sim.coaltree.sp: simulate a gene tree from the species tree
In bomeara/phybase: Basic functions for phylogenetic analysis

Description Usage Arguments Value Author(s) References See Also Examples

The function simulates a gene tree from the species tree using Rannala and Yang's formula

1	sim.coaltree.sp(rootnode, nodematrix, nspecies, seq, name)

`rootnode`	the root node of the species tree
`nodematrix`	the tree node matrix of the species tree
`nspecies`	the number of species
`seq`	a vector of number of sequences in each species
`name`	species names used in the simulated gene tree. the order of the names must be consistent with that in "nodematrix"

`gt`	the gene tree generated from the species tree
`height`	the tree height of the gene tree

Liang Liu lliu@uga.edu

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.

sim.coaltree

tree<-"(((H:0.00402#0.01,C:0.00402#0.01):0.00304#0.01,
G:0.00707#0.01):0.00929#0.01,O:0.01635#0.01)#0.01;"
spname<-species.name(tree)
nodematrix<-read.tree.nodes(tree, spname)$nodes
rootnode<-7
##define the vector seq as [2,2,2,2] which means that there are 2 sequences in each species
seq<-rep(2,4)
str<-sim.coaltree.sp(rootnode,nodematrix,4,seq,name=spname)$gt