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A Collapsing Method for Efficient Recovery of Optimal Edges

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mhu2002.pdf (544.28 KB)

Date

2002

Authors

Hu, Mike

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University of Waterloo

Abstract

In this thesis we present a novel algorithm, <I>HyperCleaning*</I>, for effectively inferring phylogenetic trees. The method is based on the quartet method paradigm and is guaranteed to recover the best supported edges of the underlying phylogeny based on the witness quartet set. This is performed efficiently using a collapsing mechanism that employs memory/time tradeoff to ensure no loss of information. This enables <I>HyperCleaning*</I> to solve the relaxed version of the Maximum-Quartet-Consistency problem feasibly, thus providing a valuable tool for inferring phylogenies using quartet based analysis.

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Keywords

Computer Science, Phylogenetics, Evolution, Quartet Method, Combinatorial Algorithm, Maximum Likelihood

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URI

http://hdl.handle.net/10012/1144

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Computer Science