[Bioperl-l] Bio::Tree development

Jason Stajich jason at bioperl.org
Fri Jan 19 21:34:29 UTC 2007

Just assume the bootstrap value will be available from bootstrap()  
and please send in the function for collapsing by bootstrap.  I never  
finished consensus_tree building from bootstrap_replicates like I  
wanted to, but this is a nice logical addition to the package.

On Jan 19, 2007, at 12:53 PM, Lucia Peixoto wrote:

> Hi
> One of the functions missing from TreeIO that will be good to  
> implement is a
> collpase bootstrap function, meaning to collapse all nodes bellow a  
> certain
> bootstrap value
> I do have a bit of code to do this, however it cannot be  
> generalized until the
> bootstrap value is consistently captured by the same function, so  
> far, for the
> trees I have at least, the internal ID is the bootstrap value, but  
> that may not
> be true for all trees.Or it can be written asuming that you already  
> set the
> boostrap to the right value.
> The function bootstrap in Bio::Tree::NodeI never gets the bootstrap  
> right in any
> tree I've used (always newick format I am talking)
This has been discussed multiple times on the list - I don't know if  
I've posted the answer on the wiki or not, but it should go to the  
FAQ and/or Tree relevant pages.
Please understand that this is a limitation of the NEWICK FORMAT.    
Everyone complains about it but I think you are complaining to the  
wrong people. We don't assume the internal node IDs are bootstrap  
values (often they are not).  Some formats use  "ID[BOOTSTRAP]" which  
we parse into node id, and bootstrap.

If you know that the internal ids represent the bootstrap you can  
easily move the data over

for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {

if this is sufficiently annoying to you, write a function and submit  
it as a patch after it has been tested....  Here is an example:

sub migrate_id_to_bootstrap {
   my $tree = shift;
   for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {


> just an idea,
> Lucia
> Quoting Chris Fields <cjfields at uiuc.edu>:
>> On Jan 19, 2007, at 1:18 PM, Sendu Bala wrote:
>> ...
>>>> * General code cleanup
>>>> Making sure everything is indented according to some standard. I've
>>>> seen previously that there doesn't seem to be any real standard for
>>>> how BioPerl code should look like. I would think that it would be a
>>>> lot clearer to understand lots of the code if it was indented
>>>> properly. As it is now, the indentation depth changes between  
>>>> 2,3 and
>>>> 4 within the same file even.
>>> My own personal preference is an indent of 4 spaces.
>> ...
>> Mine as well.  Some people also use tabs vs spaces (I prefer
>> spaces).  However, I think (Johan) you'll be hard-pressed to force a
>> standard there.
>> You're always welcome to run it through perltidy prior to commits!
>> chris
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> Lucia Peixoto
> Department of Biology,SAS
> University of Pennsylvania
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Jason Stajich
Miller Research Fellow
University of California, Berkeley
lab: 510.642.8441

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