Installed Applications

Warning

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/Website	Versions	Categories
3d-dna	3d-dna	20170330	biology, phylogenetics
3pclr	3PCLR	20150906	biology, phylogenetics
4p	4p	1.0	biology, variant_calling
aaftf	AAFTF	0.2.5, 0.4.1	biology, pipeline, assembly
abricate	ABRicate	1.0.1	phylogenetics
abruijn	ABruijn	1.0	biology, assembly, ngs
abyss	ABySS	2.1.0, 2.2.5, 2.3.7	biology, de_novo
actc	ACTC	0.3.1	biology
adapterremoval	AdapterRemoval	2.2.2	phylogenetics
adfrsuite	ADFRsuite	1.0	sequencing, biology
admb	ADMB	11.5, 12.0	math, modeling
admixtools	AdmixTools	20150311, 7.0.2	biology, genomics, ngs
admixture	ADMIXTURE	1.23, 1.3.0	biology, genomics, ngs
aegean	AEGeAn	0.14.0, 0.16.0	biology, genomics
afni	AFNI	20.3.00, 2018_04_12, 23.3.09	biology, neuroscience, imaging
afterqc	AfterQC	0.9.7	phylogenetics
agat	AGAT	0.4.0	phylogenetics
agfusion	AGFusion	1.252	phylogenetics
albacore	Albacore	2.3.1, 2.3.3	biology, phylogenetics
albumentations	Albumentations	1.0.3	ai, image_processing, imaging
alder	Alder	1.03	biology, genomics
alevin-fry	Alevin-fry	0.8.1	sequencing, biology
alfa	ALFA	1.1.1	phylogenetics
alfred	alfred	0.2.6	web, math
alienhunter	alienhunter	1.7	biology, sequencing
alistat	AliStat	1.12	phylogenetics
allelecount	alleleCount	20210713	biology
allhic	allhic	0.9.8	genomics, biology
allmaps	ALLMAPS	20180117	biology, phylogenetics
allpaths	ALLPATHS-LG	42316, 44837, 49232	biology, ngs
alphafold	AlphaFold	2.1.2, 2.3.1, 2.3.2	protein, structure, machine_learning
alphaimpute	Alphaimpute	0.0.2, 1.9.8.2, 1.9.8.3	phylogenetics
alphamate	AlphaMate	0.1.1	biology
alphapulldown	AlphaPulldown	0.30.7, 2.0.0b1, 2.0.0b2	protein, structure, machine_learning
altanalyze	AltAnalyze	2.1.0	biology, genomics
amas	AMAS	1.0	phylogenetics
amber	AMBER	20, 22, 24	chemistry, molecular_dynamics
ambertools	ambertools	23	chemistry, molecular_dynamics
amico	AMICO	1.0.1, 2.0.1	library, imaging, math
amos	AMOS	3.1.0	biology, genomics, assembly
amp	AMP	0.6.1	phylogenetics
ampeppy	amPEPpy	1.0	phylogenetics
amphora2	amphora2	20140305	biology, phylogenetics
ampligraph	Ampligraph	2.0.0	programming, library, math
amptk	AMPtk	1.5.1, 1.5.4, 1.6	biology, ngs
amptorch	amptorch	20210313	phylogenetics
amrfinderplus	amrfinderplus	3.10.18, 3.12.8	phylogenetics
amrplusplus	AMRPlusPlus	20180508	phylogenetics
amuse	AMUSE	10.0, 13.1.0	astronomy
ancestryhmm	ancestryhmm	1.0.2	genomics, biology
anchorwave	anchorwave	1.2.1	biology, genomics
andi	ANDI	0.15b	assembly
angsd	ANGSD	0.933, 0.940	biology, ngs
annocript	annocript	2.0	phylogenetics
annotale	AnnoTALE	1.4.1	phylogenetics
annovar	ANNOVAR	20130221, 20150322, 20191024	biology, genomics
ansible	Ansible	2.5.5, 2.8.1	workflow_automation
ansys	ANSYS	2023R2	modeling
ansysem	ansysem	17.0, 2022r1, 2023r1	physics
antismash	antiSMASH	4.1.0, 6.0.1, 7.0.0	phylogenetics
ants	ANTs	2.2.0, 2.3.4	biology, phylogenetics
anvio	anvio	6.2, 7.1, 8.0	biology
appreci8	Appreci8	20180530	biology, genomics
apptainer	Apptainer	1.2.2, 1.3.1	workflow_automation
apt	APT	1.18.0, 1.20.5, 2.11.8	biology, genomics
aquamis	aquamis	1.4.0	biology, genomics
arb	arb	r19270	phylogenetics
arc	ARC	1.1.4	biology, ngs
arcashla	arcashla	0.5.0	biology, genetics
arcticporechop	Arcticporechop	0.3.2	phylogenetics
aria2	Aria2	1.35.0	utility
arks	ARKS	1.0.2	phylogenetics
armadillo	Armadillo	7.900.0, 9.200.6, 9.900.4	library, compiler, math
arpack	ARPACK	1.0	math
arrayfire	ArrayFire	3.4.2	math
arriba	arriba	2.1.0	phylogenetics
art	ART	20160417, 20160605	phylogenetics
artemis	artemis	18.1.0	biology
asap	asap	2.0	visualization, biology
asaq	asaq	1.0	alignment, sequencing, phylogenetics
asdec	ASDEC	1.2	bioinformatics
ase-ani	ASE-ANI	20180712	biology, genomics, ngs
ashs	ASHS	2.0	biology, imaging
aspect	ASPECT	2.3.0, 2.5.0	geodynamics
assembly-stats	Assembly-stats	1.0.1	biology, sequencing, genomics
assemblytics	Assemblytics	1.2.1	phylogenetics
asset	asset	20210112	sequencing, data_science
assexon	Assexon	20190814	phylogenetics
astalavista	AStalavista	3.2, 4.0	biology, genomics
aster	aster	1.15, 1.16, 220718	biology, data_science, sequencing
asteroid	asteroid	1.0	genomics
astral	ASTRAL	5.6.1, 5.6.2, 5.7.7	biology, ngs, phylogenetics
astrid	ASTRID	2.2.1	phylogenetics
astropy	Astropy	2.0.8	biology, phylogenetics
atat	ATAT	3.23, 3.34	material_science
atom	Atom	1.57.0	programming
atomeye	AtomEye	3	material_science
atomman	AtomMan	1.3.3	phylogenetics
atram	aTRAM	2.2.0, 2.4.3	math
augustus	Augustus	3.3.3, 3.4.0, 3.5.0	biology, genomics
auto3dem	Auto3DEM	4.05.2	image_processing
autodock	AutoDock	4.2.6	biology
autodock-gpu	AutoDock-GPU	1.5.3	chemistry
autodock-vina	autodock-vina	1.2.3, 1.2.5	biology
autometa	Autometa	2.2.0, 20190802	phylogenetics
automlsa2	automlsa2	0.8.1	phylogenetics, biology, genomics
awscli	AWSCLI	2.11.7, 2.2.30	utility
azoo	azoo	1.3.1	phylogenetics
bactopia	bactopia	2.2.0	genomics
badread	Badread	0.1.5	phylogenetics
bakta	bakta	1.3.3, 1.9.4	genomics, biology
bali-phy	BALi-Phy	3.4.1, 3.5.0	phylogenetics
bam-matcher	BAM-matcher	20161021	phylogenetics
bam-readcount	Bam-Readcount	20150616	biology, genomics
bamaddrg	bamaddrg	20120326	phylogenetics
bambam	BamBam	1.0, 1.4	biology, genomics
bamm	bamm	2.5.0	phylogenetics
bamsnap	bamsnap	0.2.19	phylogenetics
bamstats	Bamstats	20140602	biology, ngs
bamsurgeon	Bamsurgeon	1.2	phylogenetics
bamtofastq	bamtofastq	1.3.5	phylogenetics
bamtools	Bamtools	2.5.0, 2.5.1, 2.5.2	biology, ngs, sequencing
bamutil	bamUtil	1.0.2	biology, genomics
baps	BAPS	6.0	biology, genomics
barrnap	Barrnap	0.7, 0.9	biology, rna-seq
basemount	Basemount	0.15.96, 0.25.2	biology, sequencing
batmeth2	BatMeth2	20210720	biology, genomics, mapping
bax2bam	bax2bam	0.0.9	phylogenetics
bayarea	BayArea	1.0.2	biology
bayenv	BAYENV	2.0	biology, phylogenetics
bayesass	BayesAss	3.0.4, 3.0.4.2	phylogenetics
bayesass3-snps	bayesass3-snps	1.1	phylogenetics
bayescan	BayeScan	2.1	biology, variant_calling
bayesr	BayesR	20151016	biology, phylogenetics
bayestraits	BayesTraits	3.0.2	phylogenetics
baypass	baypass	2.1	biology, phylogenetics
bbmap	BBMap	38.44, 38.90, 39.06	biology, alignment
bcftools	bcftools	1.13, 1.15, 1.19	biology, ngs
bcl2fastq	bcl2fastq	2.16.0.10, 2.20.0.422	biology, ngs
bclconvert	BCLConvert	4.2.7	biology, ngs
bdg-sequila	BDG-SeQuila	0.5.5	phylogenetics
beagle	BEAGLE	4.1, 5.0, 5.2	biology, genomics
bear	BEAR	20170209	biology, genomics
beast	BEAST	2.7.0, 2.7.3, 2.7.5	biology, phylogenetics
beast2-xml	BEAST2-XML	1.0.9	phylogenetics
beastx	BEAST	10.0.5-beta4	biology, phylogenetics
bedops	BEDOPS	2.4.30, 2.4.41	biology, sequencing, ngs
bedtools	BEDTools	2.29.1, 2.29.2, 2.30.0	biology, ngs
bertini	Bertini	1.6	math
bertopic	BERTopic	0.14.0, 0.7, 0.8.1	machine_learning
besst	BESST	2.2.4	biology, ngs
bfast	BFAST	0.7.0	biology, ngs
bfc	BFC	1.0	genome
bgenix	bgenix	1.1.7	data_science, genomics
bidscoin	BIDSCOIN	3.7.4, 4.3.0	neuroscience
bifrost	Bifrost	0.2, 1.0.3, 20200225	phylogenetics
big-scape	BiG-SCAPE	1.1.2, 1.1.9	biology, genomics, phylogenetics, pipeline
bigslice	bigslice	1.1.1, 2.0.0	biology, genomics
bindash	bindash	1.0.1, 1.0.2	genomics
binpacker	BinPacker	1.0	biology, rna-seq, assembly
binsanity	BinSanity	0.2.6.4	biology, genomics
bioawk	Bioawk	1.0	phylogenetics
biobakery	bioBakery	1.8, 3.0.0, 3.1.0	phylogenetics
biodiverse	Biodiverse	2.1	phylogenetics
biolite	Biolite	0.3.5.1	biology, genomics, variant_calling
biom	BIOM	2.1.5, 2.1.6	biology, genomics
biomart	BIOMART	1.4	biology, genomics
bionemo	BioNeMo	0.3.1, 1.2, 1.3	ai, machine_learning
biopieces	Biopieces	2.0	phylogenetics
birdnet	BirdNET	0.1.2	bioinformatics
bismark	Bismark	0.24.2, 0.7.4, 0.7.7	biology, ngs
blackfynn	Blackfynn	0.2.7	data_mining
blasr	BLASR	20130815, 20161215 (5.3), 5.3.2	biology, ngs
blast2go	Blast2GO	1.3.3, 2.5.0-20120705	biology, genomics
blat	BLAT	20121105, 20140318	genomics
blender	blender	2.77, 3.0.1, 4.0.2	graphics
blink	blink	0.01	genomics
blitz	Blitz	0.10, 1.0.2	library
blobtools	BlobTools	1.0, 2.2, 4.3.5	genomics
bloomfiltertrie	bloomfiltertrie	0.8.7	phylogenetics
bloomtree	BloomTree	0.3.5	data_mining
blupf90	BLUPF90	20160604, 20180301, 20190531	biology, phylogenetics
bmge	BMGE	1.12	biology, genomics, phylogenetics
bmtagger	bmtagger	3.101	genomics, biology
bolt-lmm	BOLT-LMM	2.3.4	phylogenetics
boltztrap	BoltzTraP	1.2.5	physics
boost	Boost	1.75.0, 1.77.0, 1.82.0	programming, library, compiler
booster	booster	0.1.2	phylogenetics
botorch	botorch	0.7.1	phylogenetics, biology
bowtie	Bowtie	1.1.1, 1.2.0, 1.2.3	biology, ngs, sequencing
bowtie2	Bowtie2	2.3.5.1, 2.4.2, 2.4.5	biology, ngs, sequencing
boxcli	BoxCLI	2.9.0	file_management, web, programming
bpga	BPGA	1.2	biology, ngs
bpp	BPP	4.1.4, 4.3.8, 4.4.1	biology, phylogenetics
bppsuite	BppSuite	2.3.2	genomics
bracken	Bracken	1.0.0, 2.5, 2.9	biology, phylogenetics
brainiak	BrainIAK	0.11	imaging
braker	braker	3.0.2, 3.0.3, 3.0.8	phylogenetics
branch	BRANCH	1.8.1	biology, ngs, mapping
bratnextgen	BRATNextGen	20150505	biology, genomics
breakdancer	BreakDancer	1.4.5	biology, phylogenetics
breakseq	breakseq	2.2	biology, phylogenetics
brewery	Brewery	20191205	phylogenetics
bridger	Bridger	20141201	ngs, genomics, biology
brig	BRIG	0.95	biology, genomics
brkraw	brkraw	0.3.5	data_science, imaging
brm	BRM	0.3	phylogenetics
bruker2nifti	Bruker2nifti	1.0.4	phylogenetics
bsmap	Bsmap	2.87	biology, ngs
bsoft	Bsoft	1.9.1	biology, image_processing
bsseeker2	BSseeker2	2.1.0, 2.1.8	biology, phylogenetics
bubbleparse	bubbleparse	20140314	biology, phylogenetics
bucky	BUCKy	1.4.4	biology, phylogenetics
busco	BUSCO	4.1.4, 5.2.0	biology, genomics
bwa	BWA	0.7.7, 0.7.8, 0.7.9a	biology, ngs
bwa-mem2	bwa-mem2	2.2.1	phylogenetics
bwa-pssm	BWA-PSSM	0.5.11	phylogenetics
bwameth	bwa-meth	0.2.7	genomics, biology
bxh_xcede_tools	bxh_xcede_tools	1.11.1	biology
byobu	BYOBU	5.133, 5.92	shell
bzip2	bzip2	1.0.6	utility, library
c-wap	c-wap	20220624	sequencing, genomics, biology
cactus	Cactus	2.0.3, 2.0.5, 2.8.0	phylogenetics
cafe	CAFE	4.1, 5.0.0	biology, phylogenetics
came	came	0.0.1	phylogenetics
camino	Camino	20140723	biology, neuroscience, imaging
cammiq	cammiq	0.1.1	genomics, biology
camp	CAMP	1.0.0	biology, sequencing
cantera	Cantera	2.1.1	physics
canu	Canu	2.0, 2.1, 2.2	biology, sequencing
canvas	CANVAS	1.40.0.1613	phylogenetics
cap3	CAP3	20120705	biology, assembly
capnp	Capnp	0.5.3	compiler
captus	captus	0.9.88, 0.9.91	phylogenetics, biology
carta	CARTA	2.0	image_processing
casava	CASAVA	1.8.2	biology, ngs
casm	CASM	0.2.0	physics
casoffinder	CasOFFinder	2.4	phylogenetics
cat	CAT	12 Standalone	biology
catch	Catch	1.4.0	biology, genomics, sequencing
caviar	CAVIAR	20171218	biology, phylogenetics
cbgpipe	CBGpipe	20190702	phylogenetics
ccmetagen	CCMetagen	1.4.0	phylogenetics
cdbfasta	CDBFasta	20181005	phylogenetics
cdhit	CD-HIT	4.6, 4.6.4, 4.6.8	biology, genomics
cdo	CDO	1.7.2rc3, 1.9.4	climate
cdrt	CDRT	23.10	machine_learning
cellprofiler	CellProfiler	3.1.9, 4.1.3, 4.2.6	phylogenetics
cellranger	CellRanger	7.0.1, 7.2.0, 8.0.0	biology, ngs, rna-seq
cellranger-arc	CellRanger-ARC	2.0.1	biology, ngs, rna-seq
cellranger-atac	CellRanger-ATAC	1.2.0	biology, ngs, rna-seq
cellranger-dna	CellRanger-DNA	1.0.0, 1.1.0	biology, ngs, rna-seq, genomics
centrifuge	Centrifuge	1.0.3, 1.0.4b	biology, phylogenetics
cfitsio	CFITSIO	3.370	library, compiler
cgal	CGAL	5.02, 5.5.2, 5.6	library, math
cgatools	CGATools	1.6.0.43	biology, ngs
cgmaptools	cgmaptools	0.1.1, 0.1.2	phylogenetics
cgmlst	cgmlst	0.2	phylogenetics
cgmlstfinder	cgmlstfinder	1.0	genetics
cgview	CGView	1.0.2	phylogenetics
charmm	CHARMM	36a3, 43b2, c48b2	chemistry, simulation
checkm	CheckM	1.0.4, 1.0.7, 1.1.2	biology, genomics
checkv	checkv	1.0.1	biology, genomics
chewbbaca	chewbbaca	3.3.0	biology, genomics
chewiesnake	chewiesnake	3.0.0	biology, genomics
chimera	Chimera	1.12	biology, modeling
chipyard	Chipyard	1.0	simulation
chopper	Chopper	0.8.0	bioinformatics
chromeister	Chromeister	1.5a	biology, genomics
chromevol	ChromEvol	2.0, 3.0	biology, ngs
cialign	CIALIGN	1.1.4	bioinformatics
cims	CIMS	4.1.2	biology, genomics
circexplorer	CIRCexplorer	1.1.10	biology, rna-seq
circexplorer2	CIRCexplorer2	2.3.5, 2.3.8	phylogenetics
