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	2.1.0, 2.2.5, 2.3.7	[7]	biology, de_novo
ACTC	actc	0.3.1	[8]	biology
AdapterRemoval	adapterremoval	2.2.2	[9]	phylogenetics
ADFRsuite	adfrsuite	1.0	[10]	sequencing, biology
ADMB	admb	11.5, 12.0	[11]	math, modeling
AdmixTools	admixtools	20150311, 7.0.2	[12]	biology, genomics, ngs
ADMIXTURE	admixture	1.23, 1.3.0	[13]	biology, genomics, ngs
AEGeAn	aegean	0.14.0, 0.16.0	[14]	biology, genomics
AFNI	afni	20.3.00, 2018_04_12, 23.3.09	[15]	biology, neuroscience, imaging
AfterQC	afterqc	0.9.7	[16]	phylogenetics
AGAT	agat	0.4.0	[17]	phylogenetics
AGFusion	agfusion	1.252	[18]	phylogenetics
Albacore	albacore	2.3.1, 2.3.3	[19]	biology, phylogenetics
Albumentations	albumentations	1.0.3	[20]	ai, image_processing, imaging
Alder	alder	1.03	[21]	biology, genomics
Alevin-fry	alevin-fry	0.8.1	[22]	sequencing, biology
ALFA	alfa	1.1.1	[23]	phylogenetics
alfred	alfred	0.2.6	[24]	web, math
alienhunter	alienhunter	1.7	[25]	biology, sequencing
AliStat	alistat	1.12	[26]	phylogenetics
alleleCount	allelecount	20210713	[27]	biology
allhic	allhic	0.9.8	[28]	genomics, biology
ALLMAPS	allmaps	20180117	[29]	biology, phylogenetics
ALLPATHS-LG	allpaths	42316, 44837, 49232	[30]	biology, ngs
AlphaFold	alphafold	2.1.2, 2.3.1, 2.3.2	[31]	protein, structure, machine_learning
Alphaimpute	alphaimpute	0.0.2, 1.9.8.2, 1.9.8.3	[32]	phylogenetics
AlphaMate	alphamate	0.1.1	[33]	biology
AlphaPulldown	alphapulldown	0.30.7, 2.0.0b1, 2.0.0b2	[34]	protein, structure, machine_learning
AltAnalyze	altanalyze	2.1.0	[35]	biology, genomics
AMAS	amas	1.0	[36]	phylogenetics
AMBER	amber	20, 22, 24	[37]	chemistry, molecular_dynamics
ambertools	ambertools	23	[38]	chemistry, molecular_dynamics
AMICO	amico	1.0.1, 2.0.1	[39]	library, imaging, math
AMOS	amos	3.1.0	[40]	biology, genomics, assembly
AMP	amp	0.6.1	[41]	phylogenetics
amPEPpy	ampeppy	1.0	[42]	phylogenetics
amphora2	amphora2	20140305	[43]	biology, phylogenetics
Ampligraph	ampligraph	2.0.0	[44]	programming, library, math
AMPtk	amptk	1.5.1, 1.5.4, 1.6	[45]	biology, ngs
amptorch	amptorch	20210313	[46]	phylogenetics
amrfinderplus	amrfinderplus	3.10.18, 3.12.8	[47]	phylogenetics
AMRPlusPlus	amrplusplus	20180508	[48]	phylogenetics
AMUSE	amuse	10.0, 13.1.0	[49]	astronomy
ancestryhmm	ancestryhmm	1.0.2	[50]	genomics, biology
anchorwave	anchorwave	1.2.1	[51]	biology, genomics
ANDI	andi	0.15b	[52]	assembly
ANGSD	angsd	0.933, 0.940	[53]	biology, ngs
annocript	annocript	2.0	[54]	phylogenetics
AnnoTALE	annotale	1.4.1	[55]	phylogenetics
ANNOVAR	annovar	20130221, 20150322, 20191024	[56]	biology, genomics
Ansible	ansible	2.5.5, 2.8.1	[57]	workflow_automation
ANSYS	ansys	2023R2	[58]	modeling
ansysem	ansysem	17.0, 2022r1, 2023r1	[59]	physics
antiSMASH	antismash	4.1.0, 6.0.1, 7.0.0	[60]	phylogenetics
ANTs	ants	2.2.0, 2.3.4	[61]	biology, phylogenetics
anvio	anvio	6.2, 7.1, 8.0	[62]	biology
Appreci8	appreci8	20180530	[63]	biology, genomics
apps	clearmap	2.0	[64]	biology, neurobiology
Apptainer	apptainer	1.2.2, 1.3.1, 1.3.5	[65]	workflow_automation
APT	apt	1.18.0, 1.20.5, 2.11.8	[66]	biology, genomics
aquamis	aquamis	1.4.0	[67]	biology, genomics
arb	arb	r19270	[68]	phylogenetics
ARC	arc	1.1.4	[69]	biology, ngs
arcashla	arcashla	0.5.0	[70]	biology, genetics
Arcticporechop	arcticporechop	0.3.2	[71]	phylogenetics
Aria2	aria2	1.35.0	[72]	utility
ARKS	arks	1.0.2	[73]	phylogenetics
Armadillo	armadillo	7.900.0, 9.200.6, 9.900.4	[74]	library, compiler, math
ARPACK	arpack	1.0	[75]	math
ArrayFire	arrayfire	3.4.2	[76]	math
arriba	arriba	2.1.0	[77]	phylogenetics
ART	art	20160417, 20160605	[78]	phylogenetics
artemis	artemis	18.1.0	[79]	biology
asap	asap	2.0	[80]	visualization, biology
asaq	asaq	1.0	[81]	alignment, sequencing, phylogenetics
ASDEC	asdec	1.2	[82]	bioinformatics
ASE-ANI	ase-ani	20180712	[83]	biology, genomics, ngs
ASHS	ashs	2.0	[84]	biology, imaging
ASPECT	aspect	2.3.0, 2.5.0	[85]	geodynamics
Assembly-stats	assembly-stats	1.0.1	[86]	biology, sequencing, genomics
Assemblytics	assemblytics	1.2.1	[87]	phylogenetics
asset	asset	20210112	[88]	sequencing, data_science
Assexon	assexon	20190814	[89]	phylogenetics
AStalavista	astalavista	3.2, 4.0	[90]	biology, genomics
aster	aster	1.15, 1.16, 220718	[91]	biology, data_science, sequencing
asteroid	asteroid	1.0	[92]	genomics
ASTRAL	astral	5.6.1, 5.6.2, 5.7.7	[93]	biology, ngs, phylogenetics
ASTRID	astrid	2.2.1	[94]	phylogenetics
Astropy	astropy	2.0.8	[95]	biology, phylogenetics
ATAT	atat	3.23, 3.34	[96]	material_science
ATLAS	atlas	3.10.1, 3.10.2, 3.11.17	[97]	library, data_science
Atom	atom	1.57.0	[98]	programming
AtomEye	atomeye	3	[99]	material_science
AtomMan	atomman	1.3.3	[100]	phylogenetics
aTRAM	atram	2.2.0, 2.4.3	[101]	math
Augustus	augustus	3.3.3, 3.4.0, 3.5.0	[102]	biology, genomics
Auto3DEM	auto3dem	4.05.2	[103]	image_processing
AutoDock	autodock	4.2.6	[104]	biology
AutoDock-GPU	autodock-gpu	1.5.3	[105]	chemistry
autodock-vina	autodock-vina	1.2.3, 1.2.5	[106]	biology
Autometa	autometa	2.2.0, 20190802	[107]	phylogenetics
automlsa2	automlsa2	0.8.1	[108]	phylogenetics, biology, genomics
AWSCLI	awscli	2.11.7, 2.2.30	[109]	utility
azoo	azoo	1.3.1	[110]	phylogenetics
bactopia	bactopia	2.2.0	[111]	genomics
Badread	badread	0.1.5	[112]	phylogenetics
bakta	bakta	1.3.3, 1.9.4	[113]	genomics, biology
BALi-Phy	bali-phy	3.4.1, 3.5.0	[114]	phylogenetics
BAM-matcher	bam-matcher	20161021	[115]	phylogenetics
Bam-Readcount	bam-readcount	20150616	[116]	biology, genomics
bamaddrg	bamaddrg	20120326	[117]	phylogenetics
BamBam	bambam	1.0, 1.4	[118]	biology, genomics
bamm	bamm	2.5.0	[119]	phylogenetics
bamsnap	bamsnap	0.2.19	[120]	phylogenetics
Bamstats	bamstats	20140602	[121]	biology, ngs
Bamsurgeon	bamsurgeon	1.2	[122]	phylogenetics
bamtofastq	bamtofastq	1.3.5	[123]	phylogenetics
Bamtools	bamtools	2.5.0, 2.5.1, 2.5.2	[124]	biology, ngs, sequencing
bamUtil	bamutil	1.0.2	[125]	biology, genomics
BAPS	baps	6.0	[126]	biology, genomics
Barrnap	barrnap	0.7, 0.9	[127]	biology, rna-seq
Basemount	basemount	0.15.96, 0.25.2	[128]	biology, sequencing
BatMeth2	batmeth2	20210720	[129]	biology, genomics, mapping
bax2bam	bax2bam	0.0.9	[130]	phylogenetics
BayArea	bayarea	1.0.2	[131]	biology
BAYENV	bayenv	2.0	[132]	biology, phylogenetics
BayesAss	bayesass	3.0.4, 3.0.4.2	[133]	phylogenetics
bayesass3-snps	bayesass3-snps	1.1	[134]	phylogenetics
BayeScan	bayescan	2.1	[135]	biology, variant_calling
BayesR	bayesr	20151016	[136]	biology, phylogenetics
BayesTraits	bayestraits	3.0.2	[137]	phylogenetics
baypass	baypass	2.1	[138]	biology, phylogenetics
BBMap	bbmap	38.44, 38.90, 39.06	[139]	biology, alignment
bcftools	bcftools	1.13, 1.15, 1.19	[140]	biology, ngs
bcl2fastq	bcl2fastq	2.16.0.10, 2.20.0.422	[141]	biology, ngs
BCLConvert	bclconvert	4.2.7	[142]	biology, ngs
BDG-SeQuila	bdg-sequila	0.5.5	[143]	phylogenetics
BEAGLE	beagle	4.1, 5.0, 5.2	[144]	biology, genomics
BEAR	bear	20170209	[145]	biology, genomics
BEAST	beast	2.7.0, 2.7.3, 2.7.5	[146]	biology, phylogenetics
BEAST2-XML	beast2-xml	1.0.9	[147]	phylogenetics
BEDOPS	bedops	2.4.30, 2.4.41	[148]	biology, sequencing, ngs
BEDTools	bedtools	2.29.1, 2.29.2, 2.30.0	[149]	biology, ngs
Bertini	bertini	1.6	[150]	math
BERTopic	bertopic	0.14.0, 0.7, 0.8.1	[151]	machine_learning
BESST	besst	2.2.4	[152]	biology, ngs
BFAST	bfast	0.7.0	[153]	biology, ngs
BFC	bfc	1.0	[154]	genome
bgenix	bgenix	1.1.7	[155]	data_science, genomics
BIDSCOIN	bidscoin	3.7.4, 4.3.0	[156]	neuroscience
Bifrost	bifrost	0.2, 1.0.3, 20200225	[157]	phylogenetics
BiG-SCAPE	big-scape	1.1.2, 1.1.9	[158]	biology, genomics, phylogenetics, pipeline
bigslice	bigslice	1.1.1, 2.0.0	[159]	biology, genomics
bindash	bindash	1.0.1, 1.0.2	[160]	genomics
BinPacker	binpacker	1.0	[161]	biology, rna-seq, assembly
BinSanity	binsanity	0.2.6.4	[162]	biology, genomics
Bioawk	bioawk	1.0	[163]	phylogenetics
bioBakery	biobakery	1.8, 3.0.0, 3.1.0	[164]	phylogenetics
Biodiverse	biodiverse	2.1	[165]	phylogenetics
Biolite	biolite	0.3.5.1	[166]	biology, genomics, variant_calling
BIOM	biom	2.1.5, 2.1.6	[167]	biology, genomics
BIOMART	biomart	1.4	[168]	biology, genomics
BioNeMo	bionemo	0.3.1, 1.2, 1.3	[169]	ai, machine_learning
Biopieces	biopieces	2.0	[170]	phylogenetics
BirdNET	birdnet	0.1.2	[171]	bioinformatics
BIRDS	fiji-birds	1.0	[172]	workflow_automation, utility, imaging
Bismark	bismark	0.24.2, 0.7.4, 0.7.7	[173]	biology, ngs
Blackfynn	blackfynn	0.2.7	[174]	data_mining
BLASR	blasr	20130815, 20161215 (5.3), 5.3.2	[175]	biology, ngs
Blast2GO	blast2go	2.5.0-20120705	[176]	biology, genomics
Blast2GO CLI	blast2go	1.3.3	[177]	biology, genomics
BLAT	blat	20121105, 20140318	[178]	genomics
blender	blender	2.77, 3.0.1, 4.0.2	[179]	graphics
blink	blink	0.01	[180]	genomics
Blitz	blitz	0.10, 1.0.2	[181]	library
BlobTools	blobtools	1.0, 2.2, 4.3.5	[182]	phylogenetics
bloomfiltertrie	bloomfiltertrie	0.8.7	[183]	phylogenetics
BloomTree	bloomtree	0.3.5	[184]	data_mining
BLUPF90	blupf90	20160604, 20180301, 20190531	[185]	biology, phylogenetics
BMGE	bmge	1.12	[186]	biology, genomics, phylogenetics
bmtagger	bmtagger	3.101	[187]	genomics, biology
BOLT-LMM	bolt-lmm	2.3.4	[188]	phylogenetics
BoltzTraP	boltztrap	1.2.5	[189]	physics
Boost	boost	1.75.0, 1.77.0, 1.82.0	[190]	programming, library, compiler
booster	booster	0.1.2	[191]	phylogenetics
botorch	botorch	0.7.1	[192]	phylogenetics, biology
Bowtie	bowtie	1.1.1, 1.2.0, 1.2.3	[193]	biology, ngs, sequencing
Bowtie2	bowtie2	2.3.5.1, 2.4.2, 2.4.5	[194]	biology, ngs, sequencing
BoxCLI	boxcli	2.9.0	[195]	file_management, web, programming
BPGA	bpga	1.2	[196]	biology, ngs
BPP	bpp	4.1.4, 4.3.8, 4.4.1	[197]	biology, phylogenetics
BppSuite	bppsuite	2.3.2	[198]	genomics
Bracken	bracken	1.0.0, 2.5, 2.9	[199]	biology, phylogenetics
BrainIAK	brainiak	0.11	[200]	imaging
braker	braker	3.0.2, 3.0.3, 3.0.8	[201]	biology, genomics, annotation
BRANCH	branch	1.8.1	[202]	biology, ngs, mapping
BRATNextGen	bratnextgen	20150505	[203]	biology, genomics
BreakDancer	breakdancer	1.4.5	[204]	biology, phylogenetics
breakseq	breakseq	2.2	[205]	biology, phylogenetics
Brewery	brewery	20191205	[206]	phylogenetics
Bridger	bridger	20141201	[207]	ngs, genomics, biology
BRIG	brig	0.95	[208]	biology, genomics
brkraw	brkraw	0.3.5	[209]	data_science, imaging
BRM	brm	0.3	[210]	phylogenetics
Bruker2nifti	bruker2nifti	1.0.4	[211]	phylogenetics
Bsmap	bsmap	2.87	[212]	biology, ngs
Bsoft	bsoft	1.9.1	[213]	biology, image_processing
BSseeker2	bsseeker2	2.1.0, 2.1.8	[214]	biology, phylogenetics
bubbleparse	bubbleparse	20140314	[215]	biology, phylogenetics
BUCKy	bucky	1.4.4	[216]	biology, phylogenetics
BUSCO	busco	4.1.4, 5.2.0	[217]	biology, genomics
BWA	bwa	0.7.7, 0.7.8, 0.7.9a	[218]	biology, ngs
bwa-mem2	bwa-mem2	2.2.1	[219]	phylogenetics
bwa-meth	bwameth	0.2.7	[220]	genomics, biology
BWA-PSSM	bwa-pssm	0.5.11	[221]	phylogenetics
bxh_xcede_tools	bxh_xcede_tools	1.11.1	[222]	biology
BYOBU	byobu	5.133, 5.92	[223]	shell
bzip2	bzip2	1.0.6	[224]	utility, library
c-wap	c-wap	20220624	[225]	sequencing, genomics, biology
Cactus	cactus	2.0.3, 2.0.5, 2.8.0	[226]	phylogenetics
CAFE	cafe	4.1, 5.0.0	[227]	phylogenetics
came	came	0.0.1	[228]	phylogenetics
Camino	camino	20140723	[229]	biology, neuroscience, imaging
cammiq	cammiq	0.1.1	[230]	genomics, biology
CAMP	camp	1.0.0	[231]	biology, sequencing
Cantera	cantera	2.1.1	[232]	physics
Canu	canu	2.0, 2.1, 2.2	[233]	biology, sequencing
CANVAS	canvas	1.40.0.1613	[234]	phylogenetics
CAP3	cap3	20120705	[235]	biology, assembly
Capnp	capnp	0.5.3	[236]	compiler
captus	captus	0.9.88, 0.9.91	[237]	phylogenetics, biology
CARTA	carta	2.0	[238]	image_processing
CASAVA	casava	1.8.2	[239]	biology, ngs
CASM	casm	0.2.0	[240]	physics
CasOFFinder	casoffinder	2.4	[241]	phylogenetics
CAT	cat	12 Standalone	[242]	biology
Catch	catch	1.4.0	[243]	biology, genomics, sequencing
CAVIAR	caviar	20171218	[244]	biology, phylogenetics
CBGpipe	cbgpipe	20190702	[245]	phylogenetics
CCMetagen	ccmetagen	1.4.0	[246]	phylogenetics
CD-HIT	cdhit	4.6, 4.6.4, 4.6.8	[247]	biology, genomics
CDBFasta	cdbfasta	20181005	[248]	phylogenetics
CDNA_Cupcake	cupcake	20180629, 22.0.0, 9.0.1	[249]	biology, ngs, sequencing
CDO	cdo	1.7.2rc3, 1.9.4	[250]	climate
CDRT	cdrt	23.10	[]	machine_learning
CellProfiler	cellprofiler	3.1.9, 4.1.3, 4.2.6	[251]	phylogenetics
CellRanger	cellranger	7.0.1, 7.2.0, 8.0.0	[252]	biology, ngs, rna-seq
CellRanger-ARC	cellranger-arc	2.0.1	[253]	biology, ngs, rna-seq
CellRanger-ATAC	cellranger-atac	1.2.0	[254]	biology, ngs, rna-seq
CellRanger-DNA	cellranger-dna	1.0.0, 1.1.0	[255]	biology, ngs, rna-seq, genomics
Centrifuge	centrifuge	1.0.3, 1.0.4b	[256]	biology, phylogenetics
CFITSIO	cfitsio	3.370	[257]	library, compiler
CGAL	cgal	5.02, 5.5.2, 5.6	[258]	library, math
CGATools	cgatools	1.6.0.43	[259]	biology, ngs
cgmaptools	cgmaptools	0.1.1, 0.1.2	[260]	phylogenetics
cgmlst	cgmlst	0.2	[261]	phylogenetics
cgmlstfinder	cgmlstfinder	1.0	[262]	genetics
CGView	cgview	1.0.2	[263]	phylogenetics
CHARMM	charmm	36a3, 43b2, c48b2	[264]	chemistry, simulation
ChartDirector	libchartdir	5.1.0	[265]	library, data_science
CheckM	checkm	1.0.4, 1.0.7, 1.1.2	[266]	biology, genomics
checkv	checkv	1.0.1	[267]	biology, genomics
chewbbaca	chewbbaca	3.3.0	[268]	biology, genomics
chewiesnake	chewiesnake	3.0.0	[269]	biology, genomics
Chimera	chimera	1.12	[270]	biology, modeling
Chipyard	chipyard	1.0	[271]	simulation
Chopper	chopper	0.8.0	[272]	bioinformatics
Chromeister	chromeister	1.5a	[273]	biology, genomics
ChromEvol	chromevol	2.0, 3.0	[274]	biology, ngs
CIALIGN	cialign	1.1.4	[275]	bioinformatics
CIMS	cims	4.1.2	[276]	biology, genomics
CIRCexplorer	circexplorer	1.1.10	[277]	biology, rna-seq
CIRCexplorer2	circexplorer2	2.3.5, 2.3.8	[278]	phylogenetics
circexplorer3	circexplorer3	01172021	[279]	RNA-Seq
Circlator	circlator	1.5.5	[280]	phylogenetics
Circleator	circleator	1.0.2	[281]	phylogenetics
circompara2	circompara2	0.1.2.1	[282]	phylogenetics
Circos	circos	0.63-pre11, 0.69-2, 0.69-9	[283]	biology, genomics, ngs
circtools	circtools	1.2.1	[284]	biology
CIRI	ciri	2.0.6	[285]	phylogenetics
ciriquant	ciriquant	1.1.2	[286]	phylogenetics
CisGenome	cisgenome	2.0	[287]	biology, genomics
