	[53]	Biology, bioinformatics, genomics, microarray
ARC	1.1.4	[54]	Biology,bioinformatics,ngs
Aria2	1.35.0	[55]	Utility
ARKS	1.0.2	[56]	Phylogenetics
Armadillo	7.900.0, 9.200.6, 9.900.4	[57]	Library, C++, math
ARPACK	1.0	[58]	Solve eigenvalue problems
ArrayFire	3.4.2	[59]	Code Optimization
arriba	2.1.0	[60]	Phylogenetics
ART	20160417, 20160605	[61]	Phylogenetics
artemis	18.1.0	[62]	Bioinformatics, biology
asap	2.0	[63]	Visualization, Biology
asaq	1.0	[64]	Alignment, Sequencing, Phylogenetics
ASE-ANI	20180712	[65]	Biology, bioinformatics, genomics, ngs
ASHS	2.0	[66]	Biology, mri
ASPECT	2.3.0	[67]	Library
Assembly-stats	1.0.1	[68]	Biology, sequencing, genomics
Assemblytics	1.2.1	[69]	Phylogenetics
Assexon	20190814	[70]	Phylogenetics
AStalavista	3.2, 4.0	[71]	Biology, bioinformatics, genomics
aster	220718	[72]	Biology, data, sequencing
ASTRAL	5.6.1, 5.6.2, 5.7.7	[73]	Biology, bioinformatics, ngs, phylogenetics
ASTRID	2.2.1	[74]	Phylogenetics
Astropy	2.0.8	[75]	Biology, bioinformatics, phylogenetics
ATAT	3.23, 3.34	[76]	Alloy Theory
ATLAS	3.10.1, 3.10.2, 3.11.17	[77]	Library, data
Atom	1.57.0	[78]	IDE
AtomEye	3	[79]	Material Science
AtomMan	1.3.3	[80]	Phylogenetics
aTRAM	2.2.0, 2.4.3	[81]	Math
Augustus	3.3.2, 3.3.3, 3.4.0	[82]	Biology,bioinformatics,genomics
Auto3DEM	4.05.2	[83]	Image Reconstruction
AutoDock	4.2.6	[84]	Biology
AutoDock-GPU	1.5.3	[85]	Molecular Docking
Autometa	20190802	[86]	Phylogenetics
automlsa2	0.8.1	[87]	Phylogenetics, biology, phylogenomics
AWSCLI	2.2.30	[88]	Utilities
azoo	1.3.1	[89]	Phylogenetics
Badread	0.1.5	[90]	Phylogenetics
bakta	1.3.3	[91]	Phylogenomics, biology
BALi-Phy	3.4.1, 3.5.0	[92]	Phylogenetics
BAM-matcher	20161021	[93]	Phylogenetics
Bam-Readcount	20150616	[94]	Biology, genomics
bamaddrg	20120326	[95]	Phylogenetics
BamBam	1.0	[96]	Biology, bioinformatics, genomics
bamm	2.5.0	[97]	Phylogenetics
bamsnap	0.2.19	[98]	Phylogenetics
Bamstats	20140602	[99]	Biology,bioinformatics,ngs
Bamsurgeon	1.2	[100]	Phylogenetics
bamtofastq	1.3.5	[101]	Phylogenetics
Bamtools	2.4.1, 2.5.0, 2.5.1	[102]	Biology,bioinformatics,ngs,sequencing
bamUtil	1.0.2	[103]	Biology, bioinformatics, genomics
BAPS	6.0	[104]	Biology, bioinformatics, genomics
Barrnap	0.7, 0.9	[105]	Biology, RNA-Seq
Basemount	0.15.96	[106]	Biology, DNA Sequencing
BatMeth2	20210720	[107]	Biology, Genomics, Mapping
bax2bam	0.0.9	[108]	Phylogenetics
BayArea	1.0.2	[109]	Biology
BAYENV	2.0	[110]	Biology, phylogenetics
BayesAss	3.0.4, 3.0.4.2	[111]	Phylogenetics
BayeScan	2.1	[112]	Biology, SNP
BayesR	20151016	[113]	Biology, phylogenetics
BayesTraits	3.0.2	[114]	Phylogenetics
baypass	2.1	[115]	Biology, phylogenetics
BBMap	38.26, 38.44, 38.90	[116]	Biology, alignment
bcftools	1.15, 1.3.1, 1.9	[117]	Biology, bioinformatics, ngs
bcl2fastq	2.16.0.10, 2.20.0.422	[118]	Biology, ngs, illumina
BDG-SeQuila	0.5.5	[119]	Phylogenetics
BEAGLE	4.1, 5.0, 5.2	[120]	Biology, genetics, genotyping
BEAR	20170209	[121]	Biology, bioinformatics, metagenomics
BEAST	2.6.2, 2.6.3, 2.6.7	[122]	Biology,phylogeny
BEAST2-XML	1.0.9	[123]	Phylogenetics
BEDOPS	2.4.30	[124]	Biology,bioinformatics,sequence,ngs
BEDTools	2.29.1, 2.29.2, 2.30.0	[125]	Biology,bioinformatics,ngs
Bertini	1.6	[126]	Mathemetics
BERTopic	0.7, 0.8.1	[127]	Machine Learning
BESST	2.2.4	[128]	Biology, NGS
BFAST	0.7.0	[129]	Biology,bioinformatics,ngs
bgenix	1.1.7	[130]	Data, genomics
Bifrost	0.2, 1.0.3, 20200225	[131]	Phylogenetics
BiG-SCAPE	1.1.2	[132]	Biology, Genomics, Phylogenetics, Pipeline
BinPacker	1.0	[133]	Biology, RNA-seq, sequence assembly
BinSanity	0.2.6.4	[134]	Biology, genomics
Bioawk	1.0	[135]	Phylogenetics
bioBakery	0.15.1, 1.8, 3.0.0	[136]	Phylogenetics
Biodiverse	2.1	[137]	Phylogenetics
Biolite	0.3.5.1	[138]	Biology, bioinformatics, genomics, SNP
BIOM	2.1.5, 2.1.6	[139]	Biology, genomics
BIOMART	1.4	[140]	Biology,genomics
Biopieces	2.0	[141]	Phylogenetics
BIRDS	1.0	[142]	Fiji, plugin, imaging
Bismark	0.22.3, 0.7.4, 0.7.7	[143]	Biology, bioinformatics, NGS
Blackfynn	0.2.7	[144]	Data Mining
BLASR	20130815, 20161215 (5.3), 5.3.2	[145]	Biology,bioinformatics,ngs
Blast2GO	2.5.0-20120705	[146]	Biology,bioinformatics,gene ontology
Blast2GO CLI	1.3.3	[147]	Biology, bioinformatics, gene ontology
BLAT	20121105, 20140318	[148]	Genomics, bioinformatics
blender	2.73, 2.77, 3.0.1	[149]	Graphics
blink	0.01	[150]	Phylogenomics
Blitz	0.10	[151]	Library
BlobTools	1.0, 2.2	[152]	Phylogenetics
bloomfiltertrie	0.8.7	[153]	Phylogenetics
BloomTree	0.3.5	[154]	Data Mining
BLUPF90	20160604, 20180301, 20190531	[155]	Biology, phylogenetics
BMGE	1.12	[156]	Biology, genetics, phylogeny
bmtagger	3.101	[157]	Phylogenomics, biology
BOLT-LMM	2.3.4	[158]	Phylogenetics
BoltzTraP	1.2.5	[159]	Physics
Boost	1.71.0, 1.75.0, 1.77.0	[160]	Programming, library, cpp
booster	0.1.2	[161]	Phylogenetics
Bowtie	1.1.1, 1.2.0, 1.2.3	[162]	Biology,bioinformatics,ngs,sequencing
Bowtie2	2.3.5.1, 2.4.2, 2.4.5	[163]	Biology,bioinformatics,ngs,sequencing
BoxCLI	2.9.0	[164]	Storage, web, api
BPGA	1.2	[165]	Biology, ngs
BPP	4.1.4, 4.3.8, 4.4.1	[166]	Biology, phylogenetics
Bracken	1.0.0, 2.5	[167]	Biology, phylogenetics
BrainIAK	0.11	[168]	Imaging
braker	2.1.2, 2.1.5, 2.1.6	[169]	Phylogenetics
BRANCH	1.8.1	[170]	Biology,bioinformatics,ngs,mapping
BRATNextGen	20150505	[171]	Biology, bioinformatics, genomics
BreakDancer	1.4.5	[172]	Biology, phylogenetics
breakseq	2.2	[173]	Biology, phylogenetics
Brewery	20191205	[174]	Phylogenetics
Bridger	20141201	[175]	NGS, Genomics, bioinformatics
BRIG	0.95	[176]	Biology, genomics
BRM	0.3	[177]	Phylogenetics
Bruker2nifti	1.0.4	[178]	Phylogenetics
Bsmap	2.87	[179]	Biology, bioinformatics, NGS
Bsoft	1.9.1	[180]	Biology, image analysis
BSseeker2	2.1.0, 2.1.8	[181]	Biology, phylogenetics
bubbleparse	20140314	[182]	Biology, phylogenetics
BUCKy	1.4.4	[183]	Biology, phylogenetics
BUSCO	4.0.6, 4.1.4, 5.2.0	[184]	Biology, genomics
BWA	0.7.7, 0.7.8, 0.7.9a	[185]	Biology,bioinformatics,ngs
bwa-mem2	2.2.1	[186]	Phylogenetics
BWA-PSSM	0.5.11	[187]	Phylogenetics
bxh_xcede_tools	1.11.1	[188]	Biology, bioinformatics
BYOBU	5.133, 5.92	[189]	Shell, screen, terminal
bzip2	1.0.6	[190]	Archiver, library
c-wap	20220624	[191]	Sequencing, Genomics, Biology, SARS-CoV2
Cactus	2.0.3, 2.0.5	[192]	Phylogenetics
CAFE	4.1, 5.0.0	[193]	Phylogenetics
came	0.0.1	[194]	Phylogenetics
Camino	20140723	[195]	Biology,bioinformatics,neuroscience,imaging
CAMP	1.0.0	[196]	Biology, Sequencing
Cantera	2.1.1	[197]	Kinetics, thermodynamics
Canu	1.9, 2.0, 2.1	[198]	Biology, sequencing
CANVAS	1.40.0.1613	[199]	Phylogenetics
CAP3	20120705	[200]	Biology,bioinformatics,assembly
Capnp	0.5.3	[201]	C++
CARTA	2.0	[202]	Image Processing
CASAVA	1.8.2	[203]	Biology,bioinformatics,ngs
CASM	0.2.0	[204]	Statistical Mechanics
CasOFFinder	2.4	[205]	Phylogenetics
Catch	1.4.0	[206]	Biology, Bioinformatics, Genomics, Sequencing
CAVIAR	20171218	[207]	Biology, phylogenetics
CBGpipe	20190702	[208]	Phylogenetics
CCMetagen	1.4.0	[209]	Phylogenetics
CD-HIT	4.6, 4.6.4, 4.6.8	[210]	Biology,genomics
CDBFasta	20181005	[211]	Phylogenetics
CDNA_Cupcake	20180629, 22.0.0, 9.0.1	[212]	Biology, bioinformatics, ngs, iso-seq
CDO	1.7.2rc3, 1.9.4	[213]	Climate
CellProfiler	3.1.9, 4.1.3	[214]	Phylogenetics
CellRanger	6.0.1, 6.1.2, 7.0.0	[215]	Biology, bioinformatics, ngs, rna-seq
CellRanger-ARC	2.0.1	[216]	Biology, bioinformatics, ngs, rna-seq
CellRanger-ATAC	1.2.0	[217]	Biology, bioinformatics, ngs, rna-seq
CellRanger-DNA	1.0.0, 1.1.0	[218]	Biology, bioinformatics, ngs, rna-seq, 10xgenomics
Centrifuge	1.0.3, 1.0.4b	[219]	Biology, phylogenetics
CFITSIO	3.370	[220]	Library, C
CGAL	4.10, 4.9, 5.02	[221]	Library, math
CGATools	1.6.0.43	[222]	Biology, bioinformatics, ngs
cgmaptools	0.1.1, 0.1.2	[223]	Phylogenetics
CGView	1.0.2	[224]	Phylogenetics
CHARMM	36a3, 43b2	[225]	Chemistry, simulation
ChartDirector	5.1.0	[226]	Library, data
CheckM	1.0.4, 1.0.7, 1.1.2	[227]	Biology, genomics
Chimera	1.12	[228]	Biology, bioinformatics, modeling
Chipyard	1.0	[229]	Hardware, design
Chromeister	1.5a	[230]	Biology, genomics
ChromEvol	2.0	[231]	Biology, NGS
CIMS	4.1.2	[232]	Biology,genomics
CIRCexplorer	1.1.10	[233]	Biology, bioinformatics, rna-seq
CIRCexplorer2	2.3.5, 2.3.8	[234]	Phylogenetics
Circlator	1.5.5	[235]	Phylogenetics
Circleator	1.0.2	[236]	Phylogenetics
circompara2	0.1.2.1	[237]	Phylogenetics
Circos	0.63-pre11, 0.69-2, 0.69-9	[238]	Biology,genomics,ngs
CIRI	2.0.6	[239]	Phylogenetics
ciriquant	1.1.2	[240]	Phylogenetics
cirspresso2	20220811	[241]	Genomics, sequencing, biology
CisGenome	2.0	[242]	Biology, bioinformatics, genomics
cisTEM	1.0.0	[243]	Phylogenetics
Clairvoyante	1.02	[244]	Phylogenetics
Clann	3.2.3	[245]	Biology,bioinformatics,phylogentics
clara	v4.0	[246]	AI, machine learning
CLARK	1.2.2-b, 1.2.3	[247]	Biology, genomics
CLHEP	2.2.0.1	[248]	High Energy Physics
CLIFinder	4.1	[249]	Biology, phylogenetics
ClinicaDL	1.0.4	[250]	Biology, bioinformatics, neuroimaging, deep learning
clipkit	1.3.0	[251]	Phylogenomics, biology
CLIPper	2.1.0	[252]	Phylogenetics
CLIPSeqTools	0.1.7	[253]	Biology, sequencing
ClonalFrame	1.1, 1.2	[254]	Biology,bioinformatics,ngs,phylogenetics
ClonalFrameML	1.0, 1.11	[255]	Biology, bioinformatics, ngs, phylogenetics
CloudCompare	2.10.3	[256]	Visualization
Clover	2.0	[257]	Biology, genomics, assembly
CLUMPP	1.1.2	[258]	Biology, bioinformatics
ClustalO	1.2.0	[259]	Biology, bioinformatics, alignment
ClustalW	2.1	[260]	Biology,bioinformatics,alignment
cluster3	1.52a	[261]	Biology, genomics
Clview	20130402	[262]	Biology, bioinformatics
CMake	3.19.1, 3.21.3	[263]	Software Development
CMS	20170518	[264]	Biology
CMWP	140518	[265]	Biology, genomics
CNCI	20180305	[266]	Phylogenetics
CNSpipeline	20170827	[267]	Phylogenetics
CNV-Seq	20110715, 20140812	[268]	Biology,bioinformatics,genomics
CNV-Sim	0.9.2	[269]	Biology, phylogenetics
CNVkit	0.9.6	[270]	Phylogenetics
CNVnator	0.3.2	[271]	Biology, genomics, CNV
cobra-tf	0.1	[272]	Nuclear Engineering
CodonPhyML	20150303	[273]	Phylogenetics
Coevol	1.3c, 1.4b, 1.6	[274]	Bio,bioinformatics,phylogenetics
Cogent	2.1	[275]	Biology, phylogenics
COLMAP	3.6	[276]	Modeling
CoMap	1.4.1	[277]	Bioinformatics, Genomics
Comp-D_MPI	1.0	[278]	Statistics
Compacta	1.02	[279]	Biology, Contig clustering
COMSOL	5.4.0	[280]	General-purpose simulation software
Concaterpillar	1.8a	[281]	Phylogenetics
