43 #include "../AbstractBiblioMixedSubstitutionModel.h" 44 #include "../MixtureOfASubstitutionModel.h" 45 #include "../FrequenciesSet/CodonFrequenciesSet.h" 47 #include <Bpp/Seq/GeneticCode/GeneticCode.h> 113 std::string
getName()
const {
return "YNGKP_M1"; }
125 #endif //_YNGKP_M1_H_ std::string getName() const
Get the name of the model.
std::auto_ptr< MixtureOfASubstitutionModel > pmixmodel_
Interface for all substitution models.
Abstract class for mixture models based on the bibliography.
YNGKP_M1(const GeneticCode *gc, FrequenciesSet *codonFreqs)
SubstitutionModel & getModel()
Parametrize a set of state frequencies.
Interface for reversible substitution models.
const MixedSubstitutionModel & getMixedModel() const
MixedSubstitutionModel & getMixedModel()
const FrequenciesSet * getFrequenciesSet() const
If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.
The Yang et al (2000) M1 substitution model for codons, with the more realistic modification in Wong ...
size_t synfrom_
indexes of 2 codons states between which the substitution is synonymous, to set a basis to the homoge...
const SubstitutionModel & getModel() const
YNGKP_M1 & operator=(const YNGKP_M1 &)
Interface for Substitution models, defined as a mixture of "simple" substitution models.