cisTEM	cistem	1.0.0	[288]	phylogenetics
Clairvoyante	clairvoyante	1.02	[289]	phylogenetics
Clann	clann	3.2.3	[290]	biology, phylogenetics
clara	clara	v4.0	[291]	ai, machine_learning
CLARK	clark	1.2.2-b, 1.2.3	[292]	biology, genomics
clean	clean	1.0.1	[293]	protein, machine_learning
CLHEP	clhep	2.2.0.1	[294]	physics
CLIFinder	clifinder	4.1	[295]	biology, phylogenetics
ClinicaDL	clinicadl	1.0.4, 1.2.0	[296]	biology, imaging, machine_learning
clipkit	clipkit	1.3.0	[297]	genomics, biology
CLIPper	clipper	2.1.0	[298]	phylogenetics
CLIPSeqTools	clipseqtools	0.1.7	[299]	biology, sequencing
CliqueSNV	cliquesnv	2.0.3	[300]	biology, phylogenetics
ClonalFrame	clonalframe	1.1, 1.2	[301]	biology, ngs, phylogenetics
ClonalFrameML	clonalframeml	1.0, 1.11	[302]	biology, ngs, phylogenetics
CloudCompare	cloudcompare	2.10.3	[303]	visualization
Clover	clover	2.0	[304]	biology, genomics, assembly
CLUMPP	clumpp	1.1.2	[305]	biology
ClustalO	clustalo	1.2.0	[306]	biology, alignment
ClustalW	clustalw	2.1	[307]	biology, alignment
cluster3	cluster3	1.52a	[308]	biology, genomics
Clview	clview	20130402	[309]	biology
CMake	cmake	3.21.3, 3.26.4, 3.30.5	[310]	programming
CMS	cms	20170518, 20240429	[311]	biology
CMWP	cmwp	140518	[312]	biology, genomics
CNCI	cnci	20180305	[313]	phylogenetics
CNSpipeline	cnspipeline	20170827	[314]	phylogenetics
CNV-Seq	cnvseq	20110715, 20140812	[315]	biology, genomics
CNV-Sim	cnv-sim	0.9.2	[316]	biology, phylogenetics
CNVkit	cnvkit	0.9.6	[317]	phylogenetics
CNVnator	cnvnator	0.3.2	[318]	biology, genomics
cobra-tf	cobra-tf	0.1	[319]	fluid_dynamics
Cobretti	cobretti	1.0	[320]	GeneExpression
CodonPhyML	codonphyml	20150303	[321]	phylogenetics
Coevol	coevol	1.3c, 1.4b, 1.6	[322]	biology, phylogenetics
Cogent	cogent	2.1	[323]	biology, phylogenetics
COLMAP	colmap	3.6	[324]	modeling
CoMap	comap	1.4.1	[325]	biology, genomics
Comp-D_MPI	comp-d_mpi	1.0	[326]	statistics
Compacta	compacta	1.02	[327]	biology, genomics
COMSOL	comsol	6.1, 6.2, 6.2.04	[328]	simulation
Concaterpillar	concaterpillar	1.8a	[329]	phylogenetics
CONCOCT	concoct	1.1.0	[330]	biology, genomics
Conda	conda	24.3.0, 24.7.1	[331]	programming
Conefor	conefor	2.7.3	[332]	software
CONN	conn	22a	[333]	imaging
CONNECT	connect	20200614	[334]	phylogenetics
connectomemapper3	connectomemapper3	3.0.0-rc1	[335]	phylogenetics
ConPADE	conpade	1.0	[336]	phylogenetics
Conpair	conpair	20161010, 20180624	[337]	biology, phylogenetics
Consed	consed	23.0, 25.0, 29.0	[338]	biology, genomics
CONSEL	consel	0.20	[339]	biology, phylogenetics
ContaVect	contavect	0.2	[340]	biology, phylogenetics
Convert3D	convert3d	1.1.0	[341]	imaging, utility
Coot	coot	0.9.5	[342]	modeling
CoPTR	coptr	1.1.6	[343]	biology
Coreutils	coreutils	8.23, 8.28	[344]	utility
Corset	corset	1.06	[345]	biology, ngs
Counterr	counterr	0.1, 20230501	[346]	phylogenetics
Coverm	coverm	0.6.1	[347]	biology, genomics, ngs
covNMR	covnmr	2014	[348]	chemistry, biology
cp2k	cp2k	2024.1, 7.0.0	[349]	imaging
CPAT	cpat	3.0.2	[350]	phylogenetics
cpc	cpc	2.0	[351]	phylogenetics
CPLEX	cplex	12.6.2, 12.7, 12.9	[352]	climate
Crass	crass	1.0.1	[353]	biology, assembly
crest	crest	12.2, 2.12, 3.0	[354]	chemistry
crisflash	crisflash	1.2.0	[355]	phylogenetics
CRISP	crisp	20181122, 20240419	[356]	phylogenetics
CRISPRanalyzer	crispranalyzer	1.50	[357]	biology, genomics, ngs
CRISPRCasFinder	crisprcasfinder	4.2.17	[358]	phylogenetics
CRISPResso2	crispresso2	20220811	[359]	genomics, sequencing, biology
CrossMap	crossmap	0.3.9, 0.6.3	[360]	biology, genomics
crossmapper	crossmapper	1.1.1	[361]	phylogenetics
Crux	crux	1.40	[362]	biology, spectroscopy
cryodrgn	cryodrgn	2.3.0	[363]	biology
CryptoMiniSat	cryptominisat	5.0.1	[364]	math
csubst	csubst	1.3.0	[365]	Biology, Phylogenetics
csvpad	csvpad	1.2	[366]	data science
csvtk	csvtk	0.23.0, 0.30.0	[367]	biology
ctk	ctk	1.1.4	[368]	biology, genomics
CUBE	cube	4.4	[369]	library, compiler, math
CUDA	cuda	12.2.2, 12.3.2, 12.4.1	[370]	programming, library, graphics
Cufflinks	cufflinks	2.1.1, 2.2.1, 2.2.1.1	[371]	biology, ngs, sequencing
cuOpt	cuopt	22.12	[372]	Accelerated AI Logistics and Route Optimization
cupy	cupy	8.3.0	[373]	phylogenetics
cutadapt	cutadapt	1.18, 2.8, 3.4	[374]	biology, ngs
CutRunTools	cutruntools	20200104	[375]	phylogenetics
cvbio	cvbio	3.0.0	[376]	phylogenetics
CViT	cvit	1.3	[377]	programming, library
CWLtool	cwltool	1.0.20190906, 2.0.20200126, 3.0.20210124104916	[378]	workflow_automation, scheduler
cx_oracle	cxoracle	8.3.0	[379]	database, utility
CycleGan	cyclegan	20201015	[380]	phylogenetics
Cytoscape	cytoscape	3.10.2, 3.4.0	[381]	biology, ngs, phylogenetics
cyvcf2	cyvcf2	20230728	[382]	library
d2go	d2go	20210702	[383]	machine_learning, ai
dadi	dadi	2.1.1	[384]	phylogenetics
DAKOTA	dakota	6.15, 6.8, 6.8-gui	[385]	math
DALIGNER	daligner	1.0	[386]	biology, phylogenetics
dammit	dammit	1.0rc2	[387]	biology, phylogenetics
dancemapper	dancemapper	1.0.0	[388]	machine learning
dapars	dapars	1.0.0	[389]	genomics, biology
darwin-gpu	darwin-gpu	20190115	[390]	genomics, alignment
DASTool	dastool	1.1.0, 1.1.2	[391]	biology, phylogenetics
datamash	datamash	1.1.0	[392]	math
DAWGPAWS	dawgpaws	1.0	[393]	biology, phylogenetics
dbcanlight	dbcanlight	1.1.0	[394]	biology, annotation
DCC	dcc	0.4.4	[395]	biology, ngs
Dcmstack	dcmstack	0.6.2	[396]	biology, imaging
DCMTK	dcmtk	3.6.0	[397]	biology, neuroscience, imaging
dDocent	ddocent	2.7.8	[398]	phylogenetics
ddprotocol	ddprotocol	20230405	[399]	biology, machine learning
DDSCAT	ddscat	7.3.0	[400]	astronomy
DDT	ddt	20.0, 20.2, 23.0	[401]	programming
DealII	dealii	8.3.0, 9.3.1, 9.5.1	[402]	library
DeconSeq	deconseq	0.4.3	[403]	biology, phylogenetics
decontaMiner	decontaminer	1.4	[404]	genomics, biology
DECX	decx	20180205	[405]	phylogenetics
DeepARG	deeparg	1.0.1	[406]	phylogenetics
deepbgc	deepbgc	0.1.18	[407]	phylogenetics
Deepcoil	deepcoil	2.0.1	[408]	sequencing, biology
deepfri	deepfri	03312021	[409]	machine learning, biology
DeepGS	deepgs	1.2	[410]	phylogenetics
DeepLabCut	deeplabcut	2.0.7-gpu, 2.1.1, 2.2.1	[411]	phylogenetics
deeplexicon	deeplexicon	1.2.0	[412]	RNAseq
DeePMD-kit	deepmd-kit	2.1.11	[413]	molecular dynamics, deep learning
DeepMD-LAMMPS	deepmd-lammps	2.2.0-02Aug23	[414]	molecular Dynamics
deepmicrobes	deepmicrobes	20200219	[415]	biology, genomics, machine_learning
DeepMReye	deepmreye	01192022	[416]	library, biology
DeepPicker	deeppicker	20161102	[417]	imaging
deepsig	deepsig	1.2.5	[418]	biology
deepTools	deeptools	2.4.3, 3.1.1, 3.5.2	[419]	biology, ngs
deepvariant	deepvariant	1.4.0, 1.5.0, 1.6.1	[420]	biology, genomics, sequencing, machine_learning
deFusion	defusion	20200305	[421]	phylogenetics
Delft3D	delft3d	4.06.01, 7545	[422]	physics
Delineate	delineate	1.2.2	[423]	biology, genomics
Delly	delly	0.7.7, 0.7.8, 1.1.5	[424]	biology, phylogenetics
delucs	delucs	20220512	[425]	sequencing, genomics, machine_learning
DeNoGAP	denogap	1.0	[426]	biology, phylogenetics, ngs
DERIVA	deriva	1.5.0	[427]	phylogenetics
deSALT	desalt	1.5.6	[428]	biology, genomics, sequencing
Desmond	desmond	6.9	[429]	biology
Detectron2	detectron2	0.4, 0.5, 0.6	[430]	library
DeTiN	detin	1.7.5.9	[431]	imaging, ngs, genomics
DEXTRACTOR	dextractor	1.0	[432]	biology, sequencing
Diamond	diamond	2.1.1, 2.1.3, 2.1.8	[433]	biology, genomics
DIANN	diann	1.8.1	[434]	protein, structure
diCal2	dical2	2.2.0.1	[435]	biology, phylogenetics
diffDomain	diffdomain	1.0.0	[436]	bioinformatics
diffReps	diffreps	1.55.4	[437]	biology
disbatch	disbatch	2.5	[438]	software
DISCOVAR de novo	discovardenovo	52488	[439]	biology, ngs, assembly
DiscoVista	discovista	20180906	[440]	phylogenetics
discvrseq	discvrseq	1.3.10	[441]	biology, phylogenetics
Distruct	distruct	2.3	[442]	phylogenetics
DIYABC	diyabc	1.0.4.43b, 2.0.3, 2.1.0	[443]	biology, phylogenetics
DL_POLY	dlpoly	1.9	[444]	molecular_dynamics
Dlib	dlib	19.19	[445]	phylogenetics
DNA Clust	dnaclust	3.0	[446]	biology, genomics
DOCK	dock	6.7, 6.8, 6.9	[447]	chemistry
DoGFinder	dogfinder	20201103	[448]	phylogenetics
dorado	dorado	0.7.0, 0.7.2, 0.8.2	[449]	genomics
DosageConvertor	dosageconvertor	1.0.3	[450]	biology
DOT	dot	2.0	[451]	biology, chemistry
Doxygen	doxygen	1.12.0, 1.8.3.1, 1.9.7	[452]	programming, documentation
dragmap	dragmap	1.2.1	[453]	phylogenetics, sequencing, biology
dragonflye	dragonflye	1.0.12	[454]	sequencing, genomics
dram	dram	1.3	[455]	biology, genomics, annotation
DRAP	drap	1.91	[456]	biology, phylogenetics
dRep	drep	2.3.2, 3.4.2	[457]	phylogenetics
dretools	dretools	0.0.1.20	[458]	rna-seq
drishti	drishti	3.2	[459]	visualization
Dropseq	dropseq	2.4.0	[460]	phylogenetics
DS9	saoimageds9	7.5, 8.0.1	[461]	imaging
DScribe	dscribe	1.2.0	[462]	machine_learning
dsistudio	dsistudio	20210123, 20220803, 20240311	[463]	imaging
DSK	dsk	2.1.0, 2.3.0	[464]	biology, ngs
DSRC	dsrc	2.0	[465]	phylogenetics
DSSAT	dssat	4.6	[466]	simulation
DSSP	dssp	2.2.1, 3.0.0	[467]	molecular_dynamics
DSuite	dsuite	0.4, 0.4-r41, 0.4-r49	[468]	biology, genomics
DTI-TK	dtitk	2.3.1	[469]	imaging
dtiprep	dtiprep	0.1.1	[470]	phylogenetics
duchamp	duchamp	1.6.2	[471]	phylogenetics
DVGfinder	dvgfinder	3.1	[472]	genomics, search, sequencing
dx-toolkit	dx-toolkit	0.347.0	[473]	biology
dynamicDBG	dynamicdbg	20181003	[474]	phylogenetics
Dynare	dynare	4.4.3	[475]	math
dynasor	dynasor	2.0	[]	Molecular_Dynamics
ea-utils	eautils	1.04.807.18, 1.1.2.537	[476]	biology, genomics, ngs
EAGLE	eagle	2.0	[477]	phylogenetics
eagle-rc	eagle-rc	1.1.1	[478]	phylogenetics
Earlgrey	earlgrey	4.2.4	[479]	biology
ECE	ece	1.2	[480]	physics
ecopcr	ecopcr	0.5.0	[481]	Biology
eddy-squeeze	eddy-squeeze	1.0.8	[482]	data_science, visualization
EDirect	edirect	10.7, 12.2	[483]	biology, phylogenetics
EDTA	edta	1.9.6, 2.1.0	[484]	phylogenetics
Edyeet	edyeet	0.1, 0.3	[485]	phylogenetics
EEGLAB	eeglab	12.0.2.1b, 13.2.2b, 13.4.4b	[486]	biology
effectorp	effectorp	2.0.1, 3.0	[487]	biology
eGene-MVN	egene-mvn	0.1	[488]	biology, genomics
eggNOG-mapper	eggnog-mapper	2.0.1, 2.1.12, 2.1.6	[489]	phylogenetics
Ego4D	ego4d	1.3.2	[490]	image processing
EGSnrc	egsnrc	2019	[491]	phylogenetics
EIGEN3	eigen3	3.4.0	[492]	libraries, mathematics
EIGENSOFT	eigensoft	5.0.1, 6.0.1, 6.1.4	[493]	biology
Elastix	elastix	4.9.0, 5.1.0	[494]	phylogenetics
ELPA	elpa	2019.11.001	[495]	library, compiler, math
elPrep	elprep	4.1.4	[496]	phylogenetics
Emacs	emacs	27.2, 28.2	[497]	programming, language
Email Alert Service	email_storage_alert	1.0.0	[498]	file_management
EMAN2	eman2	2.22, 2.31	[499]	image_processing
EMBOSS	emboss	6.6.0	[500]	biology
Embree	embree	3.6.1	[501]	graphics
EMC	emc	9.4.3	[502]	simulation
emerald	emerald	0.1	[503]	biology
EMMAX	emmax	20100307, 20120210	[504]	biology, ngs, mapping
emu	emu	3.4.5	[505]	phylogenetics
EnergyPlus	energyplus	9.3.0	[506]	simulation
enrichm	enrichm	0.6.5	[507]	biology
Ensembl Tools	ensembl_tools	100, 80	[508]	biology
enTAP	entap	0.6.1.2, 20160416	[509]	biology, phylogenetics
EPACTS	epacts	3.2.6, 3.4.2, 3.4.2.hg38	[510]	biology, genomics
EpiNano	epinano	1.2.0	[511]	biology, ngs
epiteome	epiteome	1.0	[512]	phylogenetics
epoch	epoch	4.7.3	[513]	astronomy
eQTLA	eqtla	1.1	[514]	biology, genomics
eQtlBma	eqtlbma	1.2.2, 1.3.0r20140820	[515]	biology, genomics
Erpin	erpin	5.5.4	[516]	biology, phylogenetics
esmf	esmf	8.3.0), 8.7.0)	[517]	geospatial
ESOM	esom	1.1	[518]	biology, phylogenetics
ESPRESSO	espresso	7.0, 7.1, 7.2	[519]	chemistry, modeling
ESPRIT	esprit	2009-nogap, 201102	[520]	biology
ETE3	ete3	3.0.0, 3.1.1	[521]	biology, phylogenetics
ETE4	ete	4.0.0	[522]	biology, phylogenetics
EUKulele	eukulele	2.0.7	[523]	alignment, biology, genomics
EVidenceModeler	evidencemodeler	1.1.1	[524]	phylogenetics
Evigene	evigene	20180730, 20200520	[525]	phylogenetics
EvoLSTM	evolstm	20220103	[526]	biology
ExaBayes	exabayes	1.5	[527]	phylogenetics
Exonerate	exonerate	2.2.0, 2.4.0	[528]	biology, genomics
ExpansionHunter	expansionhunter	4.0.2	[529]	biology, genomics
ExpansionHunterDenovo	expansionhunterdenovo	0.9.0	[530]	biology, genomics
export2graphlan	export2graphlan	0.22	[531]	statistics, mapping, visualization
eXpress	express	1.3.1, 1.5.1	[532]	biology, ngs
ezaai	ezaai	1.0	[533]	biology, phylogenetics
face_morpher	face_morpher	20190630	[534]	phylogenetics
face_recognition	face_recognition	1.2.2	[535]	phylogenetics
fairseq	fairseq	0.12.2	[536]	modeling, ai
falco	falco	1.2.1	[537]	biology, sequencing
FALCON	falcon	20161027, 20161222, 20190601	[538]	biology, ngs, sequencing
FALCON_unzip	falcon_unzip	20161222	[539]	biology
fanc	fanc	0.9.28	[540]	biology, genomics, ngs
faqcs	faqcs	2.10	[541]	Genomics, biology
FAR	far	2.15	[542]	biology, genomics
FAST	fast	1.06	[543]	biology, phylogenetics
fast-gep	fast-gep	1.0	[544]	phylogenetics
Fast-Plast	fast-plast	1.2.6	[545]	biology, phylogenetics
fast5tools	fast5tools	0.3.1	[546]	phylogenetics, biology
FASTA	fasta	34.26.5, 36.3.6d	[547]	biology, genomics
fastai	fastai	2.1.5, 2.6.3, 2.7.10	[548]	Machine_Learning
FastANI	fastani	1.1, 1.34	[549]	phylogenetics
fastchaos	fastchaos	0.1.0	[550]	sequencing
FastGEAR	fastgear	20161216	[551]	biology, genomics
Fastix	fastix	0.1.0	[552]	biology, ngs
FastML	fastml	3.0	[553]	biology, phylogenetics
Fastp	fastp	0.20.0, 0.22.0, 0.23.4	[554]	biology, ngs
FASTphase	fastphase	1.4.8	[555]	phylogenetics
FastPlast	fastplast	1.2.8	[556]	phylogenetics
fastq-pair	fastq-pair	1.0	[557]	phylogenetics
FastQ-Screen	fastq-screen	0.14.0	[558]	phylogenetics
Fastq-tools	fastq-tools	0.8	[559]	biology, ngs
FastQC	fastqc	0.11.7, 0.12.1, 0.9.6	[560]	biology, ngs
FastqPuri	fastqpuri	1.0.7	[561]	phylogenetics
FastQTL	fastqtl	2.184	[562]	phylogenetics
FASTRAL-constrained	fastral-constrained	20211108	[563]	phylogenetics
fastsimcoal	fastsimcoal2	2.6.0.3, 2.7.0.2	[564]	biology, phylogenetics
FastSpar	fastspar	0.0.4	[565]	biology, genomics
fastStructure	faststructure	20150112, 20240221	[566]	biology, genomics
FastTree	fasttree	2.1.11	[567]	biology, phylogenetics
FastUniq	fastuniq	1.1	[568]	biology, phylogenetics
fastv	fastv	0.10.0	[569]	bioinformatics, sequencing
Fastx Toolkit	fastx_toolkit	0.0.13.2, 0.0.14	[570]	biology, ngs
fcGENE	fcgene	1.0.7, 1.0.7.1	[571]	biology, genomics, variant_calling
