MBE Advance Access originally published online on December 5, 2003
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Mol. Biol. Evol. 21(2):255-265. 2004
DOI: 10.1093/molbev/msh018
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks
* McGill Centre for Bioinformatics, Montreal, Quebec, Canada
The Linnaeus Center for Bioinformatics, Uppsala University, Uppsala, Sweden
E-mail: bryant{at}mcb.mcgill.ca.
We present Neighbor-Net, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei. Neighbor-Net provides a snapshot of the data that can guide more detailed analysis. Unlike split decomposition, Neighbor-Net scales well and can quickly produce detailed and informative networks for several hundred taxa. We illustrate the method by reanalyzing three published data sets: a collection of 110 highly recombinant Salmonella multi-locus sequence typing sequences, the 135 "African Eve" human mitochondrial sequences published by Vigilant et al., and a collection of 12 Archeal chaperonin sequences demonstrating strong evidence for gene conversion. Neighbor-Net is available as part of the SplitsTree4 software package.
Key Words: networks • Neighbor-Joining • recombination • SplitsTree
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