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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 Models
- 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