PhylogeneticsApplicationTools.cpp File Reference

#include "../../App/PhylogeneticsApplicationTools.h"
#include "../../Io/BppOBranchModelFormat.h"
#include "../../Io/BppOFrequencySetFormat.h"
#include "../../Io/BppOMultiTreeReaderFormat.h"
#include "../../Io/BppOSubstitutionModelFormat.h"
#include "../../Io/BppOTransitionModelFormat.h"
#include "../../Io/BppOTreeReaderFormat.h"
#include "../../Io/Newick.h"
#include "../../Io/NexusIoTree.h"
#include "../../Io/Nhx.h"
#include "../../Model/FrequencySet/MvaFrequencySet.h"
#include "../../Model/MixedTransitionModel.h"
#include "../../Model/Protein/Coala.h"
#include "../../Model/SubstitutionModel.h"
#include "../../Model/WrappedModel.h"
#include "../../Tree/Tree.h"
#include "../../Tree/TreeTools.h"
#include "../OptimizationTools.h"
#include "PhylogeneticsApplicationTools.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/DataTable.h>
#include <Bpp/Numeric/Prob/DirichletDiscreteDistribution.h>
#include <Bpp/Numeric/Function/DownhillSimplexMethod.h>
#include <Bpp/Numeric/Function/PowellMultiDimensions.h>
#include <Bpp/Utils/AttributesTools.h>
#include <Bpp/Numeric/Matrix/MatrixTools.h>
#include <Bpp/Numeric/Prob/ConstantDistribution.h>
#include <Bpp/Seq/Alphabet/AlphabetTools.h>
#include <Bpp/Seq/Container/SequenceContainerTools.h>
#include <Bpp/Seq/App/SequenceApplicationTools.h>
#include <Bpp/Seq/SymbolListTools.h>
#include <fstream>
#include <memory>
#include <set>
#include <vector>

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