BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny

  • Authors:

  • Marc A. Suchard;Benjamin D. Redelings

  • Affiliations:

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

  • Venue:
  • Bioinformatics
  • Year:
  • 2006

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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@ucla.edu