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Hypothesis testing in perfect phylogeny for a bounded number of characters

  • Jens Lagergren
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 1046)

Abstract

We introduce the hypothesis testing problem (HTP). In HTP the input is a family of species F and a hypothesis, i.e., a tree where the leaves are labeled with species from some subfamily of F. The problem is to decide whether there is a perfect phylogeny for F which agrees with the hypothesis. We show that HTP can be solved in O(m2r m |F|(|F|+mr)) time, where m is the number of characters and r is the maximum number of states on any character. We obtain an O(m3rm+1 + |F|m2) algorithm for the perfect phylogeny problem (PPP), as well. The fastest previously known algorithm for PPP, with fixed m, has running time O(mm+1rm+1 + |F|m2) [10]. We also consider several variations of HTP which we either show to be solvable in polynomial time or NP-complete.

Keywords

Polynomial Time Evolutionary Tree Polynomial Time Algorithm Colored Graph Linear Time Algorithm 
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-Verlag Berlin Heidelberg 1996

Authors and Affiliations

  • Jens Lagergren
    • 1
  1. 1.Department of Numerical Analysis and Computing ScienceThe Royal Institute of TechnologyStockholmSweden

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