Why Neighbor-Joining Works

Authors:
Radu Mihaescu;Dan Levy;Lior Pachter
Affiliations:
UC Berkeley, Department of Mathematics and Computer Science, 970 Evans Hall, 94720, Berkeley, CA, USA;UC Berkeley, Department of Mathematics and Computer Science, 970 Evans Hall, 94720, Berkeley, CA, USA;UC Berkeley, Department of Mathematics and Computer Science, 970 Evans Hall, 94720, Berkeley, CA, USA
Venue:
Algorithmica
Year:
2009

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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.