Recrafting the Neighbor-Joining Method

Thomas Mailund, Gerth Stølting Brodal, Rolf Fagerberg, Christian Nørgaard Storm Pedersen, and Derek Phillips

In BMC Bioinformatics, volume 7(29), 2006.


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.

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

Copyright notice

BioMed Central Open Access

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bmc06.pdf (385 Kb)



BIBTEX entry

  author = "Thomas Mailund and Gerth St{\o}lting Brodal and Rolf Fagerberg and Christian N{\o}rgaard Storm Pedersen and Derek Phillips",
  doi = "10.1186/1471-2105-7-29",
  issn = "1471-2105",
  journal = "BMC Bioinformatics",
  number = "29",
  title = "Recrafting the Neighbor-Joining Method",
  volume = "7",
  year = "2006"

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