TreeSimGM: Simulating Phylogenetic Trees under a General Model

The package is a flexible simulation tool for phylogenetic trees under a general model. It is possible to assume any probability distribution for the waiting time until speciation and extinction independently. Thus, TreeSimGM allows to simulate stochastic phylogenetic trees using any probability distribution and parameters for speciation and extinction. The speciation modes have all binary splits and are: (i) symmetric, where for every speciation event new waiting times until speciation and extinction are drawn for both daughter lineages; and (ii) asymmetric, where a speciation event results in one species with new waiting times, and another that carries the extinction time and age of its ancestor. Those two modes were inspired by allopatric and peripatric speciation respectively.Both models (symmetric and asymmetric) were created and implemented so that different processes (distributions) for speciation and extinction could be independently and explicitly specified. It is also possible to have an implicit extinction process by setting the extinction rate to zero.

Version: 1.1
Depends: TreeSim
Published: 2013-02-21
Author: Oskar Hagen, Tanja Stadler
Maintainer: Oskar Hagen <oskar.is.hagen at gmail.com>
License: GPL-2
NeedsCompilation: no
CRAN checks: TreeSimGM results

Downloads:

Reference manual: TreeSimGM.pdf
Package source: TreeSimGM_1.1.tar.gz
OS X binary: TreeSimGM_1.1.tgz
Windows binary: TreeSimGM_1.1.zip
Old sources: TreeSimGM archive