[Bioperl-l] How to add branch labels for PAML codeml branch models

Jason Stajich jason at bioperl.org
Thu Feb 7 20:52:39 EST 2008


It will work if you just change the node's ID to be something like:  
'ID #1' (for tips) and for the internal nodes just set the id to  
("#1"), etc...

I added some code to demonstrate this one the wiki:
  http://bioperl.org/wiki/HOWTO:PAML#Setting_up_Branch-specific_labels

The format is nonstandard so you have to hack the output some to get  
what you want, hence the extra part that requires you strip out the "  
since they are required for escaping space characters.

-jason
On Feb 7, 2008, at 2:37 PM, Lucia Peixoto wrote:

> Just a small question
> in order to label the branches to use model 2 of PAML branch models
> can I use add_tag_value of Bio::Tree Node?
> or there's some other way to do it with bioperl?
>
> thanks
>
> Lucia Peixoto
> Department of Biology,SAS
> University of Pennsylvania
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> Bioperl-l at lists.open-bio.org
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