ArticleJournal of mathematical biology2020
Best match graphs and reconciliation of gene trees with species trees.
Article in Journal of mathematical biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- REvolutionH-tl 2.0: A fast and robust tool for decoding evolutionary gene histories.PLoS computational biology · 2026Article
- Orthology and near-cographs in the context of phylogenetic networks.Algorithms for molecular biology : AMB · 2025Article
- The path-label reconciliation (PLR) dissimilarity measure for gene trees.Algorithms for molecular biology : AMB · 2025Article
- The Theory of Gene Family Histories.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Relative timing information and orthology in evolutionary scenarios.Algorithms for molecular biology : AMB · 2023Article
- Indirect identification of horizontal gene transfer.Journal of mathematical biology · 2021Article
- Corrigendum to "Best match graphs".Journal of mathematical biology · 2021Article
- Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs.Journal of mathematical biology · 2021Article
- Reciprocal best match graphs.Journal of mathematical biology · 2020Article
- Reconstruction of time-consistent species trees.Algorithms for molecular biology : AMB · 2020Article
- From pairs of most similar sequences to phylogenetic best matches.Algorithms for molecular biology : AMB · 2020Article
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Authors and funding
7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the concept we clarify rigorously the relationships between reciprocal best matches, orthology, and evolutionary events under the assumption of duplication/loss scenarios. We show that the orthology graph is a subgraph of the reciprocal best match graph (RBMG). We furthermore give conditions under which an RBMG that is a cograph identifies the correct orthlogy relation. Using computer simulations we find that most false positive orthology assignments can be identified as so-called good quartets-and thus corrected-in the absence of horizontal transfer. Horizontal transfer, however, may introduce also false-negative orthology assignments.
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