sim.coaltree.sp.mu: Simulate a gene tree from the non-clock species tree model
In bomeara/phybase: Basic functions for phylogenetic analysis

Description Usage Arguments Value Author(s) Examples

The function generates a random gene tree from the species tree under the non-clock species tree model.

1	sim.coaltree.sp.mu(sptree, spname, seq, numgenetree,method="dirichlet",alpha=5.0)

`sptree`	species tree
`spname`	species names
`seq`	the species-sequences struction, i.e., which sequence belongs to which species
`numgenetree`	the number of gene trees to be generated
`alpha`	the parameter in the gamma distribution. see also `mutation_exp`
`method`	either gamma or dirichlet

`gt`	the simulated gene tree
`st`	the node matrix of the species tree
`seqname`	the names of sequences

Liang Liu

sptree<-"(((A:0.5,B:0.5):1#0.1,C:1.5):1#0.1,D:2.5)#0.1;"
spname<-c("A","B","C","D")
seq<-c(1,1,1,1) #each species has only one sequence.
sim.coaltree.sp.mu(sptree, spname, seq, numgenetree=1,method="dirichlet",alpha=5.0)