Wikipedia
BAli-Phy is a free software program for simultaneously estimating a multiple sequence alignment and its phylogenetic tree. BAli-Phy achieves high accuracy in alignment estimation by using information from the co-estimated phylogeny. BAli-Phy takes alignment uncertainty into account while estimating the phylogeny by averaging over possible alignments. Unlike most phylogeny inference software, input sequences need not be aligned beforehand. This differs from traditional approaches to alignment and phylogeny estimation, which first estimate the alignment without a high-quality tree estimate, and then estimate the tree given the alignment.
BAli-Phy produces a Bayesian posterior distribution on both the alignments and the tree. The software shows uncertainty in both the alignment and the tree. BAli-Phy uses Markov chain Monte Carlo methods for estimation. It can take several days to run.