BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny

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.