BAli---Phy

Introduction

BAli-Phy is MCMC software developed by Ben Redelings with Marc Suchard for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). [See the paper and the Application Note.]

BAli-Phy can estimate phylogenetic trees from sequence data when the alignment is uncertain. Instead of conditioning on a single alignment estimate, BAli-Phy accounts for alignment uncertainty by integrating over all alignments. BAli-Phy does not rely on a guide tree because the alignment and the tree are co-estimated. Therefore it can construct phylogeny estimates of widely divergent sequences without bias toward a guide tree.

BAli-Phy also produces high-quality alignment estimates for highly divergent sequences, because it uses advanced substitution models and a realistic model of indels occurring on an (uncertain) tree. BAli-Phy can produce alignment uncertainty (AU) plots that are colored to indicate uncertain areas of the alignment.

BAli-Phy works on the nucleotide, amino acid, and codon levels and can utilize complex substitution models, such as GTR+gamma[n], WAG+log-normal[n]+INV, M0, M7, and more. It can be used to estimate substitution rates, frequencies, and indel rates when the tree and alignment are uncertain.

References

1. Redelings BD and Suchard MA Joint Bayesian Estimation of Alignment and Phylogeny, Systematic Biology, 54(3):401-418, 2005    [PDF]
2. Suchard MA and Redelings BD BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics, 22:2047-2048, 2006.     [PDF]
3. Redelings BD and Suchard MA. Incorporating indel information into phylogeny estimation for rapidly emerging pathogens. BMC Evolutionary Biology, 7:40, 2007.    [PDF]

[See more papers on statistical alignment on my "links" page.]