[Bioperl-l] bootstrap values in cladogram
jason at bioperl.org
Thu Mar 11 15:38:50 UTC 2010
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.
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
> Even though it's inherited from the interface, as far as I can tell.
> 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.
>> Alexander Donath wrote, On 3/9/10 10:00 AM:
>>> 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:
>>> <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?
>>> By the time you've read this, you've already read it!
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
> 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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