/* This file defines the transition matrix for the Dayhoff model for amino-acids.
   The file should be used as follows:
   
   1) Read Data File and create datafilter filteredData
   2) #include this file (or use SelectTemplateModel(filteredData);)
   3) Define the tree
   4) Proceed with the likelihood function using 'equalFreqs' as the vector to pass to the constructor.
   
   This model has the following signature:
   	#Short:Dayhoff#
   	#Desc:Dayhoff model for amino-acids#
   	#Dimension:20#
    #DataType:aminoacid#
   	#FileName:Dayhoff.mdl#
   
   12/20/1999  by Sergei L. Kosakovsky Pond
*/

#include "modelParameters2.mdl";

if (!SKIP_MODEL_PARAMETER_LIST)
{
	if (modelType == 1)
	{
		#include "defineGamma.mdl";
	}	
	if (modelType == 2)
	{
		#include "defineHM.mdl";
	}
}
function PopulateModelMatrix (ModelMatrixName&, EFV)
{
	ModelMatrixName = {20,20};
	if (categoriesUsed)
	{
        ModelMatrixName[0][1] := t*c*0.036;
        ModelMatrixName[1][0] := t*c*0.036;
        ModelMatrixName[0][2] := t*c*0.12;
        ModelMatrixName[2][0] := t*c*0.12;
        ModelMatrixName[0][3] := t*c*0.198;
        ModelMatrixName[3][0] := t*c*0.198;
        ModelMatrixName[0][4] := t*c*0.018;
        ModelMatrixName[4][0] := t*c*0.018;
        ModelMatrixName[0][5] := t*c*0.24;
        ModelMatrixName[5][0] := t*c*0.24;
        ModelMatrixName[0][6] := t*c*0.023;
        ModelMatrixName[6][0] := t*c*0.023;
        ModelMatrixName[0][7] := t*c*0.065;
        ModelMatrixName[7][0] := t*c*0.065;
        ModelMatrixName[0][8] := t*c*0.026;
        ModelMatrixName[8][0] := t*c*0.026;
        ModelMatrixName[0][9] := t*c*0.041;
        ModelMatrixName[9][0] := t*c*0.041;
        ModelMatrixName[0][10] := t*c*0.072;
        ModelMatrixName[10][0] := t*c*0.072;
        ModelMatrixName[0][11] := t*c*0.098;
        ModelMatrixName[11][0] := t*c*0.098;
        ModelMatrixName[0][12] := t*c*0.25;
        ModelMatrixName[12][0] := t*c*0.25;
        ModelMatrixName[0][13] := t*c*0.089;
        ModelMatrixName[13][0] := t*c*0.089;
        ModelMatrixName[0][14] := t*c*0.027;
        ModelMatrixName[14][0] := t*c*0.027;
        ModelMatrixName[0][15] := t*c*0.409;
        ModelMatrixName[15][0] := t*c*0.409;
        ModelMatrixName[0][16] := t*c*0.371;
        ModelMatrixName[16][0] := t*c*0.371;
        ModelMatrixName[0][17] := t*c*0.208;
        ModelMatrixName[17][0] := t*c*0.208;
        ModelMatrixName[0][18] := t*c*0;
        ModelMatrixName[18][0] := t*c*0;
        ModelMatrixName[0][19] := t*c*0.024;
        ModelMatrixName[19][0] := t*c*0.024;
        ModelMatrixName[1][2] := t*c*0;
        ModelMatrixName[2][1] := t*c*0;
        ModelMatrixName[1][3] := t*c*0;
        ModelMatrixName[3][1] := t*c*0;
        ModelMatrixName[1][4] := t*c*0;
        ModelMatrixName[4][1] := t*c*0;
        ModelMatrixName[1][5] := t*c*0.011;
        ModelMatrixName[5][1] := t*c*0.011;
        ModelMatrixName[1][6] := t*c*0.028;
        ModelMatrixName[6][1] := t*c*0.028;
        ModelMatrixName[1][7] := t*c*0.044;
        ModelMatrixName[7][1] := t*c*0.044;
        ModelMatrixName[1][8] := t*c*0;
        ModelMatrixName[8][1] := t*c*0;
        ModelMatrixName[1][9] := t*c*0;
        ModelMatrixName[9][1] := t*c*0;
        ModelMatrixName[1][10] := t*c*0;
        ModelMatrixName[10][1] := t*c*0;
        ModelMatrixName[1][11] := t*c*0;
        ModelMatrixName[11][1] := t*c*0;
        ModelMatrixName[1][12] := t*c*0.019;
        ModelMatrixName[12][1] := t*c*0.019;
        ModelMatrixName[1][13] := t*c*0;
        ModelMatrixName[13][1] := t*c*0;
        ModelMatrixName[1][14] := t*c*0.023;
        ModelMatrixName[14][1] := t*c*0.023;
        ModelMatrixName[1][15] := t*c*0.161;
        ModelMatrixName[15][1] := t*c*0.161;
        ModelMatrixName[1][16] := t*c*0.016;
        ModelMatrixName[16][1] := t*c*0.016;
        ModelMatrixName[1][17] := t*c*0.049;
        ModelMatrixName[17][1] := t*c*0.049;
        ModelMatrixName[1][18] := t*c*0;
        ModelMatrixName[18][1] := t*c*0;
        ModelMatrixName[1][19] := t*c*0.096;
        ModelMatrixName[19][1] := t*c*0.096;
        ModelMatrixName[2][3] := t*c*1.153;
        ModelMatrixName[3][2] := t*c*1.153;
        ModelMatrixName[2][4] := t*c*0;
        ModelMatrixName[4][2] := t*c*0;
