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2014 ; 30
(12
): i87-95
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Pareto-optimal phylogenetic tree reconciliation
#MMPMID24932009
Libeskind-Hadas R
; Wu YC
; Bansal MS
; Kellis M
Bioinformatics
2014[Jun]; 30
(12
): i87-95
PMID24932009
show ga
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. .
free
free
free
