Applications

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

Name	Module	Versions	URL	Categories
3d-dna	3d-dna	20170330	[1]	biology, phylogenetics
3PCLR	3pclr	20150906	[2]	biology, phylogenetics
4p	4p	1.0	[3]	biology, variant_calling
AAFTF	aaftf	0.2.5, 0.4.1	[4]	biology, pipeline, assembly
ABRicate	abricate	1.0.1	[5]	phylogenetics
ABruijn	abruijn	1.0	[6]	biology, assembly, ngs
ABySS	abyss	1.5.2, 2.1.0, 2.2.5	[7]	biology, de_novo
AdapterRemoval	adapterremoval	2.2.2	[8]	phylogenetics
ADFRsuite	adfrsuite	1.0	[9]	sequencing, biology
ADMB	admb	11.5, 12.0	[10]	math, modeling
AdmixTools	admixtools	20150311, 7.0.2	[11]	biology, genomics, ngs
ADMIXTURE	admixture	1.23, 1.3.0	[12]	biology, genomics, ngs
AEGeAn	aegean	0.14.0, 0.16.0	[13]	biology, genomics
AFNI	afni	20.3.00, 2018_04_12	[14]	biology, neuroscience, imaging
AfterQC	afterqc	0.9.7	[15]	phylogenetics
AGAT	agat	0.4.0	[16]	phylogenetics
AGFusion	agfusion	1.252	[17]	phylogenetics
Albacore	albacore	2.3.1, 2.3.3	[18]	biology, phylogenetics
Albumentations	albumentations	1.0.3	[19]	ai, image_processing, imaging
Alder	alder	1.03	[20]	biology, genomics
Alevin-fry	alevin-fry	0.8.1	[21]	sequencing, biology
ALFA	alfa	1.1.1	[22]	phylogenetics
alfred	alfred	0.2.6	[23]	web, math
alienhunter	alienhunter	1.7	[24]	biology, sequencing
AliStat	alistat	1.12	[25]	phylogenetics
alleleCount	allelecount	20210713	[26]	biology
allhic	allhic	0.9.8	[27]	genomics, biology
ALLMAPS	allmaps	20180117	[28]	biology, phylogenetics
ALLPATHS-LG	allpaths	42316, 44837, 49232	[29]	biology, ngs
AlphaFold	alphafold	2.1.2, 2.2.0, 2.3.1	[30]	protein, structure, machine_learning
Alphaimpute	alphaimpute	0.0.2, 1.9.8.2, 1.9.8.3	[31]	phylogenetics
AltAnalyze	altanalyze	2.1.0	[32]	biology, genomics
AMAS	amas	1.0	[33]	phylogenetics
AMBER	amber	16.0, 18, 20	[34]	chemistry, molecular_dynamics
AMICO	amico	1.0.1	[35]	library, imaging, math
AMOS	amos	3.1.0	[36]	biology, genomics, assembly
AMP	amp	0.6.1	[37]	phylogenetics
amPEPpy	ampeppy	1.0	[38]	phylogenetics
amphora2	amphora2	20140305	[39]	biology, phylogenetics
AMPtk	amptk	1.2.4, 1.5.1, 1.5.4	[40]	biology, ngs
amptorch	amptorch	20210313	[41]	phylogenetics
amrfinderplus	amrfinderplus	3.10.18	[42]	phylogenetics
AMRPlusPlus	amrplusplus	20180508	[43]	phylogenetics
AMUSE	amuse	10.0, 13.1.0	[44]	astronomy
ANDI	andi	0.15b	[45]	assembly
ANGSD	angsd	0.933, 0.940	[46]	biology, ngs
annocript	annocript	2.0	[47]	phylogenetics
AnnoTALE	annotale	1.4.1	[48]	phylogenetics
ANNOVAR	annovar	20130221, 20150322, 20191024	[49]	biology, genomics
Ansible	ansible	2.5.5, 2.8.1	[50]	workflow_automation
ansysem	ansysem	17.0, 2022r1	[51]	physics
antiSMASH	antismash	4.1.0, 6.0.1	[52]	phylogenetics
ANTs	ants	2.2.0, 2.3.4	[53]	biology, phylogenetics
anvio	anvio	6.1, 6.2, 7.1	[54]	biology
Appreci8	appreci8	20180530	[55]	biology, genomics
Apptainer	apptainer	1.0.3, 1.1.0	[56]	workflow_automation
APT	apt	1.15.0, 1.18.0, 1.20.5	[57]	biology, genomics
ARC	arc	1.1.4	[58]	biology, ngs
Aria2	aria2	1.35.0	[59]	utility
ARKS	arks	1.0.2	[60]	phylogenetics
Armadillo	armadillo	7.900.0, 9.200.6, 9.900.4	[61]	library, compiler, math
ARPACK	arpack	1.0	[62]	math
ArrayFire	arrayfire	3.4.2	[63]	math
arriba	arriba	2.1.0	[64]	phylogenetics
ART	art	20160417, 20160605	[65]	phylogenetics
artemis	artemis	18.1.0	[66]	biology
asap	asap	2.0	[67]	visualization, biology
asaq	asaq	1.0	[68]	alignment, sequencing, phylogenetics
ASE-ANI	ase-ani	20180712	[69]	biology, genomics, ngs
ASHS	ashs	2.0	[70]	biology, imaging
ASPECT	aspect	2.3.0	[71]	library
Assembly-stats	assembly-stats	1.0.1	[72]	biology, sequencing, genomics
Assemblytics	assemblytics	1.2.1	[73]	phylogenetics
Assexon	assexon	20190814	[74]	phylogenetics
AStalavista	astalavista	3.2, 4.0	[75]	biology, genomics
aster	aster	220718	[76]	biology, data_science, sequencing
asteroid	asteroid	1.0	[77]	genomics
ASTRAL	astral	5.6.1, 5.6.2, 5.7.7	[78]	biology, ngs, phylogenetics
ASTRID	astrid	2.2.1	[79]	phylogenetics
Astropy	astropy	2.0.8	[80]	biology, phylogenetics
ATAT	atat	3.23, 3.34	[81]	material_science
ATLAS	atlas	3.10.1, 3.10.2, 3.11.17	[82]	library, data_science
Atom	atom	1.57.0	[83]	programming
AtomEye	atomeye	3	[84]	material_science
AtomMan	atomman	1.3.3	[85]	phylogenetics
aTRAM	atram	2.2.0, 2.4.3	[86]	math
Augustus	augustus	3.3.2, 3.3.3, 3.4.0	[87]	biology, genomics
Auto3DEM	auto3dem	4.05.2	[88]	image_processing
AutoDock	autodock	4.2.6	[89]	biology
AutoDock-GPU	autodock-gpu	1.5.3	[90]	chemistry
autodock-vina	autodock-vina	1.2.3	[91]	biology
Autometa	autometa	20190802	[92]	phylogenetics
automlsa2	automlsa2	0.8.1	[93]	phylogenetics, biology, genomics
AWSCLI	awscli	2.2.30	[94]	utility
azoo	azoo	1.3.1	[95]	phylogenetics
bactopia	bactopia	2.2.0	[96]	genomics
Badread	badread	0.1.5	[97]	phylogenetics
bakta	bakta	1.3.3	[98]	genomics, biology
BALi-Phy	bali-phy	3.4.1, 3.5.0	[99]	phylogenetics
BAM-matcher	bam-matcher	20161021	[100]	phylogenetics
Bam-Readcount	bam-readcount	20150616	[101]	biology, genomics
bamaddrg	bamaddrg	20120326	[102]	phylogenetics
BamBam	bambam	1.0, 1.4	[103]	biology, genomics
bamm	bamm	2.5.0	[104]	phylogenetics
bamsnap	bamsnap	0.2.19	[105]	phylogenetics
Bamstats	bamstats	20140602	[106]	biology, ngs
Bamsurgeon	bamsurgeon	1.2	[107]	phylogenetics
bamtofastq	bamtofastq	1.3.5	[108]	phylogenetics
Bamtools	bamtools	2.4.1, 2.5.0, 2.5.1	[109]	biology, ngs, sequencing
bamUtil	bamutil	1.0.2	[110]	biology, genomics
BAPS	baps	6.0	[111]	biology, genomics
Barrnap	barrnap	0.7, 0.9	[112]	biology, rna-seq
Basemount	basemount	0.15.96, 0.25.2	[113]	biology, sequencing
BatMeth2	batmeth2	20210720	[114]	biology, genomics, mapping
bax2bam	bax2bam	0.0.9	[115]	phylogenetics
BayArea	bayarea	1.0.2	[116]	biology
BAYENV	bayenv	2.0	[117]	biology, phylogenetics
BayesAss	bayesass	3.0.4, 3.0.4.2	[118]	phylogenetics
BayeScan	bayescan	2.1	[119]	biology, variant_calling
BayesR	bayesr	20151016	[120]	biology, phylogenetics
BayesTraits	bayestraits	3.0.2	[121]	phylogenetics
baypass	baypass	2.1	[122]	biology, phylogenetics
BBMap	bbmap	38.26, 38.44, 38.90	[123]	biology, alignment
bcftools	bcftools	1.15, 1.3.1, 1.9	[124]	biology, ngs
bcl2fastq	bcl2fastq	2.16.0.10, 2.20.0.422	[125]	biology, ngs
BDG-SeQuila	bdg-sequila	0.5.5	[126]	phylogenetics
BEAGLE	beagle	4.1, 5.0, 5.2	[127]	biology, genomics
BEAR	bear	20170209	[128]	biology, genomics
BEAST	beast	2.6.7, 2.7.0, 2.7.3	[129]	biology, phylogenetics
BEAST2-XML	beast2-xml	1.0.9	[130]	phylogenetics
BEDOPS	bedops	2.4.30	[131]	biology, sequencing, ngs
BEDTools	bedtools	2.29.1, 2.29.2, 2.30.0	[132]	biology, ngs
Bertini	bertini	1.6	[133]	math
BERTopic	bertopic	0.14.0, 0.7, 0.8.1	[134]	machine_learning
BESST	besst	2.2.4	[135]	biology, ngs
BFAST	bfast	0.7.0	[136]	biology, ngs
bgenix	bgenix	1.1.7	[137]	data_science, genomics
BIDSCOIN	bidscoin	3.7.4	[138]	neuroscience
Bifrost	bifrost	0.2, 1.0.3, 20200225	[139]	phylogenetics
BiG-SCAPE	big-scape	1.1.2	[140]	biology, genomics, phylogenetics, pipeline
BinPacker	binpacker	1.0	[141]	biology, rna-seq, assembly
BinSanity	binsanity	0.2.6.4	[142]	biology, genomics
Bioawk	bioawk	1.0	[143]	phylogenetics
bioBakery	biobakery	0.15.1, 1.8, 3.0.0	[144]	phylogenetics
Biodiverse	biodiverse	2.1	[145]	phylogenetics
Biolite	biolite	0.3.5.1	[146]	biology, genomics, variant_calling
BIOM	biom	2.1.5, 2.1.6	[147]	biology, genomics
BIOMART	biomart	1.4	[148]	biology, genomics
Biopieces	biopieces	2.0	[149]	phylogenetics
BIRDS	fiji-birds	1.0	[150]	workflow_automation, utility, imaging
Bismark	bismark	0.22.3, 0.7.4, 0.7.7	[151]	biology, ngs
Blackfynn	blackfynn	0.2.7	[152]	data_mining
BLASR	blasr	20130815, 20161215 (5.3), 5.3.2	[153]	biology, ngs
Blast2GO	blast2go	2.5.0-20120705	[154]	biology, genomics
Blast2GO CLI	blast2go	1.3.3	[155]	biology, genomics
BLAT	blat	20121105, 20140318	[156]	genomics
blender	blender	2.73, 2.77, 3.0.1	[157]	graphics
blink	blink	0.01	[158]	genomics
Blitz	blitz	0.10	[159]	library
BlobTools	blobtools	1.0, 2.2	[160]	phylogenetics
bloomfiltertrie	bloomfiltertrie	0.8.7	[161]	phylogenetics
BloomTree	bloomtree	0.3.5	[162]	data_mining
BLUPF90	blupf90	20160604, 20180301, 20190531	[163]	biology, phylogenetics
BMGE	bmge	1.12	[164]	biology, genomics, phylogenetics
bmtagger	bmtagger	3.101	[165]	genomics, biology
BOLT-LMM	bolt-lmm	2.3.4	[166]	phylogenetics
BoltzTraP	boltztrap	1.2.5	[167]	physics
Boost	boost	1.71.0, 1.75.0, 1.77.0	[168]	programming, library, compiler
booster	booster	0.1.2	[169]	phylogenetics
botorch	botorch	0.7.1	[170]	phylogenetics, biology
Bowtie	bowtie	1.1.1, 1.2.0, 1.2.3	[171]	biology, ngs, sequencing
Bowtie2	bowtie2	2.3.5.1, 2.4.2, 2.4.5	[172]	biology, ngs, sequencing
BoxCLI	boxcli	2.9.0	[173]	file_management, web, programming
BPGA	bpga	1.2	[174]	biology, ngs
BPP	bpp	4.1.4, 4.3.8, 4.4.1	[175]	biology, phylogenetics
BppSuite	bppsuite	2.3.2	[176]	genomics
Bracken	bracken	1.0.0, 2.5	[177]	biology, phylogenetics
BrainIAK	brainiak	0.11	[178]	imaging
braker	braker	2.1.5, 2.1.6, 3.0.2	[179]	phylogenetics
BRANCH	branch	1.8.1	[180]	biology, ngs, mapping
BRATNextGen	bratnextgen	20150505	[181]	biology, genomics
BreakDancer	breakdancer	1.4.5	[182]	biology, phylogenetics
breakseq	breakseq	2.2	[183]	biology, phylogenetics
Brewery	brewery	20191205	[184]	phylogenetics
Bridger	bridger	20141201	[185]	ngs, genomics, biology
BRIG	brig	0.95	[186]	biology, genomics
brkraw	brkraw	0.3.5	[187]	data_science, imaging
BRM	brm	0.3	[188]	phylogenetics
Bruker2nifti	bruker2nifti	1.0.4	[189]	phylogenetics
Bsmap	bsmap	2.87	[190]	biology, ngs
Bsoft	bsoft	1.9.1	[191]	biology, image_processing
BSseeker2	bsseeker2	2.1.0, 2.1.8	[192]	biology, phylogenetics
bubbleparse	bubbleparse	20140314	[193]	biology, phylogenetics
BUCKy	bucky	1.4.4	[194]	biology, phylogenetics
BUSCO	busco	4.0.6, 4.1.4, 5.2.0	[195]	biology, genomics
BWA	bwa	0.7.7, 0.7.8, 0.7.9a	[196]	biology, ngs
bwa-mem2	bwa-mem2	2.2.1	[197]	phylogenetics
BWA-PSSM	bwa-pssm	0.5.11	[198]	phylogenetics
bxh_xcede_tools	bxh_xcede_tools	1.11.1	[199]	biology
BYOBU	byobu	5.133, 5.92	[200]	shell
bzip2	bzip2	1.0.6	[201]	utility, library
c-wap	c-wap	20220624	[202]	sequencing, genomics, biology
Cactus	cactus	2.0.3, 2.0.5	[203]	phylogenetics
CAFE	cafe	4.1, 5.0.0	[204]	biology, phylogenetics
came	came	0.0.1	[205]	phylogenetics
Camino	camino	20140723	[206]	biology, neuroscience, imaging
CAMP	camp	1.0.0	[207]	biology, sequencing
Cantera	cantera	2.1.1	[208]	physics
Canu	canu	2.0, 2.1, 2.2	[209]	biology, sequencing
CANVAS	canvas	1.40.0.1613	[210]	phylogenetics
CAP3	cap3	20120705	[211]	biology, assembly
Capnp	capnp	0.5.3	[212]	compiler
captus	captus	0.9.88, 0.9.91	[213]	phylogenetics, biology
CARTA	carta	2.0	[214]	image_processing
CASAVA	casava	1.8.2	[215]	biology, ngs
CASM	casm	0.2.0	[216]	physics
CasOFFinder	casoffinder	2.4	[217]	phylogenetics
Catch	catch	1.4.0	[218]	biology, genomics, sequencing
CAVIAR	caviar	20171218	[219]	biology, phylogenetics
CBGpipe	cbgpipe	20190702	[220]	phylogenetics
CCMetagen	ccmetagen	1.4.0	[221]	phylogenetics
CD-HIT	cdhit	4.6, 4.6.4, 4.6.8	[222]	biology, genomics
CDBFasta	cdbfasta	20181005	[223]	phylogenetics
CDNA_Cupcake	cupcake	20180629, 22.0.0, 9.0.1	[224]	biology, ngs, sequencing
CDO	cdo	1.7.2rc3, 1.9.4	[225]	climate
CellProfiler	cellprofiler	3.1.9, 4.1.3	[226]	phylogenetics
CellRanger	cellranger	6.1.2, 7.0.0, 7.0.1	[227]	biology, ngs, rna-seq
CellRanger-ARC	cellranger-arc	2.0.1	[228]	biology, ngs, rna-seq
CellRanger-ATAC	cellranger-atac	1.2.0	[229]	biology, ngs, rna-seq
CellRanger-DNA	cellranger-dna	1.0.0, 1.1.0	[230]	biology, ngs, rna-seq, genomics
Centrifuge	centrifuge	1.0.3, 1.0.4b	[231]	biology, phylogenetics
CFITSIO	cfitsio	3.370	[232]	library, compiler
CGAL	cgal	4.10, 4.9, 5.02	[233]	library, math
CGATools	cgatools	1.6.0.43	[234]	biology, ngs
cgmaptools	cgmaptools	0.1.1, 0.1.2	[235]	phylogenetics
CGView	cgview	1.0.2	[236]	phylogenetics
CHARMM	charmm	36a3, 43b2	[237]	chemistry, simulation
ChartDirector	libchartdir	5.1.0	[238]	library, data_science
CheckM	checkm	1.0.4, 1.0.7, 1.1.2	[239]	biology, genomics
checkv	checkv	1.0.1	[240]	biology, genomics
Chimera	chimera	1.12	[241]	biology, modeling
Chipyard	chipyard	1.0	[242]	simulation
Chromeister	chromeister	1.5a	[243]	biology, genomics
ChromEvol	chromevol	2.0	[244]	biology, ngs
CIMS	cims	4.1.2	[245]	biology, genomics
CIRCexplorer	circexplorer	1.1.10	[246]	biology, rna-seq