        ModelMatrixName[2][5] := t*c*0.125;
        ModelMatrixName[5][2] := t*c*0.125;
        ModelMatrixName[2][6] := t*c*0.086;
        ModelMatrixName[6][2] := t*c*0.086;
        ModelMatrixName[2][7] := t*c*0.024;
        ModelMatrixName[7][2] := t*c*0.024;
        ModelMatrixName[2][8] := t*c*0.071;
        ModelMatrixName[8][2] := t*c*0.071;
        ModelMatrixName[2][9] := t*c*0;
        ModelMatrixName[9][2] := t*c*0;
        ModelMatrixName[2][10] := t*c*0;
        ModelMatrixName[10][2] := t*c*0;
        ModelMatrixName[2][11] := t*c*0.905;
        ModelMatrixName[11][2] := t*c*0.905;
        ModelMatrixName[2][12] := t*c*0.013;
        ModelMatrixName[12][2] := t*c*0.013;
        ModelMatrixName[2][13] := t*c*0.134;
        ModelMatrixName[13][2] := t*c*0.134;
        ModelMatrixName[2][14] := t*c*0;
        ModelMatrixName[14][2] := t*c*0;
        ModelMatrixName[2][15] := t*c*0.095;
        ModelMatrixName[15][2] := t*c*0.095;
        ModelMatrixName[2][16] := t*c*0.066;
        ModelMatrixName[16][2] := t*c*0.066;
        ModelMatrixName[2][17] := t*c*0.018;
        ModelMatrixName[17][2] := t*c*0.018;
        ModelMatrixName[2][18] := t*c*0;
        ModelMatrixName[18][2] := t*c*0;
        ModelMatrixName[2][19] := t*c*0;
        ModelMatrixName[19][2] := t*c*0;
        ModelMatrixName[3][4] := t*c*0;
        ModelMatrixName[4][3] := t*c*0;
        ModelMatrixName[3][5] := t*c*0.081;
        ModelMatrixName[5][3] := t*c*0.081;
        ModelMatrixName[3][6] := t*c*0.043;
        ModelMatrixName[6][3] := t*c*0.043;
        ModelMatrixName[3][7] := t*c*0.061;
        ModelMatrixName[7][3] := t*c*0.061;
        ModelMatrixName[3][8] := t*c*0.083;
        ModelMatrixName[8][3] := t*c*0.083;
        ModelMatrixName[3][9] := t*c*0.011;
        ModelMatrixName[9][3] := t*c*0.011;
        ModelMatrixName[3][10] := t*c*0.03;
        ModelMatrixName[10][3] := t*c*0.03;
        ModelMatrixName[3][11] := t*c*0.148;
        ModelMatrixName[11][3] := t*c*0.148;
        ModelMatrixName[3][12] := t*c*0.051;
        ModelMatrixName[12][3] := t*c*0.051;
        ModelMatrixName[3][13] := t*c*0.716;
        ModelMatrixName[13][3] := t*c*0.716;
        ModelMatrixName[3][14] := t*c*0.001;
        ModelMatrixName[14][3] := t*c*0.001;
        ModelMatrixName[3][15] := t*c*0.079;
        ModelMatrixName[15][3] := t*c*0.079;
        ModelMatrixName[3][16] := t*c*0.034;
        ModelMatrixName[16][3] := t*c*0.034;
        ModelMatrixName[3][17] := t*c*0.037;
        ModelMatrixName[17][3] := t*c*0.037;
        ModelMatrixName[3][18] := t*c*0;
        ModelMatrixName[18][3] := t*c*0;
        ModelMatrixName[3][19] := t*c*0.022;
        ModelMatrixName[19][3] := t*c*0.022;
        ModelMatrixName[4][5] := t*c*0.015;
        ModelMatrixName[5][4] := t*c*0.015;
        ModelMatrixName[4][6] := t*c*0.048;
        ModelMatrixName[6][4] := t*c*0.048;
        ModelMatrixName[4][7] := t*c*0.196;
        ModelMatrixName[7][4] := t*c*0.196;
        ModelMatrixName[4][8] := t*c*0;
        ModelMatrixName[8][4] := t*c*0;
        ModelMatrixName[4][9] := t*c*0.157;
        ModelMatrixName[9][4] := t*c*0.157;
        ModelMatrixName[4][10] := t*c*0.092;
        ModelMatrixName[10][4] := t*c*0.092;
        ModelMatrixName[4][11] := t*c*0.014;
        ModelMatrixName[11][4] := t*c*0.014;
        ModelMatrixName[4][12] := t*c*0.011;
        ModelMatrixName[12][4] := t*c*0.011;
        ModelMatrixName[4][13] := t*c*0;
        ModelMatrixName[13][4] := t*c*0;
        ModelMatrixName[4][14] := t*c*0.014;
        ModelMatrixName[14][4] := t*c*0.014;
        ModelMatrixName[4][15] := t*c*0.046;
        ModelMatrixName[15][4] := t*c*0.046;
        ModelMatrixName[4][16] := t*c*0.013;
        ModelMatrixName[16][4] := t*c*0.013;
        ModelMatrixName[4][17] := t*c*0.012;
        ModelMatrixName[17][4] := t*c*0.012;
        ModelMatrixName[4][18] := t*c*0.076;
        ModelMatrixName[18][4] := t*c*0.076;
        ModelMatrixName[4][19] := t*c*0.698;
        ModelMatrixName[19][4] := t*c*0.698;
        ModelMatrixName[5][6] := t*c*0.01;
        ModelMatrixName[6][5] := t*c*0.01;
        ModelMatrixName[5][7] := t*c*0;
        ModelMatrixName[7][5] := t*c*0;
        ModelMatrixName[5][8] := t*c*0.027;
