The Yang and Nielsen (1998) substitution model for codons. More...

#include <Bpp/Phyl/Model/Codon/YN98.h>

Inheritance diagram for bpp::YN98:

Collaboration diagram for bpp::YN98:

Public Member Functions
	YN98 (const GeneticCode gc, FrequenciesSet codonFreqs)

	YN98 (const YN98 &yn98)

YN98 &	operator= (const YN98 &)

virtual	~YN98 ()

YN98 *	clone () const

std::string	getName () const
	Get the name of the model. More...

const SubstitutionModel &	getModel () const

const GeneticCode *	getGeneticCode () const

double	getCodonsMulRate (size_t i, size_t j) const
	Returns the multiplicative rate specific to two codons specified by their number. The respective generator rate is this rate multiplied by the rate defined by the model defined on nucleotides. More...

const std::vector< int > &	getAlphabetStates () const

const StateMap &	getStateMap () const

int	getAlphabetStateAsInt (size_t i) const

std::string	getAlphabetStateAsChar (size_t i) const

std::vector< size_t >	getModelStates (int code) const
	Get the state in the model corresponding to a particular state in the alphabet. More...

std::vector< size_t >	getModelStates (const std::string &code) const
	Get the state in the model corresponding to a particular state in the alphabet. More...

virtual double	freq (size_t i) const

virtual double	Qij (size_t i, size_t j) const

virtual double	Pij_t (size_t i, size_t j, double t) const

virtual double	dPij_dt (size_t i, size_t j, double t) const

virtual double	d2Pij_dt2 (size_t i, size_t j, double t) const

virtual const Vdouble &	getFrequencies () const

const Matrix< double > &	getGenerator () const

const Matrix< double > &	getExchangeabilityMatrix () const

double	Sij (size_t i, size_t j) const

const Matrix< double > &	getPij_t (double t) const

const Matrix< double > &	getdPij_dt (double t) const

const Matrix< double > &	getd2Pij_dt2 (double t) const

void	enableEigenDecomposition (bool yn)
	Set if eigenValues and Vectors must be computed. More...

bool	enableEigenDecomposition ()
	Tell if eigenValues and Vectors must be computed. More...

bool	isDiagonalizable () const

bool	isNonSingular () const

const Vdouble &	getEigenValues () const

const Vdouble &	getIEigenValues () const

const Matrix< double > &	getRowLeftEigenVectors () const

const Matrix< double > &	getColumnRightEigenVectors () const

double	getRate () const
	Get the rate. More...

void	setRate (double rate)
	Set the rate of the model (must be positive). More...

void	addRateParameter ()

void	setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
	Set equilibrium frequencies equal to the frequencies estimated from the data. More...

void	setFreq (std::map< int, double > &frequ)
	Set equilibrium frequencies. More...

const Alphabet *	getAlphabet () const

size_t	getNumberOfStates () const
	Get the number of states. More...

double	getInitValue (size_t i, int state) const throw (BadIntException)

const FrequenciesSet *	getFrequenciesSet () const
	If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0. More...

virtual void	fireParameterChanged (const ParameterList &parameters)
	Tells the model that a parameter value has changed. More...

double	getScale () const
	Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale. More...

void	setScale (double scale)
	Multiplies the current generator by the given scale. More...

Protected Member Functions
virtual void	updateMatrices ()

Protected Attributes
std::map< std::string, std::string >	mapParNamesFromPmodel_
	Tools to make the link between the Parameters of the object and those of pmixmodel_. More...

ParameterList	lParPmodel_

Private Member Functions
SubstitutionModel &	getModel ()

Private Attributes
std::auto_ptr< CodonDistanceFrequenciesSubstitutionModel >	pmodel_

Detailed Description

The Yang and Nielsen (1998) substitution model for codons.

Author: Laurent Guéguen

This model has one rate of transitions and one rate of transversion. It also allows distinct equilibrium frequencies between codons. A multiplicative factor accounts for the selective restraints at the amino acid level, depending on the synonymy of the amino acids.

For codons $i=i_1i_2i_3$ and $j=j_1j_2j_3$ , the generator term $Q_{ij} (i \neq j)$ is:

0 if 2 or 3 of the pair $(i_1,j_1) (i_2,j_2) (i_3,j_3) $ are different.

