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

Jason Stajich jason at bioperl.org
Fri Feb 8 13:18:59 EST 2008


http://bioperl.org/wiki/HOWTO:Trees#Reading_and_Writing_Trees

Remember that in newick format bootstrap and internal node ids are  
effectively the same thing - that we store in them separate slots in  
bioperl is that fact that other formats can separate out this data  
but there is no standard in newick format.  In sometime cases formats  
do accept the node labels that look like NODEID[BOOTSTRAP]  for  
internal nodes (and BioPerl parses those out nicely) but most  
programs don't recognize that.

On parsing, unless you tell Bioperl that the internal IDs are  
bootstrap values it is going to store that data as an ID.
You will want to clear the bootstraps anyways to write PAML trees  
anyways.

-jason
On Feb 8, 2008, at 7:53 AM, Lucia Peixoto wrote:

> Hi
> as I have my trees right now the bootstrap support ends up as the  
> node ID
> so I guess I have to assign node ID to bootstrap first and then  
> change?
>
>
> Lucia
>
> Quoting Jason Stajich <jason at bioperl.org>:
>
>> 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
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
> Lucia Peixoto
> Department of Biology,SAS
> University of Pennsylvania



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