Performance of flip supertree construction with a heuristic algorithm

Oliver Eulenstein, Duhong Chen, J. Gordon Burleih, David Fernández-Baca, Michael J. Sanderson

Research output: Contribution to journalArticlepeer-review

49 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)299-308
Number of pages10
JournalSystematic biology
Issue number2
StatePublished - Apr 2004


  • Flipping
  • Phylogeny
  • Simulation study
  • Supertree

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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