Figure 1

An example of how RBH analysis may falsely identify a paralog as an ortholog. Illustrated is a hypothetical species tree and gene tree for the human, cattle, and mouse species, where human and cattle orthologs (unshaded genes) are being identified. If the true cattle ortholog has not yet been sequenced because of an incomplete bovine genome project, it will not be present in the gene dataset used for analysis (cattle gene crossed out with an X), and the best reciprocal BLAST hit for the human gene will be a cattle paralog (shaded gene). However, Ortholuge will detect this case as a potential paralog, because it examines the relative phylogenetic distance between genes and identifies how well their relative distances match expected species divergence.