43 #include "../AbstractBiblioSubstitutionModel.h" 94 std::auto_ptr<CodonDistanceFrequenciesSubstitutionModel>
pmodel_;
108 std::string
getName()
const {
return "YN98"; }
const GeneticCode * getGeneticCode() const
Interface for all substitution models.
std::string getName() const
Get the name of the model.
Partial implementation of the SubstitutionModel interface for models that are set for matching the bi...
std::auto_ptr< CodonDistanceFrequenciesSubstitutionModel > pmodel_
const SubstitutionModel & getModel() const
Parametrize a set of state frequencies.
YN98(const GeneticCode *gc, FrequenciesSet *codonFreqs)
Interface for reversible substitution models.
double getCodonsMulRate(size_t i, size_t j) const
Returns the multiplicative rate specific to two codons specified by their number. The respective gene...
The Yang and Nielsen (1998) substitution model for codons.
YN98 & operator=(const YN98 &)
SubstitutionModel & getModel()
Abstract class for codon models.