        ModelMatrixName[8][5] := t*c*0.027;
        ModelMatrixName[5][9] := t*c*0.007;
        ModelMatrixName[9][5] := t*c*0.007;
        ModelMatrixName[5][10] := t*c*0.017;
        ModelMatrixName[10][5] := t*c*0.017;
        ModelMatrixName[5][11] := t*c*0.139;
        ModelMatrixName[11][5] := t*c*0.139;
        ModelMatrixName[5][12] := t*c*0.034;
        ModelMatrixName[12][5] := t*c*0.034;
        ModelMatrixName[5][13] := t*c*0.028;
        ModelMatrixName[13][5] := t*c*0.028;
        ModelMatrixName[5][14] := t*c*0.009;
        ModelMatrixName[14][5] := t*c*0.009;
        ModelMatrixName[5][15] := t*c*0.234;
        ModelMatrixName[15][5] := t*c*0.234;
        ModelMatrixName[5][16] := t*c*0.03;
        ModelMatrixName[16][5] := t*c*0.03;
        ModelMatrixName[5][17] := t*c*0.054;
        ModelMatrixName[17][5] := t*c*0.054;
        ModelMatrixName[5][18] := t*c*0;
        ModelMatrixName[18][5] := t*c*0;
        ModelMatrixName[5][19] := t*c*0;
        ModelMatrixName[19][5] := t*c*0;
        ModelMatrixName[6][7] := t*c*0.007;
        ModelMatrixName[7][6] := t*c*0.007;
        ModelMatrixName[6][8] := t*c*0.026;
        ModelMatrixName[8][6] := t*c*0.026;
        ModelMatrixName[6][9] := t*c*0.044;
        ModelMatrixName[9][6] := t*c*0.044;
        ModelMatrixName[6][10] := t*c*0;
        ModelMatrixName[10][6] := t*c*0;
        ModelMatrixName[6][11] := t*c*0.535;
        ModelMatrixName[11][6] := t*c*0.535;
        ModelMatrixName[6][12] := t*c*0.094;
        ModelMatrixName[12][6] := t*c*0.094;
        ModelMatrixName[6][13] := t*c*0.606;
        ModelMatrixName[13][6] := t*c*0.606;
        ModelMatrixName[6][14] := t*c*0.24;
        ModelMatrixName[14][6] := t*c*0.24;
        ModelMatrixName[6][15] := t*c*0.035;
        ModelMatrixName[15][6] := t*c*0.035;
        ModelMatrixName[6][16] := t*c*0.022;
        ModelMatrixName[16][6] := t*c*0.022;
        ModelMatrixName[6][17] := t*c*0.044;
        ModelMatrixName[17][6] := t*c*0.044;
        ModelMatrixName[6][18] := t*c*0.027;
        ModelMatrixName[18][6] := t*c*0.027;
        ModelMatrixName[6][19] := t*c*0.127;
        ModelMatrixName[19][6] := t*c*0.127;
        ModelMatrixName[7][8] := t*c*0.046;
        ModelMatrixName[8][7] := t*c*0.046;
        ModelMatrixName[7][9] := t*c*0.257;
        ModelMatrixName[9][7] := t*c*0.257;
        ModelMatrixName[7][10] := t*c*0.336;
        ModelMatrixName[10][7] := t*c*0.336;
        ModelMatrixName[7][11] := t*c*0.077;
        ModelMatrixName[11][7] := t*c*0.077;
        ModelMatrixName[7][12] := t*c*0.012;
        ModelMatrixName[12][7] := t*c*0.012;
        ModelMatrixName[7][13] := t*c*0.018;
        ModelMatrixName[13][7] := t*c*0.018;
        ModelMatrixName[7][14] := t*c*0.064;
        ModelMatrixName[14][7] := t*c*0.064;
        ModelMatrixName[7][15] := t*c*0.024;
        ModelMatrixName[15][7] := t*c*0.024;
        ModelMatrixName[7][16] := t*c*0.192;
        ModelMatrixName[16][7] := t*c*0.192;
        ModelMatrixName[7][17] := t*c*0.889;
        ModelMatrixName[17][7] := t*c*0.889;
        ModelMatrixName[7][18] := t*c*0;
        ModelMatrixName[18][7] := t*c*0;
        ModelMatrixName[7][19] := t*c*0.037;
        ModelMatrixName[19][7] := t*c*0.037;
        ModelMatrixName[8][9] := t*c*0.018;
        ModelMatrixName[9][8] := t*c*0.018;
        ModelMatrixName[8][10] := t*c*0.243;
        ModelMatrixName[10][8] := t*c*0.243;
        ModelMatrixName[8][11] := t*c*0.318;
        ModelMatrixName[11][8] := t*c*0.318;
        ModelMatrixName[8][12] := t*c*0.033;
        ModelMatrixName[12][8] := t*c*0.033;
        ModelMatrixName[8][13] := t*c*0.153;
        ModelMatrixName[13][8] := t*c*0.153;
        ModelMatrixName[8][14] := t*c*0.464;
        ModelMatrixName[14][8] := t*c*0.464;
        ModelMatrixName[8][15] := t*c*0.096;
        ModelMatrixName[15][8] := t*c*0.096;
        ModelMatrixName[8][16] := t*c*0.136;
        ModelMatrixName[16][8] := t*c*0.136;
        ModelMatrixName[8][17] := t*c*0.01;
        ModelMatrixName[17][8] := t*c*0.01;
        ModelMatrixName[8][18] := t*c*0;
        ModelMatrixName[18][8] := t*c*0;
        ModelMatrixName[8][19] := t*c*0.013;
        ModelMatrixName[19][8] := t*c*0.013;
        ModelMatrixName[9][10] := t*c*0.527;
