Dear bioconductor users,
I have problems in having the bootstrap value from the boot.phylo() function. I actually have DNA sequences from SANGER sequencer of ITS4 region). I read the user guide of ape package and any kinds of helps that bring me to the following codes:
dna<-fasta2DNAbin("ITS4.fas") dna<-read.dna("ITS4.fas", "fasta") D<-dist.dna(dna, model = "F84") tree<-nj(D) tree<-ladderize(tree) myBoots<-boot.phylo(tree, dna,function(dna) tree) ape::plot.phylo(tree, align.tip.label = T, cex = 1, x.lim = 0.3) nodelabels(myBoots, adj = 0.7, cex=0.7, frame = "none", col = "red")
I expected to have bootstrap values in my phylogenetic tree but instead of that I got the default number of bootstrap replicates in each node.