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// Created by: Laurent Gueguen
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// Created on: July 2009
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Copyright or © or Copr. CNRS, (November 16, 2004)
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This software is a computer program whose purpose is to provide classes
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for phylogenetic data analysis.
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This software is governed by the CeCILL license under French law and
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abiding by the rules of distribution of free software. You can use,
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modify and/ or redistribute the software under the terms of the CeCILL
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license as circulated by CEA, CNRS and INRIA at the following URL
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"http://www.cecill.info".
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As a counterpart to the access to the source code and rights to copy,
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modify and redistribute granted by the license, users are provided only
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with a limited warranty and the software's author, the holder of the
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economic rights, and the successive licensors have only limited
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In this respect, the user's attention is drawn to the risks associated
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with loading, using, modifying and/or developing or reproducing the
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software by the user in light of its specific status of free software,
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that may mean that it is complicated to manipulate, and that also
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therefore means that it is reserved for developers and experienced
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professionals having in-depth computer knowledge. Users are therefore
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encouraged to load and test the software's suitability as regards their
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requirements in conditions enabling the security of their systems and/or
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data to be ensured and, more generally, to use and operate it in the
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same conditions as regards security.
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The fact that you are presently reading this means that you have had
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knowledge of the CeCILL license and that you accept its terms.
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#include "CodonAsynonymousFrequenciesReversibleSubstitutionModel.h"
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* @brief The Yang and Nielsen (1998) substitution model for codons.
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* @author Laurent Guéguen
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* This model has one rate of transitions and one rate of
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* transversion. It also allows distinct equilibrium frequencies
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* between codons. A multiplicative factor accounts for the selective
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* restraints at the amino acid level, depending on the synonymy of
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* For codons @f$i=i_1i_2i_3@f$ and @f$j=j_1j_2j_3@f$, the generator
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* term @f$Q_{ij} (i \neq j)@f$ is:
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* 0 if 2 or 3 of the pair @f$(i_1,j_1) (i_2,j_2) (i_3,j_3) @f$ are different.
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* @f$\mu \pi_j \omega@f$ if exactly 1 of the pairs @f$(i_1,j_1)
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* (i_2,j_2) (i_3,j_3) @f$ is different, that difference is a
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* transversion and amino acids coded by i and j are different.
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* @f$\mu \pi_j @f$ if exactly 1 of the pairs @f$(i_1,j_1) (i_2,j_2)
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* (i_3,j_3) @f$ is different, that difference is a transversion and
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* amino acids coded by i and j are the same.
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* @f$\mu \kappa \pi_j \omega@f$ if exactly 1 of the pairs
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* @f$(i_1,j_1) (i_2,j_2) (i_3,j_3) @f$ is different, that difference
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* is a transition and amino acids coded by i and j are different.
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* @f$\mu \kappa \pi_j @f$ if exactly 1 of the pairs @f$(i_1,j_1)
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* (i_2,j_2) (i_3,j_3) @f$ is different, that difference is a
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* transition and amino acids coded by @f$i@f$ and @f$j@f$ are the
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* @f$\mu@f$ is a normalization factor.
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* This model includes 2 parameters (@f$\kappa@f$ and @f$\omega@f$).
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* The codon frequencies @f$\pi_j@f$ are either observed or infered.
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* - Yang Z. and Nielsen R. (1998), _Journal of Molecular Evolution_ 46:409--418.
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public AbstractReversibleSubstitutionModel
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CodonAsynonymousFrequenciesReversibleSubstitutionModel pmodel_;
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* @brief Tools to make the link between the Parameters of the
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* object and those of pmodel_.
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std::map<std::string,std::string> mapParNamesFromPmodel_;
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ParameterList lParPmodel_;
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YN98(const GeneticCode* gc, FrequenciesSet* codonFreqs);
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YN98(const YN98& yn98) : AbstractReversibleSubstitutionModel(yn98),
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pmodel_(yn98.pmodel_),
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mapParNamesFromPmodel_(yn98.mapParNamesFromPmodel_),
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lParPmodel_(yn98.lParPmodel_) {}
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YN98* clone() const { return new YN98(*this); }
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std::string getName() const { return "YN98"; }
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const Vdouble& getFrequencies() const { return pmodel_.getFrequencies(); }
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const Matrix<double>& getGenerator() const { return pmodel_.getGenerator(); }
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const Vdouble& getEigenValues() const { return pmodel_.getEigenValues(); }
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const Matrix<double>& getRowLeftEigenVectors() const { return pmodel_.getRowLeftEigenVectors(); }
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const Matrix<double>& getColumnRightEigenVectors() const { return pmodel_.getColumnRightEigenVectors(); }
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double freq(unsigned int i) const { return pmodel_.freq(i); }
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double Qij(unsigned int i, unsigned int j) const { return pmodel_.Qij(i,j); }
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double Pij_t (unsigned int i, unsigned int j, double t) const { return pmodel_.Pij_t(i, j, t); }
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double dPij_dt (unsigned int i, unsigned int j, double t) const { return pmodel_.dPij_dt(i, j, t); }
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double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return pmodel_.d2Pij_dt2(i, j, t); }
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const Matrix<double>& getPij_t (double d) const { return pmodel_.getPij_t(d); }
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const Matrix<double>& getdPij_dt (double d) const { return pmodel_.getdPij_dt(d); }
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const Matrix<double>& getd2Pij_dt2(double d) const { return pmodel_.getd2Pij_dt2(d); }
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void setFreq(std::map<int, double>& m);
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unsigned int getNumberOfStates() const { return pmodel_.getNumberOfStates(); }
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double getInitValue(unsigned int i, int state) const throw (BadIntException) { return pmodel_.getInitValue(i,state); }
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void enableEigenDecomposition(bool yn) { eigenDecompose_ = 1; }
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bool enableEigenDecomposition() { return pmodel_.enableEigenDecomposition(); }
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const FrequenciesSet& getFreq() const { return pmodel_.getFreq(); }
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double getRate() const { return pmodel_.getRate();}
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void setRate(double rate) { pmodel_.setRate(rate);}
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void addRateParameter();
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void updateMatrices();
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} //end of namespace bpp.
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src/Bpp/Phyl/Model/YN98.h
