Dear all,
I am trying to create a neighbour joining tree using the nj() function
of ape. I would like to add also the bootstrap. I created a distance
matrix with the Kimura 80 algorithm using the muscle function. If I use
nj on the distance matrix without any other argument I do obtain the
tree; I saw on some examples online that I could add the bootstrap
argument with the call B. I then used the function:
tr<-nj(seq.mat, B = 100)
where tr is the resulting tree, seq.mat is the distance matrix and B is
the number of bootstraps. But I obtained the error:
Error in nj(seq.mat, B = 100) : unused argument (B = 100)
I would like to ask how to implement the bootstrap argument and how to
retrieve it for a more tuned display using the function nodelabels().
Best regards
Luigi
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