CIRCexplorer2	circexplorer2	2.3.5, 2.3.8	[247]	phylogenetics
circexplorer3	circexplorer3	01172021	[248]	RNA-Seq
Circlator	circlator	1.5.5	[249]	phylogenetics
Circleator	circleator	1.0.2	[250]	phylogenetics
circompara2	circompara2	0.1.2.1	[251]	phylogenetics
Circos	circos	0.63-pre11, 0.69-2, 0.69-9	[252]	biology, genomics, ngs
circtools	circtools	1.2.1	[253]	biology
CIRI	ciri	2.0.6	[254]	phylogenetics
ciriquant	ciriquant	1.1.2	[255]	phylogenetics
CisGenome	cisgenome	2.0	[256]	biology, genomics
cisTEM	cistem	1.0.0	[257]	phylogenetics
Clairvoyante	clairvoyante	1.02	[258]	phylogenetics
Clann	clann	3.2.3	[259]	biology, phylogenetics
clara	clara	v4.0	[260]	ai, machine_learning
CLARK	clark	1.2.2-b, 1.2.3	[261]	biology, genomics
CLHEP	clhep	2.2.0.1	[262]	physics
CLIFinder	clifinder	4.1	[263]	biology, phylogenetics
ClinicaDL	clinicadl	1.0.4	[264]	biology, imaging, machine_learning
clipkit	clipkit	1.3.0	[265]	genomics, biology
CLIPper	clipper	2.1.0	[266]	phylogenetics
CLIPSeqTools	clipseqtools	0.1.7	[267]	biology, sequencing
ClonalFrame	clonalframe	1.1, 1.2	[268]	biology, ngs, phylogenetics
ClonalFrameML	clonalframeml	1.0, 1.11	[269]	biology, ngs, phylogenetics
CloudCompare	cloudcompare	2.10.3	[270]	visualization
Clover	clover	2.0	[271]	biology, genomics, assembly
CLUMPP	clumpp	1.1.2	[272]	biology
ClustalO	clustalo	1.2.0	[273]	biology, alignment
ClustalW	clustalw	2.1	[274]	biology, alignment
cluster3	cluster3	1.52a	[275]	biology, genomics
Clview	clview	20130402	[276]	biology
CMake	cmake	3.19.1, 3.21.3	[277]	programming
CMS	cms	20170518	[278]	biology
CMWP	cmwp	140518	[279]	biology, genomics
CNCI	cnci	20180305	[280]	phylogenetics
CNSpipeline	cnspipeline	20170827	[281]	phylogenetics
CNV-Seq	cnvseq	20110715, 20140812	[282]	biology, genomics
CNV-Sim	cnv-sim	0.9.2	[283]	biology, phylogenetics
CNVkit	cnvkit	0.9.6	[284]	phylogenetics
CNVnator	cnvnator	0.3.2	[285]	biology, genomics
cobra-tf	cobra-tf	0.1	[286]	fluid_dynamics
CodonPhyML	codonphyml	20150303	[287]	phylogenetics
Coevol	coevol	1.3c, 1.4b, 1.6	[288]	biology, phylogenetics
Cogent	cogent	2.1	[289]	biology, phylogenetics
COLMAP	colmap	3.6	[290]	modeling
CoMap	comap	1.4.1	[291]	biology, genomics
Comp-D_MPI	comp-D_MPI	1.0	[292]	statistics
Compacta	compacta	1.02	[293]	biology, genomics
COMSOL	comsol	5.4.0	[294]	simulation
Concaterpillar	concaterpillar	1.8a	[295]	phylogenetics
CONCOCT	concoct	1.1.0	[296]	biology, genomics
Conda	conda	22.11.1, 4.12.0	[297]	programming
CONN	conn	18a	[298]	imaging
CONNECT	connect	20200614	[299]	phylogenetics
connectomemapper3	connectomemapper3	3.0.0-rc1	[300]	phylogenetics
ConPADE	conpade	1.0	[301]	phylogenetics
Conpair	conpair	20161010, 20180624	[302]	biology, phylogenetics
Consed	consed	23.0, 25.0, 29.0	[303]	biology, genomics
CONSEL	consel	0.20	[304]	biology, phylogenetics
ContaVect	contavect	0.2	[305]	biology, phylogenetics
Convert3D	convert3d	1.1.0	[306]	imaging, utility
Coot	coot	0.9.5	[307]	modeling
Coreutils	coreutils	8.23, 8.28	[308]	utility
Corset	corset	1.06	[309]	biology, ngs
Counterr	counterr	0.1	[310]	phylogenetics
covNMR	covnmr	2014	[311]	chemistry, biology
cp2k	cp2k	7.0.0	[312]	chemistry
CPAT	cpat	3.0.2	[313]	phylogenetics
cpc	cpc	2.0	[314]	phylogenetics
CPLEX	cplex	12.6.1, 12.6.2, 12.7	[315]	climate
Crass	crass	1.0.1	[316]	biology, assembly
crisflash	crisflash	1.2.0	[317]	phylogenetics
CRISP	crisp	20181122	[318]	phylogenetics
CRISPRanalyzer	crispranalyzer	1.50	[319]	biology, genomics, ngs
CRISPRCasFinder	crisprcasfinder	4.2.17	[320]	phylogenetics
CRISPResso2	crispresso2	20220811	[321]	genomics, sequencing, biology
CrossMap	crossmap	0.3.9, 0.6.3	[322]	biology, genomics
crossmapper	crossmapper	1.1.1	[323]	phylogenetics
Crux	crux	1.40	[324]	biology, spectroscopy
CryptoMiniSat	cryptominisat	5.0.1	[325]	math
csvpad	csvpad	1.2	[326]	data science
csvtk	csvtk	0.23.0	[327]	biology
ctk	ctk	1.1.4	[328]	biology, genomics
CUBE	cube	4.4	[329]	library, compiler, math
CUDA	cuda	11.0.207, 11.1.0, 11.4.3	[330]	programming, library, graphics
Cufflinks	cufflinks	2.1.1, 2.2.1, 2.2.1.1	[331]	biology, ngs, sequencing
cuOpt	cuopt	22.12	[332]	Accelerated AI Logistics and Route Optimization
cupy	cupy	8.3.0	[333]	phylogenetics
cutadapt	cutadapt	1.18, 2.8, 3.4	[334]	biology, ngs
CutRunTools	cutruntools	20200104	[335]	phylogenetics
cvbio	cvbio	3.0.0	[336]	phylogenetics
CViT	cvit	1.3	[337]	programming, library
CWLtool	cwltool	1.0.20190906, 2.0.20200126, 3.0.20210124104916	[338]	workflow_automation, scheduler
cx_oracle	cxoracle	8.3.0	[339]	database, utility
CycleGan	cyclegan	20201015	[340]	phylogenetics
Cytoscape	cytoscape	3.4.0	[341]	biology, ngs, phylogenetics
d2go	d2go	20210702	[342]	machine_learning, ai
dadi	dadi	2.1.1	[343]	phylogenetics
DAKOTA	dakota	6.15, 6.8, 6.8-gui	[344]	math
DALIGNER	daligner	1.0	[345]	biology, phylogenetics
dammit	dammit	1.0rc2	[346]	biology, phylogenetics
dancemapper	dancemapper	1.0.0	[347]	machine learning
DASTool	dastool	1.1.0, 1.1.2	[348]	biology, phylogenetics
datamash	datamash	1.1.0	[349]	math
DAWGPAWS	dawgpaws	1.0	[350]	biology, phylogenetics
DCC	dcc	0.4.4	[351]	biology, ngs
Dcmstack	dcmstack	0.6.2	[352]	biology, imaging
DCMTK	dcmtk	3.6.0	[353]	biology, neuroscience, imaging
dDocent	ddocent	2.7.8	[354]	phylogenetics
DDSCAT	ddscat	7.3.0	[355]	astronomy
DDT	ddt	18.2, 20.0, 20.2	[356]	programming
DealII	dealii	8.3.0, 9.3.1	[357]	library
DeconSeq	deconseq	0.4.3	[358]	biology, phylogenetics
decontaMiner	decontaminer	1.4	[359]	genomics, biology
DECX	decx	20180205	[360]	phylogenetics
DeepARG	deeparg	1.0.1	[361]	phylogenetics
deepbgc	deepbgc	0.1.18	[362]	phylogenetics
Deepcoil	deepcoil	2.0.1	[363]	sequencing, biology
deepfri	deepfri	03312021	[364]	machine learning, biology
DeepGS	deepgs	1.2	[365]	phylogenetics
DeepLabCut	deeplabcut	2.0.7-gpu, 2.1.1, 2.2.1	[366]	phylogenetics
deepmicrobes	deepmicrobes	20200219	[367]	biology, genomics, machine_learning
DeepMReye	deepmreye	01192022	[368]	library, biology
DeepPicker	deeppicker	20161102	[369]	imaging
deepsig	deepsig	1.2.5	[370]	biology
deepTools	deeptools	2.4.3, 3.1.1	[371]	biology, ngs
deepvariant	deepvariant	1.4.0	[372]	biology, genomics, sequencing, machine_learning
deFusion	defusion	20200305	[373]	phylogenetics
Delft3D	delft3d	7545	[374]	physics
Delineate	delineate	1.2.2	[375]	biology, genomics
Delly	delly	0.7.7, 0.7.8, 1.1.5	[376]	biology, phylogenetics
delucs	delucs	20220512	[377]	sequencing, genomics, machine_learning
DeNoGAP	denogap	1.0	[378]	biology, phylogenetics, ngs
DERIVA	deriva	1.5.0	[379]	phylogenetics
deSALT	desalt	1.5.6	[380]	biology, genomics, sequencing
Desmond	desmond	6.9	[381]	biology
Detectron2	detectron2	0.4, 0.5, 0.6	[382]	library
DeTiN	detin	1.7.5.9	[383]	imaging, ngs, genomics
DEXTRACTOR	dextractor	1.0	[384]	biology, sequencing
Diamond	diamond	2.0.9, 2.1.1, 2.1.3	[385]	biology, genomics
diCal2	dical2	2.2.0.1	[386]	biology, phylogenetics
diffReps	diffreps	1.55.4	[387]	biology
DISCOVAR de novo	discovardenovo	52488	[388]	biology, ngs, assembly
DiscoVista	discovista	20180906	[389]	phylogenetics
discvrseq	discvrseq	1.3.10	[390]	biology, phylogenetics
Distruct	distruct	2.3	[391]	phylogenetics
DIYABC	diyabc	1.0.4.43b, 2.0.3, 2.1.0	[392]	biology, phylogenetics
DL_POLY	dlpoly	1.9	[393]	molecular_dynamics
Dlib	dlib	19.19	[394]	phylogenetics
DNA Clust	dnaclust	3.0	[395]	biology, genomics
DOCK	dock	6.7, 6.8, 6.9	[396]	chemistry
DoGFinder	dogfinder	20201103	[397]	phylogenetics
dorado	dorado	0.1.1	[398]	genomics
DosageConvertor	dosageconvertor	1.0.3	[399]	biology
DOT	dot	2.0	[400]	biology, chemistry
Doxygen	doxygen	1.8.3.1	[401]	programming, documentation
dragmap	dragmap	1.2.1	[402]	phylogenetics, sequencing, biology
dragonflye	dragonflye	1.0.12	[403]	sequencing, genomics
dram	dram	1.3	[404]	biology, genomics, annotation
DRAP	drap	1.91	[405]	biology, phylogenetics
dRep	drep	2.3.2	[406]	phylogenetics
Dropseq	dropseq	2.4.0	[407]	phylogenetics
DS9	saoimageds9	7.5, 8.0.1	[408]	imaging
DScribe	dscribe	1.2.0	[409]	machine_learning
dsistudio	dsistudio	20210123, 20220803	[410]	imaging
DSK	dsk	2.1.0, 2.3.0	[411]	biology, ngs
DSRC	dsrc	2.0	[412]	phylogenetics
DSSAT	dssat	4.6	[413]	simulation
DSSP	dssp	2.2.1, 3.0.0	[414]	molecular_dynamics
DSuite	dsuite	0.4, 0.4-r41, 0.4-r49	[415]	biology, genomics
DTI-TK	dtitk	2.3.1	[416]	imaging
dtiprep	dtiprep	0.1.1	[417]	phylogenetics
duchamp	duchamp	1.6.2	[418]	phylogenetics
dynamicDBG	dynamicdbg	20181003	[419]	phylogenetics
Dynare	dynare	4.4.3	[420]	math
ea-utils	eautils	1.04.807.18, 1.1.2.537	[421]	biology, genomics, ngs
EAGLE	eagle	2.0	[422]	phylogenetics
eagle-rc	eagle-rc	1.1.1	[423]	phylogenetics
ECE	ece	1.2	[424]	physics
eddy-squeeze	eddy-squeeze	1.0.8	[425]	data_science, visualization
EDirect	edirect	10.7, 12.2	[426]	biology, phylogenetics
EDTA	edta	1.9.6	[427]	phylogenetics
Edyeet	edyeet	0.1, 0.3	[428]	phylogenetics
EEGLAB	eeglab	12.0.2.1b, 13.2.2b, 13.4.4b	[429]	biology
eGene-MVN	egene-mvn	0.1	[430]	biology, genomics
eggNOG-mapper	eggnog-mapper	2.0.1, 2.1.6	[431]	phylogenetics
EGSnrc	egsnrc	2019	[432]	phylogenetics
EIGENSOFT	eigensoft	4.2, 5.0.1, 6.0.1	[433]	biology
Elastix	elastix	4.9.0	[434]	phylogenetics
ELPA	elpa	2019.11.001	[435]	library, compiler, math
elPrep	elprep	4.1.4	[436]	phylogenetics
Emacs	emacs	27.2	[437]	programming, language
EMAN2	eman2	2.22, 2.31	[438]	image_processing
EMBOSS	emboss	6.6.0	[439]	biology
Embree	embree	3.6.1	[440]	graphics
EMC	emc	9.4.3	[441]	simulation
EMMAX	emmax	20100307, 20120210	[442]	biology, ngs, mapping
EnergyPlus	energyplus	9.3.0	[443]	simulation
Ensembl Tools	ensembl_tools	100, 80	[444]	biology
enTAP	entap	0.6.1.2, 20160416	[445]	biology, phylogenetics
EPACTS	epacts	3.2.6, 3.4.2, 3.4.2.hg38	[446]	biology, genomics
EpiNano	epinano	1.2.0	[447]	biology, ngs
epiteome	epiteome	1.0	[448]	phylogenetics
epoch	epoch	4.7.3	[449]	astronomy
eQTLA	eqtla	1.1	[450]	biology, genomics
eQtlBma	eqtlbma	1.2.2, 1.3.0r20140820	[451]	biology, genomics
Erpin	erpin	5.5.4	[452]	biology, phylogenetics
esmf	esmf	8.3.0)	[453]	geospatial
ESOM	esom	1.1	[454]	biology, phylogenetics
ESPRESSO	espresso	6.2.1, 6.4.1, 7.0	[455]	chemistry, modeling
ESPRIT	esprit	2009-nogap, 201102	[456]	biology
ETE3	ete3	3.0.0, 3.1.1	[457]	biology, phylogenetics
EVidenceModeler	evidencemodeler	1.1.1	[458]	phylogenetics
Evigene	evigene	20180730, 20200520	[459]	phylogenetics
EvoLSTM	evolstm	20220103	[460]	biology
ExaBayes	exabayes	1.5	[461]	phylogenetics
Exonerate	exonerate	2.2.0, 2.4.0	[462]	biology, genomics
ExpansionHunter	expansionhunter	4.0.2	[463]	biology, genomics
ExpansionHunterDenovo	expansionhunterdenovo	0.9.0	[464]	biology, genomics
export2graphlan	export2graphlan	0.22	[465]	statistics, mapping, visualization
eXpress	express	1.3.1, 1.5.1	[466]	biology, ngs
ezaai	ezaai	1.0	[467]	biology, phylogenetics
face_morpher	face_morpher	20190630	[468]	phylogenetics
face_recognition	face_recognition	1.2.2	[469]	phylogenetics
fairseq	fairseq	0.12.2	[470]	modeling, ai
falco	falco	1.2.1	[471]	biology, sequencing
FALCON	falcon	20161027, 20161222, 20190601	[472]	biology, ngs, sequencing
FALCON_unzip	falcon_unzip	20161222	[473]	biology
FAR	far	2.15	[474]	biology, genomics
FAST	fast	1.06	[475]	biology, phylogenetics
fast-gep	fast-gep	1.0	[476]	phylogenetics
Fast-Plast	fast-plast	1.2.6	[477]	biology, phylogenetics
fast5tools	fast5tools	0.3.1	[478]	phylogenetics, biology
FASTA	fasta	34.26.5, 36.3.6d	[479]	biology, genomics
fastai	fastai	2.1.5, 2.6.3, 2.7.10	[480]	Machine_Learning
FastANI	fastani	1.1	[481]	phylogenetics
fastchaos	fastchaos	0.1.0	[482]	sequencing
FastGEAR	fastgear	20161216	[483]	biology, genomics
Fastix	fastix	0.1.0	[484]	biology, ngs
FastML	fastml	3.0	[485]	biology, phylogenetics
Fastp	fastp	0.20.0, 0.22.0	[486]	biology, ngs
FASTphase	fastphase	1.4.8	[487]	phylogenetics
FastPlast	fastplast	1.2.8	[488]	phylogenetics
fastq-pair	fastq-pair	1.0	[489]	phylogenetics
FastQ-Screen	fastq-screen	0.14.0	[490]	phylogenetics
Fastq-tools	fastq-tools	0.8	[491]	biology, ngs
FastQC	fastqc	0.11.4, 0.11.7, 0.9.6	[492]	biology, ngs
FastqPuri	fastqpuri	1.0.7	[493]	phylogenetics
FastQTL	fastqtl	2.184	[494]	phylogenetics
FASTRAL-constrained	fastral-constrained	20211108	[495]	phylogenetics
fastsimcoal	fastsimcoal2	2.6.0.3, 2.7.0.2	[496]	biology, phylogenetics
FastSpar	fastspar	0.0.4	[497]	biology, genomics
