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Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005: Improved Consensus Network Techniques for Genome-Scale Phylogeny

Citation

Holland, BR and Jermiin, LS and Moulton, V, Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005: Improved Consensus Network Techniques for Genome-Scale Phylogeny, Molecular Biology and Evolution, 23, (5) pp. 848-855. ISSN 0737-4038 (2006) [Refereed Article]


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The definitive publisher-authenticated version is available online at: www.oxfordjournals.org

DOI: doi:10.1093/molbev/msj061

Abstract

Although recent studies indicate that estimating phylogenies from alignments of concatenated genes greatly reduces the stochastic error, the potential for systematic error still remains, heightening the need for reliable methods to analyze multigene data sets. Consensus methods provide an alternative, more inclusive, approach for analyzing collections of trees arising from multiple genes. We extend a previously described consensus network method for genome-scale phylogeny (Holland, B. R., K. T. Huber, V. Moulton, and P. J. Lockhart. 2004. Using consensus networks to visualize contradictory evidence for species phylogeny. Mol. Biol. Evol. 21:1459–1461.) to incorporate additional information. This additional information could come from bootstrap analysis, Bayesian analysis, or various methods to find confidence sets of trees. The new methods can be extended to include edge weights representing genetic distance. We use three data sets to illustrate the approach: 61 genes from 14 angiosperm taxa and one gymnosperm, 106 genes from eight yeast taxa, and 46 members of a gene family from 15 vertebrate taxa.

Item Details

Item Type:Refereed Article
Keywords:consensus networks • genome-scale phylogeny • gene trees
Research Division:Mathematical Sciences
Research Group:Applied Mathematics
Research Field:Biological Mathematics
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Biological Sciences
Author:Holland, BR (Associate Professor Barbara Holland)
ID Code:63273
Year Published:2006
Web of Science® Times Cited:26
Deposited By:Mathematics
Deposited On:2010-04-27
Last Modified:2010-04-30
Downloads:0

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