sim.coaltree.sp.mu {phybase} | R Documentation |
Simulate a gene tree from the non-clock species tree model
Description
The function generates a random gene tree from the species tree under the non-clock species tree model.
Usage
sim.coaltree.sp.mu(sptree, spname, seq, numgenetree,method="dirichlet",alpha=5.0)
Arguments
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 |
Value
gt |
the simulated gene tree |
st |
the node matrix of the species tree |
seqname |
the names of sequences |
Author(s)
Liang Liu
Examples
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)
[Package
phybase version 1.1
Index]