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MBE Advance Access published online on November 9, 2005
Molecular Biology and Evolution, 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
Accepted October 19, 2005

Research Article

Beyond Pairwise Distances: Neighbor Joining with Phylogenetic Diversity Estimates

Dan Levy 1, Ruriko Yoshida 2, and Lior Pachter 1*

1 Department of Mathematics, UC Berkeley
2 Department of Mathematics, Duke University

* To whom correspondence should be addressed.
Lior Pachter, E-mail: lpachter{at}math.berkeley.edu


  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/

Keywords: neighbor joining; phylogenetic diversity; subtree weights.
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