$\mu \pi_j \omega$ if exactly 1 of the pairs $(i_1,j_1) (i_2,j_2) (i_3,j_3) $ is different, that difference is a transversion and amino acids coded by i and j are different.

$\mu \pi_j$ if exactly 1 of the pairs $(i_1,j_1) (i_2,j_2) (i_3,j_3) $ is different, that difference is a transversion and amino acids coded by i and j are the same.

$\mu \kappa \pi_j \omega$ if exactly 1 of the pairs $(i_1,j_1) (i_2,j_2) (i_3,j_3) $ is different, that difference is a transition and amino acids coded by i and j are different.

$\mu \kappa \pi_j$ if exactly 1 of the pairs $(i_1,j_1) (i_2,j_2) (i_3,j_3) $ is different, that difference is a transition and amino acids coded by $i$ and $j$ are the same.

$\mu$ is a normalization factor.

This model includes 2 parameters ( $\kappa$ and $\omega$ ). The codon frequencies $\pi_j$ are either observed or infered.

Reference:

Yang Z. and Nielsen R. (1998), Journal of Molecular Evolution 46:409–418.

Definition at line 88 of file YN98.h.

Constructor & Destructor Documentation

◆ YN98() [1/2]

YN98::YN98	(	const GeneticCode *	gc,
		FrequenciesSet *	codonFreqs
	)

Definition at line 51 of file YN98.cpp.

References bpp::AbstractBiblioSubstitutionModel::lParPmodel_, bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_, pmodel_, and bpp::AbstractBiblioSubstitutionModel::updateMatrices().

Referenced by clone().

◆ YN98() [2/2]

YN98::YN98 ( const YN98 & yn98 )

Definition at line 76 of file YN98.cpp.

◆ ~YN98()

virtual bpp::YN98::~YN98 ( )

inlinevirtual

Definition at line 103 of file YN98.h.

Member Function Documentation

◆ addRateParameter()

void AbstractBiblioSubstitutionModel::addRateParameter ( )

virtualinherited

i	the index of the state in the model.
state	An observed state in the sequence/site.

IndexOutOfBoundsException	if array position is out of range.
BadIntException	if states are not allowed in the associated alphabet.

data	The sequences to use.
pseudoCount	A quantity $\psi$ to add to adjust the observed values in order to prevent issues due to missing states on small data set. The corrected frequencies shall be computed as $\pi_i = \frac{n_i+\psi}{\sum_j (f_j+\psi)}$

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ YN98() [1/2]

◆ YN98() [2/2]

◆ ~YN98()

Member Function Documentation

◆ addRateParameter()

◆ clone()

◆ d2Pij_dt2()

◆ dPij_dt()

◆ enableEigenDecomposition() [1/2]

◆ enableEigenDecomposition() [2/2]

◆ fireParameterChanged()

◆ freq()

◆ getAlphabet()

◆ getAlphabetStateAsChar()

◆ getAlphabetStateAsInt()

◆ getAlphabetStates()

◆ getCodonsMulRate()

◆ getColumnRightEigenVectors()

◆ getd2Pij_dt2()

◆ getdPij_dt()

◆ getEigenValues()

◆ getExchangeabilityMatrix()

◆ getFrequencies()

◆ getFrequenciesSet()

◆ getGenerator()

◆ getGeneticCode()

◆ getIEigenValues()

◆ getInitValue()

◆ getModel() [1/2]

◆ getModel() [2/2]

◆ getModelStates() [1/2]

◆ getModelStates() [2/2]

◆ getName()

◆ getNumberOfStates()

◆ getPij_t()

◆ getRate()

◆ getRowLeftEigenVectors()

◆ getScale()

◆ getStateMap()

◆ isDiagonalizable()

◆ isNonSingular()

◆ operator=()

◆ Pij_t()

◆ Qij()

◆ setFreq()

◆ setFreqFromData()

◆ setRate()

◆ setScale()

◆ Sij()

◆ updateMatrices()

Member Data Documentation

◆ lParPmodel_

◆ mapParNamesFromPmodel_

◆ pmodel_