[Bioperl-l] Query on tree bootstrap values

Sendu Bala bix at sendu.me.uk
Fri Oct 27 05:08:18 EDT 2006


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?

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);

and your script (with a print "--\n" between the two printing loops for 
clarity) I get...

> ##########################################
> 
> RESULTS:
> branch len is  0.007
> branch len is  0.060
> branch len is  0.038
> node is a leaf ... branch len is  0.042
> node is a leaf ... branch len is  0.052
> branch len is  0.007
> node is a leaf ... branch len is  0.060
> node is a leaf ... branch len is  0.0971
> node is a leaf ... branch len is  0.124
> branch len is  0.038
> Parent id: _0.71_ child id: ___'Human'__

...

branch len is 0.007
branch len is 0.060
branch len is 0.038
--
branch len is 0.007
node is a leaf ... branch len is 0.052
node is a leaf ... branch len is 0.042
node is a leaf ... branch len is 0.060
branch len is 0.038
node is a leaf ... branch len is 0.124
node is a leaf ... branch len is 0.0971
Parent id: 'Human_Chimp_Ancestor' child id: 'Chimp'

This seems reasonable to me. What were you expecting?


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