47 #include "../AbstractSubstitutionModel.h" 51 #include <Bpp/Seq/Alphabet/ProteicAlphabet.h> 85 Coala(
const ProteicAlphabet* alpha,
87 unsigned int nbAxes = 0,
92 #ifndef NO_VIRTUAL_COV 100 std::string
getName()
const {
return "Coala"; }
102 void setFreqFromData(
const SequenceContainer& data,
double pseudoCount = 0);
std::string getEmpiricalMatrixFile() const
void updateMatrices()
Compute and diagonalize the matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVecto...
Specialized interface for protein substitution model.
std::string getExch() const
Coala(const ProteicAlphabet *alpha, const ProteinSubstitutionModel &model, unsigned int nbAxes=0, bool param=true)
Partial implementation of the ReversibleSubstitutionModel interface.
void computeEquilibriumFrequencies()
The Coala branch-heterogeneous amino-acid substitution model.
void setFreqFromData(const SequenceContainer &data, double pseudoCount=0)
Set equilibrium frequencies equal to the frequencies estimated from the data.
void readFromFile(std::string &file)
std::string getName() const
Get the name of the model.
This class is the core class inherited by the Coala class. COaLA is a branch-heterogeneous amino-acid...