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Incomplete Directed Perfect Phylogeny

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Combinatorial Pattern Matching (CPM 2000)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1848))

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Abstract

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.

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Author information

Authors and Affiliations

  1. Department of Computer Science, Tel-Aviv University, Tel-Aviv, Israel

    Itsik Pe’er, Ron Shamir & Roded Sharan

Authors
  1. Itsik Pe’er
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  2. Ron Shamir
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  3. Roded Sharan
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Editor information

Editors and Affiliations

  1. Dipartimento di Matematica ed Applicazioni, Universitá die Palermo, Via Archirafi 34, 90123, Palermo, Italy

    Raffaele Giancarlo

  2. Centre de recherches mathématiques, Université de Montréal, CP 6128, succursale Centre-Ville, Montréal, Québec, Canada, H3C 3J7

    David Sankoff

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© 2000 Springer-Verlag Berlin Heidelberg

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Pe’er, I., Shamir, R., Sharan, R. (2000). Incomplete Directed Perfect Phylogeny. In: Giancarlo, R., Sankoff, D. (eds) Combinatorial Pattern Matching. CPM 2000. Lecture Notes in Computer Science, vol 1848. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45123-4_14

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  • DOI: https://doi.org/10.1007/3-540-45123-4_14

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-67633-1

  • Online ISBN: 978-3-540-45123-5

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