Nothing
make.mj.align <-
function(alignment){
n.taxa<-nrow(alignment)
n.nuc<-ncol(alignment)
not.in.alphabet <- ((alignment != "A")*(alignment != "G")*(alignment != "C")*(alignment != "T")*
(alignment != "a")*(alignment != "g")*(alignment != "c")*(alignment != "t"))
not.in.alphabet <- not.in.alphabet == 1
align.table = matrix(0, nrow = n.taxa, ncol = n.nuc)
rownames(align.table) = rownames(alignment)
##print(not.in.alphabet)
align.table[not.in.alphabet] = 0
align.table[alignment == "A" | alignment == "a"] = 1
align.table[alignment == "G" | alignment == "g"] = 2
align.table[alignment == "C" | alignment == "c"] = 3
align.table[alignment == "T" | alignment == "t"] = 4
return(align.table)
}
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