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Generalizing the Four Gamete Condition and Splits Equivalence Theorem: Perfect Phylogeny on Three State Characters

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Algorithms in Bioinformatics (WABI 2009)

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Abstract

We study the three state perfect phylogeny problem and show that there is a three state perfect phylogeny for a set of input sequences if and only if there is a perfect phylogeny for every subset of three characters. In establishing these results, we prove fundamental structural features of the perfect phylogeny problem on three state characters and completely characterize the obstruction sets that must occur in input sequences that do not have a perfect phylogeny. We also give a proof for a stated lower bound involved in the conjectured generalization of our main result to any number of states.

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of California, Davis, USA

    Fumei Lam & Dan Gusfield

  2. Department of Computer Science, Carnegie Mellon University, USA

    Srinath Sridhar

Authors
  1. Fumei Lam
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  2. Dan Gusfield
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  3. Srinath Sridhar
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Editor information

Editors and Affiliations

  1. Center for Bioinformatics and Computational Biology, and Department of Computer Science, University of Maryland, MD, College Park, USA

    Steven L. Salzberg

  2. Department of Computer Sciences, The University of Texas at Austin, TX, USA

    Tandy Warnow

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© 2009 Springer-Verlag Berlin Heidelberg

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Lam, F., Gusfield, D., Sridhar, S. (2009). Generalizing the Four Gamete Condition and Splits Equivalence Theorem: Perfect Phylogeny on Three State Characters. In: Salzberg, S.L., Warnow, T. (eds) Algorithms in Bioinformatics. WABI 2009. Lecture Notes in Computer Science(), vol 5724. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04241-6_18

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  • DOI: https://doi.org/10.1007/978-3-642-04241-6_18

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-04240-9

  • Online ISBN: 978-3-642-04241-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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