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Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity Estimates

Levy, Dan and Yoshida, Ruriko and Pachter, Lior (2006) Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity Estimates. Molecular Biology and Evolution, 23 (3). pp. 491-498. ISSN 0737-4038. http://resolver.caltech.edu/CaltechAUTHORS:20170307-164418033

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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/.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/molbev/msj059DOIArticle
https://academic.oup.com/mbe/article/23/3/491/1110285/Beyond-Pairwise-Distances-Neighbor-Joining-withPublisherArticle
Additional Information:© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. Accepted: 19 October 2005. Published: 09 November 2005. We thank the anonymous referees for comments that improved the manuscript. This work was partially funded by the National Institutes of Health (NIH) grant (R01HG2362). L.P. was also supported by a Sloan foundation fellowship. D.L. was also supported by NIH grant (GM68423).
Funders:
Funding AgencyGrant Number
NIHR01HG2362
Alfred P. Sloan FoundationUNSPECIFIED
NIHGM68423
Record Number:CaltechAUTHORS:20170307-164418033
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20170307-164418033
Official Citation:Dan Levy, Ruriko Yoshida, Lior Pachter; Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity Estimates. Mol Biol Evol 2006; 23 (3): 491-498. doi: 10.1093/molbev/msj059
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74876
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:08 Mar 2017 15:40
Last Modified:08 Mar 2017 15:40

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