[Bioperl-l] Bio::TreeIO: Problem rerooting with a leaf

[Ferdinand Marlétaz]

Hi Mark
 this definitely makes sense to me, and your suggestions works fine!
Thank you for your help!
Ferdi


Le 11 févr. 2010 à 18:20, Mark A. Jensen a écrit :

> Hi Ferdi-
> I'm afraid I caused your trouble. The new reroot makes the the node you provide the root, rather than
> creating a new (and arbitrary) node. Now, the user specifies that node, and so has more control.
> Sometime one wants to take an existing polytomic
> node an make it itself the root; now reroot does this
> transparently. (It also fixes some other things, I think.)
> Try this:
> 
> # put a midpoint node on the ancestral branch of the leaf:
> # this is a new method...
> $new_root = $leaf->create_node_on_branch(-fraction => 0.5);
> # reroot $tree->reroot($new_root);
> 
> (this is what reroot actually did before, essentially secretly
> changing the tree)--
> HTH -MAJ
> 
> ----- Original Message ----- From: "Ferdi" <ferdinand.marletaz at gmail.com>
> To: <bioperl-l at bioperl.org>
> Sent: Thursday, February 11, 2010 11:41 AM
> Subject: [Bioperl-l] Bio::TreeIO: Problem rerooting with a leaf
> 
> 
>> Hi-
>> I am an enthusiastic user of Bio::TreeIO module, and I got some
>> problems with it after a recent reinstall of bioperl on my new mac
>> (10.6, previous was 10.5).  Particularly, when attempting to reroot
>> ($tree->reroot($leaf))  a tree with a leaf node, it doesn't seem to
>> consider ianymore t as an outgroup but as the root itself... For
>> example, with the example provided on Howto bioperl page:
>> (((A,B),(C,D)),E);
>> what I get when reroot with A:
>> ((B,((C,D),(E))))A;
>> while I should get something like:
>> (A,((E,(C,D)),B));
>> with A considered as outgroup instead of the root node itself.
>> Thanks for your help!
>> Ferdi
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>>