Nothing
satPlot <- function(DNAbin){
Pdist <- dist.dna(DNAbin, model = "raw", pairwise.deletion = TRUE)
Tree <- nj(Pdist)
Phy <- as.phyDat(DNAbin)
Pml <- pml(Tree, Phy, model = "HKY", k = 4)
MLtree <- optim.pml(Pml, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE)
MLdist <- cophenetic(MLtree$tree)
Pdist <- as.matrix(Pdist)
satList <- list(Pdist = Pdist, MLdist = MLdist)
plot(satList$Pdist ~ satList$MLdist, xlab = "ML distance", ylab = "p-distance")
abline(a = 0, b = 1)
invisible(satList)
}
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