EggNOG

@article{huerta-cepas2019, title={Nucleic Acids Res.}, author={Jaime Huerta-Cepas and Damian Szklarczyk and Davide Heller and Ana Hernández-Plaza and Sofia K Forslund and Helen Cook and Daniel R Mende and Ivica Letunic and Thomas Rattei and Lars J Jensen and Christian von Mering and Peer Bork}, journal={Nucleic Acids Res.}, volume={47}, number={Database issue}, pages={D309--D314}, year={2019}, month={Jan}, day={8}, doi={10.1093/nar/gky1085} }

@article{10.1093/nar/gkac1022, author = {Hernández-Plaza, Ana and Szklarczyk, Damian and Botas, Jorge and Cantalapiedra, Carlos P and Giner-Lamia, Joaquín and Mende, Daniel R and Kirsch, Rebecca and Rattei, Thomas and Letunic, Ivica and Jensen, Lars J and Bork, Peer and von Mering, Christian and Huerta-Cepas, Jaime}, title = "{eggNOG 6.0: enabling comparative genomics across 12 535 organisms}", journal = {Nucleic Acids Research}, volume = {51}, number = {D1}, pages = {D389-D394}, year = {2022}, month = {11}, abstract = "{The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database is a bioinformatics resource providing orthology data and comprehensive functional information for organisms from all domains of life. Here, we present a major update of the database and website (version 6.0), which increases the number of covered organisms to 12 535 reference species, expands functional annotations, and implements new functionality. In total, eggNOG 6.0 provides a hierarchy of over 17M orthologous groups (OGs) computed at 1601 taxonomic levels, spanning 10 756 bacterial, 457 archaeal and 1322 eukaryotic organisms. OGs have been thoroughly annotated using recent knowledge from functional databases, including KEGG, Gene Ontology, UniProtKB, BiGG, CAZy, CARD, PFAM and SMART. eggNOG also offers phylogenetic trees for all OGs, maximising utility and versatility for end users while allowing researchers to investigate the evolutionary history of speciation and duplication events as well as the phylogenetic distribution of functional terms within each OG. Furthermore, the eggNOG 6.0 website contains new functionality to mine orthology and functional data with ease, including the possibility of generating phylogenetic profiles for multiple OGs across species or identifying single-copy OGs at custom taxonomic levels. eggNOG 6.0 is available at http://eggnog6.embl.de.}", issn = {0305-1048}, doi = {10.1093/nar/gkac1022}, url = {https://doi.org/10.1093/nar/gkac1022}, eprint = {https://academic.oup.com/nar/article-pdf/51/D1/D389/48441263/gkac1022.pdf}