circexplorer3	circexplorer3	01172021	RNA-Seq
circlator	Circlator	1.5.5	phylogenetics
circleator	Circleator	1.0.2	phylogenetics
circompara2	circompara2	0.1.2.1	phylogenetics
circos	Circos	0.63-pre11, 0.69-2, 0.69-9	biology, genomics, ngs
circtools	circtools	1.2.1	biology
ciri	CIRI	2.0.6	phylogenetics
ciriquant	ciriquant	1.1.2	phylogenetics
cisgenome	CisGenome	2.0	biology, genomics
cistem	cisTEM	1.0.0	phylogenetics
clairvoyante	Clairvoyante	1.02	phylogenetics
clann	Clann	3.2.3	biology, phylogenetics
clara	clara	v4.0	ai, machine_learning
clark	CLARK	1.2.2-b, 1.2.3	biology, genomics
clean	clean	1.0.1	protein, machine_learning
clearmap	apps	2.0	biology, neurobiology
clhep	CLHEP	2.2.0.1	physics
clifinder	CLIFinder	4.1	biology, phylogenetics
clinicadl	ClinicaDL	1.0.4, 1.2.0	biology, imaging, machine_learning
clipkit	clipkit	1.3.0	genomics, biology
clipper	CLIPper	2.1.0	phylogenetics
clipseqtools	CLIPSeqTools	0.1.7	biology, sequencing
cliquesnv	CliqueSNV	2.0.3	biology, phylogenetics
clonalframe	ClonalFrame	1.1, 1.2	biology, ngs, phylogenetics
clonalframeml	ClonalFrameML	1.0, 1.11	biology, ngs, phylogenetics
cloudcompare	CloudCompare	2.10.3	visualization
clover	Clover	2.0	biology, genomics, assembly
clumpp	CLUMPP	1.1.2	biology
clustalo	ClustalO	1.2.0	biology, alignment
clustalw	ClustalW	2.1	biology, alignment
cluster3	cluster3	1.52a	biology, genomics
clview	Clview	20130402	biology
cmake	CMake	3.21.3, 3.26.4, 3.30.5	programming
cms	CMS	20170518, 20240429	biology
cmwp	CMWP	140518	biology, genomics
cnci	CNCI	20180305	phylogenetics
cnspipeline	CNSpipeline	20170827	phylogenetics
cnv-sim	CNV-Sim	0.9.2	biology, phylogenetics
cnvkit	CNVkit	0.9.6	phylogenetics
cnvnator	CNVnator	0.3.2	biology, genomics
cnvseq	CNV-Seq	20110715, 20140812	biology, genomics
cobra-tf	cobra-tf	0.1	fluid_dynamics
cobretti	Cobretti	1.0	GeneExpression
codonphyml	CodonPhyML	20150303	phylogenetics
coevol	Coevol	1.3c, 1.4b, 1.6	biology, phylogenetics
cogent	Cogent	2.1	biology, phylogenetics
colmap	COLMAP	3.6	modeling
comap	CoMap	1.4.1	biology, genomics
comp-d_mpi	Comp-D_MPI	1.0	statistics
compacta	Compacta	1.02	biology, genomics
comsol	COMSOL	6.1, 6.2, 6.2.04	simulation
concaterpillar	Concaterpillar	1.8a	phylogenetics
concoct	CONCOCT	1.1.0	biology, genomics
conda	Conda	24.3.0, 24.7.1	programming
conefor	Conefor	2.7.3	software
conn	CONN	22a	imaging
connect	CONNECT	20200614	phylogenetics
connectomemapper3	connectomemapper3	3.0.0-rc1	phylogenetics
conpade	ConPADE	1.0	phylogenetics
conpair	Conpair	20161010, 20180624	biology, phylogenetics
conquest	GROMACS	2021.4	chemistry, molecular_dynamics
consed	Consed	23.0, 25.0, 29.0	biology, genomics
consel	CONSEL	0.20	biology, phylogenetics
contavect	ContaVect	0.2	biology, phylogenetics
convert3d	Convert3D	1.1.0	imaging, utility
coot	Coot	0.9.5	modeling
coptr	CoPTR	1.1.6	biology
coreutils	Coreutils	8.23, 8.28	utility
corset	Corset	1.06	biology, ngs
counterr	Counterr	0.1, 20230501	phylogenetics
coverm	Coverm	0.6.1	biology, genomics, ngs
covnmr	covNMR	2014	chemistry, biology
cp2k	cp2k	2024.1, 7.0.0	imaging
cpat	CPAT	3.0.2	phylogenetics
cpc	cpc	2.0	phylogenetics
cplex	CPLEX	12.6.2, 12.7, 12.9	climate
crass	Crass	1.0.1	biology, assembly
crest	crest	12.2, 2.12, 3.0	chemistry
crisflash	crisflash	1.2.0	phylogenetics
crisp	CRISP	20181122, 20240419	phylogenetics
crispranalyzer	CRISPRanalyzer	1.50	biology, genomics, ngs
crisprcasfinder	CRISPRCasFinder	4.2.17	phylogenetics
crispresso2	CRISPResso2	20220811	genomics, sequencing, biology
crossmap	CrossMap	0.3.9, 0.6.3	biology, genomics
crossmapper	crossmapper	1.1.1	phylogenetics
crux	Crux	1.40	biology, spectroscopy
cryodrgn	cryodrgn	2.3.0	biology
cryptominisat	CryptoMiniSat	5.0.1	math
csubst	csubst	1.3.0	Biology, Phylogenetics
csvpad	csvpad	1.2	data science
csvtk	csvtk	0.23.0, 0.30.0	biology
ctk	ctk	1.1.4	biology, genomics
cu-lammps	LAMMPS	02Aug23	molecular Dynamics
cube	CUBE	4.4	library, compiler, math
cuda	CUDA	12.2.2, 12.3.2, 12.4.1	programming, library, graphics
cufflinks	Cufflinks	2.1.1, 2.2.1, 2.2.1.1	biology, ngs, sequencing
cuopt	cuOpt	22.12	Accelerated AI Logistics and Route Optimization
cupcake	CDNA_Cupcake	22.0.0, 9.0.1	biology, ngs, sequencing
cupy	cupy	8.3.0	phylogenetics
cutadapt	cutadapt	1.18, 2.8, 3.4	biology, ngs
cutruntools	CutRunTools	20200104	phylogenetics
cvbio	cvbio	3.0.0	phylogenetics
cvit	CViT	1.3	programming, library
cwltool	CWLtool	1.0.20190906, 2.0.20200126, 3.0.20210124104916	workflow_automation, scheduler
cxoracle	cx_oracle	8.3.0	database, utility
cyclegan	CycleGan	20201015	phylogenetics
cytoscape	Cytoscape	3.10.2, 3.4.0	biology, ngs, phylogenetics
cyvcf2	cyvcf2	20230728	library
d2go	d2go	20210702	machine_learning, ai
dadi	dadi	2.1.1	phylogenetics
dakota	DAKOTA	6.15, 6.8, 6.8-gui	math
daligner	DALIGNER	1.0	biology, phylogenetics
dammit	dammit	1.0rc2	biology, phylogenetics
dancemapper	dancemapper	1.0.0	machine learning
dapars	dapars	1.0.0	genomics, biology
darwin-gpu	darwin-gpu	20190115	genomics, alignment
dastool	DASTool	1.1.0, 1.1.2	biology, phylogenetics
datamash	datamash	1.1.0	math
dawgpaws	DAWGPAWS	1.0	biology, phylogenetics
dbcanlight	dbcanlight	1.1.0	biology, annotation
dcc	DCC	0.4.4	biology, ngs
dcmstack	Dcmstack	0.6.2	biology, imaging
dcmtk	DCMTK	3.6.0	biology, neuroscience, imaging
ddocent	dDocent	2.7.8	phylogenetics
ddprotocol	ddprotocol	20230405	biology, machine learning
ddscat	DDSCAT	7.3.0	astronomy
ddt	DDT	20.0, 20.2, 23.0	programming
dealii	DealII	8.3.0, 9.3.1, 9.5.1	library
deconseq	DeconSeq	0.4.3	biology, phylogenetics
decontaminer	decontaMiner	1.4	genomics, biology
decx	DECX	20180205	phylogenetics
deeparg	DeepARG	1.0.1	phylogenetics
deepbgc	deepbgc	0.1.18	phylogenetics
deepcoil	Deepcoil	2.0.1	sequencing, biology
deepfri	deepfri	03312021	machine learning, biology
deepgs	DeepGS	1.2	phylogenetics
deeplabcut	DeepLabCut	2.0.7-gpu, 2.1.1, 2.2.1	phylogenetics
deeplexicon	deeplexicon	1.2.0	RNAseq
deepmd-kit	DeePMD-kit	2.1.11	molecular dynamics, deep learning
deepmd-lammps	DeepMD-LAMMPS	2.2.0-02Aug23	molecular Dynamics
deepmicrobes	deepmicrobes	20200219	biology, genomics, machine_learning
deepmreye	DeepMReye	01192022	library, biology
deeppicker	DeepPicker	20161102	imaging
deepsig	deepsig	1.2.5	biology
deeptools	deepTools	2.4.3, 3.1.1, 3.5.2	biology, ngs
deepvariant	deepvariant	1.4.0, 1.5.0, 1.6.1	biology, genomics, sequencing, machine_learning
defusion	deFusion	20200305	phylogenetics
delft3d	Delft3D	4.06.01, 7545	physics
delineate	Delineate	1.2.2	biology, genomics
delly	Delly	0.7.7, 0.7.8, 1.1.5	biology, phylogenetics
delucs	delucs	20220512	sequencing, genomics, machine_learning
denogap	DeNoGAP	1.0	biology, phylogenetics, ngs
deriva	DERIVA	1.5.0	phylogenetics
desalt	deSALT	1.5.6	biology, genomics, sequencing
desmond	Desmond	6.9	biology
detectron2	Detectron2	0.4, 0.5, 0.6	library
detin	DeTiN	1.7.5.9	imaging, ngs, genomics
dextractor	DEXTRACTOR	1.0	biology, sequencing
diamond	Diamond	2.1.1, 2.1.3, 2.1.8	biology, genomics
diann	DIANN	1.8.1	protein, structure
dical2	diCal2	2.2.0.1	biology, phylogenetics
diffdomain	diffDomain	1.0.0	bioinformatics
diffreps	diffReps	1.55.4	biology
disbatch	disbatch	2.5	software
discovardenovo	DISCOVAR de novo	52488	biology, ngs, assembly
discovista	DiscoVista	20180906	phylogenetics
discvrseq	discvrseq	1.3.10	biology, phylogenetics
distruct	Distruct	2.3	phylogenetics
diyabc	DIYABC	1.0.4.43b, 2.0.3, 2.1.0	biology, phylogenetics
dlib	Dlib	19.19	phylogenetics
dlpoly	DL_POLY	1.9	molecular_dynamics
dnaclust	DNA Clust	3.0	biology, genomics
dock	DOCK	6.7, 6.8, 6.9	chemistry
dogfinder	DoGFinder	20201103	phylogenetics
dorado	dorado	0.7.0, 0.7.2, 0.8.2	genomics
dosageconvertor	DosageConvertor	1.0.3	biology
dot	DOT	2.0	biology, chemistry
doxygen	Doxygen	1.12.0, 1.8.3.1, 1.9.7	programming, documentation
dragmap	dragmap	1.2.1	phylogenetics, sequencing, biology
dragonflye	dragonflye	1.0.12	sequencing, genomics
dram	dram	1.3	biology, genomics, annotation
drap	DRAP	1.91	biology, phylogenetics
drep	dRep	2.3.2, 3.4.2	phylogenetics
dretools	dretools	0.0.1.20	rna-seq
drishti	drishti	3.2	visualization
dropseq	Dropseq	2.4.0	phylogenetics
dscribe	DScribe	1.2.0	machine_learning
dsistudio	dsistudio	20210123, 20220803, 20240311	imaging
dsk	DSK	2.1.0, 2.3.0	biology, ngs
dsrc	DSRC	2.0	phylogenetics
dssat	DSSAT	4.6	simulation
dssp	DSSP	2.2.1, 3.0.0	molecular_dynamics
dsuite	DSuite	0.4, 0.4-r41, 0.4-r49	biology, genomics
dtiprep	dtiprep	0.1.1	phylogenetics
dtitk	DTI-TK	2.3.1	imaging
duchamp	duchamp	1.6.2	phylogenetics
dvgfinder	DVGfinder	3.1	genomics, search, sequencing
dx-toolkit	dx-toolkit	0.347.0	biology
dynamicdbg	dynamicDBG	20181003	phylogenetics
dynare	Dynare	4.4.3	math
dynasor	dynasor	2.0	Molecular_Dynamics
eagle	EAGLE	2.0	phylogenetics
eagle-rc	eagle-rc	1.1.1	phylogenetics
earlgrey	Earlgrey	4.2.4	biology
eautils	ea-utils	1.04.807.18, 1.1.2.537	biology, genomics, ngs
ece	ECE	1.2	physics
ecopcr	ecopcr	0.5.0	Biology
eddy-squeeze	eddy-squeeze	1.0.8	data_science, visualization
edirect	EDirect	10.7, 12.2	biology, phylogenetics
edta	EDTA	1.9.6, 2.1.0	phylogenetics
edyeet	Edyeet	0.1, 0.3	phylogenetics
eeglab	EEGLAB	12.0.2.1b, 13.2.2b, 13.4.4b	biology
effectorp	effectorp	2.0.1, 3.0	biology
egene-mvn	eGene-MVN	0.1	biology, genomics
eggnog-mapper	eggNOG-mapper	2.0.1, 2.1.12, 2.1.6	phylogenetics
ego4d	Ego4D	1.3.2	image processing
egsnrc	EGSnrc	2019	phylogenetics
eigen3	EIGEN3	3.4.0	libraries, mathematics
eigensoft	EIGENSOFT	5.0.1, 6.0.1, 6.1.4	biology
elastix	Elastix	4.9.0, 5.1.0	phylogenetics
elpa	ELPA	2019.11.001	library, compiler, math
elprep	elPrep	4.1.4	phylogenetics
emacs	Emacs	27.2, 28.2	programming, language
email_storage_alert	Email Alert Service	1.0.0	file_management
eman2	EMAN2	2.22, 2.31	image_processing
emboss	EMBOSS	6.6.0	biology
embree	Embree	3.6.1	graphics
emc	EMC	9.4.3	simulation
emerald	emerald	0.1	biology
emmax	EMMAX	20100307, 20120210	biology, ngs, mapping
emu	emu	3.4.5	phylogenetics
energyplus	EnergyPlus	9.3.0	simulation
enrichm	enrichm	0.6.5	biology
ensembl_tools	Ensembl Tools	100, 80	biology
entap	enTAP	0.6.1.2, 20160416	biology, phylogenetics
epacts	EPACTS	3.2.6, 3.4.2, 3.4.2.hg38	biology, genomics
epinano	EpiNano	1.2.0	biology, ngs
epiteome	epiteome	1.0	phylogenetics
epoch	epoch	4.7.3	astronomy
eqtla	eQTLA	1.1	biology, genomics
eqtlbma	eQtlBma	1.2.2, 1.3.0r20140820	biology, genomics
erpin	Erpin	5.5.4	biology, phylogenetics
esmf	esmf	8.3.0), 8.7.0)	geospatial
esom	ESOM	1.1	biology, phylogenetics
espresso	ESPRESSO	7.0, 7.1, 7.2	chemistry, modeling
esprit	ESPRIT	2009-nogap, 201102	biology
ete	ETE4	4.0.0	biology, phylogenetics
ete3	ETE3	3.0.0, 3.1.1	biology, phylogenetics
eukulele	EUKulele	2.0.7	alignment, biology, genomics
evidencemodeler	EVidenceModeler	1.1.1	phylogenetics
evigene	Evigene	20180730, 20200520	phylogenetics
evolstm	EvoLSTM	20220103	biology
exabayes	ExaBayes	1.5	phylogenetics
exonerate	Exonerate	2.2.0, 2.4.0	biology, genomics
expansionhunter	ExpansionHunter	4.0.2	biology, genomics
expansionhunterdenovo	ExpansionHunterDenovo	0.9.0	biology, genomics
export2graphlan	export2graphlan	0.22	statistics, mapping, visualization
express	eXpress	1.3.1, 1.5.1	biology, ngs
ezaai	ezaai	1.0	biology, phylogenetics
face_morpher	face_morpher	20190630	phylogenetics
face_recognition	face_recognition	1.2.2	phylogenetics
fairseq	fairseq	0.12.2	modeling, ai
falco	falco	1.2.1	biology, sequencing
falcon	FALCON	20161027, 20161222, 20190601	biology, ngs, sequencing
falcon_unzip	FALCON_unzip	20161222	biology
fanc	fanc	0.9.28	biology, genomics, ngs
faqcs	faqcs	2.10	Genomics, biology
far	FAR	2.15	biology, genomics
fast	FAST	1.06	biology, phylogenetics
fast-gep	fast-gep	1.0	phylogenetics
fast-plast	Fast-Plast	1.2.6	biology, phylogenetics
fast5tools	fast5tools	0.3.1	phylogenetics, biology
fasta	FASTA	34.26.5, 36.3.6d	biology, genomics
fastai	fastai	2.1.5, 2.6.3, 2.7.10	phylogenetics
fastani	FastANI	1.1, 1.34	phylogenetics
fastchaos	fastchaos	0.1.0	sequencing
fastgear	FastGEAR	20161216	biology, genomics
fastix	Fastix	0.1.0	biology, ngs
fastme	r8s	1.8	phylogenetics
fastml	FastML	3.0	biology, phylogenetics
fastp	Fastp	0.20.0, 0.22.0, 0.23.4	biology, ngs
