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Bioinformatics Advance Access published online on May 5, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl175
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received February 17, 2006
Revised April 28, 2006
Accepted May 1, 2006

Applications note

BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny

Marc A. Suchard 1 * and Benjamin D. Redelings 2

1 Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095; Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095
2 Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606

* To whom correspondence should be addressed.
Marc A. Suchard, E-mail: msuchard{at}ucla.edu


  Abstract

Summary: BAli-Phy is a Bayesian posterior sampler that employs Markov chain Monte Carlo to explore the joint space of alignment and phylogeny given molecular sequence data. Simultaneous estimation eliminates bias toward inaccurate alignment guide-trees, employs more sophisticated substitution models during alignment and automatically utilizes information in shared insertion/deletions to help infer phylogenies.

Availability: Software is available for download at http://www.biomath.ucla.edu/msuchard/bali-phy.

Associate Editor: Keith A Crandall
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