sim.coaltree.phylo: Simulate a gene tree from species tree in ape's phylo format

In bomeara/phybase: Basic functions for phylogenetic analysis

Description

The function simulates a gene tree from the species tree using Rannala and Yang's formula. It uses the same population size for all branch lengths. If you want more control, use sim.coaltree.sp().

Usage

sim.coaltree.phylo(phy, pop.size=1, nsamples=1)

Arguments

phy	a tree in phylo format
pop.size	the population size in coalescent time units on each branch
nsamples	the number of allele samples per species

Value

the gene tree in phylo format generated from the species tree

Author(s)

Brian O'Meara [e-mail]

References

Rannala, B. and Z. Yang. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645-1656.

See Also

sim.coaltree.sp

Examples

species.tree <- rcoal(7)
gene.tree <- sim.coaltree.phylo(species.tree, nsamples=2)

bomeara/phybase documentation built on May 12, 2019, 11:35 p.m.