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The Worst Case Complexity of Maximum Parsimony

  • Amir Carmel
  • Noa Musa-Lempel
  • Dekel Tsur
  • Michal Ziv-Ukelson
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8486)

Abstract

One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms. We re-examine the classical Maximum Parsimony (MP) optimization problem for the general (asymmetric) scoring matrix case, where rooted phylogenies are implied, and analyze theworst case bounds of three approaches to MP: The approach of Cavalli-Sforza and Edwards [5], the approach of Hendy and Penny [12], and a new agglomerative, “bottomup” approach we present in this paper. We show that the second and third approaches are faster than the first by a factor of \(\Theta(\sqrt{n})\) and Θ(n), respectively.

Keywords

Maximal Parsimony Search Tree Basic Operation Internal Vertex Minimum Label 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Amir Carmel
    • 1
  • Noa Musa-Lempel
    • 1
  • Dekel Tsur
    • 1
  • Michal Ziv-Ukelson
    • 1
  1. 1.Department of Computer ScienceBen-Gurion University of the NegevIsrael

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