#include <Bpp/Io/BppODiscreteDistributionFormat.h>
#include <Bpp/Io/BppOParametrizableFormat.h>
#include <Bpp/Io/FileTools.h>
#include <Bpp/Io/OutputStream.h>
#include <Bpp/Seq/Alphabet/AlphabetTools.h>
#include <Bpp/Seq/App/SequenceApplicationTools.h>
#include <Bpp/Text/KeyvalTools.h>
#include <Bpp/Text/StringTokenizer.h>
#include <Bpp/Text/TextTools.h>
#include "../App/PhylogeneticsApplicationTools.h"
#include "../Model/AbstractBiblioMixedTransitionModel.h"
#include "../Model/BinarySubstitutionModel.h"
#include "../Model/D1WalkSubstitutionModel.h"
#include "../Model/Codon/AbstractCodonAAFitnessSubstitutionModel.h"
#include "../Model/Codon/AbstractCodonAARateSubstitutionModel.h"
#include "../Model/Codon/AbstractCodonBGCSubstitutionModel.h"
#include "../Model/Codon/AbstractCodonClusterAASubstitutionModel.h"
#include "../Model/Codon/AbstractCodonCpGSubstitutionModel.h"
#include "../Model/Codon/AbstractCodonDistanceSubstitutionModel.h"
#include "../Model/Codon/AbstractCodonFitnessSubstitutionModel.h"
#include "../Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h"
#include "../Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.h"
#include "../Model/Codon/CodonAdHocSubstitutionModel.h"
#include "../Model/Codon/CodonSameAARateSubstitutionModel.h"
#include "../Model/Codon/DFP07.h"
#include "../Model/Codon/GY94.h"
#include "../Model/Codon/KCM.h"
#include "../Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.h"
#include "../Model/Codon/KroneckerCodonDistanceSubstitutionModel.h"
#include "../Model/Codon/MG94.h"
#include "../Model/Codon/SENCA.h"
#include "../Model/Codon/TripletSubstitutionModel.h"
#include "../Model/Codon/YN98.h"
#include "../Model/Codon/YNGP_M10.h"
#include "../Model/Codon/YNGP_M7.h"
#include "../Model/Codon/YNGP_M8.h"
#include "../Model/Codon/YNGP_M9.h"
#include "../Model/EquiprobableSubstitutionModel.h"
#include "../Model/FromMixtureSubstitutionModel.h"
#include "../Model/G2001.h"
#include "../Model/InMixedSubstitutionModel.h"
#include "../Model/KroneckerWordSubstitutionModel.h"
#include "../Model/MixtureOfATransitionModel.h"
#include "../Model/MixtureOfTransitionModels.h"
#include "../Model/Nucleotide/F81.h"
#include "../Model/Nucleotide/F84.h"
#include "../Model/Nucleotide/GTR.h"
#include "../Model/Nucleotide/HKY85.h"
#include "../Model/Nucleotide/JCnuc.h"
#include "../Model/Nucleotide/K80.h"
#include "../Model/Nucleotide/L95.h"
#include "../Model/Nucleotide/NucleotideSubstitutionModel.h"
#include "../Model/Nucleotide/RN95.h"
#include "../Model/Nucleotide/RN95s.h"
#include "../Model/Nucleotide/SSR.h"
#include "../Model/Nucleotide/T92.h"
#include "../Model/Nucleotide/TN93.h"
#include "../Model/Nucleotide/YpR.h"
#include "../Model/Nucleotide/gBGC.h"
#include "../Model/OneChangeRegisterTransitionModel.h"
#include "../Model/OneChangeTransitionModel.h"
#include "../Model/POMO.h"
#include "../Model/Protein/Coala.h"
#include "../Model/Protein/CoalaCore.h"
#include "../Model/Protein/DSO78.h"
#include "../Model/Protein/JCprot.h"
#include "../Model/Protein/JTT92.h"
#include "../Model/Protein/LG08.h"
#include "../Model/Protein/LGL08_CAT.h"
#include "../Model/Protein/ProteinSubstitutionModel.h"
#include "../Model/Protein/UserProteinSubstitutionModel.h"
#include "../Model/Protein/WAG01.h"
#include "../Model/RE08.h"
#include "../Model/RegisterRatesSubstitutionModel.h"
#include "../Model/TS98.h"
#include "../Model/TwoParameterBinarySubstitutionModel.h"
#include "../Model/WordSubstitutionModel.h"
#include "BppOFrequencySetFormat.h"
#include "BppORateDistributionFormat.h"
#include "BppOSubstitutionModelFormat.h"
#include "BppOTransitionModelFormat.h"
#include <Bpp/Numeric/Prob/ConstantDistribution.h>
#include <Bpp/Numeric/AutoParameter.h>
#include <iomanip>
#include <set>
#include <memory>

Include dependency graph for BppOSubstitutionModelFormat.cpp: