Neighbor joining with phylogenetic diversity estimates

2005/07/30 by Dan Levy, Ruriko Yoshida, Levy, Dan +3
Biochemistry, Genetics and Molecular Biology · Mathematics · #Combinatorics (math.CO) #FOS: Biological sciences #FOS: Mathematics #Quantitative Methods (q-bio.QM) #math.CO #q-bio.QM

paper · pdf · doi:10.48550/arxiv.q-bio/0508001

arxiv created 2005/07/30 · arxiv updated 2009/12/01

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/ .

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