geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. - Matthew W. Pennell; Jonathan M. Eastman; Graham J. Slater; Joseph W. Brown; Josef C. Uyeda; Richard G. FitzJohn; Michael E. Alfaro; Luke J. Harmon (Bioinform., 2014)

outbreaker2: a modular platform for outbreak reconstruction. - Finlay Campbell; Xavier Didelot; Richard G. FitzJohn; Neil M. Ferguson; Anne Cori; Thibaut Jombart (BMC Bioinform., 2018)