43 #include "../AbstractBiblioMixedSubstitutionModel.h" 44 #include "../MixtureOfASubstitutionModel.h" 45 #include "../FrequenciesSet/CodonFrequenciesSet.h" 47 #include <Bpp/Seq/GeneticCode/GeneticCode.h> 108 std::string
getName()
const {
return "YNGKP_M3"; }
121 #endif //_YNGKP_M3_H_ Interface for all substitution models.
size_t synfrom_
indexes of 2 codons between which the substitution is synonymous, to set a basis to the homogeneizati...
Abstract class for mixture models based on the bibliography.
std::string getName() const
Get the name of the model.
const SubstitutionModel & getModel() const
Parametrize a set of state frequencies.
std::auto_ptr< MixtureOfASubstitutionModel > pmixmodel_
Interface for reversible substitution models.
const FrequenciesSet * getFrequenciesSet() const
If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.
The Yang et al (2000) M3 substitution model for codons.
MixedSubstitutionModel & getMixedModel()
YNGKP_M3 & operator=(const YNGKP_M3 &)
const MixedSubstitutionModel & getMixedModel() const
SubstitutionModel & getModel()
YNGKP_M3(const GeneticCode *gc, FrequenciesSet *codonFreqs, unsigned int nclass=3)
Interface for Substitution models, defined as a mixture of "simple" substitution models.