PhylogeneticsApplicationTools.cpp File Reference

#include "PhylogeneticsApplicationTools.h"
#include "../Model/SubstitutionModel.h"
#include "../Model/Protein/Coala.h"
#include "../Model/FrequenciesSet/MvaFrequenciesSet.h"
#include "../Likelihood/TreeLikelihood.h"
#include "../Mapping/LaplaceSubstitutionCount.h"
#include "../Mapping/UniformizationSubstitutionCount.h"
#include "../Mapping/DecompositionSubstitutionCount.h"
#include "../Mapping/NaiveSubstitutionCount.h"
#include "../Mapping/OneJumpSubstitutionCount.h"
#include "../OptimizationTools.h"
#include "../Tree.h"
#include "../Io/Newick.h"
#include "../Io/NexusIoTree.h"
#include "../Io/Nhx.h"
#include "../Io/BppOSubstitutionModelFormat.h"
#include "../Io/BppOFrequenciesSetFormat.h"
#include "../Io/BppORateDistributionFormat.h"
#include <Bpp/Io/BppODiscreteDistributionFormat.h>
#include <Bpp/Io/BppOParametrizableFormat.h>
#include <Bpp/Io/FileTools.h>
#include <Bpp/Text/TextTools.h>
#include <Bpp/App/ApplicationTools.h>
#include <Bpp/Text/StringTokenizer.h>
#include <Bpp/Text/KeyvalTools.h>
#include <Bpp/Numeric/AutoParameter.h>
#include <Bpp/Numeric/Prob/DirichletDiscreteDistribution.h>
#include <Bpp/Numeric/Function/DownhillSimplexMethod.h>
#include <Bpp/Numeric/Function/PowellMultiDimensions.h>
#include <Bpp/Seq/Alphabet/AlphabetTools.h>
#include <Bpp/Seq/Container/SequenceContainerTools.h>
#include <Bpp/Seq/App/SequenceApplicationTools.h>
#include <fstream>
#include <memory>
#include <set>
#include <vector>

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