CONCOCT	1.1.0	[282]	Biology, bioinformatics, genomics
Conda	4.10.3, 4.12.0	[283]	Programming, development, packages
CONN	18a	[284]	MRI,fmri,matlab
CONNECT	20200614	[285]	Phylogenetics
connectomemapper3	3.0.0-rc1	[286]	Phylogenetics
ConPADE	1.0	[287]	Phylogenetics
Conpair	20161010, 20180624	[288]	Biology, phylogenetics
Consed	23.0, 25.0, 29.0	[289]	Biology, bioinformatics, genomics
CONSEL	0.20	[290]	Biology, phylogenetics
ContaVect	0.2	[291]	Biology, phylogenetics
Convert3D	1.1.0	[292]	Imaging, Data Conversion
Coot	0.9.5	[293]	Modeling
Coreutils	8.23	[294]	Software Tools
coreutils	8.28	[295]	Software Tools
Corset	1.06	[296]	Biology, NGS
Counterr	0.1	[297]	Phylogenetics
covNMR	2014	[298]	Biochemistry
cp2k	7.0.0	[299]	Quantum Chemistry
CPAT	3.0.2	[300]	Phylogenetics
cpc	2.0	[301]	Phylogenetics
CPLEX	12.6.1, 12.6.2, 12.7	[302]	Meteorology
Crass	1.0.1	[303]	Biology, assembly
crisflash	1.2.0	[304]	Phylogenetics
CRISP	20181122	[305]	Phylogenetics
CRISPRanalyzer	1.50	[306]	Biology,genomics,ngs
CRISPRCasFinder	4.2.17	[307]	Phylogenetics
CrossMap	0.3.9, 0.6.3	[308]	biology, genomics
crossmapper	1.1.1	[309]	Phylogenetics
Crux	1.40	[310]	Biology, mass-spectroscopy
CryptoMiniSat	5.0.1	[311]	SAT
csvtk	0.23.0	[312]	Bioinformatics
ctk	1.1.4	[313]	Biology, genomics
CUBE	4.4	[314]	Library,c,math
CUDA	11.0.207, 11.1.0, 11.4.3	[315]	Programming, library, graphics, runtime
Cufflinks	2.1.1, 2.2.1, 2.2.1.1	[316]	Biology,bioinformatics,ngs,sequencing
cupy	8.3.0	[317]	Phylogenetics
cutadapt	1.18, 2.8, 3.4	[318]	Biology,bioinformatics,ngs
CutRunTools	20200104	[319]	Phylogenetics
cvbio	3.0.0	[320]	Phylogenetics
CViT	1.3	[321]	Perl, library
CWLtool	1.0.20190906, 2.0.20200126, 3.0.20210124104916	[322]	Workflow, scheduler
cx_oracle	8.3.0	[323]	Oracle, Database, Software Tools
CycleGan	20201015	[324]	Phylogenetics
Cytoscape	3.4.0	[325]	Biology, bioinformatics, ngs, phylogenetics
d2go	20210702	[326]	Machine Learning, dl, ai
dadi	2.1.1	[327]	Phylogenetics
DAKOTA	6.15, 6.8, 6.8-gui	[328]	Computational Science and Engineering
DALIGNER	1.0	[329]	Biology, phylogenetics
dammit	1.0rc2	[330]	Biology, phylogenetics
DASTool	1.1.0, 1.1.2	[331]	Biology, phylogenetics
datamash	1.1.0	[332]	Math
DAWGPAWS	1.0	[333]	Biology, phylogenetics
DCC	0.4.4	[334]	Biology, bioinformatics, ngs
Dcmstack	0.6.2	[335]	Biology, imaging
DCMTK	3.6.0	[336]	Biology,neuroscience,imaging
dDocent	2.7.8	[337]	Phylogenetics
DDSCAT	7.3.0	[338]	Astrophysics
DDT	18.2, 20.0, 20.2	[339]	Software Development
DealII	8.3.0, 9.3.1	[340]	Library
DeconSeq	0.4.3	[341]	Biology, phylogenetics
decontaMiner	1.4	[342]	Genomics, biology
DECX	20180205	[343]	Phylogenetics
DeepARG	1.0.1	[344]	Phylogenetics
deepbgc	0.1.18	[345]	Phylogenetics
Deepcoil	2.0.1	[346]	Sequencing, bioinformatics
DeepGS	1.2	[347]	Phylogenetics
DeepLabCut	2.0.7-gpu, 2.1.1, 2.2.1	[348]	Phylogenetics
deepmicrobes	20200219	[349]	Biology, genomics, metagenomics, ML
DeepMReye	01192022	[350]	Library, bioinformatics
DeepPicker	20161102	[351]	Particle Picking
deepTools	2.4.3, 3.1.1	[352]	Biology, bioinformatics, NGS
deepvariant	1.4.0	[353]	bioinformatics, biology, genomics, sequencing, machine learning
deFusion	20200305	[354]	Phylogenetics
Delft3D	7545	[355]	Physics
Delineate	1.2.2	[356]	Biology, genomics
Delly	0.7.5, 0.7.7, 0.7.8	[357]	Biology, phylogenetics
delucs	20220512	[358]	sequencing, genomics, taxonomy, machine learning
DeNoGAP	1.0	[359]	Biology, phylogenetics, ngs
DERIVA	1.5.0	[360]	Phylogenetics
deSALT	1.5.6	[361]	Biology, Genomics, Sequencing
Detectron2	0.4, 0.5, 0.6	[362]	Library
DeTiN	1.7.5.9	[363]	Particle NGS, genomics
DEXTRACTOR	1.0	[364]	Biology, sequencing
Diamond	0.9.15, 0.9.34, 2.0.9	[365]	Computational Biology, genomics
diCal2	2.2.0.1	[366]	Biology, phylogenetics
diffReps	1.55.4	[367]	Bioinformatics
DISCOVAR de novo	52488	[368]	Biology, ngs, assembler
DiscoVista	20180906	[369]	Phylogenetics
discvrseq	1.3.10	[370]	Biology, Phylogenetics
Distruct	2.3	[371]	Phylogenetics
DIYABC	1.0.4.43b, 2.0.3, 2.1.0	[372]	Biology, phylogenetics
DL_POLY	1.9	[373]	Molecular Dynamics
Dlib	19.19	[374]	Phylogenetics
DNA Clust	3.0	[375]	Biology,bioinformatics,genomics
DOCK	6.7, 6.8, 6.9	[376]	Chemistry
DoGFinder	20201103	[377]	Phylogenetics
DosageConvertor	1.0.3	[378]	Biology
DOT	2.0	[379]	Biology,bioinformatics,docking
Doxygen	1.8.3.1	[380]	Programming, documentation
dragmap	1.2.1	[381]	Phylogenetics, sequencing, biology
dragonflye	1.0.12	[382]	Sequencing, Genomics
DRAP	1.91	[383]	Biology, phylogenetics
dRep	2.3.2	[384]	Phylogenetics
Dropseq	2.4.0	[385]	Phylogenetics
DS9	7.5, 8.0.1	[386]	Imaging
DScribe	1.2.0	[387]	Machine Learning
dsistudio	20210123	[388]	Machine Learning
DSK	2.1.0, 2.3.0	[389]	Biology, NGS
DSRC	2.0	[390]	Phylogenetics
DSSAT	4.6	[391]	Agriculture
DSSP	2.2.1, 3.0.0	[392]	Molecular Dynamics
DSuite	0.4, 0.4-r41	[393]	Biology, Genomics
dtiprep	0.1.1	[394]	Phylogenetics
duchamp	1.6.2	[395]	Phylogenetics
dynamicDBG	20181003	[396]	Phylogenetics
Dynare	4.4.3	[397]	Math
ea-utils	1.04.807.18, 1.1.2.537	[398]	Biology,bioinformatics,genomics,ngs
EAGLE	2.0	[399]	Phylogenetics
eagle-rc	1.1.1	[400]	Phylogenetics
ECE	1.2	[401]	ECE
EDirect	10.7, 12.2	[402]	Biology, phylogenetics
EDTA	1.9.6	[403]	Phylogenetics
Edyeet	0.1, 0.3	[404]	Phylogenetics
EEGLAB	12.0.2.1b, 13.2.2b, 13.4.4b	[405]	Biology,bioinformatics,matlab
eGene-MVN	0.1	[406]	Biology, genetics
eggNOG-mapper	2.0.1, 2.1.6	[407]	Phylogenetics
EGSnrc	2019	[408]	Phylogenetics
EIGENSOFT	4.2, 5.0.1, 6.0.1	[409]	Biology, bioinformatics
Elastix	4.9.0	[410]	Phylogenetics
ELPA	2019.11.001	[411]	Library,c,math
elPrep	4.1.4	[412]	Phylogenetics
Emacs	27.2	[413]	Programming, scripting, language
EMAN2	2.22, 2.31	[414]	Image Processing
EMBOSS	6.6.0	[415]	Biology,bioinformatics
Embree	3.6.1	[416]	Ray, tracing, kernels
EMC	9.4.3	[417]	Monte Carlo Simulations
EMMAX	20100307, 20120210	[418]	Biology, NGS, mapping
EnergyPlus	9.3.0	[419]	Simulation
Ensembl Tools	100, 80	[420]	Biology, bioinformatics
enTAP	0.6.1.2, 20160416	[421]	Biology, phylogenetics
EPACTS	3.2.6, 3.4.2, 3.4.2.hg38	[422]	Biology, bioinformatics, genomics
EpiNano	1.2.0	[423]	biology, NGS
epiteome	1.0	[424]	Phylogenetics
epoch	4.7.3	[425]	Astronomy,CCPP
eQTLA	1.1	[426]	Biology, bioinformatics, genomics
eQtlBma	1.2.2, 1.3.0r20140820	[427]	Biology, genotyping
Erpin	5.5.4	[428]	Biology, phylogenetics
ESOM	1.1	[429]	Biology, phylogenetics
ESPRESSO	6.2.1, 6.4.1, 7.0	[430]	Quantum,modeling
ESPRIT	2009-nogap, 201102	[431]	Biology,bioinformatics
ETE3	3.0.0, 3.1.1	[432]	Biology, phylogenetics
EVidenceModeler	1.1.1	[433]	Phylogenetics
Evigene	20180730, 20200520	[434]	Phylogenetics
EvoLSTM	20220103	[435]	Biology, Bioinformatics
ExaBayes	1.5	[436]	Phylogenetics
Exonerate	2.2.0	[437]	Biology,bioinformatics,genomics
ExpansionHunter	4.0.2	[438]	Biology, genomics
ExpansionHunterDenovo	0.9.0	[439]	Biology, genomics
export2graphlan	0.22	[440]	Statistics, mapping, graphing
eXpress	1.3.1, 1.5.1	[441]	Biology,bioinformatics,ngs
ezaai	1.0	[442]	Biology, phylogenetics
face_morpher	20190630	[443]	Phylogenetics
face_recognition	1.2.2	[444]	Phylogenetics
fairseq	0.12.2	[445]	modeling, ai
FALCON	20161027, 20161222, 20190601	[446]	Biology,bioinformatics,ngs,sequencing
FALCON_unzip	20161222	[447]	Biology, bioinformatics
FAR	2.15	[448]	Biology,bioinformatics,genomics
FAST	1.06	[449]	Biology phylogenetics
fast-gep	1.0	[450]	Phylogenetics
Fast-Plast	1.2.6	[451]	Biology, phylogenetics
fast5tools	0.3.1	[452]	Phylogenetics, biology
FASTA	34.26.5, 36.3.6d	[453]	Biology,bioinformatics,genomics
fastai	2.1.5, 2.6.3	[454]	Phylogenetics
FastANI	1.1	[455]	Phylogenetics
fastchaos	0.1.0	[456]	Sequencing
FastGEAR	20161216	[457]	Biology, bioinformatics, genomics
Fastix	0.1.0	[458]	Biology, NGS
FastML	3.0	[459]	Biology,bioinformatics,phylogenetics
Fastp	0.20.0, 0.22.0	[460]	Biology,bioinformatics,ngs
FASTphase	1.4.8	[461]	Phylogenetics
FastPlast	1.2.8	[462]	Phylogenetics
fastq-pair	1.0	[463]	Phylogenetics
FastQ-Screen	0.14.0	[464]	Phylogenetics
Fastq-tools	0.8	[465]	Biology, NGS,
FastQC	0.11.4, 0.11.7, 0.9.6	[466]	Biology,bioinformatics,ngs
FastqPuri	1.0.7	[467]	Phylogenetics
FastQTL	2.184	[468]	Phylogenetics
FASTRAL-constrained	20211108	[469]	Phylogenetics
fastsimcoal	2.6.0.3, 2.7.0.2	[470]	Biology, phylogenetics
FastSpar	0.0.4	[471]	Biology, genomics
fastStructure	20150112	[472]	Biology, genomics
FastTree	2.1.11	[473]	Biology,bioinformatics,phylogenetics
FastUniq	1.1	[474]	Biology, phylogenetics
Fastx Toolkit	0.0.13.2, 0.0.14	[475]	Biology,ngs
fcGENE	1.0.7, 1.0.7.1	[476]	Biology,bioinformatics,genomics,snp
FDSTools	1.2.0	[477]	Phylogenetics
fdupes	1.51	[478]	File Management
FEELnc	0.1.1	[479]	Phylogenetics
FEniCS	2018.1.0	[480]	Biology, phylogenetics
Ferret	6.82	[481]	Data Visualization and Analysis, Oceanography, Meteorology
FFmpeg	2.1.3, 2.8.3, 4.3.1	[482]	Audio, Video
FFTW	3.3.6, 3.3.7, 3.3.8	[483]	Library,c,math
fgbio	0.5.0, 0.7.0	[484]	Phylogenetics
FGMP	1.0.1	[485]	Phylogenetics
FIGARO	1.1.2	[486]	Phylogenetics
Fiji	2.0.0rc59	[487]	ImageJ
Filtlong	0.2.0	[488]	Biology, phylogenetics
Finder	20210503, 20210609	[489]	Biology, bioinformatics, finder
finemap	1.4	[490]	Phylogenetics
fineRADstructure	0.3.2	[491]	Phylogenetics
finesse	2.3.1	[492]	Simulation
fit-sne	1.2.1	[493]	Phylogenetics
FLAIR	1.5	[494]	Phylogenetics
flairNLP	0.10	[495]	Data Visualization, language
flappie	1.1.0, 2.1.3	[496]	Phylogenetics
FLASh	1.2.10, 1.2.11	[497]	Biology, genomics
FLEA	2.0.0	[498]	Phylogenetics
flex	2.6.4	[499]	Programming
Flexbar	2.3, 2.34, 3.5.0	[500]	Biology, bioinformatics, genomics, ngs
FLEXLm	1.0	[501]	Administration
FlowCraft	1.4.1	[502]	Phylogenetics
Fluent	17.2, 19.1, 2020R1	[503]	CFD
Flye	2.7.1, 2.8.1, 2.9	[504]	Biology, NGS
fMRIPrep	1.4.0a1, 1.5.4, 20.2.3	[505]	Data Mining
ForeSeqs	1.0.4	[506]	Phylogenetics
fpocket	4.0.2	[507]	sequencing, biology
fqtools	20160224	[508]	Biology,bioinformatics,ngs,sequencing
FragGeneScan	1.16	[509]	Biology,genomics
FRAMA	20151019	[510]	Biology
FrameDP	1.2.2	[511]	Biology, sequencing
FRAPOSA	20200421	[512]	Phylogenetics
FreeBayes	1.1.0-20170823, 1.3.1, 1.3.2	[513]	Biology,genomics
freesasa	2.1.2	[514]	molecular dynamics, biology
Freesurfer	7.1.0, 7.1.1, 7.2.0	[515]	Biology,bioinformatics,neuroscience,imaging
Freyja	1.3.1, 1.3.4, 1.3.8	[516]	Biology,phylogenetics,sequencing
