// VT.java // // (c) 1999-2001 PAL Development Core Team // // This package may be distributed under the // terms of the Lesser GNU General Public License (LGPL) package pal.substmodel; import pal.misc.*; import pal.util.*; import java.io.*; /** * VT (variable time matrix) model of amino acid evolution * Modeling Amino Acid Replacement Mueller, T. and Vingron, M., 2000. Journal of Computational Biology, 7(6):761-776. * * @version $Id: VT.java,v 1.7 2003/11/13 04:05:39 matt Exp $ * * @author Korbinian Strimmer * @author Alexei Drummond */ public class VT extends AminoAcidModel implements XMLConstants { /** * constructor * * @param f amino acid frequencies */ public VT(double[] f) { super(f); } // Get numerical code describing the model type public int getModelID() { return 4; } public void report(PrintWriter out) { out.println("Model of substitution: VT (Mueller-Vingron 2000)"); out.println(); printFrequencies(out); } /** * get the frequencies of the original data set that * formed the basis for the estimation of the rate matrix * * @param f array where amino acid frequencies will be stored */ public static void getOriginalFrequencies(double[] f) { f[0]=0.078837 ; f[1]=0.051238 ; f[2]=0.042313 ; f[3]=0.053066 ; f[4]=0.015175 ; f[5]=0.036713 ; f[6]=0.061924 ; f[7]=0.070852 ; f[8]=0.023082 ; f[9]=0.062056 ; f[10]=0.096371 ; f[11]=0.057324 ; f[12]=0.023771 ; f[13]=0.043296 ; f[14]=0.043911 ; f[15]=0.063403 ; f[16]=0.055897 ; f[17]=0.013272 ; f[18]=0.034399 ; f[19]=0.073101 ; } /** * @return the frequencies of the original data set that * formed the basis for the estimation of the rate matrix */ public static double[] getOriginalFrequencies() { double[] f = new double[20]; getOriginalFrequencies(f); return f; } public String getUniqueName() { return VT; } // // Private stuff // // VT model of amino acid evolution // Mueller, T. and Vingron, M. 2000. J. Comp. Biol.?:?-?. protected void rebuildRateMatrix(double[][] rate, double[] parameters) { // Q matrix rate[0][1] = 0.233108 ; rate[0][2] = 0.199097 ; rate[0][3] = 0.265145 ; rate[0][4] = 0.227333 ; rate[0][5] = 0.310084 ; rate[0][6] = 0.567957 ; rate[0][7] = 0.876213 ; rate[0][8] = 0.078692 ; rate[0][9] = 0.222972 ; rate[0][10] = 0.424630 ; rate[0][11] = 0.393245 ; rate[0][12] = 0.211550 ; rate[0][13] = 0.116646 ; rate[0][14] = 0.399143 ; rate[0][15] = 1.817198 ; rate[0][16] = 0.877877 ; rate[0][17] = 0.030309 ; rate[0][18] = 0.087061 ; rate[0][19] = 1.230985 ; rate[1][2] = 0.210797 ; rate[1][3] = 0.105191 ; rate[1][4] = 0.031726 ; rate[1][5] = 0.493763 ; rate[1][6] = 0.255240 ; rate[1][7] = 0.156945 ; rate[1][8] = 0.213164 ; rate[1][9] = 0.081510 ; rate[1][10] = 0.192364 ; rate[1][11] = 1.755838 ; rate[1][12] = 0.087930 ; rate[1][13] = 0.042569 ; rate[1][14] = 0.128480 ; rate[1][15] = 0.292327 ; rate[1][16] = 0.204109 ; rate[1][17] = 0.046417 ; rate[1][18] = 0.097010 ; rate[1][19] = 0.113146 ; rate[2][3] = 0.883422 ; rate[2][4] = 0.027495 ; rate[2][5] = 0.275700 ; rate[2][6] = 0.270417 ; rate[2][7] = 0.362028 ; rate[2][8] = 0.290006 ; rate[2][9] = 0.087225 ; rate[2][10] = 0.069245 ; rate[2][11] = 0.503060 ; rate[2][12] = 0.057420 ; rate[2][13] = 0.039769 ; rate[2][14] = 0.083956 ; rate[2][15] = 0.847049 ; rate[2][16] = 0.471268 ; rate[2][17] = 0.010459 ; rate[2][18] = 0.093268 ; rate[2][19] = 0.049824 ; rate[3][4] = 0.010313 ; rate[3][5] = 0.205842 ; rate[3][6] = 