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arXiv · 2006.02249

Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs

David Schaller·Manuela Geiß·Peter F. Stadler·Marc Hellmuth
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Abstract

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 $75\%$ 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.

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David Schaller, Manuela Geiß, Peter F. Stadler, Marc Hellmuth. 2020-11-26. Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs. https://arxiv.org/abs/2006.02249

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