[Bioperl-l] bootstrap values in cladogram
Chris Fields
cjfields at illinois.edu
Thu Mar 11 11:21:02 EST 2010
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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