[Bioperl-l] bootstrap values in cladogram

[Chris Fields]

Alex,

The best thing to do is to file this as a bug so we don't lose track of it, including demonstration code.

chris

On Mar 11, 2010, at 9:38 AM, Jason Stajich wrote:

> 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!
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