Neighbor-net: an agglomerative method for the construction of phylogenetic networks.
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.
Bryant
David
D
McGill Centre for Bioinformatics, Montreal, Quebec, Canada. bryant@mcb.mcgill.ca
Moulton
Vincent
V
D000465:Algorithms; D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics; D018833:Chaperonins / Q000235:genetics; D016000:Cluster Analysis; D003198:Computer Simulation; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D019766:Genes, Archaeal / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D008962:Models, Theoretical; D010802:Phylogeny; D012475:Salmonella / Q000235:genetics; D012984:Software
D001426:Bacterial Proteins; D004272:DNA, Mitochondrial; D018833:Chaperonins