        ModelMatrixName[10][9] := t*c*0.527;
        ModelMatrixName[9][11] := t*c*0.034;
        ModelMatrixName[11][9] := t*c*0.034;
        ModelMatrixName[9][12] := t*c*0.032;
        ModelMatrixName[12][9] := t*c*0.032;
        ModelMatrixName[9][13] := t*c*0.073;
        ModelMatrixName[13][9] := t*c*0.073;
        ModelMatrixName[9][14] := t*c*0.015;
        ModelMatrixName[14][9] := t*c*0.015;
        ModelMatrixName[9][15] := t*c*0.017;
        ModelMatrixName[15][9] := t*c*0.017;
        ModelMatrixName[9][16] := t*c*0.033;
        ModelMatrixName[16][9] := t*c*0.033;
        ModelMatrixName[9][17] := t*c*0.175;
        ModelMatrixName[17][9] := t*c*0.175;
        ModelMatrixName[9][18] := t*c*0.046;
        ModelMatrixName[18][9] := t*c*0.046;
        ModelMatrixName[9][19] := t*c*0.028;
        ModelMatrixName[19][9] := t*c*0.028;
        ModelMatrixName[10][11] := t*c*0.001;
        ModelMatrixName[11][10] := t*c*0.001;
        ModelMatrixName[10][12] := t*c*0.017;
        ModelMatrixName[12][10] := t*c*0.017;
        ModelMatrixName[10][13] := t*c*0.114;
        ModelMatrixName[13][10] := t*c*0.114;
        ModelMatrixName[10][14] := t*c*0.09;
        ModelMatrixName[14][10] := t*c*0.09;
        ModelMatrixName[10][15] := t*c*0.062;
        ModelMatrixName[15][10] := t*c*0.062;
        ModelMatrixName[10][16] := t*c*0.104;
        ModelMatrixName[16][10] := t*c*0.104;
        ModelMatrixName[10][17] := t*c*0.258;
        ModelMatrixName[17][10] := t*c*0.258;
        ModelMatrixName[10][18] := t*c*0;
        ModelMatrixName[18][10] := t*c*0;
        ModelMatrixName[10][19] := t*c*0;
        ModelMatrixName[19][10] := t*c*0;
        ModelMatrixName[11][12] := t*c*0.042;
        ModelMatrixName[12][11] := t*c*0.042;
        ModelMatrixName[11][13] := t*c*0.103;
        ModelMatrixName[13][11] := t*c*0.103;
        ModelMatrixName[11][14] := t*c*0.032;
        ModelMatrixName[14][11] := t*c*0.032;
        ModelMatrixName[11][15] := t*c*0.495;
        ModelMatrixName[15][11] := t*c*0.495;
        ModelMatrixName[11][16] := t*c*0.229;
        ModelMatrixName[16][11] := t*c*0.229;
        ModelMatrixName[11][17] := t*c*0.015;
        ModelMatrixName[17][11] := t*c*0.015;
        ModelMatrixName[11][18] := t*c*0.023;
        ModelMatrixName[18][11] := t*c*0.023;
        ModelMatrixName[11][19] := t*c*0.095;
        ModelMatrixName[19][11] := t*c*0.095;
        ModelMatrixName[12][13] := t*c*0.153;
        ModelMatrixName[13][12] := t*c*0.153;
        ModelMatrixName[12][14] := t*c*0.103;
        ModelMatrixName[14][12] := t*c*0.103;
        ModelMatrixName[12][15] := t*c*0.245;
        ModelMatrixName[15][12] := t*c*0.245;
        ModelMatrixName[12][16] := t*c*0.078;
        ModelMatrixName[16][12] := t*c*0.078;
        ModelMatrixName[12][17] := t*c*0.048;
        ModelMatrixName[17][12] := t*c*0.048;
        ModelMatrixName[12][18] := t*c*0;
        ModelMatrixName[18][12] := t*c*0;
        ModelMatrixName[12][19] := t*c*0;
        ModelMatrixName[19][12] := t*c*0;
        ModelMatrixName[13][14] := t*c*0.246;
        ModelMatrixName[14][13] := t*c*0.246;
        ModelMatrixName[13][15] := t*c*0.056;
        ModelMatrixName[15][13] := t*c*0.056;
        ModelMatrixName[13][16] := t*c*0.053;
        ModelMatrixName[16][13] := t*c*0.053;
        ModelMatrixName[13][17] := t*c*0.035;
        ModelMatrixName[17][13] := t*c*0.035;
        ModelMatrixName[13][18] := t*c*0;
        ModelMatrixName[18][13] := t*c*0;
        ModelMatrixName[13][19] := t*c*0;
        ModelMatrixName[19][13] := t*c*0;
        ModelMatrixName[14][15] := t*c*0.154;
        ModelMatrixName[15][14] := t*c*0.154;
        ModelMatrixName[14][16] := t*c*0.026;
        ModelMatrixName[16][14] := t*c*0.026;
        ModelMatrixName[14][17] := t*c*0.024;
        ModelMatrixName[17][14] := t*c*0.024;
        ModelMatrixName[14][18] := t*c*0.201;
        ModelMatrixName[18][14] := t*c*0.201;
        ModelMatrixName[14][19] := t*c*0.008;
        ModelMatrixName[19][14] := t*c*0.008;
        ModelMatrixName[15][16] := t*c*0.55;
        ModelMatrixName[16][15] := t*c*0.55;
        ModelMatrixName[15][17] := t*c*0.03;
        ModelMatrixName[17][15] := t*c*0.03;
        ModelMatrixName[15][18] := t*c*0.075;
