Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Bryant, D. & Moulton, V. Mol Biol Evol, 21(2):255–265, 2004.
doi  abstract   bibtex   
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.
@Article{bryant04neighbor-net,
  author    = {David Bryant and Vincent Moulton},
  title     = {{Neighbor-net}: an agglomerative method for the construction of phylogenetic networks.},
  journal   = {Mol Biol Evol},
  year      = {2004},
  volume    = {21},
  number    = {2},
  pages     = {255--265},
  abstract  = {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.},
  doi       = {10.1093/molbev/msh018},
  keywords  = {phylogenetics},
  optmonth  = feb,
  owner     = {Standard},
  pmid      = {14660700},
  timestamp = {2006.12.01},
}

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