/*
* WAG.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.oldevomodel.substmodel;
import dr.evolution.datatype.AminoAcids;
import dr.util.Author;
import dr.util.Citation;
import java.util.*;
/**
* WAG model of amino acid evolution (S. Whelan and N. Goldman 2000)
* Whelan, S. and N. Goldman. 2000. Bioinformatics ?.
*
* @version $Id: WAG.java,v 1.3 2005/05/24 20:25:58 rambaut Exp $
*
* @author Andrew Rambaut
* @author Alexei Drummond
*/
public class WAG extends EmpiricalRateMatrix.AbstractAminoAcid {
public static final WAG INSTANCE = new WAG();
// The rates below are specified assuming that the amino acids are in this order:
// ARNDCQEGHILKMFPSTWYV
// but the AminoAcids dataType wants them in this order:
// ACDEFGHIKLMNPQRSTVWY
// This is solved by calling the setEmpiricalRates and setEmpiricalFrequencies methods
private WAG() { super("WAG");
int n = AminoAcids.INSTANCE.getStateCount();
double[][] rate = new double[n][n];
// Q matrix
rate[0][1] = 0.610810; rate[0][2] = 0.569079;
rate[0][3] = 0.821500; rate[0][4] = 1.141050;
rate[0][5] = 1.011980; rate[0][6] = 1.756410;
rate[0][7] = 1.572160; rate[0][8] = 0.354813;
rate[0][9] = 0.219023; rate[0][10] = 0.443935;
rate[0][11] = 1.005440; rate[0][12] = 0.989475;
rate[0][13] = 0.233492; rate[0][14] = 1.594890;
rate[0][15] = 3.733380; rate[0][16] = 2.349220;
rate[0][17] = 0.125227; rate[0][18] = 0.268987;
rate[0][19] = 2.221870;
rate[1][2] = 0.711690; rate[1][3] = 0.165074;
rate[1][4] = 0.585809; rate[1][5] = 3.360330;
rate[1][6] = 0.488649; rate[1][7] = 0.650469;
rate[1][8] = 2.362040; rate[1][9] = 0.206722;
rate[1][10] = 0.551450; rate[1][11] = 5.925170;
rate[1][12] = 0.758446; rate[1][13] = 0.116821;
rate[1][14] = 0.753467; rate[1][15] = 1.357640;
rate[1][16] = 0.613776; rate[1][17] = 1.294610;
rate[1][18] = 0.423612; rate[1][19] = 0.280336;
rate[2][3] = 6.013660; rate[2][4] = 0.296524;
rate[2][5] = 1.716740; rate[2][6] = 1.056790;
rate[2][7] = 1.253910; rate[2][8] = 4.378930;
rate[2][9] = 0.615636; rate[2][10] = 0.147156;
rate[2][11] = 3.334390; rate[2][12] = 0.224747;
rate[2][13] = 0.110793; rate[2][14] = 0.217538;
rate[2][15] = 4.394450; rate[2][16] = 2.257930;
rate[2][17] = 0.078463; rate[2][18] = 1.208560;
rate[2][19] = 0.221176;
rate[3][4] = 0.033379; rate[3][5] = 0.691268;
rate[3][6] = 6.833400; rate[3][7] = 0.961142;
rate[3][8] = 1.032910; rate[3][9] = 0.043523;
rate[3][10] = 0.093930; rate[3][11] = 0.533362;
rate[3][12] = 0.116813; rate[3][13] = 0.052004;
rate[3][14] = 0.472601; rate[3][15] = 1.192810;
rate[3][16] = 0.417372; rate[3][17] = 0.146348;
rate[3][18] = 0.363243; rate[3][19] = 0.169417;
rate[4][5] = 0.109261; rate[4][6] = 0.023920;
rate[4][7] = 0.341086; rate[4][8] = 0.275403;
rate[4][9] = 0.189890; rate[4][10] = 0.428414;
rate[4][11] = 0.083649; rate[4][12] = 0.437393;
rate[4][13] = 0.441300; rate[4][14] = 0.122303;
rate[4][15] = 1.560590; rate[4][16] = 0.570186;
rate[4][17] = 0.795736; rate[4][18] = 0.604634;
rate[4][19] = 1.114570;
rate[5][6] = 6.048790; rate[5][7] = 0.366510;
rate[5][8] = 4.749460; rate[5][9] = 0.131046;
rate[5][10] = 0.964886; rate[5][11] = 4.308310;
rate[5][12] = 1.705070; rate[5][13] = 0.110744;
rate[5][14] = 1.036370; rate[5][15] = 1.141210;
rate[5][16] = 0.954144; rate[5][17] = 0.243615;
