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Phylogenetic Reconstruction Algorithms Based on Weighted 4-Trees

  • Vincent Ranwez
  • Olivier Gascuel
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2066)

Abstract

Quartet methods first compute 4-taxon trees (or 4-trees) then use a combinatorial algorithm to infer a phylogeny that closely respects the inferred 4-trees. This article focuses on the special case involving weighted 4-trees. The sum of the weights of the 4-trees induced by the inferred phylogeny is a natural measurement of the fit between this phylogeny and the 4-tree set. In order to measure the fit of each edge of the inferred tree, we propose a new criterion that takes the weights of the 4-trees along with the way they are grouped into account. However, finding the tree that optimizes the natural criterion is NP-hard [10], and optimizing our new criterion is likely not easier. We then describe two greedy heuristic algorithms that are experimentally efficient in optimizing these criteria and have an O(n 4) time complexity (where n is the number of studied taxa). We use computer simulations to show that these two algorithms have better topological accuracy than QUARTET PUZZLING [12], which is one of the few quartet methods able to take 4-trees weighting into account, and seems to be widely used.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2001

Authors and Affiliations

  • Vincent Ranwez
    • 1
  • Olivier Gascuel
    • 1
  1. 1.LIRMMUMR 9928 UNIVERSITE MONTPELLIER II/CNRSFrance

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