FDSTools	fdstools	1.2.0	[572]	phylogenetics
fdupes	fdupes	1.51	[573]	file_management
febio	febio	2.9.1	[574]	biomechanics
FEELnc	feelnc	0.1.1	[575]	phylogenetics
FEniCS	fenics	2018.1.0	[576]	biology, phylogenetics
Ferret	ferret	6.82	[577]	visualization, geospatial, climate
FFmpeg	ffmpeg	2.8.3, 4.3.1, n6.1	[578]	audio, visualization
FFTW	fftw	3.3.6, 3.3.7, 3.3.8	[579]	library, compiler, math
fgbio	fgbio	0.5.0, 0.7.0	[580]	phylogenetics
FGMP	fgmp	1.0.1	[581]	phylogenetics
FGTPartitioner	fgtpartitioner	1.0.1	[582]	genomics
FIGARO	figaro	1.1.2	[583]	phylogenetics
Fiji	fiji	2.0.0rc59	[584]	image_processing
Filtlong	filtlong	0.2.0	[585]	biology, phylogenetics
Finder	finder	20210503, 20210609	[586]	biology, search
finemap	finemap	1.4	[587]	phylogenetics
fineRADstructure	fineradstructure	0.3.2	[588]	phylogenetics
finesse	finesse	2.3.1	[589]	simulation
Firefox	firefox	1.0	[590]	linux, web
fit-sne	fit-sne	1.2.1	[591]	phylogenetics
FLAIR	flair	1.5, 2.0	[592]	phylogenetics
flairNLP	flairnlp	0.10	[593]	visualization, language
flappie	flappie	1.1.0, 2.1.3	[594]	phylogenetics
FLASh	flash	1.2.10, 1.2.11	[595]	biology, genomics
FLEA	flea	2.0.0	[596]	phylogenetics
flex	flex	2.6.4	[597]	programming
Flexbar	flexbar	2.3, 2.34, 3.5.0	[598]	biology, genomics, ngs
FLEXLm	flexlm	1.0	[599]	utility
flopp	flopp	0.2.0	[600]	genomics
FlowCraft	flowcraft	1.4.1	[601]	phylogenetics
Fluent	fluent	17.2, 19.1, 2020R1	[602]	fluid_dynamics
Flye	flye	2.9.1, 2.9.2, 2.9.3	[603]	biology, ngs
fMRIPrep	fmriprep	20.2.3, 23.1.3, 23.1.4	[604]	data_mining
foldseek	foldseek	9.427df8a	[605]	bioinformatics
forecasting	forecasting	0.10.3	[606]	Machine_Learning, Data_Science
ForeSeqs	foreseqs	1.0.4	[607]	phylogenetics
forwardgenomics	forwardgenomics	1.0	[608]	phylogenetics
fpocket	fpocket	4.0.2	[609]	sequencing, biology
fqtools	fqtools	20160224	[610]	biology, ngs, sequencing
FragGeneScan	fraggenescan	1.16	[611]	biology, genomics
FRAMA	frama	20151019	[612]	biology
FrameDP	framedp	1.2.2	[613]	biology, sequencing
FRAPOSA	fraposa	20200421	[614]	phylogenetics
FreeBayes	freebayes	1.3.1, 1.3.2, 1.3.7	[615]	biology, genomics
freecad	freecad	0.20.2	[616]	modeling
freesasa	freesasa	2.1.2	[617]	molecular_dynamics, biology
Freesurfer	freesurfer	7.2.0, 7.3.2, 7.4.1	[618]	biology, neuroscience, imaging
Freyja	freyja	1.3.1, 1.3.4, 1.3.8	[619]	biology, phylogenetics, sequencing
FSA	fsa	1.15.9	[620]	phylogenetics
FSL	fsl	6.0.4, 6.0.5, 6.0.6	[621]	biology, neuroscience, imaging
fslmrs	fslmrs	1.1.10	[622]	spectroscopy, metabolomics
funannotate	funannotate	1.8.5, 1.8.7, 1.8.9	[623]	phylogenetics
fusion_twas	fusion_twas	20210218	[624]	phylogenetics
GAL	gal	20180906	[625]	biology, genomics, annotation
Galaxy	galaxytools	1.0	[626]	biology
galaxyml	galaxyml	0.10.0	[627]	library, machine_learning
GAML	gaml	20150610	[628]	biology, genomics, assembly
GapCloser	gapcloser	1.12r6	[629]	biology, genomics, ngs
GapFiller	gapfiller	1.10, 1.11	[630]	biology, genomics
gapseq	gapseq	1.2	[631]	chemistry, biology
garfield	garfield	2	[632]	genomics
GARLI	garli	2.0, 2.01	[633]	biology, phylogenetics
GASVPro	gasvpro	201310	[634]	biology, ngs
GATE	gate	7.0	[635]	library
GATK	gatk	4.1.9.0, 4.3.0.0, 4.4.0.0	[636]	biology, ngs
Gaussian	gaussian	09 D.01, 16, 16-c02	[637]	chemistry
Gawk	gawk	4.2.0	[638]	utility
Gblocks	gblocks	0.91b	[639]	biology, alignment
GCC	gcc	7.3.0, 8.2.0, 9.3.0	[640]	compiler
GCE	gce	1.0.2	[641]	biology, genomics
gcloud	gcloud	471.0.0	[642]	cloud, google, cli
gcnenv	gcnenv	1.13	[643]	library, math
GCT	gct	6.2.1	[644]	file_management, utility
GCTA	gcta	1.26.0, 1.92.4beta, 1.93.2beta	[645]	biology, genomics, variant_calling
GDAL	gdal	2.3.1, 3.7.0, 3.9.0	[646]	geospatial, library
GDB	gdb	8.3, 9.2	[647]	programming
GDC-Client	gdc-client	1.0.1, 1.5.0	[648]	biology, sequencing, ngs
GDrive	gdrive	2.1.0	[649]	utility, file_management
GDSL	gdsl	1.18	[650]	library
Geant4	geant4	4.10, 4.10.03, 4.10.5	[651]	physics
geant4	geant4	11.0.2, 4-11.0.3	[652]	physics, simulation
GEM	gem	20130406	[653]	biology, ngs, sequencing
gem5	gem5	2.0	[654]	simulation
GEMMA	gemma	0.98.1, 0.98.5	[655]	phylogenetics
gemma_llm	gemma_llm	1	[656]	library, math
genblastg	genblastg	1.39	[657]	biology, genomics
GeneMark-ES	genemark_es	4.68, 4.69, 4.71	[658]	biology, genomics
GeneMarkS	genemark_s	2012.04	[659]	biology, genomics
GeneMarkS-T	genemark_s	3.10.001	[660]	biology, genomics
GenePainter	genepainter	2.0.4	[661]	biology, phylogenetics
GeneRax	generax	1.2.2	[662]	phylogenetics
Generic Mapping Tools	gmt	6.4.0	[663]	physics, biology
GeneSeqer	geneseqer	2014-02-26	[664]	biology, genomics
genesis	genesis	2.1.2, 2.1.2-cpu	[665]	Physics
genesum	genesum	0.1.0	[666]	biology, genomics
GeneTorrent	genetorrent	3.8.7	[667]	biology, file_management
genewalk	genewalk	1.5.3	[668]	phylogenetics
GenGen	gengen	1.0.1	[669]	biology, phylogenetics
genmap	genmap	v1.3.0	[670]	Gene mapping, biology
geNomad	genomad	1.5.1	[671]	biology, genomics
Genome STRiP	genomestrip	2.00.1602	[672]	biology, genomics, ngs
Genome_Graph_Annotation	genome_graph_annotation	20190131	[673]	phylogenetics
GenomeScope2	genomescope2	2.0	[674]	phylogenetics
GenomeThreader	genomethreader	1.7.3	[675]	phylogenetics
GenomeTools	genometools	1.5.7, 1.5.9	[676]	biology
genomic-fluidity	genomic-fluidity	20151109	[677]	phylogenetics
GenomicConsensus	genomicconsensus	2.3.3	[678]	biology, phylogenetics
GenomicNeuralnet	genomic-neuralnet	20161030	[679]	phylogenetics
GenomicTools	genomictools	2.7.0	[680]	biology, ngs, chip-seq, rna-seq
GenotypeHarmonizer	genotypeharmonizer	1.4.18	[681]	biology
Genrich	genrich	0.5	[682]	phylogenetics
GenSel	gensel	4.90	[683]	genomics
geomxngspipeline	geomxngspipeline	3.1.1.5	[684]	NGS
geopython	geopython	1.0.0, 1.0.1, 1.0.2	[685]	programming, geospatial
GEOS	geos	3.3.8, 3.6.2	[686]	library, data_science
GeP	gep	2.1	[687]	biology, phylogenetics
gepard	gepard	1.40.0, 2.1.0	[688]	phylogenetics
Gephi	gephi	0.10.0	[689]	visualization, image_processing
Gerbil	gerbil	1.11	[690]	phylogenetics
get_homologues	get_homologues	3.3.3	[691]	biology, genomics
GetOrganelle	getorganelle	1.7.3.5, 1.7.5.0	[692]	phylogenetics
GFam	gfam	1.1	[693]	biology, genomics, annotation
GFF-Ex	gff-ex	2.3	[694]	phylogenetics
GFF3toolkit	gff3toolkit	2.0.3	[695]	phylogenetics
gffcompare	gffcompare	0.12.2	[696]	phylogenetics
gffread	gffread	0.11.8, 0.12.7, 0.9.8c	[697]	biology
Gflags	gflags	2.2.1, 20150520	[698]	web, library
GFOLD	gfold	1.1.4	[699]	biology, rna-seq
ggsashimi	ggsashimi	0.5.0	[700]	phylogenetics
GHOST-MP	ghost-mp	1.3.4	[701]	phylogenetics
Ghostscript	ghostscript	9.22	[702]	documentation
giggle	giggle	20221212	[703]	Genomics
Gimmemotifs	gimmemotifs	0.18.0	[704]	biology, genetics
Giotto	giotto	0.1.0	[705]	phylogenetics
giraf	giraf	1.02	[706]	sequencing, biology
Git	git	2.14.1, 2.30.1	[707]	revision_control
git-filter-repo	git-filter-repo	2.33.0	[708]	phylogenetics
Github Cli	github-cli	2.40.1	[709]	revision_control
Gkeyll	gkeyll	2.0	[710]	Plasma Physics
glactools	glactools	1.0.8	[711]	phylogenetics
Glimmer	glimmer	3.02	[712]	biology, annotation
GlimmerHMM	glimmerhmm	3.0.4	[713]	biology, annotation
GLMsingle	glmsingle	1.0	[714]	imaging
glnexus	glnexus	1.4.1	[715]	programming
Globus	globus	2.1.3, 3.13.0, 3.18.0	[716]	file_management
glog	glog	0.3.5	[717]	web, library
GLPK	glpk	4.55, 4.65	[718]	programming
Glueviz	glueviz	0.15.2	[719]	phylogenetics
GMAP	gmap	20180212, 20180212_sse2, 20190610	[720]	biology, genomics, ngs
GMcloser	gmcloser	1.6	[721]	biology, ngs
GMP	gmp	6.1.2, 6.3.0	[722]	library
gnuastro	gnuastro	0.21	[723]	astronomy
GnuPlot	gnuplot	5.2.2, 5.2.3, 5.4.1	[724]	graphics, math
Go	go	1.15.4, 1.18.3, 1.21.0	[725]	language
goatools	goatools	1.2.3	[726]	biology, ontology
GOMAP	gomap	1.3, 1.4	[727]	biology, ngs
GoPHY	gophy	201030	[728]	phylogenetics
Gosling	gosling	0.2.2	[729]	genomics, visualization
gotcloud	gotcloud	1.17.5	[730]	phylogenetics
GPA	gpa	1.1	[731]	phylogenetics
GPhoCS	gphocs	1.2.3	[732]	phylogenetics
gptl	gptl	20140212	[733]	utility
GPTL	gptl	20140212	[734]	utility
Gpufit	gpufit	20201127	[735]	phylogenetics
Grace	grace	5.1.22	[736]	graphics, statistics
GRACKLE	grackle	3.1	[737]	library, compiler, astronomy
Grackle	grackle	3.2.1	[738]	library, compiler, astronomy
GrADS	grads	2.0.1	[739]	geospatial, math
Graftm	graftm	0.12.2	[740]	phylogenetics
GramCluster	gramcluster	1.3	[741]	biology, sequencing
graph-tool	graph-tool	2.32	[742]	phylogenetics
Graph_annotation	graph_annotation	0.1	[743]	phylogenetics
graphaligner	graphaligner	1.0.11, 1.0.16	[744]	genomics
GraPhlAn	graphlan	1.1.3	[745]	phylogenetics
GraphMap2	graphmap2	0.6.5	[746]	phylogenetics
GRAPHMB	graphmb	0.2.5	[747]	biology, genomics
GraphSplitting	graphsplitting	2.4	[748]	phylogenetics
graphtyper	graphtyper	2.7.2	[749]	phylogenetics
GraphViz	graphviz	2.38.0, 2.46.1	[750]	biology, neuroscience, imaging
GRASS	grass	7.0, 7.4	[751]	geospatial
grf	grf	1.0.0	[752]	genomics
Grib_api	grib_api	1.10.1, 1.15.1, 1.26.1	[753]	compiler, library
GRIDSS	gridss	2.6.2	[754]	phylogenetics
GROCSVs	grocsvs	0.2.5	[755]	phylogenetics
GROMACS	gromacs	2021.4, 2022.3, 2023.2	[756]	chemistry, molecular_dynamics
GroopM	groopm	0.3.5	[757]	biology, phylogenetics
Groovy	groovy	2.4.15	[758]	programming
Gscripts	gscripts	1.1	[759]	biology
GSEA	gsea	4.2.2	[760]	biology, genomics
GSL	gsl	2.6, 2.7, 2.7.1	[761]	library, data_science
GSNP	gsnp	1.0	[762]	biology, ngs
gsp	gsp	05192017	[763]	biology
GTAHunter	gtahunter	20200106	[764]	phylogenetics
GTDBTk	gtdbtk	2.0.0, 2.1.0, 2.3.2	[765]	phylogenetics
GTOOL	gtool	0.7.5	[766]	phylogenetics
GUAVA	guava	1.0	[767]	phylogenetics
Gubbins	gubbins	2.4.1, 3.2.1, 3.3.0	[768]	phylogenetics
guideseq	guideseq	1.0.2	[769]	sequencing, genomics, biology, data_science
guile	guile	2.2.2	[770]	programming
GULP	gulp	4.4, 5.0	[771]	material_science
guppy	guppy	6.1.7, 6.4.2, 6.4.3	[772]	phylogenetics
Gurobi	gurobi	10.0.0, 11.0.1, 9.5.1	[773]	math, programming
GWAMA	gwama	2.2.2	[774]	phylogenetics
Gzip	gzip	1.10	[775]	compression
hacdivsel	hacdivsel	1.4.1	[776]	genomics, biology
Hail	hail	0.2.130, 0.2.77	[777]	biology, genomics
hal	hal	2.1	[778]	phylogenetics
HALC	halc	1.1	[779]	biology, phylogenetics
halla	halla	0.8.17	[780]	phylogenetics
HaMStR	hamstr	13.2.3, 13.2.4, v8b	[781]	biology, genomics
hapbin	hapbin	1.3.0	[782]	biology, genomics
HapCompass	hapcompass	0.7.7	[783]	imaging, ngs, genomics
HAPCUT	hapcut	0.7	[784]	biology, assembly
HapCUT2	hapcut2	1.3.3	[785]	biology, genomics, sequencing
hapdup	hapdup	0.6	[786]	phylogenetics, biology
haphpipe	haphpipe	1.0.3	[787]	phylogenetics, biology
Haploflow	haploflow	0.1	[788]	biology, phylogenetics
Haplomerger2	haplomerger2	20180603	[789]	biology, genomics
HAPLOSWEEP	haplosweep	1.0	[790]	biology, phylogenetics
happy	happy	0.3.14	[791]	phylogenetics, biology
hapQTL	hapqtl	1.00	[792]	biology
hapsembler	hapsembler	2.21	[793]	biology, assembly
harvesttools	harvesttools	1.2	[794]	phylogenetics, biology
HASLR	haslr	0.8a1	[795]	phylogenetics
hclust2	hclust2	1.0.0	[796]	statistics, mapping
HDF4	hdf4	4.2.11	[797]	library, data_science
HDF5	hdf5	1.8.19, 1.8.20, 1.8.9	[798]	library, data_science
hecaton	hecaton	0.5.1	[799]	genomics, biology
HELEN	helen	20200516	[800]	phylogenetics
HelitronScanner	helitronscanner	1.1	[801]	phylogenetics
helixer	helixer	0.3.3	[802]	Genomics
herro	herro	0.1.0	[803]	Genomics
hgraph2graph	hgraph2graph	20210428	[804]	chemistry
hgtector	hgtector	2.0	[805]	biology, sequencing
hhsuite	hhsuite	3.3.0	[806]
Hi-Corrector	hi-corrector	1.2	[807]	biology, ngs, sequencing
hic-lift	hic-lift	06112023	[808]	genomics
HiC-Pro	hic-pro	3.0.0, 3.1.0	[809]	biology, pipeline, genomics
Hifiasm	hifiasm	0.19.9, 0.4, 0.8	[810]	phylogenetics
Hificnv	hificnv	0.1.7	[811]	biology, genomics, ngs
hillerlab	hillerlab	20240819	[812]	phylogenetics
hiphase	hiphase	1.4.0	[813]	biology, ngs
HipSTR	hipstr	0.7	[814]	phylogenetics
HISAT2	hisat2	2.2.1, 2.2.1-3n, 20230203	[815]	biology, alignment, ngs
hivtrace	hivtrace	1.5.0	[816]	biology,alignment
HLAminer	hlaminer	1.3.1, 1.4	[817]	biology, phylogenetics
HMM-FRAME	hmm-frame	20140724	[818]	phylogenetics
HmmCleaner	hmmcleaner	0.180750	[819]	phylogenetics
HMMER	hmmer	3.2.1, 3.3.2, 3.4	[820]	biology, genomics
hmmer2go	hmmer2go	0.18.1	[821]	phylogenetics, biology
HMMRATAC	hmmratac	1.2.10	[822]	phylogenetics
HoCoRT	hocort	1.2.2	[823]	RNA-Seq, QC
HOMER	homer	4.10, 4.11, 4.8	[824]	biology, sequencing, ngs
homopolish	homopolish	0.3.3, 0.4.1	[825]	genomics, biology
HOOMD	hoomd	2.1.7	[826]	library, math
HPL	hpl	2.1	[827]	programming, performance_analysis
hpsandbox	hpsandbox	1.0.0	[828]	Programming
HTMLDoc	htmldoc	1.8.28, 1.9.3	[829]	documentation, web
HTSeq	htseq	0.11.2, 2.0.3	[830]	biology, ngs
HUMAnN	humann	2.8.1, 3.8	[831]	sequencing, biology
humann2	humann2	0.11.2, 2.8.1	[832]	phylogenetics
hxtorch	hxtorch	0.8	[833]	imaging
hyb	hyb	20141126, 20200815	[834]	biology, ngs, rna-seq
hybkit	hybkit	0.3.4, 0.3.5, 0.3.6	[835]	biology
HybPiper	hybpiper	2.1.5, 2.1.6, 2.3.0	[836]	biology, phylogenetics
HyDe	hyde	0.4.3	[837]	phylogenetics
hylite	hylite	2.0.2	[838]	genomics, biology
Hyper-Gen	hypergen	0.1.0	[839]	Programming
HyPhy	hyphy	2.5.4, 2.5.7, 2.5.8	[840]	biology, genomics
HYPRE	hypre	2.15.1, 2.18.2, 2.19.0	[841]	math
iAnnotateSV	iannotatesv	1.0.6, 1.0.9	[842]	biology, phylogenetics
iaps	iaps	02012023	[843]	programming
iAssembler	iassembler	1.3.2	[844]	biology, assembly
IBDmix	ibdmix	1.0.1	[845]	biology
ibdne	ibdne	20150815	[846]	biology, ngs
icommands	icommands	3.3.1	[847]	utility
IDBA-MT	idba-mt	1.0	[848]	biology, ngs
IDBA-UD	idba-ud	1.1.1, 1.1.1-512, 1.1.1-512-mem	[849]	genomics, phylogenetics
IDL	idl	8.3	[850]	language, programming, data_science
IDR	idr	2.0.3	[851]	phylogenetics
IGB	igb	8.4.1	[852]	biology, genomics
igBLAST	igblast	1.5.0, 1.7.0	[853]	biology
IGoR	igor	1.4.0	[854]	phylogenetics
iGTP	igtp	1.1	[855]	biology, phylogenetics
IGV	igv	2.3.91, 2.4.16, 2.8.6	[856]	biology, ngs, phylogenetics
illumina-utils	illumina-utils	2.11	[857]	phylogenetics
Illumiprocessor	illumiprocessor	2.0.9	[858]	phylogenetics
IM and IMa	ima	20091217	[859]	biology, genomics
