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        SetDialogPrompt ("Please specify a di-nucleotide (e.g. stem RNA) file:");
      
        DataSet ds = ReadDataFile (PROMPT_FOR_FILE);
      
        DataSetFilter filteredData = CreateFilter (ds,2);
      
        fprintf (stdout,"\n______________READ THE FOLLOWING DATA______________\n",ds);
      
        SelectTemplateModel(filteredData);
      
        _DO_TREE_REBALANCE_ = 1;
      
        #include "queryTree.bf";
      
        LikelihoodFunction lf = (filteredData,givenTree);
      
        timer = Time(0);
      
        USE_ADAPTIVE_VARIABLE_STEP = 0;
      
        Optimize (res,lf);
      
        timer = Time(0)-timer;
      
        fprintf (stdout, "\n______________RESULTS______________\nTime taken = ", timer, " seconds\nAIC Score = ", 
      
        				  2(res[1][1]-res[1][0]),"\n",lf);
      
        #include "categoryEcho.bf";

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