[Bioperl-l] model 3 on Codeml.pm

[Jason Stajich]

it is in github so you can fork a version, make the change, and submit a patch which we can pick up.

I am concerned that this change can't be tested without example code.

Did you just edit the code and make sure your changes worked, the error message seems to refer to a different parameter
(ncatG) not model.

Thanks,

> MSG: parameter ncatG specified value  is not recognized, please see the documentation and the code for this module or set the no_param_checks to a true value.'


On Jun 7, 2011, at 9:26 PM, Lorenzo Carretero wrote:

> Hi,
> I'm trying to run the clade model D (Model D: model = 3, NSsites = 3 ncatG = 2, See reference. Bielawski, J. P., and Z. Yang. 2004. A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. Journal of Molecular Evolution 59:121-132. and PAML 4.4 manual page 30) from the Bio::Tools::Run::Phylo::PAML::Codeml module. However, 3 is not among the valid values that can be passed to the module (line 275 'model'    => [0..2,7],)  and consequently the following Warning message is returned from lines 689-690:
> 'MSG: parameter ncatG specified value  is not recognized, please see the documentation and the code for this module or set the no_param_checks to a true value.'
> Can line 275: 'model'    => [0..2,7], be changed to 'model'    => [0..3,7], to accept value 3 or additional changes must be done in other modules to properly run the so-called clade models of PAML.
> Thanks,
> Lorenzo
> 
> 
> -- 
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
> Lorenzo Carretero Paulet
> Institute for Plant Molecular and Cell Biology - IBMCP (CSIC-UPV)
> Integrative Systems Biology Group
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