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Bioinformatics Advance Access originally published online on May 5, 2006
Bioinformatics 2006 22(16):2047-2048; 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

BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny

Marc A. Suchard 1,2,* and Benjamin D. Redelings 3

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

*To whom correspondence should be addressed.


  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.

Contact: msuchard{at}ucla.edu

Associate Editor: Keith A Crandall

Received on February 17, 2006; revised on April 28, 2006; accepted on May 1, 2006

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