Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs
|D. Schaller, M. Geiß, P. Stadler, M. Hellmuth. Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs. Journal of Mathematical Biology, volume 82, pages 20, DOI 10.1007/s00285-021-01564-8, 2, 2021.|
|Journal||Journal of Mathematical Biology|
Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the reciprocal best match graph. We consider duplication/loss scenarios and characterize unambiguous false-positive (u-fp) orthology assignments, that is, edges in the best match graphs (BMGs) that cannot correspond to orthologs for any gene tree that explains the BMG. Moreover, we provide a polynomial-time algorithm to identify all u-fp orthology assignments in a BMG. Simulations show that at least of all incorrect orthology assignments can be detected in this manner. All results rely only on the structure of the BMGs and not on any a priori knowledge about underlying gene or species trees.