PhylogeneticsApplicationTools.cpp File Reference
#include "../Io/BppOBranchModelFormat.h"#include "../Io/BppOFrequencySetFormat.h"#include "../Io/BppOMultiTreeReaderFormat.h"#include "../Io/BppOMultiTreeWriterFormat.h"#include "../Io/BppORateDistributionFormat.h"#include "../Io/BppOTreeReaderFormat.h"#include "../Io/BppOTreeWriterFormat.h"#include "../Io/Newick.h"#include "../Io/NexusIoTree.h"#include "../Io/Nhx.h"#include "../Likelihood/AutoCorrelationSequenceEvolution.h"#include "../Likelihood/HmmSequenceEvolution.h"#include "../Likelihood/MixtureSequenceEvolution.h"#include "../Likelihood/NonHomogeneousSubstitutionProcess.h"#include "../Likelihood/OneProcessSequenceEvolution.h"#include "../Likelihood/ParametrizablePhyloTree.h"#include "../Likelihood/PartitionSequenceEvolution.h"#include "../Likelihood/PhyloLikelihoods/AlignedPhyloLikelihoodAutoCorrelation.h"#include "../Likelihood/PhyloLikelihoods/AutoCorrelationProcessPhyloLikelihood.h"#include "../Likelihood/PhyloLikelihoods/PhyloLikelihoodFormula.h"#include "../Likelihood/PhyloLikelihoods/AlignedPhyloLikelihoodHmm.h"#include "../Likelihood/PhyloLikelihoods/HmmProcessPhyloLikelihood.h"#include "../Likelihood/PhyloLikelihoods/AlignedPhyloLikelihoodMixture.h"#include "../Likelihood/PhyloLikelihoods/MixtureProcessPhyloLikelihood.h"#include "../Likelihood/PhyloLikelihoods/OneProcessSequencePhyloLikelihood.h"#include "../Likelihood/PhyloLikelihoods/PartitionProcessPhyloLikelihood.h"#include "../Likelihood/PhyloLikelihoods/AlignedPhyloLikelihoodProduct.h"#include "../Likelihood/PhyloLikelihoods/SingleDataPhyloLikelihood.h"#include "../Likelihood/PhyloLikelihoods/SingleProcessPhyloLikelihood.h"#include "../Likelihood/RateAcrossSitesSubstitutionProcess.h"#include "../Likelihood/SimpleSubstitutionProcess.h"#include "../Likelihood/SubstitutionProcessCollection.h"#include "../Likelihood/SubstitutionProcessCollectionMember.h"#include "../Mapping/DecompositionSubstitutionCount.h"#include "../Mapping/LaplaceSubstitutionCount.h"#include "../Mapping/NaiveSubstitutionCount.h"#include "../Mapping/OneJumpSubstitutionCount.h"#include "../Mapping/UniformizationSubstitutionCount.h"#include "../Model/FrequencySet/MvaFrequencySet.h"#include "../Model/MixedTransitionModel.h"#include "../Model/Protein/Coala.h"#include "../Model/SubstitutionModel.h"#include "../Model/WrappedModel.h"#include "../Model/RateDistribution/ConstantRateDistribution.h"#include "../OptimizationTools.h"#include "../Tree/PhyloTree.h"#include "../Tree/PhyloTreeTools.h"#include "PhylogeneticsApplicationTools.h"#include <Bpp/BppString.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>#include <algorithm>
Include dependency graph for PhylogeneticsApplicationTools.cpp:
