An experimental study of quartets MaxCut and other supertree methods

Authors:
M. Shel Swenson;Rahul Suri;C. Randal Linder;Tandy Warnow
Affiliations:
Department of Computer Science and Department of Mathematics, The University of Texas at Austin;Department of Computer Science, The University of Texas at Austin;Section of Integrative Biology, The University of Texas at Austin;Department of Computer Science, The University of Texas at Austin
Venue:
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Year:
2010

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Abstract

Although many supertree methods have been developed in the last few decades, none has been shown to produce more accurate trees than the popular Matrix Representation with Parsimony (MRP) method. In this paper, we evaluate the performance of several supertree methods based upon the Quartets MaxCut method of Snir and Rao. We show that two of these methods usually outperform MRP and all other supertree methods we studied under many realistic model conditions. In addition, we show that the popular criterion of minimizing the total topological distance to the source trees is only weakly correlated with topological accuracy, and therefore that evaluating supertree methods on biological datasets is problematic.