title: Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates.
abstract: The "neighbor-joining algorithm" is a recursive procedure for reconstructing trees that is based on a transformation of pairwise distances between leaves. We present a generalization of the neighbor-joining transformation, which uses estimates of phylogenetic diversity rather than pairwise distances in the tree. This leads to an improved neighbor-joining algorithm whose total running time is still polynomial in the number of taxa. On simulated data, the method outperforms other distance-based methods. We have implemented neighbor-joining for subtree weights in a program called MJOIN which is freely available under the Gnu Public License at http://bio.math.berkeley.edu/mjoin/.
authors.affiliation: Department of Mathematics, University of California, Berkeley, USA.
authors.forename: Dan
authors.initials: D
authors.lastname: Levy
authors.forename: Ruriko
authors.initials: R
authors.lastname: Yoshida
authors.forename: Lior
authors.initials: L
authors.lastname: Pachter
mesh_terms: D000465:Algorithms; D014644:Genetic Variation; D008433:Mathematics; D008957:Models, Genetic; D010802:Phylogeny