CodonFrequencySet.h File Reference
#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 for codons, with no parameter. 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 More... | |
Namespaces | |
| namespace | bpp |
| Defines the basic types of data flow nodes. | |
