BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny.
CONCLUSIONS
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.


BACKGROUND
Software is available for download at http://www.biomath.ucla.edu/msuchard/bali-phy.
Suchard
Marc A
MA
Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA. msuchard@ucla.edu
Redelings
Benjamin D
BD