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

Jason Stajich jason at bioperl.org
Mon Feb 12 13:38:11 EST 2007


I would definitely suggest getting ahold of bioperl 1.5.2 as I seem  
to remember there are several fixes in the tree module code for re- 
rooting a tree.
-jason

On Feb 12, 2007, at 10:07 AM, Wolverine Fran wrote:

> 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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--
Jason Stajich
Miller Research Fellow
University of California, Berkeley
lab: 510.642.8441
http://pmb.berkeley.edu/~taylor/people/js.html
http://fungalgenomes.org/




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