[Bioperl-l] model 3 on Codeml.pm

[Lorenzo Carretero]

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


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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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