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

Molecular biology and evolution, 2004-02, Vol.21 (2), p.255-265 [Peer Reviewed Journal]

ISSN: 0737-4038 ;EISSN: 1537-1719 ;DOI: 10.1093/molbev/msh018 ;PMID: 14660700

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Title:
Neighbor-net: an agglomerative method for the construction of phylogenetic networks
Author: Bryant, David ; Moulton, Vincent
Subjects: algorithm ; Algorithms ; Animals ; Bacterial Proteins - genetics ; chaperonins ; Chaperonins - genetics ; Cluster Analysis ; Computer Simulation ; DNA ; DNA, Mitochondrial - genetics ; evolution ; Evolution, Molecular ; gene conversion ; Genes, Archaeal - genetics ; Humans ; median networks ; Models, Genetic ; Models, Theoretical ; Phylogeny ; populations ; reconstruction ; Salmonella - genetics ; sequence data ; Software ; trees
Is Part Of: Molecular biology and evolution, 2004-02, Vol.21 (2), p.255-265
Description: 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.
Publisher: United States
Language: English;Swedish
Identifier: ISSN: 0737-4038
EISSN: 1537-1719
DOI: 10.1093/molbev/msh018
PMID: 14660700
Source: Geneva Foundation Free Medical Journals at publisher websites
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Neighbor-net: an agglomerative method for the construction of phylogenetic networks

ISSN: 0737-4038 ;EISSN: 1537-1719 ;DOI: 10.1093/molbev/msh018 ;PMID: 14660700

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