Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree Reconstruction

  • Guy E. Blelloch
  • Kedar Dhamdhere
  • Eran Halperin
  • R. Ravi
  • Russell Schwartz
  • Srinath Sridhar
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4051)


We consider the problem of finding a Steiner minimum tree in a hypercube. Specifically, given n terminal vertices in an m dimensional cube and a parameter q, we compute the Steiner minimum tree in time O(72 q + 8 q nm 2), under the assumption that the length of the minimum Steiner tree is at most m + q.

This problem has extensive applications in taxonomy and biology. The Steiner tree problem in hypercubes is equivalent to the phylogeny (evolutionary tree) reconstruction problem under the maximum parsimony criterion, when each taxon is defined over binary states. The taxa, character set and mutation of a phylogeny correspond to terminal vertices, dimensions and traversal of a dimension in a Steiner tree. Phylogenetic trees that mutate each character exactly once are called perfect phylogenies and their size is bounded by the number of characters. When a perfect phylogeny consistent with the data set exists it can be constructed in linear time. However, real data sets often do not admit perfect phylogenies. In this paper, we consider the problem of reconstructing near-perfect phylogenetic trees (referred to as BNPP). A near-perfect phylogeny relaxes the perfect phylogeny assumption by allowing at most q additional mutations. We show for the first time that the BNPP problem is fixed parameter tractable (FPT) and significantly improve the previous asymptotic bounds.


Steiner Tree Steiner Tree Problem Terminal Vertex Steiner Minimum Tree Correct Guess 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Guy E. Blelloch
    • 1
  • Kedar Dhamdhere
    • 2
  • Eran Halperin
    • 3
  • R. Ravi
    • 4
  • Russell Schwartz
    • 5
  • Srinath Sridhar
    • 1
  1. 1.Computer Science Department, CMU 
  2. 2.Google IncMountain View
  3. 3.ICSIBerkeley
  4. 4.Tepper School of Business, CMU 
  5. 5.Dept Biological Sciences, CMU 

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