I wish to prepare a a phylogenetic tree based on an aligned fasta file.
Is the script below correct?
data <- read.dna("F:/AlignedSeqs.fasta", format = "fasta")
datamat = dist.dna(data,model = "JC69")
treeUPGMA = upgma(dmmat)
And If I want to use the phangorn why this script does not work:
dm <- dist.ml(data, model="JC69")
tree <- NJ(dm)