        ModelMatrixName[18][15] := t*c*0.075;
        ModelMatrixName[15][19] := t*c*0.034;
        ModelMatrixName[19][15] := t*c*0.034;
        ModelMatrixName[16][17] := t*c*0.157;
        ModelMatrixName[17][16] := t*c*0.157;
        ModelMatrixName[16][18] := t*c*0;
        ModelMatrixName[18][16] := t*c*0;
        ModelMatrixName[16][19] := t*c*0.042;
        ModelMatrixName[19][16] := t*c*0.042;
        ModelMatrixName[17][18] := t*c*0;
        ModelMatrixName[18][17] := t*c*0;
        ModelMatrixName[17][19] := t*c*0.028;
        ModelMatrixName[19][17] := t*c*0.028;
        ModelMatrixName[18][19] := t*c*0.061;
        ModelMatrixName[19][18] := t*c*0.061;

	}
	else
	{
        ModelMatrixName[0][1] := t*0.036;
        ModelMatrixName[1][0] := t*0.036;
        ModelMatrixName[0][2] := t*0.12;
        ModelMatrixName[2][0] := t*0.12;
        ModelMatrixName[0][3] := t*0.198;
        ModelMatrixName[3][0] := t*0.198;
        ModelMatrixName[0][4] := t*0.018;
        ModelMatrixName[4][0] := t*0.018;
        ModelMatrixName[0][5] := t*0.24;
        ModelMatrixName[5][0] := t*0.24;
        ModelMatrixName[0][6] := t*0.023;
        ModelMatrixName[6][0] := t*0.023;
        ModelMatrixName[0][7] := t*0.065;
        ModelMatrixName[7][0] := t*0.065;
        ModelMatrixName[0][8] := t*0.026;
        ModelMatrixName[8][0] := t*0.026;
        ModelMatrixName[0][9] := t*0.041;
        ModelMatrixName[9][0] := t*0.041;
        ModelMatrixName[0][10] := t*0.072;
        ModelMatrixName[10][0] := t*0.072;
        ModelMatrixName[0][11] := t*0.098;
        ModelMatrixName[11][0] := t*0.098;
        ModelMatrixName[0][12] := t*0.25;
        ModelMatrixName[12][0] := t*0.25;
        ModelMatrixName[0][13] := t*0.089;
        ModelMatrixName[13][0] := t*0.089;
        ModelMatrixName[0][14] := t*0.027;
        ModelMatrixName[14][0] := t*0.027;
        ModelMatrixName[0][15] := t*0.409;
        ModelMatrixName[15][0] := t*0.409;
        ModelMatrixName[0][16] := t*0.371;
        ModelMatrixName[16][0] := t*0.371;
        ModelMatrixName[0][17] := t*0.208;
        ModelMatrixName[17][0] := t*0.208;
        ModelMatrixName[0][18] := t*0;
        ModelMatrixName[18][0] := t*0;
        ModelMatrixName[0][19] := t*0.024;
        ModelMatrixName[19][0] := t*0.024;
        ModelMatrixName[1][2] := t*0;
        ModelMatrixName[2][1] := t*0;
        ModelMatrixName[1][3] := t*0;
        ModelMatrixName[3][1] := t*0;
        ModelMatrixName[1][4] := t*0;
        ModelMatrixName[4][1] := t*0;
        ModelMatrixName[1][5] := t*0.011;
        ModelMatrixName[5][1] := t*0.011;
        ModelMatrixName[1][6] := t*0.028;
        ModelMatrixName[6][1] := t*0.028;
        ModelMatrixName[1][7] := t*0.044;
        ModelMatrixName[7][1] := t*0.044;
        ModelMatrixName[1][8] := t*0;
        ModelMatrixName[8][1] := t*0;
        ModelMatrixName[1][9] := t*0;
        ModelMatrixName[9][1] := t*0;
        ModelMatrixName[1][10] := t*0;
        ModelMatrixName[10][1] := t*0;
        ModelMatrixName[1][11] := t*0;
        ModelMatrixName[11][1] := t*0;
        ModelMatrixName[1][12] := t*0.019;
        ModelMatrixName[12][1] := t*0.019;
        ModelMatrixName[1][13] := t*0;
        ModelMatrixName[13][1] := t*0;
        ModelMatrixName[1][14] := t*0.023;
        ModelMatrixName[14][1] := t*0.023;
        ModelMatrixName[1][15] := t*0.161;
        ModelMatrixName[15][1] := t*0.161;
        ModelMatrixName[1][16] := t*0.016;
        ModelMatrixName[16][1] := t*0.016;
        ModelMatrixName[1][17] := t*0.049;
        ModelMatrixName[17][1] := t*0.049;
        ModelMatrixName[1][18] := t*0;
        ModelMatrixName[18][1] := t*0;
        ModelMatrixName[1][19] := t*0.096;
        ModelMatrixName[19][1] := t*0.096;
        ModelMatrixName[2][3] := t*1.153;
        ModelMatrixName[3][2] := t*1.153;
        ModelMatrixName[2][4] := t*0;
        ModelMatrixName[4][2] := t*0;
        ModelMatrixName[2][5] := t*0.125;
        ModelMatrixName[5][2] := t*0.125;
        ModelMatrixName[2][6] := t*0.086;
        ModelMatrixName[6][2] := t*0.086;
        ModelMatrixName[2][7] := t*0.024;
        ModelMatrixName[7][2] := t*0.024;
        ModelMatrixName[2][8] := t*0.071;
        ModelMatrixName[8][2] := t*0.071;
