44 #include "../AbstractSubstitutionModel.h" 46 #include <Bpp/Numeric/Constraints.h> 49 #include <Bpp/Seq/Alphabet/NucleicAlphabet.h> 143 double a_,
b_,
c_,
d_,
e_,
piA_,
piC_,
piG_,
piT_,
theta_,
theta1_,
theta2_,
p_;
147 const NucleicAlphabet * alpha,
160 #ifndef NO_VIRTUAL_COV 177 void setFreq(std::map<int,double>& freqs);
std::string getName() const
Get the name of the model.
GTR(const NucleicAlphabet *alpha, double a=1., double b=1., double c=1., double d=1., double e=1., double piA=0.25, double piC=0.25, double piG=0.25, double piT=0.25)
Partial implementation of the ReversibleSubstitutionModel interface.
void setFreq(std::map< int, double > &freqs)
This method is redefined to actualize the corresponding parameters piA, piT, piG and piC too...
The General Time-Reversible substitution model for nucleotides.
Specialisation interface for nucleotide substitution model.
void updateMatrices()
Compute and diagonalize the matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVecto...