Best Match Graphs with Binary Trees
Data Structures and Algorithms
2021-03-09 v2 Computational Complexity
Discrete Mathematics
Combinatorics
Populations and Evolution
Abstract
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 least 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.
Keywords
Cite
@article{arxiv.2011.00511,
title = {Best Match Graphs with Binary Trees},
author = {David Schaller and Manuela Geiß and Marc Hellmuth and Peter F. Stadler},
journal= {arXiv preprint arXiv:2011.00511},
year = {2021}
}