Rapid Neighbour-Joining

Authors:
Martin Simonsen;Thomas Mailund;Christian N. Pedersen
Affiliations:
Bioinformatics Research Center (BIRC), University of Aarhus, Århus C, Denmark DK-8000;Bioinformatics Research Center (BIRC), University of Aarhus, Århus C, Denmark DK-8000;Bioinformatics Research Center (BIRC), University of Aarhus, Århus C, Denmark DK-8000
Venue:
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Year:
2008

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Abstract

The neighbour-joining method reconstructs phylogenies by iteratively joining pairs of nodes until a single node remains. The criterion for which pair of nodes to merge is based on both the distance between the pair and the average distance to the rest of the nodes. In this paper, we present a new search strategy for the optimisation criteria used for selecting the next pair to merge and we show empirically that the new search strategy is superior to other state-of-the-art neighbour-joining implementations.