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HYPHY Package >> HyPhy bugs >> GUI - MG94_HKY85x3_4.mdl file typo?
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1250077801
Message started by flashtop on Aug 12th, 2009 at 4:50am

Title: GUI - MG94_HKY85x3_4.mdl file typo?
Post by flashtop on Aug 12th, 2009 at 4:50am
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:
if ((Abs(transition-transition2)%2)==1)

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

Title: Re: GUI - MG94_HKY85x3_4.mdl file typo?
Post by Sergei on Aug 12th, 2009 at 10:59am
Hi Gordon,

That's OK - HyPhy typically parameterizes HKY85 in terms of the transVERSION/transITION ration (1/kappa), as is done here.

Sergei

Title: Re: GUI - MG94_HKY85x3_4.mdl file typo?
Post by flashtop on Aug 13th, 2009 at 2:45am
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

Title: Re: GUI - MG94_HKY85x3_4.mdl file typo?
Post by Sergei on Aug 13th, 2009 at 8:33am
Hi Gordon,

Yes, you are absolutely correct! I didn't see that in my haste. Will correct the file in the next SVN update.

Sergei

Title: Re: GUI - MG94_HKY85x3_4.mdl file typo?
Post by flashtop on Aug 14th, 2009 at 1:59am
Cool

Keep well

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