FSA	1.15.9	[517]	Phylogenetics
FSL	6.0.3, 6.0.4, 6.0.5	[518]	Biology,bioinformatics,neuroscience,imaging
fslmrs	1.1.10	[519]	MRS, metabolomics
funannotate	1.8.7, 1.8.9	[520]	Phylogenetics
fusion_twas	20210218	[521]	Phylogenetics
GAL	20180906	[522]	Phylogenetics
Galaxy	1.0	[523]	Biology,bioinformatics
GAML	20150610	[524]	Biology, bioinformatics, genomics
GapCloser	1.12r6	[525]	Biology, genomics, ngs
GapFiller	1.10, 1.11	[526]	Biology, genomics
GARLI	2.0, 2.01	[527]	Biology,bioinformatics,phylogeny
GASVPro	201310	[528]	Biology, bioinformatics, ngs
GATE	7.0	[529]	Library
GATK	4.1.4.0, 4.1.8.1, 4.1.9.0	[530]	Biology,bioinformatics,ngs
Gaussian	09 D.01, 16, 16-c02	[531]	Computational Chemistry
Gawk	4.2.0	[532]	Software Tools
Gblocks	0.91b	[533]	Biology,bioinformatics
GCC	7.3.0, 8.2.0, 9.3.0	[534]	Compilers
GCE	1.0.2, 4.0	[535]	Biology, bioinformatics, genomics
GCT	6.2.1	[536]	Gridftp, globus, toolkit
GCTA	1.26.0, 1.92.4beta, 1.93.2beta	[537]	Biology, genomics, SNP,
GDAL	2.2.1, 2.2.4, 2.3.1	[538]	Geospatial, Library
GDB	8.3, 9.2	[539]	Software Development
GDC-Client	1.0.1	[540]	Biology, bioinformatics, sequence, ngs
gdc-client	1.5.0	[541]	Phylogenetics
GDrive	2.1.0	[542]	Applications, Utilities, Data Transfer
GDSL	1.18	[543]	Library
Geant4	4.10, 4.10.03, 4.10.5	[544]	Physics
GEM	20130406	[545]	Biology,bioinformatics,ngs,sequencing
gem5	2.0	[546]	Computer Simulator
GEMMA	0.98.1	[547]	Phylogenetics
GeneMark-ES	4.58, 4.65, 4.68	[548]	Biology, genomics
GeneMarkS	2012.04	[549]	Biology,genomics
GeneMarkS-T	3.10.001	[550]	Biology,genomics
GenePainter	2.0.4	[551]	Biology, phylogenetics
GeneRax	1.2.2	[552]	Phylogenetics
GeneSeqer	2014-02-26	[553]	Biology, genomics
genesum	0.1.0	[554]	Biology,genomics
GeneTorrent	3.8.7	[555]	Biology,bioinformatics,data download
GenGen	1.0.1	[556]	Biology, phylogenetics
Genome STRiP	2.00.1602	[557]	Biology, genomics, ngs
Genome_Graph_Annotation	20190131	[558]	Phylogenetics
GenomeScope2	2.0	[559]	Phylogenetics
GenomeThreader	1.7.3	[560]	Phylogenetics
GenomeTools	1.5.7, 1.5.9	[561]	Biology, bioinformatics
genomic-fluidity	20151109	[562]	Phylogenetics
GenomicConsensus	2.3.3	[563]	Biology, phylogenetics
GenomicNeuralnet	20161030	[564]	Phylogenetics
GenomicTools	2.7.0	[565]	Biology,bioinformatics,ngs,chip-seq,rna-seq
GenotypeHarmonizer	1.4.18	[566]	Biology, bioinformatics
Genrich	0.5	[567]	Phylogenetics
GenSel	4.90	[568]	Population Genetics
geopython	1.0.0, 1.0.1	[569]	Python, geospatial, cartography
GEOS	3.3.8, 3.6.2	[570]	Library, data
GeP	2.1	[571]	Biology, phylogenetics
gepard	1.40.0	[572]	Phylogenetics
Gerbil	1.11	[573]	Phylogenetics
get_homologues	3.3.3	[574]	Biology, genome
GetOrganelle	1.7.3.5, 1.7.5.0	[575]	Phylogenetics
GFam	1.1	[576]	Biology, genomics, annotation
GFF-Ex	2.3	[577]	Phylogenetics
GFF3toolkit	2.0.3	[578]	Phylogenetics
gffcompare	0.12.2	[579]	Phylogenetics
gffread	0.11.8, 0.12.7, 0.9.8c	[580]	Biology, bioinformatics
Gflags	2.2.1, 20150520	[581]	Google,libraries
GFOLD	1.1.4	[582]	Biology, RNA-seq
ggsashimi	0.5.0	[583]	Phylogenetics
GHOST-MP	1.3.4	[584]	Phylogenetics
Ghostscript	9.22	[585]	PDF
Giotto	0.1.0	[586]	Phylogenetics
Git	2.14.1, 2.30.1	[587]	Revision Control
git-filter-repo	2.33.0	[588]	Phylogenetics
glactools	1.0.8	[589]	Phylogenetics
Glimmer	3.02	[590]	Biology, microbial annotation
GlimmerHMM	3.0.4	[591]	Biology, microbial annotation
GLMsingle	1.0	[592]	FMRI
Globus	1.10.1, 2.1.3	[593]	Data Transfer
glog	0.3.5	[594]	Google,libraries
GLPK	4.55, 4.65	[595]	Programming
Glueviz	0.15.2	[596]	Phylogenetics
GMAP	20180212, 20180212_sse2, 20190610	[597]	Biology, bioinformatics, genomics, ngs
GMcloser	1.6	[598]	Biology, NGS
GMP	6.1.2	[599]	Library, crypto
GnuPlot	5.2.2, 5.2.3, 5.4.1	[600]	Graphics,plotting,math
Go	1.13.6, 1.15.4, 1.18.3	[601]	Language
GOMAP	1.3	[602]	Biology, bioinformatics, ngs
GoPHY	201030	[603]	Phylogenetics
gotcloud	1.17.5	[604]	Phylogenetics
GPA	1.1	[605]	Phylogenetics
GPhoCS	1.2.3	[606]	Phylogenetics
Gpufit	20201127	[607]	Phylogenetics
Grace	5.1.22	[608]	Graphics, statistics, 2D
GRACKLE	3.1	[609]	Library,c,astrophysics
GrADS	2.0.1	[610]	Environment, grid analysis
Graftm	0.12.2	[611]	Phylogenetics
GramCluster	1.3	[612]	Biology,sequencing,
graph-tool	2.32	[613]	Phylogenetics
Graph_annotation	0.1	[614]	Phylogenetics
GraPhlAn	1.1.3	[615]	Phylogenetics
GraphMap2	0.6.5	[616]	Phylogenetics
GraphSplitting	2.4	[617]	Phylogenetics
graphtyper	2.7.2	[618]	Phylogenetics
GraphViz	2.38.0, 2.46.1	[619]	Biology,bioinformatics,neuroscience,imaging
GRASS	7.0, 7.4	[620]	Geography
grf	1.0.0	[621]	Genomics, bioinformatics
Grib_api	1.10.1, 1.15.1, 1.26.1	[622]	C, fortran, library
GRIDSS	2.6.2	[623]	Phylogenetics
GROCSVs	0.2.5	[624]	Phylogenetics
GROMACS	2021.2, 2021.3, 2021.4	[625]	Computational Chemistry, Molecular Dynamics
GroopM	0.3.5	[626]	Biology, phylogenetics
Groovy	2.4.15	[627]	Programming
Gscripts	1.1	[628]	Scripts
GSEA	3.0.0, 4.2.2	[629]	Biology, bioinformatics, genomics
GSL	2.4, 2.5, 2.6	[630]	Library, data
GSNP	1.0	[631]	Biology,bioinformatics,ngs
GTAHunter	20200106	[632]	Phylogenetics
GTDBTk	1.7.0, 2.0.0, 2.1.0	[633]	Phylogenetics
GTOOL	0.7.5	[634]	Phylogenetics
GUAVA	1.0	[635]	Phylogenetics
Gubbins	2.4.1, 3.2.1	[636]	Phylogenetics
guideseq	1.0.2	[637]	sequencing, genomics, bioinformatics, data
guile	2.2.2	[638]	Programming Language
GULP	4.4, 5.0	[639]	Material Science
guppy	4.4.1, 4.5.4, 6.1.7	[640]	Phylogenetics
Gurobi	9.5.1	[641]	Math, python
GWAMA	2.2.2	[642]	Phylogenetics
Gzip	1.10	[643]	Compression
Hail	0.2.77	[644]	Biology, Genomics
hal	2.1	[645]	Phylogenetics
HALC	1.1	[646]	Biology, phylogenetics
halla	0.8.17	[647]	Phylogenetics
hamstr	v8b	[648]	Biology, genome
HaMStR	13.2.2, 13.2.3, 13.2.4	[649]	Biology, genome
hapbin	1.3.0	[650]	Biology, Genetics
HapCompass	0.7.7	[651]	Particle NGS, genomics
HAPCUT	0.7	[652]	Biology, assembly
HapCUT2	1.3.3	[653]	Biology, Genomics, Sequencing
hapdup	0.6	[654]	Phylogenetics, biology
Haploflow	0.1	[655]	Biology, Phylogenetics
Haplomerger2	20180603	[656]	Biology, genomics
HAPLOSWEEP	1.0	[657]	Biology, phylogenetics
happy	0.3.14	[658]	Phylogenetics, biology
hapQTL	1.00	[659]	Biology
hapsembler	2.21	[660]	Biology, bioinformatics, assembly
HASLR	0.8a1	[661]	Phylogenetics
hclust2	1.0.0	[662]	Statistics, mapping
HDF4	4.2.11	[663]	Library, data
HDF5	1.8.19, 1.8.20, 1.8.9	[664]	Library, data
hecaton	0.5.1	[665]	Genomics, Biology
HELEN	20200516	[666]	Phylogenetics
HelitronScanner	1.1	[667]	Phylogenetics
hgraph2graph	20210428	[668]	Chemistry
HiC-Pro	3.0.0	[669]	Biology, Pipeline, Genomics
Hifiasm	0.16.1, 0.4, 0.8	[670]	Phylogenetics
HipSTR	0.7	[671]	Phylogenetics
HISAT2	2.2.0, 2.2.1, 2.2.1-3n	[672]	Biology, Sequence Alignment, NGS
HLAminer	1.3.1, 1.4	[673]	Biology, phylogenetics
HMM-FRAME	20140724	[674]	Phylogenetics
HmmCleaner	0.180750	[675]	Phylogenetics
HMMER	3.1b1, 3.1b2, 3.2.1	[676]	Biology, genome
hmmer2go	0.18.1	[677]	Phylogenetics, biology
HMMRATAC	1.2.10	[678]	Phylogenetics
HOMER	4.10, 4.11, 4.8	[679]	Biology,bioinformatics,sequence,ngs
homopolish	0.3.3	[680]	Genomics, Biology
HOOMD	2.1.7	[681]	Library, math
HPL	2.1	[682]	Parallel Programming, benchmarks, MPI
HTMLDoc	1.8.28, 1.9.3	[683]	Pdf, docs, html
HTSeq	0.11.2	[684]	Biology,bioinformatics,ngs
humann2	0.11.2, 2.8.1	[685]	Phylogenetics
hyb	20141126, 20200815	[686]	Biology, ngs, RNA-Seq
HybPiper	1.2, 1.3.1, 2.0.1	[687]	Biology, phylogenetics
HyDe	0.4.3	[688]	Phylogenetics
HyPhy	2.5.4, 2.5.7, 2.5.8	[689]	Biology,bioinformatics,evolution
HYPRE	2.15.1, 2.18.2, 2.19.0	[690]	Math, Numerical Solvers
iAnnotateSV	1.0.6, 1.0.9	[691]	Biology, Phylogenetics
iAssembler	1.3.2	[692]	Biology, assembly
ibdne	20150815	[693]	Biology,ngs
icommands	3.3.1	[694]	IRods
IDBA-MT	1.0	[695]	Biology,NGS
IDBA-UD	1.1.1, 1.1.1-512, 1.1.1-512-mem	[696]	Genomics, bioinformatics, phylogenetics
IDL	8.3	[697]	Language, programming, science
IDR	2.0.3	[698]	Phylogenetics
IGB	8.4.1	[699]	Biology, bioinformatics, genomics
igBLAST	1.5.0, 1.7.0	[700]	Biology, bioinformatics
IGoR	1.4.0	[701]	Phylogenetics
iGTP	1.1	[702]	Biology, bioinformatics, phylogenetics
IGV	2.3.91, 2.4.16, 2.8.6	[703]	Biology, bioinformatics, ngs, phylogenetics
illumina-utils	2.11	[704]	Phylogenetics
Illumiprocessor	2.0.9	[705]	Phylogenetics
IM and IMa	20091217	[706]	Biology,bioinformatics,population genetics
Ima2	20120827	[707]	Biology,bioinformatics,population genetics
IMa2p	20170712	[708]	Biology, phylogenetics
IMA3	22Aug18	[709]	Molecular Dynamics
ImageJ	1.48	[710]	Imaging
ImageMagick	7.0.8-20	[711]	Imaging
Imaginaire	20201229	[712]	Imaging, Video, AI, synthesis
IMOD	4.7.15, 4.9.10	[713]	Image Processing
imoka	1.0	[714]	Biology, genomics
IMPUTE2	2.3.2	[715]	Phylogenetics
IMPUTE5	1.1.5	[716]	Biology, Imputation
INDELible	1.03	[717]	Phylogenetics
Infernal	1.1.1, 1.1.4	[718]	Biology, sequence alignment
INLA	20160718, 20170620	[719]	Statistics, modeling, R
InParanoid	4.1	[720]	Biology, biology
Inspector	1.0.2	[721]	Bioinformatics, genomics
InStruct	20160723	[722]	Phylogenetics
Intel Compilers and Libraries	2018.1.163, 2019.1.144, 2020.0.166	[723]	Language, development, library, math, intel
Intel MPI	5.1.1	[724]	Parallel Programming, development, MPI, library
InterProScan	5.53-87.0, 5.54-87.0, 5.56-89.0	[725]	Biology,bioinformatics
intervene	0.6.2	[726]	Biology, phylogenetics
IOAPI	3.1, 3.2	[727]	Meteorology
IPOPT	3.12.10, 3.12.6	[728]	Library, c/c++,math, solver, optimization
ipyrad	0.7.24, 0.7.30, 0.9.53	[729]	Phylogenetics
IQ-TREE	2.1.0, 2.1.2, 2.1.3	[730]	Biology, phylogenetics,
IRAP	0.8.1p7	[731]	Biology, ngs, pacbio
irep	1.10	[732]	Biology,bioinformatics,genomics
IRFinder	1.2.0, 1.3.0, 1.3.1	[733]	Biology, RNA-Seq
isONclust	0.0.6	[734]	Phylogenetics
IsoSel	1.0	[735]	Phylogenetics
IsoSeq3	3.1.0, 3.2.2, 3.4.0	[736]	Biology, bioinformatics, ngs, pacbio
ISOWN	20180820	[737]	Phylogenetics
isPcr	3.3	[738]	Biology, phylogenetics
ITK	3.20.1, 4.10.1	[739]	Bioinformatics
ITK-SNAP	3.0.0, 3.8.0	[740]	Biology,bioinformatics,neuroscience,imaging
ITSx	1.1b	[741]	Phylogenetics
IVA	1.0.11	[742]	Phylogenetics
iVar	1.3.1	[743]	Biology
Jabba	1.0	[744]	Biology, phylogenetics
JACUSA	1.2.0	[745]	Biology, bioinformatics, ngs, phylogenetics
JAGS	3.3.0, 3.4.0, 4.2.0	[746]	Statistics
Jasmine	1.1.4	[747]	Phylogenetics
jasp	0.14.3	[748]	Statistics
jbrowse2	1.7.4	[749]	Web Browser
