[Bioperl-l] PAML

[Chris Fields]

On Oct 29, 2006, at 11:06 AM, Eric Ross wrote:

> Thanks for all the help.
>
> I've been looking at the code for the PAML rst parser.  It's a bit  
> tricky.
>
> We have written a parser specific for our needs, but it looks to be  
> a pretty complicated matter to make it generic.
>
> The output of PAML can vary a lot depending upon your options and  
> this section can be repeated multiple times.  I'm sure someone with  
> a good grasp of the potential output of PAML could come up with  
> something, but I'll admit to being at a loss.

Eric,

I planned on looking at ways to integrate the protein-based PAML  
programs but I'm working on a different area at the moment.  I agree  
it may be hard to adequately genericize parsing/methods to accomplish  
this, but if you have any ideas feel free to post them.  Again, I  
would suggest adding any proposed enhancements or bugs to Bugzilla:

http://bugzilla.open-bio.org/

Suggestions or bug reports on the list sometimes get lost in the  
shuffle, esp. since we're planning on a new developer release soon.

Chris

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign