loglikeSP: loglikelihood of the species tree, i.e., Rannala and Yang...
In bomeara/phybase: Basic functions for phylogenetic analysis

Description Usage Arguments Value Author(s) References Examples

This function calculates the loglikelihood of a species tree from a set of gene trees using the Rannala and Yang formula

1	loglikeSP(gtree, sptree, taxaname,spname,species.structure,strict=T)

`gtree`	a collection of gene trees
`sptree`	a species tree in newick format
`taxaname`	the names of taxa
`spname`	the names of species
`species.structure`	define which sequence belong to which species
`strict`	whether or not to check the result

The function returns the log likelihood score.

Liang Liu

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.

gtree<-"(((A:1,B:1):3,C:4):2,D:6);"
stree<-"(((A:0.5,B:0.5):1#0.1,C:1.5):1#0.1,D:2.5)#0.1;"
taxaname<-c("A","B","C","D")
spname<-taxaname
ntax<-length(taxaname)
nspecies<-length(spname)
species.structure<-matrix(0,nrow=nspecies,ncol=ntax)
diag(species.structure)<-1
loglikeSP(gtree,stree,taxaname,spname,species.structure)