1.599461 ; rate[3][7] = 0.311718 ; rate[3][8] = 0.134252 ; rate[3][9] = 0.011720 ; rate[3][10] = 0.060863 ; rate[3][11] = 0.261101 ; rate[3][12] = 0.012182 ; rate[3][13] = 0.016577 ; rate[3][14] = 0.160063 ; rate[3][15] = 0.461519 ; rate[3][16] = 0.178197 ; rate[3][17] = 0.011393 ; rate[3][18] = 0.051664 ; rate[3][19] = 0.048769 ; rate[4][5] = 0.004315 ; rate[4][6] = 0.005321 ; rate[4][7] = 0.050876 ; rate[4][8] = 0.016695 ; rate[4][9] = 0.046398 ; rate[4][10] = 0.091709 ; rate[4][11] = 0.004067 ; rate[4][12] = 0.023690 ; rate[4][13] = 0.051127 ; rate[4][14] = 0.011137 ; rate[4][15] = 0.175270 ; rate[4][16] = 0.079511 ; rate[4][17] = 0.007732 ; rate[4][18] = 0.042823 ; rate[4][19] = 0.163831 ; rate[5][6] = 0.960976 ; rate[5][7] = 0.128660 ; rate[5][8] = 0.315521 ; rate[5][9] = 0.054602 ; rate[5][10] = 0.243530 ; rate[5][11] = 0.738208 ; rate[5][12] = 0.120801 ; rate[5][13] = 0.026235 ; rate[5][14] = 0.156570 ; rate[5][15] = 0.358017 ; rate[5][16] = 0.248992 ; rate[5][17] = 0.021248 ; rate[5][18] = 0.062544 ; rate[5][19] = 0.112027 ; rate[6][7] = 0.250447 ; rate[6][8] = 0.104458 ; rate[6][9] = 0.046589 ; rate[6][10] = 0.151924 ; rate[6][11] = 0.888630 ; rate[6][12] = 0.058643 ; rate[6][13] = 0.028168 ; rate[6][14] = 0.205134 ; rate[6][15] = 0.406035 ; rate[6][16] = 0.321028 ; rate[6][17] = 0.018844 ; rate[6][18] = 0.055200 ; rate[6][19] = 0.205868 ; rate[7][8] = 0.058131 ; rate[7][9] = 0.051089 ; rate[7][10] = 0.087056 ; rate[7][11] = 0.193243 ; rate[7][12] = 0.046560 ; rate[7][13] = 0.050143 ; rate[7][14] = 0.124492 ; rate[7][15] = 0.612843 ; rate[7][16] = 0.136266 ; rate[7][17] = 0.023990 ; rate[7][18] = 0.037568 ; rate[7][19] = 0.082579 ; rate[8][9] = 0.020039 ; rate[8][10] = 0.103552 ; rate[8][11] = 0.153323 ; rate[8][12] = 0.021157 ; rate[8][13] = 0.079807 ; rate[8][14] = 0.078892 ; rate[8][15] = 0.167406 ; rate[8][16] = 0.101117 ; rate[8][17] = 0.020009 ; rate[8][18] = 0.286027 ; rate[8][19] = 0.068575 ; rate[9][10] = 2.089890 ; rate[9][11] = 0.093181 ; rate[9][12] = 0.493845 ; rate[9][13] = 0.321020 ; rate[9][14] = 0.054797 ; rate[9][15] = 0.081567 ; rate[9][16] = 0.376588 ; rate[9][17] = 0.034954 ; rate[9][18] = 0.086237 ; rate[9][19] = 3.654430 ; rate[10][11] = 0.201204 ; rate[10][12] = 1.105667 ; rate[10][13] = 0.946499 ; rate[10][14] = 0.169784 ; rate[10][15] = 0.214977 ; rate[10][16] = 0.243227 ; rate[10][17] = 0.083439 ; rate[10][18] = 0.189842 ; rate[10][19] = 1.337571 ; rate[11][12] = 0.096474 ; rate[11][13] = 0.038261 ; rate[11][14] = 0.212302 ; rate[11][15] = 0.400072 ; rate[11][16] = 0.446646 ; rate[11][17] = 0.023321 ; rate[11][18] = 0.068689 ; rate[11][19] = 0.144587 ; rate[12][13] = 0.173052 ; rate[12][14] = 0.010363 ; rate[12][15] = 0.090515 ; rate[12][16] = 0.184609 ; rate[12][17] = 0.022019 ; rate[12][18] = 0.073223 ; rate[12][19] = 0.307309 ; rate[13][14] = 0.042564 ; rate[13][15] = 0.138119 ; rate[13][16] = 0.085870 ; rate[13][17] = 0.128050 ; rate[13][18] = 0.898663 ; rate[13][19] = 0.247329 ; rate[14][15] = 0.430431 ; rate[14][16] = 0.207143 ; rate[14][17] = 0.014584 ; rate[14][18] = 0.032043 ; rate[14][19] = 0.129315 ; rate[15][16] = 1.767766 ; rate[15][17] = 0.035933 ; rate[15][18] = 0.121979 ; rate[15][19] = 0.127700 ; rate[16][17] = 0.020437 ; rate[16][18] = 0.094617 ; rate[16][19] = 0.740372 ; rate[17][18] = 0.124746 ; rate[17][19] = 0.022134 ; rate[18][19] = 0.125733 ; } }