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FillMatrix.cpp
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FillMatrix.cpp
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// File automatically generated by the genQ.r script, don't modify!
#include "TransitionMatrix.h"
#ifndef USE_LAPACK
double TransitionMatrix::fillMatrix(double aOmega, double aK) {
mQ[0] = -aK * mCodonFreq[1] - aOmega * mCodonFreq[2] -
aOmega * mCodonFreq[3] - aK * aOmega * mCodonFreq[4] -
aOmega * mCodonFreq[8] - aOmega * mCodonFreq[10] -
aK * aOmega * mCodonFreq[13] - aOmega * mCodonFreq[29] -
aOmega * mCodonFreq[45];
mQ[1] = aK * mCodonFreq[1];
mQ[2] = aOmega * mCodonFreq[2];
mQ[3] = aOmega * mCodonFreq[3];
mQ[4] = aK * aOmega * mCodonFreq[4];
mQ[8] = aOmega * mCodonFreq[8];
mQ[10] = aOmega * mCodonFreq[10];
mQ[13] = aK * aOmega * mCodonFreq[13];
mQ[29] = aOmega * mCodonFreq[29];
mQ[45] = aOmega * mCodonFreq[45];
mQ[61] = aK * mCodonFreq[0];
mQ[62] = -aK * mCodonFreq[0] - aOmega * mCodonFreq[2] -
aOmega * mCodonFreq[3] - aK * aOmega * mCodonFreq[5] -
aOmega * mCodonFreq[9] - aOmega * mCodonFreq[11] -
aK * aOmega * mCodonFreq[14] - aOmega * mCodonFreq[30] -
aOmega * mCodonFreq[46];
mQ[63] = aOmega * mCodonFreq[2];
mQ[64] = aOmega * mCodonFreq[3];
mQ[66] = aK * aOmega * mCodonFreq[5];
mQ[70] = aOmega * mCodonFreq[9];
mQ[72] = aOmega * mCodonFreq[11];
mQ[75] = aK * aOmega * mCodonFreq[14];
mQ[91] = aOmega * mCodonFreq[30];
mQ[107] = aOmega * mCodonFreq[46];
mQ[122] = aOmega * mCodonFreq[0];
mQ[123] = aOmega * mCodonFreq[1];
mQ[124] = -aOmega * mCodonFreq[0] - aOmega * mCodonFreq[1] -
aK * mCodonFreq[3] - aK * aOmega * mCodonFreq[6] -
aK * mCodonFreq[15] - aOmega * mCodonFreq[31] -
aOmega * mCodonFreq[47];
mQ[125] = aK * mCodonFreq[3];
mQ[128] = aK * aOmega * mCodonFreq[6];
mQ[137] = aK * mCodonFreq[15];
mQ[153] = aOmega * mCodonFreq[31];
mQ[169] = aOmega * mCodonFreq[47];
mQ[183] = aOmega * mCodonFreq[0];
mQ[184] = aOmega * mCodonFreq[1];
mQ[185] = aK * mCodonFreq[2];
mQ[186] = -aOmega * mCodonFreq[0] - aOmega * mCodonFreq[1] -
aK * mCodonFreq[2] - aK * aOmega * mCodonFreq[7] -
aOmega * mCodonFreq[12] - aK * mCodonFreq[16] -
aOmega * mCodonFreq[32] - aOmega * mCodonFreq[48];
mQ[190] = aK * aOmega * mCodonFreq[7];
mQ[195] = aOmega * mCodonFreq[12];
mQ[199] = aK * mCodonFreq[16];
mQ[215] = aOmega * mCodonFreq[32];
mQ[231] = aOmega * mCodonFreq[48];
mQ[244] = aK * aOmega * mCodonFreq[0];
mQ[248] = -aK * aOmega * mCodonFreq[0] - aK * mCodonFreq[5] - mCodonFreq[6] -
mCodonFreq[7] - aOmega * mCodonFreq[8] - aOmega * mCodonFreq[10] -
aK * aOmega * mCodonFreq[17] - aOmega * mCodonFreq[33] -
aOmega * mCodonFreq[49];
mQ[249] = aK * mCodonFreq[5];
mQ[250] = mCodonFreq[6];
mQ[251] = mCodonFreq[7];
mQ[252] = aOmega * mCodonFreq[8];
mQ[254] = aOmega * mCodonFreq[10];
mQ[261] = aK * aOmega * mCodonFreq[17];
mQ[277] = aOmega * mCodonFreq[33];
mQ[293] = aOmega * mCodonFreq[49];
mQ[306] = aK * aOmega * mCodonFreq[1];
mQ[309] = aK * mCodonFreq[4];
mQ[310] = -aK * aOmega * mCodonFreq[1] - aK * mCodonFreq[4] - mCodonFreq[6] -
mCodonFreq[7] - aOmega * mCodonFreq[9] - aOmega * mCodonFreq[11] -
aK * aOmega * mCodonFreq[18] - aOmega * mCodonFreq[34] -
aOmega * mCodonFreq[50];
mQ[311] = mCodonFreq[6];
mQ[312] = mCodonFreq[7];
mQ[314] = aOmega * mCodonFreq[9];
mQ[316] = aOmega * mCodonFreq[11];
mQ[323] = aK * aOmega * mCodonFreq[18];
mQ[339] = aOmega * mCodonFreq[34];
mQ[355] = aOmega * mCodonFreq[50];
mQ[368] = aK * aOmega * mCodonFreq[2];
mQ[370] = mCodonFreq[4];
mQ[371] = mCodonFreq[5];
mQ[372] = -aK * aOmega * mCodonFreq[2] - mCodonFreq[4] - mCodonFreq[5] -
aK * mCodonFreq[7] - aK * aOmega * mCodonFreq[19] -
aOmega * mCodonFreq[35] - aOmega * mCodonFreq[51];
mQ[373] = aK * mCodonFreq[7];
mQ[385] = aK * aOmega * mCodonFreq[19];
mQ[401] = aOmega * mCodonFreq[35];
mQ[417] = aOmega * mCodonFreq[51];
mQ[430] = aK * aOmega * mCodonFreq[3];
mQ[431] = mCodonFreq[4];
mQ[432] = mCodonFreq[5];
mQ[433] = aK * mCodonFreq[6];
mQ[434] = -aK * aOmega * mCodonFreq[3] - mCodonFreq[4] - mCodonFreq[5] -
aK * mCodonFreq[6] - aOmega * mCodonFreq[12] -
aK * aOmega * mCodonFreq[20] - aOmega * mCodonFreq[36] -
aOmega * mCodonFreq[52];
mQ[439] = aOmega * mCodonFreq[12];
mQ[447] = aK * aOmega * mCodonFreq[20];
mQ[463] = aOmega * mCodonFreq[36];
mQ[479] = aOmega * mCodonFreq[52];
mQ[488] = aOmega * mCodonFreq[0];
mQ[492] = aOmega * mCodonFreq[4];
mQ[496] = -aOmega * mCodonFreq[0] - aOmega * mCodonFreq[4] -
aK * mCodonFreq[9] - aK * aOmega * mCodonFreq[10] -
aK * aOmega * mCodonFreq[21] - aOmega * mCodonFreq[37] -
aOmega * mCodonFreq[53];
mQ[497] = aK * mCodonFreq[9];
mQ[498] = aK * aOmega * mCodonFreq[10];
mQ[509] = aK * aOmega * mCodonFreq[21];
mQ[525] = aOmega * mCodonFreq[37];
mQ[541] = aOmega * mCodonFreq[53];
mQ[550] = aOmega * mCodonFreq[1];
mQ[554] = aOmega * mCodonFreq[5];
mQ[557] = aK * mCodonFreq[8];
mQ[558] = -aOmega * mCodonFreq[1] - aOmega * mCodonFreq[5] -
aK * mCodonFreq[8] - aK * aOmega * mCodonFreq[11] -
aK * aOmega * mCodonFreq[22] - aOmega * mCodonFreq[38] -
aOmega * mCodonFreq[54];
mQ[560] = aK * aOmega * mCodonFreq[11];
mQ[571] = aK * aOmega * mCodonFreq[22];
mQ[587] = aOmega * mCodonFreq[38];
mQ[603] = aOmega * mCodonFreq[54];
mQ[610] = aOmega * mCodonFreq[0];
mQ[614] = aOmega * mCodonFreq[4];
mQ[618] = aK * aOmega * mCodonFreq[8];
mQ[620] = -aOmega * mCodonFreq[0] - aOmega * mCodonFreq[4] -
aK * aOmega * mCodonFreq[8] - aK * mCodonFreq[11] -
aOmega * mCodonFreq[12] - aK * aOmega * mCodonFreq[25] -
aOmega * mCodonFreq[41] - aOmega * mCodonFreq[57];
mQ[621] = aK * mCodonFreq[11];
mQ[622] = aOmega * mCodonFreq[12];
mQ[635] = aK * aOmega * mCodonFreq[25];
mQ[651] = aOmega * mCodonFreq[41];
mQ[667] = aOmega * mCodonFreq[57];
mQ[672] = aOmega * mCodonFreq[1];
mQ[676] = aOmega * mCodonFreq[5];
mQ[680] = aK * aOmega * mCodonFreq[9];
mQ[681] = aK * mCodonFreq[10];
mQ[682] = -aOmega * mCodonFreq[1] - aOmega * mCodonFreq[5] -
aK * aOmega * mCodonFreq[9] - aK * mCodonFreq[10] -
aOmega * mCodonFreq[12] - aK * aOmega * mCodonFreq[26] -
aOmega * mCodonFreq[42] - aOmega * mCodonFreq[58];
mQ[683] = aOmega * mCodonFreq[12];
mQ[697] = aK * aOmega * mCodonFreq[26];
mQ[713] = aOmega * mCodonFreq[42];
mQ[729] = aOmega * mCodonFreq[58];
mQ[735] = aOmega * mCodonFreq[3];
mQ[739] = aOmega * mCodonFreq[7];
mQ[742] = aOmega * mCodonFreq[10];
mQ[743] = aOmega * mCodonFreq[11];
mQ[744] = -aOmega * mCodonFreq[3] - aOmega * mCodonFreq[7] -
aOmega * mCodonFreq[10] - aOmega * mCodonFreq[11] -
aK * aOmega * mCodonFreq[28] - aOmega * mCodonFreq[44] -
aOmega * mCodonFreq[60];
mQ[760] = aK * aOmega * mCodonFreq[28];
mQ[776] = aOmega * mCodonFreq[44];
mQ[792] = aOmega * mCodonFreq[60];
mQ[793] = aK * aOmega * mCodonFreq[0];
mQ[806] = -aK * aOmega * mCodonFreq[0] - aK * mCodonFreq[14] -
mCodonFreq[15] - mCodonFreq[16] - aK * aOmega * mCodonFreq[17] -
aOmega * mCodonFreq[21] - aOmega * mCodonFreq[25] -
aOmega * mCodonFreq[29] - aOmega * mCodonFreq[45];
mQ[807] = aK * mCodonFreq[14];
mQ[808] = mCodonFreq[15];
mQ[809] = mCodonFreq[16];
mQ[810] = aK * aOmega * mCodonFreq[17];
mQ[814] = aOmega * mCodonFreq[21];
mQ[818] = aOmega * mCodonFreq[25];
mQ[822] = aOmega * mCodonFreq[29];
mQ[838] = aOmega * mCodonFreq[45];
mQ[855] = aK * aOmega * mCodonFreq[1];
mQ[867] = aK * mCodonFreq[13];
mQ[868] = -aK * aOmega * mCodonFreq[1] - aK * mCodonFreq[13] -
mCodonFreq[15] - mCodonFreq[16] - aK * aOmega * mCodonFreq[18] -
aOmega * mCodonFreq[22] - aOmega * mCodonFreq[26] -
aOmega * mCodonFreq[30] - aOmega * mCodonFreq[46];
mQ[869] = mCodonFreq[15];
mQ[870] = mCodonFreq[16];
mQ[872] = aK * aOmega * mCodonFreq[18];
mQ[876] = aOmega * mCodonFreq[22];
mQ[880] = aOmega * mCodonFreq[26];
mQ[884] = aOmega * mCodonFreq[30];
mQ[900] = aOmega * mCodonFreq[46];
mQ[917] = aK * mCodonFreq[2];
mQ[928] = mCodonFreq[13];
mQ[929] = mCodonFreq[14];
mQ[930] = -aK * mCodonFreq[2] - mCodonFreq[13] - mCodonFreq[14] -
aK * mCodonFreq[16] - aK * aOmega * mCodonFreq[19] -
aOmega * mCodonFreq[23] - aOmega * mCodonFreq[27] -
aOmega * mCodonFreq[31] - aOmega * mCodonFreq[47];
mQ[931] = aK * mCodonFreq[16];
mQ[934] = aK * aOmega * mCodonFreq[19];
mQ[938] = aOmega * mCodonFreq[23];
mQ[942] = aOmega * mCodonFreq[27];
mQ[946] = aOmega * mCodonFreq[31];
mQ[962] = aOmega * mCodonFreq[47];
mQ[979] = aK * mCodonFreq[3];
mQ[989] = mCodonFreq[13];
mQ[990] = mCodonFreq[14];
mQ[991] = aK * mCodonFreq[15];
mQ[992] = -aK * mCodonFreq[3] - mCodonFreq[13] - mCodonFreq[14] -
aK * mCodonFreq[15] - aK * aOmega * mCodonFreq[20] -
aOmega * mCodonFreq[24] - aOmega * mCodonFreq[28] -
aOmega * mCodonFreq[32] - aOmega * mCodonFreq[48];
mQ[996] = aK * aOmega * mCodonFreq[20];
mQ[1000] = aOmega * mCodonFreq[24];
mQ[1004] = aOmega * mCodonFreq[28];
mQ[1008] = aOmega * mCodonFreq[32];
mQ[1024] = aOmega * mCodonFreq[48];
mQ[1041] = aK * aOmega * mCodonFreq[4];
mQ[1050] = aK * aOmega * mCodonFreq[13];
mQ[1054] = -aK * aOmega * mCodonFreq[4] - aK * aOmega * mCodonFreq[13] -
aK * mCodonFreq[18] - mCodonFreq[19] - mCodonFreq[20] -
aOmega * mCodonFreq[21] - aOmega * mCodonFreq[25] -
aOmega * mCodonFreq[33] - aOmega * mCodonFreq[49];
mQ[1055] = aK * mCodonFreq[18];
mQ[1056] = mCodonFreq[19];
mQ[1057] = mCodonFreq[20];
mQ[1058] = aOmega * mCodonFreq[21];
mQ[1062] = aOmega * mCodonFreq[25];
mQ[1070] = aOmega * mCodonFreq[33];
mQ[1086] = aOmega * mCodonFreq[49];
mQ[1103] = aK * aOmega * mCodonFreq[5];
mQ[1112] = aK * aOmega * mCodonFreq[14];
mQ[1115] = aK * mCodonFreq[17];
mQ[1116] = -aK * aOmega * mCodonFreq[5] - aK * aOmega * mCodonFreq[14] -
aK * mCodonFreq[17] - mCodonFreq[19] - mCodonFreq[20] -
aOmega * mCodonFreq[22] - aOmega * mCodonFreq[26] -
aOmega * mCodonFreq[34] - aOmega * mCodonFreq[50];
mQ[1117] = mCodonFreq[19];
mQ[1118] = mCodonFreq[20];
mQ[1120] = aOmega * mCodonFreq[22];
mQ[1124] = aOmega * mCodonFreq[26];
mQ[1132] = aOmega * mCodonFreq[34];
mQ[1148] = aOmega * mCodonFreq[50];
mQ[1165] = aK * aOmega * mCodonFreq[6];
mQ[1174] = aK * aOmega * mCodonFreq[15];
mQ[1176] = mCodonFreq[17];
mQ[1177] = mCodonFreq[18];
mQ[1178] = -aK * aOmega * mCodonFreq[6] - aK * aOmega * mCodonFreq[15] -
mCodonFreq[17] - mCodonFreq[18] - aK * mCodonFreq[20] -
aOmega * mCodonFreq[23] - aOmega * mCodonFreq[27] -
aOmega * mCodonFreq[35] - aOmega * mCodonFreq[51];
mQ[1179] = aK * mCodonFreq[20];
mQ[1182] = aOmega * mCodonFreq[23];
mQ[1186] = aOmega * mCodonFreq[27];
mQ[1194] = aOmega * mCodonFreq[35];
mQ[1210] = aOmega * mCodonFreq[51];
mQ[1227] = aK * aOmega * mCodonFreq[7];
mQ[1236] = aK * aOmega * mCodonFreq[16];
mQ[1237] = mCodonFreq[17];
mQ[1238] = mCodonFreq[18];
mQ[1239] = aK * mCodonFreq[19];
mQ[1240] = -aK * aOmega * mCodonFreq[7] - aK * aOmega * mCodonFreq[16] -
mCodonFreq[17] - mCodonFreq[18] - aK * mCodonFreq[19] -
aOmega * mCodonFreq[24] - aOmega * mCodonFreq[28] -
aOmega * mCodonFreq[36] - aOmega * mCodonFreq[52];
mQ[1244] = aOmega * mCodonFreq[24];
mQ[1248] = aOmega * mCodonFreq[28];
mQ[1256] = aOmega * mCodonFreq[36];
mQ[1272] = aOmega * mCodonFreq[52];
mQ[1289] = aK * aOmega * mCodonFreq[8];
mQ[1294] = aOmega * mCodonFreq[13];
mQ[1298] = aOmega * mCodonFreq[17];
mQ[1302] = -aK * aOmega * mCodonFreq[8] - aOmega * mCodonFreq[13] -
aOmega * mCodonFreq[17] - aK * mCodonFreq[22] -
aOmega * mCodonFreq[23] - aOmega * mCodonFreq[24] -
aK * aOmega * mCodonFreq[25] - aOmega * mCodonFreq[37] -
aOmega * mCodonFreq[53];
mQ[1303] = aK * mCodonFreq[22];
mQ[1304] = aOmega * mCodonFreq[23];
mQ[1305] = aOmega * mCodonFreq[24];
mQ[1306] = aK * aOmega * mCodonFreq[25];
mQ[1318] = aOmega * mCodonFreq[37];
mQ[1334] = aOmega * mCodonFreq[53];
mQ[1351] = aK * aOmega * mCodonFreq[9];
mQ[1356] = aOmega * mCodonFreq[14];
mQ[1360] = aOmega * mCodonFreq[18];
mQ[1363] = aK * mCodonFreq[21];
mQ[1364] = -aK * aOmega * mCodonFreq[9] - aOmega * mCodonFreq[14] -
aOmega * mCodonFreq[18] - aK * mCodonFreq[21] -
aOmega * mCodonFreq[23] - aOmega * mCodonFreq[24] -
aK * aOmega * mCodonFreq[26] - aOmega * mCodonFreq[38] -
aOmega * mCodonFreq[54];
mQ[1365] = aOmega * mCodonFreq[23];
mQ[1366] = aOmega * mCodonFreq[24];
mQ[1368] = aK * aOmega * mCodonFreq[26];
mQ[1380] = aOmega * mCodonFreq[38];
mQ[1396] = aOmega * mCodonFreq[54];
mQ[1418] = aOmega * mCodonFreq[15];
mQ[1422] = aOmega * mCodonFreq[19];
mQ[1424] = aOmega * mCodonFreq[21];
mQ[1425] = aOmega * mCodonFreq[22];
mQ[1426] = -aOmega * mCodonFreq[15] - aOmega * mCodonFreq[19] -
aOmega * mCodonFreq[21] - aOmega * mCodonFreq[22] -
aK * mCodonFreq[24] - aK * aOmega * mCodonFreq[27] -
aOmega * mCodonFreq[39] - aOmega * mCodonFreq[55];
mQ[1427] = aK * mCodonFreq[24];
mQ[1430] = aK * aOmega * mCodonFreq[27];
mQ[1442] = aOmega * mCodonFreq[39];
mQ[1458] = aOmega * mCodonFreq[55];
mQ[1480] = aOmega * mCodonFreq[16];
mQ[1484] = aOmega * mCodonFreq[20];
mQ[1485] = aOmega * mCodonFreq[21];
mQ[1486] = aOmega * mCodonFreq[22];
mQ[1487] = aK * mCodonFreq[23];
mQ[1488] = -aOmega * mCodonFreq[16] - aOmega * mCodonFreq[20] -
aOmega * mCodonFreq[21] - aOmega * mCodonFreq[22] -
aK * mCodonFreq[23] - aK * aOmega * mCodonFreq[28] -
aOmega * mCodonFreq[40] - aOmega * mCodonFreq[56];
mQ[1492] = aK * aOmega * mCodonFreq[28];
mQ[1504] = aOmega * mCodonFreq[40];
mQ[1520] = aOmega * mCodonFreq[56];
mQ[1535] = aK * aOmega * mCodonFreq[10];
mQ[1538] = aOmega * mCodonFreq[13];
mQ[1542] = aOmega * mCodonFreq[17];
mQ[1546] = aK * aOmega * mCodonFreq[21];
mQ[1550] = -aK * aOmega * mCodonFreq[10] - aOmega * mCodonFreq[13] -
aOmega * mCodonFreq[17] - aK * aOmega * mCodonFreq[21] -
aK * mCodonFreq[26] - mCodonFreq[27] - mCodonFreq[28] -
aOmega * mCodonFreq[41] - aOmega * mCodonFreq[57];
mQ[1551] = aK * mCodonFreq[26];
mQ[1552] = mCodonFreq[27];
mQ[1553] = mCodonFreq[28];
mQ[1566] = aOmega * mCodonFreq[41];
mQ[1582] = aOmega * mCodonFreq[57];
mQ[1597] = aK * aOmega * mCodonFreq[11];
mQ[1600] = aOmega * mCodonFreq[14];
mQ[1604] = aOmega * mCodonFreq[18];
mQ[1608] = aK * aOmega * mCodonFreq[22];
mQ[1611] = aK * mCodonFreq[25];
mQ[1612] = -aK * aOmega * mCodonFreq[11] - aOmega * mCodonFreq[14] -
aOmega * mCodonFreq[18] - aK * aOmega * mCodonFreq[22] -
aK * mCodonFreq[25] - mCodonFreq[27] - mCodonFreq[28] -
aOmega * mCodonFreq[42] - aOmega * mCodonFreq[58];
mQ[1613] = mCodonFreq[27];
mQ[1614] = mCodonFreq[28];
mQ[1628] = aOmega * mCodonFreq[42];
mQ[1644] = aOmega * mCodonFreq[58];
mQ[1662] = aOmega * mCodonFreq[15];
mQ[1666] = aOmega * mCodonFreq[19];
mQ[1670] = aK * aOmega * mCodonFreq[23];
mQ[1672] = mCodonFreq[25];
mQ[1673] = mCodonFreq[26];
mQ[1674] = -aOmega * mCodonFreq[15] - aOmega * mCodonFreq[19] -
aK * aOmega * mCodonFreq[23] - mCodonFreq[25] - mCodonFreq[26] -
aK * mCodonFreq[28] - mCodonFreq[43] - aOmega * mCodonFreq[59];
mQ[1675] = aK * mCodonFreq[28];
mQ[1690] = mCodonFreq[43];
mQ[1706] = aOmega * mCodonFreq[59];
mQ[1720] = aK * aOmega * mCodonFreq[12];
mQ[1724] = aOmega * mCodonFreq[16];
mQ[1728] = aOmega * mCodonFreq[20];
mQ[1732] = aK * aOmega * mCodonFreq[24];
mQ[1733] = mCodonFreq[25];
mQ[1734] = mCodonFreq[26];
mQ[1735] = aK * mCodonFreq[27];
mQ[1736] = -aK * aOmega * mCodonFreq[12] - aOmega * mCodonFreq[16] -
aOmega * mCodonFreq[20] - aK * aOmega * mCodonFreq[24] -
mCodonFreq[25] - mCodonFreq[26] - aK * mCodonFreq[27] -
mCodonFreq[44] - aOmega * mCodonFreq[60];
mQ[1752] = mCodonFreq[44];
mQ[1768] = aOmega * mCodonFreq[60];
mQ[1769] = aOmega * mCodonFreq[0];
mQ[1782] = aOmega * mCodonFreq[13];
mQ[1798] = -aOmega * mCodonFreq[0] - aOmega * mCodonFreq[13] -
aK * mCodonFreq[30] - mCodonFreq[31] - aOmega * mCodonFreq[32] -
aK * aOmega * mCodonFreq[33] - aOmega * mCodonFreq[37] -
aOmega * mCodonFreq[41] - aK * aOmega * mCodonFreq[45];
mQ[1799] = aK * mCodonFreq[30];
mQ[1800] = mCodonFreq[31];
mQ[1801] = aOmega * mCodonFreq[32];
mQ[1802] = aK * aOmega * mCodonFreq[33];
mQ[1806] = aOmega * mCodonFreq[37];
mQ[1810] = aOmega * mCodonFreq[41];
mQ[1814] = aK * aOmega * mCodonFreq[45];
mQ[1831] = aOmega * mCodonFreq[1];
mQ[1844] = aOmega * mCodonFreq[14];
mQ[1859] = aK * mCodonFreq[29];
mQ[1860] = -aOmega * mCodonFreq[1] - aOmega * mCodonFreq[14] -
aK * mCodonFreq[29] - mCodonFreq[31] - aOmega * mCodonFreq[32] -
aK * aOmega * mCodonFreq[34] - aOmega * mCodonFreq[38] -
aOmega * mCodonFreq[42] - aK * aOmega * mCodonFreq[46];
mQ[1861] = mCodonFreq[31];
mQ[1862] = aOmega * mCodonFreq[32];
mQ[1864] = aK * aOmega * mCodonFreq[34];
mQ[1868] = aOmega * mCodonFreq[38];
mQ[1872] = aOmega * mCodonFreq[42];
mQ[1876] = aK * aOmega * mCodonFreq[46];
mQ[1893] = aOmega * mCodonFreq[2];
mQ[1906] = aOmega * mCodonFreq[15];
mQ[1920] = mCodonFreq[29];
mQ[1921] = mCodonFreq[30];
mQ[1922] = -aOmega * mCodonFreq[2] - aOmega * mCodonFreq[15] -
mCodonFreq[29] - mCodonFreq[30] - aK * aOmega * mCodonFreq[32] -
aK * aOmega * mCodonFreq[35] - aOmega * mCodonFreq[39] -
aOmega * mCodonFreq[43] - aK * aOmega * mCodonFreq[47];
mQ[1923] = aK * aOmega * mCodonFreq[32];
mQ[1926] = aK * aOmega * mCodonFreq[35];
mQ[1930] = aOmega * mCodonFreq[39];
mQ[1934] = aOmega * mCodonFreq[43];
mQ[1938] = aK * aOmega * mCodonFreq[47];
mQ[1955] = aOmega * mCodonFreq[3];
mQ[1968] = aOmega * mCodonFreq[16];
mQ[1981] = aOmega * mCodonFreq[29];
mQ[1982] = aOmega * mCodonFreq[30];
mQ[1983] = aK * aOmega * mCodonFreq[31];
mQ[1984] = -aOmega * mCodonFreq[3] - aOmega * mCodonFreq[16] -
aOmega * mCodonFreq[29] - aOmega * mCodonFreq[30] -
aK * aOmega * mCodonFreq[31] - aK * aOmega * mCodonFreq[36] -
aOmega * mCodonFreq[40] - aOmega * mCodonFreq[44] -
aK * aOmega * mCodonFreq[48];
mQ[1988] = aK * aOmega * mCodonFreq[36];
mQ[1992] = aOmega * mCodonFreq[40];
mQ[1996] = aOmega * mCodonFreq[44];
mQ[2000] = aK * aOmega * mCodonFreq[48];
mQ[2017] = aOmega * mCodonFreq[4];
mQ[2030] = aOmega * mCodonFreq[17];
mQ[2042] = aK * aOmega * mCodonFreq[29];
mQ[2046] = -aOmega * mCodonFreq[4] - aOmega * mCodonFreq[17] -
aK * aOmega * mCodonFreq[29] - aK * mCodonFreq[34] -
mCodonFreq[35] - mCodonFreq[36] - aOmega * mCodonFreq[37] -
aOmega * mCodonFreq[41] - aK * aOmega * mCodonFreq[49];
mQ[2047] = aK * mCodonFreq[34];
mQ[2048] = mCodonFreq[35];
mQ[2049] = mCodonFreq[36];
mQ[2050] = aOmega * mCodonFreq[37];
mQ[2054] = aOmega * mCodonFreq[41];
mQ[2062] = aK * aOmega * mCodonFreq[49];
mQ[2079] = aOmega * mCodonFreq[5];
mQ[2092] = aOmega * mCodonFreq[18];
mQ[2104] = aK * aOmega * mCodonFreq[30];
mQ[2107] = aK * mCodonFreq[33];
mQ[2108] = -aOmega * mCodonFreq[5] - aOmega * mCodonFreq[18] -
aK * aOmega * mCodonFreq[30] - aK * mCodonFreq[33] -
mCodonFreq[35] - mCodonFreq[36] - aOmega * mCodonFreq[38] -
aOmega * mCodonFreq[42] - aK * aOmega * mCodonFreq[50];
mQ[2109] = mCodonFreq[35];
mQ[2110] = mCodonFreq[36];
mQ[2112] = aOmega * mCodonFreq[38];
mQ[2116] = aOmega * mCodonFreq[42];
mQ[2124] = aK * aOmega * mCodonFreq[50];
mQ[2141] = aOmega * mCodonFreq[6];
mQ[2154] = aOmega * mCodonFreq[19];
mQ[2166] = aK * aOmega * mCodonFreq[31];
mQ[2168] = mCodonFreq[33];
mQ[2169] = mCodonFreq[34];
mQ[2170] = -aOmega * mCodonFreq[6] - aOmega * mCodonFreq[19] -
aK * aOmega * mCodonFreq[31] - mCodonFreq[33] - mCodonFreq[34] -
aK * mCodonFreq[36] - aOmega * mCodonFreq[39] -
aOmega * mCodonFreq[43] - aK * aOmega * mCodonFreq[51];
mQ[2171] = aK * mCodonFreq[36];
mQ[2174] = aOmega * mCodonFreq[39];
mQ[2178] = aOmega * mCodonFreq[43];
mQ[2186] = aK * aOmega * mCodonFreq[51];
mQ[2203] = aOmega * mCodonFreq[7];
mQ[2216] = aOmega * mCodonFreq[20];
mQ[2228] = aK * aOmega * mCodonFreq[32];
mQ[2229] = mCodonFreq[33];
mQ[2230] = mCodonFreq[34];
mQ[2231] = aK * mCodonFreq[35];
mQ[2232] = -aOmega * mCodonFreq[7] - aOmega * mCodonFreq[20] -
aK * aOmega * mCodonFreq[32] - mCodonFreq[33] - mCodonFreq[34] -
aK * mCodonFreq[35] - aOmega * mCodonFreq[40] -
aOmega * mCodonFreq[44] - aK * aOmega * mCodonFreq[52];
mQ[2236] = aOmega * mCodonFreq[40];
mQ[2240] = aOmega * mCodonFreq[44];
mQ[2248] = aK * aOmega * mCodonFreq[52];
mQ[2265] = aOmega * mCodonFreq[8];
mQ[2278] = aOmega * mCodonFreq[21];
mQ[2286] = aOmega * mCodonFreq[29];
mQ[2290] = aOmega * mCodonFreq[33];
mQ[2294] = -aOmega * mCodonFreq[8] - aOmega * mCodonFreq[21] -
aOmega * mCodonFreq[29] - aOmega * mCodonFreq[33] -
aK * mCodonFreq[38] - aOmega * mCodonFreq[39] -
aOmega * mCodonFreq[40] - aK * aOmega * mCodonFreq[41] -
aK * aOmega * mCodonFreq[53];
mQ[2295] = aK * mCodonFreq[38];
mQ[2296] = aOmega * mCodonFreq[39];
mQ[2297] = aOmega * mCodonFreq[40];
mQ[2298] = aK * aOmega * mCodonFreq[41];
mQ[2310] = aK * aOmega * mCodonFreq[53];
mQ[2327] = aOmega * mCodonFreq[9];
mQ[2340] = aOmega * mCodonFreq[22];
mQ[2348] = aOmega * mCodonFreq[30];
mQ[2352] = aOmega * mCodonFreq[34];
mQ[2355] = aK * mCodonFreq[37];
mQ[2356] = -aOmega * mCodonFreq[9] - aOmega * mCodonFreq[22] -
aOmega * mCodonFreq[30] - aOmega * mCodonFreq[34] -
aK * mCodonFreq[37] - aOmega * mCodonFreq[39] -
aOmega * mCodonFreq[40] - aK * aOmega * mCodonFreq[42] -
aK * aOmega * mCodonFreq[54];
mQ[2357] = aOmega * mCodonFreq[39];
mQ[2358] = aOmega * mCodonFreq[40];
mQ[2360] = aK * aOmega * mCodonFreq[42];
mQ[2372] = aK * aOmega * mCodonFreq[54];
mQ[2402] = aOmega * mCodonFreq[23];
mQ[2410] = aOmega * mCodonFreq[31];
mQ[2414] = aOmega * mCodonFreq[35];
mQ[2416] = aOmega * mCodonFreq[37];
mQ[2417] = aOmega * mCodonFreq[38];
mQ[2418] = -aOmega * mCodonFreq[23] - aOmega * mCodonFreq[31] -
aOmega * mCodonFreq[35] - aOmega * mCodonFreq[37] -
aOmega * mCodonFreq[38] - aK * mCodonFreq[40] -
aK * aOmega * mCodonFreq[43] - aK * aOmega * mCodonFreq[55];
mQ[2419] = aK * mCodonFreq[40];
mQ[2422] = aK * aOmega * mCodonFreq[43];
mQ[2434] = aK * aOmega * mCodonFreq[55];
mQ[2464] = aOmega * mCodonFreq[24];
mQ[2472] = aOmega * mCodonFreq[32];
mQ[2476] = aOmega * mCodonFreq[36];
mQ[2477] = aOmega * mCodonFreq[37];
mQ[2478] = aOmega * mCodonFreq[38];
mQ[2479] = aK * mCodonFreq[39];
mQ[2480] = -aOmega * mCodonFreq[24] - aOmega * mCodonFreq[32] -
aOmega * mCodonFreq[36] - aOmega * mCodonFreq[37] -
aOmega * mCodonFreq[38] - aK * mCodonFreq[39] -
aK * aOmega * mCodonFreq[44] - aK * aOmega * mCodonFreq[56];
mQ[2484] = aK * aOmega * mCodonFreq[44];
mQ[2496] = aK * aOmega * mCodonFreq[56];
mQ[2511] = aOmega * mCodonFreq[10];
mQ[2526] = aOmega * mCodonFreq[25];
mQ[2530] = aOmega * mCodonFreq[29];
mQ[2534] = aOmega * mCodonFreq[33];
mQ[2538] = aK * aOmega * mCodonFreq[37];
mQ[2542] = -aOmega * mCodonFreq[10] - aOmega * mCodonFreq[25] -
aOmega * mCodonFreq[29] - aOmega * mCodonFreq[33] -
aK * aOmega * mCodonFreq[37] - aK * mCodonFreq[42] -
aOmega * mCodonFreq[43] - aOmega * mCodonFreq[44] -
aK * aOmega * mCodonFreq[57];
mQ[2543] = aK * mCodonFreq[42];
mQ[2544] = aOmega * mCodonFreq[43];
mQ[2545] = aOmega * mCodonFreq[44];
mQ[2558] = aK * aOmega * mCodonFreq[57];
mQ[2573] = aOmega * mCodonFreq[11];
mQ[2588] = aOmega * mCodonFreq[26];
mQ[2592] = aOmega * mCodonFreq[30];
mQ[2596] = aOmega * mCodonFreq[34];
mQ[2600] = aK * aOmega * mCodonFreq[38];
mQ[2603] = aK * mCodonFreq[41];
mQ[2604] = -aOmega * mCodonFreq[11] - aOmega * mCodonFreq[26] -
aOmega * mCodonFreq[30] - aOmega * mCodonFreq[34] -
aK * aOmega * mCodonFreq[38] - aK * mCodonFreq[41] -
aOmega * mCodonFreq[43] - aOmega * mCodonFreq[44] -
aK * aOmega * mCodonFreq[58];
mQ[2605] = aOmega * mCodonFreq[43];
mQ[2606] = aOmega * mCodonFreq[44];
mQ[2620] = aK * aOmega * mCodonFreq[58];
mQ[2650] = mCodonFreq[27];
mQ[2654] = aOmega * mCodonFreq[31];
mQ[2658] = aOmega * mCodonFreq[35];
mQ[2662] = aK * aOmega * mCodonFreq[39];
mQ[2664] = aOmega * mCodonFreq[41];
mQ[2665] = aOmega * mCodonFreq[42];
mQ[2666] = -mCodonFreq[27] - aOmega * mCodonFreq[31] -
aOmega * mCodonFreq[35] - aK * aOmega * mCodonFreq[39] -
aOmega * mCodonFreq[41] - aOmega * mCodonFreq[42] -
aK * mCodonFreq[44] - aK * aOmega * mCodonFreq[59];
mQ[2667] = aK * mCodonFreq[44];
mQ[2682] = aK * aOmega * mCodonFreq[59];
mQ[2696] = aOmega * mCodonFreq[12];
mQ[2712] = mCodonFreq[28];
mQ[2716] = aOmega * mCodonFreq[32];
mQ[2720] = aOmega * mCodonFreq[36];
mQ[2724] = aK * aOmega * mCodonFreq[40];
mQ[2725] = aOmega * mCodonFreq[41];
mQ[2726] = aOmega * mCodonFreq[42];
mQ[2727] = aK * mCodonFreq[43];
mQ[2728] = -aOmega * mCodonFreq[12] - mCodonFreq[28] -
aOmega * mCodonFreq[32] - aOmega * mCodonFreq[36] -
aK * aOmega * mCodonFreq[40] - aOmega * mCodonFreq[41] -
aOmega * mCodonFreq[42] - aK * mCodonFreq[43] -
aK * aOmega * mCodonFreq[60];
mQ[2744] = aK * aOmega * mCodonFreq[60];
mQ[2745] = aOmega * mCodonFreq[0];
mQ[2758] = aOmega * mCodonFreq[13];
mQ[2774] = aK * aOmega * mCodonFreq[29];
mQ[2790] = -aOmega * mCodonFreq[0] - aOmega * mCodonFreq[13] -
aK * aOmega * mCodonFreq[29] - aK * mCodonFreq[46] -
mCodonFreq[47] - mCodonFreq[48] - aK * aOmega * mCodonFreq[49] -
aOmega * mCodonFreq[53] - aOmega * mCodonFreq[57];
mQ[2791] = aK * mCodonFreq[46];
mQ[2792] = mCodonFreq[47];
mQ[2793] = mCodonFreq[48];
mQ[2794] = aK * aOmega * mCodonFreq[49];
mQ[2798] = aOmega * mCodonFreq[53];
mQ[2802] = aOmega * mCodonFreq[57];
mQ[2807] = aOmega * mCodonFreq[1];
mQ[2820] = aOmega * mCodonFreq[14];
mQ[2836] = aK * aOmega * mCodonFreq[30];
mQ[2851] = aK * mCodonFreq[45];
mQ[2852] = -aOmega * mCodonFreq[1] - aOmega * mCodonFreq[14] -
aK * aOmega * mCodonFreq[30] - aK * mCodonFreq[45] -
mCodonFreq[47] - mCodonFreq[48] - aK * aOmega * mCodonFreq[50] -
aOmega * mCodonFreq[54] - aOmega * mCodonFreq[58];
mQ[2853] = mCodonFreq[47];
mQ[2854] = mCodonFreq[48];
mQ[2856] = aK * aOmega * mCodonFreq[50];
mQ[2860] = aOmega * mCodonFreq[54];
mQ[2864] = aOmega * mCodonFreq[58];
mQ[2869] = aOmega * mCodonFreq[2];
mQ[2882] = aOmega * mCodonFreq[15];
mQ[2898] = aK * aOmega * mCodonFreq[31];
mQ[2912] = mCodonFreq[45];
mQ[2913] = mCodonFreq[46];
mQ[2914] = -aOmega * mCodonFreq[2] - aOmega * mCodonFreq[15] -
aK * aOmega * mCodonFreq[31] - mCodonFreq[45] - mCodonFreq[46] -
aK * mCodonFreq[48] - aK * aOmega * mCodonFreq[51] -
aOmega * mCodonFreq[55] - aOmega * mCodonFreq[59];
mQ[2915] = aK * mCodonFreq[48];
mQ[2918] = aK * aOmega * mCodonFreq[51];
mQ[2922] = aOmega * mCodonFreq[55];
mQ[2926] = aOmega * mCodonFreq[59];
mQ[2931] = aOmega * mCodonFreq[3];
mQ[2944] = aOmega * mCodonFreq[16];
mQ[2960] = aK * aOmega * mCodonFreq[32];
mQ[2973] = mCodonFreq[45];
mQ[2974] = mCodonFreq[46];
mQ[2975] = aK * mCodonFreq[47];
mQ[2976] = -aOmega * mCodonFreq[3] - aOmega * mCodonFreq[16] -
aK * aOmega * mCodonFreq[32] - mCodonFreq[45] - mCodonFreq[46] -
aK * mCodonFreq[47] - aK * aOmega * mCodonFreq[52] -
aOmega * mCodonFreq[56] - aOmega * mCodonFreq[60];
mQ[2980] = aK * aOmega * mCodonFreq[52];
mQ[2984] = aOmega * mCodonFreq[56];
mQ[2988] = aOmega * mCodonFreq[60];
mQ[2993] = aOmega * mCodonFreq[4];
mQ[3006] = aOmega * mCodonFreq[17];
mQ[3022] = aK * aOmega * mCodonFreq[33];
mQ[3034] = aK * aOmega * mCodonFreq[45];
mQ[3038] = -aOmega * mCodonFreq[4] - aOmega * mCodonFreq[17] -
aK * aOmega * mCodonFreq[33] - aK * aOmega * mCodonFreq[45] -
aK * mCodonFreq[50] - mCodonFreq[51] - mCodonFreq[52] -
aOmega * mCodonFreq[53] - aOmega * mCodonFreq[57];
mQ[3039] = aK * mCodonFreq[50];
mQ[3040] = mCodonFreq[51];
mQ[3041] = mCodonFreq[52];
mQ[3042] = aOmega * mCodonFreq[53];
mQ[3046] = aOmega * mCodonFreq[57];
mQ[3055] = aOmega * mCodonFreq[5];
mQ[3068] = aOmega * mCodonFreq[18];
mQ[3084] = aK * aOmega * mCodonFreq[34];
mQ[3096] = aK * aOmega * mCodonFreq[46];
mQ[3099] = aK * mCodonFreq[49];
mQ[3100] = -aOmega * mCodonFreq[5] - aOmega * mCodonFreq[18] -
aK * aOmega * mCodonFreq[34] - aK * aOmega * mCodonFreq[46] -
aK * mCodonFreq[49] - mCodonFreq[51] - mCodonFreq[52] -
aOmega * mCodonFreq[54] - aOmega * mCodonFreq[58];
mQ[3101] = mCodonFreq[51];
mQ[3102] = mCodonFreq[52];
mQ[3104] = aOmega * mCodonFreq[54];
mQ[3108] = aOmega * mCodonFreq[58];
mQ[3117] = aOmega * mCodonFreq[6];
mQ[3130] = aOmega * mCodonFreq[19];
mQ[3146] = aK * aOmega * mCodonFreq[35];
mQ[3158] = aK * aOmega * mCodonFreq[47];
mQ[3160] = mCodonFreq[49];
mQ[3161] = mCodonFreq[50];
mQ[3162] = -aOmega * mCodonFreq[6] - aOmega * mCodonFreq[19] -
aK * aOmega * mCodonFreq[35] - aK * aOmega * mCodonFreq[47] -
mCodonFreq[49] - mCodonFreq[50] - aK * mCodonFreq[52] -
aOmega * mCodonFreq[55] - aOmega * mCodonFreq[59];
mQ[3163] = aK * mCodonFreq[52];
mQ[3166] = aOmega * mCodonFreq[55];
mQ[3170] = aOmega * mCodonFreq[59];
mQ[3179] = aOmega * mCodonFreq[7];
mQ[3192] = aOmega * mCodonFreq[20];
mQ[3208] = aK * aOmega * mCodonFreq[36];
mQ[3220] = aK * aOmega * mCodonFreq[48];
mQ[3221] = mCodonFreq[49];
mQ[3222] = mCodonFreq[50];
mQ[3223] = aK * mCodonFreq[51];
mQ[3224] = -aOmega * mCodonFreq[7] - aOmega * mCodonFreq[20] -
aK * aOmega * mCodonFreq[36] - aK * aOmega * mCodonFreq[48] -
mCodonFreq[49] - mCodonFreq[50] - aK * mCodonFreq[51] -
aOmega * mCodonFreq[56] - aOmega * mCodonFreq[60];
mQ[3228] = aOmega * mCodonFreq[56];
mQ[3232] = aOmega * mCodonFreq[60];
mQ[3241] = aOmega * mCodonFreq[8];
mQ[3254] = aOmega * mCodonFreq[21];
mQ[3270] = aK * aOmega * mCodonFreq[37];
mQ[3278] = aOmega * mCodonFreq[45];
mQ[3282] = aOmega * mCodonFreq[49];
mQ[3286] = -aOmega * mCodonFreq[8] - aOmega * mCodonFreq[21] -
aK * aOmega * mCodonFreq[37] - aOmega * mCodonFreq[45] -
aOmega * mCodonFreq[49] - aK * mCodonFreq[54] -
aOmega * mCodonFreq[55] - aOmega * mCodonFreq[56] -
aK * aOmega * mCodonFreq[57];
mQ[3287] = aK * mCodonFreq[54];
mQ[3288] = aOmega * mCodonFreq[55];
mQ[3289] = aOmega * mCodonFreq[56];
mQ[3290] = aK * aOmega * mCodonFreq[57];
mQ[3303] = aOmega * mCodonFreq[9];
mQ[3316] = aOmega * mCodonFreq[22];
mQ[3332] = aK * aOmega * mCodonFreq[38];
mQ[3340] = aOmega * mCodonFreq[46];
mQ[3344] = aOmega * mCodonFreq[50];
mQ[3347] = aK * mCodonFreq[53];
mQ[3348] = -aOmega * mCodonFreq[9] - aOmega * mCodonFreq[22] -
aK * aOmega * mCodonFreq[38] - aOmega * mCodonFreq[46] -
aOmega * mCodonFreq[50] - aK * mCodonFreq[53] -
aOmega * mCodonFreq[55] - aOmega * mCodonFreq[56] -
aK * aOmega * mCodonFreq[58];
mQ[3349] = aOmega * mCodonFreq[55];
mQ[3350] = aOmega * mCodonFreq[56];
mQ[3352] = aK * aOmega * mCodonFreq[58];
mQ[3378] = aOmega * mCodonFreq[23];
mQ[3394] = aK * aOmega * mCodonFreq[39];
mQ[3402] = aOmega * mCodonFreq[47];
mQ[3406] = aOmega * mCodonFreq[51];
mQ[3408] = aOmega * mCodonFreq[53];
mQ[3409] = aOmega * mCodonFreq[54];
mQ[3410] = -aOmega * mCodonFreq[23] - aK * aOmega * mCodonFreq[39] -
aOmega * mCodonFreq[47] - aOmega * mCodonFreq[51] -
aOmega * mCodonFreq[53] - aOmega * mCodonFreq[54] -
aK * mCodonFreq[56] - aK * aOmega * mCodonFreq[59];
mQ[3411] = aK * mCodonFreq[56];
mQ[3414] = aK * aOmega * mCodonFreq[59];
mQ[3440] = aOmega * mCodonFreq[24];
mQ[3456] = aK * aOmega * mCodonFreq[40];
mQ[3464] = aOmega * mCodonFreq[48];
mQ[3468] = aOmega * mCodonFreq[52];
mQ[3469] = aOmega * mCodonFreq[53];
mQ[3470] = aOmega * mCodonFreq[54];
mQ[3471] = aK * mCodonFreq[55];
mQ[3472] = -aOmega * mCodonFreq[24] - aK * aOmega * mCodonFreq[40] -
aOmega * mCodonFreq[48] - aOmega * mCodonFreq[52] -
aOmega * mCodonFreq[53] - aOmega * mCodonFreq[54] -
aK * mCodonFreq[55] - aK * aOmega * mCodonFreq[60];
mQ[3476] = aK * aOmega * mCodonFreq[60];
mQ[3487] = aOmega * mCodonFreq[10];
mQ[3502] = aOmega * mCodonFreq[25];
mQ[3518] = aK * aOmega * mCodonFreq[41];
mQ[3522] = aOmega * mCodonFreq[45];
mQ[3526] = aOmega * mCodonFreq[49];
mQ[3530] = aK * aOmega * mCodonFreq[53];
mQ[3534] = -aOmega * mCodonFreq[10] - aOmega * mCodonFreq[25] -
aK * aOmega * mCodonFreq[41] - aOmega * mCodonFreq[45] -
aOmega * mCodonFreq[49] - aK * aOmega * mCodonFreq[53] -
aK * mCodonFreq[58] - mCodonFreq[59] - mCodonFreq[60];
mQ[3535] = aK * mCodonFreq[58];
mQ[3536] = mCodonFreq[59];
mQ[3537] = mCodonFreq[60];
mQ[3549] = aOmega * mCodonFreq[11];
mQ[3564] = aOmega * mCodonFreq[26];
mQ[3580] = aK * aOmega * mCodonFreq[42];
mQ[3584] = aOmega * mCodonFreq[46];
mQ[3588] = aOmega * mCodonFreq[50];
mQ[3592] = aK * aOmega * mCodonFreq[54];
mQ[3595] = aK * mCodonFreq[57];
mQ[3596] = -aOmega * mCodonFreq[11] - aOmega * mCodonFreq[26] -
aK * aOmega * mCodonFreq[42] - aOmega * mCodonFreq[46] -
aOmega * mCodonFreq[50] - aK * aOmega * mCodonFreq[54] -
aK * mCodonFreq[57] - mCodonFreq[59] - mCodonFreq[60];
mQ[3597] = mCodonFreq[59];
mQ[3598] = mCodonFreq[60];
mQ[3626] = aOmega * mCodonFreq[27];
mQ[3642] = aK * aOmega * mCodonFreq[43];
mQ[3646] = aOmega * mCodonFreq[47];
mQ[3650] = aOmega * mCodonFreq[51];
mQ[3654] = aK * aOmega * mCodonFreq[55];
mQ[3656] = mCodonFreq[57];
mQ[3657] = mCodonFreq[58];
mQ[3658] = -aOmega * mCodonFreq[27] - aK * aOmega * mCodonFreq[43] -
aOmega * mCodonFreq[47] - aOmega * mCodonFreq[51] -
aK * aOmega * mCodonFreq[55] - mCodonFreq[57] - mCodonFreq[58] -
aK * mCodonFreq[60];
mQ[3659] = aK * mCodonFreq[60];
mQ[3672] = aOmega * mCodonFreq[12];
mQ[3688] = aOmega * mCodonFreq[28];
mQ[3704] = aK * aOmega * mCodonFreq[44];
mQ[3708] = aOmega * mCodonFreq[48];
mQ[3712] = aOmega * mCodonFreq[52];
mQ[3716] = aK * aOmega * mCodonFreq[56];
mQ[3717] = mCodonFreq[57];
mQ[3718] = mCodonFreq[58];
mQ[3719] = aK * mCodonFreq[59];
mQ[3720] = -aOmega * mCodonFreq[12] - aOmega * mCodonFreq[28] -
aK * aOmega * mCodonFreq[44] - aOmega * mCodonFreq[48] -
aOmega * mCodonFreq[52] - aK * aOmega * mCodonFreq[56] -
mCodonFreq[57] - mCodonFreq[58] - aK * mCodonFreq[59];
// Compute the scale factor
double scale_q =
aK * mCodonFreq[0] * mCodonFreq[1] +
aOmega * mCodonFreq[0] * mCodonFreq[2] +
aOmega * mCodonFreq[0] * mCodonFreq[3] +
aK * aOmega * mCodonFreq[0] * mCodonFreq[4] +
aOmega * mCodonFreq[0] * mCodonFreq[8] +
aOmega * mCodonFreq[0] * mCodonFreq[10] +
aK * aOmega * mCodonFreq[0] * mCodonFreq[13] +
aOmega * mCodonFreq[0] * mCodonFreq[29] +
aOmega * mCodonFreq[0] * mCodonFreq[45] +
aOmega * mCodonFreq[1] * mCodonFreq[2] +
aOmega * mCodonFreq[1] * mCodonFreq[3] +
aK * aOmega * mCodonFreq[1] * mCodonFreq[5] +
aOmega * mCodonFreq[1] * mCodonFreq[9] +
aOmega * mCodonFreq[1] * mCodonFreq[11] +
aK * aOmega * mCodonFreq[1] * mCodonFreq[14] +
aOmega * mCodonFreq[1] * mCodonFreq[30] +
aOmega * mCodonFreq[1] * mCodonFreq[46] +
aK * mCodonFreq[2] * mCodonFreq[3] +
aK * aOmega * mCodonFreq[2] * mCodonFreq[6] +
aK * mCodonFreq[2] * mCodonFreq[15] +
aOmega * mCodonFreq[2] * mCodonFreq[31] +
aOmega * mCodonFreq[2] * mCodonFreq[47] +
aK * aOmega * mCodonFreq[3] * mCodonFreq[7] +
aOmega * mCodonFreq[3] * mCodonFreq[12] +
aK * mCodonFreq[3] * mCodonFreq[16] +
aOmega * mCodonFreq[3] * mCodonFreq[32] +
aOmega * mCodonFreq[3] * mCodonFreq[48] +
aK * mCodonFreq[4] * mCodonFreq[5] + mCodonFreq[4] * mCodonFreq[6] +
mCodonFreq[4] * mCodonFreq[7] + aOmega * mCodonFreq[4] * mCodonFreq[8] +
aOmega * mCodonFreq[4] * mCodonFreq[10] +
aK * aOmega * mCodonFreq[4] * mCodonFreq[17] +
aOmega * mCodonFreq[4] * mCodonFreq[33] +
aOmega * mCodonFreq[4] * mCodonFreq[49] + mCodonFreq[5] * mCodonFreq[6] +
mCodonFreq[5] * mCodonFreq[7] + aOmega * mCodonFreq[5] * mCodonFreq[9] +
aOmega * mCodonFreq[5] * mCodonFreq[11] +
aK * aOmega * mCodonFreq[5] * mCodonFreq[18] +
aOmega * mCodonFreq[5] * mCodonFreq[34] +
aOmega * mCodonFreq[5] * mCodonFreq[50] +
aK * mCodonFreq[6] * mCodonFreq[7] +
aK * aOmega * mCodonFreq[6] * mCodonFreq[19] +
aOmega * mCodonFreq[6] * mCodonFreq[35] +
aOmega * mCodonFreq[6] * mCodonFreq[51] +
aOmega * mCodonFreq[7] * mCodonFreq[12] +
aK * aOmega * mCodonFreq[7] * mCodonFreq[20] +
aOmega * mCodonFreq[7] * mCodonFreq[36] +
aOmega * mCodonFreq[7] * mCodonFreq[52] +
aK * mCodonFreq[8] * mCodonFreq[9] +
aK * aOmega * mCodonFreq[8] * mCodonFreq[10] +
aK * aOmega * mCodonFreq[8] * mCodonFreq[21] +
aOmega * mCodonFreq[8] * mCodonFreq[37] +
aOmega * mCodonFreq[8] * mCodonFreq[53] +
aK * aOmega * mCodonFreq[9] * mCodonFreq[11] +
aK * aOmega * mCodonFreq[9] * mCodonFreq[22] +
aOmega * mCodonFreq[9] * mCodonFreq[38] +
aOmega * mCodonFreq[9] * mCodonFreq[54] +
aK * mCodonFreq[10] * mCodonFreq[11] +
aOmega * mCodonFreq[10] * mCodonFreq[12] +
aK * aOmega * mCodonFreq[10] * mCodonFreq[25] +
aOmega * mCodonFreq[10] * mCodonFreq[41] +
aOmega * mCodonFreq[10] * mCodonFreq[57] +
aOmega * mCodonFreq[11] * mCodonFreq[12] +
aK * aOmega * mCodonFreq[11] * mCodonFreq[26] +
aOmega * mCodonFreq[11] * mCodonFreq[42] +
aOmega * mCodonFreq[11] * mCodonFreq[58] +
aK * aOmega * mCodonFreq[12] * mCodonFreq[28] +
aOmega * mCodonFreq[12] * mCodonFreq[44] +
aOmega * mCodonFreq[12] * mCodonFreq[60] +
aK * mCodonFreq[13] * mCodonFreq[14] + mCodonFreq[13] * mCodonFreq[15] +
mCodonFreq[13] * mCodonFreq[16] +
aK * aOmega * mCodonFreq[13] * mCodonFreq[17] +
aOmega * mCodonFreq[13] * mCodonFreq[21] +
aOmega * mCodonFreq[13] * mCodonFreq[25] +
aOmega * mCodonFreq[13] * mCodonFreq[29] +
aOmega * mCodonFreq[13] * mCodonFreq[45] +
mCodonFreq[14] * mCodonFreq[15] + mCodonFreq[14] * mCodonFreq[16] +
aK * aOmega * mCodonFreq[14] * mCodonFreq[18] +
aOmega * mCodonFreq[14] * mCodonFreq[22] +
aOmega * mCodonFreq[14] * mCodonFreq[26] +
aOmega * mCodonFreq[14] * mCodonFreq[30] +
aOmega * mCodonFreq[14] * mCodonFreq[46] +
aK * mCodonFreq[15] * mCodonFreq[16] +
aK * aOmega * mCodonFreq[15] * mCodonFreq[19] +
aOmega * mCodonFreq[15] * mCodonFreq[23] +
aOmega * mCodonFreq[15] * mCodonFreq[27] +
aOmega * mCodonFreq[15] * mCodonFreq[31] +
aOmega * mCodonFreq[15] * mCodonFreq[47] +
aK * aOmega * mCodonFreq[16] * mCodonFreq[20] +
aOmega * mCodonFreq[16] * mCodonFreq[24] +
aOmega * mCodonFreq[16] * mCodonFreq[28] +
aOmega * mCodonFreq[16] * mCodonFreq[32] +
aOmega * mCodonFreq[16] * mCodonFreq[48] +
aK * mCodonFreq[17] * mCodonFreq[18] + mCodonFreq[17] * mCodonFreq[19] +
mCodonFreq[17] * mCodonFreq[20] +
aOmega * mCodonFreq[17] * mCodonFreq[21] +
aOmega * mCodonFreq[17] * mCodonFreq[25] +
