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Tree Core Analysis with X-ray Computed Tomography
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Computing the distribution of a tree metric.

David Bryant1, Mike Steel

  • 1Department of Mathematics, University of Auckland, Private Bag 92010, Auckland, New Zealand. d.bryant@auckland.ac.nz

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|August 1, 2009
PubMed
Summary
This summary is machine-generated.

We present a new polynomial-time algorithm for computing the distribution of Robinson-Foulds distances between trees. This method approximates the distribution using a Poisson distribution based on tree cherries, aiding supertree construction.

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Area of Science:

  • Computational Biology
  • Phylogenetics
  • Algorithm Development

Background:

  • The Robinson-Foulds (RF) distance is a standard metric for comparing phylogenetic trees.
  • Existing methods for computing the RF distance distribution are computationally intensive.
  • A polynomial-time algorithm for RF distance distribution has been lacking.

Purpose of the Study:

  • To develop an efficient, polynomial-time algorithm for computing the Robinson-Foulds distance distribution.
  • To provide an approximation for the RF distance distribution.
  • To support advancements in supertree construction methodologies.

Main Methods:

  • Derivation of a novel polynomial-time algorithm for RF distance distribution.
  • Approximation of the RF distance distribution using a Poisson distribution.
  • Analysis of the proportion of leaves in "cherries" to determine Poisson parameters.

Main Results:

  • A polynomial-time algorithm for computing the Robinson-Foulds distance distribution is successfully derived.
  • The Poisson distribution provides an effective approximation for the RF distance distribution.
  • The results facilitate the calculation of normalization constants for maximum likelihood supertree methods.

Conclusions:

  • The developed algorithm significantly improves the computational efficiency of analyzing RF distance distributions.
  • The Poisson approximation offers a practical tool for understanding tree dissimilarities.
  • This work contributes to more robust and efficient supertree construction techniques.