eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale.
Carlos P. Cantalapiedra, Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, and Jaime Huerta-Cepas. 2021
Molecular Biology and Evolution, msab293,

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. 2019
Nucleic Acids Res. 2019 Jan 8; 47(Database issue): D309–D314. doi: 10.1093/nar/gky1085

Please, check your output files for all the references requiring citation for your job.

License of use:

eggNOG data and the eggNOG-mapper tool are open-source and fully free resources for academics. However, any kind of commercial usage requires explicit licensing; please contact for further information.


  • 19-Jul-2022
    eggNOG-mapper 2.1.9 just released! and it is running at eggNOG-mapper web, now including a new option to search against the novel families from Rodríguez et al 2022 ("Advanced Options" -> "Database" -> "Novel families")
  • 22-Oct-2021
    - New blastx-like search options for genomic and metagenomic sequences
    - New frameshift option for annotation of Nanopore reads
    - Accepting gzipped files as input (file name must end in '.gz')
  • 01-Oct-2021
    New eggNOG-mapper v2 paper in Advanced Access!

Method Overview

eggNOG-mapper v2 is a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed eggNOG v5.0 clusters and phylogenies. The method is illustrated in the following figure: