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