[Bioperl-l] bootstrap values in cladogram
alex at bioinf.uni-leipzig.de
Thu Mar 11 04:05:13 EST 2010
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
I also called move_id_to_bootstrap on the tree. But this resulted in an
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
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