JCVI	0.8.12, 1.0.13	[750]	Phylogenetics
JDK	11.0.1, 14, 9.0.1	[751]	Programming,runtime
Je	1.0	[752]	Biology, NGS
Jellyfish	2.2.4, 2.2.6, 2.3.0	[753]	Biology,ngs
jModelTest	2.1.1	[754]	Biology, bioinformatics, genomics, phylogenetics
jo	1.3	[755]	Software
jq	1.6	[756]	Software
juicer	1.22.01	[757]	Phylogenetics
Julia	1.6.2, 1.7.1, 1.7.3	[758]	Programming, language, statistics
Jupyter	5.7.8, 6.0.3, 6.2.0	[759]	Python, R, jupyter
jutils	1.0	[760]	Phylogenomics, biology
JVARKIT	20180405	[761]	Biology, phylogenetics
Kaiju	1.6.2, 1.7.2	[762]	Biology, phylogenetics
KaKs	1.2, 2.0	[763]	Biology, bioinformatics, evolution, phylogenetics
Kalign	3.3.1	[764]	Biology, Bioinformatics, Sequencing, Alignment
kallisto	0.43.0, 0.44.0, 0.48.0	[765]	Biology,NGS,RNA-Seq
khmer	2.0, 2.1	[766]	Biology, NGS
KIM	1.7.2, 1.8.2, 1.9.3	[767]	Simulation
KING	2.1.2	[768]	Biology, genome, gwas
KisSplice	2.4.0-p1	[769]	Biology, RNA
KLayout	0.26.7	[770]	Phylogenetics
KMC	3.1.0, 3.1.1, 3.2.1	[771]	Phylogenetics
kmerdb	1.9.2	[772]	Phylogenomics, biology
KMOS	0.3.21	[773]	Phylogenetics
kneaddata	0.7.4, 0.9.0	[774]	Phylogenetics
Knitro	12.2.0	[775]	Mathematical Optimization Problems
KofamScan	1.3.0	[776]	Phylogenetics
kover	2.0.3	[777]	Phylogenetics
Kraken	2.0.6b, 2.0.8b, 2.1.2	[778]	Biology, ngs
KrakenUniq	0.5.8, 0.7.3	[779]	Phylogenetics
Krona	20161019	[780]	Biology, bioinformatics
ksnp	3.021	[781]	Biology, phylogenetics, SNP
Ksrates	1.1.1	[782]	Phylogenomics, biology
LACHESIS	2.1	[783]	Phylogenetics
Lambda	0.9.4, 1.0.3, 2.0.0	[784]	Biology, sequencing, phylogenetics
LAMMPS	30Jul16, 7Aug19, 7Dec15	[785]	Molecular Dynamics
LAMP	2.5	[786]	Biology, bioinformatics, genomics
laneta	20220517, 20220808, 20220812	[787]	Bioinformatics, biology
langdetect	1.0.9	[788]	NLP, utility
LAPACK	3.8.0	[789]	Programming,library,fortran
Last	916, 979	[790]	Biology,bioinformatics,sequence,alignment
LAStools	20200114	[791]	LiDAR
LASTZ	1.02.00, 1.03.02, 1.04.00	[792]	Biology, bioinformatics, ngs
Lazypipe	1.2	[793]	Genomics,taxonomy,binning
LazyPredict	0.2.8	[794]	Phylogenetics
lbzip	2.5	[795]	Compression
LCModel	6.3	[796]	Biology, NMR
ldak	5.2	[797]	Phylogenetics, biology
LDhat	2.2a	[798]	Biology,genomics
ldsc	1.0.1	[799]	Phylogenomics, biology
leafaudio	0.1.0	[800]	Tensorflow, audio, leafaudio
LEfSe	20180219	[801]	Phylogenetics
LEMON	1.2.3	[802]	Library
LFMM	1.4, 1.5	[803]	Biology, phylogenetics
Libint	2.5.0b	[804]	Library
LIBINT	2.5.0	[805]	Library,c,math
libMesh	1.5.0	[806]	Math, Numerical Solvers
libunistring	0.9.7	[807]	Library
libvips	8.5.4	[808]	Image Processing
LIBXC	4.2.3, 4.3.4	[809]	Library, density function
LIBXSMM	1.13	[810]	Library,c,math
LIBZMQ	4.3.1	[811]	Library
Liftoff	1.4.2	[812]	Phylogenetics
LIGR	2.05	[813]	Biology,assembly
lima	2.0.0, 2.2.0	[814]	Phylogenetics
lingua	1.0.1	[815]	NLP, utility
LINKS	1.8.5, 1.8.6	[816]	Biology, genomics
Linksbrowser	2.14	[817]	Web browser
LIQA	1.0.0	[818]	Phylogenetics
LMAP	1.0.2	[819]	Biology, phylogenetics
lncScore	1.0.2	[820]	Biology, phylogenetics
lobSTR	4.0.6	[821]	Biology, phylogenetics
localbrainage	20210415	[822]	Bioinformatics, ml
localizer	1.0.4	[823]	Phylogenetics
LocusZoom	1.4	[824]	Phylogenetics
LoFreq	2.1.3.1	[825]	Phylogenetics
LongQC	1.2.0c	[826]	Phylogenetics
LongRanger	2.1.5, 2.2.2	[827]	Biology, phylogenetics
LongStitch	1.0.3	[828]	genomics, biology
LoRDEC	0.9	[829]	Phylogenetics
LoRMA	0.5	[830]	Biology, ngs, pacbio
LORMA	0.3	[831]	Biology, ngs, pacbio
LRBinner	0.1	[832]	Biology, Bioinformatics, Metagenomics, Binning
lrgapcloser	09042018	[833]	Biology, bioinformatics
LS-DYNA	700, 711, 901	[834]	Physics
LSD2	1.6.5	[835]	Phylogenetics
ltr_finder	1.07	[836]	Biology, phylogenetics
LTRRetriever	2.1, 2.5, 20170514	[837]	Biology, phylogenetics
Lua	3.5.2	[838]	Programming, scripting, language
Lucene	7.7.1, 9.1.0	[839]	Java,search,indexing
lumpy-sv	0.2.1, 0.2.13, 0.3.1	[840]	Biology, genotyping
LZO	2.09	[841]	Library, compression
M5nr	20121126	[842]	Biology, bioinformatics, genomics
Macaulay2	1.15	[843]	Phylogenetics
MACH	1.0.18	[844]	Biology,bioinformatics,genomics,ngs
Mach2VCF	20150515	[845]	Biology
MACS	2.0.10, 2.1.2, 2.2.7.1	[846]	Biology, bioinformatics, CHiP-Seq
MafFilter	1.3.0	[847]	Phylogenetics
MAFFT	7.294, 7.397, 7.490	[848]	Bio,bioinformatics,sequence
MAGeCK	0.5.9.4	[849]	Phylogenetics
MAGeCK-VISPR	0.5.6	[850]	Phylogenetics
MAGeCKFlute	1.14.0	[851]	Phylogenetics
Magenta	2.1.2	[852]	Phylogenetics
MAGMA-GWAS	1.09	[853]	Phylogenetics
magus	20220121	[854]	Sequencing, alignment
MAJIQ	2.2, 2.3	[855]	Phylogenetics
Maker	2.31.10, 2.31.6, 3.01.03	[856]	Biology,bioinformatics
MAnorm	20120316	[857]	Biology, phylogenetics
MANTA	1.6.0	[858]	Phylogenetics
mantis	1.0.4	[859]	Phylogenetics
mapclassify	2.4.2	[860]	Statistics, mapping, geography
MapThin	1.11	[861]	Phylogenetics
Maq	0.7.1	[862]	Biology,bioinformatics,ngs
MarginPolish	1.0.0	[863]	Phylogenetics
MARK	2.0.1	[864]	Application, data, capture
MarkerMiner	20150710	[865]	Biology, bioinformatics, genomics
mash	1.1	[866]	Biology, genomics
Mash	2.3	[867]	Phylogenetics
MasHmap	2.0	[868]	Phylogenetics
mashtree	1.2.0	[869]	Phylogenomics, biology
MASSMINE	0.10.0, 0.11.0, 0.9.5	[870]	Data Mining
MaSuRCA	3.4.2, 4.0.8, 4.0.9	[871]	Biology,bioinformatics,short read alignment
Mathematica	12.1.1.0	[872]	Math
MATLAB	2020a, 2020b, 2022a	[873]	Math,language
MATS	4.0.1, 4.0.2, 4.1.0	[874]	Biology,bioinformatics,ngs,rna-seq
Mauve	2.3.1	[875]	Biology,ngs,genomics
mawk	1.3.4-20150503	[876]	Language
maxbin	2.1.1	[877]	Biology,NGS
Maxima	5.41.0	[878]	Math
MC	4.6.1	[879]	Shell
mCarts	1.0.2	[880]	Biology, genomics, markov
mccortex	1.0	[881]	Phylogenetics
MCL	12-135, 14-137	[882]	Biology, genomics
MCNP	6, 6.1	[883]	Physics
MCNPX	2.7.0	[884]	Physics
MCR	2019b, 2020a, 2020b	[885]	Math, language
MCScanX	20130328	[886]	Biology, phylogenetics
mdanalysis	1.1.1	[www.mdanalysis.org]	Physics, Bioinformatics
MECAT	20180308	[887]	Phylogenetics
Medaka	1.0.1, 1.2.1, 1.6.0	[888]	Biology, phylogenetics
Medusa	1.6	[889]	Phylogenetics
MEGA	7.0.26	[890]	Biology, phylogenetics
Mega2	4.9.2, 6.0.0	[891]	Biology, phylogenetics
MEGAHIT	1.1.1, 1.1.4	[892]	Biology, phylogenetics
Megalodon	2.0.0	[893]	Phylogenetics
MEGAN	5.10.3, 6.4.15	[894]	Biology, bioinformatics, ngs
MEGASAT	1.0	[895]	Phylogenetics
Megraft	1.0.2	[896]	Biology,sequencing,
MELD	0.4.14, 0.4.19, 0.5.9	[897]	Computational Chemistry, Molecular Dynamics
MELTING	4.3.1	[898]	Biology, genome, RNA, folding
MEME	5.0.2, 5.0.5, 5.4.1	[899]	Biology,bioinformatics,sequence
MentaLiST	0.1.3	[900]	Biology, phylogenetics
Meraculous	2.0.5	[901]	Biology,NGS
Mercurial	4.8.2	[902]	Revision Control
merge_peaks	0.1.0	[903]	Workflow
Merlin	1.1.2	[904]	Biology,SNP
Merqury	1.1, 1.3	[905]	Phylogenetics
Meryl	1.0	[906]	Phylogenetics
MeShClust	1.2.0	[907]	Biology
Meshroom	2019.2.0	[908]	Phylogenetics
MET	10.0	[909]	Meteorology, Models, Verification
Meta-Marc	1.0.0	[910]	Phylogenetics
Meta-Tissue	0.4	[911]	Biology, genetics
MetaBAT	0.32.4, 2.13	[912]	Biology, genomics
MetaBCC-LR	2.0.0	[913]	Biology, Metagenomics, Binning
Metabin	1.0	[914]	Genomics, bioinformatics, metagenomics
metabolic	4.0	[915]	Phylogenetics
MetaCherchant	0.1.0	[916]	Biology, phylogenetics
MetaCluster	5.0b	[917]	Biology,bioinformatics,genomics
MetaCompare	20181016	[918]	Phylogenetics
metacrast	20200309	[919]	Phylogenetics
MetaGeneMark	2.10, 3.26	[920]	Biology,genomics
METAL	20110325	[921]	Biology, ngs, genomics
MetaLAFFA	1.0.0	[922]	Phylogenetics
MetaMaps	20201207	[923]	Phylogenetics
METANNOT	20171129	[924]	Phylogenetics
Metaphlan	3.0.14, 3.0.3, 3.1.0	[925]	Phylogenetics
MetaPhlAn2	2.7.7	[926]	Biology, phylogenetics
MetaPhysicl	1.0.0	[927]	Math, Astronomy, Numerical Simulation
MetaSV	0.5.4	[928]	Biology, phylogenetics, NGS
MetaVelvet	1.2.06	[929]	Computational Biology, genomics
metaWRAP	1.2	[930]	Phylogenetics
Metaxa2	2.1.1, 2.1.3	[931]	Biology,bioinformatics,ngs,sequencing
MethylDackel	0.5.0, 0.6.1	[932]	Phylogenetics
methylpy	1.2.9	[933]	Biology, Phylogenetics
Metilene	0.2.8	[934]	Biology, genomics, methylation
METIS	5.1.0	[935]	Software
Mfannot	20180405	[936]	Biology, phylogenetics
mfold	3.6	[937]	Bioinformatics,structure,RNA
mg-rast	20150919	[938]	Biology, genomics
MGEfinder	1.0.5	[939]	Phylogenetics
MGERT	1.0.1	[940]	Phylogenetics
MGEScan	20160416	[941]	Biology, genomics
MGLTools	1.5.7	[942]	Biology, Molecular Biology, Visualization
MHAP	1.6	[943]	Biology, sequencing
MHCflurry	1.4.3	[944]	Phylogenetics
MIA	20130201	[945]	Biology, ngs
MicrobeAnnotator	2.0.5	[946]	microbial annotation, biology
MIDAS	1.3.2, 20160830	[947]	Biology, phylogenetics
MIGRATE-N	4.2.14, 4.4.4, 5.0.4	[948]	Biology,bioinformatics,population genetics
mIGRATE-N	4.2.14	[949]	Biology, phylogenetics
Mikado	2.3.3	[950]	Biology, Genetics, Transcripts, Pipeline
MIKE	1.0	[951]	Environment,water,modeling
Minced	0.2.0	[952]	Biology, genomics
Minia	3.2.6	[953]	Phylogenomics, biology
Miniasm	0.2-r168, 0.3-r179	[954]	Biology, phylogenetics
MiniCaller	20161201	[955]	Biology,bioinformatics,ngs,phylogenetics
minigraph	0.15	[956]	Phylogenetics
minimac	1-20130717, 3-20150727	[957]	Biology, NGS,
minimac2	2-20140915	[958]	Biology, NGS,
Minimap	2.17, 2.18, 2.21	[959]	Biology, phylogenetics
minimap	2.12, 2.1t, 2.9-r720	[960]	Biology, phylogenetics
minimap2	2.24	[961]	Phylogenomics, biology
Minipolish	0.1.3	[962]	biology, genomics
MinkowskiEngine	0.5.3	[963]	Machine Learning, Deep Learning
MinPath	1.4	[964]	Biology, phylogenetics
MIRA	4.0.rc1, 4.9.6, 5rc2	[965]	Biology,bioinformatics,genomics,assembly
miRanda	1.9	[966]	Phylogenetics
miRBShunter	0.2	[967]	Phylogenetics
mirdeep	0.1.0, 0.1.1, 2.0.1.3	[968]	Phylogenetics
miRDP2	1.1.4	[969]	Biology, Genomics
Mireap	0.20	[970]	Biology
miRge	2.0	[971]	Phylogenetics
Misa	1.0	[972]	Biology, bioinformatics, genomics
MISO	0.5.3	[973]	Biology,bioinformatics,ngs,sequencing,rna-seq
MITE-Hunter	20111101	[974]	Biology, phylogenetics
MITObim	1.9.1	[975]	Phylogenetics
MitoFinder	1.0.2, 1.1, 1.4	[976]	Phylogenetics
mitohifi	2.2	[977]	genomics, sequencing
MitoPhAST	3.0	[978]	Phylogenetics
Mitsuba2	2.2.1	[979]	Rendering
MiXCR	2.1.8, 3.0.13	[980]	Biology, phylogenetics
MixMHC2pred	1.2	[981]	Phylogenetics
MixMHCpred	2.0.2	[982]	Phylogenetics
mixmogam	20190322	[983]	Phylogenetics
MKL	2018.1.163, 2019.1.144, 2020.0.166	[984]	Programming, development, library, math, intel
