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Bioinformatics Advance Access originally published online on August 6, 2009
Bioinformatics 2009 25(19):2530-2536; doi:10.1093/bioinformatics/btp473
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Improving phylogenetic analyses by incorporating additional information from genetic sequence databases

Li-Jung Liang 1,*, Robert E. Weiss 2, Benjamin Redelings 3 and Marc A. Suchard 2,4

1Department of Medicine Statistics Core, 2Department of Biostatistics, UCLA School of Public Health, Los Angeles, CA 90095, 3Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606 and 4Departments of Biomathematics and Human Genetics, UCLA School of Medicine, Los Angeles, CA 90095, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Statistical analyses of phylogenetic data culminate in uncertain estimates of underlying model parameters. Lack of additional data hinders the ability to reduce this uncertainty, as the original phylogenetic dataset is often complete, containing the entire gene or genome information available for the given set of taxa. Informative priors in a Bayesian analysis can reduce posterior uncertainty; however, publicly available phylogenetic software specifies vague priors for model parameters by default. We build objective and informative priors using hierarchical random effect models that combine additional datasets whose parameters are not of direct interest but are similar to the analysis of interest.

Results: We propose principled statistical methods that permit more precise parameter estimates in phylogenetic analyses by creating informative priors for parameters of interest. Using additional sequence datasets from our lab or public databases, we construct a fully Bayesian semiparametric hierarchical model to combine datasets. A dynamic iteratively reweighted Markov chain Monte Carlo algorithm conveniently recycles posterior samples from the individual analyses. We demonstrate the value of our approach by examining the insertion–deletion (indel) process in the enolase gene across the Tree of Life using the phylogenetic software BALI-PHY; we incorporate prior information about indels from 82 curated alignments downloaded from the BAliBASE database.

Contact: liangl{at}ucla.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on February 7, 2009; revised on July 28, 2009; accepted on July 28, 2009

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