Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.10.334003v1?rss=1 Authors: Redelings, B. D. Abstract: BAli-Phy is a Markov chain Monte Carlo (MCMC) program that jointly estimates phylogeny, alignment, and other parameters from unaligned sequence data. Version 3 is substantially faster for large trees, and implements covarion models, RNA stem models, and other new models. It implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously. Availability: Software is available for download at http://www.bali-phy.org. C++ source code is freely available on Github under the GPL2 License. Copy rights belong to original authors. Visit the link for more info