fastStructure	faststructure	20150112	[498]	biology, genomics
FastTree	fasttree	2.1.11	[499]	biology, phylogenetics
FastUniq	fastuniq	1.1	[500]	biology, phylogenetics
Fastx Toolkit	fastx_toolkit	0.0.13.2, 0.0.14	[501]	biology, ngs
fcGENE	fcgene	1.0.7, 1.0.7.1	[502]	biology, genomics, variant_calling
FDSTools	fdstools	1.2.0	[503]	phylogenetics
fdupes	fdupes	1.51	[504]	file_management
FEELnc	feelnc	0.1.1	[505]	phylogenetics
FEniCS	fenics	2018.1.0	[506]	biology, phylogenetics
Ferret	ferret	6.82	[507]	visualization, geospatial, climate
FFmpeg	ffmpeg	2.1.3, 2.8.3, 4.3.1	[508]	audio, visualization
FFTW	fftw	3.3.6, 3.3.7, 3.3.8	[509]	library, compiler, math
fgbio	fgbio	0.5.0, 0.7.0	[510]	phylogenetics
FGMP	fgmp	1.0.1	[511]	phylogenetics
FIGARO	figaro	1.1.2	[512]	phylogenetics
Fiji	fiji	2.0.0rc59	[513]	image_processing
Filtlong	filtlong	0.2.0	[514]	biology, phylogenetics
Finder	finder	20210503, 20210609	[515]	biology, search
finemap	finemap	1.4	[516]	phylogenetics
fineRADstructure	fineradstructure	0.3.2	[517]	phylogenetics
finesse	finesse	2.3.1	[518]	simulation
Firefox	firefox	1.0	[519]	linux, web
fit-sne	fit-sne	1.2.1	[520]	phylogenetics
FLAIR	flair	1.5	[521]	phylogenetics
flairNLP	flairnlp	0.10	[522]	visualization, language
flappie	flappie	1.1.0, 2.1.3	[523]	phylogenetics
FLASh	flash	1.2.10, 1.2.11	[524]	biology, genomics
FLEA	flea	2.0.0	[525]	phylogenetics
flex	flex	2.6.4	[526]	programming
Flexbar	flexbar	2.3, 2.34, 3.5.0	[527]	biology, genomics, ngs
FLEXLm	flexlm	1.0	[528]	utility
FlowCraft	flowcraft	1.4.1	[529]	phylogenetics
Fluent	fluent	17.2, 19.1, 2020R1	[530]	fluid_dynamics
Flye	flye	2.8.1, 2.9, 2.9.1	[531]	biology, ngs
fMRIPrep	fmriprep	1.4.0a1, 1.5.4, 20.2.3	[532]	data_mining
forecasting	forecasting	0.10.3	[533]	Machine_Learning, Data_Science
ForeSeqs	foreseqs	1.0.4	[534]	phylogenetics
fpocket	fpocket	4.0.2	[535]	sequencing, biology
fqtools	fqtools	20160224	[536]	biology, ngs, sequencing
FragGeneScan	fraggenescan	1.16	[537]	biology, genomics
FRAMA	frama	20151019	[538]	biology
FrameDP	framedp	1.2.2	[539]	biology, sequencing
FRAPOSA	fraposa	20200421	[540]	phylogenetics
FreeBayes	freebayes	1.1.0-20170823, 1.3.1, 1.3.2	[541]	biology, genomics
freecad	freecad	0.20.2	[542]	modeling
freesasa	freesasa	2.1.2	[543]	molecular_dynamics, biology
Freesurfer	freesurfer	7.1.1, 7.2.0, 7.3.2	[544]	biology, neuroscience, imaging
Freyja	freyja	1.3.1, 1.3.4, 1.3.8	[545]	biology, phylogenetics, sequencing
FSA	fsa	1.15.9	[546]	phylogenetics
FSL	fsl	6.0.4, 6.0.5, 6.0.6	[547]	biology, neuroscience, imaging
fslmrs	fslmrs	1.1.10	[548]	spectroscopy, metabolomics
funannotate	funannotate	1.8.13, 1.8.7, 1.8.9	[549]	phylogenetics
fusion_twas	fusion_twas	20210218	[550]	phylogenetics
GAL	gal	20180906	[551]	phylogenetics
Galaxy	galaxytools	1.0	[552]	biology
galaxyml	galaxyml	0.10.0	[553]	library, machine_learning
GAML	gaml	20150610	[554]	biology, genomics
GapCloser	gapcloser	1.12r6	[555]	biology, genomics, ngs
GapFiller	gapfiller	1.10, 1.11	[556]	biology, genomics
gapseq	gapseq	1.2	[557]	chemistry, biology
garfield	garfield	2	[558]	genomics
GARLI	garli	2.0, 2.01	[559]	biology, phylogenetics
GASVPro	gasvpro	201310	[560]	biology, ngs
GATE	gate	7.0	[561]	library
GATK	gatk	4.1.8.1, 4.1.9.0, 4.3.0.0	[562]	biology, ngs
Gaussian	gaussian	09 D.01, 16, 16-c02	[563]	chemistry
Gawk	gawk	4.2.0	[564]	utility
Gblocks	gblocks	0.91b	[565]	biology
GCC	gcc	7.3.0, 8.2.0, 9.3.0	[566]	compiler
GCE	gce	1.0.2	[567]	biology, genomics
GCT	gct	6.2.1	[568]	file_management, utility
GCTA	gcta	1.26.0, 1.92.4beta, 1.93.2beta	[569]	biology, genomics, variant_calling
GDAL	gdal	2.2.1, 2.2.4, 2.3.1	[570]	geospatial, library
GDB	gdb	8.3, 9.2	[571]	programming
GDC-Client	gdc-client	1.0.1, 1.5.0	[572]	biology, sequencing, ngs
GDrive	gdrive	2.1.0	[573]	utility, file_management
GDSL	gdsl	1.18	[574]	library
Geant4	geant4	4.10, 4.10.03, 4.10.5	[575]	physics
geant4	geant4	11.0.2, 4-11.0.3	[576]	physics, simulation
GEM	gem	20130406	[577]	biology, ngs, sequencing
gem5	gem5	2.0	[578]	simulation
GEMMA	gemma	0.98.1	[579]	phylogenetics
GeneMark-ES	genemark_es	4.65, 4.68, 4.69	[580]	biology, genomics
GeneMarkS	genemark_s	2012.04	[581]	biology, genomics
GeneMarkS-T	genemark_s	3.10.001	[582]	biology, genomics
GenePainter	genepainter	2.0.4	[583]	biology, phylogenetics
GeneRax	generax	1.2.2	[584]	phylogenetics
Generic Mapping Tools	gmt	6.4.0	[585]	physics, biology
GeneSeqer	geneseqer	2014-02-26	[586]	biology, genomics
genesum	genesum	0.1.0	[587]	biology, genomics
GeneTorrent	genetorrent	3.8.7	[588]	biology, file_management
GenGen	gengen	1.0.1	[589]	biology, phylogenetics
Genome STRiP	genomestrip	2.00.1602	[590]	biology, genomics, ngs
Genome_Graph_Annotation	genome_graph_annotation	20190131	[591]	phylogenetics
GenomeScope2	genomescope2	2.0	[592]	phylogenetics
GenomeThreader	genomethreader	1.7.3	[593]	phylogenetics
GenomeTools	genometools	1.5.7, 1.5.9	[594]	biology
genomic-fluidity	genomic-fluidity	20151109	[595]	phylogenetics
GenomicConsensus	genomicconsensus	2.3.3	[596]	biology, phylogenetics
GenomicNeuralnet	genomic-neuralnet	20161030	[597]	phylogenetics
GenomicTools	genomictools	2.7.0	[598]	biology, ngs, chip-seq, rna-seq
GenotypeHarmonizer	genotypeharmonizer	1.4.18	[599]	biology
Genrich	genrich	0.5	[600]	phylogenetics
GenSel	gensel	4.90	[601]	genomics
geopython	geopython	1.0.0, 1.0.1, 1.0.2	[602]	programming, geospatial
GEOS	geos	3.3.8, 3.6.2	[603]	library, data_science
GeP	gep	2.1	[604]	biology, phylogenetics
gepard	gepard	1.40.0	[605]	phylogenetics
Gephi	gephi	0.10.0	[606]	visualization, image_processing
Gerbil	gerbil	1.11	[607]	phylogenetics
get_homologues	get_homologues	3.3.3	[608]	biology, genomics
GetOrganelle	getorganelle	1.7.3.5, 1.7.5.0	[609]	phylogenetics
GFam	gfam	1.1	[610]	biology, genomics, annotation
GFF-Ex	gff-ex	2.3	[611]	phylogenetics
GFF3toolkit	gff3toolkit	2.0.3	[612]	phylogenetics
gffcompare	gffcompare	0.12.2	[613]	phylogenetics
gffread	gffread	0.11.8, 0.12.7, 0.9.8c	[614]	biology
Gflags	gflags	2.2.1, 20150520	[615]	web, library
GFOLD	gfold	1.1.4	[616]	biology, rna-seq
ggsashimi	ggsashimi	0.5.0	[617]	phylogenetics
GHOST-MP	ghost-mp	1.3.4	[618]	phylogenetics
Ghostscript	ghostscript	9.22	[619]	documentation
giggle	giggle	20221212	[620]	Genomics
Giotto	giotto	0.1.0	[621]	phylogenetics
giraf	giraf	1.02	[622]	sequencing, biology
Git	git	2.14.1, 2.30.1	[623]	revision_control
git-filter-repo	git-filter-repo	2.33.0	[624]	phylogenetics
glactools	glactools	1.0.8	[625]	phylogenetics
Glimmer	glimmer	3.02	[626]	biology, annotation
GlimmerHMM	glimmerhmm	3.0.4	[627]	biology, annotation
GLMsingle	glmsingle	1.0	[628]	imaging
Globus	globus	1.10.1, 2.1.3	[629]	file_management
glog	glog	0.3.5	[630]	web, library
GLPK	glpk	4.55, 4.65	[631]	programming
Glueviz	glueviz	0.15.2	[632]	phylogenetics
GMAP	gmap	20180212, 20180212_sse2, 20190610	[633]	biology, genomics, ngs
GMcloser	gmcloser	1.6	[634]	biology, ngs
GMP	gmp	6.1.2	[635]	library
GnuPlot	gnuplot	5.2.2, 5.2.3, 5.4.1	[636]	graphics, math
Go	go	1.13.6, 1.15.4, 1.18.3	[637]	language
goatools	goatools	1.2.3	[638]	biology, ontology
GOMAP	gomap	1.3	[639]	biology, ngs
GoPHY	gophy	201030	[640]	phylogenetics
gotcloud	gotcloud	1.17.5	[641]	phylogenetics
GPA	gpa	1.1	[642]	phylogenetics
GPhoCS	gphocs	1.2.3	[643]	phylogenetics
Gpufit	gpufit	20201127	[644]	phylogenetics
Grace	grace	5.1.22	[645]	graphics, statistics
GRACKLE	grackle	3.1	[646]	library, compiler, astronomy
GrADS	grads	2.0.1	[647]	geospatial, math
Graftm	graftm	0.12.2	[648]	phylogenetics
GramCluster	gramcluster	1.3	[649]	biology, sequencing
graph-tool	graph-tool	2.32	[650]	phylogenetics
Graph_annotation	graph_annotation	0.1	[651]	phylogenetics
graphaligner	graphaligner	1.0.11, 1.0.16	[652]	genomics
GraPhlAn	graphlan	1.1.3	[653]	phylogenetics
GraphMap2	graphmap2	0.6.5	[654]	phylogenetics
GraphSplitting	graphsplitting	2.4	[655]	phylogenetics
graphtyper	graphtyper	2.7.2	[656]	phylogenetics
GraphViz	graphviz	2.38.0, 2.46.1	[657]	biology, neuroscience, imaging
GRASS	grass	7.0, 7.4	[658]	geospatial
grf	grf	1.0.0	[659]	genomics
Grib_api	grib_api	1.10.1, 1.15.1, 1.26.1	[660]	compiler, library
GRIDSS	gridss	2.6.2	[661]	phylogenetics
GROCSVs	grocsvs	0.2.5	[662]	phylogenetics
GROMACS	gromacs	2021.2, 2021.3, 2021.4	[663]	chemistry, molecular_dynamics
GroopM	groopm	0.3.5	[664]	biology, phylogenetics
Groovy	groovy	2.4.15	[665]	programming
Gscripts	gscripts	1.1	[666]	biology
GSEA	gsea	3.0.0, 4.2.2	[667]	biology, genomics
GSL	gsl	2.4, 2.5, 2.6	[668]	library, data_science
GSNP	gsnp	1.0	[669]	biology, ngs
GTAHunter	gtahunter	20200106	[670]	phylogenetics
GTDBTk	gtdbtk	1.7.0, 2.0.0, 2.1.0	[671]	phylogenetics
GTOOL	gtool	0.7.5	[672]	phylogenetics
GUAVA	guava	1.0	[673]	phylogenetics
Gubbins	gubbins	2.4.1, 3.2.1	[674]	phylogenetics
guideseq	guideseq	1.0.2	[675]	sequencing, genomics, biology, data_science
guile	guile	2.2.2	[676]	programming
GULP	gulp	4.4, 5.0	[677]	material_science
guppy	guppy	6.1.7, 6.4.2, 6.4.3	[678]	phylogenetics
Gurobi	gurobi	10.0.0, 9.5.1	[679]	math, programming
GWAMA	gwama	2.2.2	[680]	phylogenetics
Gzip	gzip	1.10	[681]	compression
hacdivsel	hacdivsel	1.4.1	[682]	genomics, biology
Hail	hail	0.2.77	[683]	biology, genomics
hal	hal	2.1	[684]	phylogenetics
HALC	halc	1.1	[685]	biology, phylogenetics
halla	halla	0.8.17	[686]	phylogenetics
HaMStR	hamstr	13.2.3, 13.2.4, v8b	[687]	biology, genomics
hapbin	hapbin	1.3.0	[688]	biology, genomics
HapCompass	hapcompass	0.7.7	[689]	imaging, ngs, genomics
HAPCUT	hapcut	0.7	[690]	biology, assembly
HapCUT2	hapcut2	1.3.3	[691]	biology, genomics, sequencing
hapdup	hapdup	0.6	[692]	phylogenetics, biology
haphpipe	haphpipe	1.0.3	[693]	phylogenetics, biology
Haploflow	haploflow	0.1	[694]	biology, phylogenetics
Haplomerger2	haplomerger2	20180603	[695]	biology, genomics
HAPLOSWEEP	haplosweep	1.0	[696]	biology, phylogenetics
happy	happy	0.3.14	[697]	phylogenetics, biology
hapQTL	hapqtl	1.00	[698]	biology
hapsembler	hapsembler	2.21	[699]	biology, assembly
harvesttools	harvesttools	1.2	[700]	phylogenetics, biology
HASLR	haslr	0.8a1	[701]	phylogenetics
hclust2	hclust2	1.0.0	[702]	statistics, mapping
HDF4	hdf4	4.2.11	[703]	library, data_science
HDF5	hdf5	1.8.19, 1.8.20, 1.8.9	[704]	library, data_science
hecaton	hecaton	0.5.1	[705]	genomics, biology
HELEN	helen	20200516	[706]	phylogenetics
HelitronScanner	helitronscanner	1.1	[707]	phylogenetics
hgraph2graph	hgraph2graph	20210428	[708]	chemistry
hgtector	hgtector	2.0	[709]	biology, sequencing
HiC-Pro	hic-pro	3.0.0	[710]	biology, pipeline, genomics
Hifiasm	hifiasm	0.16.1, 0.4, 0.8	[711]	phylogenetics
HipSTR	hipstr	0.7	[712]	phylogenetics
HISAT2	hisat2	2.2.1, 2.2.1-3n, 20230203	[713]	biology, alignment, ngs
HLAminer	hlaminer	1.3.1, 1.4	[714]	biology, phylogenetics
HMM-FRAME	hmm-frame	20140724	[715]	phylogenetics
HmmCleaner	hmmcleaner	0.180750	[716]	phylogenetics
HMMER	hmmer	3.1b1, 3.1b2, 3.2.1	[717]	biology, genomics
hmmer2go	hmmer2go	0.18.1	[718]	phylogenetics, biology
HMMRATAC	hmmratac	1.2.10	[719]	phylogenetics
HOMER	homer	4.10, 4.11, 4.8	[720]	biology, sequencing, ngs
homopolish	homopolish	0.3.3	[721]	genomics, biology
HOOMD	hoomd	2.1.7	[722]	library, math
HPL	hpl	2.1	[723]	programming, performance_analysis
hpsandbox	hpsandbox	1.0.0	[724]	Programming
HTMLDoc	htmldoc	1.8.28, 1.9.3	[725]	documentation, web
HTSeq	htseq	0.11.2	[726]	biology, ngs
HUMAnN	humann	2.8.1	[727]	sequencing, biology
humann2	humann2	0.11.2, 2.8.1	[728]	phylogenetics
hyb	hyb	20141126, 20200815	[729]	biology, ngs, rna-seq
HybPiper	hybpiper	1.3.1, 2.0.1, 2.1.1	[730]	biology, phylogenetics
HyDe	hyde	0.4.3	[731]	phylogenetics
hylite	hylite	2.0.2	[732]	genomics, biology
HyPhy	hyphy	2.5.4, 2.5.7, 2.5.8	[733]	biology, genomics
HYPRE	hypre	2.15.1, 2.18.2, 2.19.0	[734]	math
iAnnotateSV	iannotatesv	1.0.6, 1.0.9	[735]	biology, phylogenetics
iaps	iaps	02012023	[736]	programming
iAssembler	iassembler	1.3.2	[737]	biology, assembly
ibdne	ibdne	20150815	[738]	biology, ngs
icommands	icommands	3.3.1	[739]	utility
IDBA-MT	idba-mt	1.0	[740]	biology, ngs
IDBA-UD	idba-ud	1.1.1, 1.1.1-512, 1.1.1-512-mem	[741]	genomics, phylogenetics
IDL	idl	8.3	[742]	language, programming, data_science
IDR	idr	2.0.3	[743]	phylogenetics
IGB	igb	8.4.1	[744]	biology, genomics
igBLAST	igblast	1.5.0, 1.7.0	[745]	biology
