An Experimental Study of Quartets MaxCut and Other Supertree Methods

  • M. Shel Swenson
  • Rahul Suri
  • C. Randal Linder
  • Tandy Warnow
Conference paper

DOI: 10.1007/978-3-642-15294-8_24

Part of the Lecture Notes in Computer Science book series (LNCS, volume 6293)
Cite this paper as:
Swenson M.S., Suri R., Linder C.R., Warnow T. (2010) An Experimental Study of Quartets MaxCut and Other Supertree Methods. In: Moulton V., Singh M. (eds) Algorithms in Bioinformatics. WABI 2010. Lecture Notes in Computer Science, vol 6293. Springer, Berlin, Heidelberg

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.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • M. Shel Swenson
    • 1
    • 2
  • Rahul Suri
    • 1
  • C. Randal Linder
    • 3
  • Tandy Warnow
    • 1
  1. 1.Department of Computer ScienceThe University of Texas at Austin 
  2. 2.Department of MathematicsThe University of Texas at Austin 
  3. 3.Section of Integrative BiologyThe University of Texas at Austin 

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