[R] APE

Beth Williams
2015-03-09T21:05:40Z

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,

Beth

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