Constructing the R* consensus tree of two trees in subcubic time

Authors:
Jesper Jansson;Wing-Kin Sung
Affiliations:
Ochanomizu University, Tokyo, Japan;School of Computing, National University of Singapore, Singapore and Genome Institute of Singapore, Genome, Singapore
Venue:
ESA'10 Proceedings of the 18th annual European conference on Algorithms: Part I
Year:
2010

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Abstract

The previously fastest algorithms for computing the R* consensus tree of two given (rooted) phylogenetic trees T1 and T2 with a leaf label set of cardinality n run in Θ(n3) time [3, 8]. In this manuscript, we describe a new O(n2 log n)-time algorithm to solve the problem. This is a significant improvement because the R* consensus tree is defined in terms of a set Rmaj which may contain Ω(n3) elements, so any direct approach which explicitly constructs Rmaj requires Ω(n3) time.