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// File: CodonNeutralReversibleSubstitutionModel.h
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// Created by: Laurent Gueguen
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// Created on: Tue Dec 24 11:03:53 2003
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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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#ifndef _CODONNEUTRALREVERSIBLESUBSTITUTIONMODEL_H_
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#define _CODONNEUTRALREVERSIBLESUBSTITUTIONMODEL_H_
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#include "AbstractCodonReversibleSubstitutionModel.h"
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#include "NucleotideSubstitutionModel.h"
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#include <Bpp/Seq/Alphabet/CodonAlphabet.h>
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* @brief Class for reversible substitution models on non stop codons.
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* Objects of this class are built from three reversible substitution
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* models of NucleicAlphabets. No model is directly accessible. </p>
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* Only substitutions with one letter changed are accepted. </p>
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* There is one substitution per word per unit of time
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* on the equilibrium frequency, and each position has its specific rate.
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* The generator is constructed in two steps:
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* First, if @f$\rho_i@f$ is the rate of model i (@f$\sum_{i=1}^{3} \rho_i = 1@f$):
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* Q_{abc \rightarrow abd} = \rho_3 Q^{(2)}_{c \rightarrow d}
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* Q_{abc \rightarrow aed} = 0
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* Q_{abc \rightarrow abc} = \rho_1 Q^{(0)}_{a \rightarrow a} + \rho_2 Q^{(1)}_{b \rightarrow b} + \rho_3 Q^{(2)}_{c \rightarrow c})
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* Second, the substitution between STOP codons and non-STOP codons are
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* nullified, and the lines of Q are normalized in accordance.
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* The parameters of this word model are the same as the ones of the
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* models used. Their names have a new suffix, "_phi" where i stands
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* for the position (i.e. the phase) in the word.
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* The rates are defined by relative rates parameters @f$r_i@f$
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* (called "relrate_i") with:
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* 1 <= i < n, \rho_i = (1-r_1).(1-r_2)...(1-r_{i-1}).r_{i}
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* \rho_n = (1-r_1).(1-r_2)...(1-r_{n-1})
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* \forall 1 <= i < n, r_i = \frac{\rho_i}{1-(\rho_0+...\rho_{i-1})}
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* The parameters of this codon model are the same as the ones of the
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* models used. Their names have a new suffix, "_phi" where i stands
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* for the position (i.e. the phase) in the word.
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class CodonNeutralReversibleSubstitutionModel :
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public AbstractCodonReversibleSubstitutionModel
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*@brief Build a new CodonNeutralReversibleSubstitutionModel object from
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*a pointer to NucleotideSubstitutionModels.
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* @author Laurent Guéguen
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*@param palph pointer to a CodonAlphabet
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*@param pmod1 pointer to the NucleotideSubstitutionModel to use in the
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* three positions. It is owned by the instabce.
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CodonNeutralReversibleSubstitutionModel(const CodonAlphabet* palph,
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NucleotideSubstitutionModel* pmod1);
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*@brief Build a new CodonNeutralReversibleSubstitutionModel object
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*from three pointers to NucleotideSubstitutionModels.
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*@param palph pointer to a CodonAlphabet
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*@param pmod1, pmod2, pmod3 pointers to the
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* NucleotideSubstitutionModel to use in the three positions.
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* All the models must be different objects to avoid parameters
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* redondancy, otherwise only the first model is used. The used models
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* are owned by the instance.
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CodonNeutralReversibleSubstitutionModel(const CodonAlphabet* palph,
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NucleotideSubstitutionModel* pmod1,
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NucleotideSubstitutionModel* pmod2,
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NucleotideSubstitutionModel* pmod3);
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~CodonNeutralReversibleSubstitutionModel(){}
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#ifndef NO_VIRTUAL_COV
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CodonNeutralReversibleSubstitutionModel*
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clone() const { return new CodonNeutralReversibleSubstitutionModel(*this); }
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void completeMatrices();
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void updateMatrices();
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std::string getName() const;
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} // end of namespace bpp.
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src/Bpp/Phyl/Model/CodonNeutralReversibleSubstitutionModel.h
