[Bioperl-l] Query on tree bootstrap values

Sendu Bala bix at sendu.me.uk
Fri Oct 27 07:16:08 EDT 2006


Nathan S. Haigh wrote:
> Sendu Bala wrote:
>> Himanshu Ardawatia wrote:
>>>
>>> EXAMPLE TREE (Newick with bootstrap values and branch lengths) :
>>> #################################
>>> (
>>>   ('Chimp'  : 0.052,
>>>    'Human'  : 0.042) 0.71 : 0.007,
>>>   'Gorilla'  : 0.060,
>>>   ('Gibbon'  : 0.124,
>>>    'Orangutan'  : 0.0971) 1 : 0.038
>>> );
>>> #################################
>>>     
>> Are you sure this is in the correct format?
>>   
> 
> He/she may have a tree that already contains bootstrap values output
> from another program. If this is so, which program did you use? Without
> reminding myself of the formats, you should lookup newick format and
> whther it is possible to store bootstraps in it. In addition you should
> also look up the nhx format.

Ah, well from a brief google it seemed like some software do store 
boostrap values for internal nodes as the node ids when outputting in 
Newick format. I don't think Bioperl should be able to tell the 
difference between a normal id and a bootstrap value, so you'll have to 
detect that yourself and manually use bootstrap() when you get an id 
that looks like a number.

Or should Bioperl be making this assumption for you? Is that a safe 
thing to do? Maybe as an option only?


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