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Systematic Biology 2004 53(2):299-308; doi:10.1080/10635150490423719
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© 2004 Society of Systematic Biologists

Performance of Flip Supertree Construction with a Heuristic Algorithm

Oliver Eulenstein1, Duhong Chen1, J. Gordon Burleigh1,2, David Fernández-Baca1 and Michael J. Sanderson2

1 Department of Computer Science, Iowa State University Ames Iowa 50011, USA; E-mail: oeulenst{at}cs.iastate.edu (O.E.)
2 Section of Evolution and Ecology, University of California Davis California 95616, USA

Edited by Junhyong Kim: Associate Editor


  Abstract

Supertree methods are used to assemble separate phylogenetic trees with shared taxa into larger trees (supertrees) in an effort to construct more comprehensive phylogenetic hypotheses. In spite of much recent interest in supertrees, there are still few methods for supertree construction. The flip supertree problem is an error correction approach that seeks to find a minimum number of changes (flips) to the matrix representation of the set of input trees to resolve their incompatibilities. A previous flip supertree algorithm was limited to finding exact solutions and was only feasible for small input trees. We developed a heuristic algorithm for the flip supertree problem suitable for much larger input trees. We used a series of 48- and 96-taxon simulations to compare supertrees constructed with the flip supertree heuristic algorithm with supertrees constructed using other approaches, including MinCut (MC), modified MC (MMC), and matrix representation with parsimony (MRP). Flip supertrees are generally far more accurate than supertrees constructed using MC or MMC algorithms and are at least as accurate as supertrees built with MRP. The flip supertree method is therefore a viable alternative to other supertree methods when the number of taxa is large.

Keywords: Flipping; phylogeny; simulation study; supertree

Received May 9, 2003; Revised August 12, 2003; Accepted November 23, 2003
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