A fast algorithmic technique for comparing large phylogenetic trees

Authors:
Gabriel Valiente
Affiliations:
Department of Software, Technical University of Catalonia, Barcelona
Venue:
SPIRE'05 Proceedings of the 12th international conference on String Processing and Information Retrieval
Year:
2005

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Abstract

The comparison of rooted phylogenetic trees is essential to querying phylogenetic databases such as TreeBASE. Current comparison methods are based on either tree edit distances or common subtrees. However, a limitation of such methods is their inherent complexity. In this paper, a new distance over fully resolved phylogenetic trees, the transposition distance, is described which is based on a well-known bijection between perfect matchings and phylogenetic trees, and simple linear-time algorithms are presented for computing the new distance.