BAli-Phy is MCMC software for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters).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.
Marc A. Suchard, M.D., Ph.D.
- Linux/MacOsX / Windows
:: MORE INFORMATION
Suchard MA and Redelings BD
BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny,
Bioinformatics, 22:2047-2048, 2006.