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Advances in Bioinformatics
Volume 2011 (2011), Article ID 524182, 21 pages
http://dx.doi.org/10.1155/2011/524182
Research Article

Polynomial Supertree Methods Revisited

Department of Computer Science, Friedrich Schiller University, 07743 Jena, Germany

Received 7 April 2011; Revised 1 August 2011; Accepted 15 September 2011

Academic Editor: David Posada

Copyright © 2011 Malte Brinkmeyer et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Supertree methods allow to reconstruct large phylogenetic trees by combining smaller trees with overlapping leaf sets into one, more comprehensive supertree. The most commonly used supertree method, matrix representation with parsimony (MRP), produces accurate supertrees but is rather slow due to the underlying hard optimization problem. In this paper, we present an extensive simulation study comparing the performance of MRP and the polynomial supertree methods MinCut Supertree, Modified MinCut Supertree, Build-with-distances, PhySIC, PhySIC_IST, and super distance matrix. We consider both quality and resolution of the reconstructed supertrees. Our findings illustrate the tradeoff between accuracy and running time in supertree construction, as well as the pros and cons of voting- and veto-based supertree approaches. Based on our results, we make some general suggestions for supertree methods yet to come.