Ima2	ima2	20120827	[860]	biology, genomics
IMa2p	ima2p	20170712	[861]	biology, phylogenetics
IMA3	ima3	22Aug18	[862]	molecular_dynamics
ImageJ	imagej	1.48	[863]	imaging
imagej2	imagej2	09302022	[864]	image processing, imaging
ImageMagick	imagemagick	7.0.8-20	[865]	imaging
Imaginaire	imaginaire	20201229	[866]	imaging, visualization, ai, machine_learning
IMOD	imod	4.7.15, 4.9.10	[867]	image_processing
imoka	imoka	1.0	[868]	biology, genomics
impg	impg	0.1.0	[869]	biology, alignment
IMPUTE2	impute2	2.3.2	[870]	phylogenetics
IMPUTE5	impute5	1.1.5, 1.2.0	[871]	biology, math
INDELible	indelible	1.03	[872]	phylogenetics
Infernal	infernal	1.1.1, 1.1.4	[873]	biology, alignment
INLA	inla	20160718, 20170620	[874]	statistics, modeling, programming
InParanoid	inparanoid	4.1	[875]	biology
Inspector	inspector	1.0.2	[876]	biology, genomics
InStruct	instruct	20160723	[877]	phylogenetics
Intel Compilers and Libraries	intel	2023.0.0, 2023.2.0, 2024.1.0	[878]	language, programming, library, math, compiler
Intel MPI	impi	5.1.1	[879]	programming, library
InterProScan	iprscan	5.60, 5.68, 5.69	[880]	biology
intervene	intervene	0.6.2	[881]	biology, phylogenetics
Intrasom	intrasom	1.0	[882]	python
IOAPI	ioapi	3.1, 3.2	[883]	climate
IPOPT	ipopt	3.12.10, 3.12.6	[884]	library, compiler, math
ipyrad	ipyrad	0.9.102, 0.9.53, 0.9.94	[885]	phylogenetics
IQ-TREE	iq-tree	2.2.2.7, 2.3.2, 2.3.6	[886]	biology, phylogenetics
IRAP	irap	0.8.1p7	[887]	biology, ngs
irep	irep	1.10	[888]	biology, genomics
IRFinder	irfinder	1.2.0, 1.3.0, 1.3.1	[889]	biology, rna-seq
isce2	isce2	2.6.3	[890]	library
ISCE3	isce3	0.23.0	[891]	library
isONclust	isonclust	0.0.6	[892]	phylogenetics
isonclust2	isonclust2	2.3	[893]	rna-seq
IsoSel	isosel	1.0	[894]	phylogenetics
IsoSeq3	isoseq3	3.7.0, 3.8.2, 4.0.0	[895]	biology, ngs
ISOWN	isown	20180820	[896]	phylogenetics
isPcr	ispcr	3.3	[897]	biology, phylogenetics
ITK	itk	3.20.1, 4.10.1	[898]	biology
ITK-SNAP	itksnap	3.0.0, 3.8.0	[899]	biology, neuroscience, imaging
ITSx	itsx	1.1b	[900]	phylogenetics
iupred2a	iupred2a	1.0	[901]	biology
IVA	iva	1.0.11	[902]	phylogenetics
iVar	ivar	1.3.1, 1.4.2	[903]	biology
Jabba	jabba	1.0	[904]	biology, phylogenetics
JACUSA	jacusa	1.2.0	[905]	biology, ngs, phylogenetics
JAGS	jags	3.3.0, 3.4.0, 4.2.0	[906]	statistics
janus	janus	20240412	[907]	biology
Jasmine	jasmine	1.1.4	[908]	phylogenetics
jasp	jasp	0.14.3	[909]	statistics
jasper	jasper	1.0.4	[910]	biology
jbrowse2	jbrowse2	1.7.4	[911]	web
JCVI	jcvi	0.8.12, 1.0.13, 1.2.10	[912]	phylogenetics
JDK	java	20, 23, 9.0.1	[913]	programming
Je	je	1.0	[914]	biology, ngs
Jellyfish	jellyfish	2.2.4, 2.2.6, 2.3.0	[915]	biology, ngs
jModelTest	jmodeltest	2.1.1	[916]	biology, genomics, phylogenetics
jo	jo	1.3	[917]	utility
jq	jq	1.6	[918]	utility
juicer	juicer	1.22.01, 2.0	[919]	phylogenetics
Julia	julia	1.7.3, 1.8.2, 1.9.2	[920]	programming, language, statistics
Jupyter	jupyter	6.2.0, 6.5.2, 6.5.4	[921]	programming
jutils	jutils	1.0	[922]	genomics, biology
JVARKIT	jvarkit	20180405	[923]	biology, phylogenetics
Kaiju	kaiju	1.6.2, 1.7.2	[924]	biology, phylogenetics
KaKs	kaks	1.2, 2.0	[925]	biology, genomics, phylogenetics
Kalign	kalign	3.3.1	[926]	biology, sequencing, alignment
kallisto	kallisto	0.46.2, 0.48.0, 0.50.1	[927]	biology, ngs, rna-seq
khmer	khmer	2.0, 2.1	[928]	biology, ngs
KIM	kim	1.7.2, 1.8.2, 1.9.3	[929]	simulation
kimmingloci	skimmingloc	1.0.0	[930]	pipeline mapping, biology
KING	king	2.1.2, 2.3.0	[931]	biology, genomics
KisSplice	kissplice	2.4.0-p1	[932]	biology, RNA
KLayout	klayout	0.26.7	[933]	phylogenetics
kma	kma	20230106	[934]	alignment
KMC	kmc	3.1.0, 3.1.1, 3.2.1	[935]	phylogenetics
kmerdb	kmerdb	1.9.2	[936]	genomics, biology
kmerfreq	kmerfreq	4.0	[937]	biology, genomics
KMOS	kmos	0.3.21	[938]	phylogenetics
kneaddata	kneaddata	0.12.0, 0.7.4, 0.9.0	[https:https://github.com/biobakery/kneaddata]	biology, genomics
knime	knime	4.7.3	[939]	data science
Knitro	knitro	12.2.0	[940]	math
KofamScan	kofamscan	1.3.0	[941]	phylogenetics
kover	kover	2.0.3	[942]	phylogenetics
Kraken	kraken	2.0.8b, 2.1.2, 2.1.3	[943]	biology, ngs
KrakenTools	krakentools	1.2	[944]	biology, ngs
KrakenUniq	krakenuniq	0.5.8, 0.7.3, 1.0.4	[945]	phylogenetics
Krona	krona	2.8.1, 20161019	[946]	biology
ksnp	ksnp	3.021, 4.0	[947]	biology, phylogenetics, variant_calling
Ksrates	ksrates	1.1.1	[948]	genomics, biology
kvarq	kvarq	0.12.2	[949]	biology
LACHESIS	lachesis	2.1	[950]	phylogenetics
Lambda	lambda	0.9.4, 1.0.3, 2.0.0	[951]	biology, sequencing, phylogenetics
LAMMPS	lammps	3Nov2022, 7Aug19, 7Dec15	[952]	molecular_dynamics
LAMMPS-PPA	lammps-ppa	23Jun2022	[953]	molecular Dynamics
LAMP	lamp	2.5	[954]	biology, genomics
laneta	laneta	20220517, 20220808, 20220812	[955]	biology
langdetect	langdetect	1.0.9	[956]	language, utility
LAPACK	lapack	3.11.0, 3.8.0	[957]	programming, library, compiler
Last	last	916, 979	[958]	biology, sequencing, alignment
LAStools	lastools	20200114	[959]	image_processing
LASTZ	lastz	1.02.00, 1.03.02, 1.04.00	[960]	biology, ngs
Lazypipe	lazypipe	1.2	[961]	genomics
LazyPredict	lazypredict	0.2.8	[962]	phylogenetics
lbzip	lbzip	2.5	[963]	compression
LCModel	lcmodel	6.3	[964]	biology, spectroscopy
ldak	ldak	5.2	[965]	phylogenetics, biology
ldblockshow	ldblockshow	1.40	[966]	biology
LDhat	ldhat	2.2a	[967]	biology, genomics
ldsc	ldsc	1.0.1	[968]	genomics, biology
leafaudio	leafaudio	0.1.0	[969]	machine_learning, audio
LEfSe	lefse	20180219	[970]	phylogenetics
LEMON	liblemon	1.2.3	[971]	library
LFMM	lfmm	1.4, 1.5	[972]	biology, phylogenetics
libgfortran	libgfortran	3.0.0	[973]	programming
Libint	libint	2.5.0, 2.5.0b	[974]	library
libMesh	libmesh	1.5.0	[975]	math
libunistring	libunistring	0.9.7	[976]	library
libvips	libvips	8.5.4	[977]	image_processing
LIBXC	libxc	4.3.4, 6.2.2, 7.0.0	[978]	library, math
LIBXSMM	libxsmm	1.13	[979]	library, compiler, math
LIBZMQ	libzmq	4.3.1	[980]	library
Liftoff	liftoff	1.4.2, 1.6.2	[981]	phylogenetics
Lighter	lighter	1.1.3	[982]	genome
LIGR	ligr	2.05	[983]	biology, assembly
LillyMol	lillymol	6.1	[984]
lima	lima	2.0.0, 2.2.0, 2.7.1	[985]	phylogenetics
lingua	lingua	1.0.1	[986]	language, utility
LINKS	links	1.8.5, 1.8.6	[987]	biology, genomics
Linksbrowser	linksbrowser	2.14	[988]	web
LIQA	liqa	1.0.0, 1.1.16	[989]	phylogenetics
llama	llama	2, 3	[990]	library, math
llama-alex	llama	alex	[991]	library, math
llava	llava	1.6	[992]	Machine Learning
LMAP	lmap	1.0.2	[993]	biology, phylogenetics
lncScore	lncscore	1.0.2	[994]	biology, phylogenetics
lobSTR	lobstr	4.0.6	[995]	biology, phylogenetics
localbrainage	localbrainage	20210415	[996]	biology, machine_learning
localizer	localizer	1.0.4, 1.0.5	[997]	phylogenetics
LocusZoom	locuszoom	1.4	[998]	phylogenetics
LoFreq	lofreq	2.1.3.1	[999]	phylogenetics
LongQC	longqc	1.2.0c	[1,000]	phylogenetics
LongRanger	longranger	2.1.5, 2.2.2	[1,001]	biology, phylogenetics
longshot	longshot	0.4.5	[1,002]	genomics
LongStitch	longstitch	1.0.3	[1,003]	genomics, biology
LoRDEC	lordec	0.9	[1,004]	phylogenetics
LoRMA	lorma	0.3, 0.5	[1,005]	biology, ngs
loter	loter	1.0	[1,006]	genomics,
LRBinner	lrbinner	0.1	[1,007]	biology, genomics
lrgapcloser	lrgapcloser	09042018	[1,008]	biology
LS-DYNA	ls-dyna	700, 711, 901	[1,009]	physics
LSD2	lsd2	1.6.5	[1,010]	phylogenetics
ltr_finder	ltr_finder	1.07	[1,011]	biology, phylogenetics
LTRRetriever	ltrretriever	2.1, 2.5, 2.9.0	[1,012]	biology, phylogenetics
Lua	lua	5.3.2, 5.3.4, 5.4.6	[1,013]	programming, language
Lucene	pylucene	7.7.1, 9.1.0	[1,014]	programming, search
lumpy-sv	lumpy	0.2.1, 0.2.13, 0.3.1	[1,015]	biology, genomics
LZO	lzo	2.09	[1,016]	library, compression
M5nr	m5tools	20121126	[1,017]	biology, genomics
Macaulay2	macaulay2	1.15	[1,018]	phylogenetics
MACH	mach	1.0.18	[1,019]	biology, genomics, ngs
Mach2VCF	mach2vcf	20150515	[1,020]	biology
Macrel	macrel	1.3.0	[1,021]	biology, genomics
MACS	macs	2.0.10, 2.1.2, 2.2.7.1	[1,022]	biology, chip-seq
MafFilter	maffilter	1.3.0	[1,023]	phylogenetics
MAFFT	mafft	7.490, 7.505, 7.520	[1,024]	biology, sequencing
MAGeCK	mageck	0.5.9.4	[1,025]	phylogenetics
MAGeCK-VISPR	mageck-vispr	0.5.6	[1,026]	phylogenetics
MAGeCKFlute	mageckflute	1.14.0	[1,027]	phylogenetics
Magenta	magenta	2.1.2	[1,028]	phylogenetics
magicblast	magicblast	1.6.0	[1,029]	genomics, biology
MAGMA-GWAS	magma-gwas	1.09	[1,030]	phylogenetics
magpurify	magpurify	2.1.2	[1,031]	genomics
magus	magus	20220121	[1,032]	sequencing, alignment
MAJIQ	majiq	2.2, 2.3, 2.5.7	[1,033]	phylogenetics
Maker	maker	2.31.10, 2.31.6, 3.01.03	[1,034]	biology
MAnorm	manorm	20120316	[1,035]	biology, phylogenetics
MANTA	manta	1.6.0	[1,036]	phylogenetics
mantis	mantis	1.0.4	[1,037]	phylogenetics
mapclassify	mapclassify	2.4.2	[1,038]	statistics, mapping, geospatial
mapdamage	mapdamage	2.2.1	[1,039]	ngs, sequencing, biology
MapThin	mapthin	1.11	[1,040]	phylogenetics
Maq	maq	0.7.1	[1,041]	biology, ngs
MarginPolish	marginpolish	1.0.0	[1,042]	phylogenetics
MARK	mark	2.0.1	[1,043]	data_science, math
MarkerMiner	markerminer	20150710	[1,044]	biology, genomics
Mash	mash	1.1, 2.3	[1,045]	biology, genomics
MasHmap	mashmap	2.0	[1,046]	phylogenetics
mashtree	mashtree	1.2.0	[1,047]	genomics, biology
maskrc-svg	maskrc-svg	0.5	[1,048]	genomics
MASS	mass	1.1.1	[1,049]	genomics, biology
MASSMINE	massmine	0.10.0, 0.11.0, 0.9.5	[1,050]	data_mining
MaSuRCA	masurca	4.0.8, 4.0.9, 4.1.0	[1,051]	biology, alignment
Mathematica	mathematica	13.1, 14.0	[1,052]	math
MATLAB	matlab	2023b, 2024a, 2024b	[1,053]	math, language
MATS	mats	4.0.2, 4.1.0, 4.2.0	[1,054]	biology, ngs, rna-seq
matt	matt	1.3.1	[1,055]
Mauve	mauve	2.3.1	[1,056]	biology, ngs, genomics
mawk	mawk	1.3.4-20150503	[1,057]	language
maxbin	maxbin	2.1.1	[1,058]	biology, ngs
Maxima	maxima	5.41.0	[1,059]	math
MC	mc	4.6.1	[1,060]	shell
mCarts	mcarts	1.0.2	[1,061]	biology, genomics, math
mccortex	mccortex	1.0	[1,062]	phylogenetics
mcfost	mcfost	4.1.07	[1,063]	astronomy
MCL	mcl	12-135, 14-137	[1,064]	biology, genomics
MCNP	mcnp	6, 6.1, 6.3.0	[1,065]	physics
MCNPX	mcnpx	2.7.0	[1,066]	physics
MCR	mcr	2020a, 2020b, 2023b	[1,067]	math, language
MCScanX	mcscanx	20130328	[1,068]	biology, phylogenetics
mdanalysis	mdanalysis	1.1.1	[1,069]	physics, biology
MECAT	mecat	20180308	[1,070]	phylogenetics
Medaka	medaka	1.7.2, 1.8.0, 2.0	[1,071]	biology, phylogenetics
Medusa	medusa	1.6	[1,072]	phylogenetics
MEGA	mega	11.0.13, 7.0.26	[1,073]	biology, phylogenetics
Mega2	mega2	4.9.2, 6.0.0	[1,074]	biology, phylogenetics
MEGAHIT	megahit	1.1.1, 1.1.4, 1.2.9	[1,075]	biology, phylogenetics
Megalodon	megalodon	2.0.0, 2.4.1	[1,076]	phylogenetics
MEGAN	megan	6.23.4, 6.25.9, 6.4.15	[1,077]	biology, ngs
MEGASAT	megasat	1.0	[1,078]	phylogenetics
Megraft	megraft	1.0.2	[1,079]	biology, sequencing
MELD	meld	0.4.14, 0.4.19, 0.5.9	[1,080]	chemistry, molecular_dynamics
MELTING	melting	4.3.1	[1,081]	biology, genomics, rna
MEME	meme	5.0.2, 5.0.5, 5.4.1	[1,082]	biology, sequencing
MentaLiST	mentalist	0.1.3	[1,083]	biology, phylogenetics
Meraculous	meraculous	2.0.5	[1,084]	biology, ngs
Mercurial	mercurial	4.8.2	[1,085]	revision_control
merge_peaks	merge_peaks	0.1.0	[1,086]	workflow_automation
Merlin	merlin	1.1.2	[1,087]	biology, variant_calling
Merqury	merqury	1.1, 1.3	[1,088]	phylogenetics
Meryl	meryl	1.0	[1,089]	phylogenetics
MeShClust	meshclust	1.2.0	[1,090]	biology
Meshroom	meshroom	2019.2.0	[1,091]	phylogenetics
Meson	meson	1.2.3	[1,092]	biology, ngs, sequencing
MET	met	10.0	[1,093]	climate, modeling
Meta-Marc	meta-marc	1.0.0	[1,094]	phylogenetics
Meta-Tissue	meta-tissue	0.4	[1,095]	biology, genomics
MetaBAT	metabat	0.32.4, 2.13	[1,096]	biology, genomics
MetaBCC-LR	metabcc_lr	2.0.0	[1,097]	biology, genomics
Metabin	metabin	1.0	[1,098]	genomics
metabolic	metabolic	4.0	[1,099]	phylogenetics
MetaCherchant	metacherchant	0.1.0	[1,100]	biology, phylogenetics
MetaCluster	metacluster	5.0b	[1,101]	biology, genomics
MetaCompare	metacompare	20181016	[1,102]	phylogenetics
metacrast	metacrast	20200309	[1,103]	phylogenetics
Metaeuk	metaeuk	6.0	[1,104]	phylogenetics
MetaGeneMark	metagenemark	2.10, 3.26	[1,105]	biology, genomics
METAL	metal	20110325	[1,106]	biology, ngs, genomics
MetaLAFFA	metalaffa	1.0.0	[1,107]	phylogenetics
MetaMaps	metamaps	20201207	[1,108]	phylogenetics
METANNOT	metannot	20171129	[1,109]	phylogenetics
Metaphlan	metaphlan	4.0.6, 4.1.0, 4.1.1	[1,110]	phylogenetics
MetaPhlAn2	metaphlan2	2.7.7	[1,111]	biology, phylogenetics
MetaPhysicl	metaphysicl	1.0.0	[1,112]	math, astronomy, simulation
Metashape	metashape	1.8.4, 2.1.1	[1,113]
MetaSV	metasv	0.5.4	[1,114]	biology, phylogenetics, ngs
MetaVelvet	metavelvet	1.2.06	[1,115]	biology, genomics
metaWRAP	metawrap	1.2	[1,116]	phylogenetics
Metaxa2	metaxa2	2.1.1, 2.1.3, 2.2.3	[1,117]	biology, ngs, sequencing
methylartist	methylartist	1.3.0	[1,118]	biology
MethylDackel	methyldackel	0.5.0, 0.6.1	[1,119]	phylogenetics
methylpy	methylpy	1.2.9	[1,120]	biology, phylogenetics
Metilene	metilene	0.2.8	[1,121]	biology, genomics, methylation
METIS	metis	5.1.0, 5.2.1	[1,122]	utility
Mfannot	mfannot	20180405	[1,123]	biology, phylogenetics
mfold	mfold	3.6	[1,124]	biology, structure, rna
mg-rast	mg-rast	20150919	[1,125]	biology, genomics
MGEfinder	mgefinder	1.0.5	[1,126]	phylogenetics
MGERT	mgert	1.0.1	[1,127]	phylogenetics
MGEScan	mgescan	20160416	[1,128]	biology, genomics
MGLTools	mgltools	1.5.7	[1,129]	biology, visualization
Mgs2amr	mgs2amr	2.0.1	[1,130]	genomics
MHAP	mhap	1.6	[1,131]	biology, sequencing
MHCflurry	mhcflurry	1.4.3	[1,132]	phylogenetics
MIA	mia	20130201	[1,133]	biology, ngs
micop	micop	03312022	[1,134]	genomics
MicrobeAnnotator	microbeannotator	2.0.5	[1,135]	annotation, biology
MIDAS	midas	1.3.2, 20160830	[1,136]	biology, phylogenetics
MIGRATE-N	migraten	4.2.14, 4.4.4, 5.0.4	[1,137]	biology, genomics
Mikado	mikado	2.3.3	[1,138]	biology, genomics, sequencing, pipeline
MIKE	mike	1.0	[1,139]	geospatial, fluid_dynamics, modeling
milvus	milvus	2.4.15	[1,140]	database, llm, container
Minced	minced	0.2.0	[1,141]	biology, genomics
Minia	minia	3.2.6	[1,142]	genomics, biology
Miniasm	miniasm	0.2-r168, 0.3-r179	[1,143]	biology, phylogenetics
