Best Match Graphs with Binary Trees [article]

David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
2021 arXiv   pre-print
Best match graphs (BMG) are a key intermediate in graph-based orthology detection and contain a large amount of information on the gene tree. We provide a near-cubic algorithm to determine whether a BMG is binary-explainable, i.e., whether it can be explained by a fully resolved gene tree and, if so, to construct such a tree. Moreover, we show that all such binary trees are refinements of the unique binary-resolvable tree (BRT), which in general is a substantial refinement of the also unique
more » ... st resolved tree of a BMG. Finally, we show that the problem of editing an arbitrary vertex-colored graph to a binary-explainable BMG is NP-complete and provide an integer linear program formulation for this task.
arXiv:2011.00511v2 fatcat:7gkl3b3m6vcrxofkifrw7zk4fa