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Approximating Subtree Distances Between Phylogenies Maria Luisa Bonet

Summary: Approximating Subtree Distances Between Phylogenies
Maria Luisa Bonet
Katherine St. John
Ruchi Mahindru§
Nina Amenta¶
August 14, 2006
We give a 5-approximation algorithm to the rooted Subtree-Prune-and-Regraft
(rSPR) distance between two phylogenies, which was recently shown to be NP-complete
by Bordewich and Semple [Bordewich and Semple, 2005]. This paper presents the first
approximation result for this important tree distance. The algorithm follows a standard
format for tree distances such as Rodrigues et al. [Rodrigues et al., 2001] and Hein et
al. [Hein et al., 1996]. The novel ideas are in the analysis. In the analysis, the cost of
the algorithm uses a "cascading" scheme that accounts for possible wrong moves. This
accounting is missing from previous analysis of tree distance approximation algorithms.

Lenguajes y Sistemas Informaticos (LSI), Universidad Politecnica de Catalunya (UPC), 08034 Barcelona,
Spain bonet@lsi.upc.edu.

Department of Math & Computer Science, Lehman College­ City University of New York (CUNY),


Source: Amenta, Nina - Department of Computer Science, University of California, Davis


Collections: Biology and Medicine; Computer Technologies and Information Sciences