IGoR	igor	1.4.0	[746]	phylogenetics
iGTP	igtp	1.1	[747]	biology, phylogenetics
IGV	igv	2.3.91, 2.4.16, 2.8.6	[748]	biology, ngs, phylogenetics
illumina-utils	illumina-utils	2.11	[749]	phylogenetics
Illumiprocessor	illumiprocessor	2.0.9	[750]	phylogenetics
IM and IMa	ima	20091217	[751]	biology, genomics
Ima2	ima2	20120827	[752]	biology, genomics
IMa2p	ima2p	20170712	[753]	biology, phylogenetics
IMA3	ima3	22Aug18	[754]	molecular_dynamics
ImageJ	imagej	1.48	[755]	imaging
imagej2	imagej2	09302022	[756]	image processing, imaging
ImageMagick	imagemagick	7.0.8-20	[757]	imaging
Imaginaire	imaginaire	20201229	[758]	imaging, visualization, ai, machine_learning
IMOD	imod	4.7.15, 4.9.10	[759]	image_processing
imoka	imoka	1.0	[760]	biology, genomics
IMPUTE2	impute2	2.3.2	[761]	phylogenetics
IMPUTE5	impute5	1.1.5	[762]	biology, math
INDELible	indelible	1.03	[763]	phylogenetics
Infernal	infernal	1.1.1, 1.1.4	[764]	biology, alignment
INLA	inla	20160718, 20170620	[765]	statistics, modeling, programming
InParanoid	inparanoid	4.1	[766]	biology
Inspector	inspector	1.0.2	[767]	biology, genomics
InStruct	instruct	20160723	[768]	phylogenetics
Intel Compilers and Libraries	intel	2018.1.163, 2019.1.144, 2020.0.166	[769]	language, programming, library, math, compiler
Intel MPI	impi	5.1.1	[770]	programming, library
InterProScan	iprscan	5.57, 5.59, 5.60	[771]	biology
intervene	intervene	0.6.2	[772]	biology, phylogenetics
IOAPI	ioapi	3.1, 3.2	[773]	climate
IPOPT	ipopt	3.12.10, 3.12.6	[774]	library, compiler, math
ipyrad	ipyrad	0.7.24, 0.7.30, 0.9.53	[775]	phylogenetics
IQ-TREE	iq-tree	2.1.2, 2.1.3, 2.2.2	[776]	biology, phylogenetics
IRAP	irap	0.8.1p7	[777]	biology, ngs
irep	irep	1.10	[778]	biology, genomics
IRFinder	irfinder	1.2.0, 1.3.0, 1.3.1	[779]	biology, rna-seq
isONclust	isonclust	0.0.6	[780]	phylogenetics
isonclust2	isonclust2	2.3	[781]	rna-seq
IsoSel	isosel	1.0	[782]	phylogenetics
IsoSeq3	isoseq3	3.4.0, 3.7.0, 3.8.2	[783]	biology, ngs
ISOWN	isown	20180820	[784]	phylogenetics
isPcr	ispcr	3.3	[785]	biology, phylogenetics
ITK	itk	3.20.1, 4.10.1	[786]	biology
ITK-SNAP	itksnap	3.0.0, 3.8.0	[787]	biology, neuroscience, imaging
ITSx	itsx	1.1b	[788]	phylogenetics
IVA	iva	1.0.11	[789]	phylogenetics
iVar	ivar	1.3.1	[790]	biology
Jabba	jabba	1.0	[791]	biology, phylogenetics
JACUSA	jacusa	1.2.0	[792]	biology, ngs, phylogenetics
JAGS	jags	3.3.0, 3.4.0, 4.2.0	[793]	statistics
Jasmine	jasmine	1.1.4	[794]	phylogenetics
jasp	jasp	0.14.3	[795]	statistics
jbrowse2	jbrowse2	1.7.4	[796]	web
JCVI	jcvi	0.8.12, 1.0.13, 1.2.10	[797]	phylogenetics
JDK	java	11.0.1, 14, 9.0.1	[798]	programming
Je	je	1.0	[799]	biology, ngs
Jellyfish	jellyfish	2.2.4, 2.2.6, 2.3.0	[800]	biology, ngs
jModelTest	jmodeltest	2.1.1	[801]	biology, genomics, phylogenetics
jo	jo	1.3	[802]	utility
jq	jq	1.6	[803]	utility
juicer	juicer	1.22.01	[804]	phylogenetics
Julia	julia	1.7.1, 1.7.3, 1.8.2	[805]	programming, language, statistics
Jupyter	jupyter	6.0.3, 6.2.0, 6.5.2	[806]	programming
jutils	jutils	1.0	[807]	genomics, biology
JVARKIT	jvarkit	20180405	[808]	biology, phylogenetics
Kaiju	kaiju	1.6.2, 1.7.2	[809]	biology, phylogenetics
KaKs	kaks	1.2, 2.0	[810]	biology, genomics, phylogenetics
Kalign	kalign	3.3.1	[811]	biology, sequencing, alignment
kallisto	kallisto	0.43.0, 0.44.0, 0.48.0	[812]	biology, ngs, rna-seq
khmer	khmer	2.0, 2.1	[813]	biology, ngs
KIM	kim	1.7.2, 1.8.2, 1.9.3	[814]	simulation
KING	king	2.1.2, 2.3.0	[815]	biology, genomics
KisSplice	kissplice	2.4.0-p1	[816]	biology, RNA
KLayout	klayout	0.26.7	[817]	phylogenetics
kma	kma	20230106	[818]	alignment
KMC	kmc	3.1.0, 3.1.1, 3.2.1	[819]	phylogenetics
kmerdb	kmerdb	1.9.2	[820]	genomics, biology
kmerfreq	kmerfreq	4.0	[821]	biology, genomics
KMOS	kmos	0.3.21	[822]	phylogenetics
kneaddata	kneaddata	0.7.4, 0.9.0	[823]	phylogenetics
Knitro	knitro	12.2.0	[824]	math
KofamScan	kofamscan	1.3.0	[825]	phylogenetics
kover	kover	2.0.3	[826]	phylogenetics
Kraken	kraken	2.0.6b, 2.0.8b, 2.1.2	[827]	biology, ngs
KrakenUniq	krakenuniq	0.5.8, 0.7.3	[828]	phylogenetics
Krona	krona	2.8.1, 20161019	[829]	biology
ksnp	ksnp	3.021	[830]	biology, phylogenetics, variant_calling
Ksrates	ksrates	1.1.1	[831]	genomics, biology
LACHESIS	lachesis	2.1	[832]	phylogenetics
Lambda	lambda	0.9.4, 1.0.3, 2.0.0	[833]	biology, sequencing, phylogenetics
LAMMPS	lammps	30Jul16, 7Aug19, 7Dec15	[834]	molecular_dynamics
LAMP	lamp	2.5	[835]	biology, genomics
laneta	laneta	20220517, 20220808, 20220812	[836]	biology
langdetect	langdetect	1.0.9	[837]	language, utility
LAPACK	lapack	3.8.0	[838]	programming, library, compiler
Last	last	916, 979	[839]	biology, sequencing, alignment
LAStools	lastools	20200114	[840]	image_processing
LASTZ	lastz	1.02.00, 1.03.02, 1.04.00	[841]	biology, ngs
Lazypipe	lazypipe	1.2	[842]	genomics
LazyPredict	lazypredict	0.2.8	[843]	phylogenetics
lbzip	lbzip	2.5	[844]	compression
LCModel	lcmodel	6.3	[845]	biology, spectroscopy
ldak	ldak	5.2	[846]	phylogenetics, biology
LDhat	ldhat	2.2a	[847]	biology, genomics
ldsc	ldsc	1.0.1	[848]	genomics, biology
leafaudio	leafaudio	0.1.0	[849]	machine_learning, audio
LEfSe	lefse	20180219	[850]	phylogenetics
LEMON	liblemon	1.2.3	[851]	library
LFMM	lfmm	1.4, 1.5	[852]	biology, phylogenetics
Libint	libint	2.5.0, 2.5.0b	[853]	library
libMesh	libmesh	1.5.0	[854]	math
libunistring	libunistring	0.9.7	[855]	library
libvips	libvips	8.5.4	[856]	image_processing
LIBXC	libxc	4.2.3, 4.3.4	[857]	library, math
LIBXSMM	libxsmm	1.13	[858]	library, compiler, math
LIBZMQ	libzmq	4.3.1	[859]	library
Liftoff	liftoff	1.4.2	[860]	phylogenetics
LIGR	ligr	2.05	[861]	biology, assembly
LillyMol	lillymol	6.1	[862]
lima	lima	2.0.0, 2.2.0, 2.7.1	[863]	phylogenetics
lingua	lingua	1.0.1	[864]	language, utility
LINKS	links	1.8.5, 1.8.6	[865]	biology, genomics
Linksbrowser	linksbrowser	2.14	[866]	web
LIQA	liqa	1.0.0	[867]	phylogenetics
LMAP	lmap	1.0.2	[868]	biology, phylogenetics
lncScore	lncscore	1.0.2	[869]	biology, phylogenetics
lobSTR	lobstr	4.0.6	[870]	biology, phylogenetics
localbrainage	localbrainage	20210415	[871]	biology, machine_learning
localizer	localizer	1.0.4	[872]	phylogenetics
LocusZoom	locuszoom	1.4	[873]	phylogenetics
LoFreq	lofreq	2.1.3.1	[874]	phylogenetics
LongQC	longqc	1.2.0c	[875]	phylogenetics
LongRanger	longranger	2.1.5, 2.2.2	[876]	biology, phylogenetics
LongStitch	longstitch	1.0.3	[877]	genomics, biology
LoRDEC	lordec	0.9	[878]	phylogenetics
LoRMA	lorma	0.3, 0.5	[879]	biology, ngs
loter	loter	1.0	[880]	genomics,
LRBinner	lrbinner	0.1	[881]	biology, genomics
lrgapcloser	lrgapcloser	09042018	[882]	biology
LS-DYNA	ls-dyna	700, 711, 901	[883]	physics
LSD2	lsd2	1.6.5	[884]	phylogenetics
ltr_finder	ltr_finder	1.07	[885]	biology, phylogenetics
LTRRetriever	ltrretriever	2.5, 2.9.0, 20170514	[886]	biology, phylogenetics
Lua	lua	5.3.2, 5.3.4	[887]	programming, language
Lucene	pylucene	7.7.1, 9.1.0	[888]	programming, search
lumpy-sv	lumpy	0.2.1, 0.2.13, 0.3.1	[889]	biology, genomics
LZO	lzo	2.09	[890]	library, compression
M5nr	m5tools	20121126	[891]	biology, genomics
Macaulay2	macaulay2	1.15	[892]	phylogenetics
MACH	mach	1.0.18	[893]	biology, genomics, ngs
Mach2VCF	mach2vcf	20150515	[894]	biology
MACS	macs	2.0.10, 2.1.2, 2.2.7.1	[895]	biology, chip-seq
MafFilter	maffilter	1.3.0	[896]	phylogenetics
MAFFT	mafft	7.397, 7.490, 7.505	[897]	biology, sequencing
MAGeCK	mageck	0.5.9.4	[898]	phylogenetics
MAGeCK-VISPR	mageck-vispr	0.5.6	[899]	phylogenetics
MAGeCKFlute	mageckflute	1.14.0	[900]	phylogenetics
Magenta	magenta	2.1.2	[901]	phylogenetics
magicblast	magicblast	1.6.0	[902]	genomics, biology
MAGMA-GWAS	magma-gwas	1.09	[903]	phylogenetics
magus	magus	20220121	[904]	sequencing, alignment
MAJIQ	majiq	2.2, 2.3	[905]	phylogenetics
Maker	maker	2.31.10, 2.31.6, 3.01.03	[906]	biology
MAnorm	manorm	20120316	[907]	biology, phylogenetics
MANTA	manta	1.6.0	[908]	phylogenetics
mantis	mantis	1.0.4	[909]	phylogenetics
mapclassify	mapclassify	2.4.2	[910]	statistics, mapping, geospatial
mapdamage	mapdamage	2.2.1	[911]	ngs, sequencing, biology
MapThin	mapthin	1.11	[912]	phylogenetics
Maq	maq	0.7.1	[913]	biology, ngs
MarginPolish	marginpolish	1.0.0	[914]	phylogenetics
MARK	mark	2.0.1	[915]	data_science, math
MarkerMiner	markerminer	20150710	[916]	biology, genomics
Mash	mash	1.1, 2.3	[917]	biology, genomics
MasHmap	mashmap	2.0	[918]	phylogenetics
mashtree	mashtree	1.2.0	[919]	genomics, biology
maskrc-svg	maskrc-svg	0.5	[920]	genomics
MASS	mass	1.1.1	[921]	genomics, biology
MASSMINE	massmine	0.10.0, 0.11.0, 0.9.5	[922]	data_mining
MaSuRCA	masurca	4.0.8, 4.0.9, 4.1.0	[923]	biology, alignment
Mathematica	mathematica	12.1.1.0	[924]	math
MATLAB	matlab	2020a, 2020b, 2022a	[925]	math, language
MATS	mats	4.0.1, 4.0.2, 4.1.0	[926]	biology, ngs, rna-seq
matt	matt	1.3.1	[927]
Mauve	mauve	2.3.1	[928]	biology, ngs, genomics
mawk	mawk	1.3.4-20150503	[929]	language
maxbin	maxbin	2.1.1	[930]	biology, ngs
Maxima	maxima	5.41.0	[931]	math
MC	mc	4.6.1	[932]	shell
mCarts	mcarts	1.0.2	[933]	biology, genomics, math
mccortex	mccortex	1.0	[934]	phylogenetics
MCL	mcl	12-135, 14-137	[935]	biology, genomics
MCNP	mcnp	6, 6.1	[936]	physics
MCNPX	mcnpx	2.7.0	[937]	physics
MCR	mcr	2019b, 2020a, 2020b	[938]	math, language
MCScanX	mcscanx	20130328	[939]	biology, phylogenetics
mdanalysis	mdanalysis	1.1.1	[www.mdanalysis.org]	physics, biology
MECAT	mecat	20180308	[940]	phylogenetics
Medaka	medaka	1.2.1, 1.6.0, 1.7.3	[941]	biology, phylogenetics
Medusa	medusa	1.6	[942]	phylogenetics
MEGA	mega	7.0.26	[943]	biology, phylogenetics
Mega2	mega2	4.9.2, 6.0.0	[944]	biology, phylogenetics
MEGAHIT	megahit	1.1.1, 1.1.4	[945]	biology, phylogenetics
Megalodon	megalodon	2.0.0, 2.4.1	[946]	ngs, genomics
MEGAN	megan	5.10.3, 6.23.4, 6.4.15	[947]	biology, ngs
MEGASAT	megasat	1.0	[948]	phylogenetics
Megraft	megraft	1.0.2	[949]	biology, sequencing
MELD	meld	0.4.14, 0.4.19, 0.5.9	[950]	chemistry, molecular_dynamics
MELTING	melting	4.3.1	[951]	biology, genomics, rna
MEME	meme	5.0.2, 5.0.5, 5.4.1	[952]	biology, sequencing
MentaLiST	mentalist	0.1.3	[953]	biology, phylogenetics
Meraculous	meraculous	2.0.5	[954]	biology, ngs
Mercurial	mercurial	4.8.2	[955]	revision_control
merge_peaks	merge_peaks	0.1.0	[956]	workflow_automation
Merlin	merlin	1.1.2	[957]	biology, variant_calling
Merqury	merqury	1.1, 1.3	[958]	phylogenetics
Meryl	meryl	1.0	[959]	phylogenetics
MeShClust	meshclust	1.2.0	[960]	biology
Meshroom	meshroom	2019.2.0	[961]	phylogenetics
MET	met	10.0	[962]	climate, modeling
Meta-Marc	meta-marc	1.0.0	[963]	phylogenetics
Meta-Tissue	meta-tissue	0.4	[964]	biology, genomics
MetaBAT	metabat	0.32.4, 2.13	[965]	biology, genomics
MetaBCC-LR	metabcc_lr	2.0.0	[966]	biology, genomics
Metabin	metabin	1.0	[967]	genomics
metabolic	metabolic	4.0	[968]	phylogenetics
MetaCherchant	metacherchant	0.1.0	[969]	biology, phylogenetics
MetaCluster	metacluster	5.0b	[970]	biology, genomics
MetaCompare	metacompare	20181016	[971]	phylogenetics
metacrast	metacrast	20200309	[972]	phylogenetics
MetaGeneMark	metagenemark	2.10, 3.26	[973]	biology, genomics
METAL	metal	20110325	[974]	biology, ngs, genomics
MetaLAFFA	metalaffa	1.0.0	[975]	phylogenetics
MetaMaps	metamaps	20201207	[976]	phylogenetics
METANNOT	metannot	20171129	[977]	phylogenetics
Metaphlan	metaphlan	3.0.3, 3.1.0, 4.0.1	[978]	phylogenetics
MetaPhlAn2	metaphlan2	2.7.7	[979]	biology, phylogenetics
MetaPhysicl	metaphysicl	1.0.0	[980]	math, astronomy, simulation
Metashape	metashape	1.8.4	[981]
MetaSV	metasv	0.5.4	[982]	biology, phylogenetics, ngs
MetaVelvet	metavelvet	1.2.06	[983]	biology, genomics
metaWRAP	metawrap	1.2	[984]	phylogenetics
Metaxa2	metaxa2	2.1.1, 2.1.3, 2.2.3	[985]	biology, ngs, sequencing
MethylDackel	methyldackel	0.5.0, 0.6.1	[986]	phylogenetics
methylpy	methylpy	1.2.9	[987]	biology, phylogenetics
Metilene	metilene	0.2.8	[988]	biology, genomics, methylation
METIS	metis	5.1.0	[989]	utility
Mfannot	mfannot	20180405	[990]	biology, phylogenetics
mfold	mfold	3.6	[991]	biology, structure, rna
mg-rast	mg-rast	20150919	[992]	biology, genomics
MGEfinder	mgefinder	1.0.5	[993]	phylogenetics
MGERT	mgert	1.0.1	[994]	phylogenetics
MGEScan	mgescan	20160416	[995]	biology, genomics
MGLTools	mgltools	1.5.7	[996]	biology, visualization
MHAP	mhap	1.6	[997]	biology, sequencing
MHCflurry	mhcflurry	1.4.3	[998]	phylogenetics
