ArticleJournal of mathematical biology2013
Orthology relations, symbolic ultrametrics, and cographs.
Article in Journal of mathematical biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- REvolutionH-tl 2.0: A fast and robust tool for decoding evolutionary gene histories.PLoS computational biology · 2026Article
- Arboreal networks and their underlying trees.Journal of mathematical 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
- 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
- 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
- Evolutionary Perspective and Expression Analysis of Intronless Genes Highlight the Conservation of Their Regulatory Role.Frontiers in genetics · 2021Article
- Best match graphs and reconciliation of gene trees with species trees.Journal of mathematical biology · 2020Article
- Reciprocal best match graphs.Journal of mathematical biology · 2020Article
- Reconstruction of time-consistent species trees.Algorithms for molecular biology : AMB · 2020Article
- Reconciling event-labeled gene trees with MUL-trees and species networks.Journal of mathematical biology · 2019Article
- Alternative characterizations of Fitch's xenology relation.Journal of mathematical biology · 2019Article
- Best match graphs.Journal of mathematical biology · 2019Article
- Reconstructing gene trees from Fitch's xenology relation.Journal of mathematical biology · 2018Article
- Accurate prediction of orthologs in the presence of divergence after duplication.Bioinformatics (Oxford, England) · 2018Article
- Inferring phylogenetic trees from the knowledge of rare evolutionary events.Journal of mathematical biology · 2018Article
- Time-consistent reconciliation maps and forbidden time travel.Algorithms for molecular biology : AMB · 2018Article
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6 authors.
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Abstract
Orthology detection is an important problem in comparative and evolutionary genomics and, consequently, a variety of orthology detection methods have been devised in recent years. Although many of these methods are dependent on generating gene and/or species trees, it has been shown that orthology can be estimated at acceptable levels of accuracy without having to infer gene trees and/or reconciling gene trees with species trees. Thus, it is of interest to understand how much information about the gene tree, the species tree, and their reconciliation is already contained in the orthology relation on the underlying set of genes. Here we shall show that a result by Böcker and Dress concerning symbolic ultrametrics, and subsequent algorithmic results by Semple and Steel for processing these structures can throw a considerable amount of light on this problem. More specifically, building upon these authors' results, we present some new characterizations for symbolic ultrametrics and new algorithms for recovering the associated trees, with an emphasis on how these algorithms could be potentially extended to deal with arbitrary orthology relations. In so doing we shall also show that, somewhat surprisingly, symbolic ultrametrics are very closely related to cographs, graphs that do not contain an induced path on any subset of four vertices. We conclude with a discussion on how our results might be applied in practice to orthology detection.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.