ArticleAlgorithms for molecular biology : AMB2020
From pairs of most similar sequences to phylogenetic best matches.
Article in Algorithms for molecular biology : AMB, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- REvolutionH-tl 2.0: A fast and robust tool for decoding evolutionary gene histories.PLoS computational biology · 2026Article
- 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
- Heuristic algorithms for best match graph editing.Algorithms for molecular biology : AMB · 2021Article
- Indirect identification of horizontal gene transfer.Journal of mathematical biology · 2021Article
- Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs.Journal of mathematical biology · 2021Article
- Reconstruction of time-consistent species trees.Algorithms for molecular biology : AMB · 2020Article
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Authors and funding
8 authors.
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Abstract
backgroundMany of the commonly used methods for orthology detection start from mutually most similar pairs of genes (reciprocal best hits) as an approximation for evolutionary most closely related pairs of genes (reciprocal best matches). This approximation of best matches by best hits becomes exact for ultrametric dissimilarities, i.e., under the Molecular Clock Hypothesis. It fails, however, whenever there are large lineage specific rate variations among paralogous genes. In practice, this introduces a high level of noise into the input data for best-hit-based orthology detection methods.
resultsIf additive distances between genes are known, then evolutionary most closely related pairs can be identified by considering certain quartets of genes provided that in each quartet the outgroup relative to the remaining three genes is known.
conclusionImprovements of tree-free orthology assessment methods can be expected from a combination of the accurate inference of best matches reported here and recent mathematical advances in the understanding of (reciprocal) best match graphs and orthology relations. AVAILABILITY: Accompanying software is available at https://github.com/david-schaller/AsymmeTree.
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