#include <codonevodiscr.hh>

Inheritance diagram for CodonEvoDiscr:

Public Member Functions
void	setM ()

int	getM ()

void	writeRateMatrices (string filename)

void	readMatrices (MatrixFormat fmt=fmt_TXT)

void	computeLogPmatrices ()

gsl_matrix *	getSubMatrixLogP (double omega, double t)

double	subLogProb (int from, int to, double omega, double t)

double	logLik (const char e1, const char e2, int u, double t)

vector< double >	loglikForCodonTuple (vector< string > &seqtuple, PhyloTree *ctree)

vector< double >	loglikForCodonTuple (vector< string > &seqtuple, PhyloTree ctree, PhyloTree tree, int &subs)

void	addBranchLength (double b)

void	produceComb (vector< vector< int > > &config)

double	getProb (const vector< double > &lls)

Public Member Functions inherited from Evo
	Evo (int s)

int	getNumStates ()

void	setBranchLengths (vector< double > b, int m=-1)

void	printBranchLengths ()

virtual void	getRateMatrices ()

double	getPi (int i) const

double	getLogPi (int i) const

gsl_matrix *	getSubMatrixQ (int u)

gsl_matrix *	getSubMatrixP (int u, double t)

gsl_matrix *	getSubMatrixLogP (int u, double t)

gsl_matrix *	expQt (double t, gsl_vector lambda, gsl_matrix U, gsl_matrix *Uinv)

Additional Inherited Members
Protected Member Functions inherited from Evo
int	findClosestIndex (vector< double > &v, double val)

Protected Attributes inherited from Evo
const int	states

int	m

double *	pi

vector< double >	times

vector< gsl_matrix * >	allQs

Matrix< gsl_matrix * >	allPs

Matrix< gsl_matrix * >	allLogPs

Detailed Description

class CodonEvoDiscr

Computes and stores 64x64 codon substitution probability matrices P(t,omega,kappa,pi) = exp(Q(omega,kappa,pi)*t) for a sample of values for t and omega (dN/dS, selection) and a fixed given value of kappa (transition/transversion ratio) and vector pi (codon usage). Matrices are precomputed and retrieval of P(t,omega) is then a constant time lookup as this is needed very often during estimation of omega for a given tree.

Author: Mario Stanke; Stefanie König adapted by Giovanna Migliorelli

Member Function Documentation

◆ addBranchLength()

void CodonEvoDiscr::addBranchLength ( double b )

inlinevirtual

Implements Evo.

◆ computeLogPmatrices()

void CodonEvoDiscr::computeLogPmatrices ( )

virtual

Implements Evo.

The documentation for this class was generated from the following files:

include/codonevodiscr.hh
src/codonevodiscr.cc

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ addBranchLength()

◆ computeLogPmatrices()