fastphase	FASTphase	1.4.8	phylogenetics
fastplast	FastPlast	1.2.8	phylogenetics
fastq-pair	fastq-pair	1.0	phylogenetics
fastq-screen	FastQ-Screen	0.14.0	phylogenetics
fastq-tools	Fastq-tools	0.8	biology, ngs
fastqc	FastQC	0.11.7, 0.12.1, 0.9.6	biology, ngs
fastqpuri	FastqPuri	1.0.7	phylogenetics
fastqtl	FastQTL	2.184	phylogenetics
fastral-constrained	FASTRAL-constrained	20211108	phylogenetics
fastsimcoal2	fastsimcoal	2.6.0.3, 2.7.0.2	biology, phylogenetics
fastspar	FastSpar	0.0.4	biology, genomics
faststructure	fastStructure	20150112, 20240221	biology, genomics
fasttree	FastTree	2.1.11	biology, phylogenetics
fastuniq	FastUniq	1.1	biology, phylogenetics
fastv	fastv	0.10.0	bioinformatics, sequencing
fastx_toolkit	Fastx Toolkit	0.0.13.2, 0.0.14	biology, ngs
fcgene	fcGENE	1.0.7, 1.0.7.1	biology, genomics, variant_calling
fdstools	FDSTools	1.2.0	phylogenetics
fdupes	fdupes	1.51	file_management
febio	febio	2.9.1	biomechanics
feelnc	FEELnc	0.1.1	phylogenetics
fenics	FEniCS	2018.1.0	biology, phylogenetics
ferret	Ferret	6.82	visualization, geospatial, climate
ffmpeg	FFmpeg	2.8.3, 4.3.1, n6.1	audio, visualization
fftw	FFTW	3.3.6, 3.3.7, 3.3.8	library, compiler, math
fgbio	fgbio	0.5.0, 0.7.0	phylogenetics
fgmp	FGMP	1.0.1	phylogenetics
fgtpartitioner	FGTPartitioner	1.0.1	genomics
figaro	FIGARO	1.1.2	phylogenetics
fiji	Fiji	2.0.0rc59	image_processing
fiji-birds	BIRDS	1.0	workflow_automation, utility, imaging
filtlong	Filtlong	0.2.0	biology, phylogenetics
finder	Finder	20210503, 20210609	biology, search
finemap	finemap	1.4	phylogenetics
fineradstructure	fineRADstructure	0.3.2	phylogenetics
finesse	finesse	2.3.1	simulation
finestructure	r8s	1.8	phylogenetics
firefox	Firefox	1.0	linux, web
fit-sne	fit-sne	1.2.1	phylogenetics
flair	FLAIR	1.5, 2.0	phylogenetics
flairnlp	flairNLP	0.10	visualization, language
flappie	flappie	1.1.0, 2.1.3	phylogenetics
flash	FLASh	1.2.10, 1.2.11	biology, genomics
flea	FLEA	2.0.0	phylogenetics
flex	flex	2.6.4	programming
flexbar	Flexbar	2.3, 2.34, 3.5.0	biology, genomics, ngs
flexlm	FLEXLm	1.0	utility
flopp	flopp	0.2.0	genomics
flowcraft	FlowCraft	1.4.1	phylogenetics
fluent	Fluent	17.2, 19.1, 2020R1	fluid_dynamics
flye	Flye	2.9.1, 2.9.2, 2.9.3	biology, ngs
fmriprep	fMRIPrep	20.2.3, 23.1.3, 23.1.4	data_mining
foldseek	foldseek	9.427df8a	bioinformatics
forecasting	forecasting	0.10.3	Machine_Learning, Data_Science
foreseqs	ForeSeqs	1.0.4	phylogenetics
forwardgenomics	forwardgenomics	1.0	phylogenetics
fpc	Pascal	3.0.0	compiler, programming
fpocket	fpocket	4.0.2	sequencing, biology
fqtools	fqtools	20160224	biology, ngs, sequencing
fraggenescan	FragGeneScan	1.16	biology, genomics
frama	FRAMA	20151019	biology
framedp	FrameDP	1.2.2	biology, sequencing
fraposa	FRAPOSA	20200421	phylogenetics
freebayes	FreeBayes	1.3.1, 1.3.2, 1.3.7	biology, genomics
freecad	freecad	0.20.2	modeling
freesasa	freesasa	2.1.2	molecular_dynamics, biology
freesurfer	Freesurfer	7.2.0, 7.3.2, 7.4.1	biology, neuroscience, imaging
freyja	Freyja	1.3.1, 1.3.4, 1.3.8	biology, phylogenetics, sequencing
fsa	FSA	1.15.9	phylogenetics
fsl	FSL	6.0.4, 6.0.5, 6.0.6	biology, neuroscience, imaging
fslmrs	fslmrs	1.1.10	spectroscopy, metabolomics
funannotate	funannotate	1.8.5, 1.8.7, 1.8.9	phylogenetics
fusion_twas	fusion_twas	20210218	phylogenetics
gal	GAL	20180906	biology, genomics, annotation
galaxyml	galaxyml	0.10.0	library, machine_learning
galaxytools	Galaxy	1.0	biology
gaml	GAML	20150610	biology, genomics, assembly
gapcloser	GapCloser	1.12r6	biology, genomics, ngs
gapfiller	GapFiller	1.10, 1.11	biology, genomics
gapseq	gapseq	1.2	chemistry, biology
garfield	garfield	2	genomics
garli	GARLI	2.0, 2.01	biology, phylogenetics
gasvpro	GASVPro	201310	biology, ngs
gate	GATE	7.0	library
gatk	GATK	4.1.9.0, 4.3.0.0, 4.4.0.0	biology, ngs
gaussian	Gaussian	09 D.01, 16, 16-c02	chemistry
gawk	Gawk	4.2.0	utility
gblocks	Gblocks	0.91b	biology, alignment
gcc	GCC	7.3.0, 8.2.0, 9.3.0	compiler
gce	GCE	1.0.2	biology, genomics
gcloud	gcloud	471.0.0	cloud, google, cli
gcnenv	gcnenv	1.13	library, math
gct	GCT	6.2.1	file_management, utility
gcta	GCTA	1.26.0, 1.92.4beta, 1.93.2beta	biology, genomics, variant_calling
gdal	GDAL	2.3.1, 3.7.0, 3.9.0	geospatial, library
gdb	GDB	8.3, 9.2	programming
gdc-client	GDC-Client	1.0.1, 1.5.0	biology, sequencing, ngs
gdrive	GDrive	2.1.0	utility, file_management
gdsl	GDSL	1.18	library
geant4	Geant4	4.10, 4.10.03, 4.10.5	physics
gem	GEM	20130406	biology, ngs, sequencing
gem5	gem5	2.0	simulation
gemma	GEMMA	0.98.1, 0.98.5	phylogenetics
gemma_llm	gemma_llm	1	library, math
genbank_tools	NCBI GenBank Tools	20140130	biology
genblastg	genblastg	1.39	biology, genomics
genemark_es	GeneMark-ES	4.68, 4.69, 4.71	biology, genomics
genemark_s	GeneMarkS-T	2012.04, 3.10.001	biology, genomics
genepainter	GenePainter	2.0.4	biology, phylogenetics
generax	GeneRax	1.2.2	phylogenetics
geneseqer	GeneSeqer	2014-02-26	biology, genomics
genesis	genesis	2.1.2, 2.1.2-cpu	Physics
genesum	genesum	0.1.0	biology, genomics
genetorrent	GeneTorrent	3.8.7	biology, file_management
genewalk	genewalk	1.5.3	phylogenetics
gengen	GenGen	1.0.1	biology, phylogenetics
genmap	genmap	v1.3.0	Gene mapping, biology
genomad	geNomad	1.5.1	biology, genomics
genome_graph_annotation	Genome_Graph_Annotation	20190131	phylogenetics
genomescope2	GenomeScope2	2.0	phylogenetics
genomestrip	Genome STRiP	2.00.1602	biology, genomics, ngs
genomethreader	GenomeThreader	1.7.3	phylogenetics
genometools	GenomeTools	1.5.7, 1.5.9	biology
genomic-fluidity	genomic-fluidity	20151109	phylogenetics
genomic-neuralnet	GenomicNeuralnet	20161030	phylogenetics
genomicconsensus	GenomicConsensus	2.3.3	biology, phylogenetics
genomictools	GenomicTools	2.7.0	biology, ngs, chip-seq, rna-seq
genotypeharmonizer	GenotypeHarmonizer	1.4.18	biology
genrich	Genrich	0.5	phylogenetics
gensel	GenSel	4.90	genomics
geomxngspipeline	geomxngspipeline	3.1.1.5	NGS
geopython	geopython	1.0.0, 1.0.1, 1.0.2	programming, geospatial
geos	GEOS	3.3.8, 3.6.2	library, data_science
gep	GeP	2.1	biology, phylogenetics
gepard	gepard	1.40.0, 2.1.0	phylogenetics
gephi	Gephi	0.10.0	visualization, image_processing
gerbil	Gerbil	1.11	phylogenetics
get_homologues	get_homologues	3.3.3	biology, genomics
getorganelle	GetOrganelle	1.7.3.5, 1.7.5.0	phylogenetics
gfam	GFam	1.1	biology, genomics, annotation
gff-ex	GFF-Ex	2.3	phylogenetics
gff3toolkit	GFF3toolkit	2.0.3	phylogenetics
gffcompare	gffcompare	0.12.2	phylogenetics
gffread	gffread	0.11.8, 0.12.7, 0.9.8c	biology
gflags	Gflags	2.2.1, 20150520	web, library
gfold	GFOLD	1.1.4	biology, rna-seq
ggsashimi	ggsashimi	0.5.0	phylogenetics
ghost-mp	GHOST-MP	1.3.4	phylogenetics
ghostscript	Ghostscript	9.22	documentation
giggle	giggle	20221212	Genomics
gimmemotifs	Gimmemotifs	0.18.0	biology, genetics
giotto	Giotto	0.1.0	phylogenetics
giraf	giraf	1.02	sequencing, biology
git	Git	2.14.1, 2.30.1	revision_control
git-filter-repo	git-filter-repo	2.33.0	phylogenetics
github-cli	Github Cli	2.40.1	revision_control
gkeyll	Gkeyll	2.0	Plasma Physics
glactools	glactools	1.0.8	phylogenetics
glimmer	Glimmer	3.02	biology, annotation
glimmerhmm	GlimmerHMM	3.0.4	biology, annotation
glmsingle	GLMsingle	1.0	imaging
glnexus	glnexus	1.4.1	programming
globus	Globus	2.1.3, 3.13.0, 3.18.0	file_management
glog	glog	0.3.5	web, library
glpk	GLPK	4.55, 4.65	programming
glueviz	Glueviz	0.15.2	phylogenetics
gmap	GMAP	20180212, 20180212_sse2, 20190610	biology, genomics, ngs
gmcloser	GMcloser	1.6	biology, ngs
gmp	GMP	6.1.2, 6.3.0	library
gmt	Generic Mapping Tools	6.4.0	physics, biology
gnuastro	gnuastro	0.21	astronomy
gnuplot	GnuPlot	5.2.2, 5.2.3, 5.4.1	graphics, math
go	Go	1.15.4, 1.18.3, 1.21.0	language
goatools	goatools	1.2.3	biology, ontology
gomap	GOMAP	1.3, 1.4	biology, ngs
gophy	GoPHY	201030	phylogenetics
gosling	Gosling	0.2.2	genomics, visualization
gotcloud	gotcloud	1.17.5	phylogenetics
gpa	GPA	1.1	phylogenetics
gphocs	GPhoCS	1.2.3	phylogenetics
gptl	GPTL	20140212	utility
gpufit	Gpufit	20201127	phylogenetics
grace	Grace	5.1.22	graphics, statistics
grackle	GRACKLE	3.1, 3.2.1	library, compiler, astronomy
grads	GrADS	2.0.1	geospatial, math
graftm	Graftm	0.12.2	phylogenetics
gramcluster	GramCluster	1.3	biology, sequencing
graph-tool	graph-tool	2.32	phylogenetics
graph_annotation	Graph_annotation	0.1	phylogenetics
graphaligner	graphaligner	1.0.11, 1.0.16	genomics
graphlan	GraPhlAn	1.1.3	phylogenetics
graphmap2	GraphMap2	0.6.5	phylogenetics
graphmb	GRAPHMB	0.2.5	biology, genomics
graphsplitting	GraphSplitting	2.4	phylogenetics
graphtyper	graphtyper	2.7.2	phylogenetics
graphviz	GraphViz	2.38.0, 2.46.1	biology, neuroscience, imaging
grass	GRASS	7.0, 7.4	geospatial
grf	grf	1.0.0	genomics
grib_api	Grib_api	1.10.1, 1.15.1, 1.26.1	compiler, library
gridss	GRIDSS	2.6.2	phylogenetics
grocsvs	GROCSVs	0.2.5	phylogenetics
gromacs	GROMACS	2021.3, 2021.4, 2023.2	chemistry, molecular_dynamics
groopm	GroopM	0.3.5	biology, phylogenetics
groovy	Groovy	2.4.15	programming
gscripts	Gscripts	1.1	biology
gsea	GSEA	4.2.2	biology, genomics
gsl	GSL	2.6, 2.7, 2.7.1	library, data_science
gsnp	GSNP	1.0	biology, ngs
gsp	gsp	05192017	biology
gtahunter	GTAHunter	20200106	phylogenetics
gtdbtk	GTDBTk	2.0.0, 2.1.0, 2.3.2	phylogenetics
gtool	GTOOL	0.7.5	phylogenetics
guava	GUAVA	1.0	phylogenetics
gubbins	Gubbins	2.4.1, 3.2.1, 3.3.0	phylogenetics
guideseq	guideseq	1.0.2	sequencing, genomics, biology, data_science
guile	guile	2.2.2	programming
gulp	GULP	4.4, 5.0	material_science
guppy	guppy	6.1.7, 6.4.2, 6.4.3	phylogenetics
gurobi	Gurobi	10.0.0, 11.0.1, 9.5.1	math, programming
gwama	GWAMA	2.2.2	phylogenetics
gzip	Gzip	1.10	compression
hacdivsel	hacdivsel	1.4.1	genomics, biology
hail	Hail	0.2.130, 0.2.77	biology, genomics
hal	hal	2.1	phylogenetics
halc	HALC	1.1	biology, phylogenetics
halla	halla	0.8.17	phylogenetics
hamstr	HaMStR	13.2.3, 13.2.4, v8b	biology, genomics
hapbin	hapbin	1.3.0	biology, genomics
hapcompass	HapCompass	0.7.7	imaging, ngs, genomics
hapcut	HAPCUT	0.7	biology, assembly
hapcut2	HapCUT2	1.3.3	biology, genomics, sequencing
hapdup	hapdup	0.6	phylogenetics, biology
haphpipe	haphpipe	1.0.3	phylogenetics, biology
haploflow	Haploflow	0.1	biology, phylogenetics
haplomerger2	Haplomerger2	20180603	biology, genomics
haplosweep	HAPLOSWEEP	1.0	biology, phylogenetics
happy	happy	0.3.14	phylogenetics, biology
hapqtl	hapQTL	1.00	biology
hapsembler	hapsembler	2.21	biology, assembly
harvesttools	harvesttools	1.2	phylogenetics, biology
haslr	HASLR	0.8a1	phylogenetics
hclust2	hclust2	1.0.0	statistics, mapping
hdf4	HDF4	4.2.11	library, data_science
hdf5	HDF5	1.8.19, 1.8.20, 1.8.9	library, data_science
hecaton	hecaton	0.5.1	genomics, biology
helen	HELEN	20200516	phylogenetics
helitronscanner	HelitronScanner	1.1	phylogenetics
helixer	helixer	0.3.3	Genomics
herro	herro	0.1.0	Genomics
hgraph2graph	hgraph2graph	20210428	chemistry
hgtector	hgtector	2.0	biology, sequencing
hhsuite	hhsuite	3.3.0	nan
hi-corrector	Hi-Corrector	1.2	biology, ngs, sequencing
hic-lift	hic-lift	06112023	genomics
hic-pro	HiC-Pro	3.0.0	biology, pipeline, genomics
hicpro	HiC-Pro	3.1.0	HiC
hifiasm	Hifiasm	0.19.9, 0.4, 0.8	phylogenetics
hificnv	Hificnv	0.1.7	biology, genomics, ngs
hillerlab	hillerlab	20240819	phylogenetics
hiphase	hiphase	1.4.0	biology, ngs
hipstr	HipSTR	0.7	phylogenetics
hisat2	HISAT2	2.2.1, 2.2.1-3n, 20230203	biology, alignment, ngs
hivtrace	hivtrace	1.5.0	biology,alignment
hlaminer	HLAminer	1.3.1, 1.4	biology, phylogenetics
hmm-frame	HMM-FRAME	20140724	phylogenetics
hmmcleaner	HmmCleaner	0.180750	phylogenetics
hmmer	HMMER	3.2.1, 3.3.2, 3.4	biology, genomics
hmmer2go	hmmer2go	0.18.1	phylogenetics, biology
hmmratac	HMMRATAC	1.2.10	phylogenetics
hocort	HoCoRT	1.2.2	RNA-Seq, QC
homer	HOMER	4.10, 4.11, 4.8	biology, sequencing, ngs
homopolish	homopolish	0.3.3, 0.4.1	biology
hoomd	HOOMD	2.1.7	library, math
hpl	HPL	2.1	programming, performance_analysis
hpsandbox	hpsandbox	1.0.0	Programming
htmldoc	HTMLDoc	1.8.28, 1.9.3	documentation, web
htseq	HTSeq	0.11.2, 2.0.3	biology, ngs
humann	HUMAnN	2.8.1, 3.8	sequencing, biology
humann2	humann2	0.11.2, 2.8.1	phylogenetics
hxtorch	hxtorch	0.8	imaging
hyb	hyb	20141126, 20200815	biology, ngs, rna-seq
