ArticleBioinformatics (Oxford, England)2014
Polytomy refinement for the correction of dubious duplications in gene trees.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- REvolutionH-tl 2.0: A fast and robust tool for decoding evolutionary gene histories.PLoS computational biology · 2026Article
- Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs.Journal of mathematical biology · 2021Article
- ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy.Molecular biology and evolution · 2020Article
- Unblended disjoint tree merging using GTM improves species tree estimation.BMC genomics · 2020Article
- The link between orthology relations and gene trees: a correction perspective.Algorithms for molecular biology : AMB · 2016Article
- Efficient Gene Tree Correction Guided by Genome Evolution.PloS one · 2016Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationLarge-scale methods for inferring gene trees are error-prone. Correcting gene trees for weakly supported features often results in non-binary trees, i.e. trees with polytomies, thus raising the natural question of refining such polytomies into binary trees. A feature pointing toward potential errors in gene trees are duplications that are not supported by the presence of multiple gene copies.
resultsWe introduce the problem of refining polytomies in a gene tree while minimizing the number of created non-apparent duplications in the resulting tree. We show that this problem can be described as a graph-theoretical optimization problem. We provide a bounded heuristic with guaranteed optimality for well-characterized instances. We apply our algorithm to a set of ray-finned fish gene trees from the Ensembl database to illustrate its ability to correct dubious duplications. AVAILABILITY AND IMPLEMENTATION: The C++ source code for the algorithms and simulations described in the article are available at http://www-ens.iro.umontreal.ca/~lafonman/software.php. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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