This course will provide foundational knowledge in complex models for phylogenetic inference. Our focus will be primarily on Bayesian inference using MCMC. Each component of the course will be accompanied by a hands-on tutorial using cutting-edge phylogenetic inference software. Specifically, we will use this course to introduce and build a user base for RevBayes. RevBayes is a rich statistical package for inference of evolutionary parameters (open source: http://sourceforge.net/projects/revbayes/). This program coupled with detailed lectures on phylogenetic theory and applications will provide a rich learning environment for Ph.D. students and postdocs in evolutionary biology.