File List

Here is a list of all files with brief descriptions:

[detail level 12345]

▼ Bpp
▼ Phyl
► App
BppPhylogeneticsApplication.cpp
BppPhylogeneticsApplication.h
PhylogeneticsApplicationTools.cpp
PhylogeneticsApplicationTools.h
► Distance
AbstractAgglomerativeDistanceMethod.cpp
AbstractAgglomerativeDistanceMethod.h
BioNJ.cpp
BioNJ.h
DistanceEstimation.cpp
DistanceEstimation.h
DistanceMethod.h
HierarchicalClustering.cpp
HierarchicalClustering.h
NeighborJoining.cpp
NeighborJoining.h
PGMA.cpp
PGMA.h
► Graphics
AbstractDendrogramPlot.cpp
AbstractDendrogramPlot.h
AbstractTreeDrawing.cpp
AbstractTreeDrawing.h
CladogramPlot.cpp
CladogramPlot.h
PhylogramPlot.cpp
PhylogramPlot.h
TreeDrawing.h
TreeDrawingDisplayControler.cpp
TreeDrawingDisplayControler.h
TreeDrawingListener.cpp
TreeDrawingListener.h
► Io
BppOBranchModelFormat.cpp
BppOBranchModelFormat.h
BppOFrequencySetFormat.cpp
BppOFrequencySetFormat.h
BppOMultiTreeReaderFormat.cpp
BppOMultiTreeReaderFormat.h
BppOMultiTreeWriterFormat.cpp
BppOMultiTreeWriterFormat.h
BppORateDistributionFormat.cpp
BppORateDistributionFormat.h
BppOSubstitutionModelFormat.cpp
BppOSubstitutionModelFormat.h
BppOTransitionModelFormat.cpp
BppOTransitionModelFormat.h
BppOTreeReaderFormat.cpp
BppOTreeReaderFormat.h
BppOTreeWriterFormat.cpp
BppOTreeWriterFormat.h
ExtendedNewick.cpp
ExtendedNewick.h
IoDAG.h
IoFrequencySet.h
IoFrequencySetFactory.cpp
IoFrequencySetFactory.h
IoSubstitutionModel.h
IoSubstitutionModelFactory.cpp
IoSubstitutionModelFactory.h
IoTree.h
IoTreeFactory.cpp
IoTreeFactory.h
Newick.cpp
Newick.h
NexusIoTree.cpp
NexusIoTree.h
Nhx.cpp
Nhx.h
► Legacy
► App
PhylogeneticsApplicationTools.cpp
PhylogeneticsApplicationTools.h
► Io
IoPairedSiteLikelihoods.cpp
IoPairedSiteLikelihoods.h
► Likelihood
AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp
AbstractDiscreteRatesAcrossSitesTreeLikelihood.h
AbstractHomogeneousTreeLikelihood.cpp
AbstractHomogeneousTreeLikelihood.h
AbstractNonHomogeneousTreeLikelihood.cpp
AbstractNonHomogeneousTreeLikelihood.h
AbstractTreeLikelihood.cpp
AbstractTreeLikelihood.h
AbstractTreeLikelihoodData.h
DiscreteRatesAcrossSitesTreeLikelihood.h
DRASDRTreeLikelihoodData.cpp
DRASDRTreeLikelihoodData.h
DRASRTreeLikelihoodData.cpp
DRASRTreeLikelihoodData.h
DRHomogeneousMixedTreeLikelihood.cpp
DRHomogeneousMixedTreeLikelihood.h
DRHomogeneousTreeLikelihood.cpp
DRHomogeneousTreeLikelihood.h
DRNonHomogeneousTreeLikelihood.cpp
DRNonHomogeneousTreeLikelihood.h
DRTreeLikelihood.h
DRTreeLikelihoodTools.cpp
DRTreeLikelihoodTools.h
GlobalClockTreeLikelihoodFunctionWrapper.cpp
GlobalClockTreeLikelihoodFunctionWrapper.h
HomogeneousTreeLikelihood.h
MarginalAncestralStateReconstruction.cpp
MarginalAncestralStateReconstruction.h
NNIHomogeneousTreeLikelihood.cpp
NNIHomogeneousTreeLikelihood.h
NonHomogeneousTreeLikelihood.h
PairedSiteLikelihoods.cpp
PairedSiteLikelihoods.h
RASTools.cpp
RASTools.h
RHomogeneousMixedTreeLikelihood.cpp
RHomogeneousMixedTreeLikelihood.h
RHomogeneousTreeLikelihood.cpp
RHomogeneousTreeLikelihood.h
RNonHomogeneousMixedTreeLikelihood.cpp
RNonHomogeneousMixedTreeLikelihood.h
RNonHomogeneousTreeLikelihood.cpp
RNonHomogeneousTreeLikelihood.h
SitePartitionTreeLikelihood.h
TreeLikelihood.h
TreeLikelihoodData.h
TreeLikelihoodTools.cpp
TreeLikelihoodTools.h
► Mapping
Mapping.h
ProbabilisticRewardMapping.cpp
ProbabilisticRewardMapping.h
ProbabilisticSubstitutionMapping.cpp
ProbabilisticSubstitutionMapping.h
RewardMapping.h
RewardMappingTools.cpp
RewardMappingTools.h
SubstitutionMapping.h
SubstitutionMappingTools.cpp
SubstitutionMappingTools.h
