Methodology article

Recrafting the neighbor-joining method

Thomas Mailund^1*, Gerth S Brodal², Rolf Fagerberg³, Christian NS Pedersen^4,1 and Derek Phillips⁵

• * Corresponding author: Thomas Mailund mailund@birc.dk

Author Affiliations

¹ Bioinformatics Research Center (BiRC), University of Aarhus, Denmark

² Basic Research in Computer Sciences (BRICS), Department of Computer Science, University of Aarhus, Denmark

³ Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark

⁴ Department of Computer Science, University of Aarhus, Denmark

⁵ School of Computer Science, University of Waterloo, Canada

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BMC Bioinformatics 2006, 7:29 doi:10.1186/1471-2105-7-29

Published: 19 January 2006

Abstract

Background

The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical Θ(n³) algorithm upon which all existing implementations are based.

Results

In this paper we present techniques for speeding up the canonical neighbor-joining method. Our algorithms construct the same phylogenetic trees as the canonical neighbor-joining method. The best-case running time of our algorithms are O(n²) but the worst-case remains O(n³). We empirically evaluate the performance of our algoritms on distance matrices obtained from the Pfam collection of alignments. The experiments indicate that the running time of our algorithms evolve as Θ(n²) on the examined instance collection. We also compare the running time with that of the QuickTree tool, a widely used efficient implementation of the canonical neighbor-joining method.

Conclusion

The experiments show that our algorithms also yield a significant speed-up, already for medium sized instances.