/*
* FLU.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;
/**
* FLU model of amino acid evolution (add reference).
*
* Cuong Cao Dang, Quang Si Le, Olivier Gascuel and Vinh Sy Le (2010)
* FLU, an amino acid substitution model for influenza proteins. BMC Evol Biol 10:99
*
* @version 08/01/2010
*
* @author Marc A. Suchard
* @author Yu-Nong Gong
*/
public class FLU extends EmpiricalRateMatrix.AbstractAminoAcid {
public static final FLU INSTANCE = new FLU();
// 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 FLU() { super("FLU");
int n = AminoAcids.INSTANCE.getStateCount();
double[][] rate = new double[n][n];
// Q matrix
rate[0][1] = 0.138659; rate[0][2] = 0.053367;
rate[0][3] = 0.584852; rate[0][4] = 0.026447;
rate[0][5] = 0.353754; rate[0][6] = 1.484235;
rate[0][7] = 1.132313; rate[0][8] = 0.214758;
rate[0][9] = 0.149927; rate[0][10] = 0.023117;
rate[0][11] = 0.474334; rate[0][12] = 0.058745;
rate[0][13] = 0.080491; rate[0][14] = 0.659311;
rate[0][15] = 3.011345; rate[0][16] = 5.418298;
rate[0][17] = 0.195966; rate[0][18] = 0.018289;
rate[0][19] = 3.532005;
rate[1][2] = 0.161001; rate[1][3] = 0.006772;
rate[1][4] = 0.167207; rate[1][5] = 3.292717;
rate[1][6] = 0.124898; rate[1][7] = 1.190624;
rate[1][8] = 1.879570; rate[1][9] = 0.246117;
rate[1][10] = 0.296046; rate[1][11] = 15.300097;
rate[1][12] = 0.890162; rate[1][13] = 0.016055;
rate[1][14] = 0.154027; rate[1][15] = 0.950138;
rate[1][16] = 0.183077; rate[1][17] = 1.369429;
rate[1][18] = 0.099855; rate[1][19] = 0.103964;
rate[2][3] = 7.737393; rate[2][4] = 0.000013;
rate[2][5] = 0.530643; rate[2][6] = 0.061652;
rate[2][7] = 0.322525; rate[2][8] = 1.387096;
rate[2][9] = 0.218572; rate[2][10] = 0.000836;
rate[2][11] = 2.646848; rate[2][12] = 0.005252;
rate[2][13] = 0.000836; rate[2][14] = 0.036442;
rate[2][15] = 3.881311; rate[2][16] = 2.140332;
rate[2][17] = 0.000536; rate[2][18] = 0.373102;
rate[2][19] = 0.010258;
rate[3][4] = 0.014132; rate[3][5] = 0.145469;
rate[3][6] = 5.370511; rate[3][7] = 1.934833;
rate[3][8] = 0.887571; rate[3][9] = 0.014086;
rate[3][10] = 0.005731; rate[3][11] = 0.290043;
rate[3][12] = 0.041763; rate[3][13] = 0.000001;
rate[3][14] = 0.188539; rate[3][15] = 0.338372;
rate[3][16] = 0.135481; rate[3][17] = 0.000015;
rate[3][18] = 0.525399; rate[3][19] = 0.297124;
rate[4][5] = 0.002547; rate[4][6] = 0.000000;
rate[4][7] = 0.116941; rate[4][8] = 0.021845;
rate[4][9] = 0.001112; rate[4][10] = 0.005614;
rate[4][11] = 0.000004; rate[4][12] = 0.111457;
rate[4][13] = 0.104054; rate[4][14] = 0.000000;
rate[4][15] = 0.336263; rate[4][16] = 0.011975;
rate[4][17] = 0.094107; rate[4][18] = 0.601692;
rate[4][19] = 0.054905;
rate[5][6] = 1.195629; rate[5][7] = 0.108051;
rate[5][8] = 5.330313; rate[5][9] = 0.028840;
rate[5][10] = 1.020367; rate[5][11] = 2.559587;
rate[5][12] = 0.190259; rate[5][13] = 0.032681;
rate[5][14] = 0.712770; rate[5][15] = 0.487822;
rate[5][16] = 0.602341; rate[5][17] = 0.044021;
rate[5][18] = 0.072206; rate[5][19] = 0.406698;
rate[6][7] = 1.593099; rate[6][8] = 0.256492;
rate[6][9] = 0.014211; rate[6][10] = 0.016500;
rate[6][11] = 3.881489; rate[6][12] = 0.313974;
rate[6][13] = 0.001004; rate[6][14] = 0.319559;
rate[6][15] = 0.307140; rate[6][16] = 0.280125;
rate[6][17] = 0.155245; rate[6][18] = 0.104093;
rate[6][19] = 0.285048;
rate[7][8] = 0.058775; rate[7][9] = 0.000016;
rate[7][10] = 0.006516; rate[7][11] = 0.264149;
rate[7][12] = 0.001500; rate[7][13] = 0.001237;
rate[7][14] = 0.038632; rate[7][15] = 1.585647;
rate[7][16] = 0.018808; rate[7][17] = 0.196486;
rate[7][18] = 0.074815; rate[7][19] = 0.337230;
rate[8][9] = 0.243190; rate[8][10] = 0.321612;
rate[8][11] = 0.347303; rate[8][12] = 0.001274;
rate[8][13] = 0.119029; rate[8][14] = 0.924467;
rate[8][15] = 0.580704; rate[8][16] = 0.368714;
rate[8][17] = 0.022373; rate[8][18] = 6.448954;
rate[8][19] = 0.098631;
rate[9][10] = 3.512072; rate[9][11] = 0.227708;
rate[9][12] = 9.017954; rate[9][13] = 1.463357;
rate[9][14] = 0.080543; rate[9][15] = 0.290381;
rate[9][16] = 2.904052; rate[9][17] = 0.032132;
rate[9][18] = 0.273934; rate[9][19] = 14.394052;
rate[10][11] = 0.129224; rate[10][12] = 6.746936;
rate[10][13] = 2.986800; rate[10][14] = 0.634309;
rate[10][15] = 0.570767; rate[10][16] = 0.044926;
rate[10][17] = 0.431278; rate[10][18] = 0.340058;
rate[10][19] = 0.890599;
rate[11][12] = 1.331292; rate[11][13] = 0.319896;
rate[11][14] = 0.195751; rate[11][15] = 0.283808;
rate[11][16] = 1.526964; rate[11][17] = 0.000050;
rate[11][18] = 0.012416; rate[11][19] = 0.073128;
rate[12][13] = 0.279911; rate[12][14] = 0.056869;
rate[12][15] = 0.007027; rate[12][16] = 2.031511;
rate[12][17] = 0.070460; rate[12][18] = 0.874272;
rate[12][19] = 4.904842;
rate[13][14] = 0.007132; rate[13][15] = 0.996686;
rate[13][16] = 0.000135; rate[13][17] = 0.814753;
rate[13][18] = 5.393924; rate[13][19] = 0.592588;
rate[14][15] = 2.087385; rate[14][16] = 0.542251;
rate[14][17] = 0.000431; rate[14][18] = 0.000182;
rate[14][19] = 0.058972;
rate[15][16] = 2.206860; rate[15][17] = 0.099836;
rate[15][18] = 0.392552; rate[15][19] = 0.088256;
rate[16][17] = 0.207066; rate[16][18] = 0.124898;
rate[16][19] = 0.654109;
rate[17][18] = 0.427755; rate[17][19] = 0.256900;
rate[18][19] = 0.167582;
setEmpiricalRates(rate, "ARNDCQEGHILKMFPSTWYV");
double[] f = new double[n];
f[0] = 0.0470718; // A
f[1] = 0.0509102; // R
f[2] = 0.0742143; // N
f[3] = 0.0478596; // D
f[4] = 0.0250216; // C
f[5] = 0.0333036; // Q
f[6] = 0.0545874; // E
f[7] = 0.0763734; // G
f[8] = 0.0199642; // H
f[9] = 0.0671336; // I
f[10] = 0.0714981; // L
f[11] = 0.0567845; // K
f[12] = 0.0181507; // M
f[13] = 0.0304961; // F
f[14] = 0.0506561; // P
f[15] = 0.0884091; // S
f[16] = 0.0743386; // T
f[17] = 0.0185237; // W
f[18] = 0.0314741; // Y
f[19] = 0.0632292; // V
setEmpiricalFrequencies(f, "ARNDCQEGHILKMFPSTWYV");
}
@Override
public Citation.Category getCategory() {
return Citation.Category.SUBSTITUTION_MODELS;
}
@Override
public String getDescription() {
return "FLU amino acid substitution model";
}
@Override
public List<Citation> getCitations() {
return Collections.singletonList(CITATION);
}
public static Citation CITATION = new Citation(
new Author[]{
new Author("CC", "Dang"),
new Author("QS", "Le"),
new Author("O", "Gascuel"),
new Author("VS", "Le")
},
"FLU, an amino acid substitution model for influenza proteins",
2010, "BMC Evolutionary Biology", 10, 99, -1
);
}