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

Lucia Peixoto luciap at sas.upenn.edu
Fri Feb 8 10:53:36 EST 2008


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


More information about the Bioperl-l mailing list