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Multiple sequence alignment is an important task in bioinformatics, and alignments of large datasets containing hundreds or thousands of sequences are increasingly of interest. While many alignment methods exist, the most accurate alignments are likely to be based on stochastic models where sequences evolve down a tree with substitutions, insertions, and deletions. While some methods have been developed to estimate alignments under these stochastic models, only the Bayesian method BAli-Phy hasdoi:10.1186/s12864-016-3101-8 pmid:28185555 fatcat:n6f3wttyo5bsxnevdkyukvapvq