CodonFrequenciesSet.h File Reference
#include "WordFrequenciesSet.h"#include "FrequenciesSet.h"#include "ProteinFrequenciesSet.h"#include <Bpp/Seq/Alphabet/CodonAlphabet.h>#include <Bpp/Seq/GeneticCode/GeneticCode.h>#include <Bpp/Numeric/Prob/Simplex.h>
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Classes | |
| class | bpp::CodonFrequenciesSet |
| Parametrize a set of state frequencies for codons. More... | |
| class | bpp::FullCodonFrequenciesSet |
| A generic FrequenciesSet for Full Codon alphabets. More... | |
| class | bpp::FixedCodonFrequenciesSet |
| FrequenciesSet useful for homogeneous and stationary models, codon implementation. More... | |
| class | bpp::FullPerAACodonFrequenciesSet |
| FrequenciesSet integrating ProteinFrequenciesSet inside CodonFrequenciesSet. In this case, FrequencieSet defined inside each amino acid is parametrized as a FullFrequenciesSet. Hence there are 61-20=41 parameters in addition of the parameters of the ProteinFrequenciesSet. More... | |
| class | bpp::CodonFromIndependentFrequenciesSet |
| the Frequencies in codons are the product of Independent Frequencies in letters with the frequencies of stop codons set to zero. More... | |
| class | bpp::CodonFromUniqueFrequenciesSet |
| the Frequencies in codons are the product of the frequencies for a unique FrequenciesSet in letters, with the frequencies of stop codons set to zero. More... | |
Namespaces | |
| bpp | |
