[Bioperl-l] bootstrap values in cladogram

[Alexander Donath]

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
>> 
>> ---
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---
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!