Best match graphs

Manuela Geiß, Edgar Chávez, Marcos González Laffitte, Alitzel López Sánchez, Bärbel M. R. Stadler, Dulce I. Valdivia, Marc Hellmuth, Maribel Hernández Rosales, Peter F. Stadler
2019 Journal of Mathematical Biology  
Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let T be a phylogenetic (gene) tree T and [Formula: see text] an assignment of leaves of T to species. The best match graph [Formula: see text] is a digraph that contains an arc from x to y if the genes x and y reside in different species and y is one of possibly many (evolutionary) closest relatives of x compared to all other genes contained in the species [Formula: see text]. Here, we
more » ... characterize best match graphs and show that it can be decided in cubic time and quadratic space whether [Formula: see text] derived from a tree in this manner. If the answer is affirmative, there is a unique least resolved tree that explains [Formula: see text], which can also be constructed in cubic time.
doi:10.1007/s00285-019-01332-9 pmid:30968198 pmcid:PMC6534531 fatcat:nsiwxfrxpzcxncjenndfnvpv44