Hello,

I am trying to run a likelihood analysis using the GY94_3x4 model matrix which comes with the hyphy package. Upon running my batch file, however, I always receive the error message as follows:

Error:
Operation 'MAccess' is not implemented/defined for a Number

Function call stack
1 : Branch  under condition ModelGeneticCode[h]==10 to 9 else 12
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2 : codonfreq=GUIBuildCodonFrequencies(observedFreq_outer)


I have tried several other codon models as well and the same error (more or less) is returned for each.

In my troubleshooting efforts, I tried to use a codon model formatted by the GUI rather than the ones in the trunk directory. Interestingly, I found that the "buildcodonfrequencies" function included in the model file that the GUI returns does not work but the other/standard buildcodonfrequencies model works fine with that matrix.

Any thoughts? I've attached my batch file as well.

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Hi there,

The models inside "SubstitutionModels" directory are only meant to work through the HyPhy GUI, which sets a lot of variables behind the scenes to make them work (sorry about the lack of documentation on this). I modified the file you include to work. The missing bits were:

• The model definition expects to have a genetic code defined and stored in the variable ModelGeneticCode
  
• The call to GUIBuildCodonFrequencies must follow the call to GUIPopulateModelMatrix
  

HTH,
Sergei

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