ArticleAlgorithms for molecular biology : AMB2016
The link between orthology relations and gene trees: a correction perspective.
Article in Algorithms for molecular biology : AMB, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Simplifying and Characterizing DAGs and Phylogenetic Networks via Least Common Ancestor Constraints.Bulletin of mathematical biology · 2025Article
- 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
- Best match graphs and reconciliation of gene trees with species trees.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
- Best match graphs.Journal of mathematical biology · 2019Article
- Reconciling multiple genes trees via segmental duplications and losses.Algorithms for molecular biology : AMB · 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
- Time-consistent reconciliation maps and forbidden time travel.Algorithms for molecular biology : AMB · 2018Article
- The mathematics of xenology: di-cographs, symbolic ultrametrics, 2-structures and tree-representable systems of binary relations.Journal of mathematical biology · 2017Article
- Biologically feasible gene trees, reconciliation maps and informative triples.Algorithms for molecular biology : AMB · 2017Article
- Approximating the correction of weighted and unweighted orthology and paralogy relations.Algorithms for molecular biology : AMB · 2017Article
- Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies.BMC genomics · 2016Article
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3 authors.
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Abstract
backgroundWhile tree-oriented methods for inferring orthology and paralogy relations between genes are based on reconciling a gene tree with a species tree, many tree-free methods are also available (usually based on sequence similarity). Recently, the link between orthology relations and gene trees has been formally considered from the perspective of reconstructing phylogenies from orthology relations. In this paper, we consider this link from a correction point of view. Indeed, a gene tree induces a set of relations, but the converse is not always true: a set of relations is not necessarily in agreement with any gene tree. A natural question is thus how to minimally correct an infeasible set of relations. Another natural question, given a gene tree and a set of relations, is how to minimally correct a gene tree so that the resulting gene tree fits the set of relations.
resultsWe consider four variants of relation and gene tree correction problems, and provide hardness results for all of them. More specifically, we show that it is NP-Hard to edit a minimum of set of relations to make them consistent with a given species tree. We also show that the problem of finding a maximum subset of genes that share consistent relations is hard to approximate. We then demonstrate that editing a gene tree to satisfy a given set of relations in a minimum way is NP-Hard, where "minimum" refers either to the number of modified relations depicted by the gene tree or the number of clades that are lost. We also discuss some of the algorithmic perspectives given these hardness results.
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