Polynomial supertree methods revisited

Authors:
Malte Brinkmeyer;Thasso Griebel;Sebastian Böcker
Affiliations:
Department of Computer Science, Friedrich Schiller University, Jena, Germany;Department of Computer Science, Friedrich Schiller University, Jena, Germany;Department of Computer Science, Friedrich Schiller University, Jena, Germany
Venue:
PRIB'10 Proceedings of the 5th IAPR international conference on Pattern recognition in bioinformatics
Year:
2010

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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 Min-Cut Supertree, Modified MinCut Supertree, Build-with-distances, PhySIC, and PhySIC IST. We consider both quality and resolution of the reconstructed supertrees. Our findings illustrate the trade-off between accuracy and running time in supertree construction, as well as the pros and cons of voting- and veto-based supertree approaches.