[Bioperl-l] Getting distance matrix from phylogenetic tree

[joris meys]

Hi,

I'm currently exploring the phylogenetic parts of Bio Perl, but I
can't seem to find a quick solution to following problem :
Say you have a tree obtained by a certain method. From this tree, you
want to have the evolutionary distances between species, defined as
the sum of the branch lengths between any 2 species. There is as far
as I know no function for doing that. But is there a possibility to
get a list of some sort of "shortest paths" from one species to
another, allowing to easily calculate that matrix?

>From the phylip package, I get following data if I run the neighbor or
fitch program. From there I can easily get an algorithm to calculate
the distances I need. But I also need to do that for maximum
likelihood trees and the like. Is there a way to get this information
in Bio Perl?
>From     to       dist
node1  sp1     xxxxx
node2 sp3      xxxxxx
node1 node2 xxxxx
node 1 sp2    xxxxx

Kind regards
Joris