Nothing
calc.null.pboot <-
function(data,B,l,m,exhaustive=F,codeml="codeml",evolver="evolverNSsites"){
IDnum<-which(!is.na(suppressWarnings(as.numeric(substring(data$nam,1,1)))))
if(length(IDnum)>0){
for(i in 1:length(IDnum)){
data$nam[IDnum[i]]<-paste("N",data$nam[IDnum[i]],sep="")
}
} # append "N" in front of taxa names that start with a number; codeml tanks otherwise
distance<-dist.dna(as.DNAbin(data),model="F84")*3
ols.tree<-nnls.tree(distance,bionj(distance),trace=0)
params<-paml.codeml(data,ols.tree,codeml)
data<-as.matrix.alignment(data)
length.codons<-dim(data)[2]/3
n.taxa<-dim(data)[1]
Dss.null<-rep(NA,B)
for(i in 1:B){
align.taxa<-sim.codon(n.taxa,length.codons,1,ols.tree,freqs=params$freqs,omega=params$omega,kap=params$kap,evolver)[[1]]
data<-t(matrix(as.vector(unlist(apply(align.taxa,1,strsplit,""))),ncol=nrow(align.taxa))) # for calc.dss
data.tmp<-ape::as.alignment(data)
Dss.null[i]<-max(calc.Dss(data.tmp,l,m,exhaustive))
}
return(Dss.null[order(Dss.null)])
}
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