Bayesian Inference of Alignment and Phylogeny

 BAli-Phy estimates multiple sequence alignments and evolutionary trees
 from unaligned DNA, amino acid, or codon sequences. BAli-Phy uses MCMC
 to estimate evolutionary trees, positive selection, and branch lengths
 while averaging over alternative alignments. BAli-Phy can display
 alignment ambiguity graphically in an alignment uncertainty (AU) plot.
 .
 BAli-Phy can also estimate phylogenies from a fixed alignment (like MrBayes
 and BEAST) using substitution models like GTR+gamma. BAli-Phy automatically
 estimates relative rates for each gene.