SamW
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Feed your monkey!
Posts: 18
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Thanks for the incredibly quick reply! Below is the actual code I'm running and getting a flat likelihood. I get the same likelihood if I insert a matrix designated as matrix = {61,61};
DataSet myData = ReadDataFile ("brown.nuc"); DataSetFilter codonFilter = CreateFilter (myData,3,"","","TAA,TAG,TGA");
HarvestFrequencies (obsFreqs, codonFilter, 3, 3, 1);
CFreqs = {61,1}; for(i=0; i<64; i=i+1) { count=0; if(i!=48 && i!=50 && i!=56) { CFreqs[count][1] = obsFreqs[i][1]; count = count+1; } }
TMatrix = {61,61}; for(j=0; j<61; j=j+1) { for(z=0; z<61; z=z+1) { if(j!=z) { TMatrix[j][z]:=mu; } } }
Model eval = (TMatrix , CFreqs); Tree myTree = (((Human,Chimpanzee),Gorilla),(Orangutan,Gibbon)); LikelihoodFunction theLikFun = (codonFilter , myTree); Optimize (MLEs, theLikFun); fprintf (stdout, "\n","\n", MLEs[1][0], "\n","\n");
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