Why neighbor-joining works

Abstract

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.

Revision 2

Cited by in corpus (2)

• On the optimality of the neighbor-joining algorithm
• Partitioning the Sample Space on Five Taxa for the Neighbor Joining Algorithm