Hi guys

In the .mdl file above under the Substitution/Codon/ directory, I think there might be a typo in the GUIPopulateModelMatrix function. Should the line
Quote:

not also be ==0?

here is the code:

Code:

if (ModelGeneticCode[0][h]==ModelGeneticCode[0][v])
			  		{
			  			if ((Abs(transition-transition2)%2)==1)
			  			{
			  				ModelMatrixName[h-hshift][v-vshift] := globalVariable_TVTS*synRate*EFV__[transition__][nucPosInCodon__];
			  				ModelMatrixName[v-vshift][h-hshift] := globalVariable_TVTS*synRate*EFV__[transition2__][nucPosInCodon__];
			  
			  			}
			  			else
			  			{
			  				ModelMatrixName[h-hshift][v-vshift] := synRate*EFV__[transition__][nucPosInCodon__];
			  				ModelMatrixName[v-vshift][h-hshift] := synRate*EFV__[transition2__][nucPosInCodon__];
			  			}
				  	}
			  		else
			  		{
			  			if ((Abs(transition-transition2)%2)==0)
			  			{
			  				ModelMatrixName[h-hshift][v-vshift] := globalVariable_TVTS*nonSynRate*EFV__[transition__][nucPosInCodon__];
			  				ModelMatrixName[v-vshift][h-hshift] := globalVariable_TVTS*nonSynRate*EFV__[transition2__][nucPosInCodon__];
			  
			  			}
			  			else
			  			{
			  				ModelMatrixName[h-hshift][v-vshift] := nonSynRate*EFV__[transition__][nucPosInCodon__];
			  				ModelMatrixName[v-vshift][h-hshift] := nonSynRate*EFV__[transition2__][nucPosInCodon__];
			  			}
				  	} 

Might be that my distro is a bit old and this has been fixed already as well...

O yeah and just to make sure, the default nucleotide rate matrix when fitting codon models is HKY85 right?

keep well
gordon

Hi Sergei

Ok... but should the second "if (Abs(...))" line then not be ==1 as well?

Can't figure out why the two should be different?

ciao

Cool

Keep well