ArticleJournal of mathematical biology2021
Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs.
Article in Journal of mathematical biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 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
- Unbiased anchors for reliable genome-wide synteny detection.Algorithms for molecular biology : AMB · 2025Article
- Simplifying and Characterizing DAGs and Phylogenetic Networks via Least Common Ancestor Constraints.Bulletin of mathematical biology · 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
- Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs.Frontiers in bioinformatics · 2023Article
- Heuristic algorithms for best match graph editing.Algorithms for molecular biology : AMB · 2021Article
- Indirect identification of horizontal gene transfer.Journal of mathematical biology · 2021Article
- Corrigendum to "Best match graphs".Journal of mathematical biology · 2021Article
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4 authors.
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Abstract
Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the reciprocal best match graph. We consider duplication/loss scenarios and characterize unambiguous false-positive (u-fp) orthology assignments, that is, edges in the best match graphs (BMGs) that cannot correspond to orthologs for any gene tree that explains the BMG. Moreover, we provide a polynomial-time algorithm to identify all u-fp orthology assignments in a BMG. Simulations show that at least [Formula: see text] of all incorrect orthology assignments can be detected in this manner. All results rely only on the structure of the BMGs and not on any a priori knowledge about underlying gene or species trees.
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