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Best Match Graphs With Binary Trees
Stockholm University, Faculty of Science, Department of Mathematics.ORCID iD: 0000-0002-1620-5508
Number of Authors: 42023 (English)In: IEEE/ACM Transactions on Computational Biology & Bioinformatics, ISSN 1545-5963, E-ISSN 1557-9964, Vol. 20, no 3, p. 1679-1690Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2023. Vol. 20, no 3, p. 1679-1690
Keywords [en]
Best match graphs, binary trees, rooted triple consistency, polynomial-time algorithm, NP-hardness, integer linear program
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:su:diva-230074DOI: 10.1109/TCBB.2022.3143870ISI: 001006656100006PubMedID: 35044918Scopus ID: 2-s2.0-85123353824OAI: oai:DiVA.org:su-230074DiVA, id: diva2:1867194
Available from: 2024-06-10 Created: 2024-06-10 Last updated: 2024-06-10Bibliographically approved

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Hellmuth, Marc

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