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Bioinformatics DOI:10.1093/bioinformatics/btu289

Pareto-optimal phylogenetic tree reconciliation.

Publication TypeJournal Article
Year of Publication2014
AuthorsLibeskind-Hadas, R, Wu, Y-C, Bansal, MS, Kellis, M
JournalBioinformatics
Volume30
Issue12
Pagesi87-95
Date Published2014 Jun 15
ISSN1367-4811
KeywordsAlgorithms, Genomics, Multigene Family, Phylogeny, Software
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.

AVAILABILITY AND IMPLEMENTATION: Our Python tools are freely available at www.cs.hmc.edu/∼hadas/xscape. .

URLhttp://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=24932009
DOI10.1093/bioinformatics/btu289
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/24932009?dopt=Abstract

Alternate JournalBioinformatics
PubMed ID24932009
PubMed Central IDPMC4058917