ArticleBioMed research international2014
Reconciliation of gene and species trees.
Article in BioMed research international, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- The Theory of Gene Family Histories.Methods in molecular biology (Clifton, N.J.) · 2024Article
- 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
- From pairs of most similar sequences to phylogenetic best matches.Algorithms for molecular biology : AMB · 2020Article
- Reconciling event-labeled gene trees with MUL-trees and species networks.Journal of mathematical biology · 2019Article
- Biologically feasible gene trees, reconciliation maps and informative triples.Algorithms for molecular biology : AMB · 2017Article
- Functional Annotations of Paralogs: A Blessing and a Curse.Life (Basel, Switzerland) · 2016Article
- Algorithms for reconstruction of chromosomal structures.BMC bioinformatics · 2016Article
- Algorithms of ancestral gene length reconstruction.BioMed research international · 2013Article
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Authors and funding
4 authors.
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Abstract
The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree.
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