spacodiR: structuring of phylogenetic diversity in ecological communities. - Jonathan M. Eastman; C. E. Timothy Paine; Olivier J. Hardy (Bioinform., 2011)

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)