/*
* LG.java
*
* Copyright (c) 2002-2016 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.evomodel.substmodel.aminoacid;
import dr.evomodel.substmodel.EmpiricalRateMatrix;
import dr.evolution.datatype.AminoAcids;
import dr.util.Author;
import dr.util.Citation;
import java.util.Collections;
import java.util.List;
/**
* LG model of amino acid evolution (Le and Gascuel, 2008)
* Le, S. Q. and O. Gascuel. 2008. Mol. Biol. Evol. 25(7):1307-1320.
*
* @author Guy Baele
*/
public class LG extends EmpiricalRateMatrix.AbstractAminoAcid {
public static final LG INSTANCE = new LG();
// 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 LG() { super("LG");
int n = AminoAcids.INSTANCE.getStateCount();
double[][] rate = new double[n][n];
// Q matrix
rate[0][1] = 0.425093;
rate[0][2] = 0.276818;
rate[0][3] = 0.395144;
rate[0][4] = 2.489084;
rate[0][5] = 0.969894;
rate[0][6] = 1.038545;
rate[0][7] = 2.066040;
rate[0][8] = 0.358858;
rate[0][9] = 0.149830;
rate[0][10] = 0.395337;
rate[0][11] = 0.536518;
rate[0][12] = 1.124035;
rate[0][13] = 0.253701;
rate[0][14] = 1.177651;
rate[0][15] = 4.727182;
rate[0][16] = 2.139501;
rate[0][17] = 0.180717;
rate[0][18] = 0.218959;
rate[0][19] = 2.547870;
rate[1][2] = 0.751878;
rate[1][3] = 0.123954;
rate[1][4] = 0.534551;
rate[1][5] = 2.807908;
rate[1][6] = 0.363970;
rate[1][7] = 0.390192;
rate[1][8] = 2.426601;
rate[1][9] = 0.126991;
rate[1][10] = 0.301848;
rate[1][11] = 6.326067;
rate[1][12] = 0.484133;
rate[1][13] = 0.052722;
rate[1][14] = 0.332533;
rate[1][15] = 0.858151;
rate[1][16] = 0.578987;
rate[1][17] = 0.593607;
rate[1][18] = 0.314440;
rate[1][19] = 0.170887;
rate[2][3] = 5.076149;
rate[2][4] = 0.528768;
rate[2][5] = 1.695752;
rate[2][6] = 0.541712;
rate[2][7] = 1.437645;
rate[2][8] = 4.509238;
rate[2][9] = 0.191503;
rate[2][10] = 0.068427;
rate[2][11] = 2.145078;
rate[2][12] = 0.371004;
rate[2][13] = 0.089525;
rate[2][14] = 0.161787;
rate[2][15] = 4.008358;
rate[2][16] = 2.000679;
rate[2][17] = 0.045376;
rate[2][18] = 0.612025;
rate[2][19] = 0.083688;
rate[3][4] = 0.062556;
rate[3][5] = 0.523386;
rate[3][6] = 5.243870;
rate[3][7] = 0.844926;
rate[3][8] = 0.927114;
rate[3][9] = 0.010690;
rate[3][10] = 0.015076;
rate[3][11] = 0.282959;
rate[3][12] = 0.025548;
rate[3][13] = 0.017416;
rate[3][14] = 0.394456;
rate[3][15] = 1.240275;
rate[3][16] = 0.425860;
rate[3][17] = 0.029890;
rate[3][18] = 0.135107;
rate[3][19] = 0.037967;
rate[4][5] = 0.084808;
rate[4][6] = 0.003499;
rate[4][7] = 0.569265;
rate[4][8] = 0.640543;
rate[4][9] = 0.320627;
rate[4][10] = 0.594007;
rate[4][11] = 0.013266;
rate[4][12] = 0.893680;
rate[4][13] = 1.105251;
rate[4][14] = 0.075382;
rate[4][15] = 2.784478;
rate[4][16] = 1.143480;
rate[4][17] = 0.670128;
rate[4][18] = 1.165532;
rate[4][19] = 1.959291;
rate[5][6] = 4.128591;
rate[5][7] = 0.267959;
rate[5][8] = 4.813505;
rate[5][9] = 0.072854;
rate[5][10] = 0.582457;
rate[5][11] = 3.234294;
rate[5][12] = 1.672569;
rate[5][13] = 0.035855;
rate[5][14] = 0.624294;
rate[5][15] = 1.223828;
rate[5][16] = 1.080136;
rate[5][17] = 0.236199;
rate[5][18] = 0.257336;
rate[5][19] = 0.210332;
rate[6][7] = 0.348847;
rate[6][8] = 0.423881;
rate[6][9] = 0.044265;
rate[6][10] = 0.069673;
rate[6][11] = 1.807177;
rate[6][12] = 0.173735;
rate[6][13] = 0.018811;
rate[6][14] = 0.419409;
rate[6][15] = 0.611973;
rate[6][16] = 0.604545;
rate[6][17] = 0.077852;
rate[6][18] = 0.120037;
rate[6][19] = 0.245034;
rate[7][8] = 0.311484;
rate[7][9] = 0.008705;
rate[7][10] = 0.044261;
rate[7][11] = 0.296636;
rate[7][12] = 0.139538;
rate[7][13] = 0.089586;
rate[7][14] = 0.196961;
rate[7][15] = 1.739990;
rate[7][16] = 0.129836;
rate[7][17] = 0.268491;
rate[7][18] = 0.054679;
rate[7][19] = 0.076701;
rate[8][9] = 0.108882;
rate[8][10] = 0.366317;
rate[8][11] = 0.697264;
rate[8][12] = 0.442472;
rate[8][13] = 0.682139;
rate[8][14] = 0.508851;
rate[8][15] = 0.990012;
rate[8][16] = 0.584262;
rate[8][17] = 0.597054;
rate[8][18] = 5.306834;
rate[8][19] = 0.119013;
rate[9][10] = 4.145067;
rate[9][11] = 0.159069;
rate[9][12] = 4.273607;
rate[9][13] = 1.112727;
rate[9][14] = 0.078281;
rate[9][15] = 0.064105;
rate[9][16] = 1.033739;
rate[9][17] = 0.111660;
rate[9][18] = 0.232523;
rate[9][19] = 10.649107;
rate[10][11] = 0.137500;
rate[10][12] = 6.312358;
rate[10][13] = 2.592692;
rate[10][14] = 0.249060;
rate[10][15] = 0.182287;
rate[10][16] = 0.302936;
rate[10][17] = 0.619632;
rate[10][18] = 0.299648;
rate[10][19] = 1.702745;
rate[11][12] = 0.656604;
rate[11][13] = 0.023918;
rate[11][14] = 0.390322;
rate[11][15] = 0.748683;
rate[11][16] = 1.136863;
rate[11][17] = 0.049906;
rate[11][18] = 0.131932;
rate[11][19] = 0.185202;
rate[12][13] = 1.798853;
rate[12][14] = 0.099849;
rate[12][15] = 0.346960;
rate[12][16] = 2.020366;
rate[12][17] = 0.696175;
rate[12][18] = 0.481306;
rate[12][19] = 1.898718;
rate[13][14] = 0.094464;
rate[13][15] = 0.361819;
rate[13][16] = 0.165001;
rate[13][17] = 2.457121;
rate[13][18] = 7.803902;
rate[13][19] = 0.654683;
rate[14][15] = 1.338132;
rate[14][16] = 0.571468;
rate[14][17] = 0.095131;
rate[14][18] = 0.089613;
rate[14][19] = 0.296501;
rate[15][16] = 6.472279;
rate[15][17] = 0.248862;
rate[15][18] = 0.400547;
rate[15][19] = 0.098369;
rate[16][17] = 0.140825;
rate[16][18] = 0.245841;
rate[16][19] = 2.188158;
rate[17][18] = 3.151815;
rate[17][19] = 0.189510;
rate[18][19] = 0.249313;
setEmpiricalRates(rate, "ARNDCQEGHILKMFPSTWYV");
//the order of the amino acid codes below
//Ala = A
//Arg = R
//Asn = N
//Asp = D
//Cys = C
//Gln = Q
//Glu = E
//Gly = G
//His = H
//Ile = I
//Leu = L
//Lys = K
//Met = M
//Phe = F
//Pro = P
//Ser = S
//Thr = T
//Trp = W
//Tyr = Y
//Val = V
double[] f = new double[n];
f[0] = 0.079066;
f[1] = 0.055941;
f[2] = 0.041977;
f[3] = 0.053052;
f[4] = 0.012937;
f[5] = 0.040767;
f[6] = 0.071586;
f[7] = 0.057337;
f[8] = 0.022355;
f[9] = 0.062157;
f[10] = 0.099081;
f[11] = 0.064600;
f[12] = 0.022951;
f[13] = 0.042302;
f[14] = 0.044040;
f[15] = 0.061197;
f[16] = 0.053287;
f[17] = 0.012066;
f[18] = 0.034155;
f[19] = 0.069147;
setEmpiricalFrequencies(f, "ARNDCQEGHILKMFPSTWYV");
}
@Override
public Citation.Category getCategory() {
return Citation.Category.SUBSTITUTION_MODELS;
}
@Override
public String getDescription() {
return "LG amino acid substitution model";
}
@Override
public List<Citation> getCitations() {
return Collections.singletonList(CITATION);
}
public static Citation CITATION = new Citation(
new Author[]{
new Author("S. Q.", "Le"),
new Author("O.", "Gascuel")
},
"An Improved General Amino Acid Replacement Matrix",
2008,
"Mol. Biol. Evol.",
25,
1307, 1320,
Citation.Status.PUBLISHED
);
}