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MBE Advance Access originally published online on November 9, 2005
Molecular Biology and Evolution 2006 23(3):491-498; doi:10.1093/molbev/msj059
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity Estimates

Dan Levy*, Ruriko Yoshida{dagger} and Lior Pachter*

* Department of Mathematics, University of California, Berkeley and {dagger} Department of Mathematics, Duke University

E-mail: lpachter{at}math.berkeley.edu.

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/.

Key Words: neighbor-joining • phylogenetic diversity • subtree weights


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