MIA	mia	20130201	[999]	biology, ngs
micop	micop	03312022	[1,000]	genomics
MicrobeAnnotator	microbeannotator	2.0.5	[1,001]	annotation, biology
MIDAS	midas	1.3.2, 20160830	[1,002]	biology, phylogenetics
MIGRATE-N	migraten	4.2.14, 4.4.4, 5.0.4	[1,003]	biology, genomics
Mikado	mikado	2.3.3	[1,004]	biology, genomics, sequencing, pipeline
MIKE	mike	1.0	[1,005]	geospatial, fluid_dynamics, modeling
Minced	minced	0.2.0	[1,006]	biology, genomics
Minia	minia	3.2.6	[1,007]	genomics, biology
Miniasm	miniasm	0.2-r168, 0.3-r179	[1,008]	biology, phylogenetics
MiniCaller	minicaller	20161201	[1,009]	biology, ngs, phylogenetics
minigraph	minigraph	0.15	[1,010]	phylogenetics
minimac	minimac	1-20130717, 3-20150727	[1,011]	biology, ngs
minimac2	minimac	2-20140915	[1,012]	biology, ngs
minimap	minimap	2.1t, 2.21, 2.9-r720	[1,013]	biology, phylogenetics
minimap2	minimap2	2.24	[1,014]	genomics, biology
Minipolish	minipolish	0.1.3	[1,015]	biology, genomics
MinkowskiEngine	minkowskiengine	0.5.3	[1,016]	machine_learning
MinPath	minpath	1.4	[1,017]	biology, phylogenetics
MIRA	mira	4.0.rc1, 4.9.6, 5rc2	[1,018]	biology, genomics, assembly
miRanda	miranda	1.9	[1,019]	phylogenetics
miRBShunter	mirbshunter	0.2	[1,020]	phylogenetics
mirdeep	mirdeep	0.1.0, 0.1.1, 2.0.1.3	[1,021]	phylogenetics
miRDP2	mirdp2	1.1.4	[1,022]	biology, genomics
Mireap	mireap	0.20	[1,023]	biology
miRge	mirge	2.0	[1,024]	phylogenetics
Misa	misa	1.0	[1,025]	biology, genomics
MISO	miso	0.5.3	[1,026]	biology, ngs, sequencing, rna-seq
MITE-Hunter	mite-hunter	20111101	[1,027]	biology, phylogenetics
MITObim	mitobim	1.9.1	[1,028]	phylogenetics
MitoFinder	mitofinder	1.0.2, 1.1, 1.4	[1,029]	phylogenetics
mitohifi	mitohifi	2.2	[1,030]	genomics, sequencing
MitoPhAST	mitophast	3.0	[1,031]	phylogenetics
Mitsuba2	mitsuba2	2.2.1	[1,032]	graphics
MiXCR	mixcr	2.1.8, 3.0.13	[1,033]	biology, phylogenetics
MixMHC2pred	mixmhc2pred	1.2	[1,034]	phylogenetics
MixMHCpred	mixmhcpred	2.0.2	[1,035]	phylogenetics
mixmogam	mixmogam	20190322	[1,036]	phylogenetics
MKL	mkl	2018.1.163, 2019.1.144, 2020.0.166	[1,037]	programming, library, math, compiler
mlcoalsim	mlcoalsim	1.9916b	[1,038]	biology, phylogenetics
mlpack	mlpack	3.4.2	[1,039]	library
mlst	mlst	2.15.2	[1,040]	phylogenetics
mlstcheck	mlst-check	2.1	[1,041]	phylogenetics
MMSEQ	mmseq	1.0.8	[1,042]	biology, genomics
MMseqs2	mmseqs2	11, 12	[1,043]	phylogenetics
MMvec	mmvec	1.0.5, 1.0.6	[1,044]	metabolomics
MNEtools	mnetools	0.22.0, 1.3.1	[1,045]	phylogenetics
MOABS	moabs	1.2.9, 1.3.2, 1.3.4	[1,046]	biology, ngs
mobsuite	mobsuite	3.1.0	[1,047]	sequencing, biology
MOCCASIN	moccasin	0.25	[1,048]	phylogenetics
MODELLER	modeller	9.14, 9.23	[1,049]	biology, modeling, structure
MODELTEST	modeltest	0.1.2, 0.1.7	[1,050]	biology, phylogenetics
Modulus	modulus	21.06, 22.03	[1,051]	physics, ai, neural_network
Molden	molden	5.0	[1,052]	chemistry, structure
MolProbity	molprobity	20221216	[1,053]	biology
momi	momi	2.1.19	[1,054]	phylogenetics, biology
monai	monai	0.8, 0.8.1, 0.9.0	[1,055]	healthcare
MONAI label	ngc-monailabel	0.3.2	[1,056]	healthcare
MongoDB	mongodb	4.0.3	[1,057]	database
Moni	moni	0.2.0	[1,058]	genomics, biology
mono	mono	5.18	[1,059]	linux, programming
Monolix	monolix	4.3.2	[1,060]	modeling, biology
MOOSE	moose	20210726, 20220610, 20230320	[1,061]	physics, simulation
MORPHEUS	morpheus	23.01	[1,062]	machine_learning
Mosaic	mosaic	1.7.4	[1,063]	phylogenetics
MOSAIK	mosaik	2.1.33, 2.2.3, 2.2.30	[1,064]	biology, alignment
Mosdepth	mosdepth	0.2.3, 0.3.1	[1,065]	biology, phylogenetics
moses	moses	0.3.1	[1,066]	machine learning, data science
Mothur	mothur	1.38.1, 1.41.3, 1.46.1	[1,067]	biology
MotionCor2	motioncor2	1.2.3, 1.3.1	[1,068]	imaging
mOTU	motu	1.1	[1,069]	biology, genomics
mOTUs	motus	2.5.1	[1,070]	phylogenetics
MountainSort	mountainsort	0.9.0	[1,071]	library
MP-EST	mpest	1.4	[1,072]	biology, ngs, sequencing
MPACK	mpack	0.8.0	[1,073]	library
MPB	mpb	1.5	[1,074]	library, math
MPBoot	mpboot	1.1.0	[1,075]	biology, phylogenetics
MPFR	mpfr	3.1.6	[1,076]	library, math
mpinterfaces	mpinterfaces	20170613	[1,077]	math
MrBayes	mrbayes	3.2.4, 3.2.5, 3.2.6	[1,078]	biology, phylogenetics
MRIcroGL	mricrogl	20201102, 20210327, 20211006	[1,079]	biology, imaging
MRIcron	mricron	201306, 20161012, 20190911	[1,080]	biology, imaging
mriqc	mriqc	0.11.0, 0.16.1, 22.0.1	[1,081]	imaging, biology
MRtrix	mrtrix	3.0.1, 3.0.3, 3.0rc2	[1,082]	biology, imaging
mrtrix3tissue	mrtrix3tissue	5.2.9	[1,083]	phylogenetics
ms	ms	20171108	[1,084]	phylogenetics
ms-dial	ms-dial	4.4.8	[1,085]	biology, metabolomics
msfinder	msfinder	3.52	[1,086]	biology, metabolomics
mSINGS	msings	20180810	[1,087]	phylogenetics
MSMC-Tools	msmc-tools	20190614	[1,088]	phylogenetics
msprime	msprime	0.7.4	[1,089]	phylogenetics
MstatX	mstatx	1.0	[1,090]	biology, phylogenetics
MSTmap	mstmap	1.0	[1,091]	phylogenetics
msvar	msvar	1.3	[1,092]	biology, genomics
MTG2	mtg2	2.15	[1,093]	phylogenetics
mTR	mtr	20210526	[1,094]	biology, genomics
Mugsy	mugsy	1.2.3	[1,095]	biology, phylogenetics
MultiQC	multiqc	1.12, 1.7	[1,096]	biology, chip-seq
MUMmer	mummer	3.23, 4.0.0beta2	[1,097]	biology, genomics
MUSCLE	muscle	3.8.31, 5.1	[1,098]	biology, alignment
MuSE	muse	1.0rc	[1,099]	phylogenetics
Musket	musket	1.1	[1,100]	biology, genomics, ngs
MuTect	mutect	1.1.4, 1.1.7	[1,101]	biology, genomics
MutSig	mutsig	1.4, 1.41	[1,102]	biology, genomics
mvftools	mvftools	20191124	[1,103]	phylogenetics
mvrsion	mvrsion	07302018	[1,104]	sequencing
mxnet	ngc-mxnet	22.08	[1,105]	healthcare
MZMine	mzmine	2.52, 2.53, 3.3.0	[1,106]	biology, spectroscopy
NAMD	namd	2.14, 2.14b2, 3.0 Alpha	[1,107]	molecular_dynamics
NANO	nano	2.8.2	[1,108]	programming
nanocaller	nanocaller	3.1.0	[1,109]	sequencing
nanocomp	nanocomp	1.17.0	[1,110]	programming, sequencing
NanoCount	nanocount	0.2.1	[1,111]	phylogenetics
Nanodisco	nanodisco	1.0.3	[1,112]	phylogenetics
Nanofilt	nanofilt	2.7.1	[1,113]	phylogenetics
nanolyse	nanolyse	1.2.0	[1,114]	genomics, biology
NanoPlot	nanoplot	1.30.1	[1,115]	phylogenetics
Nanopolish	nanopolish	0.11.1, 0.13.2, 20171006	[1,116]	biology
nanostripper	nanostripper	0.1	[1,117]	phylogenetics, biology
NanoSV	nanosv	1.2.0, 1.2.3, 1.2.4	[1,118]	biology, genomics
NanoVar	nanovar	1.3.9	[1,119]	phylogenetics
Napari	napari	0.3.8, 0.4.7	[1,120]	phylogenetics
NBODY	nbody	6	[1,121]	astronomy
NCBI BLAST+	ncbi_blast	2.7.1, 2.8.1, 2.9.0	[1,122]	biology
NCBI C++ Toolkit	ncbi_toolkit	12.0.0, 21.0.0, 7.0.0	[1,123]	biology, programming, library, compiler
NCBI GenBank Tools	genbank_tools	20140130	[1,124]	biology
ncbi-vdb	ncbi-vdb	2.6.3, 2.8.2	[1,125]	ngs
nccl	nccl	20.11	[1,126]	programming, library, gpu
ncftp	ncftp	3.2.5	[1,127]	file_management
NCL	ncl	6.1.2, 6.3.0	[1,128]	climate
NCO	nco	4.2.1, 4.4.3	[1,129]	data_science
ncview	ncview	2.1.2, 2.1.7	[1,130]	visualization
NECAT	necat	202001019, 20200803	[1,131]	genomics
Necklace	necklace	1.00	[1,132]	biology, phylogenetics
NeEstimator	neestimator	2.1	[1,133]	biology
nemo	nemo	1.0.0rc1, 1.0.1, 1.2.0	[1,134]	ai, machine_learning
neovim	neovim	0.2.0, 0.8.1, 0.8.3	[1,135]	programming, shell
NetCDF	netcdf	4.3, 4.3.3, 4.4.3	[1,136]	data_science
NetCDF-C	netcdf-c	4.7.4, 4.8.1, 4.9.0	[1,137]	data_science
NetCDF-F	netcdf-f	4.4.4, 4.5.3, 4.5.4	[1,138]	data_science
NetLogo	netlogo	5.3.64, 6.1.1, 6.2.0	[1,139]	modeling
NEURON	neuron	7.7.2, 8.0.0, 8.2.1	[1,140]	biology, neuroscience
Newbler	newbler	2.7, 2.8, 2.9	[1,141]	biology, ngs, assembly, de_novo
newick-utils	newickutils	1.6	[1,142]	biology, genomics, phylogenetics
newick_utils	newick_utils	1.6, 1.7	[1,143]	biology, phylogenetics
NewTargets	newtargets	20210215	[1,144]	biology
nextclade	nextclade	2.9.1	[1,145]	phylogenetics, genomics
NextDenovo	nextdenovo	2.4.0	[1,146]	phylogenetics
Nextflow	nextflow	22.04.5, 22.10.6, 22.11.0	[1,147]	biology, workflow_automation
NextGenMap	nextgenmap	0.5.5	[1,148]	phylogenetics
NextPolish	nextpolish	1.3.1	[1,149]	phylogenetics
Nextstrain	nextstrain	1.16.1	[1,150]	phylogenetics
nf-core	nf-core	1.12.1, 2.1, 2.7.2	[1,151]	biology, workflow_automation
NGC CLI	ngccli	2.10.1	[1,152]	shell
NGmerge	ngmerge	0.3	[1,153]	phylogenetics
ngmlr	ngmlr	0.2.6, 0.2.7	[1,154]	biology, phylogenetics
ngs-bits	ngsbits	0.1	[1,155]	biology, sequencing
NGS-SDK	ngs-sdk	1.2.4, 1.3.0	[1,156]	biology, healthcare, programming, library
ngscheckmate	ngscheckmate	1.0	[1,157]	phylogenetics
ngsremix	ngsremix	20221117	[1,158]	genomics
ngstools	ngstools	20150816	[1,159]	biology, ngs
nilearn	nilearn	0.7.0, 0.9.0	[1,160]	phylogenetics
nimare	nimare	0.0.5	[1,161]	neuroscience
Nipype	nipype	1.6.0, 1.7.0, 1.8.0	[1,162]	biology, neuroscience, imaging
nlp	nlp	1.1, 1.2	[N/A]	machine_learning
nlr-annotator	nlr-annotator	0.7	[1,163]	phylogenetics
NLR-Parser	nlr-parser	1.0	[1,164]	phylogenetics
NMRPipe	nmrpipe	7.9, 8.2	[1,165]	chemistry, biology
NONMEM	nonmem	7.3.0, 7.4.4	[1,166]	modeling
nonpareil	nonpareil	3.3.4	[1,167]	phylogenetics
Novoalign	novoalign	2.08.02, 3.00.02	[1,168]	biology, ngs
NOVOPlasty	novoplasty	3.7, 4.2, 4.3	[1,169]	phylogenetics
nPhase	nphase	1.1.3	[1,170]	biology, pipeline
npScarf	japsa	1.7	[1,171]	phylogenetics
nQuire	nquire	20180405	[1,172]	phylogenetics
Nsight	nsight	2022.1	[1,173]	gpu, performance_analysis, utility
Nsightsys	nsightsys	2022.2.1	[1,174]	gpu, performance_analysis, utility
nt	nt	20220404	[1,175]	sequencing, neuroscience
ntEdit	ntedit	1.2.1	[1,176]	phylogenetics
nubeamdedup	nubeamdedup	20200907	[1,177]	phylogenetics
NucDiff	nucdiff	2.0.3	[1,178]	phylogenetics
NucleoATAC	nucleoatac	0.3.1	[1,179]	biology
Nullarbor	nullarbor	1.41	[1,180]	biology, phylogenetics
Numba	numba	0.36.2, 0.43.1, 0.48.0	[1,181]	compiler
NUPACK	nupack	3.2.2	[1,182]	phylogenetics
nvhpc	nvhpc	11.1, 21.7	[1,183]	language, programming, library, math, gpu
nVidia HPC Compilers	nvidia	20.11	[1,184]	compiler
NWChem	nwchem	6.8	[1,185]	chemistry
NxTrim	nxtrim	0.4.1	[1,186]	biology, ngs
Oases	oases	0.2.08	[1,187]	biology, ngs, assembly
OCaml	ocaml	4.02.3	[1,188]	language, programming
OCOCO	ococo	0.1.2.6	[1,189]	biology, phylogenetics
octave	octave	6.4.0, 7.2.0, 7.3.0	[1,190]	math
odgi	odgi	0.6	[1,191]	phylogenetics
Olego	olego	1.1.2, 1.1.5, 1.1.6	[1,192]	biology, ngs, rna-seq
OMindel	omindel	20180129	[1,193]	phylogenetics
omniCLIP	omniclip	0.1.0	[1,194]	phylogenetics
OMNIVERSE	omniverse	beta211004	[1,195]	gpu
OMSV	omsv	1.0.1	[1,196]	phylogenetics
ONT-Bonito	ont-bonito	0.1.5, 0.5.3, 0.6.0	[1,197]	phylogenetics
ont_fast5_api	ont-fast5-api	2.0.1, 4.0.2	[1,198]	phylogenetics
ont_tutorial_cas9	ont_tutorial_cas9	20190705	[1,199]	phylogenetics
open-cravat	open-cravat	2.0.1	[1,200]	biology, genomics
open3d	open3d	0.13.0	[1,201]	phylogenetics
OPENACC	openacc	16.7	[1,202]	programming
OpenBabel	openbabel	2.3.2, 2.4.1, 3.1.1	[1,203]	biology
OpenBLAS	openblas	0.2.20	[1,204]	programming, library
OpenCL	opencl	18.1.0.013	[1,205]	phylogenetics
OpenCV	opencv	4.5.2, 4.7.0	[1,206]	library
OpenFOAM	openfoam	4.1, 5.0, 8.0	[1,207]	fluid_dynamics
OpenMM	openmm	7.5, 7.5.0, 7.6.0	[1,208]	chemistry, molecular_dynamics
OpenMPI	openmpi	4.0.5, 4.1.1, 4.1.4	[1,209]	programming, library
OpenNeuro	openneuro	3.17.4, 3.37.4	[1,210]	biology, data_science
OpenPIV-python	openpiv	0.21.2	[1,211]	programming, imaging
OpenPIV-python-gpu	openpiv	20190506-gpu	[1,212]	programming, imaging
OpenPose	openpose	20230106	[1,213]	image_processing
OpenSim	opensim	4.3	[1,214]	phylogenetics
OpenSlide	openslide	3.4.1	[1,215]	imaging
openstructure	openstructure	2.3.1	[1,216]	biology
OptiType	optitype	1.3.1	[1,217]	biology, phylogenetics
Orange3	orange3	3.3.6	[1,218]	data_mining
ORCA	orca	4.0.1.2	[1,219]	chemistry, structure
OrganellePBA	organellepba	20180904	[1,220]	phylogenetics
OrthoFiller	orthofiller	1.1.4	[1,221]	phylogenetics
OrthoFinder	orthofinder	1.1.10, 2.3.11, 2.5.2	[1,222]	biology, ngs
Orthofisher	orthofisher	0.1.2	[1,223]	biology, genomics
Orthograph	orthograph	0.6.3	[1,224]	orthology
Orthologer	orthologer	2.2.0	[1,225]	biology
OrthoMCL	orthomcl	2.0.3, 2.0.7	[1,226]	biology, genomics
osprey	osprey	1.1.0	[1,227]	spectroscopy, neuroscience
OTB	otb	5.8.0	[1,228]	geospatial
p4est	p4est	1.1, 2.8	[1,229]	library
p4vasp	p4vasp	0.3.29, 0.3.30	[1,230]	chemistry, structure
p53MH	p53mh	20020901	[1,231]	biology, sequencing
p7zip	p7zip	9.20.1	[1,232]	utility
