'BEAST2' (< https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'mcbette' allows to do a Bayesian model comparison over some site and clock models, using 'babette' (< https://github.com/ropensci/babette/>).