- [eggNOG-mapper v2] - [Python, v2.1.12, 2023.08] - [2021.10, Mol Biol Evol]- [eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale.]
- [KofamScan] - [Ruby, v1.3.0, 2020.05] - [2019.11, Bioinformatics] - [KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold.]
- [Macrel] - [Python, v1.5.0, 2024.09] - [2020.12, PeerJ] - [Macrel: antimicrobial peptide screening in genomes and metagenomes.]
- [RGI] - [Python, 6.0.3, 2023.09] - [2023.01, Nucleic Acids Res] - [CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.]
- [MetaCerberus] - [Python, v1.4.0, 2024.08] - [2024.02, Bioinformatics] - [MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life.]
- [GMSC-mapper] - [Python, v0.1.0, 2024.04] - [2024.08, Nat Commun] - [A catalog of small proteins from the global microbiome.]
- [Bakta] - [Python, v1.10.1, 2024.11] - [2021.11, Microbial Genomics] Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. - [web version]
- [DRAM] - [Python, v1.5.0, 2024.1] - [2020.9, Nucleic Acids Res] - [DRAM for distilling microbial metabolism to automate the curation of microbiome function]
- [graftM] - [Python, v0.14.0, 2022.5] - [2018.6, Nucleic Acids Res] - [GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes.]
- CD-Search - [Web] - [2004.7, Nucleic Acids Res] - CD-Search: protein domain annotations on the fly.
- [HMMER3] - [C, v3.4, 2023.8] - [2011.10, PLoS Comput Biol] - [Accelerated profile HMM searches.]
- [DeepARG] - [Python2.7, NA, 2023.11] - [2018.2, Microbiome] - [DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data]
- ARG-OAP
- [argNorm] - [Python, v0.6.0, 2024.8] - [2024.10, QUT ePrints] - [argNorm: Normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)]
- [OrthoLoger] - [bash, v3.5.0, 2024.10] - [2022.11, Nucleic Acids Res] - [OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity]
- [nail] - [Rust, 2024.7, v0.2.0] - [2024.1, bioRxiv] - [nail: software for high-speed, high-sensitivity protein sequence annotation]
- [FastOMA] - [Python, 2024.9,v0.3.4] - [2025.1, Nat Methods] - [Orthology inference at scale with FastOMA.]
- [BenchAMRking] - [web workflow AAMR detection] - [BenchAMRking: a Galaxy-based platform for illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows.]
- [eggNOG 6.0] - [AA Genes, v6.0, 2022.09] - [2022.11, Nucleic Acids Res] - [eggNOG 6.0: Enabling comparative genomics across 12,535 organisms.]
- [KEGG] - [AA Genes, 111.0, 2024.08] - [2016.1, Nucleic Acids Res] - [KEGG as a reference resource for gene and protein annotation]
- [CAZy] - [AA, web] - [2022.1, Nucleic Acids Res] - [The carbohydrate-active enzyme database: functions and literature.]
- [CARD] - [ARG, v3.3.0, 2024.08] - [2023.01, Nucleic Acids Res] - [CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.]
- [UniProt] - [AA genes, v2024_04, 2024.07] - [2022.11, Nucleic Acids Res] - [The UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2023.]
- [UniProt] - [AA genes, v2024_5] - [2024.11, Nucleic Acids Res] - UniProt: the Universal Protein Knowledgebase in 2025.
- [ISOSDB] - [IS Sequences, v3, 2023.12] - [2024.05, Cell Host Microbe] - [A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.]
- [AMPSphere] - [AMP, v2022-03, 2022.03] - [2024.07, cell] - [Discovery of antimicrobial peptides in the global microbiome with machine learning.]
- [DRAMP] - [AMP, v4.0, 2024.09] - [2022.01, Nucleic Acids Res] - [DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides.]
- [GMSC] - [smORF, v1.0, 2024.08] - [2024.08, Nat Commun] - [A catalog of small proteins from the global microbiome.]
- [TCDB] - [transporters, 2024-09, 2024.09] - [2021.01, Nucleic Acids Res] - [The Transporter Classification Database (TCDB): 2021 update]
- [VFDB] - [virulence factors, 2024.9] - [2022.1, Nucleic Acids Res] - VFDB 2022: a general classification scheme for bacterial virulence factors
- [DoriC] - [oriC, v12.1, NA] - [2023.1, Nucleic Acids Res] - [DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes.]
- [TIGRAFMs] - [protein sequence, v15.0, 2014.9] [2001.1, Nucleic Acids Res] - TIGRFAMs: a protein family resource for the functional identification of proteins.
- [Pfam] - [protein sequences, v37.0, 2024.5] - [2021.1, Nucleic Acids Res] - [Pfam: The protein families database in 2021.]
- [Rfam] - [microRNA, v15, 2024.9] - [2021.1, Nucleic Acids Res] - [Rfam 14: expanded coverage of metagenomic, viral and microRNA families.]
- [PHI] - [Pathogen Host Interactions, v5.0, 2024.3] [2022.1, Nucleic Acids Res] [PHI-base in 2022: a multi-species phenotype database for Pathogen–Host Interactions.]
- [oriTDB] - [2024.10, Nucleic Acids Res] - [oriTDB: a database of the origin-of-transfer regions of bacterial mobile genetic elements.]
- [COG] - [2024.11, Nucleic Acids Res] - [COG database update 2024.] - [FTP]
- [OrthoDB] - [v11.0] - [2022.11, Nucleic Acids Res] - [OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity]
- CAZyme3D - [web] - [2024.12, bioRxiv] - [CAZyme3D: a database of 3D structures for carbohydrate-active enzymes]
- S9BactDB - [S9 proteases, web] - [2025.1, bioRxiv] - [S9BactDB: A database for S9 family of proteases in bacterial genomes.]
- [Chai-1] - [Python, v0.0.1, 2024.09] - [2024.09, Web] - [Introducing Chai-1: Decoding the molecular interactions of life.]
- [AlphaFold2] - [Python, v2.3.2, 2023.04] - [2021.07, Nature] - [Highly accurate protein structure prediction with AlphaFold.]
- [AlphaFold3] - [Web Service, NA, NA] - [2024.05, Nature] - [Accurate structure prediction of biomolecular interactions with AlphaFold 3.]
- [DNAproDB] - [Online database] - [2024.11, Nucleic Acids Res] - [DNAproDB: an updated database for the automated and interactive analysis of protein–DNA complexes.]