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// Created by: Laurent Guéguen
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// Created on: samedi 12 mars 2011, à 06h 49
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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 "NucleotideSubstitutionModel.h"
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#include "AbstractSubstitutionModel.h"
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#include <Bpp/Numeric/Constraints.h>
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#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>
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* @brief Intersection of models RN95 and L95.
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* The two hypotheses are that the transversion rates are only
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* dependent of the target nucleotide, and strand symmetry.
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* After normalization this model has 3 parameters:
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* . & \gamma & \alpha & \delta \\
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* \delta & . & \gamma & \beta \\
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* \beta & \gamma & . & \delta \\
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* \delta & \alpha & \gamma & .\\
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* so in the parametrization process we set: \f[\gamma+\delta=\frac 12\f]
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* The stationnary distribution
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* \pi = \left(\pi_A, \pi_C, \pi_G, \pi_T\right)
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* is such as \f[\pi_A=\pi_T\f] and \f[\pi_C=\pi_G\f]. It can be computed analytically.
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* We use as parameters:
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* \gamma \in ]0;1/2[\\
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* where \f[\alpha'=\frac{2\alpha\pi_A+min(0.5-\pi_A,\gamma)}{0.5-\pi_A}\f].
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* The generator is then computed as:
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* \delta=\frac 12-\gamma\\
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* \alpha=\frac{\alpha'(0.5-\pi_A)-min(0.5-\pi_A,\gamma)}{2\pi_A}\\
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* \beta=\frac{\delta-2*\pi_A*(\alpha+\frac 12)}{2*\pi_A-1}\\
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* and \f[P\f] is set for normalization.
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* The parameters are named \c "piA", \c "gamma", \c "alphaP".
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* - Rhetsky A. \& Ney M. (1995) MBE 12(1) 131-151.
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* - Lobry J R (1995), Journal_ Of Molecular Evolution_ 40 326-330.
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* - Schadt, Sinsheimer \& Lange (1998) Genome Research 8 222-233.
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public virtual NucleotideSubstitutionModel,
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public AbstractSubstitutionModel
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double alpha_, beta_, gamma_, delta_;
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* For calculation purposes as in Schadt & al. (with c1_=1)
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double c3_, c4_, c8_;
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mutable RowMatrix<double> p_;
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mutable double exp1_,exp3_,l_;
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const NucleicAlphabet* alphabet,
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#ifndef NO_VIRTUAL_COV
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clone() const { return new RN95s(*this); }
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double Pij_t (int i, int j, double d) const;
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double dPij_dt (int i, int j, double d) const;
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double d2Pij_dt2(int i, int j, double d) const;
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const Matrix<double>& getPij_t (double d) const;
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const Matrix<double>& getdPij_dt (double d) const;
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const Matrix<double>& getd2Pij_dt2(double d) const;
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std::string getName() const { return "RN95s"; }
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void updateMatrices();
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* @brief This method takes the average value between observed \f[\pi_A\f] and \f[\pi_T\f].
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void setFreq(std::map<int, double>&);
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} //end of namespace bpp.
added
removed
src/Bpp/Phyl/Model/RN95s.h
