Beth Williams WilliamsBL at cardiff.ac.uk
Mon Mar 9 22:05:40 CET 2015

Dear All,

I am having some trouble with R and would be extremely grateful if anyone has a way around this. I have loaded a nexus tree from PAUP into R using the command read.nexus and this loaded,  it was reported as "rooted; with no branch lengths". I then used the command "compute.brlen(mytree)" to compute the branch lengths and this was reported as "rooted; includes branch lengths". I added my community data (samp) and then tried to compute the phylogenetic diversity with the command "> pd(samp, mytree, include.root=TRUE)" however it said it could not calculate the PD as there were no branch lengths. Is there a way to incorporate the branch lengths into the calculation for PD?

Thanks for your time,


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