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

Mol Biol Evol. 2004 Feb;21(2):255-65. doi: 10.1093/molbev/msh018. Epub 2003 Dec 5.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

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


  • Bacterial Proteins
  • DNA, Mitochondrial
  • Chaperonins