[Bioperl-l] TreeIO, how (does) it work?

[Wolverine Fran]

thanks for your reply!

I am using Bioperl 1.4.

>Node 6 is to hold the root or a fake root with a trifurcation for
>unrooted trees.  Did you actually call the reroot method to set the
>root to node 5?

Yes, I tried the following with the same result:
$tree->reroot($tree->find_node(-internal_id => '5'));
or
$tree->set_root_node($tree->find_node(-internal_id => '5'));

Even if I use a rooted tree: 
(((dog:0.04,cat:0.08):0.12,human:0.15):0.1,mouse:0.1);
I get the node #6. So, is it always present? Am I not representing properly 
a rooted tree  in newick format?

>The distance method is just summing branch lengths on the path
>between two nodes.  Is that what are you trying to do?
>
>The error message you report doesn't make sense as
>"Must provide a valid array reference for -nodes"
>is only printed when you call is_monophyletic or is_paraphyletic as
>far as I can tell.

I do not know yet what I was doing incorrectly but now It works. Yes, I was 
using the distance method to know where the node 6 was located. For the 
unrooted tree, node 6 was node 5 (an internal node) and for the rooted tree 
node 6 was 0.1 from the mouse leaf and the internal node (root).
The error message: "Must provide a valid array reference for -nodes" is 
shown if I indicate a node which is not present in the tree.

>You are trying to calculate the likelihood of a tree or are you
>trying to generate a ML tree from an alignment?

I am trying to calculate the likelihood of a tree, as a practice. Probably 
there are other  bioperl modules, besides AlignIO and TreeIO, which can help 
me in the process and I do not know them.

Again, thank you for your time!

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