PacBio	pacbio	10.2.0.133434, 11.0.0.146107, 7.0.1	[1,233]	biology, ngs, workflow_automation
Package-GFE	package-gfe	20150701	[1,234]	biology, genomics
PacMAP	pacmap	0.7.0	[1,235]	genomics
PALADIN	paladin	1.3.1	[1,236]	biology, phylogenetics
PALES	pales	122	[1,237]	physics
PAML	paml	4.8a, 4.9a, 4.9h	[1,238]	biology, phylogenetics
Pandaseq	pandaseq	20140808, 20150627	[1,239]	biology, ngs, sequencing
Pandoc	pandoc	2.2.2.1	[1,240]	utility
pangolin	pangolin	2	[1,241]	phylogenetics
panseq	panseq	3.2.1	[1,242]	phylogenetics
panX	panx	1.6.0	[1,243]	phylogenetics
PAPI	papi	5.5.1, 5.7.0	[1,244]	programming, performance_analysis
parabricks	parabricks	3.5.0, 3.7.0	[1,245]	phylogenetics
parallel	parallel	20150122, 20170322	[1,246]	shell, workflow_automation
paralyzer	paralyzer	1.5	[1,247]	phylogenetics
ParaView	paraview	5.4.1, 5.7.0, 5.9.1.1	[1,248]	data_science
ParaView Server	paraview_server	5.10.1	[1,249]	data_science
ParGenes	pargenes	1.2.0	[1,250]	phylogenetics
ParlAI	parlai	1.3.0, 1.5.0	[1,251]	phylogenetics
Parsnp	parsnp	1.2, 1.5.0, 1.6.2	[1,252]	biology, phylogenetics
PartitionFinder	partitionfinder	2.0.0-pre-20160513, 2.1.1-20161205, 2.1.1.0	[1,253]	biology, phylogenetics, genomics
PASA	pasa	2.0.2-r20151207, 2.2.0-r20171013, 2.4.1	[1,254]	biology, genomics, ngs
Pascal	fpc	3.0.0	[1,255]	compiler, programming
PASTA	pasta	0.2.0, 1.7.8, 20160616	[1,256]	biology, alignment
PATHd8	pathd8	1.0	[1,257]	biology, phylogenetics
pathoscope	pathoscope	2.0.7	[1,258]	sequencing, genomics, biology
PATRIC	patric	1.034	[1,259]	machine_learning
PAUDA	pauda	1.0.1	[1,260]	biology, ngs, phylogenetics
PAUP	paup	4.0a166, 4.0a168, 4.0b10	[1,261]	biology, phylogenetics
PB-Assembly	pb-assembly	0.0.6, 0.0.8	[1,262]	biology, ngs, sequencing
pbalign	pbalign	20160921, 20161221	[1,263]	biology
PBCCS	pbccs	5.0.0, 6.4.0	[1,264]	phylogenetics
pbcore	pbcore	1.7.1	[1,265]	biology
PBGCpp	pbgcpp	1.9.0	[1,266]	phylogenetics
pbipa	pbipa	1.8.0	[1,267]	phylogenetics, biology
PBJelly	pbjelly	15.8.24	[1,268]	biology, ngs
pbmm2	pbmm2	1.3.0	[1,269]	phylogenetics
pbrt	pbrt	20181017	[1,270]	phylogenetics
pbsmrtpipe	pbsmrtpipe	0.63.0	[1,271]	biology, programming
pbtk	pbtk	3.1.0	[1,272]	biology
pbtranscript-tofu	pbtranscript-tofu	20150317, 20160119	[1,273]	biology, ngs
PCIT	pcit	2014	[1,274]	biology
PCRE	pcre	8.38, 8.39	[1,275]	programming, library
PDA	pda	1.0.3	[1,276]	biology, phylogenetics
pdb2pqr	pdb2pqr	2.1.0	[1,277]	protein, modeling, biology
PeakSplitter	peaksplitter	1.0	[1,278]	biology, chip-seq
PEAR	pear	0.9.2	[1,279]	biology, genomics, ngs
peneasy	peneasy	20150530	[1,280]	physics
PennCNV	penncnv	1.0.5	[1,281]	phylogenetics
Perl	perl	5.16.0, 5.20.0, 5.24.1	[1,282]	programming, language
PerM	perm	0.4.0	[1,283]	biology, ngs, mapping
PETSc	petsc	3.8.1, 3.8.3, 3.8.4	[1,284]	math
PfamScan	pfamscan	1.3, 1.5	[1,285]	biology, genomics
PGAP	pgap	20220414	[1,286]	biology, genomics, annotation, pipeline
PGDSpider	pgdspider	2.0.9.0, 2.1.1.5	[1,287]	biology, ngs
pggb	pggb	0.4.1, 20201106, 20210121	[1,288]	phylogenetics
PhaME	phame	1.0.3	[1,289]	phylogenetics
phanotate	phanotate	1.5.0	[1,290]	genomics
pharmcat	pharmcat	1.8.0	[1,291]	biology, phylogenetics
PHASE	phase	2.1.1	[1,292]	phylogenetics
PHAST	phast	1.5	[1,293]	biology, phylogenetics
Phenix	phenix	1.10.2155, 1.17.1, 1.8.1069	[1,294]	material_science
PHI	phi	3.1.1, 3.1.2b, 3.1.6	[1,295]	math
PhiSpy	phispy	3.2	[1,296]	phylogenetics
PHITS	phits	2.76, 2.82, 2.84	[1,297]	physics
PHLAWD	phlawd	20170427	[1,298]	biology, phylogenetics
PhotoScan	photoscan-pro	1.4.1, 1.4.5	[1,299]	image_processing
Photutils	photutils	0.5	[1,300]	astronomy
PHYling	phyling	1.0	[1,301]	biology, phylogenetics, genomics
PHYLIP	phylip	3.696	[1,302]	biology, phylogenetics
PhyloAcc	phyloacc	1.0	[1,303]	phylogenetics
PhyloBayes	phylobayes	3.3f	[1,304]	biology, phylogenetics
phyloFlash	phyloflash	3.3b4	[1,305]	phylogenetics
phylonet	phylonet	3.5.7, 3.8.2	[1,306]	biology, phylogenetics
PhyloParser	phyloparser	20180404	[1,307]	phylogenetics
PhyloPhlAn2	phylophlan2	0.41	[1,308]	phylogenetics
phylopypruner	phylopypruner	1.2.3	[1,309]	phylogenetics
PhyloSift	phylosift	1.1	[1,310]	biology, genomics, phylogenetics
phyloTF2	phylotf2	20210726	[1,311]	biology, genomics, alignment
Phyluce	phyluce	20180727, 20190308, 20191015	[1,312]	biology, ngs, sequencing
PhyML	phyml	3.0, 3.1	[1,313]	biology, phylogenetics
phynd	phynd	20200409	[1,314]	phylogenetics
Physher	physher	1.0.2	[1,315]	phylogenetics
PHYUTILITY	phyutility	2.7.1	[1,316]	biology
Phyx	phyx	1.1	[1,317]	phylogenetics
PIA2	pia2	20180305	[1,318]	biology, phylogenetics
Picard-tools	picard	2.5.0, 2.9.0, 2.9.2	[1,319]	biology, ngs
PICRUSt	picrust	1.1.3, 1.1.4, 2.3.0b	[1,320]	biology, phylogenetics
PICSL	picsl	1.3	[1,321]	imaging
Piggy	piggy	20171220	[1,322]	biology, ngs
Pigz	pigz	2.4	[1,323]	compression
PILON	pilon	1.22, 1.24	[1,324]	biology, ngs, phylogenetics
Pindel	pindel	0.2.5b8	[1,325]	biology, phylogenetics
pipe-clip	pipe-clip	1.1.0	[1,326]	biology, ngs
pipits	pipits	1.3.6, 1.4.0	[1,327]	biology, sequencing
Piranha	piranha	1.2.1	[1,328]	biology, phylogenetics
PlantTribes	planttribes	1.0.4	[1,329]	phylogenetics
plasflow	plasflow	1.1	[1,330]	biology, phylogenetics
PLAST	plast	1.0, 2.3.2	[1,331]	biology
platanus	platanus	1.2.4	[1,332]	phylogenetics
Platon	platon	1.6	[1,333]	biology, sequencing
Platypus	platypus	0.8.1	[1,334]	biology, ngs
PLEK	plek	1.2.2	[1,335]	biology, phylogenetics
Plink	plink	1.90b3.39, 2.00a2, 2.00a3LM	[1,336]	biology, genomics, phylogenetics
plinkseq	plinkseq	0.10	[1,337]	biology, library
plotsr	plotsr	0.5.4	[1,338]	genomics, biology
PLUMED	plumed	2.7.3, 2021.2	[1,339]	chemistry, molecular_dynamics
pod5	pod5	0.1.5, 20220621	[1,340]	sequencing
PolyGembler	polygembler	1.0	[1,341]	phylogenetics
PolyPHen	polyphen	2.2.2.r405b	[1,342]	biology, genomics
polyply	polyply	1.3.0	[1,343]	phylogenetics, biology
pomoxis	pomoxis	0.1.11, 0.2.5, 0.3.2	[1,344]	biology, phylogenetics
popcorn	popcorn	20211104	[1,345]	phylogenetics, biology
PopLDdecay	poplddecay	3.40	[1,346]	phylogenetics
popoolation	popoolation	1.2.2	[1,347]	biology, phylogenetics
Porechop	porechop	0.2.4	[1,348]	phylogenetics
Poretools	poretools	0.6.1	[1,349]	phylogenetics
portcullis	portcullis	1.2.3	[1,350]	phylogenetics
PosiGene	posigene	20171113	[1,351]	biology, phylogenetics
POV-Ray	povray	3.7	[1,352]	graphics
powerfit	powerfit	2.0.0	[1,353]	Physics
pplacer	pplacer	1.1.alpha19	[1,354]	biology, phylogenetics, genomics
PRANK	prank	170427, 20150803	[1,355]	biology, alignment
Predector	predector	20201110	[1,356]	phylogenetics
preplot	preplot	14.0.2	[]
Preseq	preseq	0.0.4	[1,357]	biology, ngs
PRICE	price	1.2	[1,358]	biology, ngs
Primer3	primer3	2.3.4	[1,359]	biology, genomics
primus	primus	1.8.0	[1,360]	biology, phylogenetics
PRINSEQ	prinseq	0.20.4	[1,361]	biology, sequencing
PRINSEQ++	prinseq++	1.2	[1,362]	phylogenetics
ProbABEL	probabel	0.4.2, 0.4.3, 0.4.5	[1,363]	genomics
probalign	probalign	1.4	[1,364]	biology, ngs
Processing	processing	3.4	[1,365]	programming, language, visualization
Prodigal	prodigal	2.6.2, 2.6.3	[1,366]	biology, genomics
ProDy	prody	2.0	[1,367]	phylogenetics
Program Database Toolkit	pdt	3.20, 3.22, 3.24	[1,368]	language, programming, performance_analysis
PROJ	proj	4.9.3, 5.1.0, 8.0.1	[1,369]	library, geospatial
Prokka	prokka	1.12, 1.14.6	[1,370]	biology, genomics, assembly
Proovread	proovread	1.03rcl, 2.12, 2.13	[1,371]	biology, genomics, ngs
ProSplign	prosplign	1.0.0	[1,372]	phylogenetics
Protege	protege	5.1.0	[1,373]	genomics
Proteinortho	proteinortho	4.26, 5.11, 5.16	[1,374]	biology, genomics
ProtExcluder	protexcluder	1.2	[1,375]	biology, phylogenetics
ProtHint	prothint	2.6.0	[1,376]	biology, genomics
protobuf	protobuf	2.5.0, 3.5.1	[1,377]	web, library
prottest3	prottest3	3.4.2	[1,378]	biology
PROVEAN	provean	1.1.5	[1,379]	biology, genomics
PRSice	prsice	2.3.3	[1,380]	phylogenetics
Pseudofinder	pseudofinder	1.0	[1,381]	phylogenetics
PsiCLASS	psiclass	1.0.1	[1,382]	phylogenetics
PSMC	psmc	0.6.5	[1,383]	phylogenetics
psRobot	psrobot	1.2	[1,384]	phylogenetics
Pufferfish	pufferfish	20200417	[1,385]	phylogenetics
PureCLIP	pureclip	1.1.1	[1,386]	phylogenetics
Purge_Dups	purge_dups	1.0.1	[1,387]	phylogenetics
purge_haplotigs	purge_haplotigs	1.1.2	[1,388]	sequencing, biology
pvconv	pvconv	10152018	[1,389]	imaging
pyani	pyani	0.2.10	[1,390]	phylogenetics
Pybedtools	pybedtools	0.8.2	[1,391]	phylogenetics
PyBSASeq	pybsaseq	20200623	[1,392]	phylogenetics
PyCharm	pycharm	2018.3	[1,393]	programming
pychopper	pychopper	2.5.0, 2.7.1	[1,394]	phylogenetics, sequencing
PyCogent	pycogent	1.9	[1,395]	biology, genomics
pycoqc	pycoqc	2.5.2	[1,396]	sequencing, data_science
PyDeface	pydeface	2.0.0	[1,397]	imaging
pyEGA3	pyega3	3.4.1	[1,398]	biology, genomics, utility
PyEXR	pyexr	0.3.10	[1,399]	programming
Pyfaidx	pyfaidx	0.5.2	[1,400]	biology, ngs, sequencing
pyfasta	pyfasta	0.5.2	[1,401]	phylogenetics
pygot	pygot	20170518	[1,402]	biology, phylogenetics
pyhdf	pyhdf	0.9.0	[1,403]	library
PyHIST	pyhist	1.0	[1,404]	biology, imaging, image_processing
pymesh	pymesh	0.3.0	[1,405]	math, graphics
PyPHLAWD	pyphlawd	20180416, 20190414	[1,406]	biology, phylogenetics
Pyroms	pyroms	1.0	[1,407]	geospatial
PyRosetta	pyrosetta	r56324	[1,408]	biology, structure, modeling
pyrpipe	pyrpipe	0.0.3	[1,409]	phylogenetics
Pysamstats	pysamstats	1.1.2	[1,410]	phylogenetics
PySLURM	pyslurm	18.08.04	[1,411]	scheduler
Python	python	3.6.3, 3.6.5, 3.8	[1,412]	language, programming
Python-core	python-core	3.6.5, 3.7, 3.8	[1,413]	language, programming
Python2	python	2.7.11	[1,414]	language, programming
PyTorch	ngc-pytorch	1.11.0, 1.9.0	[1,415]	library, math
pytorch	pytorch	1.7.1, 1.8.1, 1.9.0	[1,416]	library, math
PyVCF	pyvcf	0.6.0, 0.6.8	[1,417]	biology, phylogenetics
PyVista	pyvista	0.26.1	[1,418]	phylogenetics
pyweka	pyweka	0.3.18	[1,419]	phylogenetics
QAPA	qapa	1.3.1, 1.3.3	[1,420]	phylogenetics
qcat	qcat	1.1.0	[1,421]	phylogenetics
qctool	qctool	2.0.1	[1,422]	phylogenetics
QD	qd	2.3.22	[1,423]	library, compiler, math
QDD	qdd	3.1.2	[1,424]	biology, genomics, ngs
QGIS	qgis	2.18.0, 3.14.0	[1,425]	geospatial
QIIME	qiime	1.9.1	[1,426]	biology, genomics
QIIME2	qiime2	2021.11, 2021.4, 2022.8	[1,427]	biology, bioinformatics, metagenomics
QMCPACK	qmcpack	3.4.0	[1,428]	library
QRNA	qrna	2.0.4	[1,429]	phylogenetics
QT	qt	4.8.3, 5.12.9, 5.15.4	[1,430]	library
QTL-seq	qtl-seq	2.2.2	[1,431]	biology, sequencing, pipeline
QTLtools	qtltools	1.2, 1.3.1	[1,432]	phylogenetics
Quake	quake	0.3	[1,433]	biology, sequencing
QualiMap	qualimap	2.1.2	[1,434]	biology, sequencing, alignment
Quantas	quantas	1.0.4, 1.0.8, 1.0.9	[1,435]	biology, ngs
quantisnp	quantisnp	2	[1,436]	biology, genomics
QuartetScores	quartetscores	1.0.0	[1,437]	phylogenetics
QUAST	quast	4.4, 5.0.0, 5.0.2	[1,438]	biology, ngs, sequencing, rna-seq
quickmerge	quickmerge	0.3	[1,439]	phylogenetics
Quickquartet	quickquartet	1.0.0	[1,440]	biology, ngs
QUIP	quip	20201029, 20210626	[1,441]	phylogenetics
QuorUM	quorum	1.0.0	[1,442]	biology
R	R	4.0, 4.1, 4.2	[1,443]	statistics
r-index	r-index	20190711	[1,444]	phylogenetics
r8s	r8s	1.8, 1.81	[1,445]	phylogenetics
RACA	raca	0.9.1.1	[1,446]	biology, ngs
Racon	racon	1.3.3, 1.4.10, 1.4.13	[1,447]	phylogenetics
RADICAL	radical	0.2	[1,448]	biology, genomics
radorgminer	radorgminer	0.9	[1,449]	genomics, biology, sequencing
RaGOO	ragoo	1.11	[1,450]	phylogenetics
Ragout	ragout	2.3	[1,451]	genomics
RagTag	ragtag	1.0.0, 2.0.1	[1,452]	phylogenetics
rainbow	rainbow	2.0.4	[1,453]	biology, sequencing
Rainbowfish	rainbowfish	0.1.0	[1,454]	phylogenetics
RAiSD	raisd	2.8	[1,455]	phylogenetics
Randfold	randfold	2.0.1	[1,456]	biology, RNA
ranger	ranger	1.9.3	[1,457]	file_management
rapidsai	rapidsai	21.12, 22.04, 23.02	[1,458]	data_science
rapidtide	rapidtide	1.9.0	[1,459]	phylogenetics
RAPSearch	rapsearch	2.24	[1,460]	biology, phylogenetics
Rascaf	rascaf	1.0.2	[1,461]	biology
RAVE	rave	2.1	[1,462]	biology, phylogenetics
Raven	raven	1.8.1	[1,463]	assembly
RAxML	raxml	8.2.10, 8.2.12, 8.2.8	[1,464]	biology, phylogenetics
RAxML-NG	raxml-ng	0.9.0, 1.0.2, 1.1.0	[1,465]	phylogenetics
razers3	razers3	3.5.7	[1,466]	biology, phylogenetics
rbp-maps	rbp-maps	0.1.4	[1,467]	phylogenetics
rclone	rclone	1.57.0, 1.58.1	[1,468]	web
Rcorrector	rcorrector	1.0.4	[1,469]	phylogenetics
