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Approximating subtree distances between Phylogenies
Bonet Carbonell, Maria Luisa; St. John, Katherine; Mahindru, Ruchi; Amenta, Nina
Centre de Recerca Matemàtica
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 [5]. 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. [24] and Hein et al. [13]. 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. Further, we show how all algorithms of this type can be implemented in linear time and give experimental results.
2006-03
Filogènia
Mètodes estadístics
Arbres (Teoria dels grafs)
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Centre de Recerca Matemàtica
Prepublicacions del Centre de Recerca Matemàtica;669
         

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