Hi Eugen,
to compute a distance matrix from a phylogeny, you can use the
cophenetic.phylo function in {ape}.
You then have to rescale all distances in you matrix (which are expressed
in million years) by the total depth of the tree:
dist=cophenetic.phylo(tree)
dist2=dist/max(dist)
Best,
Florian
2013/7/12 Eugen
> Hi folks,
>
> I have phylogeny with absolute branch lengths in million years. How do I
> get a distance matrix with values between 0 and 1?
>
> Best,
>
> Eugen
>
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