1NICETY_LEVEL = 2;
2
3#include "modelParameters2.mdl";
4
5aaNames = {{"Alanine",
6"Cysteine",
7"Aspartic_Acid",
8"Glutamic_Acid",
9"Phenylalanine",
10"Glycine",
11"Histidine",
12"Isoleucine",
13"Lysine",
14"Leucine",
15"Methionine",
16"Asparagine",
17"Proline",
18"Glutamine",
19"Arginine",
20"Serine",
21"Threonine",
22"Valine",
23"Tryptophan",
24"Tyrosine"}};
25
26
27if (!SKIP_MODEL_PARAMETER_LIST)
28{
29	if (modelType == 1)
30	{
31		#include "defineGamma.mdl";
32	}
33	if (modelType == 2)
34	{
35		#include "defineHM.mdl";
36	}
37}
38
39function PopulateModelMatrix (ModelMatrixName&, EFV)
40{
41
42	ModelMatrixName = {20,20};
43	if (categoriesUsed)
44	{
45		for (k=0; k<19; k=k+1)
46		{
47			for (k2 = k+1; k2 < 20; k2=k2+1)
48			{
49				subString = aaNames[k]+aaNames[k2];
50				ExecuteCommands("global "+subString +"=1; ModelMatrixName[k][k2]:= c*t*"+subString+
51								";ModelMatrixName[k2][k]:= c*t*"+subString+";");
52			}
53		}
54	}
55	else
56	{
57		for (k=0; k<19; k=k+1)
58		{
59			for (k2 = k+1; k2 < 20; k2=k2+1)
60			{
61				subString = aaNames[k]+aaNames[k2];
62				ExecuteCommands("global "+subString +"=1; ModelMatrixName[k][k2]:= t*"+subString+
63								";ModelMatrixName[k2][k]:= t*"+subString+";");
64			}
65		}
66	}
67
68	subString = aaNames[7]+aaNames[9];
69	ExecuteCommands(subString +":=1;");
70	return 1;
71}
72
73
74
75mtREVMatrix = 0;
76
77HarvestFrequencies (vectorOfFrequencies,filteredData,1,1,0);
78
79MULTIPLY_BY_FREQS = PopulateModelMatrix ("mtREVMatrix",equalFreqs);
80
81Model mtREVModel = (mtREVMatrix, vectorOfFrequencies, MULTIPLY_BY_FREQS);
82
83FREQUENCY_SENSITIVE = 1;
84