mlcoalsim	1.9916b	[985]	Biology, phylogenetics
Mlcoalsim	1.9916b	[986]	Biology, phylogenetics
mlpack	3.4.2	[987]	Library
mlst	2.15.2	[988]	Phylogenetics
mlstcheck	2.1	[989]	Phylogenetics
MMSEQ	1.0.8	[990]	Biology,bioinformatics,genomics
MMseqs2	11, 12	[991]	Phylogenetics
MMvec	1.0.5, 1.0.6	[992]	Metabolomics
MNEtools	0.22.0	[993]	Phylogenetics
MOABS	1.2.9, 1.3.2, 1.3.4	[994]	Biology, ngs
mobsuite	3.1.0	[995]	Sequencing, biology
MOCCASIN	0.25	[996]	Phylogenetics
MODELLER	9.14, 9.23	[997]	Biology,bioinformatics,modelling,structure
MODELTEST	0.1.2, 0.1.7	[998]	Biology, phylogenetics
Modulus	21.06, 22.03	[999]	Physics, AI, Neural Network
Molden	5.0	[1,000]	Molecular, Electronic Structure
momi	2.1.19	[1,001]	Phylogenetics, biology
monai	0.8, 0.8.1, 0.9.0	[1,002]	Data Science in Healthcare
MONAI label	0.3.2	[1,003]	Data Science in Healthcare
MongoDB	4.0.3	[1,004]	Database
Moni	0.2.0	[1,005]	Phylogenomics, biology
mono	5.18	[1,006]	Linux, runtime
Monolix	4.3.2	[1,007]	Modeling, pharmacokinetics
MOOSE	20200316, 20200722, 20210726	[1,008]	Physics, simulation
Mosaic	1.7.4	[1,009]	Phylogenetics
MOSAIK	2.1.33, 2.2.3, 2.2.30	[1,010]	Biology,bioinformatics,short read alignment
Mosdepth	0.2.3, 0.3.1	[1,011]	Biology, phylogenetics
Mothur	1.38.1, 1.41.3, 1.46.1	[1,012]	Biology, microbial ecology
MotionCor2	1.2.3, 1.3.1	[1,013]	Motion Correction
mOTU	1.1	[1,014]	Biology, bioinformatics, genomics
mOTUs	2.5.1	[1,015]	Phylogenetics
MountainSort	0.9.0	[1,016]	Library
MP-EST	1.4	[1,017]	Biology,bioinformatics,ngs,sequencing
MPACK	0.8.0	[1,018]	Library
MPB	1.5	[1,019]	Library, math
MPBoot	1.1.0	[1,020]	Biology, phylogenetics
MPFR	3.1.6	[1,021]	Library, math
mpinterfaces	20170613	[1,022]	DFT
MrBayes	3.2.4, 3.2.5, 3.2.6	[1,023]	Application, biology, phylogenetics
MRIcroGL	20201102, 20210327, 20211006	[1,024]	Biology, mri, imaging
MRIcron	201306, 20161012, 20190911	[1,025]	Biology, mri, imaging
mriqc	0.11.0, 0.16.1, 22.0.1	[1,026]	MRI, imaging, biology
MRtrix	3.0.1, 3.0.3, 3.0rc2	[1,027]	Biology, mri, imaging
ms	20171108	[1,028]	Phylogenetics
ms-dial	4.4.8	[1,029]	Biology, bioinformatics, metabolomics
msfinder	3.52	[1,030]	Biology, Metabolomics
mSINGS	20180810	[1,031]	Phylogenetics
MSMC-Tools	20190614	[1,032]	Phylogenetics
msprime	0.7.4	[1,033]	Phylogenetics
MstatX	1.0	[1,034]	Biology, phylogenetics
MSTmap	1.0	[1,035]	Phylogenetics
msvar	1.3	[1,036]	Biology,bioinformatics,population genetics
MTG2	2.15	[1,037]	Phylogenetics
mTR	20210526	[1,038]	Biology, Genomics
Mugsy	1.2.3	[1,039]	Biology, phylogenetics
MultiQC	1.12, 1.7	[1,040]	Biology, bioinformatics, CHiP-Seq
MUMmer	3.23, 4.0.0beta2	[1,041]	Biology,bioinformatics,genomics
MUSCLE	3.8.31	[1,042]	Biology, bioinformatics, alignment
MuSE	1.0rc	[1,043]	Phylogenetics
Musket	1.1	[1,044]	Biology, genomics, ngs
MuTect	1.1.4, 1.1.7	[1,045]	Biology,genomics
MutSig	1.4, 1.41	[1,046]	Biology,genomics
mvftools	20191124	[1,047]	Phylogenetics
MZMine	2.41, 2.52, 2.53	[1,048]	Biology, bioinformatics, spectrometry, NMR
NAMD	2.14, 2.14b2, 3.0 Alpha	[1,049]	Molecular Dynamics
NANO	2.8.2	[1,050]	Text Editor
nanocomp	1.17.0	[1,051]	Programming, python, sequencing
NanoCount	0.2.1	[1,052]	Phylogenetics
Nanodisco	1.0.3	[1,053]	Phylogenetics
Nanofilt	2.7.1	[1,054]	Phylogenetics
NanoPlot	1.30.1	[1,055]	Phylogenetics
Nanopolish	0.11.1, 0.13.2, 20171006	[1,056]	Biology
nanostripper	0.1	[1,057]	Phylogenetics, biology
NanoSV	1.2.0, 1.2.3, 1.2.4	[1,058]	Biology, genomics
NanoVar	1.3.9	[1,059]	Phylogenetics
Napari	0.3.8, 0.4.7	[1,060]	Phylogenetics
NBODY	6	[1,061]	Astronomy
NCBI BLAST+	2.7.1, 2.8.1, 2.9.0	[1,062]	Biology, bioinformatics
NCBI C++ Toolkit	12.0.0, 21.0.0, 7.0.0	[1,063]	Biology,bioinformatics,NCBI,programming,library,cpp
NCBI GenBank Tools	20140130	[1,064]	Biology,bioinformatics,NCBI,GenBank
ncbi-vdb	2.6.3, 2.8.2	[1,065]	SRA toolkit library
nccl	20.11	[1,066]	Development, library, communication, nvidia
ncftp	3.2.5	[1,067]	File transfer
NCL	6.1.2, 6.3.0	[1,068]	Atmosphere Science
NCO	4.2.1, 4.4.3	[1,069]	Data Analysis
ncview	2.1.2, 2.1.7	[1,070]	Data Visualization
NECAT	202001019	[1,071]	Phylogenetics
Necklace	1.00	[1,072]	Biology, phylogenetics
NeEstimator	2.1	[1,073]	Biology, Bioinformatics
nemo	1.0.0rc1, 1.0.1, 1.2.0	[1,074]	AI, machine learning
neovim	0.2.0	[1,075]	Editor, text, ide, vim
NetCDF	4.3, 4.3.3, 4.4.3	[1,076]	Data, exchange
NetCDF-C	4.7.4, 4.8.1, 4.9.0	[1,077]	Data, exchange
NetCDF-F	4.5.4	[1,078]	Data, exchange
NetCDF-Fortran	4.4.3, 4.4.4	[1,079]	Data, exchange
NetCDF-FORTRAN	4.5.3	[1,080]	Data, exchange
NetLogo	5.3.64, 6.1.1, 6.2.0	[1,081]	Modeling
NEURON	7.7.2, 8.0.0, 8.2.1	[1,082]	Biology, neuroscience
Newbler	2.7, 2.8, 2.9	[1,083]	Biology,bioinformatics,ngs,454,assembly,denovo
newick-utils	1.6	[1,084]	Biology, bioinformatics, genomics, phylogenetics
newick_utils	1.6, 1.7	[1,085]	Biology, phylogenetics
NewTargets	20210215	[1,086]	Bioinformatics
NextDenovo	2.4.0	[1,087]	Phylogenetics
Nextflow	21.04.0, 21.10.6, 22.04.5	[1,088]	Biology, bioinformatics, workflow
NextGenMap	0.5.5	[1,089]	Phylogenetics
NextPolish	1.3.1	[1,090]	Phylogenetics
Nextstrain	1.16.1	[1,091]	Phylogenetics
nf-core	1.12.1, 2.1	[1,092]	Biology, bioinformatics, workflow
NGC CLI	2.10.1	[1,093]	Command Line Interface
NGmerge	0.3	[1,094]	Phylogenetics
ngmlr	0.2.6, 0.2.7	[1,095]	Biology, phylogenetics
ngs-bits	0.1	[1,096]	Biology, sequencing
NGS-SDK	1.2.4, 1.3.0	[1,097]	Biology,bioinformatics,ncbi,sdk,library
ngscheckmate	1.0	[1,098]	Phylogenetics
ngstools	20150816	[1,099]	Biology, ngs
nilearn	0.7.0, 0.9.0	[1,100]	Phylogenetics
nimare	0.0.5	[1,101]	neuroimaging
Nipype	1.6.0, 1.7.0, 1.8.0	[1,102]	Biology,bioinformatics,neuroscience,imaging
nlp	1.1, 1.2	[N/A]	Machine Learning
nlr-annotator	0.7	[1,103]	Phylogenetics
NLR-Parser	1.0	[1,104]	Phylogenetics
NMRPipe	7.9, 8.2	[1,105]	Biochemistry
NONMEM	7.3.0, 7.4.4	[1,106]	Modeling
nonpareil	3.3.4	[1,107]	Phylogenetics
Novoalign	2.08.02, 3.00.02	[1,108]	Biology,bioinformatics,ngs
NOVOPlasty	3.7, 4.2, 4.3	[1,109]	Phylogenetics
nPhase	1.1.3	[1,110]	Bioinformatics,pipeline,phasing,polyploid
npScarf	1.7	[1,111]	Phylogenetics
nQuire	20180405	[1,112]	Phylogenetics
Nsight	2022.1	[1,113]	GPU, profiler, tools
Nsightsys	2022.2.1	[1,114]	GPU, profiler, tools
nt	20220404	[1,115]	sequencing, neuroscience
ntEdit	1.2.1	[1,116]	Phylogenetics
nubeamdedup	20200907	[1,117]	Phylogenetics
NucDiff	2.0.3	[1,118]	Phylogenetics
NucleoATAC	0.3.1	[1,119]	Biology, bioinformatics
Nullarbor	1.41	[1,120]	Biology, phylogenetics
Numba	0.36.2	[1,121]	Compiler
NUMBA	0.43.1, 0.48.0	[1,122]	Phylogenetics
NUPACK	3.2.2	[1,123]	Phylogenetics
nvhpc	11.1, 21.7	[1,124]	Language, development, library, math, nvidia
nVidia HPC Compilers	20.11	[1,125]	Compilers
NWChem	6.8	[1,126]	Chemistry
NxTrim	0.4.1	[1,127]	Biology, bioinformatics, ngs
Oases	0.2.08	[1,128]	Biology,ngs,assembler
OCaml	4.02.3	[1,129]	Language, scripting, development
OCOCO	0.1.2.6	[1,130]	Biology, phylogenetics
octave	6.4.0	[1,131]	Numerical Computation
odgi	0.6	[1,132]	Phylogenetics
Olego	1.1.2, 1.1.5, 1.1.6	[1,133]	Biology,bioinformatics,ngs,rna-seq
OmicsBox	1.1.78	[1,134]	Image Processing
OMindel	20180129	[1,135]	Phylogenetics
omniCLIP	0.1.0	[1,136]	Phylogenetics
OMNIVERSE	beta211004	[1,137]	NVIDIA Omniverse
OMSV	1.0.1	[1,138]	Phylogenetics
ONT-Bonito	0.0.5, 0.1.5	[1,139]	Phylogenetics
ont_fast5_api	2.0.1, 4.0.2	[1,140]	phylogenetics
ont_tutorial_cas9	20190705	[1,141]	Phylogenetics
open-cravat	2.0.1	[1,142]	Bioinformatics, genomics
open3d	0.13.0	[1,143]	Phylogenetics
OPENACC	16.7	[1,144]	Programming, Accelerator toolkit
OpenBabel	2.3.2, 2.4.1, 3.1.1	[1,145]	Biology, bioinformatics
OpenBLAS	0.2.20	[1,146]	Programming,library
OpenCL	18.1.0.013	[1,147]	Phylogenetics
OpenCV	4.5.2	[1,148]	Library
OpenFOAM	4.1, 5.0, 8.0	[1,149]	Computational Fluid Dynamics
OPENMM	7.4.2, 7.5	[1,150]	Computational Chemistry, Molecular Dynamics
OpenMM	7.4.2, 7.5.0, 7.6.0	[1,151]	Computational Chemistry, Molecular Dynamics
OpenMPI	4.0.4, 4.0.5, 4.1.1	[1,152]	Parallel Programming, development, MPI, library
OpenNeuro	3.17.4, 3.37.4	[1,153]	Biology, data
OpenPIV-python	0.21.2	[1,154]	Python, imaging
OpenPIV-python-gpu	20190506-gpu	[1,155]	Python, imaging
OpenSim	4.3	[1,156]	Phylogenetics
OpenSlide	3.4.1	[1,157]	Imaging
OptiType	1.3.1	[1,158]	Biology, phylogenetics
Orange3	3.3.6	[1,159]	Data Mining
ORCA	4.0.1.2	[1,160]	Molecular, Electronic Structure
OrganellePBA	20180904	[1,161]	Phylogenetics
OrthoFiller	1.1.4	[1,162]	Phylogenetics
OrthoFinder	1.1.10, 2.3.11, 2.5.2	[1,163]	Biology, ngs
Orthofisher	0.1.2	[1,164]	Biology, Genetics
Orthograph	0.6.3	[1,165]	Orthology
Orthologer	2.2.0	[1,166]	Biology,
OrthoMCL	2.0.3, 2.0.7	[1,167]	Biology,genomics
osprey	1.1.0	[1,168]	MRS,matlab,neuroscience
OTB	5.8.0	[1,169]	Geospatial Data Modeling
p4est	1.1, 2.8	[1,170]	Library
p4vasp	0.3.29, 0.3.30	[1,171]	Molecular, Electronic Structure
p53MH	20020901	[1,172]	Biology, DNA-sequencing
p7zip	9.20.1	[1,173]	Archiver
PacBio	10.2.0.133434, 11.0.0.146107, 7.0.1	[1,174]	Biology, bioinformatics, ngs, pacbio, smrtlink
Package-GFE	20150701	[1,175]	Biology,genomics
PALADIN	1.3.1	[1,176]	Biology, phylogenetics
PALES	122	[1,177]	Physics
PAML	4.8a, 4.9a, 4.9h	[1,178]	Biology, phylogenetics
Pandaseq	20140808, 20150627	[1,179]	Biology,bioinformatics,ngs,sequencing
Pandoc	2.2.2.1	[1,180]	Converter
pangolin	2	[1,181]	Phylogenetics
panseq	3.2.1	[1,182]	Phylogenetics
panX	1.6.0	[1,183]	Phylogenetics
PAPI	5.5.1, 5.7.0	[1,184]	Programming interface, performance analysis
parabricks	3.5.0, 3.7.0	[1,185]	Phylogenetics
parallel	20150122, 20170322	[1,186]	Shell, process management
paralyzer	1.5	[1,187]	Phylogenetics
ParaView	5.4.1, 5.7.0, 5.9.1.1	[1,188]	Data Analysis
ParaView Server	5.10.1	[1,189]	Data Analysis
ParGenes	1.2.0	[1,190]	Phylogenetics
ParlAI	1.3.0, 1.5.0	[1,191]	Phylogenetics
Parsnp	1.2, 1.5.0, 1.6.2	[1,192]	Biology, phylogenetics
PartitionFinder	2.0.0-pre-20160513, 2.1.1-20161205, 2.1.1.0	[1,193]	Biology,phylogenetics,evolution
PASA	2.0.2-r20151207, 2.2.0-r20171013, 2.4.1	[1,194]	Biology, bioinformatics, genomics, ngs
Pascal	3.0.0	[1,195]	Compiler, Programming
PASTA	0.2.0, 1.7.8, 20160616	[1,196]	Biology, sequence alignment
PATHd8	1.0	[1,197]	Biology, phylogenetics
pathoscope	2.0.7	[1,198]	Sequencing, Genomics, Biology
PATRIC	1.034	[1,199]	Machine Learning
