Hi,

I worked on HyPhy and PAUP with same data, tree topology, and model (GTR). They gave very closed branch length for the tree but very different Log likelihood(-3594 from Hyphy, -3815 from PAUP).  

Any reasons for this different result? Thanks.

my HyPhy code:

DataSet myData = ReadDataFile Hominoid.txt");
DataSetFilter myFilter = CreateFilter (myData,1);

HarvestFrequencies (obsFreqs, myFilter, 1, 1, 1);
REVRateMatrix = {{*,a,b,c}{a,*,d,e}{b,d,*,f}{c,e,f,*}};
Model REV = (REVRateMatrix, obsFreqs);
Tree myTree = ((((((Ch,Bo),Gr),Hm),Or),Gb),Mc);

LikelihoodFunction theLikFun = (myFilter, myTree, obsFreqs);
Optimize (paramValues, theLikFun);
fprintf (out.txt, theLikFun);

Dear Sergei ,

Thank you for your reply. How can i make a global analysis on GTR model? Is V always 2?should i put V into the RateMatrix?

global V=2.0
REVRateMatrix = {{*,av,bv,cv}{av,*,dv,ev}{bv,dv,*,fv}{cv,ev,fv,*}};

Thanks.

jxn