44 #include "../AbstractSubstitutionModel.h" 46 #include <Bpp/Numeric/Constraints.h> 49 #include <Bpp/Seq/Alphabet/NucleicAlphabet.h> 106 SSR(
const NucleicAlphabet* alpha,
114 #ifndef NO_VIRTUAL_COV 122 std::string
getName()
const {
return "Strand Symmetric Reversible"; }
129 void setFreq(std::map<int, double>&);
The Strand Symmetric Reversible substitution model for nucleotides.
std::string getName() const
Get the name of the model.
void setFreq(std::map< int, double > &)
This method is redefined to actualize the corresponding parameters theta too.
Partial implementation of the ReversibleSubstitutionModel interface.
Specialisation interface for nucleotide substitution model.
void updateMatrices()
Compute and diagonalize the matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVecto...
SSR(const NucleicAlphabet *alpha, double beta=1., double gamma=1., double delta=1., double theta=0.5)