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Carlos P Cantalapiedra edited this page Aug 18, 2023 · 64 revisions


EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed Orthologous Groups (OGs) and phylogenies from the EggNOG database ( to transfer functional information from fine-grained orthologs only.

Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.

The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches (i.e. BLAST searches), as it avoids transferring annotations from close paralogs (duplicate genes with a higher chance of being involved in functional divergence).

Benchmarks comparing different eggNOG-mapper options against BLAST and InterProScan are available here.

EggNOG-mapper is also available as a public online web resource:


Current versions

Previous versions


[1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain                                                                         
      prediction at the metagenomic scale. Carlos P. Cantalapiedra,                                                                                    
      Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas.                                                                               
      biorxiv (2021). doi:

[2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated
      orthology resource based on 5090 organisms and 2502 viruses. Jaime
      Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia
      K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars
      J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8;
      47(Database issue): D309–D314. doi: 10.1093/nar/gky1085 

Or, if you use the novel families database instead of eggNOG 5, please cite:

[2] Functional and evolutionary significance of unknown genes from uncultivated taxa.                                                                                                                                                                                                Álvaro Rodríguez del Río, Joaquín Giner-Lamia, Carlos P. Cantalapiedra,                                                                                                                                                                                                      Jorge Botas, Ziqi Deng, Ana Hernández-Plaza, Lucas Paoli, Thomas S.B. Schmidt,                                                                                                                                                                                               Shinichi Sunagawa, Peer Bork, Luis Pedro Coelho, Jaime Huerta-Cepas.                                                                                                                                                                                                         2022. bioRxiv 2022.01.26.477801. 


Depending on the tools used, you may want to cite also:


Accelerated Profile HMM Searches. Eddy SR. 2011. PLoS Comput. Biol. 7:e1002195.                                                                                                                                                                                                                         

* Diamond

Sensitive protein alignments at tree-of-life scale using DIAMOND. Buchfink B, Reuter K, Drost HG. 2021. Nature Methods 18, 366–368 (2021).                                                                                                                                                                                         

* MMseqs

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Steinegger M & Söding J. 2017. Nat. Biotech. 35, 1026–1028.                                                                                                                                                                          

* Prodigal

Prodigal: prokaryotic gene recognition and translation initiation site identification. Hyatt et al. 2010. BMC Bioinformatics 11, 119. 


Original eggNOG-mapper paper:

    Fast genome-wide functional annotation through orthology assignment by
      eggNOG-mapper. Jaime Huerta-Cepas, Damian Szklarczyk, Lars Juhl Jensen,
      Christian von Mering and Peer Bork. Submitted (2016).