Next-generation sequencing technologies are now generating a vast amount of sequence data. This leads to a dramatic increase in the number of predicted protein sequences, which serve as a starting point for structural, functional and phylogenomic studies. In such studies, high-throughput comparative analyses are often required to transfer information between organisms, for which the concept of orthology is crucial. The original definition by Fitch describes orthologs as genes that diverged through a speciation event, as opposed to paralogs, which diverged after a duplication event (1). eggNOG, namely evolutionary genealogy of genes Non-supervised Orthologous Groups, is a database providing clusters of orthologous groups for a vast majority of genes covered by the whole tree of life. The database contains a hierarchy of orthologous groups to balance phylogenetic coverage and resolution, and provides automatic function annotation.