Incomplete Directed Perfect Phylogeny

  • Itsik Pe’er
  • Ron Shamir
  • Roded Sharan
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 1848)


Perfect phylogeny is one of the fundamental models for studying evolution. We investigate the following generalization of the problem: The input is a species-characters matrix. The characters are binary and directed, i.e., a species can only gain characters. The difference from standard perfect phylogeny is that for some species the state of some characters is unknown. The question is whether one can complete the missing states in a way admitting a perfect phylogeny. The problem arises in classical phylogenetic studies, when some states are missing or undetermined. Quite recently, studies that infer phylogenies using inserted repeat elements in DNA gave rise to the same problem. The best known algorithm for the problem requires O(n 2 m) time for m characters and n species. We provide a near optimal ÕO(nm)-time algorithm for the problem.


Binary Matrix Edge Deletion Dynamic Data Structure Perfect Phylogeny Canonical Matrix 
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 2000

Authors and Affiliations

  • Itsik Pe’er
    • 1
  • Ron Shamir
    • 1
  • Roded Sharan
    • 1
  1. 1.Department of Computer ScienceTel-Aviv UniversityTel-AvivIsrael

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