hybkit	hybkit	0.3.4, 0.3.5, 0.3.6	biology
hybpiper	HybPiper	2.1.5, 2.1.6, 2.3.0	biology, phylogenetics
hyde	HyDe	0.4.3	phylogenetics
hylite	hylite	2.0.2	genomics, biology
hypergen	Hyper-Gen	0.1.0	Programming
hyphy	HyPhy	2.5.4, 2.5.7, 2.5.8	biology, genomics
hypre	HYPRE	2.15.1, 2.18.2, 2.19.0	math
iannotatesv	iAnnotateSV	1.0.6, 1.0.9	biology, phylogenetics
iaps	iaps	02012023	programming
iassembler	iAssembler	1.3.2	biology, assembly
ibdmix	IBDmix	1.0.1	biology
ibdne	ibdne	20150815	biology, ngs
icommands	icommands	3.3.1	utility
idba-mt	IDBA-MT	1.0	biology, ngs
idba-ud	IDBA-UD	1.1.1, 1.1.1-512, 1.1.1-512-mem	genomics, phylogenetics
idl	IDL	8.3	language, programming, data_science
idr	IDR	2.0.3	phylogenetics
igb	IGB	8.4.1	biology, genomics
igblast	igBLAST	1.5.0, 1.7.0	biology
igor	IGoR	1.4.0	phylogenetics
igtp	iGTP	1.1	biology, phylogenetics
igv	IGV	2.3.91, 2.4.16, 2.8.6	biology, ngs, phylogenetics
illumina-utils	illumina-utils	2.11	phylogenetics
illumiprocessor	Illumiprocessor	2.0.9	phylogenetics
ima	IM and IMa	20091217	biology, genomics
ima2	Ima2	20120827	biology, genomics
ima2p	IMa2p	20170712	biology, phylogenetics
ima3	IMA3	22Aug18	molecular_dynamics
imagej	ImageJ	1.48	imaging
imagej2	imagej2	09302022	image processing, imaging
imagemagick	ImageMagick	7.0.8-20	imaging
imaginaire	Imaginaire	20201229	imaging, visualization, ai, machine_learning
imod	IMOD	4.7.15, 4.9.10	image_processing
imoka	imoka	1.0	biology, genomics
impg	impg	0.1.0	biology, alignment
impi	Intel MPI	5.1.1	programming, library
impute2	IMPUTE2	2.3.2	phylogenetics
impute5	IMPUTE5	1.1.5, 1.2.0	biology, math
indelible	INDELible	1.03	phylogenetics
infernal	Infernal	1.1.1, 1.1.4	biology, alignment
inla	INLA	20160718, 20170620	statistics, modeling, programming
inparanoid	InParanoid	4.1	biology
inspector	Inspector	1.0.2	biology, genomics
instruct	InStruct	20160723	phylogenetics
intel	Intel Compilers and Libraries	2023.0.0, 2023.2.0, 2024.1.0	language, programming, library, math, compiler
intervene	intervene	0.6.2	biology, phylogenetics
intrasom	Intrasom	1.0	python
ioapi	IOAPI	3.1, 3.2	climate
ipopt	IPOPT	3.12.10, 3.12.6	library, compiler, math
iprscan	InterProScan	5.60, 5.68, 5.69	biology
ipyrad	ipyrad	0.9.102, 0.9.53, 0.9.94	phylogenetics
iq-tree	IQ-TREE	2.2.2.7, 2.3.2, 2.3.6	biology, phylogenetics
irap	IRAP	0.8.1p7	biology, ngs
irep	irep	1.10	biology, genomics
irfinder	IRFinder	1.2.0, 1.3.0, 1.3.1	biology, rna-seq
isce2	isce2	2.6.3	library
isce3	ISCE3	0.23.0	library
isonclust	isONclust	0.0.6	phylogenetics
isonclust2	isonclust2	2.3	rna-seq
isosel	IsoSel	1.0	phylogenetics
isoseq3	IsoSeq3	3.7.0, 3.8.2, 4.0.0	biology, ngs
isown	ISOWN	20180820	phylogenetics
ispcr	isPcr	3.3	biology, phylogenetics
itk	ITK	3.20.1, 4.10.1	biology
itksnap	ITK-SNAP	3.0.0, 3.8.0	biology, neuroscience, imaging
itsx	ITSx	1.1b	phylogenetics
iupred2a	iupred2a	1.0	biology
iva	IVA	1.0.11	phylogenetics
ivar	iVar	1.3.1, 1.4.2	biology
jabba	Jabba	1.0	biology, phylogenetics
jacusa	JACUSA	1.2.0	biology, ngs, phylogenetics
jags	JAGS	3.3.0, 3.4.0, 4.2.0	statistics
janus	janus	20240412	biology
japsa	npScarf	1.7	phylogenetics
jasmine	Jasmine	1.1.4	phylogenetics
jasp	jasp	0.14.3	statistics
jasper	jasper	1.0.4	biology
java	JDK	20, 23, 9.0.1	programming
jbrowse2	jbrowse2	1.7.4	web
jcvi	JCVI	0.8.12, 1.0.13, 1.2.10	phylogenetics
je	Je	1.0	biology, ngs
jellyfish	Jellyfish	2.2.4, 2.2.6, 2.3.0	biology, ngs
jmodeltest	jModelTest	2.1.1	biology, genomics, phylogenetics
jo	jo	1.3	utility
jq	jq	1.6	utility
juicer	juicer	1.22.01, 2.0	phylogenetics
julia	Julia	1.7.3, 1.8.2, 1.9.2	programming, language, statistics
jupyter	Jupyter	6.2.0, 6.5.2, 6.5.4	programming
jutils	jutils	1.0	genomics, biology
jvarkit	JVARKIT	20180405	biology, phylogenetics
kaiju	Kaiju	1.6.2, 1.7.2	biology, phylogenetics
kaks	KaKs	1.2, 2.0	biology, genomics, phylogenetics
kalign	Kalign	3.3.1	biology, sequencing, alignment
kallisto	kallisto	0.46.2, 0.48.0, 0.50.1	biology, ngs, rna-seq
khmer	khmer	2.0, 2.1	biology, ngs
kim	KIM	1.7.2, 1.8.2, 1.9.3	simulation
king	KING	2.1.2, 2.3.0	biology, genomics
kissplice	KisSplice	2.4.0-p1	biology, RNA
klayout	KLayout	0.26.7	phylogenetics
kma	kma	20230106	alignment
kmc	KMC	3.1.0, 3.1.1, 3.2.1	phylogenetics
kmerdb	kmerdb	1.9.2	genomics, biology
kmerfreq	kmerfreq	4.0	biology, genomics
kmos	KMOS	0.3.21	phylogenetics
kneaddata	kneaddata	0.12.0, 0.7.4, 0.9.0	phylogenetics
knime	knime	4.7.3	data science
knitro	Knitro	12.2.0	math
kofamscan	KofamScan	1.3.0	phylogenetics
kover	kover	2.0.3	phylogenetics
kraken	Kraken	2.0.8b, 2.1.2, 2.1.3	biology, ngs
krakentools	KrakenTools	1.2	biology, ngs
krakenuniq	KrakenUniq	0.5.8, 0.7.3, 1.0.4	genomics, annotation
krona	Krona	2.8.1, 20161019	biology
ksnp	ksnp	3.021, 4.0	biology, phylogenetics, variant_calling
ksrates	Ksrates	1.1.1	genomics, biology
kvarq	kvarq	0.12.2	biology
lachesis	LACHESIS	2.1	phylogenetics
lambda	Lambda	0.9.4, 1.0.3, 2.0.0	biology, sequencing, phylogenetics
lammps	LAMMPS	30Jul16, 7Aug19, 7Dec15	molecular_dynamics
lammps-ppa	LAMMPS-PPA	23Jun2022	molecular Dynamics
lamp	LAMP	2.5	biology, genomics
laneta	laneta	20220517, 20220808, 20220812	biology
langdetect	langdetect	1.0.9	language, utility
lapack	LAPACK	3.11.0, 3.8.0	programming, library, compiler
last	Last	916, 979	biology, sequencing, alignment
lastools	LAStools	20200114	image_processing
lastz	LASTZ	1.02.00, 1.03.02, 1.04.00	biology, ngs
lazypipe	Lazypipe	1.2	genomics
lazypredict	LazyPredict	0.2.8	phylogenetics
lbzip	lbzip	2.5	compression
lcmodel	LCModel	6.3	biology, spectroscopy
ldak	ldak	5.2	phylogenetics, biology
ldblockshow	ldblockshow	1.40	biology
ldhat	LDhat	2.2a	biology, genomics
ldsc	ldsc	1.0.1	genomics, biology
leafaudio	leafaudio	0.1.0	machine_learning, audio
lefse	LEfSe	20180219	phylogenetics
lfmm	LFMM	1.4, 1.5	biology, phylogenetics
libchartdir	ChartDirector	5.1.0	library, data_science
libgfortran	libgfortran	3.0.0	programming
libint	Libint	2.5.0, 2.5.0b	library
liblemon	LEMON	1.2.3	library
libmesh	libMesh	1.5.0	math
libunistring	libunistring	0.9.7	library
libvips	libvips	8.5.4	image_processing
libxc	LIBXC	4.3.4, 6.2.2, 7.0.0	library, math
libxsmm	LIBXSMM	1.13	library, compiler, math
libzmq	LIBZMQ	4.3.1	library
liftoff	Liftoff	1.4.2, 1.6.2	phylogenetics
lighter	Lighter	1.1.3	genome
ligr	LIGR	2.05	biology, assembly
lillymol	LillyMol	6.1	nan
lima	lima	2.0.0, 2.2.0, 2.7.1	phylogenetics
lingua	lingua	1.0.1	language, utility
links	LINKS	1.8.5, 1.8.6	biology, genomics
linksbrowser	Linksbrowser	2.14	web
liqa	LIQA	1.0.0, 1.1.16	phylogenetics
llama	llama	2, 3	library, math
llava	llava	1.6	Machine Learning
lmap	LMAP	1.0.2	biology, phylogenetics
lncscore	lncScore	1.0.2	biology, phylogenetics
lobstr	lobSTR	4.0.6	biology, phylogenetics
localbrainage	localbrainage	20210415	biology, machine_learning
localizer	localizer	1.0.4, 1.0.5	phylogenetics
locuszoom	LocusZoom	1.4	phylogenetics
lofreq	LoFreq	2.1.3.1	phylogenetics
longqc	LongQC	1.2.0c	phylogenetics
longranger	LongRanger	2.1.5, 2.2.2	biology, phylogenetics
longshot	longshot	0.4.5	genomics
longstitch	LongStitch	1.0.3	genomics, biology
lordec	LoRDEC	0.9	phylogenetics
lorma	LoRMA	0.3, 0.5	biology, ngs
loter	loter	1.0	genomics,
lrbinner	LRBinner	0.1	biology, genomics
lrgapcloser	lrgapcloser	09042018	biology
ls-dyna	LS-DYNA	700, 711, 901	physics
lsd2	LSD2	1.6.5	phylogenetics
ltr_finder	ltr_finder	1.07	biology, phylogenetics
ltrretriever	LTRRetriever	2.1, 2.5, 2.9.0	biology, phylogenetics
lua	Lua	5.3.2, 5.3.4, 5.4.6	programming, language
lumpy	lumpy-sv	0.2.1, 0.2.13, 0.3.1	biology, genomics
lzo	LZO	2.09	library, compression
m5tools	M5nr	20121126	biology, genomics
macaulay2	Macaulay2	1.15	phylogenetics
mach	MACH	1.0.18	biology, genomics, ngs
mach2vcf	Mach2VCF	20150515	biology
macrel	Macrel	1.3.0	biology, genomics
macs	MACS	2.0.10, 2.1.2, 2.2.7.1	biology, chip-seq
maestro	Schrodinger Maestro	2024-1	chemistry, molecular_dynamics
maffilter	MafFilter	1.3.0	phylogenetics
mafft	MAFFT	7.490, 7.505, 7.520	biology, sequencing
mageck	MAGeCK	0.5.9.4	phylogenetics
mageck-vispr	MAGeCK-VISPR	0.5.6	phylogenetics
mageckflute	MAGeCKFlute	1.14.0	phylogenetics
magenta	Magenta	2.1.2	phylogenetics
magicblast	magicblast	1.6.0	genomics, biology
magma-gwas	MAGMA-GWAS	1.09	phylogenetics
magpurify	magpurify	2.1.2	genomics
magus	magus	20220121	sequencing, alignment
majiq	MAJIQ	2.2, 2.3, 2.5.7	phylogenetics
maker	Maker	2.31.10, 2.31.6, 3.01.03	biology
manorm	MAnorm	20120316	biology, phylogenetics
manta	MANTA	1.6.0	phylogenetics
mantis	mantis	1.0.4	phylogenetics
mapclassify	mapclassify	2.4.2	statistics, mapping, geospatial
mapdamage	mapdamage	2.2.1	ngs, sequencing, biology
mapthin	MapThin	1.11	phylogenetics
maq	Maq	0.7.1	biology, ngs
marginpolish	MarginPolish	1.0.0	phylogenetics
mark	MARK	2.0.1	data_science, math
markerminer	MarkerMiner	20150710	biology, genomics
mash	Mash	1.1, 2.3	biology, genomics
mashmap	MasHmap	2.0	phylogenetics
mashtree	mashtree	1.2.0	genomics, biology
maskrc-svg	maskrc-svg	0.5	genomics
mass	MASS	1.1.1	genomics, biology
massmine	MASSMINE	0.10.0, 0.11.0, 0.9.5	data_mining
masurca	MaSuRCA	4.0.8, 4.0.9, 4.1.0	biology, alignment
mathematica	Mathematica	13.1, 14.0	math
matlab	MATLAB	2023b, 2024a, 2024b	math, language
mats	MATS	4.0.2, 4.1.0, 4.2.0	biology, ngs, rna-seq
matt	matt	1.3.1	nan
mauve	Mauve	2.3.1	biology, ngs, genomics
mawk	mawk	1.3.4-20150503	language
maxbin	maxbin	2.1.1	biology, ngs
maxima	Maxima	5.41.0	math
mc	MC	4.6.1	shell
mcarts	mCarts	1.0.2	biology, genomics, math
mccortex	mccortex	1.0	phylogenetics
mcfost	mcfost	4.1.07	astronomy
mcl	MCL	12-135, 14-137	biology, genomics
mcnp	MCNP	6, 6.1, 6.3.0	physics
mcnpx	MCNPX	2.7.0	physics
mcr	MCR	2020a, 2020b, 2023b	math, language
mcscanx	MCScanX	20130328	biology, phylogenetics
mdanalysis	mdanalysis	1.1.1	physics, biology
mecat	MECAT	20180308	phylogenetics
medaka	Medaka	1.7.2, 1.8.0, 2.0	biology, phylogenetics
medusa	Medusa	1.6	phylogenetics
mega	MEGA	11.0.13, 7.0.26	biology, phylogenetics
mega2	Mega2	4.9.2, 6.0.0	biology, phylogenetics
megahit	MEGAHIT	1.1.1, 1.1.4, 1.2.9	biology, phylogenetics
megalodon	Megalodon	2.0.0, 2.4.1	ngs, genomics
megan	MEGAN	6.23.4, 6.25.9, 6.4.15	biology, ngs
megasat	MEGASAT	1.0	phylogenetics
megraft	Megraft	1.0.2	biology, sequencing
meld	MELD	0.4.14, 0.4.19, 0.5.9	chemistry, molecular_dynamics
melting	MELTING	4.3.1	biology, genomics, rna
meme	MEME	5.0.2, 5.0.5, 5.4.1	biology, sequencing
mentalist	MentaLiST	0.1.3	biology, phylogenetics
meraculous	Meraculous	2.0.5	biology, ngs
mercurial	Mercurial	4.8.2	revision_control
merge_peaks	merge_peaks	0.1.0	workflow_automation
merlin	Merlin	1.1.2	biology, variant_calling
merqury	Merqury	1.1, 1.3	phylogenetics
meryl	Meryl	1.0	phylogenetics
meshclust	MeShClust	1.2.0	biology
meshroom	Meshroom	2019.2.0	phylogenetics
meson	Meson	1.2.3	biology, ngs, sequencing
met	MET	10.0	climate, modeling
meta-marc	Meta-Marc	1.0.0	phylogenetics
meta-tissue	Meta-Tissue	0.4	biology, genomics
metabat	MetaBAT	0.32.4, 2.13	biology, genomics
metabcc_lr	MetaBCC-LR	2.0.0	biology, genomics
metabin	Metabin	1.0	genomics
metabolic	metabolic	4.0	phylogenetics
metacherchant	MetaCherchant	0.1.0	biology, phylogenetics
metacluster	MetaCluster	5.0b	biology, genomics
metacompare	MetaCompare	20181016	phylogenetics
metacrast	metacrast	20200309	phylogenetics
metaeuk	Metaeuk	6.0	phylogenetics
metagenemark	MetaGeneMark	2.10, 3.26	biology, genomics
metal	METAL	20110325	biology, ngs, genomics
metalaffa	MetaLAFFA	1.0.0	phylogenetics
metamaps	MetaMaps	20201207	phylogenetics
metannot	METANNOT	20171129	phylogenetics
metaphlan	Metaphlan	4.0.6, 4.1.0, 4.1.1	phylogenetics
metaphlan2	MetaPhlAn2	2.7.7, 2.96.1, 3.0.3	biology, phylogenetics
metaphysicl	MetaPhysicl	1.0.0	math, astronomy, simulation
metashape	Metashape	1.8.4, 2.1.1	nan
metasv	MetaSV	0.5.4	biology, phylogenetics, ngs
metavelvet	MetaVelvet	1.2.06	biology, genomics
metawrap	metaWRAP	1.2	phylogenetics
metaxa2	Metaxa2	2.1.1, 2.1.3, 2.2.3	biology, ngs, sequencing
methylartist	methylartist	1.3.0	biology
methyldackel	MethylDackel	0.5.0, 0.6.1	phylogenetics
methylpy	methylpy	1.2.9	biology, phylogenetics
metilene	Metilene	0.2.8	biology, genomics, methylation
metis	METIS	5.1.0, 5.2.1	utility
