, Volume 54, Issue 1, pp 1–24 | Cite as

Why Neighbor-Joining Works

  • Radu Mihaescu
  • Dan Levy
  • Lior PachterEmail author


We show that the neighbor-joining algorithm is a robust quartet method for constructing trees from distances. This leads to a new performance guarantee that contains Atteson’s optimal radius bound as a special case and explains many cases where neighbor-joining is successful even when Atteson’s criterion is not satisfied. We also provide a proof for Atteson’s conjecture on the optimal edge radius of the neighbor-joining algorithm. The strong performance guarantees we provide also hold for the quadratic time fast neighbor-joining algorithm, thus providing a theoretical basis for inferring very large phylogenies with neighbor-joining.


Distance methods Edge radius Neighbor-joining Quartets 


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Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  1. 1.Department of Mathematics and Computer ScienceUC BerkeleyBerkeleyUSA

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