PAUDA	1.0.1	[1,200]	Biology,bioinformatics,ngs,phylogenetics
PAUP	4.0a166, 4.0a168, 4.0b10	[1,201]	Bioinformatics, Phylogenetics
PB-Assembly	0.0.6, 0.0.8	[1,202]	Biology,bioinformatics,ngs,sequencing,pacbio
pbalign	20160921, 20161221	[1,203]	Biology, bioinformatics
PBCCS	5.0.0	[1,204]	Phylogenetics
pbcore	1.7.1	[1,205]	Biology,bioinformatics
PBGCpp	1.9.0	[1,206]	Phylogenetics
pbipa	1.8.0	[1,207]	Phylogenetics, biology
PBJelly	15.8.24	[1,208]	Biology,bioinformatics,ngs
pbmm2	1.3.0	[1,209]	Phylogenetics
pbrt	20181017	[1,210]	Phylogenetics
pbsmrtpipe	0.63.0	[1,211]	Biology,API
pbtranscript-tofu	20150317, 20160119	[1,212]	Biology, bioinformatics, ngs, pacbio
PCIT	2014	[1,213]	Bioinformatics
PCRE	8.38, 8.39	[1,214]	Perl, library
PDA	1.0.3	[1,215]	Biology, phylogenetics
pdb2pqr	2.1.0	[1,216]	Protein, modeling, pdb
PeakSplitter	1.0	[1,217]	Biology, bioinformatics, CHiP-Seq
PEAR	0.9.2	[1,218]	Biology, genomics, ngs
peneasy	20150530	[1,219]	Physics
PennCNV	1.0.5	[1,220]	Phylogenetics
Perl	5.16.0, 5.20.0, 5.24.1	[1,221]	Programming,scripting,language
PerM	0.4.0	[1,222]	Biology,bioinformatics,ngs,mapping
PETSc	3.8.1, 3.8.3, 3.8.4	[1,223]	Math, Numerical Solvers
PfamScan	1.3, 1.5	[1,224]	Biology, genomics
PGAP	20220414	[1,225]	Biology, Genomics, Annotation, Pipeline
PGDSpider	2.0.9.0, 2.1.1.5	[1,226]	Biology, NGS
pggb	0.2.0, 20201106, 20210121	[1,227]	Phylogenetics
PhaME	1.0.3	[1,228]	Phylogenetics
pharmcat	1.8.0	[1,229]	Biology, Bioinformatics, Phylogenetics
PHASE	2.1.1	[1,230]	Phylogenetics
PHAST	1.5	[1,231]	Biology,phylogeny
Phenix	1.10.2155, 1.17.1, 1.8.1069	[1,232]	Crystallography
PHI	3.1.1, 3.1.2b, 3.1.6	[1,233]	Calculations
PhiSpy	3.2	[1,234]	Phylogenetics
PHITS	2.76, 2.82, 2.84	[1,235]	Physics
PHLAWD	20170427	[1,236]	Biology, phylogenetics
PhotoScan	1.4.1, 1.4.5	[1,237]	Image Processing
Photutils	0.5	[1,238]	Astronomy, photometry
PHYLDOG	20130116-dbg	[1,239]	Biology,bioinformatics,phylogenetics
PHYling	1.0	[1,240]	Biology, Phylogenetics, Markers, Genomics
PHYLIP	3.696	[1,241]	Biology,phylogenetics
PhyloAcc	1.0	[1,242]	Phylogenetics
PhyloBayes	3.3f	[1,243]	Biology,bioinformatics,phylogenetics
phyloFlash	3.3b4	[1,244]	Phylogenetics
phylonet	3.5.7, 3.8.2	[1,245]	Biology, phylogenetics
PhyloParser	20180404	[1,246]	Phylogenetics
PhyloPhlAn2	0.41	[1,247]	Phylogenetics
phylopypruner	1.2.3	[1,248]	Phylogenetics
PhyloSift	1.1	[1,249]	Biology, genomics, phylogenetics, taxonomy
phyloTF2	20210726	[1,250]	Bioinformatics, genomics, alignment
Phyluce	20180727, 20190308, 20191015	[1,251]	Biology,bioinformatics,ngs,sequencing
PhyML	3.0, 3.1	[1,252]	Biology,bioinformatics,phylogenetics
phynd	20200409	[1,253]	Phylogenetics
Physher	1.0.2	[1,254]	Phylogenetics
PHYUTILITY	2.7.1	[1,255]	Biology, bioinformatics
Phyx	1.1	[1,256]	Phylogenetics
PIA2	20180305	[1,257]	Biology, phylogenetics
Picard-tools	2.5.0, 2.9.0, 2.9.2	[1,258]	Biology,bioinformatics,ngs
PICRUSt	1.1.3, 1.1.4, 2.3.0b	[1,259]	Biology, phylogenics
PICSL	1.3	[1,260]	Imaging, Atlas, Segmentation
Piggy	20171220	[1,261]	Biology, bioinformatics, ngs
Pigz	2.4	[1,262]	Compression
PILON	1.22, 1.24	[1,263]	Biology, bioinformatics, ngs, phylogenetics
Pindel	0.2.5b8	[1,264]	Biology, phylogenetics
pipe-clip	1.1.0	[1,265]	Biology,NGS
pipits	1.3.6, 1.4.0	[1,266]	Biology, sequencing
Piranha	1.2.1	[1,267]	Biology,phylogenetics
PlantTribes	1.0.4	[1,268]	Phylogenetics
plasflow	1.1	[1,269]	Biology, phylogenetics
PLAST	1.0, 2.3.2	[1,270]	Biology,bioinformatics
platanus	1.2.4	[1,271]	Phylogenetics
Platypus	0.8.1	[1,272]	Biology,bioinformatics,ngs
PLEK	1.2.2	[1,273]	Biology, phylogenetics
Plink	1.90b3.39, 2.00a2, 2.00a3LM	[1,274]	Biology,bioinformatics,genomics,phylogenetics
plinkseq	0.10	[1,275]	Biology, bioinformatics, library
plotsr	0.5.4	[1,276]	genomics, biology
PLUMED	2.7.3, 2021.2	[1,277]	Computational Chemistry, Molecular Dynamics
pod5	20220621	[1,278]	sequencing
PolyGembler	1.0	[1,279]	Phylogenetics
PolyPHen	2.2.2.r405b	[1,280]	Biology, genomics
polyply	1.3.0	[1,281]	Phylogenetics, Biology
pomoxis	0.1.11, 0.2.5, 0.3.2	[1,282]	Biology, phylogenetics
popcorn	20211104	[1,283]	Phylogenetics, biology
PopLDdecay	3.40	[1,284]	Phylogenetics
popoolation	1.2.2	[1,285]	Biology, phylogenetics
Porechop	0.2.4	[1,286]	Phylogenetics
Poretools	0.6.1	[1,287]	Phylogenetics
portcullis	1.2.3	[1,288]	Phylogenetics
PosiGene	20171113	[1,289]	Biology, phylogenetics
POV-Ray	3.7	[1,290]	3D Graphics
pplacer	1.1.alpha19	[1,291]	Biology, bioinformatics, phylogenics, taxonomy
PRANK	170427, 20150803	[1,292]	Biology, bioinformatics, alignment
Predector	20201110	[1,293]	Phylogenetics
preplot	14.0.2	[]
Preseq	0.0.4	[1,294]	Biology, bioinformatics, ngs
PRICE	1.2	[1,295]	Biology, bioinformatics, ngs
Primer3	2.3.4	[1,296]	Biology,bioinformatics,genomics
primus	1.8.0	[1,297]	Biology, phylogenetics
PRINSEQ	0.20.4	[1,298]	Biology, sequencing
PRINSEQ++	1.2	[1,299]	Phylogenetics
ProbABEL	0.4.2, 0.4.3, 0.4.5	[1,300]	Genomics, bioinformatics, gwas
probalign	1.4	[1,301]	Biology, bioinformatics, ngs
Processing	3.4	[1,302]	Java, language, programming, visual
Prodigal	2.6.2, 2.6.3	[1,303]	Biology, genomics
ProDy	2.0	[1,304]	Phylogenetics
Program Database Toolkit	3.20, 3.22, 3.24	[1,305]	Language, development, performance analysis
PROJ	4.9.3, 5.1.0, 8.0.1	[1,306]	Library, geospatial, cartography
Prokka	1.12, 1.14.6	[1,307]	Biology, bioinformatics, genomics, assembly
Proovread	1.03rcl, 2.12, 2.13	[1,308]	Biology, genomics, ngs
ProSplign	1.0.0	[1,309]	Phylogenetics
Protege	5.1.0	[1,310]	Ontology
Proteinortho	4.26, 5.11, 5.16	[1,311]	Biology, genomics
ProtExcluder	1.2	[1,312]	Biology, phylogenetics
ProtHint	2.6.0	[1,313]	Biology, bioinformatics, genomics
protobuf	2.5.0, 3.5.1	[1,314]	Google, libraries
PROVEAN	1.1.5	[1,315]	Biology, genomics
PRSice	2.3.3	[1,316]	Phylogenetics
Pseudofinder	1.0	[1,317]	Phylogenetics
PsiCLASS	1.0.1	[1,318]	Phylogenetics
PSMC	0.6.5	[1,319]	Phylogenetics
psRobot	1.2	[1,320]	Phylogenetics
Pufferfish	20200417	[1,321]	Phylogenetics
PureCLIP	1.1.1	[1,322]	Phylogenetics
Purge_Dups	1.0.1	[1,323]	Phylogenetics
purge_haplotigs	1.1.2	[1,324]	Sequencing, bioinformatics, biology
pyani	0.2.10	[1,325]	Phylogenetics
Pybedtools	0.8.2	[1,326]	Phylogenetics
PyBSASeq	20200623	[1,327]	Phylogenetics
PyCharm	2018.3	[1,328]	Editor, ide, programming, python
pychopper	2.5.0, 2.7.1	[1,329]	Phylogenetics, sequencing
PyCogent	1.9	[1,330]	Biology, genomics
PyDeface	2.0.0	[1,331]	MRI, imaging
pyEGA3	3.4.1	[1,332]	Biology, Genomics, Utility
PyEXR	0.3.10	[1,333]	Programming, python, openexr
Pyfaidx	0.5.2	[1,334]	Biology, bioinformatics, ngs, sequencing
pyfasta	0.5.2	[1,335]	Phylogenetics
pygot	20170518	[1,336]	Biology, phylogenetics
pyhdf	0.9.0	[1,337]	Library, hdf4
PyHIST	1.0	[1,338]	Biology, Histology, Image segmentation
PyPHLAWD	20180416, 20190414	[1,339]	Biology, phylogenetics
Pyroms	1.0	[1,340]	Oceanography
PyRosetta	r56324	[1,341]	Biology,structure,modeling
pyrpipe	0.0.3	[1,342]	Phylogenetics
Pysamstats	1.1.2	[1,343]	Phylogenetics
PySLURM	18.08.04	[1,344]	SLURM
Python	3.6.3, 3.6.5, 3.8	[1,345]	Language, scripting, development
Python-core	3.6.5, 3.7, 3.8	[1,346]	Language, scripting, development
Python2	2.7.11	[1,347]	Language, scripting, development
PyTorch	1.11.0, 1.9.0	[1,348]	Library, math
pytorch	1.7.1, 1.8.1, 1.9.0	[1,349]	Library, math
PyVCF	0.6.0, 0.6.8	[1,350]	Biology, phylogenetics
PyVista	0.26.1	[1,351]	Phylogenetics
pyweka	0.3.18	[1,352]	Phylogenetics
QAPA	1.3.1	[1,353]	Phylogenetics
qcat	1.1.0	[1,354]	Phylogenetics
qctool	2.0.1	[1,355]	Phylogenetics
QD	2.3.22	[1,356]	Library,c,math
QDD	3.1.2	[1,357]	Biology, genomics, ngs
QGIS	2.18.0, 3.14.0	[1,358]	GIS
QIIME	1.9.1	[1,359]	Biology, bioinformatics, metagenomics
QIIME2	2020.8, 2021.11, 2021.4	[1,360]	Biology, bioinformatics, metagenomics
QMCPACK	3.4.0	[1,361]	Library
QRNA	2.0.4	[1,362]	Phylogenetics
QT	4.8.3, 5.12.9, 5.15.4	[1,363]	UI Framework
QTL-seq	2.2.2	[1,364]	Biology, Sequencing, Pipeline
QTLtools	1.2, 1.3.1	[1,365]	Phylogenetics
Quake	0.3	[1,366]	Biology, sequencing
QualiMap	2.1.2	[1,367]	Biology,sequence alignment
Quantas	1.0.4, 1.0.8, 1.0.9	[1,368]	Biology,bioinformatics,ngs
quantisnp	2	[1,369]	bioinformatics, genomics
QuartetScores	1.0.0	[1,370]	Phylogenetics
QUAST	4.4, 5.0.0, 5.0.2	[1,371]	Biology, bioinformatics, ngs, sequencing, rna-seq
quickmerge	0.3	[1,372]	Phylogenetics
Quickquartet	1.0.0	[1,373]	Biology,bioinformatics,ngs
QUIP	20201029, 20210626	[1,374]	Phylogenetics
QuorUM	1.0.0	[1,375]	Biology
R	4.0, 4.1, 4.2	[1,376]	Statistics
r-index	20190711	[1,377]	Phylogenetics
r8s	1.8, 1.81	[1,378]	Phylogenetics
RACA	0.9.1.1	[1,379]	Biology, ngs
Racon	1.3.3, 1.4.10, 1.4.13	[1,380]	Phylogenetics
RADICAL	0.2	[1,381]	Biology, bioinformatics, genomics
radorgminer	0.9	[1,382]	Genomics, Biology, Sequencing
RaGOO	1.11	[1,383]	Phylogenetics
Ragout	2.3	[1,384]	Genomics
RagTag	1.0.0, 2.0.1	[1,385]	Phylogenetics
rainbow	2.0.4	[1,386]	Biology, sequencing
Rainbowfish	0.1.0	[1,387]	Phylogenetics
RAiSD	2.8	[1,388]	Phylogenetics
Randfold	2.0.1	[1,389]	Biology, RNA
ranger	1.9.3	[1,390]	File Management
rapidsai	21.10, 21.12, 22.04	[1,391]	Data Science
rapidtide	1.9.0	[1,392]	Phylogenetics
RAPSearch	2.24	[1,393]	Biology, phylogenetics
Rascaf	1.0.2	[1,394]	Biology, bioinformatics
RAVE	2.1	[1,395]	Biology, phylogenetics
Raven	1.8.1	[1,396]	assembler
RAxML	8.2.10, 8.2.12, 8.2.8	[1,397]	Application, biology, philogenetics
RAxML-NG	0.9.0, 1.0.2, 1.1.0	[1,398]	Phylogenetics
razers3	3.5.7	[1,399]	Biology, phylogenetics
rbp-maps	0.1.4	[1,400]	Phylogenetics
rclone	1.57.0, 1.58.1	[1,401]	Cloud
Rcorrector	1.0.4	[1,402]	Phylogenetics
RDKit	2020092	[1,403]	Chemiformatics
rDnaTools	0.1.3	[1,404]	Phylogenetics
READemption	1.0.0	[1,405]	Phylogenetics
REAPR	1.0.18	[1,406]	Biology,bioinformatics,assembly
Rebaler	0.2.0	[1,407]	Phylogenetics
reCOGnizer	1.3.3	[1,408]	Phylogenetics
recon	1.08	[1,409]	Biology,sequencing
Redis	2.8.13, 2.8.19	[1,410]	Daemon, data, server
REDItools2	20200701	[1,411]	Phylogenetics
Redundans	0.14a	[1,412]	Biology, phylogenetics
ReFrame	3.2	[1,413]	Hpc, internal
regtools	0.5.2	[1,414]	Biology, RNA-seq, Genitics
RELION	3.0.2, 3.0b, 3.1.0	[1,415]	Biology, imaging
RelocaTE2	2.0.1	[1,416]	Phylogenetics
REMORA	1.8.2, 1.8.3, 1.8.5	[1,417]	System, profiler
REPdenovo	20170222	[1,418]	Biology, phylogenetics
