[Bioperl-l] bootstrap values in cladogram

[Jason Stajich]

Yeah sorry then I don't know what the problem is. The usual - are you 
using the latest version question applies, but sounds like something 
else is wrong with this module.

I don't have any time to try out any code sorry but maybe someone else 
can step in to give a hand.
-jason

Alexander Donath wrote, On 3/11/10 1:05 AM:
> I tried both, with -internal_node_id => 'bootstrap' and without. Nothing.
>
> Nevertheless, iterating through the tree and printing $node->bootstrap 
> worked in both cases and gave me the correct bootstrap values of the 
> inner nodes.
>
> I also called move_id_to_bootstrap on the tree. But this resulted in 
> an error:
>
> Can't locate object method "move_id_to_bootstrap" via package 
> "Bio::Tree::Tree".
> Even though it's inherited from the interface, as far as I can tell.
>
>
> alex
>
>
> On Thu, 11 Mar 2010, Jason Stajich wrote:
>
>> not sure if the cladogram is printing bootstraps from the internal id 
>> or the bootstrap function.
>>
>> See the example code here  http://bioperl.org/wiki/HOWTO:Trees that 
>> shows how to automatically convert internal IDs to boostrap slots 
>> basically by using
>> -internal_node_id => 'bootstrap'
>> in the TreeIO initialization.
>>
>> You may want to iterate through the tree and print $node->bootstrap 
>> where you think it should be so you can verify that it is working too.
>>
>> -jason
>>
>> Alexander Donath wrote, On 3/9/10 10:00 AM:
>>> Hi,
>>>
>>> using Bioperl 1.6.1, I'm reading a newick tree with branch lengths 
>>> and bootstrap values and try to plot the tree as cladogram. But 
>>> somehow I cannot print the bootstrap values.
>>>
>>> Short example:
>>>
>>> test.nwk
>>> ((seq_1:0.18484,seq_3:0.23183):0.17826[879],seq_2:0.36341,seq_4:0.30326); 
>>>
>>>
>>>
>>> <code snippet>
>>> [..]
>>> use Bio::TreeIO;
>>> use Bio::Tree::Draw::Cladogram;
>>> [..]
>>> my $trees = Bio::TreeIO->new( -file => "test.nwk",
>>>                          -format => 'newick');
>>> my $tree = $trees->next_tree();
>>> [..]
>>> my $out = Bio::Tree::Draw::Cladogram->new( -bootstrap => 1,
>>>                             -tree => $tree,
>>>                        -compact => 0);
>>>
>>> $out->print(-file => "test.eps");
>>> </code snippet>
>>>
>>> I already tried it by copying the bootstrap values into the ids of the
>>> internal nodes - nothing. Any suggestions?
>>>
>>>
>>> Thanks,
>>> Alex
>>>
>>> ---
>>> By the time you've read this, you've already read it!
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>
>
> ---
> Alexander Donath
> Professur für Bioinformatik
> Institut für Informatik
> Universität Leipzig
> Härtelstr. 16-18
> D-04107 Leipzig, Germany
>
> phone:  +49 (0)341 97-16702
> fax:    +49 (0)341 97-16679
>
> By the time you've read this, you've already read it!