Pareto-optimal phylogenetic tree reconciliation
Name
Liebeskind-Hadas-2014-Pareto-optimal phylogenetic.pdf
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550.63 KB
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Author(s)
Libeskind-Hadas, Ran
Wu, Yi-Chieh
Bansal, Mukul S.
Kellis, Manolis
Wu, Yi-Chieh
Date Issued
June 2014
Journal
Bioinformatics
Publisher
Oxford University Press
Citation
Libeskind-Hadas, R., Y.-C. Wu, M. S. Bansal, and M. Kellis. “Pareto-Optimal Phylogenetic Tree Reconciliation.” Bioinformatics 30, no. 12 (June 15, 2014): i87–i95.
Version
Final published version
Abstract
Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem.
Results: We address this problem by giving an efficient algorithm for computing Pareto-optimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robust statistical tests. We provide new software tools and demonstrate their use on a number of datasets from evolutionary genomic and cophylogenetic studies.
MIT Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1093/bioinformatics/btu289
