[Bioperl-l] Query on tree bootstrap values

Nathan S. Haigh n.haigh at sheffield.ac.uk
Fri Oct 27 07:36:10 EDT 2006


Sendu Bala wrote:
> Himanshu Ardawatia wrote:
>   
>> Hi,
>>
>> 2 questions :
>>
>> 1. I have a phylogenetic tree and I wish to set (or modify or query)
>> bootstrap values for all internal nodes. How do I do that using BioPerl ?
>>     
>
> Does bootstrap() not do what you need?
>
>
>   
>> 2. I tried the example script attached below for general purpose for the
>> example newick tree with bootstrap values (also attached below) and It gives
>> strange results even for branch length. It shows Parent ID as 0.71 which
>> actually is the bootstrap value for the last ancestral node for human and
>> chimp and It shows the Child node ID as 'Human' ! Am I missing something in
>> the tree formatting ? Results also attached below. Also how to extract /
>> modify/ add bootstrap values in this tree ?
>>     
> [snip]
>   
>> 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.

> For example, with the tree:
> ( ('Chimp':0.052,'Human':0.042)'Human_Chimp_Ancestor':0.007, 
> 'Gorilla':0.060, 
> ('Gibbon':0.124,'Orangutan':0.0971)'Gibbon_Orangutan_Ancestor':0.038);
>
>   

This tree does not contain any bootstrap values - only branch lengths.

Sorry I can't be much more help at the moment - if i get a spare 10 mins
i'll have a closer look.
Nath


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