[Bioperl-l] codeml

Filipe Garrett fgarret at ub.edu
Mon Dec 18 15:07:46 EST 2006

Right now it's impossible for me to write it.
By February or March I should have more time but I'll let you know.


Jason Stajich wrote:
> 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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