RDKit	rdkit	2020092	[1,470]	chemistry
rDnaTools	rdnatools	0.1.3	[1,471]	phylogenetics
READemption	reademption	1.0.0	[1,472]	phylogenetics
REAPR	reapr	1.0.18	[1,473]	biology, assembly
Rebaler	rebaler	0.2.0	[1,474]	phylogenetics
reCOGnizer	recognizer	1.3.3	[1,475]	phylogenetics
recon	recon	1.08	[1,476]	biology, sequencing
recycler	recycler	0.7	[1,477]	biology, sequencing
Redis	redis	2.8.13, 2.8.19	[1,478]	database, data_science
REDItools2	reditools2	20200701	[1,479]	phylogenetics
Redundans	redundans	0.14a	[1,480]	biology, phylogenetics
ReFrame	reframe	3.2	[1,481]	performance_analysis, utility
regtools	regtools	0.5.2	[1,482]	biology, rna-seq, genomics
release	release	12082021	[1,483]	molecular_dynamics, machine_learning
RELION	relion	3.0.2, 3.0b, 3.1.0	[1,484]	biology, imaging
RelocaTE2	relocate2	2.0.1	[1,485]	phylogenetics
REMORA	remora	1.8.2, 1.8.3, 1.8.5	[1,486]	performance_analysis
REPdenovo	repdenovo	20170222	[1,487]	biology, phylogenetics
RepeatAnalysis	repeatanalysis	0.10.0, 0.12.2	[]	biology, phylogenetics
RepeatAnalysisTools	repeatanalysistools	20210506	[1,488]	biology, genomics, sequencing, utility
RepeatExplorer	repeatexplorer	20150506, 20180517	[1,489]	biology, ngs
RepeatMasker	repeatmasker	4.0.5, 4.0.9, 4.1.1	[1,490]	biology
RepeatModeler	repeatmodeler	1.0.8, 2.0	[1,491]	biology
repeatscout	repeatscout	1.0.5	[1,492]	biology
RepeatSeq	repeatseq	0.8.2	[1,493]	phylogenetics
reptile	reptile	1.1	[1,494]	biology, ngs, math
ResFinder	resfinder	4.0	[1,495]	biology, genomics
Resistome	resistome	20170111	[1,496]	phylogenetics
RevBayes	revbayes	1.0.7, 1.0.9, 1.1.1	[1,497]	biology, phylogenetics
RFMIX	rfmix	2.03	[1,498]	phylogenetics
RGAugury	rgaugury	20220107	[1,499]	sequencing, biology
RGI	rgi	4.2.2, 5.1.1, 6.0.2	[1,500]	phylogenetics
RGIS	rgis	20180211, 20180814	[1,501]	geospatial
RHash	rhash	1.3.3	[1,502]	programming
RiboCode	ribocode	1.2.11	[1,503]	phylogenetics
riboPicker	ribopicker	0.4.3	[1,504]	biology, sequencing
RiboTaper	ribotaper	1.3.1a	[1,505]	phylogenetics
RIGERJ	rigerj	2.0.2	[1,506]	phylogenetics
rMATS turbo	rmats-turbo	4.1.2	[1,507]	biology, sequencing, genomics
rmats2sashimiplot	rmats2sashimiplot	2.0.3, 2.0.4	[1,508]	phylogenetics
Rmpi	Rmpi	3.5.1, 4.0.3	[1,509]	statistics, programming
RNAFramework	rnaframework	2.7.2	[1,510]	biology, RNA, sequencing
RNAhybrid	rnahybrid	2.1.1	[1,511]	biology, genomics
RNAmmer	rnammer	1.2	[1,512]	biology, rna-seq
rnaQUAST	rnaquast	1.5.1	[1,513]	biology, ngs, sequencing, rna-seq
RNAsalsa	rnasalsa	0.8.1	[1,514]	biology, phylogenetics
rnaseqlib	rnaseqlib	20150721	[1,515]	biology, phylogenetics, rna-seq
RNAstructure	rnastructure	6.3	[1,516]	biology, sequencing
Roary	roary	3.12.0, 3.4.1	[1,517]	biology, genomics
ROOT	root	5.34.17, 6.0, 6.06.02	[1,518]	data_science
ROOTPy	rootpy	20160323	[1,519]	data_science
Rosetta	rosetta	2014wk4, 2019.35.60890, 2021.16.61629	[1,520]	biology, structure, modeling
RoseTTAFold	rosettafold	1.0.0	[1,521]	phylogenetics
rrnaselector	rrnaselector	1.0	[1,522]	biology, sequencing
RSEG	rseg	0.4.8	[1,523]	biology, genomics
RSEM	rsem	1.2.31, 1.2.7, 1.3.3	[1,524]	biology, ngs, sequencing
RSeQC	rseqc	2.6.4, 3.0.0	[1,525]	biology, ngs, rna-seq
RStudio	rstudio	1.4, 2021.09.0, 2022.02.3	[1,526]	statistics
RTGTools	rtgtools	3.7.1	[1,527]	biology, ngs
Ruby	ruby	2.5.1	[1,528]	programming, language
Rust	rust	1.48.0, 1.52.1, 1.62.1	[1,529]	programming
rvtests	rvtests	2.1.0	[1,530]	genomics, biology, sequencing
S.A.G.E	s.a.g.e	6.4.2	[1,531]	phylogenetics
Sabre	sabre	1.0	[1,532]	phylogenetics
saffrontree	saffrontree	0.1.2	[1,533]	phylogenetics
saige	saige	0.45.0	[1,534]	genomics
Sailfish	sailfish	0.6.3	[1,535]	biology, genomics, ngs, rna-seq
Salmon	salmon	1.5.2, 1.8.0, 1.9.0	[1,536]	biology, rna-seq
SALSA	salsa	20171009, 20191001	[1,537]	biology, ngs
Sambamba	sambamba	0.6.3, 0.6.6, 0.6.9	[1,538]	biology, ngs
samblaster	samblaster	0.1.14, 0.1.24	[1,539]	biology, ngs, sequencing
sampledock	sampledock	0.5.1	[1,540]	molecular_dynamics, AI
SAMStat	samstat	1.08	[1,541]	biology, ngs, sequencing
Samtools	samtools	1.7, 1.8, 1.9	[1,542]	biology, ngs, sequencing
SAS	sas	9.4	[1,543]	statistics, data_science
Sate	sate	2.2.7	[1,544]	biology, phylogenetics
Satsuma	satsuma	3.0	[1,545]	phylogenetics
Satsuma2	satsuma2	20161123, 3.1	[1,546]	phylogenetics
sc-im	scim	0.8.2	[1,547]	utility, visualization
Scala	scala	2.11.5, 3.0.1	[1,548]	programming, language
Scalablast	scalablast	2.4.53	[1,549]	biology, genomics
ScaLAPACK	scalapack	2.0.2, 2.1.0	[1,550]	programming, library
scallop	scallop	0.10.5	[1,551]	phylogenetics
Scalpel	scalpel	0.1.1, 0.5.3	[1,552]	biology, ngs
Schrodinger Suite	schrodinger	2019-3, 2020-4, 2021-2	[1,553]	chemistry, molecular_dynamics
Scipion	scipion	1.2	[1,554]	image_processing
SCIrun	scirun	5.0.Z	[1,555]	phylogenetics
Scoary	scoary	1.6.16	[1,556]	phylogenetics
Scons	scons	2.5.1, 3.1.2	[1,557]	programming
SCOP	scop	20180311	[1,558]	biology, assembly
Scrappie	scrappie	1.4.2	[1,559]	biology, genomics
SCRATCH-1D	scratch1d	1.0, 2.0	[1,560]	biology, ngs
Screen	screen	4.8.0	[1,561]	programming, shell
SCRIPTURE	scripture	20101211	[1,562]	biology, genomics
Scythe	scythe	0.991	[1,563]	biology, ngs
sdsl	sdsl	2.1.1	[1,564]	library, compiler
SE-MEI	se-mei	0.1.0	[1,565]	phylogenetics
SeCaPr	secapr	1.1.12, 2.0.2, 2.1.1	[1,566]	phylogenetics
Segemehl	segemehl	0.1.9, 0.3.4	[1,567]	biology, ngs, sequencing
segment-liftover	segment-liftover	20211021	[1,568]	biology, genomics
SEPP	sepp	20160614	[1,569]	biology, phylogenetics
Seq-Gen	seq-gen	1.3.3	[1,570]	biology, phylogenetics
seq_crumbs	seq_crumbs	20150120	[1,571]	biology, sequencing, genomics, utility
SeqKit	seqkit	0.10.2, 0.8.0, 2.0.0	[1,572]	biology, phylogenetics
seqmagick	seqmagick	0.8.4	[1,573]	biology
SeqMap	seqmap	1.0.13	[1,574]	biology, sequencing, ngs
seqmule	seqmule	1.2.6	[1,575]	biology, sequencing
SEQPower	seqpower	1.1.1	[1,576]	genomics, phylogenetics
SeqPrep	seqprep	0.5, 1.1	[1,577]	biology, ngs, sequencing
seqscreen	seqscreen	3.3	[1,578]	sequencing, biology
seqtk	seqtk	1.3, 20140729	[1,579]	biology, genomics, ngs
SEQuel	sequel	1.0.1	[1,580]	biology, ngs
SequelQC	sequelqc	1.1.0	[1,581]	phylogenetics
seqwish	seqwish	0.7, 20190509	[1,582]	phylogenetics
SeqyClean	seqyclean	1.8.10	[1,583]	biology, ngs, sequencing
SeSiMCMC	sesimcmc	4.36	[1,584]	biology, sequencing
SExtractor	sextractor	2.19.5	[1,585]	astronomy
SHAPE-MaP	shapemap	1.2	[1,586]	biology, phylogenetics
SHAPEIT	shapeit	2.12, 2.5	[1,587]	biology, variant_calling
SHAPEIT4	shapeit4	4.2.2	[1,588]	biology, sequencing
ShapeMapper	shapemapper	2.1.3, 2.1.5	[1,589]	biology, phylogenetics
SHARCGS	sharcgs	1.2.11	[1,590]	biology, ngs, de_novo
Shasta	shasta	0.1.0	[1,591]	phylogenetics
SHEsisPlus	shesisplus	1.0, 1.01	[1,592]	biology, genomics
shogun	shogun	6.1.3	[1,593]	phylogenetics
Shortbred	shortbred	0.9.4	[1,594]	phylogenetics
shovill	shovill	1.1.0	[1,595]	genomics, sequencing, biology
SHRiMP	shrimp	2.2.3	[1,596]	biology, genomics, ngs
shustring	shustring	2.6	[1,597]	biology, sequencing
SibeliaZ	sibeliaz	1.2.2, 1.2.3, 1.2.4	[1,598]	biology, genomics, alignment
SICER	sicer	1.1	[1,599]	biology, chip-seq
Sickle	sickle	1.200, 1.33	[1,600]	biology, ngs
Siesta	siesta	3.2, 4.1b2, 4.1b3	[1,601]	chemistry
SIFT	sift	4.0.3b	[1,602]	biology, genomics
SIGffRid	sigffrid	1.1	[1,603]	phylogenetics
SignalP	signalp	4.1c, 5.0b	[1,604]	biology, phylogenetics
SiLiX	silix	1.2.11, 1.3.0	[1,605]	phylogenetics
silo	silo	4.7	[1,606]	library
sim4	sim4	20121010	[1,607]	biology, genomics
Sim4Life	sim4life	7.0.1	[1,608]	biology, simulation
Simka	simka	1.5.3	[1,609]	phylogenetics
SimNIBS	simnibs	3.2.1, 4.0.0	[1,610]	phylogenetics
SimSeq	simseq	4.12.2011	[1,611]	biology, ngs, phylogenetics
Simulia	simulia	2019	[1,612]	simulation, visualization
SInC	sinc	20140120	[1,613]	biology, phylogenetics
sine_scan	sine_scan	1.1.1	[1,614]	phylogenetics
Singularity	singularity	3.10.4, 3.7.4	[1,615]	workflow_automation
SIPeS	sipes	2.0	[1,616]	biology, chip-seq
sisl	sisl	0.8.3	[1,617]	physics, structure
skmer	skmer	3.2.1	[1,618]	genomics, biology
Slamdunk	slamdunk	0.4.1, 0.4.2	[1,619]	phylogenetics
SLAW	slaw	20211217	[1,620]	chemistry, spectroscopy
Slicer	slicer	4.3.1, 5.0.3, 5.2.1	[1,621]	biology, neuroscience, imaging
slow5tools	slow5tools	0.5.1	[1,622]	biology, sequencing
slurm-drmaa	slurm-drmaa	1.1.2, 1.1.3	[1,623]	library, scheduler, programming
smalt	smalt	0.7.6	[1,624]	biology, phylogenetics
SMARTdenovo	smartdenovo	20180219	[1,625]	biology, phylogenetics
smartie-sv	smartie-sv	20180308	[1,626]	phylogenetics
SMC++	smcpp	1.15.4	[1,627]	biology, genomics, sequencing
Smetana	smetana	1.1.0	[1,628]	phylogenetics
SMR	smr	1.03	[1,629]	biology, genomics
SMRT-SV	smrtsv2	2.0.0	[1,630]	biology, ngs
SMS	sms	1.7	[1,631]	biology
Smudgeplot	smudgeplot	0.2.4	[1,632]	phylogenetics
Snakemake	snakemake	6.4.1, 7.16, 7.5.0	[1,633]	biology, workflow_automation
SNAP	snap	0.15.4, 2.0.0, 20100728	[1,634]	biology, sequencing
SNAPE-pooled	snape-pooled	20130407	[1,635]	biology, variant_calling
SNeP	snep	1.1	[1,636]	biology, phylogenetics
Sniffles	sniffles	1.0.11, 1.0.6, 1.0.8	[1,637]	phylogenetics
Sniffles2	sniffles2	2.0.6	[1,638]	biology
Snippy	snippy	20160419, 4.6.0	[1,639]	biology, phylogenetics
SNP-Pipeline	snp-pipeline	1.0.1	[1,640]	biology, phylogenetics
SNP-sites	snp-sites	2.0.3	[1,641]	biology, variant_calling
snp2hla	snp2hla	1.0.3	[1,642]	biology, genomics
SnpEff	snpeff	4.3t, 5.0, 5.1d	[1,643]	biology, annotation
snpflip	snpflip	20190515	[1,644]	biology, phylogenetics
SNPGenie	snpgenie	20190620	[1,645]	phylogenetics
SNPhylo	snphylo	20140701	[1,646]	biology, phylogenetics
SNPsplit	snpsplit	0.5.0	[1,647]	biology, sequencing
SNPTEST	snptest	2.5.2	[1,648]	phylogenetics
SOAPaligner	soapaligner	2.21	[1,649]	phylogenetics
SOAPdenovo	soapdenovo	1.05, 2.04	[1,650]	biology, ngs
SOAPdenovo-Trans	soapdenovo-trans	1.01, 1.03	[1,651]	biology, ngs
SOAPec	soapec	2.03	[1,652]	biology, phylogenetics
SOAPnuke	soapnuke	2.1.0	[1,653]	phylogenetics
SOAPsplice	soapsplice	1.10	[1,654]	biology, ngs
SODA	soda	20200930	[1,655]	biology
SOLAR	solar	8.4.2	[1,656]	phylogenetics
SomaticSeq	somaticseq	3.6.2	[1,657]	phylogenetics
SortaDate	sortadate	20190705	[1,658]	phylogenetics
SortMeRNA	sortmerna	2.1, 4.0, 4.3.6	[1,659]	biology, sequencing, ngs
SourceTracker2	sourcetracker2	2.0.1	[1,660]	phylogenetics
Sourmash	sourmash	2.0.1, 4.5.0	[1,661]	phylogenetics
SoX	sox	14.4.2	[1,662]	phylogenetics
spacemake	spacemake	0.5.5	[1,663]	sequencing
SpaceRanger	spaceranger	1.3.1	[1,664]	phylogenetics
SPAdes	spades	3.15.3, 3.7.1, 3.8.0	[1,665]	biology, ngs
SparCC	sparcc	201608	[1,666]	biology
Spark	spark	2.2.0, 3.1.1	[1,667]	utility
sparsehash	sparsehash	2.0.3	[1,668]	web, programming
SPARTA+	sparta+	2.60	[1,669]	chemistry
Spec2nii	spec2nii	0.3.4	[1,670]	phylogenetics
SpeedSeq	speedseq	0.1.2	[1,671]	phylogenetics
Spidey	spidey	20150922	[1,672]	biology, genomics
SpinalCordToolbox	spinalcordtoolbox	5.4	[1,673]	phylogenetics
SplAdder	spladder	2.4.2	[1,674]	phylogenetics
SpliceGrapher	splicegrapher	0.2.5	[1,675]	biology, sequencing
SpliceTrap	splicetrap	0.90.5	[1,676]	biology, genomics, ngs
SPM	spm	12b, 8, 8r5236	[1,677]	biology
spruceup	spruceup	2019.2.3	[1,678]	phylogenetics
Sputnik	sputnik	1.0	[1,679]	biology
spyder	spyder	4.1.4, 5.1.1, 5.3.2	[1,680]	programming
SQANTI	sqanti	1.2	[1,681]	phylogenetics
SQANTI2	sqanti2	5.0	[1,682]	phylogenetics
SQANTI3	sqanti3	0.1, 1.6, 4.2	[1,683]	phylogenetics
SQL Developer	sqldeveloper	4.1.2	[1,684]	programming, database
SQLite	sqlite	3.33.0, 3.8.8.2	[1,685]	database
SqueezeMeta	squeezemeta	1.4.0, 1.5.2, 1.6.0	[1,686]	phylogenetics
squigglekit	squigglekit	1.0.0	[1,687]	visualization, biology
squigglenet	squigglenet	1.0	[1,688]	sequencing, biology
SRA	sra	2.10.9, 3.0.0, 3.0.2	[1,689]	biology, ngs
sra-human-scrubber	sra_human_scrubber	1.1	[1,690]	genomics
SRAssembler	srassembler	1.0.0	[1,691]	phylogenetics
srst2	srst2	0.2.0	[1,692]	sequencing, genomics, biology
SSM	ssm	20210511	[1,693]	phylogenetics
SSPACE	sspace	2.0, 3.0	[1,694]	biology, ngs
ssr_pipeline	ssr_pipeline	0.951	[1,695]	biology, sequencing
stable-diffusion	stable-diffusion	20221116	[1,696]	machine_learning
Stacks	stacks	2.53, 2.55, 20190403	[1,697]	biology, genomics, ngs
Staden	staden	1.14.6	[1,698]	biology, phylogenetics
