[R] add bootstrap to neighbour joining tree using nj function (ape package)

Luigi Marongiu marongiu.luigi at gmail.com
Wed Jan 7 00:03:38 CET 2015

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

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