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Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04)
An Improved Algorithm for the Maximum Agreement Subtree Problem
Taichung, Taiwan, ROC
May 19-May 21
ISBN: 0-7695-2173-8
Chuan-Min Lee, National Chung Cheng University, Taiwan
Ling-Ju Hung, National Chung Cheng University, Taiwan
Maw-Shang Chang, National Chung Cheng University, Taiwan
Chuan-Yi Tang, National Tsing Hua University, Taiwan
In this paper, we solve the maximum agreement subtree problem for a set T of k rooted, leaf-labelled evolutionary trees on n leaves where T contains a binary tree. We show that the O(kn{3})-time dynamic programming algorithm proposed by Farach et al. [On the agreement of many trees] and Bryant [Hunting for trees, building trees and comparing trees: theory and methods in phylogenetic analysis] can be implemented in {\text{O(n}}^{\text{2}} {\text{log}}^{{\text{k - 1}}} {\text{n)}} and {\text{O(k\cdotn}}^{{\text{3 - }}\frac{1}{{k - 1}}}) using the k-dimensional binary search tree and the k-dimensional range search tree, respectively.
Index Terms:
Evolutionary tree, maximum agreement sub-tree, leaf-labelled tree, k-dimensional range search tree, k-dimensional binary search tree
Citation:
Chuan-Min Lee, Ling-Ju Hung, Maw-Shang Chang, Chuan-Yi Tang, "An Improved Algorithm for the Maximum Agreement Subtree Problem," bibe, pp.533, Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04), 2004
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