mfannot	Mfannot	20180405	biology, phylogenetics
mfold	mfold	3.6	biology, structure, rna
mg-rast	mg-rast	20150919	biology, genomics
mgefinder	MGEfinder	1.0.5	phylogenetics
mgert	MGERT	1.0.1	phylogenetics
mgescan	MGEScan	20160416	biology, genomics
mgltools	MGLTools	1.5.7	biology, visualization
mgs2amr	Mgs2amr	2.0.1	genomics
mhap	MHAP	1.6	biology, sequencing
mhcflurry	MHCflurry	1.4.3	phylogenetics
mia	MIA	20130201	biology, ngs
micop	micop	03312022	genomics
microbeannotator	MicrobeAnnotator	2.0.5	annotation, biology
midas	MIDAS	1.3.2, 20160830	biology, phylogenetics
migraten	MIGRATE-N	4.2.14, 4.4.4, 5.0.4	biology, genomics
mikado	Mikado	2.3.3	biology, genomics, sequencing, pipeline
mike	MIKE	1.0	geospatial, fluid_dynamics, modeling
milvus	milvus	2.4.15	database, llm, container
minced	Minced	0.2.0	biology, genomics
minia	Minia	3.2.6	genomics, biology
miniasm	Miniasm	0.2-r168, 0.3-r179	biology, phylogenetics
minicaller	MiniCaller	20161201	biology, ngs, phylogenetics
minigraph	minigraph	0.15, 0.20	phylogenetics
minimac	minimac2	1-20130717, 2-20140915, 3-20150727	biology, ngs
minimap	minimap	2.21, 2.9-r720, 2.ax	biology, phylogenetics
minimap2	minimap2	2.24, 2.28	genomics, biology
minipolish	Minipolish	0.1.3	biology, genomics
miniprot	Miniprot	0.12	biology, genomics
miniwdl	miniwdl	1.11.1	bioinfomatics
minkowskiengine	MinkowskiEngine	0.5.3, 0.5.4a	machine_learning
minpath	MinPath	1.4	biology, phylogenetics
mira	MIRA	4.0.rc1, 4.9.6, 5rc2	biology, genomics, assembly
miranda	miRanda	1.9	phylogenetics
mirbshunter	miRBShunter	0.2	phylogenetics
mirdeep	mirdeep	0.1.0, 0.1.1, 2.0.1.3	phylogenetics
mirdp2	miRDP2	1.1.4	biology, genomics
mireap	Mireap	0.20	biology
mirge	miRge	2.0	phylogenetics
misa	Misa	1.0	biology, genomics
miso	MISO	0.5.3	biology, ngs, sequencing, rna-seq
mistral	mistral	0.1.5	library, math
mite-hunter	MITE-Hunter	20111101	biology, phylogenetics
mitobim	MITObim	1.9.1	phylogenetics
mitofinder	MitoFinder	1.4.1	phylogenetics
mitohifi	mitohifi	2.2, 3.2	genomics, sequencing
mitophast	MitoPhAST	3.0	phylogenetics
mitos	Mitos	2.1.9	biology, phylogenetics
mitsuba2	Mitsuba2	2.2.1	graphics
mixcr	MiXCR	2.1.8, 3.0.13	biology, phylogenetics
mixmhc2pred	MixMHC2pred	1.2	phylogenetics
mixmhcpred	MixMHCpred	2.0.2	phylogenetics
mixmogam	mixmogam	20190322	phylogenetics
mkl	MKL	2019.1.144, 2020.0.166, 2020.2.0	programming, library, math, compiler
mlcoalsim	mlcoalsim	1.9916b	biology, phylogenetics
mlpack	mlpack	3.4.2	library
mlst	mlst	2.15.2, 2.23.0	phylogenetics
mlst-check	mlstcheck	2.1	phylogenetics
mmaction2	mmaction2	1.0.0	Machine_Learning, Visualization
mmseq	MMSEQ	1.0.8	biology, genomics
mmseqs2	MMseqs2	11, 12, 14	phylogenetics
mmvec	MMvec	1.0.5, 1.0.6	metabolomics
mnetools	MNEtools	0.22.0, 1.3.1, 1.4.0	phylogenetics
moabs	MOABS	1.2.9, 1.3.2, 1.3.4	biology, ngs
mobsuite	mobsuite	3.1.0, 3.1.9	sequencing, biology
moccasin	MOCCASIN	0.25	phylogenetics
moco	moco	0.4.0	modeling, tools
model_card_toolkit	Model Card Toolkit	2.0.0	Machine_Learning, Utility, Workflow_automation
modeller	MODELLER	9.14, 9.23	biology, modeling, structure
modeltest	MODELTEST	0.1.2, 0.1.7	biology, phylogenetics
moderncsv	ModernCSV	2.0.2	editor, viewer
modkit	Modkit	0.4.1	genomics, bioinformatics
modulus	Modulus	23.11, 24.01, 24.07	physics, ai, neural_network
molden	Molden	5.0, 7.3	chemistry, structure
molpro	MolPro	0.1	biology
molprobity	MolProbity	20221216	biology
momi	momi	2.1.19	phylogenetics, biology
monai	monai	0.5.3, 0.8, 0.8.1	healthcare
mongodb	MongoDB	4.0.3	database
moni	Moni	0.2.0	genomics, biology
mono	mono	5.18	linux, programming
monolix	Monolix	2023R1, 4.3.2	modeling, biology
moose	MOOSE	20220610, 20230320, 20230711	physics, simulation
mopac	mopac	22.1.1	chemistry
morpheus	MORPHEUS	23.01	machine_learning
mosaic	Mosaic	1.7.4	phylogenetics
mosaik	MOSAIK	2.1.33, 2.2.3, 2.2.30	biology, alignment
mosdepth	Mosdepth	0.2.3, 0.3.1	biology, phylogenetics
moses	moses	0.3.1	machine learning, data science
mothur	Mothur	1.41.3, 1.46.1, 1.48.0	biology
motioncor2	MotionCor2	1.2.3, 1.3.1, 1.6.4	imaging
motu	mOTU	1.1	biology, genomics
motus	mOTUs	2.5.1	phylogenetics
mountainsort	MountainSort	0.9.0	library
mpack	MPACK	0.8.0	library
mpb	MPB	1.5	library, math
mpboot	MPBoot	1.1.0	biology, phylogenetics
mpest	MP-EST	1.4	biology, ngs, sequencing
mpfr	MPFR	3.1.6, 4.2.1	library, math
mpi-test-suite	mpi-test-suite	1.1.1	utility
mpinterfaces	mpinterfaces	20170613	math
mrbayes	MrBayes	3.2.4, 3.2.5, 3.2.6	biology, phylogenetics
mricrogl	MRIcroGL	20201102, 20210327, 20211006	biology, imaging
mricron	MRIcron	201306, 20161012, 20190911	biology, imaging
mriqc	mriqc	0.11.0, 0.16.1, 22.0.1	imaging, biology
mrtrix	MRtrix	3.0.1, 3.0.3, 3.0rc2	statistics
mrtrix3tissue	mrtrix3tissue	5.2.9	phylogenetics
ms	ms	20171108	phylogenetics
ms-dial	ms-dial	4.4.8	biology, metabolomics
msfinder	msfinder	3.52	biology, metabolomics
msings	mSINGS	20180810	phylogenetics
msmc-tools	MSMC-Tools	20190614	phylogenetics
msprime	msprime	0.7.4, 1.2.0	phylogenetics
mstatx	MstatX	1.0	biology, phylogenetics
mstmap	MSTmap	1.0	phylogenetics
msvar	msvar	1.3	biology, genomics
mtg2	MTG2	2.15	phylogenetics
mtr	mTR	20210526, 20240801	biology, genomics
mugsy	Mugsy	1.2.3	biology, phylogenetics
multimatchgaze	Multimatch-gaze	0.1.3	math, data_science
multiqc	MultiQC	1.21, 1.24, 1.7	biology, ngs, sequencing
mummer	MUMmer	3.23, 4.0.0beta2	biology, genomics
muscle	MUSCLE	3.8.31, 5.1	biology, alignment
muse	MuSE	1.0rc	phylogenetics
musket	Musket	1.1	biology, genomics, ngs
mutect	MuTect	1.1.4, 1.1.7	biology, genomics
mutmap	mutmap	2.3.3	biology
mutsig	MutSig	1.4, 1.41	biology, genomics
mvftools	mvftools	20191124	phylogenetics
mvrsion	mvrsion	07302018	sequencing
mykrobe	mykrobe	0.12.2	biology
mzmine	MZMine	2.53, 3.3.0	biology, spectroscopy
namd	NAMD	2.14b2, 3.0 Alpha, 3.0b2	molecular_dynamics
nano	NANO	2.8.2	programming
nanocaller	nanocaller	3.1.0	sequencing
nanocomp	nanocomp	1.17.0	programming, sequencing
nanocompore	Nanocompore	1.3.0	biology, genomics
nanocount	NanoCount	0.2.1	phylogenetics
nanodisco	Nanodisco	1.0.3	phylogenetics
nanofilt	Nanofilt	2.7.1	phylogenetics
nanolyse	nanolyse	1.2.0	genomics, biology
nanoplot	NanoPlot	1.30.1, 1.42.0	phylogenetics
nanopolish	Nanopolish	0.11.1, 0.13.2, 20171006	biology
nanoq	nanoq	0.10.0	biology, ngs, nanopore
nanostripper	nanostripper	0.1	phylogenetics, biology
nanosv	NanoSV	1.2.0, 1.2.3, 1.2.4	biology, genomics
nanovar	NanoVar	1.3.9	phylogenetics
napari	Napari	0.3.8, 0.4.7	phylogenetics
nbody	NBODY	6	astronomy
ncbi-fcs	ncbi-fcs	0.4.0, 0.5.0, 0.5.4	genomics
ncbi-genome-download	ncbi-genome-download	0.3.3	biology, genomics
ncbi-vdb	ncbi-vdb	2.6.3, 2.8.2	ngs
ncbi_blast	NCBI BLAST+	2.7.1, 2.8.1, 2.9.0	biology
ncbi_cli	ncbi_cli	15.3.1	biology, sequencing, library
ncbi_toolkit	NCBI C++ Toolkit	12.0.0, 21.0.0, 7.0.0	biology, programming, library, compiler
nccl	nccl	20.11	programming, library, gpu
ncftp	ncftp	3.2.5	file_management
ncl	NCL	6.1.2, 6.3.0, 6.6.2	climate
nco	NCO	4.2.1, 4.4.3	data_science
ncview	ncview	2.1.2, 2.1.7	visualization
necat	NECAT	202001019, 20200803	phylogenetics
necklace	Necklace	1.00	biology, phylogenetics
neestimator	NeEstimator	2.1	biology
nemo	nemo	1.2.0, 1.22.0, 1.23.0	ai, machine_learning
neovim	neovim	0.8.1, 0.8.3, 0.9.5	programming, shell
nerfstudio	nerfstudio	1.1.3	Machine Learning
netcdf	NetCDF	4.3.3, 4.4.3, 4.7.2	data_science
netcdf-c	NetCDF-C	4.8.1, 4.9.0, 4.9.2	data_science
netcdf-f	NetCDF-F	4.5.3, 4.5.4, 4.6.1	data_science
netlogo	NetLogo	5.3.64, 6.1.1, 6.2.0	modeling
neuron	NEURON	7.7.2, 8.0.0, 8.2.1	biology, neuroscience
newbler	Newbler	2.7, 2.8, 2.9	biology, ngs, assembly, de_novo
newick_utils	newick_utils	1.6, 1.7	biology, phylogenetics
newickutils	newick-utils	1.6	biology, genomics, phylogenetics
newtargets	NewTargets	20210215	biology
nextclade	nextclade	2.9.1, 3.2.0, 3.8.2	phylogenetics, genomics
nextdenovo	NextDenovo	2.4.0	phylogenetics
nextflow	Nextflow	23.10.0, 23.10.1, 24.04.2	biology, workflow_automation
nextgenmap	NextGenMap	0.5.5	phylogenetics
nextpolish	NextPolish	1.3.1	phylogenetics
nextstrain	Nextstrain	1.16.1	phylogenetics
nf-core	nf-core	2.11.1, 2.14.1, 2.7.2	biology, workflow_automation
ngc-gromacs	GROMACS	2022.3	Chemistry, Molecular Dynamics
ngc-lammps	LAMMPS	15Jun2023, 20220504, 3Nov2022	Molecular Dynamics
ngc-monai	monai	0.8.1, 0.9.0, 1.0.1	healthcare
ngc-monailabel	MONAI label	0.3.2, 0.6.0	healthcare
ngc-mxnet	mxnet	22.08	healthcare
ngc-pytorch	PyTorch	1.9.0, 2.3.0, 2.5.0	library, math
ngc-tensorflow	TensorFlow	1.15.5, 2.15.0, 2.4.0	library, math
ngccli	NGC CLI	2.10.1	shell
ngmerge	NGmerge	0.3	phylogenetics
ngmlr	ngmlr	0.2.6, 0.2.7	biology, phylogenetics
ngs-sdk	NGS-SDK	1.2.4, 1.3.0	biology, healthcare, programming, library
ngsbits	ngs-bits	0.1	biology, sequencing
ngsremix	ngsremix	20221117	genomics
ngstools	ngstools	20150816	biology, ngs
nilearn	nilearn	0.7.0, 0.9.0	phylogenetics
nimare	nimare	0.0.5	neuroscience
nipype	Nipype	1.6.0, 1.7.0, 1.8.0	biology, neuroscience, imaging
nlp	nlp	1.1, 1.2, 1.3	machine_learning
nlr-annotator	nlr-annotator	0.7	phylogenetics
nlr-parser	NLR-Parser	1.0	phylogenetics
nlrtracker	nlrtracker	20240306	biology
nmrpipe	NMRPipe	7.9, 8.2	chemistry, biology
nonmem	NONMEM	7.3.0, 7.4.4	modeling
nonpareil	nonpareil	3.3.4	phylogenetics
novoalign	Novoalign	2.08.02, 3.00.02	biology, ngs
novoplasty	NOVOPlasty	3.7, 4.2, 4.3	phylogenetics
nphase	nPhase	1.1.3	biology, pipeline
nquire	nQuire	20180405	phylogenetics
nsight	Nsight	2022.1, 2024.3.2.0	gpu, performance_analysis, utility
nsightsys	Nsightsys	2022.2.1, 2024.5.1	gpu, performance_analysis, utility
nt	nt	20220404	sequencing, neuroscience
ntedit	ntEdit	1.2.1	phylogenetics
ntjoin	ntJoin	1.1.4	biology, genomics
nubeamdedup	nubeamdedup	20200907	phylogenetics
nucdiff	NucDiff	2.0.3	phylogenetics
nucleoatac	NucleoATAC	0.3.1	biology
nuke	Nuke	14.0v5	Graphics, Utility, Visualization
nullarbor	Nullarbor	1.41	biology, phylogenetics
numba	Numba	0.36.2, 0.43.1, 0.48.0	compiler
nupack	NUPACK	3.2.2	phylogenetics
nvhpc	nvhpc	23.7, 24.3, 24.5	language, programming, library, math, gpu
nvidia	nVidia HPC Compilers	20.11	compiler
nwchem	NWChem	6.8, 7.2	chemistry
nxtrim	NxTrim	0.4.1	biology, ngs
oases	Oases	0.2.08	biology, ngs, assembly
oatk	Oatk	1.0	genomics
obitools	Obitools	1.2.13, 3.0	biology, ngs, sequencing
ocaml	OCaml	4.02.3	language, programming
ococo	OCOCO	0.1.2.6	biology, phylogenetics
octave	octave	6.4.0, 7.2.0, 7.3.0	math
odgi	odgi	0.6, 0.8.4	phylogenetics
olego	Olego	1.1.2, 1.1.5, 1.1.6	biology, ngs, rna-seq
ollama	ollama	0.3.8	LLM
omindel	OMindel	20180129	phylogenetics
omnic	OMNI-C	1.0	genomics
omniclip	omniCLIP	0.1.0	phylogenetics
omniverse	OMNIVERSE	beta211004	gpu
omsv	OMSV	1.0.1	phylogenetics
oneformer	OneFormer	1.0	ai, image_processing, imaging
ont-bonito	ONT-Bonito	0.1.5, 0.5.3, 0.6.0	phylogenetics
ont-fast5-api	ont_fast5_api	2.0.1, 4.0.2	phylogenetics
ont_tutorial_cas9	ont_tutorial_cas9	20190705	phylogenetics
open-cravat	open-cravat	2.0.1	biology, genomics
open3d	open3d	0.13.0, 0.17.0	graphics
openacc	OPENACC	16.7	programming
openbabel	OpenBabel	2.3.2, 2.4.1, 3.1.1	biology
openblas	OpenBLAS	0.2.20, 0.3.24	programming, library
opencl	OpenCL	18.1.0.013	phylogenetics
opencv	OpenCV	4.5.2, 4.7.0	library
openfoam	OpenFOAM	4.1, 5.0, 8.0	fluid_dynamics
openmc	openmc	0.14.0, 0.15.0	physics
openmm	OpenMM	7.6.0, 8.0.0, 8.1.2	chemistry, molecular_dynamics
openmpi	OpenMPI	4.1.4, 4.1.5, 4.1.6	programming, library
openneuro	OpenNeuro	3.17.4, 3.37.4, 4.19.2	biology, data_science
opennmt-py	opennmt-py	3.1.0	language, machine_learning
openpiv	OpenPIV-python-gpu	0.21.2, 20190506-gpu	programming, imaging
openpose	OpenPose	20230106	image_processing
openrdp	openrdp	0.1.0-rc2	biology
opensim	OpenSim	4.3	phylogenetics
openslide	OpenSlide	3.4.1	imaging
openssl	Openssl	3.3.0	libray
openstructure	openstructure	2.3.1	biology
openusd	OpenUSD	23.08	digital twin, simulation
optitype	OptiType	1.3.1	biology, phylogenetics
orange3	Orange3	3.3.6	data_mining
orca	Orca	4.0.1.2, 5.0.1, 5.0.4	chemistry
organellepba	OrganellePBA	20180904	phylogenetics
orthofiller	OrthoFiller	1.1.4	phylogenetics
orthofinder	OrthoFinder	2.3.11, 2.5.2, 2.5.5	biology, ngs
