Oh interesting.
sequence alignment isn't the interesting problem here though, for the most part that's probably going to be inferring proto-forms and rules from correspondences. Which I'm able to get fairly handily. Without training on my Chechen-Ingush-Batsbi data, the system was able to pick out correspondence which I know to be correct. What will be interesting is seeing if it can use a (probably statistical) model to infer reasonable ancestor forms, and identify conditioning environments.