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Best Match Graphs With Binary Trees
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DOI：10.1109/TCBB.2022.3143870.png)
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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-refinable 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.
Keyword:
Best match graphs
binary trees
rooted triple consistency
polynomial-time algorithm
NP-hardness
integer linear program
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3.4
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3.3K
被引数:
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