orthofisher	Orthofisher	0.1.2	biology, genomics
orthograph	Orthograph	0.6.3	orthology
orthologer	Orthologer	2.2.0	biology
orthomcl	OrthoMCL	2.0.9	biology, genomics
osl	OSL	1.1.0	biology, neuroscience, imaging
oslom	oslom	0.3.0	plotting
osprey	osprey	1.1.0, 2.5.0	spectroscopy, neuroscience
otb	OTB	5.8.0	geospatial
ovito	ovito	3.8.5, 3.9.4	programming
owitools	owitools	1.0	metabarcoding, bioinformatics, ecology
p4est	p4est	1.1, 2.8	library
p4vasp	p4vasp	0.3.29, 0.3.30	chemistry, structure
p53mh	p53MH	20020901	biology, sequencing
p7zip	p7zip	9.20.1	utility
pacbio	PacBio	10.2.0.133434, 11.0.0.146107, 7.0.1	biology, ngs, workflow_automation
package-gfe	Package-GFE	20150701	biology, genomics
pacmap	PacMAP	0.7.0	genomics
paladin	PALADIN	1.3.1	biology, phylogenetics
pales	PALES	122	physics
paml	PAML	4.8a, 4.9a, 4.9h	biology, phylogenetics
panaroo	panaroo	1.3.3	biology, genomics
pandaseq	Pandaseq	20140808, 20150627	biology, ngs, sequencing
pandoc	Pandoc	2.2.2.1	utility
pangolin	pangolin	2, 4.3	phylogenetics
panseq	panseq	3.2.1	phylogenetics
pantools	pantools	4.3.1	biology, genomics
panx	panX	1.6.0	phylogenetics
papi	PAPI	5.5.1, 5.7.0	programming, performance_analysis
parabricks	parabricks	4.2.1, 4.3.0, 4.3.1	phylogenetics
parallel	parallel	20150122, 20170322	shell, workflow_automation
paralyzer	paralyzer	1.5	phylogenetics
paraview	ParaView	5.4.1, 5.7.0, 5.9.1.1	data_science
paraview_server	ParaView Server	5.10.1	data_science
pargenes	ParGenes	1.2.0	phylogenetics
parlai	ParlAI	1.3.0, 1.5.0	phylogenetics
parmetis	PARMETIS	4.0.3	utility
parsnp	Parsnp	1.2, 1.5.0, 1.6.2	biology, phylogenetics
partitionfinder	PartitionFinder	2.0.0-pre-20160513, 2.1.1-20161205, 2.1.1.0	biology, phylogenetics, genomics
pasa	PASA	2.2.0-r20171013, 2.4.1, 2.5.3	biology, genomics, ngs
pasta	PASTA	0.2.0, 1.7.8, 20160616	biology, alignment
pathd8	PATHd8	1.0	biology, phylogenetics
pathoscope	pathoscope	2.0.7	sequencing, genomics, biology
patric	PATRIC	1.034	machine_learning
pauda	PAUDA	1.0.1	biology, ngs, phylogenetics
paup	PAUP	4.0a166, 4.0a168, 4.0b10	biology, phylogenetics
pb-assembly	PB-Assembly	0.0.6, 0.0.8	biology, ngs, sequencing
pbalign	pbalign	20160921, 20161221	biology
pbccs	PBCCS	5.0.0, 6.4.0	phylogenetics
pbcore	pbcore	1.7.1	biology
pbgcpp	PBGCpp	1.9.0	phylogenetics
pbipa	pbipa	1.8.0	phylogenetics, biology
pbjelly	PBJelly	15.8.24	biology, ngs
pbmm2	pbmm2	1.13.1, 1.3.0	phylogenetics
pbpigeon	pbpigeon	1.2.0	biology, ngs
pbrt	pbrt	20181017	phylogenetics
pbsmrtpipe	pbsmrtpipe	0.63.0	biology, programming
pbtk	pbtk	3.1.0	biology
pbtranscript-tofu	pbtranscript-tofu	20150317, 20160119	biology, ngs
pcangsd	pcangsd	1.2	biology
pcit	PCIT	2014	biology
pcre	PCRE	8.38, 8.39	programming, library
pda	PDA	1.0.3	biology, phylogenetics
pdb2pqr	pdb2pqr	2.1.0	protein, modeling, biology
pdt	Program Database Toolkit	3.20, 3.22, 3.24	language, programming, performance_analysis
peaksplitter	PeakSplitter	1.0	biology, chip-seq
pear	PEAR	0.9.2	biology, genomics, ngs
peneasy	peneasy	20150530	physics
penncnv	PennCNV	1.0.5	phylogenetics
perl	Perl	5.16.0, 5.20.0, 5.24.1	programming, language
perm	PerM	0.4.0	biology, ngs, mapping
petsc	PETSc	3.8.1, 3.8.3, 3.8.4	math
pfamscan	PfamScan	1.3, 1.5	biology, genomics
pgap	PGAP	20230306, 20231003, 20240703	biology, genomics, annotation, pipeline
pgdspider	PGDSpider	2.0.9.0, 2.1.1.5	biology, ngs
pggb	pggb	0.6.0, 20201106, 20210121	phylogenetics
phame	PhaME	1.0.3	phylogenetics
phanotate	phanotate	1.5.0	genomics
pharmcat	pharmcat	1.8.0	biology, phylogenetics
phase	PHASE	2.1.1	phylogenetics
phast	PHAST	1.5	biology, phylogenetics
phenix	Phenix	1.10.2155, 1.17.1, 1.8.1069	material_science
phi	PHI	3.1.1, 3.1.2b, 3.1.6	math
phispy	PhiSpy	3.2	phylogenetics
phlawd	PHLAWD	20170427	biology, phylogenetics
photoscan-pro	PhotoScan	1.4.1, 1.4.5	image_processing
photutils	Photutils	0.5	astronomy
phyling	PHYling	1.0	biology, phylogenetics, genomics
phylip	PHYLIP	3.696	biology, phylogenetics
phyloacc	PhyloAcc	1.0	phylogenetics
phylobayes	PhyloBayes	3.3f	biology, phylogenetics
phyloflash	phyloFlash	3.3b4	phylogenetics
phylonet	phylonet	3.5.7, 3.8.2	biology, phylogenetics
phyloparser	PhyloParser	20180404	phylogenetics
phylophlan2	PhyloPhlAn2	0.41	phylogenetics
phylopypruner	phylopypruner	1.2.3	phylogenetics
phylosift	PhyloSift	1.1	biology, genomics, phylogenetics
phylotf2	phyloTF2	20210726	biology, genomics, alignment
phyluce	Phyluce	20180727, 20190308, 20191015	biology, ngs, sequencing
phyml	PhyML	3.0, 3.1, 3.3.20220408	biology, phylogenetics
phynd	phynd	20200409	phylogenetics
physher	Physher	1.0.2	phylogenetics
phyutility	PHYUTILITY	2.7.1	biology
phyx	Phyx	1.1	phylogenetics
pia2	PIA2	20180305	biology, phylogenetics
picard	Picard-tools	2.9.2, 3.1.1, 3.2.0	biology, ngs
picrust	PICRUSt	1.1.0, 1.1.3, 1.1.4	biology, phylogenetics
picrust2	PICRUSt	2.3.0b	biology,phylogenics
picsl	PICSL	1.3	imaging
piggy	Piggy	20171220	biology, ngs
pigz	Pigz	2.4	compression
pilon	PILON	1.22, 1.24	biology, ngs, phylogenetics
pindel	Pindel	0.2.5b8	biology, phylogenetics
pipe-clip	pipe-clip	1.1.0	biology, ngs
pipits	pipits	1.3.6, 1.4.0	biology, sequencing
piranha	Piranha	1.2.1	biology, phylogenetics
plantismash	PLantismash	1.0	biology, genomics
planttribes	PlantTribes	1.0.4	phylogenetics
plasme	plasme	1.1	Genomics
plast	PLAST	1.0, 2.3.2	biology
platanus	platanus	1.2.4	phylogenetics
platon	Platon	1.6	biology, sequencing
platypus	Platypus	0.8.1	biology, ngs
plek	PLEK	1.2.2	biology, phylogenetics
plink	Plink	2.00a2, 2.00a3LM, 2.00a5LM	biology, genomics, phylogenetics
plinkseq	plinkseq	0.10	biology, library
plip	plip	2.3.0	Protein-structure
plotsr	plotsr	0.5.4	genomics, biology
plumed	PLUMED	2.7.3, 2.9.0, 2021.2	chemistry, molecular_dynamics
pm4py	pm4py	2.7.4	Data_Mining, Machine_Learning
pod5	pod5	0.1.5, 0.3.6, 20220621	sequencing
polygembler	PolyGembler	1.0	phylogenetics
polyphen	PolyPHen	2.2.2.r405b	biology, genomics
polyply	polyply	1.3.0	phylogenetics, biology
polypolish	Polypolish	0.5.0	biology, genomics
pomdp	pomdp	1.3.4	software
pomoxis	pomoxis	0.1.11, 0.2.5, 0.3.2	biology, phylogenetics
popcorn	popcorn	20211104	phylogenetics, biology
poplddecay	PopLDdecay	3.40	phylogenetics
popoolation	popoolation	1.2.2	biology, phylogenetics
popoolation2	popoolation2	1.201	biology, phylogenetics
porechop	Porechop	0.2.4	phylogenetics
poretools	Poretools	0.6.1	phylogenetics
portcullis	portcullis	1.2.3	phylogenetics
posigene	PosiGene	20171113	biology, phylogenetics
povray	POV-Ray	3.7, 3.7.0.8	graphics
powerfit	powerfit	2.0.0	Physics
pplacer	pplacer	1.1.alpha19	biology, phylogenetics, genomics
prank	PRANK	170427, 20150803	biology, alignment
predector	Predector	20201110	phylogenetics
predectorutils	predectorutils	0.9.1	biology, genomics
preplot	preplot	14.0.2	nan
preseq	Preseq	0.0.4	biology, ngs
price	PRICE	1.2	biology, ngs
primer3	Primer3	2.3.4	biology, genomics
primus	primus	1.8.0	biology, phylogenetics
prinseq	PRINSEQ	0.20.4	biology, sequencing
prinseq++	PRINSEQ++	1.2	phylogenetics
probabel	ProbABEL	0.4.2, 0.4.3, 0.4.5	genomics
probalign	probalign	1.4	biology, ngs
processing	Processing	3.4	programming, language, visualization
prodigal	Prodigal	2.6.2, 2.6.3	biology, genomics
prody	ProDy	2.0	phylogenetics
proj	PROJ	5.1.0, 8.0.1, 9.4.0	library, Cartographic Projections and Coordinate Transformations
prokka	Prokka	1.12, 1.14.6	biology, genomics, assembly
proovread	Proovread	1.03rcl, 2.12, 2.13	biology, genomics, ngs
prosplign	ProSplign	1.0.0	phylogenetics
protege	Protege	5.1.0	genomics
proteinortho	Proteinortho	4.26, 5.11, 5.16	biology, genomics
protexcluder	ProtExcluder	1.2	biology, phylogenetics
prothint	ProtHint	2.6.0	biology, genomics
protobuf	protobuf	2.5.0, 3.5.1	web, library
prottest3	prottest3	3.4.2	biology
provean	PROVEAN	1.1.5	biology, genomics
prsice	PRSice	2.3.3	phylogenetics
pseudofinder	Pseudofinder	1.0	phylogenetics
psiclass	PsiCLASS	1.0.1	phylogenetics
psmc	PSMC	0.6.5	phylogenetics
psrobot	psRobot	1.2	phylogenetics
pufferfish	Pufferfish	20200417, 20230223	phylogenetics
pureclip	PureCLIP	1.1.1	phylogenetics
purge_dups	Purge_Dups	1.0.1	phylogenetics
purge_haplotigs	purge_haplotigs	1.1.2, 1.1.3	sequencing, biology
pvconv	pvconv	10152018	imaging
pyani	pyani	0.2.10, 0.2.12	phylogenetics
pybedtools	Pybedtools	0.8.2, 0.9.0	phylogenetics
pybind11	Pybind11	2.13.5	programming
pybsaseq	PyBSASeq	20200623	phylogenetics
pycharm	PyCharm	2018.3, 2023.1.2	programming
pycharm-pro	Pycharm Pro	23.1.3	software
pychopper	pychopper	2.5.0, 2.7.1	phylogenetics, sequencing
pycogent	PyCogent	1.9	biology, genomics
pycoqc	pycoqc	2.5.2	sequencing
pycuda	PyCUDA	2024.1	GPU programming
pydarwin	pydarwin	3.0.0	machine_learning
pydeface	PyDeface	2.0.0	imaging
pydock3	pydock3	20240513	biology
pyega3	pyEGA3	3.4.1, 5.0.2	biology, genomics, utility
pyexr	PyEXR	0.3.10	programming
pyfaidx	Pyfaidx	0.5.2	biology, ngs, sequencing
pyfasta	pyfasta	0.5.2	phylogenetics
pyfastx	pyfastx	2.1.0	bioinformatics
pygenometracks	pygenometracks	3.8	genomics, biology
pygot	pygot	20170518	biology, phylogenetics
pyhdf	pyhdf	0.9.0	library
pyhist	PyHIST	1.0	biology, imaging, image_processing
pylucene	Lucene	7.7.1, 9.1.0	programming, search
pymesh	pymesh	0.3.0	math, graphics
pypaftol	pypaftol	1.0	biology, ngs, phylogenetics
pyphlawd	PyPHLAWD	20180416, 20190414	biology, phylogenetics
pyroms	Pyroms	1.0	geospatial
pyrosetta	PyRosetta	r56324	biology, structure, modeling
pyrpipe	pyrpipe	0.0.3	phylogenetics
pysamstats	Pysamstats	1.1.2	phylogenetics
pyslurm	PySLURM	18.08.04	scheduler
python	Python	3.6.3, 3.6.5, 3.8	programming, language
python-core	Python-core	3.6.5, 3.7, 3.8	language, programming
pytorch	pytorch	1.9.0, 2.0.1, 2.2.0	library, math
pytorch_lightning	Pytorch Lightning	2.2.0	library, math
pyvcf	PyVCF	0.6.0, 0.6.8	biology, phylogenetics
pyvista	PyVista	0.26.1	phylogenetics
pyweka	pyweka	0.3.18	phylogenetics
qapa	QAPA	1.3.1, 1.3.3	phylogenetics
qcat	qcat	1.1.0	phylogenetics
qctool	qctool	2.0.1	phylogenetics
qcustomplot-pyqt5	qcustomplot-pyqt5	2.1.1.2	plotting, visualization
qd	QD	2.3.22	library, compiler, math
qdd	QDD	3.1.2	biology, genomics, ngs
qgis	QGIS	2.18.0, 3.14.0	geospatial
qiime2	QIIME2	2024.10, 2024.2, 2024.5	biology, bioinformatics, metagenomics
qmcpack	QMCPACK	3.4.0	library
qrna	QRNA	2.0.4	phylogenetics
qsiprep	qsirep	0.19.1	data_mining
qt	QT	5.15.4, 5.15.9, 6.7.3	library
qtl-seq	QTL-seq	2.2.2	biology, sequencing, pipeline
qtltools	QTLtools	1.2, 1.3.1	phylogenetics
quake	Quake	0.3	biology, sequencing
qualimap	QualiMap	2.1.2, 2.3	biology, sequencing, alignment
quantas	Quantas	1.0.8, 1.0.9	biology, ngs
quantisnp	quantisnp	2	biology, genomics
quantlib	QuantLib	1.34	financial, quantitative analysis
quartet	quarTeT	1.1.6	phylogenetics
quartetscores	QuartetScores	1.0.0	phylogenetics
quarto	QUARTO	1.4.550	desktop publishing
quast	QUAST	5.0.0, 5.0.2, 5.2.0	biology, ngs, sequencing, rna-seq
quickmerge	quickmerge	0.3	phylogenetics
quickquartet	Quickquartet	1.0.0	biology, ngs
quip	QUIP	20201029, 20210626	phylogenetics
quorum	QuorUM	1.0.0	biology
qupath	qupath	0.4.3	biology, Imaging
R	R	4.2, 4.3, 4.4	statistics
r-index	r-index	20190711	phylogenetics
r8s	r8s	1.8, 1.81	phylogenetics
raca	RACA	0.9.1.1	biology, ngs
racon	Racon	1.4.10, 1.4.13, 1.5.0	phylogenetics
radical	RADICAL	0.2	biology, genomics
radinitio	radinitio	1.2.3	biology
radorgminer	radorgminer	0.9	genomics, biology, sequencing
ragoo	RaGOO	1.11	phylogenetics
ragout	Ragout	2.3	genomics
ragtag	RagTag	1.0.0, 2.0.1	phylogenetics
rainbow	rainbow	2.0.4	biology, sequencing
rainbowfish	Rainbowfish	0.1.0	phylogenetics
raisd	RAiSD	2.8, 3.1	phylogenetics
randfold	Randfold	2.0.1	biology, RNA
ranger	ranger	1.9.3	file_management
rapidnj	Rapidnj	2.3.3	biology, phylogenetics
rapidsai	rapidsai	24.02, 24.04, 24.08	data_science
rapidtide	rapidtide	1.9.0	phylogenetics
rapsearch	RAPSearch	2.24	biology, phylogenetics
rapt	RAPT	0.5.5	biology,assembly
rar	Unrar	0.0.1, 4.20	utility
rascaf	Rascaf	1.0.2	biology
rasterio	Rasterio	1.3.10	geospatial
rattle	RATTLE	1.0	Sequencing
rave	RAVE	2.1	biology, phylogenetics
raven	Raven	1.8.1	assembly
raxml	RAxML	8.2.10, 8.2.12, 8.2.8	biology, phylogenetics
