File List

Here is a list of all files with brief descriptions:

Bpp/Phyl/AncestralStateReconstruction.h [code]
Bpp/Phyl/BipartitionList.cpp [code]
Bpp/Phyl/BipartitionList.h [code]
Bpp/Phyl/BipartitionTools.cpp [code]
Bpp/Phyl/BipartitionTools.h [code]
Bpp/Phyl/NNISearchable.h [code]
Bpp/Phyl/NNITopologySearch.cpp [code]
Bpp/Phyl/NNITopologySearch.h [code]
Bpp/Phyl/Node.cpp [code]
Bpp/Phyl/Node.h [code]
Bpp/Phyl/NodeTemplate.h [code]
Bpp/Phyl/OptimizationTools.cpp [code]
Bpp/Phyl/OptimizationTools.h [code]
Bpp/Phyl/PatternTools.cpp [code]
Bpp/Phyl/PatternTools.h [code]
Bpp/Phyl/PhyloStatistics.cpp [code]
Bpp/Phyl/PhyloStatistics.h [code]
Bpp/Phyl/SitePatterns.cpp [code]
Bpp/Phyl/SitePatterns.h [code]
Bpp/Phyl/TopologySearch.h [code]
Bpp/Phyl/Tree.h [code]
Bpp/Phyl/TreeExceptions.cpp [code]
Bpp/Phyl/TreeExceptions.h [code]
Bpp/Phyl/TreeTemplate.h [code]
Bpp/Phyl/TreeTemplateTools.cpp [code]
Bpp/Phyl/TreeTemplateTools.h [code]
Bpp/Phyl/TreeTools.cpp [code]
Bpp/Phyl/TreeTools.h [code]
Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp [code]
Bpp/Phyl/App/PhylogeneticsApplicationTools.h [code]
Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp [code]
Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h [code]
Bpp/Phyl/Distance/BioNJ.cpp [code]
Bpp/Phyl/Distance/BioNJ.h [code]
Bpp/Phyl/Distance/DistanceEstimation.cpp [code]
Bpp/Phyl/Distance/DistanceEstimation.h [code]
Bpp/Phyl/Distance/DistanceMethod.h [code]
Bpp/Phyl/Distance/HierarchicalClustering.cpp [code]
Bpp/Phyl/Distance/HierarchicalClustering.h [code]
Bpp/Phyl/Distance/NeighborJoining.cpp [code]
Bpp/Phyl/Distance/NeighborJoining.h [code]
Bpp/Phyl/Distance/PGMA.cpp [code]
Bpp/Phyl/Distance/PGMA.h [code]
Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp [code]
Bpp/Phyl/Graphics/AbstractDendrogramPlot.h [code]
Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp [code]
Bpp/Phyl/Graphics/AbstractTreeDrawing.h [code]
Bpp/Phyl/Graphics/CladogramPlot.cpp [code]
Bpp/Phyl/Graphics/CladogramPlot.h [code]
Bpp/Phyl/Graphics/PhylogramPlot.cpp [code]
Bpp/Phyl/Graphics/PhylogramPlot.h [code]
Bpp/Phyl/Graphics/TreeDrawing.h [code]
Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp [code]
Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h [code]
Bpp/Phyl/Graphics/TreeDrawingListener.cpp [code]
Bpp/Phyl/Graphics/TreeDrawingListener.h [code]
Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp [code]
Bpp/Phyl/Io/BppOFrequenciesSetFormat.h [code]
Bpp/Phyl/Io/BppORateDistributionFormat.cpp [code]
Bpp/Phyl/Io/BppORateDistributionFormat.h [code]
Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp [code]
Bpp/Phyl/Io/BppOSubstitutionModelFormat.h [code]
Bpp/Phyl/Io/IoDistanceMatrix.h [code]
Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp [code]
Bpp/Phyl/Io/IoDistanceMatrixFactory.h [code]
Bpp/Phyl/Io/IoFrequenciesSet.h [code]
Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp [code]
Bpp/Phyl/Io/IoFrequenciesSetFactory.h [code]
Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp [code]
Bpp/Phyl/Io/IoPairedSiteLikelihoods.h [code]
Bpp/Phyl/Io/IoSubstitutionModel.h [code]
Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp [code]
Bpp/Phyl/Io/IoSubstitutionModelFactory.h [code]
Bpp/Phyl/Io/IoTree.h [code]
Bpp/Phyl/Io/IoTreeFactory.cpp [code]
Bpp/Phyl/Io/IoTreeFactory.h [code]
Bpp/Phyl/Io/Newick.cpp [code]
Bpp/Phyl/Io/Newick.h [code]
Bpp/Phyl/Io/NexusIoTree.cpp [code]
Bpp/Phyl/Io/NexusIoTree.h [code]
Bpp/Phyl/Io/Nhx.cpp [code]
Bpp/Phyl/Io/Nhx.h [code]
Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp [code]
Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h [code]
Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp [code]
Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp [code]
Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp [code]
Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp [code]
Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h [code]
Bpp/Phyl/Likelihood/ClockTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp [code]
Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h [code]
Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp [code]
Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h [code]
Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp [code]
Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp [code]
Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp [code]
Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/DRTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp [code]
Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h [code]
Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp [code]
Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h [code]
Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp [code]
Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h [code]
Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp [code]
Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp [code]
Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h [code]
Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp [code]
Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h [code]
Bpp/Phyl/Likelihood/RASTools.cpp [code]
Bpp/Phyl/Likelihood/RASTools.h [code]
Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp [code]
Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp [code]
Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp [code]
Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp [code]
Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp [code]
Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/SitePartitionTreeLikelihood.h [code]
Bpp/Phyl/Likelihood/TreeLikelihood.h [code]
Bpp/Phyl/Likelihood/TreeLikelihoodData.h [code]
Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp [code]
Bpp/Phyl/Likelihood/TreeLikelihoodTools.h [code]
Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp [code]
Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h [code]
Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp [code]
Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h [code]
Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp [code]
Bpp/Phyl/Mapping/NaiveSubstitutionCount.h [code]
Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp [code]
Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h [code]
Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp [code]
Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h [code]
Bpp/Phyl/Mapping/SubstitutionCount.h [code]
Bpp/Phyl/Mapping/SubstitutionMapping.h [code]
Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp [code]
Bpp/Phyl/Mapping/SubstitutionMappingTools.h [code]
Bpp/Phyl/Mapping/SubstitutionRegister.h [code]
Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp [code]
Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h [code]
Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp [code]
Bpp/Phyl/Mapping/WeightedSubstitutionCount.h [code]
Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp [code]
Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h [code]
Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp [code]
Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h [code]
Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp [code]
Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h [code]
Bpp/Phyl/Model/AbstractSubstitutionModel.cpp [code]
Bpp/Phyl/Model/AbstractSubstitutionModel.h [code]
Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp [code]
Bpp/Phyl/Model/AbstractWordSubstitutionModel.h [code]
Bpp/Phyl/Model/BinarySubstitutionModel.cpp [code]
Bpp/Phyl/Model/BinarySubstitutionModel.h [code]
Bpp/Phyl/Model/G2001.h [code]
Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp [code]
Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h [code]
