[Bioperl-l] Representation of phylogenetic trees

[Jutta Buschbom]

Moin!

Some weeks ago a colleague suggested to use Bioperl for the 
modification of phylogenetic trees in newick format en route from one 
phylogenetic program to another one. From what I understand of the 
Bio::TreeIO and Bio::Tree classes, I think that they will be very 
useful tools for tree manipulation. Unfortunatly, having no previous 
experience with object-orientated programming, I find the theory and 
its application quite some disparate pair of socks. I have not been 
able to find the answer to the following question in the 
documentation or literature and would appreciate it very much if 
somebody could help me with it.

I am able to read trees into the object structure, but cannot get 
helpful information on the created objects represented by, eg., 
$treeio, $tree, $nodes, back out. What I would need is a list that 
gives me the names, attributes and relationships/ inheritances of the 
elements of the data structures. If I know the name and "location" of 
the object that represents taxon1, I should be able to manipulate it. 
So far, everything I tried has failed. Thus, any help with this would 
be appreciated very much.

Thanks a lot in advance,

Jutta