raxml-ng	RAxML-NG	0.9.0, 1.0.2, 1.1.0	phylogenetics
razers3	razers3	3.5.7	biology, phylogenetics
rbp-maps	rbp-maps	0.1.4	phylogenetics
rcapptests	rcapptests	1.0	software
rclone	rclone	1.57.0, 1.58.1, 1.65.2	web
rcorrector	Rcorrector	1.0.4	phylogenetics
rdkit	RDKit	2020092	chemistry
rdnatools	rDnaTools	0.1.3	phylogenetics
read2tree	read2tree	0.1.5	alignment, biology, genomics, phylogenetics
reademption	READemption	1.0.0	phylogenetics
reapr	REAPR	1.0.18	biology, assembly
rebaler	Rebaler	0.2.0	phylogenetics
recognizer	reCOGnizer	1.3.3	phylogenetics
recon	recon	1.08	biology, sequencing
recycler	recycler	0.7	biology, sequencing
redis	Redis	2.8.13, 2.8.19	database, data_science
reditools2	REDItools2	20200701	phylogenetics
redundans	Redundans	0.14a	biology, phylogenetics
refmaker	refmaker	1.0	biology, phylogenomics
reframe	ReFrame	3.2	performance_analysis, utility
regtools	regtools	0.5.2	biology, rna-seq, genomics
release	release	12082021	molecular_dynamics, machine_learning
relernn	ReLERNN	1.0.0	biology/AI
relion	RELION	3.0.2, 3.1.0, 4.0.1	biology, imaging
relocate2	RelocaTE2	2.0.1	phylogenetics
remora	REMORA	1.8.3, 1.8.5, 2.0.0	performance_analysis
repdenovo	REPdenovo	20170222	biology, phylogenetics
repeatanalysis	RepeatAnalysis	0.10.0, 0.12.2	biology, phylogenetics
repeatanalysistools	RepeatAnalysisTools	20210506	biology, genomics, sequencing, utility
repeatexplorer	RepeatExplorer	20150506, 20180517	biology, ngs
repeatmasker	RepeatMasker	4.0.9, 4.1.1, 4.1.7	biology, genomics
repeatmodeler	RepeatModeler	1.0.8, 2.0	biology
repeatscout	repeatscout	1.0.5	biology
repeatseq	RepeatSeq	0.8.2	phylogenetics
reptile	reptile	1.1	biology, ngs, math
resfinder	ResFinder	4.0	biology, genomics
resistify	resistify	0.1.0	biology, molecular
resistome	Resistome	20170111	phylogenetics
resolve	Resolve	18.1.4	Graphics, Utility, Visualization
revbayes	RevBayes	1.0.9, 1.1.1, 1.2.3	biology, phylogenetics
rfaa	RFAA	20240323	biology, genomics
rfmix	RFMIX	2.03	phylogenetics
rgaugury	RGAugury	2.2	sequencing, biology
rgi	RGI	4.2.2, 5.1.1, 6.0.2	phylogenetics
rgis	RGIS	20180211, 20180814	geospatial
rhash	RHash	1.3.3	programming
ribocode	RiboCode	1.2.11	phylogenetics
ribodetector	ribodetector	0.3.1	biology
ribopicker	riboPicker	0.4.3	biology, sequencing
ribotaper	RiboTaper	1.3.1a	phylogenetics
ribotricer	Ribotricer	1.3.3	phylogenetics
rigerj	RIGERJ	2.0.2	phylogenetics
rmats-turbo	rMATS turbo	4.1.2	biology, sequencing, genomics
rmats2sashimiplot	rmats2sashimiplot	2.0.3, 2.0.4	phylogenetics
Rmpi	Rmpi	3.5.1	statistics, programming
rmpi	Rmpi	3.5.1, 4.0.3	statistics, programming
rnabloom	rnabloom	2.0.1	biology, ngs, sequencing, rna-seq
rnaeditingindexer	rnaeditingindexer	12152022	data_mining
rnaframework	RNAFramework	2.7.2	biology, RNA, sequencing
rnahybrid	RNAhybrid	2.1.1	biology, genomics
rnalysis	rnalysis	3.7.0	sequencing, biology
rnammer	RNAmmer	1.2	biology, rna-seq
rnaquast	rnaQUAST	1.5.1	biology, ngs, sequencing, rna-seq
rnasalsa	RNAsalsa	0.8.1	biology, phylogenetics
rnaseqlib	rnaseqlib	20150721	biology, phylogenetics, rna-seq
rnastructure	RNAstructure	6.3	biology, sequencing
rndatools	rDnaTools	0.1.3	phylogenetics
roary	Roary	3.12.0, 3.13.0, 3.4.1	biology, genomics
roguenarok	roguenarok	20230418	phylogenetics
root	ROOT	5.34.17, 6.0, 6.06.02	data_science
rootpy	ROOTPy	20160323	data_science
rosetta	Rosetta	2019.35.60890, 2021.16.61629, 2023.11.30	biology, structure, modeling
rosettafold	RoseTTAFold	1.0.0	phylogenetics
rrnaselector	rrnaselector	1.0	biology, sequencing
rseg	RSEG	0.4.8	biology, genomics
rsem	RSEM	1.2.31, 1.2.7, 1.3.3	biology, ngs, sequencing
rseqc	RSeQC	2.6.4, 3.0.0, 5.0.3	biology, ngs, rna-seq
rstudio	RStudio	1.4, 2021.09.0, 2022.02.3	statistics
rsync	rsync	3.2.7	software, utility
rtgtools	RTGTools	3.7.1	biology, ngs
ruby	Ruby	2.5.1	programming, language
run_dbcan	run_dbcan	4.0.0, 4.1.4	biology
rust	Rust	1.62.1, 1.70.0, 1.76.0	programming
rvtests	rvtests	2.1.0	genomics, biology, sequencing
s.a.g.e	S.A.G.E	6.4.2	phylogenetics
sabre	Sabre	1.0	phylogenetics
saffrontree	saffrontree	0.1.2	phylogenetics
saige	saige	0.45.0	genomics
sailfish	Sailfish	0.6.3	biology, genomics, ngs, rna-seq
salmon	Salmon	1.5.2, 1.8.0, 1.9.0	biology, rna-seq
salsa	SALSA	20171009, 20191001, 20220408	biology, ngs
samapi	samapi	0.4.0	Imaging
sambamba	Sambamba	0.6.3, 0.6.6, 0.6.9	biology, ngs
samblaster	samblaster	0.1.14, 0.1.24	biology, ngs, sequencing
sampledock	sampledock	0.5.1	molecular_dynamics, AI
samstat	SAMStat	1.08	biology, ngs, sequencing
samtools	Samtools	1.7, 1.8, 1.9	biology, ngs, sequencing
saoimageds9	DS9	7.5, 8.0.1	imaging
sas	SAS	9.4.8	statistics, data_science
sate	Sate	2.2.7	biology, phylogenetics
satsuma	Satsuma	3.0	phylogenetics
satsuma2	Satsuma2	20161123, 3.1	phylogenetics
scala	Scala	2.11.5, 3.0.1	programming, language
scalablast	Scalablast	2.4.53	biology, genomics
scalapack	ScaLAPACK	2.1.0, 2.2.0, 2.2.1.5	programming, library
scallop	scallop	0.10.5	phylogenetics
scalpel	Scalpel	0.1.1, 0.5.3	biology, ngs
scanpy	scanpy	1.8.2	biology
scapp	scapp	0.1.4	genomics, assembly
scgpt	scGPT	0.1.2	Biology, Data_Science, Genomics
schrodinger	Schrodinger Suite	2023-2, 2023-3, 2024-2	chemistry, molecular_dynamics
sciann	sciann	0.7.0.1	machine_learning
scikit-learn	scikit-learn	1.4.1.post1	Data_Science
scim	sc-im	0.8.2	utility, visualization
scipion	scipion	1.2, 3.0.0, 3.1.0	image_processing
scirun	SCIrun	5.0.Z	phylogenetics
scnic	scnic	1.0	library
scoary	Scoary	1.6.16	phylogenetics
scons	Scons	2.5.1, 3.1.2	programming
scop	SCOP	20180311	biology, assembly
score-sde	score-sde	20221110	Machine_Learning
scrappie	Scrappie	1.4.2	biology, genomics
scratch1d	SCRATCH-1D	1.0, 1.2, 2.0	biology, ngs
screen	Screen	4.8.0, 4.9.1	programming, shell
scripture	SCRIPTURE	20101211	biology, genomics
scvelo	scVelo	0.2.5	biology
scythe	Scythe	0.991	biology, ngs
sdsl	sdsl	2.1.1	library, compiler
se-mei	SE-MEI	0.1.0	phylogenetics
secapr	SeCaPr	1.1.12, 2.0.2, 2.1.1	phylogenetics
seekdeep	seekdeep	3.0.1	biology, sequencing
segemehl	Segemehl	0.1.9, 0.3.4	biology, ngs, sequencing
segment-liftover	segment-liftover	20211021	biology, genomics
seismometer	seismometer	0.2.1	AI, utility
semibin	SemiBin	2.1.0	bioinformatics
sepp	SEPP	20160614	biology, phylogenetics
seq-gen	Seq-Gen	1.3.3	biology, phylogenetics
seq_crumbs	seq_crumbs	20150120	biology, sequencing, genomics, utility
seqkit	SeqKit	0.8.0, 2.0.0, 2.4.0	biology, phylogenetics
seqmagick	seqmagick	0.8.4	biology
seqmap	SeqMap	1.0.13	biology, sequencing, ngs
seqmule	seqmule	1.2.6	biology, sequencing
seqpower	SEQPower	1.1.1	genomics, phylogenetics
seqprep	SeqPrep	0.5, 1.1	biology, ngs, sequencing
seqscreen	seqscreen	3.3	sequencing, biology
seqtk	seqtk	1.3, 20140729	biology, genomics, ngs
sequel	SEQuel	1.0.1	biology, ngs
sequelqc	SequelQC	1.1.0	phylogenetics
seqwish	seqwish	0.7, 20190509	phylogenetics
seqyclean	SeqyClean	1.8.10	biology, ngs, sequencing
sesimcmc	SeSiMCMC	4.36	biology, sequencing
sextractor	SExtractor	2.19.5	astronomy
shapeit	SHAPEIT	2.12, 2.5	biology, variant_calling
shapeit4	SHAPEIT4	4.2.2	biology, sequencing
shapemap	SHAPE-MaP	1.2	biology, phylogenetics
shapemapper	ShapeMapper	2.1.3, 2.1.5, 2.2.2	biology, phylogenetics
sharcgs	SHARCGS	1.2.11	biology, ngs, de_novo
shasta	Shasta	0.1.0	phylogenetics
shesisplus	SHEsisPlus	1.0, 1.01	biology, genomics
shogun	shogun	6.1.3	phylogenetics
shortbred	Shortbred	0.9.4	phylogenetics
shortstack	shortstack	4.0.3	biology
shovill	shovill	1.1.0	genomics, sequencing, biology
shrimp	SHRiMP	2.2.3	biology, genomics, ngs
shustring	shustring	2.6	biology, sequencing
sibeliaz	SibeliaZ	1.2.2, 1.2.3, 1.2.4	biology, genomics, alignment
sicer	SICER	1.1	biology, chip-seq
sickle	Sickle	1.200, 1.33	biology, ngs
siesta	Siesta	3.2, 4.1b2, 4.1b3	chemistry
sift	SIFT	4.0.3b	biology, genomics
sigffrid	SIGffRid	1.1	phylogenetics
signalp	SignalP	4.1c, 5.0b, 6.0h	biology, phylogenetics
silix	SiLiX	1.2.11, 1.3.0	phylogenetics
silo	silo	4.7	library
sim4	sim4	20121010	biology, genomics
sim4life	Sim4Life	7.0.1, 7.2.3	biology, simulation
simka	Simka	1.5.3	phylogenetics
simnibs	SimNIBS	3.2.1, 4.0.0, 4.1.0	phylogenetics
simseq	SimSeq	4.12.2011	biology, ngs, phylogenetics
simulia	Simulia	2019	simulation, visualization
sinc	SInC	20140120	biology, phylogenetics
sine_scan	sine_scan	1.1.1	phylogenetics
singularity	Singularity	3.10.4	workflow_automation
sipes	SIPeS	2.0	biology, chip-seq
siril	SIRIL	1.2.0	image processing
sisl	sisl	0.8.3	physics, structure
ska2	Ska2	0.3.0	alignment, biology, genomics
skimmingloc	kimmingloci	1.0.0	pipeline mapping, biology
skmer	skmer	3.2.1	genomics, biology
slamdunk	Slamdunk	0.4.1, 0.4.2	phylogenetics
slaw	SLAW	20211217	chemistry, spectroscopy
sleap	Sleap	1.3.3	machine learning
slicer	Slicer	5.0.3, 5.2.1, 5.6.2	biology, neuroscience, imaging
slivar	slivar	0.3.0	biology
slow5tools	slow5tools	0.5.1, 1.1.0	biology, sequencing
slr	SLR	1.0.0	genomics
slurm-drmaa	slurm-drmaa	1.1.3, 1.1.4, 1.1.4.1	library, scheduler, programming
smalt	smalt	0.7.6	biology, phylogenetics
smartdenovo	SMARTdenovo	20180219	biology, phylogenetics
smartie-sv	smartie-sv	20180308	phylogenetics
smcpp	SMC++	1.15.4	biology, genomics, sequencing
smetana	Smetana	1.1.0	phylogenetics
smr	SMR	1.03	biology, genomics
smrtsv2	SMRT-SV	2.0.0	biology, ngs
sms	SMS	1.7	biology
smudgeplot	Smudgeplot	0.2.4	phylogenetics
snakemake	Snakemake	7.5.0, 8.10.8, 8.4.0	biology, workflow_automation
snap	SNAP	2.0.0, 2.0.3, 20100728	biology, sequencing
snape-pooled	SNAPE-pooled	20130407	biology, variant_calling
snep	SNeP	1.1	biology, phylogenetics
sniffles	Sniffles	1.0.11, 1.0.6, 1.0.8	phylogenetics
sniffles2	Sniffles2	2.0.6	biology
snippy	Snippy	20160419, 4.6.0	biology, phylogenetics
snp-pipeline	SNP-Pipeline	1.0.1	biology, phylogenetics
snp-sites	SNP-sites	2.0.3	biology, variant_calling
snp2hla	snp2hla	1.0.3	biology, genomics
snpeff	SnpEff	5.0, 5.1d, 5.2e	biology, annotation
snpflip	snpflip	20190515	biology, phylogenetics
snpgenie	SNPGenie	20190620	phylogenetics
snphylo	SNPhylo	20140701, 3.0	biology, phylogenetics
snpsplit	SNPsplit	0.5.0	biology, sequencing
snptest	SNPTEST	2.5.2	phylogenetics
soapaligner	SOAPaligner	2.21	phylogenetics
soapdenovo	SOAPdenovo	1.05, 2.04	biology, ngs
soapdenovo-trans	SOAPdenovo-Trans	1.01, 1.03	biology, ngs
soapec	SOAPec	2.03	biology, phylogenetics
soapnuke	SOAPnuke	2.1.0	phylogenetics
soapsplice	SOAPsplice	1.10	biology, ngs
soda	SODA	20200930	biology
solar	SOLAR	8.4.2	phylogenetics
somaticseq	SomaticSeq	3.6.2	phylogenetics
sortadate	SortaDate	20190705	phylogenetics
sortmerna	SortMeRNA	2.1, 4.0, 4.3.6	biology, sequencing, ngs
sourcetracker2	SourceTracker2	2.0.1	phylogenetics
sourmash	Sourmash	2.0.1, 4.5.0	phylogenetics
sox	SoX	14.4.2	phylogenetics
spacemake	spacemake	0.5.5	sequencing
spaceranger	SpaceRanger	2.1.0, 3.0.1, 3.1.1	phylogenetics
spades	SPAdes	3.7.1, 3.8.0, 4.0.0	biology, ngs
sparcc	SparCC	201608	biology
spark	Spark	2.2.0, 3.1.1	utility
sparsehash	sparsehash	2.0.3	web, programming
sparta+	SPARTA+	2.60	chemistry
spec2nii	Spec2nii	0.3.4	phylogenetics
speedseq	SpeedSeq	0.1.2	phylogenetics
spidey	Spidey	20150922	biology, genomics
spinalcordtoolbox	SpinalCordToolbox	5.4	phylogenetics
spladder	SplAdder	2.4.2	phylogenetics
splicegrapher	SpliceGrapher	0.2.5	biology, sequencing
splicetrap	SpliceTrap	0.90.5	biology, genomics, ngs
spm	SPM	12b, 8, 8r5236	biology
spruceup	spruceup	2019.2.3	phylogenetics
sputnik	Sputnik	1.0	biology
spyder	spyder	4.1.4, 5.1.1, 5.3.2	programming
sqanti	SQANTI	1.2	phylogenetics
sqanti2	SQANTI2	5.0	phylogenetics
sqanti3	SQANTI3	1.6, 4.2, 5.1.1	phylogenetics
sqldeveloper	SQL Developer	4.1.2	programming, database
sqlite	SQLite	3.33.0, 3.8.8.2	database
sqlite3	SQLite	3.45.3	database
squashfuse	squashfuse	0.5.2	containers, library
squeezemeta	SqueezeMeta	1.4.0, 1.5.2, 1.6.0	phylogenetics
squigglekit	squigglekit	1.0.0	visualization, biology
squigglenet	squigglenet	1.0	sequencing, biology
sra	SRA	3.0.2, 3.0.5, 3.0.8	biology, ngs
sra_human_scrubber	sra-human-scrubber	1.1	genomics
srassembler	SRAssembler	1.0.0	phylogenetics
srst2	srst2	0.2.0	sequencing, genomics, biology
ssm	SSM	20210511	phylogenetics
sspace	SSPACE	2.0, 3.0	biology, ngs
