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      Neighbor-net: an agglomerative method for the construction of phylogenetic networks.

      Molecular Biology and Evolution
      Algorithms, Animals, Bacterial Proteins, genetics, Chaperonins, Cluster Analysis, Computer Simulation, DNA, Mitochondrial, Evolution, Molecular, Genes, Archaeal, Humans, Models, Genetic, Models, Theoretical, Phylogeny, Salmonella, Software

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          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.

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