MiniCaller	minicaller	20161201	[1,144]	biology, ngs, phylogenetics
minigraph	minigraph	0.15, 0.20	[1,145]	phylogenetics
minimac	minimac	1-20130717, 3-20150727	[1,146]	biology, ngs
minimac2	minimac	2-20140915	[1,147]	biology, ngs
minimap	minimap	2.21, 2.9-r720, 2.ax	[1,148]	biology, phylogenetics
minimap2	minimap2	2.24, 2.28	[1,149]	genomics, biology
Minipolish	minipolish	0.1.3	[1,150]	biology, genomics
Miniprot	miniprot	0.12	[1,151]	biology, genomics
miniwdl	miniwdl	1.11.1	[1,152]	bioinfomatics
MinkowskiEngine	minkowskiengine	0.5.3, 0.5.4a	[1,153]	machine_learning
MinPath	minpath	1.4	[1,154]	biology, phylogenetics
MIRA	mira	4.0.rc1, 4.9.6, 5rc2	[1,155]	biology, genomics, assembly
miRanda	miranda	1.9	[1,156]	phylogenetics
miRBShunter	mirbshunter	0.2	[1,157]	phylogenetics
mirdeep	mirdeep	0.1.0, 0.1.1, 2.0.1.3	[1,158]	phylogenetics
miRDP2	mirdp2	1.1.4	[1,159]	biology, genomics
Mireap	mireap	0.20	[1,160]	biology
miRge	mirge	2.0	[1,161]	phylogenetics
Misa	misa	1.0	[1,162]	biology, genomics
MISO	miso	0.5.3	[1,163]	biology, ngs, sequencing, rna-seq
mistral	mistral	0.1.5	[1,164]	library, math
MITE-Hunter	mite-hunter	20111101	[1,165]	biology, phylogenetics
MITObim	mitobim	1.9.1	[1,166]	phylogenetics
MitoFinder	mitofinder	1.4.1	[1,167]	phylogenetics
mitohifi	mitohifi	2.2, 3.2	[1,168]	genomics, sequencing
MitoPhAST	mitophast	3.0	[1,169]	phylogenetics
Mitos	mitos	2.1.9	[1,170]	biology, phylogenetics
Mitsuba2	mitsuba2	2.2.1	[1,171]	graphics
MiXCR	mixcr	2.1.8, 3.0.13	[1,172]	biology, phylogenetics
MixMHC2pred	mixmhc2pred	1.2	[1,173]	phylogenetics
MixMHCpred	mixmhcpred	2.0.2	[1,174]	phylogenetics
mixmogam	mixmogam	20190322	[1,175]	phylogenetics
MKL	mkl	2019.1.144, 2020.0.166, 2020.2.0	[1,176]	programming, library, math, compiler
mlcoalsim	mlcoalsim	1.9916b	[1,177]	biology, phylogenetics
mlpack	mlpack	3.4.2	[1,178]	library
mlst	mlst	2.15.2, 2.23.0	[1,179]	phylogenetics
mlstcheck	mlst-check	2.1	[1,180]	phylogenetics
mmaction2	mmaction2	1.0.0	[1,181]	Machine_Learning, Visualization
MMSEQ	mmseq	1.0.8	[1,182]	biology, genomics
MMseqs2	mmseqs2	11, 12, 14	[1,183]	phylogenetics
MMvec	mmvec	1.0.5, 1.0.6	[1,184]	metabolomics
MNEtools	mnetools	0.22.0, 1.3.1, 1.4.0	[1,185]	phylogenetics
MOABS	moabs	1.2.9, 1.3.2, 1.3.4	[1,186]	biology, ngs
mobsuite	mobsuite	3.1.0, 3.1.9	[1,187]	sequencing, biology
MOCCASIN	moccasin	0.25	[1,188]	phylogenetics
moco	moco	0.4.0	[1,189]	modeling, tools
Model Card Toolkit	model_card_toolkit	2.0.0	[1,190]	Machine_Learning, Utility, Workflow_automation
MODELLER	modeller	9.14, 9.23	[1,191]	biology, modeling, structure
MODELTEST	modeltest	0.1.2, 0.1.7	[1,192]	biology, phylogenetics
ModernCSV	moderncsv	2.0.2	[1,193]	editor, viewer
Modkit	modkit	0.4.1	[1,194]	genomics, bioinformatics
Modulus	modulus	23.11, 24.01, 24.07	[1,195]	physics, ai, neural_network
Molden	molden	5.0, 7.3	[1,196]	chemistry, structure
MolPro	molpro	0.1	[1,197]	biology
MolProbity	molprobity	20221216	[1,198]	biology
momi	momi	2.1.19	[1,199]	phylogenetics, biology
monai	monai	0.8.1, 0.9.0, 1.0.1	[1,200]	healthcare
MONAI label	ngc-monailabel	0.3.2, 0.6.0	[1,201]	healthcare
MongoDB	mongodb	4.0.3	[1,202]	database
Moni	moni	0.2.0	[1,203]	genomics, biology
mono	mono	5.18	[1,204]	linux, programming
Monolix	monolix	2023R1, 4.3.2	[1,205]	modeling, biology
MOOSE	moose	20220610, 20230320, 20230711	[1,206]	physics, simulation
mopac	mopac	22.1.1	[1,207]	chemistry
MORPHEUS	morpheus	23.01	[1,208]	machine_learning
Mosaic	mosaic	1.7.4	[1,209]	phylogenetics
MOSAIK	mosaik	2.1.33, 2.2.3, 2.2.30	[1,210]	biology, alignment
Mosdepth	mosdepth	0.2.3, 0.3.1	[1,211]	biology, phylogenetics
moses	moses	0.3.1	[1,212]	machine learning, data science
Mothur	mothur	1.41.3, 1.46.1, 1.48.0	[1,213]	biology
MotionCor2	motioncor2	1.2.3, 1.3.1, 1.6.4	[1,214]	imaging
mOTU	motu	1.1	[1,215]	biology, genomics
mOTUs	motus	2.5.1	[1,216]	phylogenetics
MountainSort	mountainsort	0.9.0	[1,217]	library
MP-EST	mpest	1.4	[1,218]	biology, ngs, sequencing
MPACK	mpack	0.8.0	[1,219]	library
MPB	mpb	1.5	[1,220]	library, math
MPBoot	mpboot	1.1.0	[1,221]	biology, phylogenetics
MPFR	mpfr	3.1.6, 4.2.1	[1,222]	library, math
mpi-test-suite	mpi-test-suite	1.1.1	[1,223]	utility
mpinterfaces	mpinterfaces	20170613	[1,224]	math
MrBayes	mrbayes	3.2.4, 3.2.5, 3.2.6	[1,225]	biology, phylogenetics
MRIcroGL	mricrogl	20201102, 20210327, 20211006	[1,226]	biology, imaging
MRIcron	mricron	201306, 20161012, 20190911	[1,227]	biology, imaging
mriqc	mriqc	0.11.0, 0.16.1, 22.0.1	[1,228]	imaging, biology
MRtrix	mrtrix	3.0.1, 3.0.3, 3.0rc2	[1,229]	statistics
mrtrix3tissue	mrtrix3tissue	5.2.9	[1,230]	phylogenetics
ms	ms	20171108	[1,231]	phylogenetics
ms-dial	ms-dial	4.4.8	[1,232]	biology, metabolomics
msfinder	msfinder	3.52	[1,233]	biology, metabolomics
mSINGS	msings	20180810	[1,234]	phylogenetics
MSMC-Tools	msmc-tools	20190614	[1,235]	phylogenetics
msprime	msprime	0.7.4, 1.2.0	[1,236]	phylogenetics
MstatX	mstatx	1.0	[1,237]	biology, phylogenetics
MSTmap	mstmap	1.0	[1,238]	phylogenetics
msvar	msvar	1.3	[1,239]	biology, genomics
MTG2	mtg2	2.15	[1,240]	phylogenetics
mTR	mtr	20210526, 20240801	[1,241]	biology, genomics
Mugsy	mugsy	1.2.3	[1,242]	biology, phylogenetics
Multimatch-gaze	multimatchgaze	0.1.3	[1,243]	math, data_science
MultiQC	multiqc	1.21, 1.24, 1.7	[1,244]	biology, ngs, sequencing
MUMmer	mummer	3.23, 4.0.0beta2	[1,245]	biology, genomics
MUSCLE	muscle	3.8.31, 5.1	[1,246]	biology, alignment
MuSE	muse	1.0rc	[1,247]	phylogenetics
Musket	musket	1.1	[1,248]	biology, genomics, ngs
MuTect	mutect	1.1.4, 1.1.7	[1,249]	biology, genomics
mutmap	mutmap	2.3.3	[1,250]	biology
MutSig	mutsig	1.4, 1.41	[1,251]	biology, genomics
mvftools	mvftools	20191124	[1,252]	phylogenetics
mvrsion	mvrsion	07302018	[1,253]	sequencing
mxnet	ngc-mxnet	22.08	[1,254]	healthcare
mykrobe	mykrobe	0.12.2	[1,255]	biology
MZMine	mzmine	2.53, 3.3.0	[1,256]	biology, spectroscopy
NAMD	namd	2.14b2, 3.0 Alpha, 3.0b2	[1,257]	molecular_dynamics
NANO	nano	2.8.2	[1,258]	programming
nanocaller	nanocaller	3.1.0	[1,259]	sequencing
nanocomp	nanocomp	1.17.0	[1,260]	programming, sequencing
Nanocompore	nanocompore	1.3.0	[1,261]	biology, genomics
NanoCount	nanocount	0.2.1	[1,262]	phylogenetics
Nanodisco	nanodisco	1.0.3	[1,263]	phylogenetics
Nanofilt	nanofilt	2.7.1	[1,264]	phylogenetics
nanolyse	nanolyse	1.2.0	[1,265]	genomics, biology
NanoPlot	nanoplot	1.30.1, 1.42.0	[1,266]	phylogenetics
Nanopolish	nanopolish	0.11.1, 0.13.2, 20171006	[1,267]	biology
nanoq	nanoq	0.10.0	[1,268]	biology, ngs, nanopore
nanostripper	nanostripper	0.1	[1,269]	phylogenetics, biology
NanoSV	nanosv	1.2.0, 1.2.3, 1.2.4	[1,270]	biology, genomics
NanoVar	nanovar	1.3.9	[1,271]	phylogenetics
Napari	napari	0.3.8, 0.4.7	[1,272]	phylogenetics
NBODY	nbody	6	[1,273]	astronomy
NCBI BLAST+	ncbi_blast	2.7.1, 2.8.1, 2.9.0	[1,274]	biology
NCBI C++ Toolkit	ncbi_toolkit	12.0.0, 21.0.0, 7.0.0	[1,275]	biology, programming, library, compiler
NCBI GenBank Tools	genbank_tools	20140130	[1,276]	biology
ncbi-fcs	ncbi-fcs	0.4.0, 0.5.0, 0.5.4	[1,277]	genomics
ncbi-genome-download	ncbi-genome-download	0.3.3	[1,278]	biology, genomics
ncbi-vdb	ncbi-vdb	2.6.3, 2.8.2	[1,279]	ngs
ncbi_cli	ncbi_cli	15.3.1	[1,280]	biology, sequencing, library
nccl	nccl	20.11	[1,281]	programming, library, gpu
ncftp	ncftp	3.2.5	[1,282]	file_management
NCL	ncl	6.1.2, 6.3.0, 6.6.2	[1,283]	climate
NCO	nco	4.2.1, 4.4.3	[1,284]	data_science
ncview	ncview	2.1.2, 2.1.7	[1,285]	visualization
NECAT	necat	202001019, 20200803	[1,286]	phylogenetics
Necklace	necklace	1.00	[1,287]	biology, phylogenetics
NeEstimator	neestimator	2.1	[1,288]	biology
nemo	nemo	1.2.0, 1.22.0, 1.23.0	[1,289]	ai, machine_learning
neovim	neovim	0.8.1, 0.8.3, 0.9.5	[1,290]	programming, shell
nerfstudio	nerfstudio	1.1.3	[1,291]	Machine Learning
NetCDF	netcdf	4.3, 4.3.3, 4.4.3	[1,292]	data_science
NetCDF-C	netcdf-c	4.8.1, 4.9.0, 4.9.2	[1,293]	data_science
NetCDF-F	netcdf-f	4.5.3, 4.5.4, 4.6.1	[1,294]	data_science
NetLogo	netlogo	5.3.64, 6.1.1, 6.2.0	[1,295]	modeling
NEURON	neuron	7.7.2, 8.0.0, 8.2.1	[1,296]	biology, neuroscience
Newbler	newbler	2.7, 2.8, 2.9	[1,297]	biology, ngs, assembly, de_novo
newick-utils	newickutils	1.6	[1,298]	biology, genomics, phylogenetics
newick_utils	newick_utils	1.6, 1.7	[1,299]	biology, phylogenetics
NewTargets	newtargets	20210215	[1,300]	biology
nextclade	nextclade	2.9.1, 3.2.0, 3.8.2	[1,301]	phylogenetics, genomics
NextDenovo	nextdenovo	2.4.0	[1,302]	phylogenetics
Nextflow	nextflow	23.10.0, 23.10.1, 24.04.2	[1,303]	biology, workflow_automation
NextGenMap	nextgenmap	0.5.5	[1,304]	phylogenetics
NextPolish	nextpolish	1.3.1	[1,305]	phylogenetics
Nextstrain	nextstrain	1.16.1	[1,306]	phylogenetics
nf-core	nf-core	2.11.1, 2.14.1, 2.7.2	[1,307]	biology, workflow_automation
NGC CLI	ngccli	2.10.1	[1,308]	shell
NGmerge	ngmerge	0.3	[1,309]	phylogenetics
ngmlr	ngmlr	0.2.6, 0.2.7	[1,310]	biology, phylogenetics
ngs-bits	ngsbits	0.1	[1,311]	biology, sequencing
NGS-SDK	ngs-sdk	1.2.4, 1.3.0	[1,312]	biology, healthcare, programming, library
ngsremix	ngsremix	20221117	[1,313]	genomics
ngstools	ngstools	20150816	[1,314]	biology, ngs
nilearn	nilearn	0.7.0, 0.9.0	[1,315]	phylogenetics
nimare	nimare	0.0.5	[1,316]	neuroscience
Nipype	nipype	1.6.0, 1.7.0, 1.8.0	[1,317]	biology, neuroscience, imaging
nlp	nlp	1.1, 1.2, 1.3	[1,318]	machine_learning
nlr-annotator	nlr-annotator	0.7	[1,319]	phylogenetics
NLR-Parser	nlr-parser	1.0	[1,320]	phylogenetics
nlrtracker	nlrtracker	20240306	[1,321]	biology
NMRPipe	nmrpipe	7.9, 8.2	[1,322]	chemistry, biology
NONMEM	nonmem	7.3.0, 7.4.4	[1,323]	modeling
nonpareil	nonpareil	3.3.4	[1,324]	phylogenetics
Novoalign	novoalign	2.08.02, 3.00.02	[1,325]	biology, ngs
NOVOPlasty	novoplasty	3.7, 4.2, 4.3	[1,326]	phylogenetics
nPhase	nphase	1.1.3	[1,327]	biology, pipeline
npScarf	japsa	1.7	[1,328]	phylogenetics
nQuire	nquire	20180405	[1,329]	phylogenetics
Nsight	nsight	2022.1, 2024.3.2.0	[1,330]	gpu, performance_analysis, utility
Nsightsys	nsightsys	2022.2.1, 2024.5.1	[1,331]	gpu, performance_analysis, utility
nt	nt	20220404	[1,332]	sequencing, neuroscience
ntEdit	ntedit	1.2.1	[1,333]	phylogenetics
ntJoin	ntjoin	1.1.4	[1,334]	biology, genomics
nubeamdedup	nubeamdedup	20200907	[1,335]	phylogenetics
NucDiff	nucdiff	2.0.3	[1,336]	phylogenetics
NucleoATAC	nucleoatac	0.3.1	[1,337]	biology
Nuke	nuke	14.0v5	[1,338]	Graphics, Utility, Visualization
Nullarbor	nullarbor	1.41	[1,339]	biology, phylogenetics
Numba	numba	0.36.2, 0.43.1, 0.48.0	[1,340]	compiler
NUPACK	nupack	3.2.2	[1,341]	phylogenetics
nvhpc	nvhpc	23.7, 24.3, 24.5	[1,342]	language, programming, library, math, gpu
nVidia HPC Compilers	nvidia	20.11	[1,343]	compiler
NWChem	nwchem	6.8, 7.2	[1,344]	chemistry
NxTrim	nxtrim	0.4.1	[1,345]	biology, ngs
Oases	oases	0.2.08	[1,346]	biology, ngs, assembly
Oatk	oatk	1.0	[1,347]	genomics
Obitools	obitools	1.2.13, 3.0	[1,348]	biology, ngs, sequencing
OCaml	ocaml	4.02.3	[1,349]	language, programming
OCOCO	ococo	0.1.2.6	[1,350]	biology, phylogenetics
octave	octave	6.4.0, 7.2.0, 7.3.0	[1,351]	math
odgi	odgi	0.6, 0.8.4	[1,352]	phylogenetics
Olego	olego	1.1.2, 1.1.5, 1.1.6	[1,353]	biology, ngs, rna-seq
ollama	ollama	0.3.8	[1,354]	LLM
OMindel	omindel	20180129	[1,355]	phylogenetics
OMNI-C	omnic	1.0	[1,356]	genomics
omniCLIP	omniclip	0.1.0	[1,357]	phylogenetics
OMNIVERSE	omniverse	beta211004	[1,358]	gpu
OMSV	omsv	1.0.1	[1,359]	phylogenetics
OneFormer	oneformer	1.0	[1,360]	ai, image_processing, imaging
ONT-Bonito	ont-bonito	0.1.5, 0.5.3, 0.6.0	[1,361]	phylogenetics
ont_fast5_api	ont-fast5-api	2.0.1, 4.0.2	[1,362]	phylogenetics
ont_tutorial_cas9	ont_tutorial_cas9	20190705	[1,363]	phylogenetics
open-cravat	open-cravat	2.0.1	[1,364]	biology, genomics
open3d	open3d	0.13.0, 0.17.0	[1,365]	graphics
OPENACC	openacc	16.7	[1,366]	programming
OpenBabel	openbabel	2.3.2, 2.4.1, 3.1.1	[1,367]	biology
OpenBLAS	openblas	0.2.20, 0.3.24	[1,368]	programming, library
OpenCL	opencl	18.1.0.013	[1,369]	phylogenetics
OpenCV	opencv	4.5.2, 4.7.0	[1,370]	library
OpenFOAM	openfoam	4.1, 5.0, 8.0	[1,371]	fluid_dynamics
openmc	openmc	0.14.0, 0.15.0	[1,372]	physics
OpenMM	openmm	7.6.0, 8.0.0, 8.1.2	[1,373]	chemistry, molecular_dynamics
OpenMPI	openmpi	4.1.4, 4.1.5, 4.1.6	[1,374]	programming, library
OpenNeuro	openneuro	3.17.4, 3.37.4, 4.19.2	[1,375]	biology, data_science
opennmt-py	opennmt-py	3.1.0	[1,376]	language, machine_learning
OpenPIV-python	openpiv	0.21.2	[1,377]	programming, imaging
OpenPIV-python-gpu	openpiv	20190506-gpu	[1,378]	programming, imaging
OpenPose	openpose	20230106	[1,379]	image_processing
openrdp	openrdp	0.1.0-rc2	[1,380]	biology
OpenSim	opensim	4.3	[1,381]	phylogenetics
OpenSlide	openslide	3.4.1	[1,382]	imaging
Openssl	openssl	3.3.0	[1,383]	libray
openstructure	openstructure	2.3.1	[1,384]	biology
OpenUSD	openusd	23.08	[1,385]	digital twin, simulation
OptiType	optitype	1.3.1	[1,386]	biology, phylogenetics
Orange3	orange3	3.3.6	[1,387]	data_mining
Orca	orca	5.0.1, 5.0.4	[1,388]	chemistry
ORCA	orca	4.0.1.2	[1,389]	chemistry, structure
OrganellePBA	organellepba	20180904	[1,390]	phylogenetics
OrthoFiller	orthofiller	1.1.4	[1,391]	phylogenetics
OrthoFinder	orthofinder	2.3.11, 2.5.2, 2.5.5	[1,392]	biology, ngs
Orthofisher	orthofisher	0.1.2	[1,393]	biology, genomics
Orthograph	orthograph	0.6.3	[1,394]	orthology
Orthologer	orthologer	2.2.0	[1,395]	biology
OrthoMCL	orthomcl	2.0.9	[1,396]	biology, genomics
OSL	osl	1.1.0	[1,397]	biology, neuroscience, imaging
oslom	oslom	0.3.0	[1,398]	plotting
osprey	osprey	1.1.0, 2.5.0	[1,399]	spectroscopy, neuroscience
OTB	otb	5.8.0	[1,400]	geospatial
ovito	ovito	3.8.5, 3.9.4	[1,401]	programming
owitools	owitools	1.0	[1,402]	metabarcoding, bioinformatics, ecology
p4est	p4est	1.1, 2.8	[1,403]	library
p4vasp	p4vasp	0.3.29, 0.3.30	[1,404]	chemistry, structure
p53MH	p53mh	20020901	[1,405]	biology, sequencing
p7zip	p7zip	9.20.1	[1,406]	utility
PacBio	pacbio	10.2.0.133434, 11.0.0.146107, 7.0.1	[1,407]	biology, ngs
Package-GFE	package-gfe	20150701	[1,408]	biology, genomics
PacMAP	pacmap	0.7.0	[1,409]	genomics
PALADIN	paladin	1.3.1	[1,410]	biology, phylogenetics
PALES	pales	122	[1,411]	physics
PAML	paml	4.8a, 4.9a, 4.9h	[1,412]	biology, phylogenetics