RepeatAnalysis	0.10.0, 0.12.2	[]	Biology, phylogenetics
RepeatAnalysisTools	20210506	[1,419]	Biology, Genomics, Sequencing, Utility
RepeatExplorer	20150506, 20180517	[1,420]	Biology, bioinformatics, ngs
RepeatMasker	4.0.5, 4.0.9, 4.1.1	[1,421]	Biology, bioinformatics
RepeatModeler	1.0.8, 2.0	[1,422]	Biology,bioinformatics
repeatscout	1.0.5	[1,423]	Biology
RepeatSeq	0.8.2	[1,424]	Phylogenetics
reptile	1.1	[1,425]	Biology,NGS,error correction
ResFinder	4.0	[1,426]	Biology, genomics
Resistome	20170111	[1,427]	Phylogenetics
RevBayes	1.0.7, 1.0.9, 1.1.1	[1,428]	Biology, phylogenetics
RFMIX	2.03	[1,429]	Phylogenetics
RGAugury	20220107	[1,430]	Sequencing, biology
RGI	4.2.2, 5.1.1	[1,431]	Phylogenetics
RGIS	20180211, 20180814	[1,432]	RiverGIS
RHash	1.3.3	[1,433]	GNU
RiboCode	1.2.11	[1,434]	Phylogenetics
riboPicker	0.4.3	[1,435]	Biology,sequence
RiboTaper	1.3.1a	[1,436]	Phylogenetics
RIGERJ	2.0.2	[1,437]	Phylogenetics
rMATS turbo	4.1.2	[1,438]	Biology, Sequencing, Genomics
rmats2sashimiplot	2.0.3	[1,439]	Phylogenetics
Rmpi	0.6.9	[1,440]	Statistics, R, mpi
RNAFramework	2.7.2	[1,441]	Biology, RNA, Sequencing
RNAhybrid	2.1.1	[1,442]	Biology, bioinformatics, genomics
RNAmmer	1.2	[1,443]	Biology, RNA-seq
rnaQUAST	1.5.1	[1,444]	Biology,bioinformatics,ngs,sequencing,rna-seq
RNAsalsa	0.8.1	[1,445]	Biology, phylogenetics
rnaseqlib	20150721	[1,446]	Biology, phylogenetics, RNA-seq
RNAstructure	6.3	[1,447]	Biology, sequencing
Roary	3.12.0, 3.4.1	[1,448]	Biology,genomics
ROOT	5.34.17, 6.0, 6.06.02	[1,449]	Data Analysis
ROOTPy	20160323	[1,450]	Data Analysis
Rosetta	2014wk4, 2019.35.60890	[1,451]	Biology,structure,modeling
RoseTTAFold	1.0.0	[1,452]	Phylogenetics
rrnaselector	1.0	[1,453]	Biology, sequencing
RSEG	0.4.8	[1,454]	Biology, bioinformatics, genomics
RSEM	1.2.31, 1.2.7, 1.3.3	[1,455]	Biology,bioinformatics,ngs,sequencing
RSeQC	2.6.4, 3.0.0	[1,456]	Biology,ngs,rna-seq
RStudio	1.4, 2021.09.0, 2022.02.3	[1,457]	Statistics
RTGTools	3.7.1	[1,458]	Biology, NGS
Ruby	2.5.1	[1,459]	Programming,scripting,language
Rust	1.48.0, 1.52.1, 1.62.1	[1,460]	Programming
rvtests	2.1.0	[1,461]	Genomics, Biology, Sequencing
S.A.G.E	6.4.2	[1,462]	Phylogenetics
Sabre	1.0	[1,463]	Phylogenetics
saffrontree	0.1.2	[1,464]	Phylogenetics
Sailfish	0.6.3	[1,465]	Biology,genomics,ngs,rna-seq
Salmon	1.1.0, 1.5.2, 1.8.0	[1,466]	Biology, RNA-seq
SALSA	20171009, 20191001	[1,467]	Biology, ngs, pacbio
Sambamba	0.6.3, 0.6.6, 0.6.9	[1,468]	Biology, NGS
samblaster	0.1.14, 0.1.24	[1,469]	Biology,bioinformatics,ngs,sequencing
sampledock	0.5.1	[1,470]	molecular dynamics, AI
SAMStat	1.08	[1,471]	Biology,bioinformatics,ngs,sequencing
Samtools	1.7, 1.8, 1.9	[1,472]	Biology,bioinformatics,ngs,sequencing
SAS	9.3, 9.4	[1,473]	Statistics, data analysis
Sate	2.2.7	[1,474]	Biology, bioinformatics, phylogenetics
Satsuma	3.0	[1,475]	Phylogenetics
Satsuma2	3.1	[1,476]	Phylogenetics
satsuma2	20161123	[1,477]	Phylogenetics
sc-im	0.8.2	[1,478]	Software, data visualization
Scala	2.11.5, 3.0.1	[1,479]	Programming, language, java
Scalablast	2.4.53	[1,480]	Application, biology, genomics
ScaLAPACK	2.0.2, 2.1.0	[1,481]	Programming,library
scallop	0.10.5	[1,482]	Phylogenetics
Scalpel	0.1.1, 0.5.3	[1,483]	Biology, NGS
Schrodinger Suite	2019-3, 2020-4, 2021-2	[1,484]	Computational Chemistry, Molecular Dynamics
Scipion	1.2	[1,485]	Image Processing
SCIrun	5.0.Z	[1,486]	Phylogenetics
Scoary	1.6.16	[1,487]	Phylogenetics
Scons	2.5.1, 3.1.2	[1,488]	Programming
SCOP	20180311	[1,489]	Biology, Scaffolding, Assembly
Scrappie	1.4.2	[1,490]	Biology, Genomics
SCRATCH-1D	1.0, 2.0	[1,491]	Biology, bioinformatics, ngs
Screen	4.8.0	[1,492]	GNU, Terminal Multiplexer
SCRIPTURE	20101211	[1,493]	Biology, bioinformatics, genomics
Scythe	0.991	[1,494]	Biology, NGS
sdsl	2.1.1	[1,495]	Library, c++
SE-MEI	0.1.0	[1,496]	Phylogenetics
SeCaPr	1.1.12, 2.0.2, 2.1.1	[1,497]	Phylogenetics
Segemehl	0.1.9, 0.3.4	[1,498]	Biology,bioinformatics,ngs,sequencing
segment-liftover	20211021	[1,499]	bioinformatics, biology, genome
SEPP	20160614	[1,500]	Biology, phylogenetics
Seq-Gen	1.3.3	[1,501]	Biology,phylogenetics
seq_crumbs	20150120	[1,502]	Biology, sequence, genomics, utilities
SeqKit	0.10.2, 0.8.0, 2.0.0	[1,503]	Biology, phylogenetics
seqmagick	0.8.4	[1,504]	Biology, bioinformatics
SeqMap	1.0.13	[1,505]	Biology,bioinformatics,sequence,ngs
SEQPower	1.1.1	[1,506]	Genomics, bioinformatics, phylogenetics
SeqPrep	0.5, 1.1	[1,507]	Biology,bioinformatics,ngs,sequencing
seqscreen	3.3	[1,508]	Sequencing, biology
seqtk	1.3, 20140729	[1,509]	Bioinformatics, Genomics, NGS
SEQuel	1.0.1	[1,510]	Biology,bioinformatics,ngs
SequelQC	1.1.0	[1,511]	Phylogenetics
seqwish	0.7, 20190509	[1,512]	Phylogenetics
SeqyClean	1.8.10	[1,513]	Biology,bioinformatics,ngs,sequencing
SeSiMCMC	4.36	[1,514]	Biology, Sequencing
SExtractor	2.19.5	[1,515]	Astronomy
SHAPE-MaP	1.2	[1,516]	Biology, phylogenetics
SHAPEIT	2.12, 2.5	[1,517]	Biology,SNP
SHAPEIT4	4.2.2	[1,518]	Biology, Sequencing, Phasing
ShapeMapper	2.1.3, 2.1.5	[1,519]	Biology, phylogenetics
SHARCGS	1.2.11	[1,520]	Biology, NGS, de novo assembly
Shasta	0.1.0	[1,521]	Phylogenetics
SHEsisPlus	1.0, 1.01	[1,522]	Biology, genetics
shogun	6.1.3	[1,523]	Phylogenetics
Shortbred	0.9.4	[1,524]	Phylogenetics
SHRiMP	2.2.3	[1,525]	Biology, genomics, ngs
shustring	2.6	[1,526]	Biology, sequencing
SibeliaZ	1.2.2, 1.2.3, 1.2.4	[1,527]	Bioinformatics, genomics, alignment
SICER	1.1	[1,528]	Biology, ChIP-Seq
Sickle	1.200, 1.33	[1,529]	Biology, bioinformatics, ngs
Siesta	3.2, 4.1b2, 4.1b3	[1,530]	Chemistry
SIFT	4.0.3b	[1,531]	Biology,bioinformatics,genomics
SIGffRid	1.1	[1,532]	Phylogenetics
SignalP	4.1c, 5.0b	[1,533]	Biology, phylogenetics
SiLiX	1.2.11, 1.3.0	[1,534]	Phylogenetics
silo	4.7	[1,535]	IO,library
sim4	20121010	[1,536]	Biology, bioinformatics, genomics
Sim4Life	7.0.1	[1,537]	Biology,simulation
Simka	1.5.3	[1,538]	Phylogenetics
SimNIBS	3.2.1	[1,539]	Phylogenetics
SimSeq	4.12.2011	[1,540]	Biology, bioinformatics, ngs, phylogenetics
Simulia	2019	[1,541]	Simulation, visualization
SInC	20140120	[1,542]	Biology, phylogenetics
sine_scan	1.1.1	[1,543]	Phylogenetics
Singularity	3.7.4	[1,544]	Containers
SIPeS	2.0	[1,545]	Biology, bioinformatics, ChIP-Seq
sisl	0.8.3	[1,546]	Physics, Tight-binding
skmer	3.2.1	[1,547]	Phylogenomics, biology
Slamdunk	0.4.1, 0.4.2	[1,548]	Phylogenetics
SLAW	20211217	[1,549]	Chromatography, Spectrometry
Slicer	4.13.0, 4.3.1, 5.0.3	[1,550]	biology,bioinformatics,neuroscience,imaging
slow5tools	0.5.1	[1,551]	biology, sequencing
slurm-drmaa	1.1.2, 1.1.3	[1,552]	Libraries, slurm, api, drmaa
smalt	0.7.6	[1,553]	Application, biology, phylogenetics
SMARTdenovo	20180219	[1,554]	Biology, phylogenetics
smartie-sv	20180308	[1,555]	Phylogenetics
SMC++	1.15.4	[1,556]	Biology, Genomics, Sequencing
Smetana	1.1.0	[1,557]	Phylogenetics
SMR	1.03	[1,558]	Biology, Genomics
SMRT-SV	2.0.0	[1,559]	Biology, bioinformatics, ngs
SMS	1.7	[1,560]	Biology, bioinformatics
Smudgeplot	0.2.4	[1,561]	Phylogenetics
Snakemake	6.4.1, 7.5.0	[1,562]	Biology, bioinformatics, workflow
SNAP	0.15.4, 2.0.0, 20100728	[1,563]	Biology,bioinformatics,sequencing
SNAPE-pooled	20130407	[1,564]	Biology, SNP
SNeP	1.1	[1,565]	Biology,phylogenetics
Sniffles	1.0.11, 1.0.6, 1.0.8	[1,566]	Phylogenetics
Sniffles2	2.0.6	[1,567]	Biology, Bioinformatics
Snippy	20160419, 4.6.0	[1,568]	Biology, phylogenetics
SNP-Pipeline	1.0.1	[1,569]	Biology, phylogenics
SNP-sites	2.0.3	[1,570]	Biology, SNP
snp2hla	1.0.3	[1,571]	Biology, Bioinformatics, Genomics
SnpEff	4.3r, 4.3t, 5.0	[1,572]	Biology,bioinformatics,variant annotation
snpflip	20190515	[1,573]	Biology, Phylogenetics
SNPGenie	20190620	[1,574]	Phylogenetics
SNPhylo	20140701	[1,575]	Biology,phylogenetics
SNPsplit	0.5.0	[1,576]	Biology,bioinformatics,sequencing
SNPTEST	2.5.2	[1,577]	Phylogenetics
SOAPaligner	2.21	[1,578]	Phylogenetics
SOAPdenovo	1.05, 2.04	[1,579]	Biology,ngs
SOAPdenovo-Trans	1.01, 1.03	[1,580]	Biology,ngs
SOAPec	2.03	[1,581]	Biology, phylogenetics
SOAPnuke	2.1.0	[1,582]	Phylogenetics
SOAPsplice	1.10	[1,583]	Biology,ngs
SODA	20200930	[1,584]	Biology
SOLAR	8.4.2	[1,585]	Phylogenetics
SomaticSeq	3.6.2	[1,586]	Phylogenetics
SortaDate	20190705	[1,587]	Phylogenetics
SortMeRNA	2.1, 4.0	[1,588]	Biology, sequencing, NGS
SourceTracker2	2.0.1	[1,589]	Phylogenetics
Sourmash	2.0.1	[1,590]	Phylogenetics
SoX	14.4.2	[1,591]	Phylogenetics
SpaceRanger	1.3.1	[1,592]	Phylogenetics
SPAdes	3.15.3, 3.7.1, 3.8.0	[1,593]	Biology,bioinformatics,ngs
SparCC	201608	[1,594]	Microbial Ecology
Spark	2.2.0, 3.1.1	[1,595]	Spark, hadoop
sparsehash	2.0.3	[1,596]	Google, API
SPARTA+	2.60	[1,597]	Chemistry
Spec2nii	0.3.4	[1,598]	Phylogenetics
SpeedSeq	0.1.2	[1,599]	Phylogenetics
Spidey	20150922	[1,600]	Biology, genomics, bioinformatics
SpinalCordToolbox	5.4	[1,601]	Phylogenetics
SplAdder	2.4.2	[1,602]	Phylogenetics
SpliceGrapher	0.2.5	[1,603]	Biology, sequencing
SpliceTrap	0.90.5	[1,604]	Biology, bioinformatics, genomics, NGS
SPM	12b, 8, 8r5236	[1,605]	Biology,bioinformatics,matlab
spruceup	2019.2.3	[1,606]	Phylogenetics
Sputnik	1.0	[1,607]	Biology,bioinformatics,repeats
spyder	4.1.4, 5.1.1	[1,608]	IDE, editor, programming, scripting
SQANTI	1.2	[1,609]	Phylogenetics
SQANTI2	5.0	[1,610]	Phylogenetics
SQANTI3	0.1, 1.6, 4.2	[1,611]	Phylogenetics
SQL Developer	4.1.2	[1,612]	Programming, oracle, sql
SQLite	3.33.0, 3.8.8.2	[1,613]	Database
SqueezeMeta	1.4.0, 1.5.2	[1,614]	Phylogenetics
squigglekit	1.0.0	[1,615]	Data Visualization and Analysis, biology
squigglenet	1.0	[1,616]	Sequencing, biology
SRA	2.10.9, 3.0.0	[1,617]	Biology,bioinformatics,sra
sra-human-scrubber	1.1	[1,618]	CSV_categories
SRAssembler	1.0.0	[1,619]	Phylogenetics
SSM	20210511	[1,620]	Phylogenetics
SSPACE	2.0, 3.0	[1,621]	Biology,bioinformatics,ngs
ssr_pipeline	0.951	[1,622]	Biology, DNA sequencing,
Stacks	2.53, 2.55, 20190403	[1,623]	Biology, bioinformatics, genomics, ngs
Staden	1.14.6	[1,624]	Biology, phylogenetics
Stampy	1.0.31	[1,625]	Biology, bioinformatics, sequencing
staphb-toolkit	1.2.0, 1.3.10	[1,626]	Biology
STAR	2.7.5c, 2.7.6a, 2.7.9a	[1,627]	Biology, ngs, rna-seq
STAR-CCM+	14.04.011, 15.02.009, 8.06	[1,628]	Mechanical Engineering
STAR-Fusion	1.1.0, 1.3.1, 1.9.1	[1,629]	Biology, transcriptome
starseqr	0.6.7	[1,630]	Phylogenetics
Stata	10.1, 13	[1,631]	Statistics
