40 #include "../Nucleotide/K80.h" 41 #include "../FrequenciesSet/CodonFrequenciesSet.h" 54 addParameter_(
new Parameter(
"GY94.kappa",1,&Parameter::R_PLUS_STAR));
55 addParameter_(
new Parameter(
"GY94.V",10000,&Parameter::R_PLUS_STAR));
58 addParameters_(codonFreqs->getParameters());
62 vector<std::string> v=
pmodel_->getFrequenciesSet()->getParameters().getParameterNames();
63 for (
unsigned int i=0;i<v.size();i++)
GY94 & operator=(const GY94 &gy94)
std::map< std::string, std::string > mapParNamesFromPmodel_
Tools to make the link between the Parameters of the object and those of pmixmodel_.
ParameterList lParPmodel_
Partial implementation of the SubstitutionModel interface for models that are set for matching the bi...
GY94(const GeneticCode *gc, FrequenciesSet *codonFreqs)
virtual void updateMatrices()
The Kimura 2-rates substitution model for nucleotides.
AbstractBiblioSubstitutionModel & operator=(const AbstractBiblioSubstitutionModel &model)
The Goldman and Yang (1994) substitution model for codons.
Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nu...
Parametrize a set of state frequencies.
std::auto_ptr< CodonDistanceFrequenciesSubstitutionModel > pmodel_