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rstatistics-bootstrapphylogeny

How to include bootstrap values in phylogenetic trees in ape package

I am using the R package ape to analyze some sequences stored in a DNAbin object:

library(ape)
my.seq  <- read.dna("sequences.txt", format = "clustal")
my.dist <- dist.dna(my.seq)
my.tree <- nj(my.dist)

I want to find the bootstrap values, so I use boot.phylo:

boot <- boot.phylo(my.tree, my.seq, FUN = function(xx) nj(dist.dna(xx)), B = 100)

But I get an error message saying:

Error in if (drop[j]) next : missing value where TRUE/FALSE needed

Any idea what this means, and how to fix it? I tried googling the error message, and I could not find anything.

Solution

  • Your if condition resulted in an NA.

    It must have either TRUE or FALSEresult.