Sergei
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Dear Konrad, [quote author=konrad link=1129736474/0#2 date=1130246542]
The modelType flag is set by chooseGeneticCode.def, where it is used to identify the genetic code. But in PopulateModelMatrix it seems to mean something else: kappa is only used for modelType = 2 and 3.
[/quote]
Before 'PopulateModelMatrix' is called, 'modelType' (I don't think PopulateModelMatrix uses 'modelFlag') is set by the user response to a dialog:
[code]ChoiceList (modelType,"Choose a model",1,SKIP_NONE, "MG94 1x4","Muse-Gaut 94 model with 4(-1) nucleotide frequency parameters (intra-codon position independent).", "MG94 3x4","Muse-Gaut 94 model with 12(-3) nucleotide frequency parameters (intra-codon position specific).", "GY94 1x4","Goldman-Yang 94 model with 4(-1) nucleotide frequency parameters (intra-codon position independent).", "GY94 3x4","Goldman-Yang 94 model with 12(-3) nucleotide frequency parameters (intra-codon position specific).", "MG94 Custom 1x4", "Muse-Gaut 94 crossed with an arbitrary nucelotide substitution model with 4(-1) nucleotide frequency parameters (intra-codon position independent).", "MG94 Custom 3x4", "Muse-Gaut 94 crossed with an arbitrary nucelotide substitution model with 12(-3) nucleotide frequency parameters (intra-codon position specific)." ); [/code]
Since selection is zero based, you will see that agreement with PAML (which uses GY94 for most analysis) is only to be expected for [tt]modelType == 2[/tt] or [tt]modelType == 3[/tt].
Sorry for my undocumented code. Hopefully this helps.
Cheers, Sergei
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