[R] Select best maximum likelihood tree with raxml (package ips)

[Luigi Marongiu]

Dear all,
I am trying to build a maximum likelihood (ML) tree using the raxml 
function of the package ips. I implemented the following script:
     tr<-raxml(seq.align,    exec = "/usr/bin/raxmlHPC",    b = 100,    
N = 10)
where tr is the resulting tree, seq.align is the DNA alignment created 
with the function muscle of the package ape, "/usr/bin/raxmlHPC" is the 
path for the executable of raxml, b is the number of bootstraps per 
tree, and N is the number of trees created (I reckon this should be 
enough because to build 10 trees it took several hours).
The resulting tree tr is an object of class 'multiPhylo' so my first 
question is how to extract an individual tree and create a standard 
object of class 'Phylo'.
My second question is on what basis select such tree: what function 
should I implement to obtain the best ML tree?
Finally, how could I extract the bootstrap values from the best tree in 
order to use it as a vector for the nodelabel function of the package ape?
Thank you
Best regards
Luigi