stringMLST	0.4	[1,632]	Biology, bioinformatics, CHiP-Seq
Stringtie	1.3.4d, 2.0.4, 2.1.3b	[1,633]	Biology,bioinformatics,ngs,sequencing,alignment
Structure	2.3.3, 2.3.4	[1,634]	Biology,bioinformatics,population genetics
Structure_threader	1.3.10	[1,635]	Utility, Wrapper, Structure
stylegan3	20211028	[1,636]	AI, Image Processing
SU2	7.0.6	[1,637]	Phylogenetics
Subread	1.6.2, 2.0.0, 2.0.3	[1,638]	Biology, sequencing, SNP
Subversion	1.9.7	[1,639]	Revision Control
SUMO	1.13.0, 1.2.0, 1.9.2	[1,640]	Simulation, traffic, engineering
SUNDIALS	2.3.0, 2.5.0, 3.0.0	[1,641]	Math, Numerical Solvers
supercell	20170602	[1,642]	Biology, NGS
SuperCRUNCH	1.2.1	[1,643]	Phylogenetics
Supernova	1.2.1, 2.0.0, 2.1.1	[1,644]	Biology, phylogenetics, ngs
SUPPA	2.3	[1,645]	Phylogenetics
Survival_Kit	6.12	[1,646]	Clinical Biometrics
SURVIVOR	1.0.6	[1,647]	Phylogenetics
SVDetect	0.8b	[1,648]	Biology,ngs,genomics
svim	1.4.2	[1,649]	Biology
svim-asm	1.0.2	[1,650]	Biology
swarm	1.2.11	[1,651]	Data Analysis
Sweed	3.3.2	[1,652]	Biology, phylogenetics
SWIG	2.0.9, 3.0.12, 3.0.8	[1,653]	Library, development, C++, python
SWSC-EN	1.0.0	[1,654]	Phylogenetics
Synima	20210908	[1,655]	Phylogenetics
syri	1.5.4	[1,656]	Phylogenomics, biology
TACO	0.7.3	[1,657]	Phylogenetics
Taiyaki	5.0.1	[1,658]	Phylogenetics
talesf	20160814	[1,659]	Phylogenetics
Tandem-Genotypes	1.4.0	[1,660]	Phylogenetics
Tantan	13	[1,661]	Particle NGS, genomics
Tapestri	2.0.1	[1,662]	Phylogenetics
tapir	20160825	[1,663]	Biology, phylogenetics
TAPIS	1.2.1	[1,664]	Biology, sequencing
TASSEL	5.0, 5.2.20, 5.2.29	[1,665]	Biology,bioinformatics,genomics,wga
TAU	2.23, 2.26, 2.26.3	[1,666]	Library, profiling and optimization
Tax4Fun	0.3.1	[1,667]	Phylogenetics
taxMaps	0.1	[1,668]	Biology, phylogenetics, taxonomy
TaxonKit	0.9.0	[1,669]	Phylogenetics
Taxtastic	0.5.7	[1,670]	Biology, taxonomy
taxtastic	0.9.1	[1,671]	Biology, bioinformatics, phylogenics, taxonomy
tbb	2017_20161128	[1,672]	Library
tcllib	1.18	[1,673]	Library
tcoffee	10.00.r1613, 9.03.r1318	[1,674]	Bioinformatics
TDNAscan	20210304	[1,675]	Phylogenetics
Tecplot 360 EX	2015R1	[1,676]	Plotting, animation, cfd, simulations
tellseq	1.0.0	[1,677]	Sequencing, Phylogenetics
TEMP	20170731	[1,678]	Phylogenetics
TEMP2	0.1.4	[1,679]	Phylogenetics
TensorFlow	2.6.0, 2.7.0, 2.8.0	[1,680]	Library, math
TESS	2.3.1	[1,681]	Biology, bioinformatics, genomics, markov
Test	1.0	[1,682]	Shell
TetGen	1.5.0	[1,683]	Tetrahedral meshes
TEToolkit	1.5.1	[1,684]	Biology, bioinformatics, sequencing
TEtools	20180213	[1,685]	Biology, phylogenetics
Texlive	20191127, 2020	[1,686]	Formatting, typesetting, document preparataion
TGICL	2.1	[1,687]	Biology,bioinformatics,ngs,sequencing
TGSGapCloser	1.0.3	[1,688]	Phylogenetics
the_silver_searcher	2.2.0	[1,689]	Search
Theano	1.0.4	[1,690]	Library, math, gpu
Themisto	0.2.0, 1.1.0	[1,691]	Genomics, Alignment
Tiara	1.0.2	[1,692]	Phylogenetics
tiff	3.8.0, 4.0.10	[1,693]	Imaging
Tigmint	1.1.2	[1,694]	Phylogenetics
Tmux	2.9, 3.1	[1,695]	GNU
TNTBLAST	2.04	[1,696]	Biology
ToFU2	v17	[1,697]	Biology, bioinformatics, ngs, iso-seq
toil	3.3.0, 3.3.3	[1,698]	Biology, bioinformatics
Tombo	1.4, 1.5, 1.5.1	[1,699]	Biology, genomics, ngs
Tophat	2.1.0, 2.1.1, 2.1.2	[1,700]	Biology,bioinformatics,ngs,sequencing
torch-geometric	1.3.2	[1,701]	Phylogenetics
TotalView	8.12	[1,702]	Parallel Computing
TPMcalculator	0.0.3	[1,703]	Phylogenetics
TPP	4.7.0, 4.7.1, 5.0.0	[1,704]	Biology, chemistry, nmr
TraCeR	20160519	[1,705]	Biology, phylogenetics
TrackTools	2011	[1,706]	Software
TrackVis/DTK	0.5.2.2, 0.6.0.1	[1,707]	Biology,bioinformatics,neuroscience,imaging
Tracula	5.3.2014_05_26	[1,708]	Biology,bioinformatics,neuroscience,imaging
traitRate	1.1	[1,709]	Biology, evolution
Trans-ABySS	2.0.1	[1,710]	Biology, phylogenetics
TransDecoder	5.3.0, 5.4.0, 5.5.0	[1,711]	Biology, ngs
TRANSIT	2.5.2, 3.2.3	[1,712]	Phylogenetics
Transrate	1.0.1	[1,713]	Biology,assembly
TransVar	2.3.3	[1,714]	Biology, bioinformatics, phylogenetics
TreeBreaker	20160621	[1,715]	Biology, phylogenetics
TreeMix	1.12	[1,716]	Biology, phylogenetics
treePL	20150305	[1,717]	Biology, bioinformatics, phylogenetics
TREEPUZZLE	5.3	[1,718]	Biology, phylogenetics
TreeShrink	1.3.1, 1.3.2	[1,719]	Phylogenetics
TreeTime	0.7.5, 0.8.1	[1,720]	Phylogenetics
trelis	16.3	[1,721]	Geometry
TRF	4.04, 4.09.1	[1,722]	Biology,bioinformatics,genomics
Trilinos	12.12.1, 12.18.1, 12.6.4	[1,723]	Mathematical Algorithms
Trim Galore	0.4.4, 0.5.0, 0.6.5	[1,724]	Biology,bioinformatics,ngs
trim_isoseq_polya	0.0.3	[1,725]	Biology, Genetics, Sequencing
trimAl	1.2	[1,726]	Biology,genomics,sequence alignment
TriMetAss	1.1	[1,727]	Biology,bioinformatics,ngs
Trimmomatic	0.33, 0.36, 0.39	[1,728]	Biology,bioinformatics,ngs
Trinity	r20130225, r20131110, r20140413	[1,729]	Biology,bioinformatics,ngs,sequencing,rna-seq
Trinotate	3.0.1, 3.2.0	[1,730]	Biology
triobinning	0.2.3	[1,731]	Phylogenomics, biology
TRIPLEC	1.0	[1,732]	Biology, bioinformatics
TRITONSERVER	21.08	[1,733]	Machine Learning Inference Server
tRNAscan-Se	1.23	[1,734]	Biology,bioinformatics,ngs
TRUST4	1.0.2b	[1,735]	Phylogenetics
Trycycler	0.4.2	[1,736]	Phylogenetics
TURBOMOLE	7.4.1	[1,737]	Quantum Chemistry
TWINSCAN	4.1.2	[1,738]	Biology,genomics
Ubuntu	20.04	[1,739]	Ubuntu Linux
UCSC	20200320, 20210803	[1,740]	Genomics, bioinformatics
ucsc-fafiltern	377	[1,741]	Phylogenetics
ucsc-maskoutfa	377	[1,742]	Phylogenetics
UCX	1.11.2, 1.9.0	[1,743]	Parallel Programming, development, library
UDUNITS	2.2.17	[1,744]	Library, data, units
ufraw	0.22	[1,745]	Data Mining
ugtm	1.1.6	[1,746]	Statistics, modeling
UKFractography	20200127	[1,747]	Phylogenetics
umi-tools	0.5.5	[1,748]	Phylogenetics
UNAFold	3.8	[1,749]	Biology, genome, RNA, folding
Unanimity	20171108, 3.4.1	[1,750]	Programming,library,cpp
UNCALLED	2.2	[1,751]	Biology, bioinformatics, genomics
Unicycler	0.4.8	[1,752]	Phylogenetics
Unrar	0.0.1, 4.20	[1,753]	Unarchiver, utility
uproc	1.2.0	[1,754]	Biology, genome
USEARCH	9.0.2132, 9.1.13, 9.2.64	[1,755]	Biology,bioinformatics,alignment,sequence analysis
UShER	0.1.4, 0.4.1, 0.5.2	[1,756]	Phylogenetics
V-Phaser	02112013	[1,757]	Biology, phylogenetics
v-pipe	2.0.0	[1,758]	Biology, bioinformatics, genomics, sequencing, virus
VAIR	0.7.0	[1,759]	Geospatial Data Modeling
Valgrind	3.11.0, 3.15.0, 3.8.1	[1,760]	Computer Programming
Valouev	20160325	[1,761]	Biology, Phylogenetics
vamb	3.0.2	[1,762]	Biology
VAMPIR	9.1	[1,763]	High Performance Computing
VarDictJava	1.6.0, 20160521, 20170531	[1,764]	Biology, phylogenetics
varnorm	0.21	[1,765]	Biology, bioinformatics
VarScan	2.3.6	[1,766]	Biology,bioinformatics,ngs
VarSim	0.8.4, 0.8.6	[1,767]	Phylogenetics
VarSimLab	20180220, 20180921	[1,768]	Biology, simulation, genomics
vasp	5.4.4, 6.1.0, 6.2.0	[1,769]	Quantum Chemistry
vaspkit	1.2.5	[1,770]	Phylogenetics
VAST-TOOLS	2.5.1, 20150506	[1,771]	Biology, rna-seq, ngs, splicing
VCF-kit	0.2.6	[1,772]	Phylogenetics
vcf-validator	0.6	[1,773]	Biology, phylogenetics
vcfanno	0.2.8, 0.3.3	[1,774]	Biology, phylogenetics
vcflib	1.0.1	[1,775]	Biology,bioinformatics,genomics
vcftools	0.1.15, 0.1.16, 0.1.9	[1,776]	Biology,bioinformatics,genomics
vcontact	20190512	[1,777]	Phylogenetics
VDJtools	1.1.7, 1.2.1	[1,778]	Biology, phylogenetics
Velvet	1.2.10, 1.2.10-long	[1,779]	Computational Biology, genomics
VEP	83, 88.8, 92	[1,780]	Biology, genomics, ngs
Vermouth-martinize	0.7.2	[1,781]	Phylogenetics
VeryFastTree	3.0.1	[1,782]	Phylogenetics
vg	1.33.0, 1.38.0, 1.39.0	[1,783]	Phylogenetics
vibrant	1.2.0	[1,784]	genomics, virus
ViennaRNA	2.2.6, 2.4.18	[1,785]	Biology, RNA-seq
ViewBS	0.1.10, 0.1.9	[1,786]	Phylogenetics
Vim	8.1.1566, 8.2.2465	[1,787]	Programming,scripting,language
viralmsa	1.1.10, 1.1.12	[1,788]	Phylogenetics
VirSIeve	20210406	[1,789]	Biology, Pipeline
VirtualCell	7.1	[1,790]	Phylogenetics
VIRULIGN	1.0.2	[1,791]	Phylogenetics
VirusDetect	1.7	[1,792]	Phylogenetics
VirusFinder	2.0	[1,793]	Biology, phylogenetics
visit	2.13.3, 3.0.1, 3.1.4	[1,794]	Visualization, Animation and Analysis
VISPR	0.4.14	[1,795]	Phylogenetics
VMD	1.9.1, 1.9.3	[1,796]	Visualization, animation, 3d
vscode	1.38.1, 1.65.2	[1,797]	IDE, editor, programming, scripting
VSearch	20151022, 20161209-2.3.4	[1,798]	Biology,NGS
vt	0.57721, 20140903, 20160129	[1,799]	Biology, genomics
VTC	0.9.3	[1,800]	Biology, bioinformatics, VCF
VTK	8.2.0, 9.0.3, 9.1.0	[1,801]	Biology,bioinformatics,neuroscience,imaging
w2rap-contigger	20161124	[1,802]	Biology, genomics
Wannier90	1.2, 2.1.0	[1,803]	Computational Physics
WarpedLMM	0.21	[1,804]	Modeling
WaveGAN	20190829	[1,805]	Machine Learning, Audio, GAN, Synthesis
WDSSII	5	[1,806]	Weather, Meteorology
WebLogo	2.8.2, 3.3, 3.5.0	[1,807]	Biology,bioinformatics,sequence,graphics
Weka	3.8, 3.8.5	[1,808]	Statistics,machine learning
Wengan	0.2	[1,809]	Biology,bioinformatics,genomics
wgd	1.1.1	[1,810]	Phylogenetics
WGS Assembler	8.3rc1.r4638, 8.3rc2	[1,811]	Biology, bioinformatics, genomics
Wgsim	0.3.1-r13	[1,812]	Biology, phylogenetics
WHAMM	0.14a	[1,813]	Biology, phylogenetics
WhatsHap	1.1	[1,814]	Biology, phylogenetics
whiteboxtools	1.5.0	[1,815]	Phylogenetics
Wine	4.0.0, 7.0.0	[1,816]	Windows, emulator
Wise	2.2.0, 2.4.1	[1,817]	Biology, genome
WIsH	1.0	[1,818]	Phylogenetics
WoLFPSort	0.2	[1,819]	Phylogenetics
WOMBAT	20180118	[1,820]	Biology, phylogenetics
workbench	4.1.1	[1,821]	Nuclear Engineering
wtdbg	2.1, 2.4, 2.5	[1,822]	Phylogenetics
WU BLAST	2.0	[1,823]	Biology, bioinformatics
Wub	0.2.0, 0.4.0	[1,824]	Biology, genomics, ngs
xander	20151222	[1,825]	Biology, phylogenetics
Xapian	1.4.4	[1,826]	Library
XCrySDen	1.5.60	[1,827]	Computational Material Science
Xerces	3.1.4	[1,828]	Phylogenetics
xesmf	0.6.2	[1,829]	Grid Analysis, Climate
xpclr	1.0, 1.1.1	[1,830]	Phylogenetics
Xterm	1.1	[1,831]	Shell
XWAS	3.0	[1,832]	Phylogenetics
XY-Meta	20200413	[1,833]	Phylogenetics
XZ	5.2.2	[1,834]	Compression, library
YAGO	4	[1,835]	Data
YAHA	0.1.82	[1,836]	Biology, ngs
YAK	0.1	[1,837]	Phylogenetics
YASM	1.3.0	[1,838]	Computer Programming
YASRA	2.33	[1,839]	Biology,bioinformatics,ngs,sequencing
yolov4_darknet	4-pre	[1,840]	Machine Learning
yolov5	4.0	[1,841]	Machine Learning
Zagros	1.0.0	[1,842]	Biology,phylogenetics
ZEO++	0.2.2	[1,843]	Chemistry
zorro	2.2	[1,844]	Biology, sequencing
Zstd	1.5.0	[1,845]	Phylogenetics
ZUMIS	2.6.0	[1,846]	Biology, bioinformatics, ngs, sequencing