On the Generality of Phylogenies from Incomplete Directed Characters

  • Itsik Pe’er
  • Ron Shamir
  • Roded Sharan
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2368)


We study a problem that arises in computational biology, when wishing to reconstruct the phylogeny of a set of species. In Incomplete Directed Perfect Phylogeny (IDP), the characters are binary and directed (i.e., species can only gain characters), and the states of some characters are unknown. The goal is to complete the missing states in a way consistent with a perfect phylogenetic tree. This problem arises in classical phylogenetic studies, when some states are missing or undetermined, and in recent phylogenetic studies based on repeat elements in DNA. The problem was recently shown to be polynomial. As different completions induce different trees, it is desirable to find a general solution tree. Such a solution is consistent with the data, and every other consistent solution can be obtained from it by node splitting. Unlike the situation for complete datasets, a general solution may not exist for IDP instances. We provide a polynomial algorithm to find a general solution for an IDP instance, or determine that none exists.


General Solution Binary Matrix Recursive Call Node Splitting Character Species 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2002

Authors and Affiliations

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

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