eggnog-mapper is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments. Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. The use of orthology predictions for functional annotation is considered more precise than traditional homology searches, as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
EggNOG-mapper is also available as a public online resource: http://eggnog-mapper.embl.de
If you use this software, please cite:
 Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering and Peer Bork. Mol Biol Evol (2017). [doi: 10.1093/molbev/msx148](https://doi.org/10.1093/molbev/msx148)  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