MrBayes (v3.2.2) adds the gamma-Dirichlet and inverseGamma-Dirichlet priors for branch lengths (Rannala et al. 2012; Zhang et al. 2012). It also includes the two-exponential prior on internal and external branch lengths (Yang & Rannala 2005; Yang 2007). The gamma-Dirichlet prior is default since v3.2.3.
MrBayes (v3.2.6) adds the fossilized birth-death priors (Stadler 2010, Heath et al. 2014, Gavryushkina et al. 2014, Zhang et al. 2016) for Bayesian total-evidence dating analyses. A tutorial is available on arXiv.
Diversified sampling in FBD model is available in BDSky.
SpeciesNetwork: a package to infer species networks and gene trees from multilocus sequence alignments (Zhang et al. 2018). A tutorial is included in the package.