rate[5][18] = 0.252457; rate[5][19] = 0.333890;
rate[6][7] = 0.630832; rate[6][8] = 0.635025;
rate[6][9] = 0.141320; rate[6][10] = 0.172579;
rate[6][11] = 2.867580; rate[6][12] = 0.353912;
rate[6][13] = 0.092310; rate[6][14] = 0.755791;
rate[6][15] = 0.782467; rate[6][16] = 0.914814;
rate[6][17] = 0.172682; rate[6][18] = 0.217549;
rate[6][19] = 0.655045;
rate[7][8] = 0.276379; rate[7][9] = 0.034151;
rate[7][10] = 0.068651; rate[7][11] = 0.415992;
rate[7][12] = 0.194220; rate[7][13] = 0.055288;
rate[7][14] = 0.273149; rate[7][15] = 1.486700;
rate[7][16] = 0.251477; rate[7][17] = 0.374321;
rate[7][18] = 0.114187; rate[7][19] = 0.209108;
rate[8][9] = 0.152215; rate[8][10] = 0.555096;
rate[8][11] = 0.992083; rate[8][12] = 0.450867;
rate[8][13] = 0.756080; rate[8][14] = 0.771387;
rate[8][15] = 0.822459; rate[8][16] = 0.525511;
rate[8][17] = 0.289998; rate[8][18] = 4.290350;
rate[8][19] = 0.131869;
rate[9][10] = 3.517820; rate[9][11] = 0.360574;
rate[9][12] = 4.714220; rate[9][13] = 1.177640;
rate[9][14] = 0.111502; rate[9][15] = 0.353443;
rate[9][16] = 1.615050; rate[9][17] = 0.234326;
rate[9][18] = 0.468951; rate[9][19] = 8.659740;
rate[10][11] = 0.287583; rate[10][12] = 5.375250;
rate[10][13] = 2.348200; rate[10][14] = 0.462018;
rate[10][15] = 0.382421; rate[10][16] = 0.364222;
rate[10][17] = 0.740259; rate[10][18] = 0.443205;
rate[10][19] = 1.997370;
rate[11][12] = 1.032220; rate[11][13] = 0.098843;
rate[11][14] = 0.619503; rate[11][15] = 1.073780;
rate[11][16] = 1.537920; rate[11][17] = 0.152232;
rate[11][18] = 0.147411; rate[11][19] = 0.342012;
rate[12][13] = 1.320870; rate[12][14] = 0.194864;
rate[12][15] = 0.556353; rate[12][16] = 1.681970;
rate[12][17] = 0.570369; rate[12][18] = 0.473810;
rate[12][19] = 2.282020;
rate[13][14] = 0.179896; rate[13][15] = 0.606814;
rate[13][16] = 0.191467; rate[13][17] = 1.699780;
rate[13][18] = 7.154480; rate[13][19] = 0.725096;
rate[14][15] = 1.786490; rate[14][16] = 0.885349;
rate[14][17] = 0.156619; rate[14][18] = 0.239607;
rate[14][19] = 0.351250;
rate[15][16] = 4.847130; rate[15][17] = 0.578784;
rate[15][18] = 0.872519; rate[15][19] = 0.258861;
rate[16][17] = 0.126678; rate[16][18] = 0.325490;
rate[16][19] = 1.547670;
rate[17][18] = 2.763540; rate[17][19] = 0.409817;
rate[18][19] = 0.347826;
setEmpiricalRates(rate, "ARNDCQEGHILKMFPSTWYV");
double[] f = new double[n];
f[0] = 0.0866;
f[1] = 0.0440;
f[2] = 0.0391;
f[3] = 0.0570;
f[4] = 0.0193;
f[5] = 0.0367;
f[6] = 0.0581;
f[7] = 0.0833;
f[8] = 0.0244;
f[9] = 0.0485;
f[10] = 0.0862;
f[11] = 0.0620;
f[12] = 0.0195;
f[13] = 0.0384;
f[14] = 0.0458;
f[15] = 0.0695;
f[16] = 0.0610;
f[17] = 0.0144;
f[18] = 0.0353;
f[19] = 0.0709;
setEmpiricalFrequencies(f, "ARNDCQEGHILKMFPSTWYV");
}
@Override
public Citation.Category getCategory() {
return Citation.Category.SUBSTITUTION_MODELS;
}
@Override
public String getDescription() {
return "WAG amino acid substitution model";
}
@Override
public List<Citation> getCitations() {
return Collections.singletonList(CITATION);
}
public static Citation CITATION = new Citation(
new Author[]{
new Author("S", "Whelan"),
new Author("N", "Goldman")
},
"A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach",
2001,
"Mol Biol Evol",
18,
691, 699,
Citation.Status.PUBLISHED
);
}