        ModelMatrixName[2][9] := t*0;
        ModelMatrixName[9][2] := t*0;
        ModelMatrixName[2][10] := t*0;
        ModelMatrixName[10][2] := t*0;
        ModelMatrixName[2][11] := t*0.905;
        ModelMatrixName[11][2] := t*0.905;
        ModelMatrixName[2][12] := t*0.013;
        ModelMatrixName[12][2] := t*0.013;
        ModelMatrixName[2][13] := t*0.134;
        ModelMatrixName[13][2] := t*0.134;
        ModelMatrixName[2][14] := t*0;
        ModelMatrixName[14][2] := t*0;
        ModelMatrixName[2][15] := t*0.095;
        ModelMatrixName[15][2] := t*0.095;
        ModelMatrixName[2][16] := t*0.066;
        ModelMatrixName[16][2] := t*0.066;
        ModelMatrixName[2][17] := t*0.018;
        ModelMatrixName[17][2] := t*0.018;
        ModelMatrixName[2][18] := t*0;
        ModelMatrixName[18][2] := t*0;
        ModelMatrixName[2][19] := t*0;
        ModelMatrixName[19][2] := t*0;
        ModelMatrixName[3][4] := t*0;
        ModelMatrixName[4][3] := t*0;
        ModelMatrixName[3][5] := t*0.081;
        ModelMatrixName[5][3] := t*0.081;
        ModelMatrixName[3][6] := t*0.043;
        ModelMatrixName[6][3] := t*0.043;
        ModelMatrixName[3][7] := t*0.061;
        ModelMatrixName[7][3] := t*0.061;
        ModelMatrixName[3][8] := t*0.083;
        ModelMatrixName[8][3] := t*0.083;
        ModelMatrixName[3][9] := t*0.011;
        ModelMatrixName[9][3] := t*0.011;
        ModelMatrixName[3][10] := t*0.03;
        ModelMatrixName[10][3] := t*0.03;
        ModelMatrixName[3][11] := t*0.148;
        ModelMatrixName[11][3] := t*0.148;
        ModelMatrixName[3][12] := t*0.051;
        ModelMatrixName[12][3] := t*0.051;
        ModelMatrixName[3][13] := t*0.716;
        ModelMatrixName[13][3] := t*0.716;
        ModelMatrixName[3][14] := t*0.001;
        ModelMatrixName[14][3] := t*0.001;
        ModelMatrixName[3][15] := t*0.079;
        ModelMatrixName[15][3] := t*0.079;
        ModelMatrixName[3][16] := t*0.034;
        ModelMatrixName[16][3] := t*0.034;
        ModelMatrixName[3][17] := t*0.037;
        ModelMatrixName[17][3] := t*0.037;
        ModelMatrixName[3][18] := t*0;
        ModelMatrixName[18][3] := t*0;
        ModelMatrixName[3][19] := t*0.022;
        ModelMatrixName[19][3] := t*0.022;
        ModelMatrixName[4][5] := t*0.015;
        ModelMatrixName[5][4] := t*0.015;
        ModelMatrixName[4][6] := t*0.048;
        ModelMatrixName[6][4] := t*0.048;
        ModelMatrixName[4][7] := t*0.196;
        ModelMatrixName[7][4] := t*0.196;
        ModelMatrixName[4][8] := t*0;
        ModelMatrixName[8][4] := t*0;
        ModelMatrixName[4][9] := t*0.157;
        ModelMatrixName[9][4] := t*0.157;
        ModelMatrixName[4][10] := t*0.092;
        ModelMatrixName[10][4] := t*0.092;
        ModelMatrixName[4][11] := t*0.014;
        ModelMatrixName[11][4] := t*0.014;
        ModelMatrixName[4][12] := t*0.011;
        ModelMatrixName[12][4] := t*0.011;
        ModelMatrixName[4][13] := t*0;
        ModelMatrixName[13][4] := t*0;
        ModelMatrixName[4][14] := t*0.014;
        ModelMatrixName[14][4] := t*0.014;
        ModelMatrixName[4][15] := t*0.046;
        ModelMatrixName[15][4] := t*0.046;
        ModelMatrixName[4][16] := t*0.013;
        ModelMatrixName[16][4] := t*0.013;
        ModelMatrixName[4][17] := t*0.012;
        ModelMatrixName[17][4] := t*0.012;
        ModelMatrixName[4][18] := t*0.076;
        ModelMatrixName[18][4] := t*0.076;
        ModelMatrixName[4][19] := t*0.698;
        ModelMatrixName[19][4] := t*0.698;
        ModelMatrixName[5][6] := t*0.01;
        ModelMatrixName[6][5] := t*0.01;
        ModelMatrixName[5][7] := t*0;
        ModelMatrixName[7][5] := t*0;
        ModelMatrixName[5][8] := t*0.027;
        ModelMatrixName[8][5] := t*0.027;
        ModelMatrixName[5][9] := t*0.007;
        ModelMatrixName[9][5] := t*0.007;
        ModelMatrixName[5][10] := t*0.017;
        ModelMatrixName[10][5] := t*0.017;
        ModelMatrixName[5][11] := t*0.139;
        ModelMatrixName[11][5] := t*0.139;
        ModelMatrixName[5][12] := t*0.034;
        ModelMatrixName[12][5] := t*0.034;
        ModelMatrixName[5][13] := t*0.028;
        ModelMatrixName[13][5] := t*0.028;
        ModelMatrixName[5][14] := t*0.009;
        ModelMatrixName[14][5] := t*0.009;