panaroo	panaroo	1.3.3	[1,413]	biology, genomics
Pandaseq	pandaseq	20140808, 20150627	[1,414]	biology, ngs, sequencing
Pandoc	pandoc	2.2.2.1	[1,415]	utility
pangolin	pangolin	2, 4.3	[1,416]	phylogenetics
panseq	panseq	3.2.1	[1,417]	phylogenetics
pantools	pantools	4.3.1	[1,418]	biology, genomics
panX	panx	1.6.0	[1,419]	phylogenetics
PAPI	papi	5.5.1, 5.7.0	[1,420]	programming, performance_analysis
parabricks	parabricks	4.2.1, 4.3.0, 4.3.1	[1,421]	phylogenetics
parallel	parallel	20150122, 20170322	[1,422]	shell, workflow_automation
paralyzer	paralyzer	1.5	[1,423]	phylogenetics
ParaView	paraview	5.4.1, 5.7.0, 5.9.1.1	[1,424]	data_science
ParaView Server	paraview_server	5.10.1	[1,425]	data_science
ParGenes	pargenes	1.2.0	[1,426]	phylogenetics
ParlAI	parlai	1.3.0, 1.5.0	[1,427]	phylogenetics
PARMETIS	parmetis	4.0.3	[1,428]	utility
Parsnp	parsnp	1.2, 1.5.0, 1.6.2	[1,429]	biology, phylogenetics
PartitionFinder	partitionfinder	2.0.0-pre-20160513, 2.1.1-20161205, 2.1.1.0	[1,430]	biology, phylogenetics, genomics
PASA	pasa	2.2.0-r20171013, 2.4.1, 2.5.3	[1,431]	biology, genomics, ngs
Pascal	fpc	3.0.0	[1,432]	compiler, programming
PASTA	pasta	0.2.0, 1.7.8, 20160616	[1,433]	biology, alignment
PATHd8	pathd8	1.0	[1,434]	biology, phylogenetics
pathoscope	pathoscope	2.0.7	[1,435]	sequencing, genomics, biology
PATRIC	patric	1.034	[1,436]	machine_learning
PAUDA	pauda	1.0.1	[1,437]	biology, ngs, phylogenetics
PAUP	paup	4.0a166, 4.0a168, 4.0b10	[1,438]	biology, phylogenetics
PB-Assembly	pb-assembly	0.0.6, 0.0.8	[1,439]	biology, ngs, sequencing
pbalign	pbalign	20160921, 20161221	[1,440]	biology
PBCCS	pbccs	5.0.0, 6.4.0	[1,441]	phylogenetics
pbcore	pbcore	1.7.1	[1,442]	biology
PBGCpp	pbgcpp	1.9.0	[1,443]	phylogenetics
pbipa	pbipa	1.8.0	[1,444]	phylogenetics, biology
PBJelly	pbjelly	15.8.24	[1,445]	biology, ngs
pbmm2	pbmm2	1.13.1, 1.3.0	[1,446]	phylogenetics
pbpigeon	pbpigeon	1.2.0	[1,447]	biology, ngs
pbrt	pbrt	20181017	[1,448]	phylogenetics
pbsmrtpipe	pbsmrtpipe	0.63.0	[1,449]	biology, programming
pbtk	pbtk	3.1.0	[1,450]	biology
pbtranscript-tofu	pbtranscript-tofu	20150317, 20160119	[1,451]	biology, ngs
pcangsd	pcangsd	1.2	[1,452]	biology
PCIT	pcit	2014	[1,453]	biology
PCRE	pcre	8.38, 8.39	[1,454]	programming, library
PDA	pda	1.0.3	[1,455]	biology, phylogenetics
pdb2pqr	pdb2pqr	2.1.0	[1,456]	protein, modeling, biology
PeakSplitter	peaksplitter	1.0	[1,457]	biology, chip-seq
PEAR	pear	0.9.2	[1,458]	biology, genomics, ngs
peneasy	peneasy	20150530	[1,459]	physics
PennCNV	penncnv	1.0.5	[1,460]	phylogenetics
Perl	perl	5.16.0, 5.20.0, 5.24.1	[1,461]	programming, language
PerM	perm	0.4.0	[1,462]	biology, ngs, mapping
PETSc	petsc	3.8.1, 3.8.3, 3.8.4	[1,463]	math
PfamScan	pfamscan	1.3, 1.5	[1,464]	biology, genomics
PGAP	pgap	20230306, 20231003, 20240703	[1,465]	biology, genomics, annotation, pipeline
PGDSpider	pgdspider	2.0.9.0, 2.1.1.5	[1,466]	biology, ngs
pggb	pggb	0.6.0, 20201106, 20210121	[1,467]	phylogenetics
PhaME	phame	1.0.3	[1,468]	phylogenetics
phanotate	phanotate	1.5.0	[1,469]	genomics
pharmcat	pharmcat	1.8.0	[1,470]	biology, phylogenetics
PHASE	phase	2.1.1	[1,471]	phylogenetics
PHAST	phast	1.5	[1,472]	biology, phylogenetics
Phenix	phenix	1.10.2155, 1.17.1, 1.8.1069	[1,473]	material_science
PHI	phi	3.1.1, 3.1.2b, 3.1.6	[1,474]	math
PhiSpy	phispy	3.2	[1,475]	phylogenetics
PHLAWD	phlawd	20170427	[1,476]	biology, phylogenetics
PhotoScan	photoscan-pro	1.4.1, 1.4.5	[1,477]	image_processing
Photutils	photutils	0.5	[1,478]	astronomy
PHYling	phyling	1.0	[1,479]	biology, phylogenetics, genomics
PHYLIP	phylip	3.696	[1,480]	biology, phylogenetics
PhyloAcc	phyloacc	1.0	[1,481]	phylogenetics
PhyloBayes	phylobayes	3.3f	[1,482]	biology, phylogenetics
phyloFlash	phyloflash	3.3b4	[1,483]	phylogenetics
phylonet	phylonet	3.5.7, 3.8.2	[1,484]	biology, phylogenetics
PhyloParser	phyloparser	20180404	[1,485]	phylogenetics
PhyloPhlAn2	phylophlan2	0.41	[1,486]	phylogenetics
phylopypruner	phylopypruner	1.2.3	[1,487]	phylogenetics
PhyloSift	phylosift	1.1	[1,488]	biology, genomics, phylogenetics
phyloTF2	phylotf2	20210726	[1,489]	biology, genomics, alignment
Phyluce	phyluce	20180727, 20190308, 20191015	[1,490]	biology, ngs, sequencing
PhyML	phyml	3.0, 3.1, 3.3.20220408	[1,491]	biology, phylogenetics
phynd	phynd	20200409	[1,492]	phylogenetics
Physher	physher	1.0.2	[1,493]	phylogenetics
PHYUTILITY	phyutility	2.7.1	[1,494]	biology
Phyx	phyx	1.1	[1,495]	phylogenetics
PIA2	pia2	20180305	[1,496]	biology, phylogenetics
Picard-tools	picard	2.9.2, 3.1.1, 3.2.0	[1,497]	biology, ngs
PICRUSt	picrust	1.1.3, 1.1.4, 2.3.0b	[1,498]	biology, phylogenetics
PICSL	picsl	1.3	[1,499]	imaging
Piggy	piggy	20171220	[1,500]	biology, ngs
Pigz	pigz	2.4	[1,501]	compression
PILON	pilon	1.22, 1.24	[1,502]	biology, ngs, phylogenetics
Pindel	pindel	0.2.5b8	[1,503]	biology, phylogenetics
pipe-clip	pipe-clip	1.1.0	[1,504]	biology, ngs
pipits	pipits	1.3.6, 1.4.0	[1,505]	biology, sequencing
Piranha	piranha	1.2.1	[1,506]	biology, phylogenetics
PLantismash	plantismash	1.0	[1,507]	biology, genomics
PlantTribes	planttribes	1.0.4	[1,508]	phylogenetics
plasme	plasme	1.1	[1,509]	Genomics
PLAST	plast	1.0, 2.3.2	[1,510]	biology
platanus	platanus	1.2.4	[1,511]	phylogenetics
Platon	platon	1.6	[1,512]	biology, sequencing
Platypus	platypus	0.8.1	[1,513]	biology, ngs
PLEK	plek	1.2.2	[1,514]	biology, phylogenetics
Plink	plink	2.00a2, 2.00a3LM, 2.00a5LM	[1,515]	biology, genomics, phylogenetics
plinkseq	plinkseq	0.10	[1,516]	biology, library
plip	plip	2.3.0	[1,517]	Protein-structure
plotsr	plotsr	0.5.4	[1,518]	genomics, biology
PLUMED	plumed	2.7.3, 2.9.0, 2021.2	[1,519]	chemistry, molecular_dynamics
pm4py	pm4py	2.7.4	[1,520]	Data_Mining, Machine_Learning
pod5	pod5	0.1.5, 0.3.6, 20220621	[1,521]	sequencing
PolyGembler	polygembler	1.0	[1,522]	phylogenetics
PolyPHen	polyphen	2.2.2.r405b	[1,523]	biology, genomics
polyply	polyply	1.3.0	[1,524]	phylogenetics, biology
Polypolish	polypolish	0.5.0	[1,525]	biology, genomics
pomdp	pomdp	1.3.4	[1,526]	software
pomoxis	pomoxis	0.1.11, 0.2.5, 0.3.2	[1,527]	biology, phylogenetics
popcorn	popcorn	20211104	[1,528]	phylogenetics, biology
PopLDdecay	poplddecay	3.40	[1,529]	phylogenetics
popoolation	popoolation	1.2.2	[1,530]	biology, phylogenetics
popoolation2	popoolation2	1.201	[1,531]	biology, phylogenetics
Porechop	porechop	0.2.4	[1,532]	phylogenetics
Poretools	poretools	0.6.1	[1,533]	phylogenetics
portcullis	portcullis	1.2.3	[1,534]	phylogenetics
PosiGene	posigene	20171113	[1,535]	biology, phylogenetics
POV-Ray	povray	3.7, 3.7.0.8	[1,536]	graphics
powerfit	powerfit	2.0.0	[1,537]	Physics
pplacer	pplacer	1.1.alpha19	[1,538]	biology, phylogenetics, genomics
PRANK	prank	170427, 20150803	[1,539]	biology, alignment
Predector	predector	20201110	[1,540]	phylogenetics
predectorutils	predectorutils	0.9.1	[1,541]	biology, genomics
preplot	preplot	14.0.2	[]
Preseq	preseq	0.0.4	[1,542]	biology, ngs
PRICE	price	1.2	[1,543]	biology, ngs
Primer3	primer3	2.3.4	[1,544]	biology, genomics
primus	primus	1.8.0	[1,545]	biology, phylogenetics
PRINSEQ	prinseq	0.20.4	[1,546]	biology, sequencing
PRINSEQ++	prinseq++	1.2	[1,547]	phylogenetics
ProbABEL	probabel	0.4.2, 0.4.3, 0.4.5	[1,548]	genomics
probalign	probalign	1.4	[1,549]	biology, ngs
Processing	processing	3.4	[1,550]	programming, language, visualization
Prodigal	prodigal	2.6.2, 2.6.3	[1,551]	biology, genomics
ProDy	prody	2.0	[1,552]	phylogenetics
Program Database Toolkit	pdt	3.20, 3.22, 3.24	[1,553]	language, programming, performance_analysis
PROJ	proj	5.1.0, 8.0.1, 9.4.0	[1,554]	library, Cartographic Projections and Coordinate Transformations
Prokka	prokka	1.12, 1.14.6	[1,555]	biology, genomics, assembly
Proovread	proovread	1.03rcl, 2.12, 2.13	[1,556]	biology, genomics, ngs
ProSplign	prosplign	1.0.0	[1,557]	phylogenetics
Protege	protege	5.1.0	[1,558]	genomics
Proteinortho	proteinortho	4.26, 5.11, 5.16	[1,559]	biology, genomics
ProtExcluder	protexcluder	1.2	[1,560]	biology, phylogenetics
ProtHint	prothint	2.6.0	[1,561]	biology, genomics
protobuf	protobuf	2.5.0, 3.5.1	[1,562]	web, library
prottest3	prottest3	3.4.2	[1,563]	biology
PROVEAN	provean	1.1.5	[1,564]	biology, genomics
PRSice	prsice	2.3.3	[1,565]	phylogenetics
Pseudofinder	pseudofinder	1.0	[1,566]	phylogenetics
PsiCLASS	psiclass	1.0.1	[1,567]	phylogenetics
PSMC	psmc	0.6.5	[1,568]	phylogenetics
psRobot	psrobot	1.2	[1,569]	phylogenetics
Pufferfish	pufferfish	20200417, 20230223	[1,570]	phylogenetics
PureCLIP	pureclip	1.1.1	[1,571]	phylogenetics
Purge_Dups	purge_dups	1.0.1	[1,572]	phylogenetics
purge_haplotigs	purge_haplotigs	1.1.2, 1.1.3	[1,573]	sequencing, biology
pvconv	pvconv	10152018	[1,574]	imaging
pyani	pyani	0.2.10, 0.2.12	[1,575]	phylogenetics
Pybedtools	pybedtools	0.8.2, 0.9.0	[1,576]	phylogenetics
Pybind11	pybind11	2.13.5	[1,577]	programming
PyBSASeq	pybsaseq	20200623	[1,578]	phylogenetics
PyCharm	pycharm	2018.3, 2023.1.2	[1,579]	programming
Pycharm Pro	pycharm-pro	23.1.3	[1,580]	software
pychopper	pychopper	2.5.0, 2.7.1	[1,581]	phylogenetics, sequencing
PyCogent	pycogent	1.9	[1,582]	biology, genomics
pycoqc	pycoqc	2.5.2	[1,583]	sequencing
PyCUDA	pycuda	2024.1	[1,584]	GPU programming
pydarwin	pydarwin	3.0.0	[1,585]	machine_learning
PyDeface	pydeface	2.0.0	[1,586]	imaging
pydock3	pydock3	20240513	[1,587]	biology
pyEGA3	pyega3	3.4.1, 5.0.2	[1,588]	biology, genomics, utility
PyEXR	pyexr	0.3.10	[1,589]	programming
Pyfaidx	pyfaidx	0.5.2	[1,590]	biology, ngs, sequencing
pyfasta	pyfasta	0.5.2	[1,591]	phylogenetics
pyfastx	pyfastx	2.1.0	[1,592]	bioinformatics
pygenometracks	pygenometracks	3.8	[1,593]	genomics, biology
pygot	pygot	20170518	[1,594]	biology, phylogenetics
pyhdf	pyhdf	0.9.0	[1,595]	library
PyHIST	pyhist	1.0	[1,596]	biology, imaging, image_processing
pymesh	pymesh	0.3.0	[1,597]	math, graphics
pypaftol	pypaftol	1.0	[1,598]	biology, ngs, phylogenetics
PyPHLAWD	pyphlawd	20180416, 20190414	[1,599]	biology, phylogenetics
Pyroms	pyroms	1.0	[1,600]	geospatial
PyRosetta	pyrosetta	r56324	[1,601]	biology, structure, modeling
pyrpipe	pyrpipe	0.0.3	[1,602]	phylogenetics
Pysamstats	pysamstats	1.1.2	[1,603]	phylogenetics
PySLURM	pyslurm	18.08.04	[1,604]	scheduler
Python	python	3.6.3, 3.6.5, 3.8	[1,605]	programming, language
Python-core	python-core	3.6.5, 3.7, 3.8	[1,606]	language, programming
Python2	python	2.7.11	[1,607]	language, programming
PyTorch	ngc-pytorch	1.9.0, 2.3.0, 2.5.0	[1,608]	library, math
pytorch	pytorch	1.9.0, 2.0.1, 2.2.0	[1,609]	library, math
Pytorch Lightning	pytorch_lightning	2.2.0	[1,610]	library, math
PyVCF	pyvcf	0.6.0, 0.6.8	[1,611]	biology, phylogenetics
PyVista	pyvista	0.26.1	[1,612]	phylogenetics
pyweka	pyweka	0.3.18	[1,613]	phylogenetics
QAPA	qapa	1.3.1, 1.3.3	[1,614]	phylogenetics
qcat	qcat	1.1.0	[1,615]	phylogenetics
qctool	qctool	2.0.1	[1,616]	phylogenetics
qcustomplot-pyqt5	qcustomplot-pyqt5	2.1.1.2	[1,617]	plotting, visualization
QD	qd	2.3.22	[1,618]	library, compiler, math
QDD	qdd	3.1.2	[1,619]	biology, genomics, ngs
QGIS	qgis	2.18.0, 3.14.0	[1,620]	geospatial
QIIME2	qiime2	2024.10, 2024.2, 2024.5	[1,621]	biology, genomics
QMCPACK	qmcpack	3.4.0	[1,622]	library
QRNA	qrna	2.0.4	[1,623]	phylogenetics
qsirep	qsiprep	0.19.1	[1,624]	data_mining
QT	qt	5.15.4, 5.15.9, 6.7.3	[1,625]	library
QTL-seq	qtl-seq	2.2.2	[1,626]	biology, sequencing, pipeline
QTLtools	qtltools	1.2, 1.3.1	[1,627]	phylogenetics
Quake	quake	0.3	[1,628]	biology, sequencing
QualiMap	qualimap	2.1.2, 2.3	[1,629]	biology, sequencing, alignment
Quantas	quantas	1.0.4, 1.0.8, 1.0.9	[1,630]	biology, ngs
quantisnp	quantisnp	2	[1,631]	biology, genomics
QuantLib	quantlib	1.34	[1,632]	financial, quantitative analysis
quarTeT	quartet	1.1.6	[1,633]	phylogenetics
QuartetScores	quartetscores	1.0.0	[1,634]	phylogenetics
QUARTO	quarto	1.4.550	[1,635]	desktop publishing
QUAST	quast	5.0.0, 5.0.2, 5.2.0	[1,636]	biology, ngs, sequencing, rna-seq
quickmerge	quickmerge	0.3	[1,637]	phylogenetics
Quickquartet	quickquartet	1.0.0	[1,638]	biology, ngs
QUIP	quip	20201029, 20210626	[1,639]	phylogenetics
QuorUM	quorum	1.0.0	[1,640]	biology
qupath	qupath	0.4.3	[1,641]	biology, Imaging
R	R	4.2, 4.3, 4.4	[1,642]	statistics
r-index	r-index	20190711	[1,643]	phylogenetics
r8s	r8s	1.8, 1.81	[1,644]	phylogenetics
RACA	raca	0.9.1.1	[1,645]	biology, ngs
Racon	racon	1.4.10, 1.4.13, 1.5.0	[1,646]	phylogenetics
RADICAL	radical	0.2	[1,647]	biology, genomics
radinitio	radinitio	1.2.3	[1,648]	biology
radorgminer	radorgminer	0.9	[1,649]	genomics, biology, sequencing
RaGOO	ragoo	1.11	[1,650]	phylogenetics
Ragout	ragout	2.3	[1,651]	genomics
RagTag	ragtag	1.0.0, 2.0.1	[1,652]	phylogenetics
rainbow	rainbow	2.0.4	[1,653]	biology, sequencing
Rainbowfish	rainbowfish	0.1.0	[1,654]	phylogenetics
RAiSD	raisd	2.8, 3.1	[1,655]	phylogenetics
Randfold	randfold	2.0.1	[1,656]	biology, RNA
ranger	ranger	1.9.3	[1,657]	file_management
Rapidnj	rapidnj	2.3.3	[1,658]	biology, phylogenetics
Rapids Base	rapidsai	24.02, 24.08	[1,659]	data_science
rapidsai	rapidsai	23.02, 23.06, 24.04	[1,660]	data_science
rapidtide	rapidtide	1.9.0	[1,661]	phylogenetics
RAPSearch	rapsearch	2.24	[1,662]	biology, phylogenetics
RAPT	rapt	0.5.5	[1,663]	biology,assembly
Rascaf	rascaf	1.0.2	[1,664]	biology
Rasterio	rasterio	1.3.10	[1,665]	geospatial
RATTLE	rattle	1.0	[1,666]	Sequencing
RAVE	rave	2.1	[1,667]	biology, phylogenetics
Raven	raven	1.8.1	[1,668]	assembly
RAxML	raxml	8.2.10, 8.2.12, 8.2.8	[1,669]	biology, phylogenetics
RAxML-NG	raxml-ng	0.9.0, 1.0.2, 1.1.0	[1,670]	phylogenetics
razers3	razers3	3.5.7	[1,671]	biology, phylogenetics
rbp-maps	rbp-maps	0.1.4	[1,672]	phylogenetics
rcapptests	rcapptests	1.0	[1,673]	software
rclone	rclone	1.57.0, 1.58.1, 1.65.2	[1,674]	web
Rcorrector	rcorrector	1.0.4	[1,675]	phylogenetics
RDKit	rdkit	2020092	[1,676]	chemistry
rDnaTools	rdnatools	0.1.3	[1,677]	phylogenetics
read2tree	read2tree	0.1.5	[1,678]	alignment, biology, genomics, phylogenetics
READemption	reademption	1.0.0	[1,679]	phylogenetics
REAPR	reapr	1.0.18	[1,680]	biology, assembly
Rebaler	rebaler	0.2.0	[1,681]	phylogenetics
reCOGnizer	recognizer	1.3.3	[1,682]	phylogenetics
recon	recon	1.08	[1,683]	biology, sequencing
