Pattern identification in biogeography

Authors:
Ganeshkumar Ganapathy;Barbara Goodson;Robert Jansen;Vijaya Ramachandran;Tandy Warnow
Affiliations:
Department of Computer Sciences, The University of Texas at Austin, TX;Section of Integrative Biology, School of Biological Sciences, The University of Texas at Austin, TX;Section of Integrative Biology, School of Biological Sciences, The University of Texas at Austin, TX;Department of Computer Sciences, The University of Texas at Austin, TX;Department of Computer Sciences, The University of Texas at Austin, TX
Venue:
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Year:
2005

Citing 4
Cited 0

Kaikoura tree theorems: computing the maximum agreement subtree

Information Processing Letters
On the agreement of many trees

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Maximum Agreement Subtree in a Set of Evolutionary Trees: Metrics and Efficient Algorithms

SIAM Journal on Computing
The Design and Analysis of Computer Algorithms

The Design and Analysis of Computer Algorithms

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Abstract

We develop and study two distance metrics for area cladograms (leaf-labeled trees where many leaves can share the same label): the edge contract-and-refine metric and the MAAC distance metric. We demonstrate that in contrast to phylogenies, the contract-and-refine distance between two area cladograms is not identical to the character encoding distance, and the latter is not a metric. We present a polynomial time algorithm to compute the MAAC distance, based on a polynomial-time algorithm for computing the largest common pruned subtree of two area cladograms. We also describe a linear time algorithm to decide if two area cladograms are identical.