'bootstrap.mulgene' <-
function(sequence,gene,name,boot,outfile=""){
write.table("",file=outfile,col.names=FALSE,row.names=FALSE,quote=FALSE)
#row:taxa, col:sites
sequence<-t(sequence)
ntaxa<-dim(sequence)[2]
for(j in 1:boot){
ngene<-dim(gene)[1]
index<-sample(1:ngene,ngene,replace=TRUE)
bootgene<-gene[index,]
for(i in 1:ngene){
gene1<-sequence[bootgene[i,1]:bootgene[i,2],]
index<-sample(1:dim(gene1)[1],dim(gene1)[1],replace=TRUE)
gene2<-gene1[index,]
#delete the missing taxa
missing<-rep(1,ntaxa)
for(k in 1:ntaxa)
{
if((sum(gene2[,k]=="?")+sum(gene2[,k]=="-")+sum(gene2[,k]=="N")+sum(gene2[,k]=="n")) == length(gene2[,k])) missing[k]<-0
}
nomissing<-(1:ntaxa)*missing
nomissing<-nomissing[nomissing>0]
write.dna(t(gene2[,nomissing]),name[nomissing],format="phylip",file=outfile,append=TRUE)
}
}
}
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