Fast error-tolerant quartet phylogeny algorithms

  • Authors:
  • Daniel G. Brown;Jakub Truszkowski

  • Affiliations:
  • David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, Canada;David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, Canada

  • Venue:
  • CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
  • Year:
  • 2011

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Abstract

We present a quartet-based phylogeny algorithm that returns the correct topology for n taxa in O(n log n) time with high probability, assuming each quartet is inconsistent with the true tree topology with constant probability, independent of other quartets. Our incremental algorithm relies upon a search tree structure for the phylogeny that is balanced, with high probability, no matter the true topology. In experiments, our prototype was as fast as the fastest heuristics, but because real data do not typically satisfy our probabilistic assumptions, its overall performance is not as good as our theoretical results predict.