Common Newick Trees with "proximities" for use with PhyloGibbs

Question

[Monika515]

The program PhyloGibbs available for use: http://www.phylogibbs.unibas.ch/cgi-bin/phylogibbs.pl has a requirement for a species tree in newick format where the numbers do not correspond to branch length but proximity to common ancestor defined as " A proximity gives the probability that no mutation has taken place along the branch". I was hoping someone may know where I could find examples of such trees that may be useful to me in my analysis.

[Chirag Parsania]

A tree showing universal relation between species can be downloaded from NCBI taxonomy database using common tree functionality. In that, for given taxonomical ids you can download species tree in newick format. For more details about tree download and loading in the R follow this thread.