TreeSim (1.4)

Simulating trees under the birth-death model.

The package simulates phylogenetic trees under a constant-rate birth-death process, conditioned on having a fixed number of final tips, or a fixed age, or a fixed age and number of tips. When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process. TreeSim further samples appropriately trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of leaves is first reached. This latter method is appropriate for m-tip trees generated under a big class of models (details in the bd.gsa.taxa man page). For incomplete phylogeny, the missing speciation events can be added through simulations.

Maintainer: Tanja Stadler
Author(s): Tanja Stadler

License: GPL-2

Uses: ape, geiger
Reverse depends: TreePar, TreeSimGM
Reverse suggests: nLTT, PhylogeneticEM, POUMM

Released over 6 years ago.