Bpp/Phyl/Model/MixedSubstitutionModel.h [code]
Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp [code]
Bpp/Phyl/Model/MixedSubstitutionModelSet.h [code]
Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp [code]
Bpp/Phyl/Model/MixtureOfASubstitutionModel.h [code]
Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp [code]
Bpp/Phyl/Model/MixtureOfSubstitutionModels.h [code]
Bpp/Phyl/Model/RateDistributionFactory.cpp [code]
Bpp/Phyl/Model/RateDistributionFactory.h [code]
Bpp/Phyl/Model/RE08.cpp [code]
Bpp/Phyl/Model/RE08.h [code]
Bpp/Phyl/Model/StateMap.cpp [code]
Bpp/Phyl/Model/StateMap.h [code]
Bpp/Phyl/Model/SubstitutionModel.h [code]
Bpp/Phyl/Model/SubstitutionModelFactory.cpp [code]
Bpp/Phyl/Model/SubstitutionModelFactory.h [code]
Bpp/Phyl/Model/SubstitutionModelSet.cpp [code]
Bpp/Phyl/Model/SubstitutionModelSet.h [code]
Bpp/Phyl/Model/SubstitutionModelSetTools.cpp [code]
Bpp/Phyl/Model/SubstitutionModelSetTools.h [code]
Bpp/Phyl/Model/TS98.h [code]
Bpp/Phyl/Model/WordSubstitutionModel.cpp [code]
Bpp/Phyl/Model/WordSubstitutionModel.h [code]
Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp [code]
Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h [code]
Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp [code]
Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h [code]
Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp [code]
Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h [code]
Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp [code]
Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.h [code]
Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp [code]
Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h [code]
Bpp/Phyl/Model/Codon/CodonDistanceFitnessPhaseFrequenciesSubstitutionModel.cpp [code]
Bpp/Phyl/Model/Codon/CodonDistanceFitnessPhaseFrequenciesSubstitutionModel.h [code]
Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp [code]
Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h [code]
Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp [code]
Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h [code]
Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp [code]
Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h [code]
Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp [code]
Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.h [code]
Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp [code]
Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.h [code]
Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h [code]
Bpp/Phyl/Model/Codon/GY94.cpp [code]
Bpp/Phyl/Model/Codon/GY94.h [code]
Bpp/Phyl/Model/Codon/MG94.cpp [code]
Bpp/Phyl/Model/Codon/MG94.h [code]
Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp [code]
Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h [code]
Bpp/Phyl/Model/Codon/YN98.cpp [code]
Bpp/Phyl/Model/Codon/YN98.h [code]
Bpp/Phyl/Model/Codon/YNGKP_M1.cpp [code]
Bpp/Phyl/Model/Codon/YNGKP_M1.h [code]
Bpp/Phyl/Model/Codon/YNGKP_M2.cpp [code]
Bpp/Phyl/Model/Codon/YNGKP_M2.h [code]
Bpp/Phyl/Model/Codon/YNGKP_M3.cpp [code]
Bpp/Phyl/Model/Codon/YNGKP_M3.h [code]
Bpp/Phyl/Model/Codon/YNGKP_M7.cpp [code]
Bpp/Phyl/Model/Codon/YNGKP_M7.h [code]
Bpp/Phyl/Model/Codon/YNGKP_M8.cpp [code]
Bpp/Phyl/Model/Codon/YNGKP_M8.h [code]
Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp [code]
Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h [code]
Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp [code]
Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h [code]
Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp [code]
Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h [code]
Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp [code]
Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.h [code]
Bpp/Phyl/Model/FrequenciesSet/ProteinFrequenciesSet.h [code]
Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp [code]
Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h [code]
Bpp/Phyl/Model/Nucleotide/F84.cpp [code]
Bpp/Phyl/Model/Nucleotide/F84.h [code]
Bpp/Phyl/Model/Nucleotide/gBGC.cpp [code]
Bpp/Phyl/Model/Nucleotide/gBGC.h [code]
Bpp/Phyl/Model/Nucleotide/GTR.cpp [code]
Bpp/Phyl/Model/Nucleotide/GTR.h [code]
Bpp/Phyl/Model/Nucleotide/HKY85.cpp [code]
Bpp/Phyl/Model/Nucleotide/HKY85.h [code]
Bpp/Phyl/Model/Nucleotide/JCnuc.cpp [code]
Bpp/Phyl/Model/Nucleotide/JCnuc.h [code]
Bpp/Phyl/Model/Nucleotide/K80.cpp [code]
Bpp/Phyl/Model/Nucleotide/K80.h [code]
Bpp/Phyl/Model/Nucleotide/L95.cpp [code]
Bpp/Phyl/Model/Nucleotide/L95.h [code]
Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h [code]
Bpp/Phyl/Model/Nucleotide/RN95.cpp [code]
Bpp/Phyl/Model/Nucleotide/RN95.h [code]
Bpp/Phyl/Model/Nucleotide/RN95s.cpp [code]
Bpp/Phyl/Model/Nucleotide/RN95s.h [code]
Bpp/Phyl/Model/Nucleotide/SSR.cpp [code]
Bpp/Phyl/Model/Nucleotide/SSR.h [code]
Bpp/Phyl/Model/Nucleotide/T92.cpp [code]
Bpp/Phyl/Model/Nucleotide/T92.h [code]
Bpp/Phyl/Model/Nucleotide/TN93.cpp [code]
Bpp/Phyl/Model/Nucleotide/TN93.h [code]
Bpp/Phyl/Model/Nucleotide/YpR.cpp [code]
Bpp/Phyl/Model/Nucleotide/YpR.h [code]
Bpp/Phyl/Model/Protein/Coala.cpp [code]
Bpp/Phyl/Model/Protein/Coala.h [code]
Bpp/Phyl/Model/Protein/CoalaCore.cpp [code]
Bpp/Phyl/Model/Protein/CoalaCore.h [code]
Bpp/Phyl/Model/Protein/DSO78.cpp [code]
Bpp/Phyl/Model/Protein/DSO78.h [code]
Bpp/Phyl/Model/Protein/JCprot.cpp [code]
Bpp/Phyl/Model/Protein/JCprot.h [code]
Bpp/Phyl/Model/Protein/JTT92.cpp [code]
Bpp/Phyl/Model/Protein/JTT92.h [code]
Bpp/Phyl/Model/Protein/LG08.cpp [code]
Bpp/Phyl/Model/Protein/LG08.h [code]
Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp [code]
Bpp/Phyl/Model/Protein/LG10_EX_EHO.h [code]
Bpp/Phyl/Model/Protein/LGL08_CAT.cpp [code]
Bpp/Phyl/Model/Protein/LGL08_CAT.h [code]
Bpp/Phyl/Model/Protein/LLG08_EHO.cpp [code]
Bpp/Phyl/Model/Protein/LLG08_EHO.h [code]
Bpp/Phyl/Model/Protein/LLG08_EX2.cpp [code]
Bpp/Phyl/Model/Protein/LLG08_EX2.h [code]
Bpp/Phyl/Model/Protein/LLG08_EX3.cpp [code]
Bpp/Phyl/Model/Protein/LLG08_EX3.h [code]
Bpp/Phyl/Model/Protein/LLG08_UL2.cpp [code]
Bpp/Phyl/Model/Protein/LLG08_UL2.h [code]
Bpp/Phyl/Model/Protein/LLG08_UL3.cpp [code]
Bpp/Phyl/Model/Protein/LLG08_UL3.h [code]
Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h [code]
Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp [code]
Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h [code]
Bpp/Phyl/Model/Protein/WAG01.cpp [code]
Bpp/Phyl/Model/Protein/WAG01.h [code]
Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h [code]
Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h [code]
Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h [code]
Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h [code]
Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h [code]
Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp [code]
Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h [code]
Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp [code]
Bpp/Phyl/Parsimony/DRTreeParsimonyData.h [code]
Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp [code]
Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h [code]
Bpp/Phyl/Parsimony/TreeParsimonyData.h [code]
Bpp/Phyl/Parsimony/TreeParsimonyScore.h [code]
Bpp/Phyl/Simulation/DetailedSiteSimulator.h [code]
Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h [code]
Bpp/Phyl/Simulation/MutationProcess.cpp [code]
Bpp/Phyl/Simulation/MutationProcess.h [code]
Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp [code]
Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h [code]
Bpp/Phyl/Simulation/SequenceSimulationTools.cpp [code]
Bpp/Phyl/Simulation/SequenceSimulationTools.h [code]
Bpp/Phyl/Simulation/SequenceSimulator.h [code]
Bpp/Phyl/Simulation/SiteSimulator.h [code]