Stampy	stampy	1.0.31	[1,699]	biology, sequencing
staphb-toolkit	staphb-toolkit	1.2.0, 1.3.10	[1,700]	biology
STAR	star	2.7.5c, 2.7.6a, 2.7.9a	[1,701]	biology, ngs, rna-seq
STAR-CCM+	starccm+	14.04.011, 15.02.009, 8.06	[1,702]	fluid_dynamics
STAR-Fusion	star-fusion	1.1.0, 1.3.1, 1.9.1	[1,703]	biology, sequencing
starseqr	starseqr	0.6.7	[1,704]	phylogenetics
Stata	stata	10.1, 13	[1,705]	statistics
stringMLST	stringmlst	0.4	[1,706]	biology, chip-seq
Stringtie	stringtie	1.3.4d, 2.0.4, 2.1.3b	[1,707]	biology, ngs, sequencing, alignment
Structure	structure	2.3.3, 2.3.4	[1,708]	biology, genomics
Structure_threader	structure_threader	1.3.10	[1,709]	utility, structure
stumpy	stumpy	1.11.1	[1,710]	library, math
stylegan3	stylegan3	20211028	[1,711]	ai, image_processing
SU2	su2	7.0.6	[1,712]	phylogenetics
Subread	subread	1.6.2, 2.0.0, 2.0.3	[1,713]	biology, sequencing, variant_calling
Subversion	subversion	1.9.7	[1,714]	revision_control
SUMO	sumo	1.13.0, 1.2.0, 1.9.2	[1,715]	simulation, mapping
SUNDIALS	sundials	2.3.0, 2.5.0, 3.0.0	[1,716]	math
supercell	supercell	20170602	[1,717]	biology, ngs
SuperCRUNCH	supercrunch	1.2.1	[1,718]	phylogenetics
Supernova	supernova	1.2.1, 2.0.0, 2.1.1	[1,719]	biology, phylogenetics, ngs
SUPPA	suppa	2.3	[1,720]	phylogenetics
Survival_Kit	survival_kit	6.12	[1,721]	healthcare
SURVIVOR	survivor	1.0.6	[1,722]	phylogenetics
SVDetect	svdetect	0.8b	[1,723]	biology, ngs, genomics
svim	svim	1.4.2	[1,724]	biology
svim-asm	svim-asm	1.0.2	[1,725]	biology
svtyper	svtyper	0.7.1	[1,726]	biology, genomics, sequencing
swarm	swarm	1.2.11	[1,727]	data_science
Sweed	sweed	3.3.2	[1,728]	biology, phylogenetics
SWIG	swig	2.0.9, 3.0.12, 3.0.8	[1,729]	library, programming, compiler
SWSC-EN	swsc-en	1.0.0	[1,730]	phylogenetics
Synima	synima	20210908	[1,731]	phylogenetics
syri	syri	1.5.4	[1,732]	genomics, biology
TACO	taco	0.7.3	[1,733]	phylogenetics
Taiyaki	taiyaki	5.0.1	[1,734]	phylogenetics
talesf	talesf	20160814	[1,735]	phylogenetics
talon	talon	5.0	[1,736]	biology, sequencing
Tandem-Genotypes	tandem-genotypes	1.4.0	[1,737]	phylogenetics
Tantan	tantan	13	[1,738]	imaging, ngs, genomics
Tapestri	tapestri	2.0.1	[1,739]	phylogenetics
tapir	tapir	20160825	[1,740]	biology, phylogenetics
TAPIS	tapis	1.2.1	[1,741]	biology, sequencing
TASSEL	tassel	5.0, 5.2.20, 5.2.29	[1,742]	biology, genomics, sequencing
TAU	tau	2.23, 2.26, 2.26.3	[1,743]	library, performance_analysis
Tax4Fun	tax4fun	0.3.1	[1,744]	phylogenetics
taxMaps	taxmaps	0.1	[1,745]	biology, phylogenetics, genomics
TaxonKit	taxonkit	0.13.0, 0.9.0	[1,746]	phylogenetics
Taxtastic	taxtastic	0.5.7, 0.9.1	[1,747]	biology, genomics
tbb	tbb	2017_20161128	[1,748]	library
tbprofiler	tbprofiler	4.4.1	[1,749]	genomics, biology
tcllib	tcllib	1.18	[1,750]	library
tcoffee	tcoffee	10.00.r1613, 9.03.r1318	[1,751]	biology
TDNAscan	tdnascan	20210304	[1,752]	phylogenetics
Tecplot 360 EX	tecplot	2015R1	[1,753]	math, animation, fluid_dynamics, simulation
tellseq	tellseq	1.0.0	[1,754]	sequencing, phylogenetics
TEMP	temp	20170731	[1,755]	phylogenetics
TEMP2	temp2	0.1.4	[1,756]	phylogenetics
TensorFlow	ngc-tensorflow	2.6.0, 2.7.0, 2.8.0	[1,757]	library, math
TESS	tess	2.3.1	[1,758]	biology, genomics, math
Test	test	1.0	[1,759]	shell
TetGen	tetgen	1.5.0	[1,760]	modeling
TEToolkit	tetoolkit	1.5.1	[1,761]	biology, sequencing
TEtools	tetools	20180213	[1,762]	biology, phylogenetics
Texlive	texlive	20191127, 2020	[1,763]	documentation
textract	textract	1.6.1	[1,764]	data_science, file_management
TGICL	tgicl	2.1	[1,765]	biology, ngs, sequencing
TGSGapCloser	tgsgapcloser	1.0.3	[1,766]	phylogenetics
the_silver_searcher	the_silver_searcher	2.2.0	[1,767]	search
Theano	theano	1.0.4	[1,768]	library, math, gpu
Themisto	themisto	0.2.0, 1.1.0	[1,769]	genomics, alignment
Tiara	tiara	1.0.2	[1,770]	phylogenetics
tiff	tiff	3.8.0, 4.0.10	[1,771]	imaging
Tigmint	tigmint	1.1.2	[1,772]	phylogenetics
Tmux	tmux	2.9, 3.1	[1,773]	programming
TNTBLAST	tntblast	2.04	[1,774]	biology
ToFU2	tofu2	v17	[1,775]	biology, ngs, sequencing
toil	toil	3.3.0, 3.3.3	[1,776]	biology
Tombo	tombo	1.4, 1.5, 1.5.1	[1,777]	biology, genomics, ngs
Tophat	tophat	2.1.0, 2.1.1, 2.1.2	[1,778]	biology, ngs, sequencing
torch-geometric	torch-geometric	1.3.2, 2.0.4	[1,779]	math, machine_learning
TotalView	totalview	8.12	[1,780]	programming
TPMcalculator	tpmcalculator	0.0.3	[1,781]	phylogenetics
TPP	tpp	4.7.0, 4.7.1, 5.0.0	[1,782]	biology, chemistry, spectroscopy
TraCeR	tracer	20160519	[1,783]	biology, phylogenetics
TrackTools	tracktools	2011	[1,784]	utility
TrackVis/DTK	trackvis	0.5.2.2, 0.6.0.1	[1,785]	biology, neuroscience, imaging
Tracula	tracula	5.3.2014_05_26	[1,786]	biology, neuroscience, imaging
traitRate	traitrate	1.1	[1,787]	biology, genomics
Trans-ABySS	transabyss	2.0.1	[1,788]	biology, phylogenetics
TransDecoder	transdecoder	5.3.0, 5.4.0, 5.5.0	[1,789]	biology, ngs
TRANSIT	transit	2.5.2, 3.2.3	[1,790]	phylogenetics
Transrate	transrate	1.0.1	[1,791]	biology, assembly
TransVar	transvar	2.3.3	[1,792]	biology, phylogenetics
TreeBreaker	treebreaker	20160621	[1,793]	biology, phylogenetics
TreeMix	treemix	1.12	[1,794]	biology, phylogenetics
treePL	treepl	20150305	[1,795]	biology, phylogenetics
TREEPUZZLE	treepuzzle	5.3	[1,796]	biology, phylogenetics
TreeShrink	treeshrink	1.3.1, 1.3.2	[1,797]	phylogenetics
TreeTime	treetime	0.7.5, 0.8.1	[1,798]	phylogenetics
trelis	trelis	16.3	[1,799]	math
TRF	trf	4.04, 4.09.1	[1,800]	biology, genomics
Trilinos	trilinos	12.12.1, 12.18.1, 12.6.4	[1,801]	math
Trim Galore	trim_galore	0.4.4, 0.5.0, 0.6.5	[1,802]	biology, ngs
trim_isoseq_polya	trim_isoseq_polya	0.0.3	[1,803]	biology, genomics, sequencing
trimAl	trimal	1.2, 1.4.1	[1,804]	biology, genomics, alignment
trimesh	trimesh	3.20.2	[1,805]	graphics, math
TriMetAss	trimetass	1.1	[1,806]	biology, ngs
Trimmomatic	trimmomatic	0.33, 0.36, 0.39	[1,807]	biology, ngs
Trinity	trinity	r20130225, r20131110, r20140413	[1,808]	biology, ngs, sequencing, rna-seq
Trinotate	trinotate	3.0.1, 3.2.0	[1,809]	biology
triobinning	triobinning	0.2.3	[1,810]	genomics, biology
TRIPLEC	triplec	1.0	[1,811]	biology
TRITONSERVER	tritonserver	21.08, 23.01	[1,812]	machine_learning
tRNAscan-Se	trnascan-se	1.23	[1,813]	biology, ngs
TRUST4	trust4	1.0.2b	[1,814]	phylogenetics
Trycycler	trycycler	0.4.2	[1,815]	phylogenetics
TURBOMOLE	turbomole	7.4.1	[1,816]	chemistry
TWINSCAN	twinscan	4.1.2	[1,817]	biology, genomics
Ubuntu	ubuntu	20.04, 22.04	[1,818]	linux
UCSC	ucsc	20200320, 20210803	[1,819]	genomics
ucsc-fafiltern	ucsc-fafiltern	377	[1,820]	phylogenetics
ucsc-maskoutfa	ucsc-maskoutfa	377	[1,821]	phylogenetics
UCX	ucx	1.11.2, 1.9.0	[1,822]	programming, library
UDUNITS	udunits	2.2.17	[1,823]	library, data_science, math
ufraw	ufraw	0.22	[1,824]	data_mining
ugtm	ugtm	1.1.6	[1,825]	statistics, modeling
UKFractography	ukfractography	20200127	[1,826]	phylogenetics
umi-tools	umi-tools	0.5.5	[1,827]	phylogenetics
UMICollapse	umicollapse	02072021	[1,828]	chemestry
UNAFold	unafold	3.8	[1,829]	biology, genomics, rna
Unanimity	unanimity	20171108, 3.4.1	[1,830]	programming, library, compiler
UNCALLED	uncalled	2.2	[1,831]	biology, genomics
Unicycler	unicycler	0.4.8	[1,832]	phylogenetics
Unrar	rar	0.0.1, 4.20	[1,833]	utility
uproc	uproc	1.2.0	[1,834]	biology, genomics
uropa	uropa	4.0.2	[1,835]	genomics, sequencing, biology
USEARCH	usearch	9.0.2132, 9.1.13, 9.2.64	[1,836]	biology, alignment, sequencing
UShER	usher	0.1.4, 0.4.1, 0.5.2	[1,837]	phylogenetics
V-Phaser	vphaser2	02112013	[1,838]	biology, phylogenetics
v-pipe	v-pipe	2.0.0, 2.99.3	[1,839]	biology, genomics, sequencing
Valgrind	valgrind	3.11.0, 3.15.0, 3.8.1	[1,840]	programming
Valouev	valouev	20160325	[1,841]	biology, phylogenetics
vamb	vamb	3.0.2	[1,842]	biology
VAMPIR	vampir	9.1	[1,843]	performance_analysis
VarDictJava	vardictjava	1.6.0, 20160521, 20170531	[1,844]	biology, phylogenetics
VARI	vari	0.7.0	[1,845]	math, visualization
varnorm	varnorm	0.21	[1,846]	biology
varpipe-wgs	varpipe-wgs	20230222	[1,847]	sequencing, biology
VarScan	varscan	2.3.6	[1,848]	biology, ngs
VarSim	varsim	0.8.4, 0.8.6	[1,849]	phylogenetics
VarSimLab	varsimlab	20180220, 20180921	[1,850]	biology, simulation, genomics
vasp	vasp	5.4.4, 6.1.0, 6.2.0	[1,851]	chemistry
vaspkit	vaspkit	1.2.5	[1,852]	phylogenetics
VAST-TOOLS	vast-tools	2.5.1, 20150506	[1,853]	biology, rna-seq, ngs
VCF-kit	vcf-kit	0.2.6	[1,854]	phylogenetics
vcf-validator	vcfvalidator	0.6	[1,855]	biology, phylogenetics
vcfanno	vcfanno	0.2.8, 0.3.3	[1,856]	biology, phylogenetics
vcflib	vcflib	1.0.1	[1,857]	biology, genomics
vcftools	vcftools	0.1.15, 0.1.16, 0.1.9	[1,858]	biology, genomics
vcontact	vcontact	20190512	[1,859]	phylogenetics
VDJtools	vdjtools	1.1.7, 1.2.1	[1,860]	biology, phylogenetics
Velocyto	velocyto	0.17	[1,861]	biology, RNA seq
Velvet	velvet	1.2.10, 1.2.10-long	[1,862]	biology, genomics
VEP	vep	83, 88.8, 92	[1,863]	biology, genomics, ngs
Vermouth-martinize	vermouth-martinize	0.7.2	[1,864]	phylogenetics
VeryFastTree	veryfasttree	3.0.1	[1,865]	phylogenetics
vg	vg	1.39.0, 1.43.0, 1.45.0	[1,866]	phylogenetics
vibrant	vibrant	1.2.0	[1,867]	genomics
ViennaRNA	viennarna	2.2.6, 2.4.18	[1,868]	biology, rna-seq
ViewBS	viewbs	0.1.10, 0.1.9	[1,869]	phylogenetics
Vim	vim	8.1.1566, 8.2.2465	[1,870]	programming, language
viralmsa	viralmsa	1.1.10, 1.1.12	[1,871]	phylogenetics
VirSieve	virsieve	20210406	[1,872]	biology, pipeline
virsorter	virsorter	2.2.3	[1,873]	genomics
VirtualCell	virtualcell	7.1	[1,874]	phylogenetics
VIRULIGN	virulign	1.0.2	[1,875]	phylogenetics
VirusDetect	virusdetect	1.7	[1,876]	phylogenetics
VirusFinder	virusfinder	2.0	[1,877]	biology, phylogenetics
visit	visit	2.13.3, 3.0.1, 3.1.4	[1,878]	visualization, animation
VISPR	vispr	0.4.14	[1,879]	phylogenetics
VMD	vmd	1.9.1, 1.9.3, 1.9.4	[1,880]	visualization, animation, graphics
vscode	vscode	1.72.2, 1.74.3	[1,881]	programming
VSearch	vsearch	2.22.1, 20151022, 20161209-2.3.4	[1,882]	biology, ngs
vt	vt	0.57721, 20140903, 20160129	[1,883]	biology, genomics
VTC	vtc	0.9.3	[1,884]	biology
VTK	vtk	9.0.3, 9.1.0, 9.2.6	[1,885]	biology, neuroscience, imaging
w2rap-contigger	w2rap-contigger	20161124	[1,886]	biology, genomics
Wannier90	wannier90	1.2, 2.1.0	[1,887]	physics
WarpedLMM	warpedlmm	0.21	[1,888]	modeling
WaveGAN	wavegan	20190829	[1,889]	machine_learning, audio, GAN
WDSSII	wdss2	5, 6	[1,890]	climate
WebLogo	weblogo	2.8.2, 3.3, 3.5.0	[1,891]	biology, sequencing, graphics
Weka	weka	3.8, 3.8.5	[1,892]	statistics, machine_learning
Wengan	wengan	0.2	[1,893]	biology, genomics
wgd	wgd	1.1.1	[1,894]	phylogenetics
WGS Assembler	wgs	8.3rc1.r4638, 8.3rc2	[1,895]	biology, genomics
Wgsim	wgsim	0.3.1-r13	[1,896]	biology, phylogenetics
WHAMM	whamm	0.14a	[1,897]	biology, phylogenetics
WhatsHap	whatshap	1.1	[1,898]	biology, phylogenetics
whiteboxtools	whiteboxtools	1.5.0	[1,899]	phylogenetics
Wine	wine	4.0.0, 7.0.0	[1,900]	linux, utility
Wise	wise	2.2.0, 2.4.1	[1,901]	biology, genomics
WIsH	wish	1.0	[1,902]	phylogenetics
WoLFPSort	wolfpsort	0.2	[1,903]	phylogenetics
WOMBAT	wombat	20180118	[1,904]	biology, phylogenetics
workbench	workbench	4.1.1	[1,905]	modeling, simulation
wtdbg	wtdbg	2.1, 2.4, 2.5	[1,906]	phylogenetics
WU BLAST	wublast	2.0	[1,907]	biology
Wub	wub	0.2.0, 0.4.0	[1,908]	biology, genomics, ngs
xander	xander	20151222	[1,909]	biology, phylogenetics
Xapian	xapian	1.4.4	[1,910]	library
XCrySDen	xcrysden	1.5.60	[1,911]	material_science
Xerces	xerces	3.1.4	[1,912]	phylogenetics
xesmf	xesmf	0.6.2	[1,913]	math, climate
xlsx2csv	xlsx2csv	0.8.0	[1,914]	utility
xpclr	xpclr	1.0, 1.1.1	[1,915]	phylogenetics
Xterm	xterm	1.1	[1,916]	utility
xwalk	xwalk	0.6	[1,917]	biology
XWAS	xwas	3.0	[1,918]	phylogenetics
XY-Meta	xy-meta	20200413	[1,919]	phylogenetics
XZ	xz	5.2.2	[1,920]	compression, library
YAGO	yago	4	[1,921]	data_science
YAHA	yaha	0.1.82	[1,922]	biology, ngs
YAK	yak	0.1	[1,923]	phylogenetics
YASM	yasm	1.3.0	[1,924]	programming
YASRA	yasra	2.33	[1,925]	biology, ngs, sequencing
yolov4_darknet	yolov4_darknet	4-pre	[1,926]	machine_learning
yolov5	yolo	4.0, 8	[1,927]	machine_learning
Zagros	zagros	1.0.0	[1,928]	biology, phylogenetics
ZEO++	zeo++	0.2.2	[1,929]	chemistry
zorro	zorro	2.2	[1,930]	biology, sequencing
Zstd	zstd	1.5.0	[1,931]	phylogenetics
ZUMIS	zumis	2.6.0	[1,932]	biology, ngs, sequencing