Citation:

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, https://doi.org/10.1093/molbev/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

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• 18-Aug-2023
  eggNOG-mapper 2.1.12 just released! and it is running at eggNOG-mapper web, now including new annotations when searching against the novel families from Rodríguez et al 2022 (try it at eggnog-mapper.embl.de/FESNOV or go to "Advanced Options" -> "Database" -> "Novel families")
• 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!

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: