RevBayes - Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language. RevBayes provides a flexible framework for performing Bayesian statistical analysis of phylogeny and related topics, such as divergence time estimation, diversification rate estimation, continuous and discrete trait evolution and historical biogeography.

TESS - An R package for Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction Events. TESS both provides the likelihood function as well as reversible-jump method to estimate global diversification rates and rate shifts.