On the optimality of the neighbor-joining algorithm

The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a dissimilarity map. From this point of view, NJ is "optimal" when the algorithm outputs the tree which minimizes the balanced minimum evolution criterion.

We use the fact that the NJ tree topology and the BME tree topology are determined by polyhedral subdivisions of the spaces of dissimilarity maps IR_{+}^{n choose 2} to study the optimality of the neighbor-joining algorithm. In particular, we investigate and compare the polyhedral subdivisions for n less than or equal to 8.

A key requirement is the measurement of volumesof spherical polytopes in high dimension, which we obtain using a combination of Monte Carlo methods and polyhedral algorithms. We show that highly unrelated trees can be co-optimal in BME reconstruction, and that NJ regions are not convex.

We obtain the l2 radius for neighbor-joining for n = 5 and we conjecture that the ability of the neighbor-joining algorithm to recover the BME tree depends on the diameter of the BME tree.

Author: Kord Eickmeyer, Peter Huggins, Lior Pachter and Ruriko Yoshida
Credits/Source: Algorithms for Molecular Biology 2008, 3:5

Published on: 2008-04-30

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