#include <Bpp/Numeric/Prob/Simplex.h>
#include <Bpp/Seq/Alphabet/CodonAlphabet.h>
#include <Bpp/Seq/GeneticCode/GeneticCode.h>
#include "FrequencySet.h"
#include "ProteinFrequencySet.h"
#include "WordFrequencySet.h"

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Classes
class	bpp::CodonFrequencySetInterface
	Parametrize a set of state frequencies for codons. More...

class	bpp::FullCodonFrequencySet
	A generic FrequencySet for Full Codon alphabets. More...

class	bpp::FixedCodonFrequencySet
	FrequencySet useful for homogeneous and stationary models, codon implementation. More...

class	bpp::UserCodonFrequencySet

class	bpp::FullPerAACodonFrequencySet
	FrequencySet integrating ProteinFrequencySet inside CodonFrequencySet. In this case, FrequencieSet defined inside each amino acid is parametrized as a FullFrequencySet. Hence there are 61-20=41 parameters in addition of the parameters of the ProteinFrequencySet. More...

class	bpp::CodonFromIndependentFrequencySet
	the Frequencies in codons are the product of Independent Frequencies in letters with the frequencies of stop codons set to zero. More...

class	bpp::CodonFromUniqueFrequencySet
	the Frequencies in codons are the product of the frequencies for a unique FrequencySet in letters, with the frequencies of stop codons set to zero. More...

Namespaces
	bpp
	Defines the basic types of data flow nodes.

Classes

Namespaces