43 #include "../AbstractBiblioMixedSubstitutionModel.h" 44 #include "../MixtureOfASubstitutionModel.h" 45 #include "../FrequenciesSet/CodonFrequenciesSet.h" 47 #include <Bpp/Seq/GeneticCode/GeneticCode.h> 111 std::string
getName()
const {
return "YNGKP_M8"; }
123 #endif //_YNGKP_M8_H_ Interface for all substitution models.
Abstract class for mixture models based on the bibliography.
MixedSubstitutionModel & getMixedModel()
Parametrize a set of state frequencies.
size_t synfrom_
indexes of 2 codons between which the substitution is synonymous, to set a basis to the homogeneizati...
Interface for reversible substitution models.
YNGKP_M8 & operator=(const YNGKP_M8 &)
const FrequenciesSet * getFrequenciesSet() const
If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.
The Yang et al (2000) M8 substitution model for codons.
SubstitutionModel & getModel()
const SubstitutionModel & getModel() const
const MixedSubstitutionModel & getMixedModel() const
std::string getName() const
Get the name of the model.
std::auto_ptr< MixtureOfASubstitutionModel > pmixmodel_
YNGKP_M8(const GeneticCode *gc, FrequenciesSet *codonFreqs, unsigned int nbclass)
Interface for Substitution models, defined as a mixture of "simple" substitution models.