        ModelMatrixName[5][15] := t*0.234;
        ModelMatrixName[15][5] := t*0.234;
        ModelMatrixName[5][16] := t*0.03;
        ModelMatrixName[16][5] := t*0.03;
        ModelMatrixName[5][17] := t*0.054;
        ModelMatrixName[17][5] := t*0.054;
        ModelMatrixName[5][18] := t*0;
        ModelMatrixName[18][5] := t*0;
        ModelMatrixName[5][19] := t*0;
        ModelMatrixName[19][5] := t*0;
        ModelMatrixName[6][7] := t*0.007;
        ModelMatrixName[7][6] := t*0.007;
        ModelMatrixName[6][8] := t*0.026;
        ModelMatrixName[8][6] := t*0.026;
        ModelMatrixName[6][9] := t*0.044;
        ModelMatrixName[9][6] := t*0.044;
        ModelMatrixName[6][10] := t*0;
        ModelMatrixName[10][6] := t*0;
        ModelMatrixName[6][11] := t*0.535;
        ModelMatrixName[11][6] := t*0.535;
        ModelMatrixName[6][12] := t*0.094;
        ModelMatrixName[12][6] := t*0.094;
        ModelMatrixName[6][13] := t*0.606;
        ModelMatrixName[13][6] := t*0.606;
        ModelMatrixName[6][14] := t*0.24;
        ModelMatrixName[14][6] := t*0.24;
        ModelMatrixName[6][15] := t*0.035;
        ModelMatrixName[15][6] := t*0.035;
        ModelMatrixName[6][16] := t*0.022;
        ModelMatrixName[16][6] := t*0.022;
        ModelMatrixName[6][17] := t*0.044;
        ModelMatrixName[17][6] := t*0.044;
        ModelMatrixName[6][18] := t*0.027;
        ModelMatrixName[18][6] := t*0.027;
        ModelMatrixName[6][19] := t*0.127;
        ModelMatrixName[19][6] := t*0.127;
        ModelMatrixName[7][8] := t*0.046;
        ModelMatrixName[8][7] := t*0.046;
        ModelMatrixName[7][9] := t*0.257;
        ModelMatrixName[9][7] := t*0.257;
        ModelMatrixName[7][10] := t*0.336;
        ModelMatrixName[10][7] := t*0.336;
        ModelMatrixName[7][11] := t*0.077;
        ModelMatrixName[11][7] := t*0.077;
        ModelMatrixName[7][12] := t*0.012;
        ModelMatrixName[12][7] := t*0.012;
        ModelMatrixName[7][13] := t*0.018;
        ModelMatrixName[13][7] := t*0.018;
        ModelMatrixName[7][14] := t*0.064;
        ModelMatrixName[14][7] := t*0.064;
        ModelMatrixName[7][15] := t*0.024;
        ModelMatrixName[15][7] := t*0.024;
        ModelMatrixName[7][16] := t*0.192;
        ModelMatrixName[16][7] := t*0.192;
        ModelMatrixName[7][17] := t*0.889;
        ModelMatrixName[17][7] := t*0.889;
        ModelMatrixName[7][18] := t*0;
        ModelMatrixName[18][7] := t*0;
        ModelMatrixName[7][19] := t*0.037;
        ModelMatrixName[19][7] := t*0.037;
        ModelMatrixName[8][9] := t*0.018;
        ModelMatrixName[9][8] := t*0.018;
        ModelMatrixName[8][10] := t*0.243;
        ModelMatrixName[10][8] := t*0.243;
        ModelMatrixName[8][11] := t*0.318;
        ModelMatrixName[11][8] := t*0.318;
        ModelMatrixName[8][12] := t*0.033;
        ModelMatrixName[12][8] := t*0.033;
        ModelMatrixName[8][13] := t*0.153;
        ModelMatrixName[13][8] := t*0.153;
        ModelMatrixName[8][14] := t*0.464;
        ModelMatrixName[14][8] := t*0.464;
        ModelMatrixName[8][15] := t*0.096;
        ModelMatrixName[15][8] := t*0.096;
        ModelMatrixName[8][16] := t*0.136;
        ModelMatrixName[16][8] := t*0.136;
        ModelMatrixName[8][17] := t*0.01;
        ModelMatrixName[17][8] := t*0.01;
        ModelMatrixName[8][18] := t*0;
        ModelMatrixName[18][8] := t*0;
        ModelMatrixName[8][19] := t*0.013;
        ModelMatrixName[19][8] := t*0.013;
        ModelMatrixName[9][10] := t*0.527;
        ModelMatrixName[10][9] := t*0.527;
        ModelMatrixName[9][11] := t*0.034;
        ModelMatrixName[11][9] := t*0.034;
        ModelMatrixName[9][12] := t*0.032;
        ModelMatrixName[12][9] := t*0.032;
        ModelMatrixName[9][13] := t*0.073;
        ModelMatrixName[13][9] := t*0.073;
        ModelMatrixName[9][14] := t*0.015;
        ModelMatrixName[14][9] := t*0.015;
        ModelMatrixName[9][15] := t*0.017;
        ModelMatrixName[15][9] := t*0.017;
        ModelMatrixName[9][16] := t*0.033;
        ModelMatrixName[16][9] := t*0.033;
        ModelMatrixName[9][17] := t*0.175;
        ModelMatrixName[17][9] := t*0.175;
        ModelMatrixName[9][18] := t*0.046;
        ModelMatrixName[18][9] := t*0.046;
        ModelMatrixName[9][19] := t*0.028;
        ModelMatrixName[19][9] := t*0.028;
        ModelMatrixName[10][11] := t*0.001;
        ModelMatrixName[11][10] := t*0.001;
        ModelMatrixName[10][12] := t*0.017;
        ModelMatrixName[12][10] := t*0.017;
        ModelMatrixName[10][13] := t*0.114;
        ModelMatrixName[13][10] := t*0.114;
        ModelMatrixName[10][14] := t*0.09;
        ModelMatrixName[14][10] := t*0.09;
        ModelMatrixName[10][15] := t*0.062;
        ModelMatrixName[15][10] := t*0.062;
        ModelMatrixName[10][16] := t*0.104;
        ModelMatrixName[16][10] := t*0.104;
        ModelMatrixName[10][17] := t*0.258;
        ModelMatrixName[17][10] := t*0.258;
        ModelMatrixName[10][18] := t*0;
        ModelMatrixName[18][10] := t*0;
        ModelMatrixName[10][19] := t*0;
        ModelMatrixName[19][10] := t*0;
        ModelMatrixName[11][12] := t*0.042;
        ModelMatrixName[12][11] := t*0.042;
        ModelMatrixName[11][13] := t*0.103;
        ModelMatrixName[13][11] := t*0.103;
        ModelMatrixName[11][14] := t*0.032;
        ModelMatrixName[14][11] := t*0.032;
        ModelMatrixName[11][15] := t*0.495;
        ModelMatrixName[15][11] := t*0.495;
        ModelMatrixName[11][16] := t*0.229;
        ModelMatrixName[16][11] := t*0.229;
        ModelMatrixName[11][17] := t*0.015;
        ModelMatrixName[17][11] := t*0.015;
        ModelMatrixName[11][18] := t*0.023;
        ModelMatrixName[18][11] := t*0.023;
        ModelMatrixName[11][19] := t*0.095;
        ModelMatrixName[19][11] := t*0.095;
        ModelMatrixName[12][13] := t*0.153;
        ModelMatrixName[13][12] := t*0.153;
        ModelMatrixName[12][14] := t*0.103;
        ModelMatrixName[14][12] := t*0.103;
        ModelMatrixName[12][15] := t*0.245;
        ModelMatrixName[15][12] := t*0.245;
        ModelMatrixName[12][16] := t*0.078;
        ModelMatrixName[16][12] := t*0.078;
        ModelMatrixName[12][17] := t*0.048;
        ModelMatrixName[17][12] := t*0.048;
        ModelMatrixName[12][18] := t*0;
        ModelMatrixName[18][12] := t*0;
        ModelMatrixName[12][19] := t*0;
        ModelMatrixName[19][12] := t*0;
        ModelMatrixName[13][14] := t*0.246;
        ModelMatrixName[14][13] := t*0.246;
        ModelMatrixName[13][15] := t*0.056;
        ModelMatrixName[15][13] := t*0.056;
        ModelMatrixName[13][16] := t*0.053;
        ModelMatrixName[16][13] := t*0.053;
        ModelMatrixName[13][17] := t*0.035;
        ModelMatrixName[17][13] := t*0.035;
        ModelMatrixName[13][18] := t*0;
        ModelMatrixName[18][13] := t*0;
        ModelMatrixName[13][19] := t*0;
        ModelMatrixName[19][13] := t*0;
        ModelMatrixName[14][15] := t*0.154;
        ModelMatrixName[15][14] := t*0.154;
        ModelMatrixName[14][16] := t*0.026;
        ModelMatrixName[16][14] := t*0.026;
        ModelMatrixName[14][17] := t*0.024;
        ModelMatrixName[17][14] := t*0.024;
        ModelMatrixName[14][18] := t*0.201;
        ModelMatrixName[18][14] := t*0.201;
        ModelMatrixName[14][19] := t*0.008;
        ModelMatrixName[19][14] := t*0.008;
        ModelMatrixName[15][16] := t*0.55;
        ModelMatrixName[16][15] := t*0.55;
        ModelMatrixName[15][17] := t*0.03;
        ModelMatrixName[17][15] := t*0.03;
        ModelMatrixName[15][18] := t*0.075;
        ModelMatrixName[18][15] := t*0.075;
        ModelMatrixName[15][19] := t*0.034;
        ModelMatrixName[19][15] := t*0.034;
        ModelMatrixName[16][17] := t*0.157;
        ModelMatrixName[17][16] := t*0.157;
        ModelMatrixName[16][18] := t*0;
        ModelMatrixName[18][16] := t*0;
        ModelMatrixName[16][19] := t*0.042;
        ModelMatrixName[19][16] := t*0.042;
        ModelMatrixName[17][18] := t*0;
        ModelMatrixName[18][17] := t*0;
        ModelMatrixName[17][19] := t*0.028;
        ModelMatrixName[19][17] := t*0.028;
        ModelMatrixName[18][19] := t*0.061;
        ModelMatrixName[19][18] := t*0.061;
	}
	return 1;
}




HarvestFrequencies (vectorOfFrequencies,filteredData,1,1,0);
dayhoffModelF = 0;
MULTIPLY_BY_FREQS = PopulateModelMatrix ("dayhoffModelF",vectorOfFrequencies);
Model DayhoffModel = (dayhoffModelF, vectorOfFrequencies, MULTIPLY_BY_FREQS);
FREQUENCY_SENSITIVE = 1;
