The Performance of Neighbor-Joining Algorithms of Phylogeny Recronstruction

Biologists have hotly debated the merits of various algorithms for phylogenetic reconstruction for many years. In this paper, we analyze the performance of the popular neighbor-joining algorithm. In particular, we determine the L∞ radius under which the method will determine the correct tree topology. In fact, this radius is optimal for all distance-based methods, the class of methods which includes all known tractable methods for which there is any sort of performance guarantee. We also gauge the performance of the algorithm when it is not possible to determine the correct tree topology.