ssr_pipeline	ssr_pipeline	0.951	biology, sequencing
ssu-align	SSU-ALIGN	0.1.1	phylogenetics
stable-diffusion	stable-diffusion	20221116	machine_learning
stacks	Stacks	2.61, 2.64, 20190403	biology, genomics, ngs
staden	Staden	1.14.6	biology, phylogenetics
stampy	Stampy	1.0.31	biology, sequencing
staphb-toolkit	staphb-toolkit	1.2.0, 1.3.10, 2.0.1	biology
star	STAR	2.7.5c, 2.7.6a, 2.7.9a	biology, ngs, rna-seq
star-fusion	STAR-Fusion	1.13.0, 1.3.1, 1.9.1	biology, sequencing
starccm+	STAR-CCM+	14.04.011, 15.02.009, 8.06	fluid_dynamics
starseqr	starseqr	0.6.7	phylogenetics
stata	Stata	10.1, 13, 18	statistics
strainline	Strainline	1.0	biology
strelka	Strelka	2.9.2	biology, genomics
stringmlst	stringMLST	0.4	biology, chip-seq
stringtie	Stringtie	2.0.4, 2.1.3b, 2.2.3	biology, ngs, sequencing, alignment
structure	Structure	2.3.3, 2.3.4	biology, genomics
structure_threader	Structure_threader	1.3.10	utility, structure
stumpy	stumpy	1.11.1	library, math
stylegan3	stylegan3	20211028	ai, image_processing
su2	SU2	7.0.6	phylogenetics
subphaser	subphaser	1.2.6	sequencing, biology
subread	Subread	2.0.0, 2.0.3, 2.0.6	biology, sequencing, variant_calling
subversion	Subversion	1.14.2, 1.9.7	revision_control
sumo	SUMO	1.2.0, 1.20.0, 1.9.2	simulation, mapping
sundials	SUNDIALS	2.5.0, 3.0.0, 6.1.1	math
supercell	supercell	20170602	biology, ngs
supercrunch	SuperCRUNCH	1.2.1	phylogenetics
superlu_dist	SUperLU-DIST	6.0.1, 8.2.1	linear algebra
supernova	Supernova	1.2.1, 2.0.0, 2.1.1	biology, phylogenetics, ngs
suppa	SUPPA	2.3	phylogenetics
support	support	24.03.20	ufrc, admin, tools
surrealdb	SurrealDB	1.3.1, 1.5.0, 2.0.1	database
survival_kit	Survival_Kit	6.12	healthcare
survivor	SURVIVOR	1.0.6	phylogenetics
svdetect	SVDetect	0.8b	biology, ngs, genomics
svim	svim	1.4.2	biology
svim-asm	svim-asm	1.0.2	biology
svtyper	svtyper	0.7.1	biology, genomics, sequencing
swarm	swarm	1.2.11	data_science
sweed	Sweed	3.3.2	biology, phylogenetics
swig	SWIG	3.0.8, 4.1.1, 4.2.1	library, programming, compiler
swsc-en	SWSC-EN	1.0.0	phylogenetics
synima	Synima	20210908	phylogenetics
syri	syri	1.5.4	genomics, biology
taco	TACO	0.7.3	phylogenetics
taiyaki	Taiyaki	5.0.1	phylogenetics
talesf	talesf	20160814	phylogenetics
talon	talon	5.0	biology, sequencing
tandem-genotypes	Tandem-Genotypes	1.4.0	phylogenetics
tantan	Tantan	13	imaging, ngs, genomics
tapestri	Tapestri	2.0.1	phylogenetics
tapir	tapir	20160825	biology, phylogenetics
tapis	TAPIS	1.2.1	biology, sequencing
tassel	TASSEL	5.2.20, 5.2.29, 5.2.82	biology, genomics, sequencing
tau	TAU	2.23, 2.26, 2.26.3	library, performance_analysis
tax4fun	Tax4Fun	0.3.1	phylogenetics
taxmaps	taxMaps	0.1	biology, phylogenetics, genomics
taxonkit	TaxonKit	0.13.0, 0.9.0	phylogenetics
taxtastic	Taxtastic	0.5.7, 0.9.1	biology, genomics
tbb	tbb	2017_20161128	library
tbprofiler	tbprofiler	4.4.1	genomics, biology
tcllib	tcllib	1.18	library
tcoffee	tcoffee	10.00.r1613, 9.03.r1318	biology
tdnascan	TDNAscan	20210304	phylogenetics
tecplot	Tecplot 360 EX	2015R1	math, animation, fluid_dynamics, simulation
tellseq	tellseq	1.0.0	sequencing, phylogenetics
temp	TEMP	20170731	phylogenetics
temp2	TEMP2	0.1.4	phylogenetics
tensorflow	TensorFlow	2.6.0, 2.7.0, 2.8.0	library, math
tess	TESS	2.3.1	biology, genomics, math
tesseract	tesseract	5.3.4	OCR
tetgen	TetGen	1.5.0	modeling
tetoolkit	TEToolkit	1.5.1	biology, sequencing
tetools	TEtools	20180213	biology, phylogenetics
texlive	Texlive	20191127, 2020, 2023	documentation
textract	textract	1.6.1	data_science, file_management
tgicl	TGICL	2.1	biology, ngs, sequencing
tgsgapcloser	TGSGapCloser	1.0.3	phylogenetics
the_silver_searcher	the_silver_searcher	2.2.0	search
themisto	Themisto	0.2.0, 1.1.0	genomics, alignment
tiara	Tiara	1.0.2	phylogenetics
tidk	tidk	0.2.41	bioinformatics
tiff	tiff	3.8.0, 4.0.10, 4.6.0	imaging
tighe-r	tighe-r	4.2, studio	statistics
tigmint	Tigmint	1.1.2	phylogenetics
tmhmm	TMHMM	2.0	biology
tmux	Tmux	2.9, 3.1, 3.4	programming
tntblast	TNTBLAST	2.04	biology
tofu2	CDNA_Cupcake	20180629, v17	biology, ngs, sequencing
toil	toil	3.3.0, 3.3.3	biology
tombo	Tombo	1.4, 1.5, 1.5.1	biology, genomics, ngs
topd	topd	4.6	phylogenetics
tophat	Tophat	2.1.0, 2.1.1, 2.1.2	biology, ngs, sequencing
torch-geometric	torch-geometric	1.3.2, 2.0.4	phylogenetics
totalview	TotalView	8.12	programming
tpmcalculator	TPMcalculator	0.0.3	phylogenetics
tpp	TPP	4.7.0, 4.7.1, 5.0.0	biology, chemistry, spectroscopy
tracer	TraCeR	20160519	biology, phylogenetics
tracktools	TrackTools	2011	utility
trackvis	TrackVis/DTK	0.5.2.2, 0.6.0.1	biology, neuroscience, imaging
tracula	Tracula	5.3.2014_05_26	biology, neuroscience, imaging
traitrate	traitRate	1.1	biology, genomics
transabyss	Trans-ABySS	2.0.1	biology, phylogenetics
transdecoder	TransDecoder	5.3.0, 5.4.0, 5.5.0	biology, ngs
transit	TRANSIT	2.5.2, 3.2.3	phylogenetics
transrate	Transrate	1.0.1, 1.0.3	biology, assembly
transvar	TransVar	2.3.3	biology, phylogenetics
treebreaker	TreeBreaker	20160621	biology, phylogenetics
treemix	TreeMix	1.12	biology, phylogenetics
treepl	treePL	20150305	biology, phylogenetics
treepuzzle	TREEPUZZLE	5.3	biology, phylogenetics
treeshrink	TreeShrink	1.3.1, 1.3.2, 1.3.9	phylogenetics
treetime	TreeTime	0.10.1, 0.7.5, 0.8.1	phylogenetics
trelis	trelis	16.3	math
trf	TRF	4.04, 4.09.1	biology, genomics
trgt	trgt	0.4.0	genetics, biology
trilinos	Trilinos	12.6.4, 14.4.0, 16.6.0	math
trim_galore	Trim Galore	0.5.0, 0.6.10, 0.6.5	biology, ngs
trim_isoseq_polya	trim_isoseq_polya	0.0.3	biology, genomics, sequencing
trimal	trimAl	1.2, 1.4.1	biology, genomics, alignment
trimesh	trimesh	3.20.2	graphics, math
trimetass	TriMetAss	1.1	biology, ngs
trimmomatic	Trimmomatic	0.33, 0.36, 0.39	biology, ngs
trinity	Trinity	r20130225, r20131110, r20140413	biology, ngs, sequencing, rna-seq
trinotate	Trinotate	3.0.1, 3.2.0, 4.0.0	biology
triobinning	triobinning	0.2.3	genomics, biology
triplec	TRIPLEC	1.0	biology
tritonserver	TRITONSERVER	21.08, 23.01	machine_learning
trnascan-se	tRNAscan-Se	1.23, 2.0.12	biology, ngs
trust4	TRUST4	1.0.2b	phylogenetics
trvz	trvz	0.4.0	genetics, biology
trycycler	Trycycler	0.4.2	phylogenetics
turbomole	TURBOMOLE	7.4.1	chemistry
twinscan	TWINSCAN	4.1.2	biology, genomics
ubuntu	Ubuntu	20.04, 22.04, 24.04	linux
ucsc	UCSC	20200320, 20210803	genomics
ucsc-fafiltern	ucsc-fafiltern	377	phylogenetics
ucsc-maskoutfa	ucsc-maskoutfa	377	phylogenetics
ucx	UCX	1.11.2, 1.15.0, 1.9.0	programming, library
udunits	UDUNITS	2.2.17	library, data_science, math
ufcg	UFCG	1.0.3, 1.0.5	biology, genomics
ufraw	ufraw	0.22	data_mining
ugtm	ugtm	1.1.6	statistics, modeling
ukfractography	UKFractography	20200127	phylogenetics
umi-tools	umi-tools	0.5.5, 1.1.4, 1.1.5	phylogenetics
umicollapse	UMICollapse	02072021	chemestry
unafold	UNAFold	3.8	biology, genomics, rna
unanimity	Unanimity	20171108, 3.4.1	programming, library, compiler
uncalled	UNCALLED	2.2	biology, genomics
unicycler	Unicycler	0.4.8	phylogenetics
unrealengine	unrealengine editor	5.2.1	programming, design, digitaltwin
uproc	uproc	1.2.0	biology, genomics
upscayl	UPSCAYL	2.5.5, 2.8.1, 2.9.1	image processing
uropa	uropa	4.0.2	genomics, sequencing, biology
usearch	USEARCH	9.0.2132, 9.1.13, 9.2.64	biology, alignment, sequencing
usher	UShER	0.1.4, 0.4.1, 0.5.2	phylogenetics
v-pipe	v-pipe	2.0.0, 2.99.3	biology, genomics, sequencing
valgrind	Valgrind	3.11.0, 3.15.0, 3.8.1	programming
valouev	Valouev	20160325	biology, phylogenetics
vamb	vamb	3.0.2	biology
vampir	VAMPIR	9.1	performance_analysis
vardictjava	VarDictJava	1.6.0, 20160521, 20170531	biology, phylogenetics
vari	VARI	0.7.0	math, visualization
varnorm	varnorm	0.21	biology
varpipe-wgs	varpipe-wgs	20230222	sequencing, biology
varscan	VarScan	2.3.6	biology, ngs
varsim	VarSim	0.8.4, 0.8.6	phylogenetics
varsimlab	VarSimLab	20180220, 20180921	biology, simulation, genomics
vasp	vasp	6.2.0, 6.4.1, 6.4.3	chemistry
vaspkit	vaspkit	1.2.5, 1.4.1	phylogenetics
vast-tools	VAST-TOOLS	2.5.1, 20150506	biology, rna-seq, ngs
vcf-kit	VCF-kit	0.2.6	phylogenetics
vcfanno	vcfanno	0.2.8, 0.3.3	biology, phylogenetics
vcflib	vcflib	1.0.1	biology, genomics
vcftools	vcftools	0.1.15, 0.1.16, 0.1.9	biology, genomics
vcfvalidator	vcf-validator	0.6	biology, phylogenetics
vcontact	vcontact	20190512	phylogenetics
vdjtools	VDJtools	1.1.7, 1.2.1	biology, phylogenetics
velocyto	Velocyto	0.17	biology, RNA seq
velvet	Velvet	1.2.10, 1.2.10-long	biology, genomics
vep	VEP	83, 88.8, 92	biology, genomics, ngs
verkko	Verkko	1.3.1	genomics
vermouth-martinize	vermouth-martinize	0.11.0, 0.7.2	biology, molecular
veryfasttree	VeryFastTree	3.0.1	phylogenetics
vfuparr	VFUparr	20240320	sequencing, biology
vg	vg	1.45.0, 1.49.0, 1.55.0	phylogenetics
vibrant	vibrant	1.2.0	genomics
viennarna	ViennaRNA	2.2.6, 2.4.18	biology, rna-seq
viewbs	ViewBS	0.1.10, 0.1.9	phylogenetics
vigor4	vigor4	20200702	biology, annotation
vim	Vim	8.1.1566, 8.2.2465, 9.0.1946i	programming, language
vina-gpu	vina-gpu	20230530	biology
viralmsa	viralmsa	1.1.10, 1.1.12, 1.1.14	phylogenetics
virclust	VIRCLUST	2.0	biology, annotation
viromescan	viromescan	2015	genomics, biology
virsieve	VirSieve	20210406	biology, pipeline
virsorter	virsorter	2.2.3	genomics
virtualcell	VirtualCell	7.1	phylogenetics
virulign	VIRULIGN	1.0.2	phylogenetics
virusdetect	VirusDetect	1.7	phylogenetics
virusfinder	VirusFinder	2.0	biology, phylogenetics
visit	visit	3.3.3, 3.3.3-mpi, 3.3.3_mpi	visualization, animation
vispr	VISPR	0.4.14	phylogenetics
vmamba	vmamba	2.0	machine_learning
vmd	VMD	1.9.1, 1.9.3, 1.9.4	visualization, animation, graphics
vphaser2	V-Phaser	02112013	biology, phylogenetics
vray	vray	6.10.04	graphics
vscode	vscode	1.86.2, 1.87, 1.92	programming
vsearch	VSearch	2.22.1, 20151022, 20161209-2.3.4	biology, ngs
vt	vt	0.57721, 20140903, 20160129	biology, genomics
vtc	VTC	0.9.3	biology
vtk	VTK	9.1.0, 9.2.6, 9.3.0	biology, neuroscience, imaging
w2rap-contigger	w2rap-contigger	20161124	biology, genomics
wannier90	Wannier90	1.2, 2.1.0, 3.1.0	computational Physics
warpedlmm	WarpedLMM	0.21	modeling
wavegan	WaveGAN	20190829	machine_learning, audio, GAN
wdss2	WDSSII	5, 6	climate
weblogo	WebLogo	3.3, 3.5.0, 3.7	biology, sequencing, graphics
webodm	webodm	20240718	graphics
weka	Weka	3.8, 3.8.5	statistics, machine_learning
wengan	Wengan	0.2	biology, genomics
wfmash	wfmash	0.13.0	phylogenetics
wgd	wgd	1.1.1	phylogenetics
wgs	WGS Assembler	8.3rc1.r4638, 8.3rc2	biology, genomics
wgsim	Wgsim	0.3.1-r13	biology, phylogenetics
whamm	WHAMM	0.14a	biology, phylogenetics
whatshap	WhatsHap	1.1, 2.1	biology, phylogenetics
whiteboxtools	whiteboxtools	1.5.0	phylogenetics
widis-lstm-tools	widis-lstm-tools	0.4	ML
wine	Wine	4.0.0, 7.0.0	linux, utility
wise	Wise	2.2.0, 2.4.1	biology, genomics
wish	WIsH	1.0	phylogenetics
wolfpsort	WoLFPSort	0.2	phylogenetics
wombat	WOMBAT	20180118	biology, phylogenetics
workbench	workbench	4.1.1	modeling, simulation
wtdbg	wtdbg	2.1, 2.4, 2.5	phylogenetics
wub	Wub	0.2.0, 0.4.0	biology, genomics, ngs
wublast	WU BLAST	2.0	biology
xander	xander	20151222	biology, phylogenetics
xapian	Xapian	1.4.4	library
xcrysden	XCrySDen	1.5.60	material_science
xerces	Xerces	3.1.4	phylogenetics
xesmf	xesmf	0.6.2	math, climate
xlsx2csv	xlsx2csv	0.8.0	utility
xpclr	xpclr	1.0, 1.1.1	phylogenetics
xppaut	xppaut	8.0	math
xroms	xroms	v0.5.4	geospatial
xterm	Xterm	1.1	utility
xwalk	xwalk	0.6	biology
xwas	XWAS	3.0	phylogenetics
xy-meta	XY-Meta	20200413	phylogenetics
xz	XZ	5.2.2	compression, library
yagcloser	yagcloser	1.0.0	biology, genomics, assembly
yago	YAGO	4	data_science
yaha	YAHA	0.1.82	biology, ngs
yahs	Yaha	1.1	biology
yak	YAK	0.1	phylogenetics
yasm	YASM	1.3.0	programming
yasra	YASRA	2.33	biology, ngs, sequencing
ydata-profiling	ydata-profiling	4.6.1	biology, ai, machine learning
yolo	yolo-nas	8.1, 8.2, NAS	machine_learning
yolov4_darknet	yolov4_darknet	4-pre	machine_learning
yolov5	yolov5	4.0, 7.0	machine_learning
z1plus	Z1Plus	1.0	molecular_dynamics
zagros	Zagros	1.0.0	biology, phylogenetics
zbar	Zbar	0.23.90	ai, image_processing, imaging
zeo++	ZEO++	0.2.2	chemistry
zerosum	ZeroSum	20231113	programming
zorro	zorro	2.2	biology, sequencing
zstd	Zstd	1.5.0	phylogenetics
zumis	ZUMIS	2.6.0	biology, ngs, sequencing