triplenumber <- function(dna)
{
ntaxa<-dim(dna)[1]
ntriple<-ntaxa*(ntaxa-1)*(ntaxa-2)/6
triple<-matrix(0,nrow=ntriple,ncol=5)
for(i in 1:(ntaxa-2))
for(j in (i+1):(ntaxa-1))
for(k in (j+1):ntaxa)
{
seq<-dna[c(i,j,k),]
triple[i+j+k-5,]<-site.pattern(seq)[,4]
}
triple
}
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