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Neighbor joining with phylogenetic diversity estimates

Levy, Dan and Yoshida, Ruriko and Pachter, Lior (2005) Neighbor joining with phylogenetic diversity estimates. . (Submitted) http://resolver.caltech.edu/CaltechAUTHORS:20170307-090555699

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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:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://arxiv.org/abs/q-bio/0508001arXivDiscussion Paper
Additional Information:This work was partially funded by an 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
Subject Keywords:neighbor joining, phylogenetic diversity, subtree weights
Record Number:CaltechAUTHORS:20170307-090555699
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20170307-090555699
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74832
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:07 Mar 2017 17:46
Last Modified:07 Mar 2017 17:46

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