aOmega * mCodonFreq[17] * mCodonFreq[33] +
aOmega * mCodonFreq[17] * mCodonFreq[49] +
mCodonFreq[18] * mCodonFreq[19] + mCodonFreq[18] * mCodonFreq[20] +
aOmega * mCodonFreq[18] * mCodonFreq[22] +
aOmega * mCodonFreq[18] * mCodonFreq[26] +
aOmega * mCodonFreq[18] * mCodonFreq[34] +
aOmega * mCodonFreq[18] * mCodonFreq[50] +
aK * mCodonFreq[19] * mCodonFreq[20] +
aOmega * mCodonFreq[19] * mCodonFreq[23] +
aOmega * mCodonFreq[19] * mCodonFreq[27] +
aOmega * mCodonFreq[19] * mCodonFreq[35] +
aOmega * mCodonFreq[19] * mCodonFreq[51] +
aOmega * mCodonFreq[20] * mCodonFreq[24] +
aOmega * mCodonFreq[20] * mCodonFreq[28] +
aOmega * mCodonFreq[20] * mCodonFreq[36] +
aOmega * mCodonFreq[20] * mCodonFreq[52] +
aK * mCodonFreq[21] * mCodonFreq[22] +
aOmega * mCodonFreq[21] * mCodonFreq[23] +
aOmega * mCodonFreq[21] * mCodonFreq[24] +
aK * aOmega * mCodonFreq[21] * mCodonFreq[25] +
aOmega * mCodonFreq[21] * mCodonFreq[37] +
aOmega * mCodonFreq[21] * mCodonFreq[53] +
aOmega * mCodonFreq[22] * mCodonFreq[23] +
aOmega * mCodonFreq[22] * mCodonFreq[24] +
aK * aOmega * mCodonFreq[22] * mCodonFreq[26] +
aOmega * mCodonFreq[22] * mCodonFreq[38] +
aOmega * mCodonFreq[22] * mCodonFreq[54] +
aK * mCodonFreq[23] * mCodonFreq[24] +
aK * aOmega * mCodonFreq[23] * mCodonFreq[27] +
aOmega * mCodonFreq[23] * mCodonFreq[39] +
aOmega * mCodonFreq[23] * mCodonFreq[55] +
aK * aOmega * mCodonFreq[24] * mCodonFreq[28] +
aOmega * mCodonFreq[24] * mCodonFreq[40] +
aOmega * mCodonFreq[24] * mCodonFreq[56] +
aK * mCodonFreq[25] * mCodonFreq[26] + mCodonFreq[25] * mCodonFreq[27] +
mCodonFreq[25] * mCodonFreq[28] +
aOmega * mCodonFreq[25] * mCodonFreq[41] +
aOmega * mCodonFreq[25] * mCodonFreq[57] +
mCodonFreq[26] * mCodonFreq[27] + mCodonFreq[26] * mCodonFreq[28] +
aOmega * mCodonFreq[26] * mCodonFreq[42] +
aOmega * mCodonFreq[26] * mCodonFreq[58] +
aK * mCodonFreq[27] * mCodonFreq[28] + mCodonFreq[27] * mCodonFreq[43] +
aOmega * mCodonFreq[27] * mCodonFreq[59] +
mCodonFreq[28] * mCodonFreq[44] +
aOmega * mCodonFreq[28] * mCodonFreq[60] +
aK * mCodonFreq[29] * mCodonFreq[30] + mCodonFreq[29] * mCodonFreq[31] +
aOmega * mCodonFreq[29] * mCodonFreq[32] +
aK * aOmega * mCodonFreq[29] * mCodonFreq[33] +
aOmega * mCodonFreq[29] * mCodonFreq[37] +
aOmega * mCodonFreq[29] * mCodonFreq[41] +
aK * aOmega * mCodonFreq[29] * mCodonFreq[45] +
mCodonFreq[30] * mCodonFreq[31] +
aOmega * mCodonFreq[30] * mCodonFreq[32] +
aK * aOmega * mCodonFreq[30] * mCodonFreq[34] +
aOmega * mCodonFreq[30] * mCodonFreq[38] +
aOmega * mCodonFreq[30] * mCodonFreq[42] +
aK * aOmega * mCodonFreq[30] * mCodonFreq[46] +
aK * aOmega * mCodonFreq[31] * mCodonFreq[32] +
aK * aOmega * mCodonFreq[31] * mCodonFreq[35] +
aOmega * mCodonFreq[31] * mCodonFreq[39] +
aOmega * mCodonFreq[31] * mCodonFreq[43] +
aK * aOmega * mCodonFreq[31] * mCodonFreq[47] +
aK * aOmega * mCodonFreq[32] * mCodonFreq[36] +
aOmega * mCodonFreq[32] * mCodonFreq[40] +
aOmega * mCodonFreq[32] * mCodonFreq[44] +
aK * aOmega * mCodonFreq[32] * mCodonFreq[48] +
aK * mCodonFreq[33] * mCodonFreq[34] + mCodonFreq[33] * mCodonFreq[35] +
mCodonFreq[33] * mCodonFreq[36] +
aOmega * mCodonFreq[33] * mCodonFreq[37] +
aOmega * mCodonFreq[33] * mCodonFreq[41] +
aK * aOmega * mCodonFreq[33] * mCodonFreq[49] +
mCodonFreq[34] * mCodonFreq[35] + mCodonFreq[34] * mCodonFreq[36] +
aOmega * mCodonFreq[34] * mCodonFreq[38] +
aOmega * mCodonFreq[34] * mCodonFreq[42] +
aK * aOmega * mCodonFreq[34] * mCodonFreq[50] +
aK * mCodonFreq[35] * mCodonFreq[36] +
aOmega * mCodonFreq[35] * mCodonFreq[39] +
aOmega * mCodonFreq[35] * mCodonFreq[43] +
aK * aOmega * mCodonFreq[35] * mCodonFreq[51] +
aOmega * mCodonFreq[36] * mCodonFreq[40] +
aOmega * mCodonFreq[36] * mCodonFreq[44] +
aK * aOmega * mCodonFreq[36] * mCodonFreq[52] +
aK * mCodonFreq[37] * mCodonFreq[38] +
aOmega * mCodonFreq[37] * mCodonFreq[39] +
aOmega * mCodonFreq[37] * mCodonFreq[40] +
aK * aOmega * mCodonFreq[37] * mCodonFreq[41] +
aK * aOmega * mCodonFreq[37] * mCodonFreq[53] +
aOmega * mCodonFreq[38] * mCodonFreq[39] +
aOmega * mCodonFreq[38] * mCodonFreq[40] +
aK * aOmega * mCodonFreq[38] * mCodonFreq[42] +
aK * aOmega * mCodonFreq[38] * mCodonFreq[54] +
aK * mCodonFreq[39] * mCodonFreq[40] +
aK * aOmega * mCodonFreq[39] * mCodonFreq[43] +
aK * aOmega * mCodonFreq[39] * mCodonFreq[55] +
aK * aOmega * mCodonFreq[40] * mCodonFreq[44] +
aK * aOmega * mCodonFreq[40] * mCodonFreq[56] +
aK * mCodonFreq[41] * mCodonFreq[42] +
aOmega * mCodonFreq[41] * mCodonFreq[43] +
aOmega * mCodonFreq[41] * mCodonFreq[44] +
aK * aOmega * mCodonFreq[41] * mCodonFreq[57] +
aOmega * mCodonFreq[42] * mCodonFreq[43] +
aOmega * mCodonFreq[42] * mCodonFreq[44] +
aK * aOmega * mCodonFreq[42] * mCodonFreq[58] +
aK * mCodonFreq[43] * mCodonFreq[44] +
aK * aOmega * mCodonFreq[43] * mCodonFreq[59] +
aK * aOmega * mCodonFreq[44] * mCodonFreq[60] +
aK * mCodonFreq[45] * mCodonFreq[46] + mCodonFreq[45] * mCodonFreq[47] +
mCodonFreq[45] * mCodonFreq[48] +
aK * aOmega * mCodonFreq[45] * mCodonFreq[49] +
aOmega * mCodonFreq[45] * mCodonFreq[53] +
aOmega * mCodonFreq[45] * mCodonFreq[57] +
mCodonFreq[46] * mCodonFreq[47] + mCodonFreq[46] * mCodonFreq[48] +
aK * aOmega * mCodonFreq[46] * mCodonFreq[50] +
aOmega * mCodonFreq[46] * mCodonFreq[54] +
aOmega * mCodonFreq[46] * mCodonFreq[58] +