Representation in stochastic search for phylogenetic tree reconstruction

Authors:
Griffin Weber;Lucila Ohno-Machado;Stuart Shieber
Affiliations:
Decision Systems Group, Brigham and Women's Hospital, Division of Health Sciences and Technology, Harvard and MIT and Division of Engineering and Applied Sciences, Harvard University;Decision Systems Group, Brigham and Women's Hospital, Division of Health Sciences and Technology, Harvard and MIT;Division of Engineering and Applied Sciences, Harvard University
Venue:
Journal of Biomedical Informatics - Special issue: Phylogenetic inferencing: Beyond biology
Year:
2006

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Abstract

Phylogenetic tree reconstruction is a process in which the ancestral relationships among a group of organisms are inferred from their DNA sequences. For all but trivial sized data sets, finding the optimal tree is computationally intractable. Many heuristic algorithms exist, but the branch-swapping algorithm used in the software package PAUP* is the most popular. This method performs a stochastic search over the space of trees, using a branch-swapping operation to construct neighboring trees in the search space. This study introduces a new stochastic search algorithm that operates over an alternative representation of trees, namely as permutations of taxa giving the order in which they are processed during stepwise addition. Experiments on several data sets suggest that this algorithm for generating an initial tree. When followed by branch-swapping, can produce better trees for a given total amount of time.