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FAQ Frequently Asked Questions
While eggNOG provides groups of orthologs where in-paralogs at different levels might exist, phylogenetic analysis allows restricting the list of orthologs for a given sequence to those that where not the result of a duplication event. Basically, fine-grained orthologs refer to phylogeneticly refined orthology assignments.
In our latest tests, DIAMOND mode worked much faster and obtained similar or even better results than with the HMM approach. Note that eggnog-mapper needs to identify a seed_ortholog for each query sequence. The seed ortholog is expected to have a minimum level of similarity with the query, so eggNOG-mapper cannot really benefit from very distant homologies catched by HMM searches.
Optionally, queries without any DIAMOND hit can be assigned to eggNOG groups using HMM searches. In that case, functional inferences will be more general and less reliable.