[Bioperl-l] codeml

Jason Stajich jason at bioperl.org
Mon Dec 18 14:35:50 EST 2006


This is shortcoming in the Run::Phylo::PAML::Codeml implementation -  
I guess we'll need to allow the -tree option to accept and arrayref  
of trees.
Are you willing to try write this patch?  It should be added as a bug/ 
feature request to bugzilla so it can be corrected in short order.

-jason
On Dec 18, 2006, at 7:07 AM, Filipe Garrett wrote:

> Hi all,
>
> I've been using bioperl's PAML module (specifically the codeml  
> part) but
> with just one tree.
>
> Since the program accepts several trees as input (and runs the  
> analysis
> for each tree outputting the difference in likelihoods for each one) I
> was wondering if there's some way to do it through bioperl?
>
> thanks in adv,
> FG
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--
Jason Stajich
Miller Research Fellow
University of California, Berkeley
lab: 510.642.8441
http://pmb.berkeley.edu/~taylor/people/js.html




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