recycler	recycler	0.7	[1,684]	biology, sequencing
Redis	redis	2.8.13, 2.8.19	[1,685]	database, data_science
REDItools2	reditools2	20200701	[1,686]	phylogenetics
Redundans	redundans	0.14a	[1,687]	biology, phylogenetics
refmaker	refmaker	1.0	[1,688]	biology, phylogenomics
ReFrame	reframe	3.2	[1,689]	performance_analysis, utility
regtools	regtools	0.5.2	[1,690]	biology, rna-seq, genomics
release	release	12082021	[1,691]	molecular_dynamics, machine_learning
ReLERNN	relernn	1.0.0	[1,692]	biology/AI
RELION	relion	3.0.2, 3.1.0, 4.0.1	[1,693]	biology, imaging
RelocaTE2	relocate2	2.0.1	[1,694]	phylogenetics
REMORA	remora	1.8.3, 1.8.5, 2.0.0	[1,695]	performance_analysis
REPdenovo	repdenovo	20170222	[1,696]	biology, phylogenetics
RepeatAnalysis	repeatanalysis	0.10.0, 0.12.2	[]	biology, phylogenetics
RepeatAnalysisTools	repeatanalysistools	20210506	[1,697]	biology, genomics, sequencing, utility
RepeatExplorer	repeatexplorer	20150506, 20180517	[1,698]	biology, ngs
RepeatMasker	repeatmasker	4.0.9, 4.1.1, 4.1.7	[1,699]	biology
RepeatModeler	repeatmodeler	1.0.8, 2.0	[1,700]	biology
repeatscout	repeatscout	1.0.5	[1,701]	biology
RepeatSeq	repeatseq	0.8.2	[1,702]	phylogenetics
reptile	reptile	1.1	[1,703]	biology, ngs, math
ResFinder	resfinder	4.0	[1,704]	biology, genomics
resistify	resistify	0.1.0	[1,705]	biology, molecular
Resistome	resistome	20170111	[1,706]	phylogenetics
Resolve	resolve	18.1.4	[1,707]	Graphics, Utility, Visualization
RevBayes	revbayes	1.0.9, 1.1.1, 1.2.3	[1,708]	biology, phylogenetics
RFAA	rfaa	20240323	[1,709]	biology, genomics
RFMIX	rfmix	2.03	[1,710]	phylogenetics
RGAugury	rgaugury	2.2	[1,711]	sequencing, biology
RGI	rgi	4.2.2, 5.1.1, 6.0.2	[1,712]	phylogenetics
RGIS	rgis	20180211, 20180814	[1,713]	geospatial
RHash	rhash	1.3.3	[1,714]	programming
RiboCode	ribocode	1.2.11	[1,715]	phylogenetics
ribodetector	ribodetector	0.3.1	[1,716]	biology
riboPicker	ribopicker	0.4.3	[1,717]	biology, sequencing
RiboTaper	ribotaper	1.3.1a	[1,718]	phylogenetics
Ribotricer	ribotricer	1.3.3	[1,719]	phylogenetics
RIGERJ	rigerj	2.0.2	[1,720]	phylogenetics
rMATS turbo	rmats-turbo	4.1.2	[1,721]	biology, sequencing, genomics
rmats2sashimiplot	rmats2sashimiplot	2.0.3, 2.0.4	[1,722]	phylogenetics
Rmpi	Rmpi	3.5.1, 4.0.3	[1,723]	statistics, programming
rnabloom	rnabloom	2.0.1	[1,724]	biology, ngs, sequencing, rna-seq
rnaeditingindexer	rnaeditingindexer	12152022	[1,725]	data_mining
RNAFramework	rnaframework	2.7.2	[1,726]	biology, RNA, sequencing
RNAhybrid	rnahybrid	2.1.1	[1,727]	biology, genomics
rnalysis	rnalysis	3.7.0	[1,728]	sequencing, biology
RNAmmer	rnammer	1.2	[1,729]	biology, rna-seq
rnaQUAST	rnaquast	1.5.1	[1,730]	biology, ngs, sequencing, rna-seq
RNAsalsa	rnasalsa	0.8.1	[1,731]	biology, phylogenetics
rnaseqlib	rnaseqlib	20150721	[1,732]	biology, phylogenetics, rna-seq
RNAstructure	rnastructure	6.3	[1,733]	biology, sequencing
Roary	roary	3.12.0, 3.13.0, 3.4.1	[1,734]	biology, genomics
roguenarok	roguenarok	20230418	[1,735]	phylogenetics
ROOT	root	5.34.17, 6.0, 6.06.02	[1,736]	data_science
ROOTPy	rootpy	20160323	[1,737]	data_science
Rosetta	rosetta	2019.35.60890, 2021.16.61629, 2023.11.30	[1,738]	biology, structure, modeling
RoseTTAFold	rosettafold	1.0.0	[1,739]	phylogenetics
rrnaselector	rrnaselector	1.0	[1,740]	biology, sequencing
RSEG	rseg	0.4.8	[1,741]	biology, genomics
RSEM	rsem	1.2.31, 1.2.7, 1.3.3	[1,742]	biology, ngs, sequencing
RSeQC	rseqc	2.6.4, 3.0.0, 5.0.3	[1,743]	biology, ngs, rna-seq
RStudio	rstudio	1.4, 2021.09.0, 2022.02.3	[1,744]	statistics
rsync	rsync	3.2.7	[1,745]	software, utility
RTGTools	rtgtools	3.7.1	[1,746]	biology, ngs
Ruby	ruby	2.5.1	[1,747]	programming, language
run_dbcan	run_dbcan	4.0.0, 4.1.4	[1,748]	biology
Rust	rust	1.62.1, 1.70.0, 1.76.0	[1,749]	programming
rvtests	rvtests	2.1.0	[1,750]	genomics, biology, sequencing
S.A.G.E	s.a.g.e	6.4.2	[1,751]	phylogenetics
Sabre	sabre	1.0	[1,752]	phylogenetics
saffrontree	saffrontree	0.1.2	[1,753]	phylogenetics
saige	saige	0.45.0	[1,754]	genomics
Sailfish	sailfish	0.6.3	[1,755]	biology, genomics, ngs, rna-seq
Salmon	salmon	1.5.2, 1.8.0, 1.9.0	[1,756]	biology, rna-seq
SALSA	salsa	20171009, 20191001, 20220408	[1,757]	biology, ngs
samapi	samapi	0.4.0	[1,758]	Imaging
Sambamba	sambamba	0.6.3, 0.6.6, 0.6.9	[1,759]	biology, ngs
samblaster	samblaster	0.1.14, 0.1.24	[1,760]	biology, ngs, sequencing
sampledock	sampledock	0.5.1	[1,761]	molecular_dynamics, AI
SAMStat	samstat	1.08	[1,762]	biology, ngs, sequencing
Samtools	samtools	1.7, 1.8, 1.9	[1,763]	biology, ngs, sequencing
SAS	sas	9.4.8	[1,764]	statistics, data_science
Sate	sate	2.2.7	[1,765]	biology, phylogenetics
Satsuma	satsuma	3.0	[1,766]	phylogenetics
Satsuma2	satsuma2	20161123, 3.1	[1,767]	phylogenetics
sc-im	scim	0.8.2	[1,768]	utility, visualization
Scala	scala	2.11.5, 3.0.1	[1,769]	programming, language
Scalablast	scalablast	2.4.53	[1,770]	biology, genomics
ScaLAPACK	scalapack	2.1.0, 2.2.0, 2.2.1.5	[1,771]	programming, library
scallop	scallop	0.10.5	[1,772]	phylogenetics
Scalpel	scalpel	0.1.1, 0.5.3	[1,773]	biology, ngs
scanpy	scanpy	1.8.2	[1,774]	biology
scapp	scapp	0.1.4	[1,775]	genomics, assembly
scGPT	scgpt	0.1.2	[1,776]	Biology, Data_Science, Genomics
Schrodinger Maestro	maestro	2024-1	[1,777]	chemistry, molecular_dynamics
Schrodinger Suite	schrodinger	2023-2, 2023-3, 2024-2	[1,778]	chemistry, molecular_dynamics
sciann	sciann	0.7.0.1	[1,779]	machine_learning
scikit-learn	scikit-learn	1.4.1.post1	[1,780]	Data_Science
scipion	scipion	3.0.0, 3.1.0	[1,781]	image_processing
Scipion	scipion	1.2	[1,782]	image_processing
SCIrun	scirun	5.0.Z	[1,783]	phylogenetics
scnic	scnic	1.0	[1,784]	library
Scoary	scoary	1.6.16	[1,785]	phylogenetics
Scons	scons	2.5.1, 3.1.2	[1,786]	programming
SCOP	scop	20180311	[1,787]	biology, assembly
score-sde	score-sde	20221110	[1,788]	Machine_Learning
Scrappie	scrappie	1.4.2	[1,789]	biology, genomics
SCRATCH-1D	scratch1d	1.0, 1.2, 2.0	[1,790]	biology, ngs
Screen	screen	4.8.0, 4.9.1	[1,791]	programming, shell
SCRIPTURE	scripture	20101211	[1,792]	biology, genomics
scVelo	scvelo	0.2.5	[1,793]	biology
Scythe	scythe	0.991	[1,794]	biology, ngs
sdsl	sdsl	2.1.1	[1,795]	library, compiler
SE-MEI	se-mei	0.1.0	[1,796]	phylogenetics
SeCaPr	secapr	1.1.12, 2.0.2, 2.1.1	[1,797]	phylogenetics
seekdeep	seekdeep	3.0.1	[1,798]	biology, sequencing
Segemehl	segemehl	0.1.9, 0.3.4	[1,799]	biology, ngs, sequencing
segment-liftover	segment-liftover	20211021	[1,800]	biology, genomics
seismometer	seismometer	0.2.1	[1,801]	AI, utility
SemiBin	semibin	2.1.0	[1,802]	bioinformatics
SEPP	sepp	20160614	[1,803]	biology, phylogenetics
Seq-Gen	seq-gen	1.3.3	[1,804]	biology, phylogenetics
seq_crumbs	seq_crumbs	20150120	[1,805]	biology, sequencing, genomics, utility
SeqKit	seqkit	0.8.0, 2.0.0, 2.4.0	[1,806]	biology, phylogenetics
seqmagick	seqmagick	0.8.4	[1,807]	biology
SeqMap	seqmap	1.0.13	[1,808]	biology, sequencing, ngs
seqmule	seqmule	1.2.6	[1,809]	biology, sequencing
SEQPower	seqpower	1.1.1	[1,810]	genomics, phylogenetics
SeqPrep	seqprep	0.5, 1.1	[1,811]	biology, ngs, sequencing
seqscreen	seqscreen	3.3	[1,812]	sequencing, biology
seqtk	seqtk	1.3, 20140729	[1,813]	biology, genomics, ngs
SEQuel	sequel	1.0.1	[1,814]	biology, ngs
SequelQC	sequelqc	1.1.0	[1,815]	phylogenetics
seqwish	seqwish	0.7, 20190509	[1,816]	phylogenetics
SeqyClean	seqyclean	1.8.10	[1,817]	biology, ngs, sequencing
SeSiMCMC	sesimcmc	4.36	[1,818]	biology, sequencing
SExtractor	sextractor	2.19.5	[1,819]	astronomy
SHAPE-MaP	shapemap	1.2	[1,820]	biology, phylogenetics
SHAPEIT	shapeit	2.12, 2.5	[1,821]	biology, variant_calling
SHAPEIT4	shapeit4	4.2.2	[1,822]	biology, sequencing
ShapeMapper	shapemapper	2.1.3, 2.1.5, 2.2.2	[1,823]	biology, phylogenetics
SHARCGS	sharcgs	1.2.11	[1,824]	biology, ngs, de_novo
Shasta	shasta	0.1.0	[1,825]	phylogenetics
SHEsisPlus	shesisplus	1.0, 1.01	[1,826]	biology, genomics
shogun	shogun	6.1.3	[1,827]	phylogenetics
Shortbred	shortbred	0.9.4	[1,828]	phylogenetics
shortstack	shortstack	4.0.3	[1,829]	biology
shovill	shovill	1.1.0	[1,830]	genomics, sequencing, biology
SHRiMP	shrimp	2.2.3	[1,831]	biology, genomics, ngs
shustring	shustring	2.6	[1,832]	biology, sequencing
SibeliaZ	sibeliaz	1.2.2, 1.2.3, 1.2.4	[1,833]	biology, genomics, alignment
SICER	sicer	1.1	[1,834]	biology, chip-seq
Sickle	sickle	1.200, 1.33	[1,835]	biology, ngs
Siesta	siesta	3.2, 4.1b2, 4.1b3	[1,836]	chemistry
SIFT	sift	4.0.3b	[1,837]	biology, genomics
SIGffRid	sigffrid	1.1	[1,838]	phylogenetics
SignalP	signalp	4.1c, 5.0b, 6.0h	[1,839]	biology, phylogenetics
SiLiX	silix	1.2.11, 1.3.0	[1,840]	phylogenetics
silo	silo	4.7	[1,841]	library
sim4	sim4	20121010	[1,842]	biology, genomics
Sim4Life	sim4life	7.0.1, 7.2.3	[1,843]	biology, simulation
Simka	simka	1.5.3	[1,844]	phylogenetics
SimNIBS	simnibs	3.2.1, 4.0.0, 4.1.0	[1,845]	phylogenetics
SimSeq	simseq	4.12.2011	[1,846]	biology, ngs, phylogenetics
Simulia	simulia	2019	[1,847]	simulation, visualization
SInC	sinc	20140120	[1,848]	biology, phylogenetics
sine_scan	sine_scan	1.1.1	[1,849]	phylogenetics
Singularity	singularity	3.10.4	[1,850]	workflow_automation
SIPeS	sipes	2.0	[1,851]	biology, chip-seq
SIRIL	siril	1.2.0	[1,852]	image processing
sisl	sisl	0.8.3	[1,853]	physics, structure
Ska2	ska2	0.3.0	[1,854]	alignment, biology, genomics
skmer	skmer	3.2.1	[1,855]	genomics, biology
Slamdunk	slamdunk	0.4.1, 0.4.2	[1,856]	phylogenetics
SLAW	slaw	20211217	[1,857]	chemistry, spectroscopy
Sleap	sleap	1.3.3	[1,858]	machine learning
Slicer	slicer	4.3.1, 5.0.3, 5.2.1	[1,859]	biology, neuroscience, imaging
slicer	slicer	5.6.2	[1,860]	biology, neuroscience, medicine, imaging
slivar	slivar	0.3.0	[1,861]	biology
slow5tools	slow5tools	0.5.1, 1.1.0	[1,862]	biology, sequencing
SLR	slr	1.0.0	[1,863]	genomics
slurm-drmaa	slurm-drmaa	1.1.3, 1.1.4, 1.1.4.1	[1,864]	library, scheduler, programming
smalt	smalt	0.7.6	[1,865]	biology, phylogenetics
SMARTdenovo	smartdenovo	20180219	[1,866]	biology, phylogenetics
smartie-sv	smartie-sv	20180308	[1,867]	phylogenetics
SMC++	smcpp	1.15.4	[1,868]	biology, genomics, sequencing
Smetana	smetana	1.1.0	[1,869]	phylogenetics
SMR	smr	1.03	[1,870]	biology, genomics
SMRT-SV	smrtsv2	2.0.0	[1,871]	biology, ngs
SMS	sms	1.7	[1,872]	biology
Smudgeplot	smudgeplot	0.2.4	[1,873]	phylogenetics
Snakemake	snakemake	7.5.0, 8.10.8, 8.4.0	[1,874]	biology, workflow_automation
SNAP	snap	2.0.0, 2.0.3, 20100728	[1,875]	biology, sequencing
SNAPE-pooled	snape-pooled	20130407	[1,876]	biology, variant_calling
SNeP	snep	1.1	[1,877]	biology, phylogenetics
Sniffles	sniffles	1.0.11, 1.0.6, 1.0.8	[1,878]	phylogenetics
Sniffles2	sniffles2	2.0.6	[1,879]	biology
Snippy	snippy	20160419, 4.6.0	[1,880]	biology, phylogenetics
SNP-Pipeline	snp-pipeline	1.0.1	[1,881]	biology, phylogenetics
SNP-sites	snp-sites	2.0.3	[1,882]	biology, variant_calling
snp2hla	snp2hla	1.0.3	[1,883]	biology, genomics
SnpEff	snpeff	5.0, 5.1d, 5.2e	[1,884]	biology, annotation
snpflip	snpflip	20190515	[1,885]	biology, phylogenetics
SNPGenie	snpgenie	20190620	[1,886]	phylogenetics
SNPhylo	snphylo	20140701, 3.0	[1,887]	biology, phylogenetics
SNPsplit	snpsplit	0.5.0	[1,888]	biology, sequencing
SNPTEST	snptest	2.5.2	[1,889]	phylogenetics
SOAPaligner	soapaligner	2.21	[1,890]	phylogenetics
SOAPdenovo	soapdenovo	1.05, 2.04	[1,891]	biology, ngs
SOAPdenovo-Trans	soapdenovo-trans	1.01, 1.03	[1,892]	biology, ngs
SOAPec	soapec	2.03	[1,893]	biology, phylogenetics
SOAPnuke	soapnuke	2.1.0	[1,894]	phylogenetics
SOAPsplice	soapsplice	1.10	[1,895]	biology, ngs
SODA	soda	20200930	[1,896]	biology
SOLAR	solar	8.4.2	[1,897]	phylogenetics
SomaticSeq	somaticseq	3.6.2	[1,898]	phylogenetics
SortaDate	sortadate	20190705	[1,899]	phylogenetics
SortMeRNA	sortmerna	2.1, 4.0, 4.3.6	[1,900]	biology, sequencing, ngs
SourceTracker2	sourcetracker2	2.0.1	[1,901]	phylogenetics
Sourmash	sourmash	2.0.1, 4.5.0	[1,902]	genomics
SoX	sox	14.4.2	[1,903]	phylogenetics
spacemake	spacemake	0.5.5	[1,904]	sequencing
SpaceRanger	spaceranger	2.1.0, 3.0.1, 3.1.1	[1,905]	phylogenetics
SPAdes	spades	3.7.1, 3.8.0, 4.0.0	[1,906]	biology, ngs
SparCC	sparcc	201608	[1,907]	biology
Spark	spark	2.2.0, 3.1.1	[1,908]	utility
sparsehash	sparsehash	2.0.3	[1,909]	web, programming
SPARTA+	sparta+	2.60	[1,910]	chemistry
Spec2nii	spec2nii	0.3.4	[1,911]	phylogenetics
SpeedSeq	speedseq	0.1.2	[1,912]	phylogenetics
Spidey	spidey	20150922	[1,913]	biology, genomics
SpinalCordToolbox	spinalcordtoolbox	5.4	[1,914]	phylogenetics
SplAdder	spladder	2.4.2	[1,915]	phylogenetics
SpliceGrapher	splicegrapher	0.2.5	[1,916]	biology, sequencing
SpliceTrap	splicetrap	0.90.5	[1,917]	biology, genomics, ngs
SPM	spm	12b, 8, 8r5236	[1,918]	biology
spruceup	spruceup	2019.2.3	[1,919]	phylogenetics
Sputnik	sputnik	1.0	[1,920]	biology
spyder	spyder	4.1.4, 5.1.1, 5.3.2	[1,921]	programming
SQANTI	sqanti	1.2	[1,922]	phylogenetics
SQANTI2	sqanti2	5.0	[1,923]	phylogenetics
SQANTI3	sqanti3	1.6, 4.2, 5.1.1	[1,924]	phylogenetics
SQL Developer	sqldeveloper	4.1.2	[1,925]	programming, database
SQLite	sqlite3	3.33.0, 3.45.3, 3.8.8.2	[1,926]	database
squashfuse	squashfuse	0.5.2	[1,927]	containers, library
SqueezeMeta	squeezemeta	1.4.0, 1.5.2, 1.6.0	[1,928]	phylogenetics
squigglekit	squigglekit	1.0.0	[1,929]	visualization, biology
squigglenet	squigglenet	1.0	[1,930]	sequencing, biology
SRA	sra	3.0.2, 3.0.5, 3.0.8	[1,931]	biology, ngs
sra-human-scrubber	sra_human_scrubber	1.1	[1,932]	genomics
SRAssembler	srassembler	1.0.0	[1,933]	phylogenetics
srst2	srst2	0.2.0	[1,934]	sequencing, genomics, biology
SSM	ssm	20210511	[1,935]	phylogenetics
SSPACE	sspace	2.0, 3.0	[1,936]	biology, ngs
ssr_pipeline	ssr_pipeline	0.951	[1,937]	biology, sequencing
SSU-ALIGN	ssu-align	0.1.1	[1,938]	phylogenetics
stable-diffusion	stable-diffusion	20221116	[1,939]	machine_learning
Stacks	stacks	2.53, 2.55, 20190403	[1,940]	biology, genomics, ngs
stacks	stacks	2.61, 2.64	[1,941]	biology, genomics, ngs
Staden	staden	1.14.6	[1,942]	biology, phylogenetics
Stampy	stampy	1.0.31	[1,943]	biology, sequencing
staphb-toolkit	staphb-toolkit	1.2.0, 1.3.10, 2.0.1	[1,944]	biology
STAR	star	2.7.5c, 2.7.6a, 2.7.9a	[1,945]	biology, ngs, rna-seq
STAR-CCM+	starccm+	14.04.011, 15.02.009, 8.06	[1,946]	fluid_dynamics
STAR-Fusion	star-fusion	1.13.0, 1.3.1, 1.9.1	[1,947]	biology, sequencing
starseqr	starseqr	0.6.7	[1,948]	phylogenetics
Stata	stata	10.1, 13, 18	[1,949]	statistics
Strainline	strainline	1.0	[1,950]	biology
Strelka	strelka	2.9.2	[1,951]	biology, genomics
stringMLST	stringmlst	0.4	[1,952]	biology, chip-seq
Stringtie	stringtie	2.0.4, 2.1.3b, 2.2.3	[1,953]	biology, ngs, sequencing, alignment
Structure	structure	2.3.3, 2.3.4	[1,954]	biology, genomics
Structure_threader	structure_threader	1.3.10	[1,955]	utility, structure
stumpy	stumpy	1.11.1	[1,956]	library, math
stylegan3	stylegan3	20211028	[1,957]	ai, image_processing
SU2	su2	7.0.6	[1,958]	phylogenetics
subphaser	subphaser	1.2.6	[1,959]	sequencing, biology
Subread	subread	2.0.0, 2.0.3, 2.0.6	[1,960]	biology, sequencing, variant_calling
Subversion	subversion	1.14.2, 1.9.7	[1,961]	revision_control
SUMO	sumo	1.2.0, 1.20.0, 1.9.2	[1,962]	phylogenetics
SUNDIALS	sundials	2.5.0, 3.0.0, 6.1.1	[1,963]	math
supercell	supercell	20170602	[1,964]	biology, ngs
SuperCRUNCH	supercrunch	1.2.1	[1,965]	phylogenetics
SUperLU-DIST	superlu_dist	6.0.1, 8.2.1	[1,966]	linear algebra
Supernova	supernova	1.2.1, 2.0.0, 2.1.1	[1,967]	biology, phylogenetics, ngs
SUPPA	suppa	2.3	[1,968]	phylogenetics
support	support	24.03.20	[1,969]	ufrc, admin, tools
SurrealDB	surrealdb	1.3.1, 1.5.0, 2.0.1	[1,970]	database
Survival_Kit	survival_kit	6.12	[1,971]	healthcare
SURVIVOR	survivor	1.0.6	[1,972]	phylogenetics
SVDetect	svdetect	0.8b	[1,973]	biology, ngs, genomics
svim	svim	1.4.2	[1,974]	biology
svim-asm	svim-asm	1.0.2	[1,975]	biology
svtyper	svtyper	0.7.1	[1,976]	biology, genomics, sequencing
swarm	swarm	1.2.11	[1,977]	data_science
Sweed	sweed	3.3.2	[1,978]	biology, phylogenetics
SWIG	swig	3.0.8, 4.1.1, 4.2.1	[1,979]	library, programming, compiler
SWSC-EN	swsc-en	1.0.0	[1,980]	phylogenetics
Synima	synima	20210908	[1,981]	phylogenetics
syri	syri	1.5.4	[1,982]	genomics, biology
TACO	taco	0.7.3	[1,983]	phylogenetics
Taiyaki	taiyaki	5.0.1	[1,984]	phylogenetics
talesf	talesf	20160814	[1,985]	phylogenetics
talon	talon	5.0	[1,986]	biology, sequencing
Tandem-Genotypes	tandem-genotypes	1.4.0	[1,987]	phylogenetics
Tantan	tantan	13	[1,988]	imaging, ngs, genomics
Tapestri	tapestri	2.0.1	[1,989]	phylogenetics
tapir	tapir	20160825	[1,990]	biology, phylogenetics
TAPIS	tapis	1.2.1	[1,991]	biology, sequencing
TASSEL	tassel	5.2.20, 5.2.29, 5.2.82	[1,992]	biology, genomics, sequencing
TAU	tau	2.23, 2.26, 2.26.3	[1,993]	library, performance_analysis
Tax4Fun	tax4fun	0.3.1	[1,994]	phylogenetics
taxMaps	taxmaps	0.1	[1,995]	biology, phylogenetics, genomics
TaxonKit	taxonkit	0.13.0, 0.9.0	[1,996]	phylogenetics
Taxtastic	taxtastic	0.5.7, 0.9.1	[1,997]	biology, genomics
tbb	tbb	2017_20161128	[1,998]	library
tbprofiler	tbprofiler	4.4.1	[1,999]	genomics, biology
tcllib	tcllib	1.18	[2,000]	library
tcoffee	tcoffee	10.00.r1613, 9.03.r1318	[2,001]	biology
TDNAscan	tdnascan	20210304	[2,002]	phylogenetics
Tecplot 360 EX	tecplot	2015R1	[2,003]	math, animation, fluid_dynamics, simulation
tellseq	tellseq	1.0.0	[2,004]	sequencing, phylogenetics
TEMP	temp	20170731	[2,005]	phylogenetics
TEMP2	temp2	0.1.4	[2,006]	phylogenetics
TensorFlow	ngc-tensorflow	2.6.0, 2.7.0, 2.8.0	[2,007]	library, math
TESS	tess	2.3.1	[2,008]	biology, genomics, math
tesseract	tesseract	5.3.4	[2,009]	OCR
Test	test	1.0	[2,010]	shell
TetGen	tetgen	1.5.0	[2,011]	modeling
TEToolkit	tetoolkit	1.5.1	[2,012]	biology, sequencing
TEtools	tetools	20180213	[2,013]	biology, phylogenetics
Texlive	texlive	20191127, 2020, 2023	[2,014]	documentation
textract	textract	1.6.1	[2,015]	data_science, file_management
TGICL	tgicl	2.1	[2,016]	biology, ngs, sequencing
TGSGapCloser	tgsgapcloser	1.0.3	[2,017]	phylogenetics
the_silver_searcher	the_silver_searcher	2.2.0	[2,018]	search
Themisto	themisto	0.2.0, 1.1.0	[2,019]	genomics, alignment
Tiara	tiara	1.0.2	[2,020]	phylogenetics
tidk	tidk	0.2.41	[2,021]	bioinformatics
tiff	tiff	3.8.0, 4.0.10, 4.6.0	[2,022]	imaging
tighe-r	tighe-r	4.2, studio	[2,023]	statistics
Tigmint	tigmint	1.1.2	[2,024]	phylogenetics
TMHMM	tmhmm	2.0	[2,025]	biology
Tmux	tmux	2.9, 3.1, 3.4	[2,026]	programming
TNTBLAST	tntblast	2.04	[2,027]	biology
ToFU2	tofu2	v17	[2,028]	biology, ngs, sequencing
toil	toil	3.3.0, 3.3.3	[2,029]	biology
Tombo	tombo	1.4, 1.5, 1.5.1	[2,030]	biology, genomics, ngs
topd	topd	4.6	[2,031]	phylogenetics
Tophat	tophat	2.1.0, 2.1.1, 2.1.2	[2,032]	biology, ngs, sequencing
torch-geometric	torch-geometric	1.3.2, 2.0.4	[2,033]	math, machine_learning
TotalView	totalview	8.12	[2,034]	programming
TPMcalculator	tpmcalculator	0.0.3	[2,035]	phylogenetics
TPP	tpp	4.7.0, 4.7.1, 5.0.0	[2,036]	biology, chemistry, spectroscopy
TraCeR	tracer	20160519	[2,037]	biology, phylogenetics
TrackTools	tracktools	2011	[2,038]	utility
TrackVis/DTK	trackvis	0.5.2.2, 0.6.0.1	[2,039]	biology, neuroscience, imaging
Tracula	tracula	5.3.2014_05_26	[2,040]	biology, neuroscience, imaging
traitRate	traitrate	1.1	[2,041]	biology, genomics
Trans-ABySS	transabyss	2.0.1	[2,042]	biology, phylogenetics
TransDecoder	transdecoder	5.3.0, 5.4.0, 5.5.0	[2,043]	biology, ngs
TRANSIT	transit	2.5.2, 3.2.3	[2,044]	phylogenetics
Transrate	transrate	1.0.1, 1.0.3	[2,045]	biology, assembly
TransVar	transvar	2.3.3	[2,046]	biology, phylogenetics
TreeBreaker	treebreaker	20160621	[2,047]	biology, phylogenetics
TreeMix	treemix	1.12	[2,048]	biology, phylogenetics
treePL	treepl	20150305	[2,049]	biology, phylogenetics
TREEPUZZLE	treepuzzle	5.3	[2,050]	biology, phylogenetics
TreeShrink	treeshrink	1.3.1, 1.3.2, 1.3.9	[2,051]	phylogenetics
TreeTime	treetime	0.10.1, 0.7.5, 0.8.1	[2,052]	phylogenetics
trelis	trelis	16.3	[2,053]	math
TRF	trf	4.04, 4.09.1	[2,054]	biology, genomics
trgt	trgt	0.4.0	[2,055]	genetics, biology
Trilinos	trilinos	12.6.4, 14.4.0, 16.6.0	[2,056]	math
Trim Galore	trim_galore	0.5.0, 0.6.10, 0.6.5	[2,057]	biology, ngs
trim_isoseq_polya	trim_isoseq_polya	0.0.3	[2,058]	biology, genomics, sequencing
trimAl	trimal	1.2, 1.4.1	[2,059]	biology, genomics, alignment
trimesh	trimesh	3.20.2	[2,060]	graphics, math
TriMetAss	trimetass	1.1	[2,061]	biology, ngs
Trimmomatic	trimmomatic	0.33, 0.36, 0.39	[2,062]	biology, ngs
Trinity	trinity	r20130225, r20131110, r20140413	[2,063]	biology, ngs, sequencing, rna-seq
Trinotate	trinotate	3.0.1, 3.2.0, 4.0.0	[2,064]	biology
triobinning	triobinning	0.2.3	[2,065]	genomics, biology
TRIPLEC	triplec	1.0	[2,066]	biology
TRITONSERVER	tritonserver	21.08, 23.01	[2,067]	machine_learning
tRNAscan-Se	trnascan-se	1.23, 2.0.12	[2,068]	biology, ngs
TRUST4	trust4	1.0.2b	[2,069]	phylogenetics
trvz	trvz	0.4.0	[2,070]	genetics, biology
Trycycler	trycycler	0.4.2	[2,071]	phylogenetics
TURBOMOLE	turbomole	7.4.1	[2,072]	chemistry
TWINSCAN	twinscan	4.1.2	[2,073]	biology, genomics
Ubuntu	ubuntu	20.04, 22.04, 24.04	[2,074]	linux
UCSC	ucsc	20200320, 20210803	[2,075]	genomics
ucsc-fafiltern	ucsc-fafiltern	377	[2,076]	phylogenetics
ucsc-maskoutfa	ucsc-maskoutfa	377	[2,077]	phylogenetics
UCX	ucx	1.11.2, 1.15.0, 1.9.0	[2,078]	programming, library
UDUNITS	udunits	2.2.17	[2,079]	library, data_science, math
UFCG	ufcg	1.0.3, 1.0.5	[2,080]	biology, genomics
ufraw	ufraw	0.22	[2,081]	data_mining
ugtm	ugtm	1.1.6	[2,082]	statistics, modeling
UKFractography	ukfractography	20200127	[2,083]	phylogenetics
umi-tools	umi-tools	0.5.5, 1.1.4, 1.1.5	[2,084]	phylogenetics
UMICollapse	umicollapse	02072021	[2,085]	chemestry
UNAFold	unafold	3.8	[2,086]	biology, genomics, rna
Unanimity	unanimity	20171108, 3.4.1	[2,087]	programming, library, compiler
UNCALLED	uncalled	2.2	[2,088]	biology, genomics
Unicycler	unicycler	0.4.8	[2,089]	phylogenetics
Unrar	rar	0.0.1, 4.20	[2,090]	utility
unrealengine editor	unrealengine	5.2.1	[2,091]	programming, design, digitaltwin
uproc	uproc	1.2.0	[2,092]	biology, genomics
UPSCAYL	upscayl	2.5.5, 2.8.1, 2.9.1	[2,093]	image processing
uropa	uropa	4.0.2	[2,094]	genomics, sequencing, biology
USEARCH	usearch	9.0.2132, 9.1.13, 9.2.64	[2,095]	biology, alignment, sequencing
UShER	usher	0.1.4, 0.4.1, 0.5.2	[2,096]	phylogenetics
V-Phaser	vphaser2	02112013	[2,097]	biology, phylogenetics
v-pipe	v-pipe	2.0.0, 2.99.3	[2,098]	biology, genomics, sequencing
Valgrind	valgrind	3.11.0, 3.15.0, 3.8.1	[2,099]	programming
Valouev	valouev	20160325	[2,100]	biology, phylogenetics
vamb	vamb	3.0.2	[2,101]	biology
VAMPIR	vampir	9.1	[2,102]	performance_analysis
VarDictJava	vardictjava	1.6.0, 20160521, 20170531	[2,103]	biology, phylogenetics
VARI	vari	0.7.0	[2,104]	math, visualization
varnorm	varnorm	0.21	[2,105]	biology
varpipe-wgs	varpipe-wgs	20230222	[2,106]	sequencing, biology
VarScan	varscan	2.3.6	[2,107]	biology, ngs
VarSim	varsim	0.8.4, 0.8.6	[2,108]	phylogenetics
VarSimLab	varsimlab	20180220, 20180921	[2,109]	biology, simulation, genomics
vasp	vasp	5.4.4, 6.1.0, 6.2.0	[2,110]	chemistry
VASP	vasp	5.4.4, 6.4.1, 6.4.3	[2,111]	chemistry
vaspkit	vaspkit	1.2.5, 1.4.1	[2,112]	phylogenetics
VAST-TOOLS	vast-tools	2.5.1, 20150506	[2,113]	biology, rna-seq, ngs
VCF-kit	vcf-kit	0.2.6	[2,114]	phylogenetics
vcf-validator	vcfvalidator	0.6	[2,115]	biology, phylogenetics
vcfanno	vcfanno	0.2.8, 0.3.3	[2,116]	biology, phylogenetics
vcflib	vcflib	1.0.1	[2,117]	biology, genomics
vcftools	vcftools	0.1.15, 0.1.16, 0.1.9	[2,118]	biology, genomics
vcontact	vcontact	20190512	[2,119]	phylogenetics
VDJtools	vdjtools	1.1.7, 1.2.1	[2,120]	biology, phylogenetics
Velocyto	velocyto	0.17	[2,121]	biology, RNA seq
Velvet	velvet	1.2.10, 1.2.10-long	[2,122]	biology, genomics
VEP	vep	83, 88.8, 92	[2,123]	biology, genomics, ngs
Verkko	verkko	1.3.1	[2,124]	genomics
vermouth-martinize	vermouth-martinize	0.11.0	[2,125]	biology, molecular
Vermouth-martinize	vermouth-martinize	0.7.2	[2,126]	phylogenetics
VeryFastTree	veryfasttree	3.0.1	[2,127]	phylogenetics
VFUparr	vfuparr	20240320	[2,128]	sequencing, biology
vg	vg	1.45.0, 1.49.0, 1.55.0	[2,129]	phylogenetics
vibrant	vibrant	1.2.0	[2,130]	genomics
ViennaRNA	viennarna	2.2.6, 2.4.18	[2,131]	biology, rna-seq
ViewBS	viewbs	0.1.10, 0.1.9	[2,132]	phylogenetics
vigor4	vigor4	20200702	[2,133]	biology, annotation
Vim	vim	8.1.1566, 8.2.2465, 9.0.1946i	[2,134]	programming, language
vina-gpu	vina-gpu	20230530	[2,135]	biology
viralmsa	viralmsa	1.1.10, 1.1.12, 1.1.14	[2,136]	phylogenetics
VIRCLUST	virclust	2.0	[2,137]	biology, annotation
viromescan	viromescan	2015	[2,138]	genomics, biology
VirSieve	virsieve	20210406	[2,139]	biology, pipeline
virsorter	virsorter	2.2.3	[2,140]	genomics
VirtualCell	virtualcell	7.1	[2,141]	phylogenetics
VIRULIGN	virulign	1.0.2	[2,142]	phylogenetics
VirusDetect	virusdetect	1.7	[2,143]	phylogenetics
VirusFinder	virusfinder	2.0	[2,144]	biology, phylogenetics
visit	visit	3.3.3, 3.3.3-mpi, 3.3.3_mpi	[2,145]	visualization, animation
VISPR	vispr	0.4.14	[2,146]	phylogenetics
vmamba	vmamba	2.0	[2,147]	machine_learning
VMD	vmd	1.9.1, 1.9.3, 1.9.4	[2,148]	visualization, animation, graphics
vray	vray	6.10.04	[2,149]	graphics
vscode	vscode	1.86.2, 1.87, 1.92	[2,150]	programming
VSearch	vsearch	2.22.1, 20151022, 20161209-2.3.4	[2,151]	biology, ngs
vt	vt	0.57721, 20140903, 20160129	[2,152]	biology, genomics
VTC	vtc	0.9.3	[2,153]	biology
VTK	vtk	9.1.0, 9.2.6, 9.3.0	[2,154]	biology, neuroscience, imaging
w2rap-contigger	w2rap-contigger	20161124	[2,155]	biology, genomics
Wannier90	wannier90	1.2, 2.1.0, 3.1.0	[2,156]	computational Physics
WarpedLMM	warpedlmm	0.21	[2,157]	modeling
WaveGAN	wavegan	20190829	[2,158]	machine_learning, audio, GAN
WDSSII	wdss2	5, 6	[2,159]	climate
WebLogo	weblogo	3.3, 3.5.0, 3.7	[2,160]	biology, sequencing, graphics
webodm	webodm	20240718	[2,161]	graphics
Weka	weka	3.8, 3.8.5	[2,162]	statistics, machine_learning
Wengan	wengan	0.2	[2,163]	biology, genomics
wfmash	wfmash	0.13.0	[2,164]	phylogenetics
wgd	wgd	1.1.1	[2,165]	phylogenetics
WGS Assembler	wgs	8.3rc1.r4638, 8.3rc2	[2,166]	biology, genomics
Wgsim	wgsim	0.3.1-r13	[2,167]	biology, phylogenetics
WHAMM	whamm	0.14a	[2,168]	biology, phylogenetics
WhatsHap	whatshap	1.1, 2.1	[2,169]	biology, phylogenetics
whiteboxtools	whiteboxtools	1.5.0	[2,170]	phylogenetics
widis-lstm-tools	widis-lstm-tools	0.4	[2,171]	ML
Wine	wine	4.0.0, 7.0.0	[2,172]	linux, utility
Wise	wise	2.2.0, 2.4.1	[2,173]	biology, genomics
WIsH	wish	1.0	[2,174]	phylogenetics
WoLFPSort	wolfpsort	0.2	[2,175]	phylogenetics
WOMBAT	wombat	20180118	[2,176]	biology, phylogenetics
workbench	workbench	4.1.1	[2,177]	modeling, simulation
wtdbg	wtdbg	2.1, 2.4, 2.5	[2,178]	phylogenetics
WU BLAST	wublast	2.0	[2,179]	biology
Wub	wub	0.2.0, 0.4.0	[2,180]	biology, genomics, ngs
xander	xander	20151222	[2,181]	biology, phylogenetics
Xapian	xapian	1.4.4	[2,182]	library
XCrySDen	xcrysden	1.5.60	[2,183]	material_science
Xerces	xerces	3.1.4	[2,184]	phylogenetics
xesmf	xesmf	0.6.2	[2,185]	math, climate
xlsx2csv	xlsx2csv	0.8.0	[2,186]	utility
xpclr	xpclr	1.0, 1.1.1	[2,187]	phylogenetics
xppaut	xppaut	8.0	[2,188]	math
xroms	xroms	v0.5.4	[2,189]	geospatial
Xterm	xterm	1.1	[2,190]	utility
xwalk	xwalk	0.6	[2,191]	biology
XWAS	xwas	3.0	[2,192]	phylogenetics
XY-Meta	xy-meta	20200413	[2,193]	phylogenetics
XZ	xz	5.2.2	[2,194]	compression, library
yagcloser	yagcloser	1.0.0	[2,195]	biology, genomics, assembly
YAGO	yago	4	[2,196]	data_science
YAHA	yaha	0.1.82	[2,197]	biology, ngs
Yaha	yahs	1.1	[2,198]	biology
YAK	yak	0.1	[2,199]	phylogenetics
YASM	yasm	1.3.0	[2,200]	programming
YASRA	yasra	2.33	[2,201]	biology, ngs, sequencing
ydata-profiling	ydata-profiling	4.6.1	[2,202]	biology, ai, machine learning
yolo	yolo	10.0, 8.2	[2,203]	machine_learning
yolo-nas	yolo	NAS	[2,204]	machine_learning
yolov4_darknet	yolov4_darknet	4-pre	[2,205]	machine_learning
yolov5	yolo	7.0, 8, 8.1	[2,206]	machine_learning
Z1Plus	z1plus	1.0	[2,207]	molecular_dynamics
Zagros	zagros	1.0.0	[2,208]	biology, phylogenetics
Zbar	zbar	0.23.90	[2,209]	ai, image_processing, imaging
ZEO++	zeo++	0.2.2	[2,210]	chemistry
ZeroSum	zerosum	20231113	[2,211]	programming
zorro	zorro	2.2	[2,212]	biology, sequencing
Zstd	zstd	1.5.0	[2,213]	phylogenetics
ZUMIS	zumis	2.6.0	[2,214]	biology, ngs, sequencing