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- 3PCLR
- 3d-dna
- 4p
- AAFTF
- ABRicate
- ABruijn
- ABySS
- ACLs
- ACTC
- ADFRsuite
- ADMB
- ADMIXTURE
- AEGeAn
- AFNI
- AGAT
- AGfusion
- AI Education and Training
- AI Examples
- AI Help
- AI Reference Datasets
- AI reference dataset hosting policy
- ALFA
- ALLMAPS
- ALLPATHS-LG
- AMAS
- AMBER
- AMICO
- AMOS
- AMP
- AMPtk
- AMRPlusPlus
- ANDI
- ANGSD
- ANNOVAR
- ANTs
- APT
- ARC
- ARKS
- ARPACK
- ART
- ASE-ANI
- ASHS
- ASPECT
- ASTRAL
- ASTRID
- AStalavista
- ATAT
- ATLAS
- ATRAM
- AWSCLI
- Account and QOS limits under SLURM
- AdapterRemoval
- Add New App Page
- Admin Tools
- AdmixTools
- AfterQC
- Albacore
- Albumentations
- Alder
- Alevin-fry
- Alfred
- AliStat
- Alienhunter
- AlleleCount
- Allhic
- AlphaFold
- AlphaMate
- AlphaPulldown
- Alphaimpute
- AltAnalyze
- AmPEPpy
- Amber Job Sample Scripts
- Ambertools
- Amphora2
- Ampligraph
- Amptorch
- Amrfinderplus
- Amuse
- Ancestryhmm
- Anchorwave
- AnnoTALE
- Annocript
- Annotated SLURM Script
- Ansible
- Ansysem
- AntiSMASH
- Anvio
- Applications
- Applications FAQ
- Appreci8
- Apptainer
- Apptests
- Aquamis
- Arcashla
- Aria2
- Armadillo
- ArrayFire
- Array ID Indexes
- Arriba
- Artemis
- Asap
- Asaq
- Assembly-stats
- Assemblytics
- Asset
- Assexon
- Aster
- Asteroid
- Astropy
- Atom
- AtomEye
- AtomMan
- Augustus
- Authentication
- Authentication With MFA
- Auto3DEM
- AutoDock
- AutoDock-GPU
- AutoDock-GPU Job Scripts
- Autodock-vina
- Autometa
- Automlsa2
- Available Node Features
- Azoo
- BALi-Phy
- BAM-matcher
- BAPS
- BBMap
- BDG-SeQuila
- BEAGLE
- BEAR
- BEAST
- BEAST2-XML
- BEDOPS
- BEDTools
- BERTopic
- BESST
- BFAST
- BIDSCOIN
- BIOM
- BIOMART
- BIRDS
- BLASR
- BLASTDB
- BLAT
- BLUPF90
- BMGE
- BOLT-LMM
- BPGA
- BPP
- BRANCH
- BRATNextGen
- BRIG
- BRM
- BSseeker2
- BUCKy
- BUSCO
- BWA
- BWA-PSSM
- BYOBU
- Bactopia
- Badread
- Bakta
- Bam-Readcount
- BamBam
- BamUtil
- Bamaddrg
- Bamm
- Bamsnap
- Bamstats
- Bamsurgeon
- Bamtofastq
- Bamtools
- Barrnap
- Basemount
- Basic Linux Use
- BatMeth2
- Bax2bam
- BayArea
- BayeScan
- Bayenv
- BayesAss
- BayesR
- BayesTraits
- Baypass
- Bcftools
- Bcl2fastq
- Bertini
- Bgenix
- BiG-SCAPE
- Bifrost
- Bigslice
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- BioBakery
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- Biodiverse
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- Biology
- Biopieces
- Bismark
- Bitvise
- Blackfynn
- Blast
- Blast2GO
- Blast2GO CLI
- Blast Job Scripts
- Blender
- Blink
- Blitz
- BlobTools
- Blocked Accounts
- BloomTree
- Bloomfiltertrie
- Bmtagger
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- Boost
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- Bowtie
- Bowtie2
- BoxCLI
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- Bracken
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- Bsmap
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- Bwa-meth
- Bxh xcede tools
- Bzip2
- C-wap
- CAFE
- CAMP
- CANVAS
- CAP3
- CARTA
- CASAVA
- CASM
- CAVIAR
- CBGpipe
- CCMetagen