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| TreePar-package | Estimating speciation and extinction rates based on phylogenies |
| bd.densdep.optim | bd.densdep.optim: Estimating speciation and extinction rates in phylogenies under a density-dependent speciation model |
| bd.groups.optim | bd.groups.optim: Estimating speciation and extinction rates in higher-taxonomic-level phylogenies |
| bd.shifts.optim | bd.shifts.optim: Estimating speciation and extinction rate changes and mass extinction events in phylogenies |
| getx | getx: Getting the vector of speciation times x from a phylogenetic tree |
| treemrcashifts | treemrcashifts: calculates the likelihood of a tree |
| TreePar | Estimating speciation and extinction rates based on phylogenies |