Fig. 6.

Bottom-up GETHOGs reconstruction example. (A) Orthology graph, where circles represent extant genes with a species-specific color and edges represent pairwise orthologous relations between genes. The red edge represents a spurious orthologous relation between the mouse gene A and the monkey gene B₁. (B) Reconciled gene trees corresponding to the orthology graph in (A). Extant genes are represented by squares, speciation events by circles and duplication events by stars. (C) Corresponding species tree. (D) HOGs reconstruction using bottom-up GETHOGs with a minimal edges removal threshold of 0.8. The algorithm starts by reconstructing HOGs at the level of the primates and finishes at the level of mammals. The left panel displays the sub-orthology graph composed of HOGs (or extant genes) as nodes connected by weighted edges according to the number of existing orthologous relations between HOG genes. In the middle panel, to identify spurious edges, GETHOGs computes the fraction of orthologous pairs over the maximal number of possible pairs. The algorithm removes the red edge because the score is smaller than the minimal edge removal threshold. The right panel depicts the HOGs reconstructed from the connected component of the corrected graph