Luigi Marongiu
2015-Jan-06 23:03 UTC
[R] add bootstrap to neighbour joining tree using nj function (ape package)
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