[Bioperl-l] model 3 on Codeml.pm

[Lorenzo Carretero]

Jason,
I tried to change codeml.pm on my computer to accept 3 as model value 
but still have the same message. The  warning message I have, even after 
doing the mentioned change in codeml.pm, is actually complaining about 
the value passed to model (I wrongly posted a warning message from a 
different script).  Despite that, the program seems to run fine but 
results seem not to be exactly the same as those resulting from manual 
run of codeml.
Thanks a lot,
Lorenzo
PS: Let me take a look at github and all this. I really don't know what 
is it.

   On 6/8/11 7:15 AM, Jason Stajich wrote:
> 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
>> C/ Ingeniero Fausto Elio s/n.
>> 46022 Valencia, Spain
>>
>> Phone:  +34 963879934
>> Fax:    +34 963877859
>> e-mail: locarpau at upvnet.upv.es
>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>
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-- 
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Lorenzo Carretero Paulet
Institute for Plant Molecular and Cell Biology - IBMCP (CSIC-UPV)
Integrative Systems Biology Group
C/ Ingeniero Fausto Elio s/n.
46022 Valencia, Spain

Phone:  +34 963879934
Fax:    +34 963877859
e-mail: locarpau at upvnet.upv.es
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