Non-shared edges and nearest neighbor interchanges revisited

Authors:
Wing-Kai Hon;Ming-Yang Kao;Tak-Wah Lam;Wing-Kin Sung;Siu-Ming Yiu
Affiliations:
Department of Computer Science, University of Hong Kong, Hong Kong;Department of Computer Science, Northwestern University, Evanston, IL;Department of Computer Science, University of Hong Kong, Hong Kong;Department of Computer Science, National University of Singapore, Singapore;Department of Computer Science, University of Hong Kong, Hong Kong
Venue:
Information Processing Letters
Year:
2004

Citing 2
Cited 1

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ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation

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Abstract

The number of non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edge distance is also a building block for approximating a more sophisticated measure called the nearest neighbor interchange (NNI) distance. In this paper, we give the first sub-quadratic time algorithm for computing the non-shared edge distance, whose running time is O(n log n). Based on this result, we can speed up the existing approximation algorithm for the NNI distance from O(n2) time to O(n log n) time.