► Model
MixedSubstitutionModelSet.cpp
MixedSubstitutionModelSet.h
SubstitutionModelSet.cpp
SubstitutionModelSet.h
SubstitutionModelSetTools.cpp
SubstitutionModelSetTools.h
► Simulation
NonHomogeneousSequenceSimulator.cpp
NonHomogeneousSequenceSimulator.h
► Tree
AwareNode.cpp
AwareNode.h
NNITopologySearch.cpp
NNITopologySearch.h
AncestralStateReconstruction.h
OptimizationTools.cpp
OptimizationTools.h
TreeIterator.cpp
TreeIterator.h
► Likelihood
► DataFlow
BackwardLikelihoodTree.cpp
BackwardLikelihoodTree.h
CollectionNodes.cpp
CollectionNodes.h
DataFlow.cpp
DataFlow.h
DataFlowCWise.cpp
DataFlowCWise.h
DataFlowCWiseComputing.cpp
DataFlowCWiseComputing.h
DataFlowNumeric.cpp
DataFlowNumeric.h
Definitions.h
DiscreteDistribution.cpp
DiscreteDistribution.h
ExtendedFloat.cpp
ExtendedFloat.h
ExtendedFloatEigen.h
ExtendedFloatEigenTools.h
ForwardLikelihoodTree.cpp
ForwardLikelihoodTree.h
FrequencySet.cpp
FrequencySet.h
LikelihoodCalculation.h
LikelihoodCalculationOnABranch.cpp
LikelihoodCalculationOnABranch.h
LikelihoodCalculationSingleProcess.cpp
LikelihoodCalculationSingleProcess.h
Model.cpp
Model.h
Parameter.cpp
Parameter.h
Parametrizable.cpp
Parametrizable.h
ProcessTree.cpp
ProcessTree.h
Sequence_DF.h
Simplex_DF.cpp
Simplex_DF.h
TransitionMatrix.cpp
TransitionMatrix.h
► PhyloLikelihoods
AbstractPhyloLikelihood.h
AlignedPhyloLikelihood.h
AlignedPhyloLikelihoodAutoCorrelation.cpp
AlignedPhyloLikelihoodAutoCorrelation.h
AlignedPhyloLikelihoodHmm.cpp
AlignedPhyloLikelihoodHmm.h
AlignedPhyloLikelihoodMixture.cpp
AlignedPhyloLikelihoodMixture.h
AlignedPhyloLikelihoodProduct.cpp
AlignedPhyloLikelihoodProduct.h
AlignedPhyloLikelihoodSet.cpp
AlignedPhyloLikelihoodSet.h
AutoCorrelationProcessPhyloLikelihood.cpp
AutoCorrelationProcessPhyloLikelihood.h
HmmLikelihood_DF.cpp
HmmLikelihood_DF.h
HmmLikelihoodComputation.cpp
HmmLikelihoodComputation.h
HmmPhyloAlphabet.h
HmmPhyloEmissionProbabilities.cpp
HmmPhyloEmissionProbabilities.h
HmmProcessPhyloLikelihood.cpp
HmmProcessPhyloLikelihood.h
MixtureProcessPhyloLikelihood.cpp
MixtureProcessPhyloLikelihood.h
MultiProcessSequencePhyloLikelihood.cpp
MultiProcessSequencePhyloLikelihood.h
OnABranchPhyloLikelihood.cpp
OnABranchPhyloLikelihood.h
OneProcessSequencePhyloLikelihood.cpp
OneProcessSequencePhyloLikelihood.h
PartitionProcessPhyloLikelihood.cpp
PartitionProcessPhyloLikelihood.h
PhyloLikelihood.h
PhyloLikelihoodContainer.h
PhyloLikelihoodFormula.cpp
PhyloLikelihoodFormula.h
PhyloLikelihoodSet.cpp
PhyloLikelihoodSet.h
SequencePhyloLikelihood.h
SingleDataPhyloLikelihood.h
SingleProcessPhyloLikelihood.cpp
SingleProcessPhyloLikelihood.h
WeightedAutoCorrelationProcessPhyloLikelihood.cpp
WeightedAutoCorrelationProcessPhyloLikelihood.h
AbstractAutonomousSubstitutionProcess.cpp
AbstractAutonomousSubstitutionProcess.h
AbstractSubstitutionProcess.cpp
AbstractSubstitutionProcess.h
AutoCorrelationSequenceEvolution.cpp
AutoCorrelationSequenceEvolution.h
AutonomousSubstitutionProcess.h
HmmEmissionProbabilities_Eigen.h
HmmProcessAlphabet.h
HmmSequenceEvolution.cpp
HmmSequenceEvolution.h
MarginalAncestralReconstruction.cpp
MarginalAncestralReconstruction.h
MixtureSequenceEvolution.cpp
MixtureSequenceEvolution.h
ModelPath.cpp
ModelPath.h
ModelScenario.cpp
ModelScenario.h
MultiProcessSequenceEvolution.cpp
MultiProcessSequenceEvolution.h
NonHomogeneousSubstitutionProcess.cpp
NonHomogeneousSubstitutionProcess.h
OneProcessSequenceEvolution.cpp
OneProcessSequenceEvolution.h
ParametrizablePhyloTree.cpp
ParametrizablePhyloTree.h
PartitionSequenceEvolution.cpp
PartitionSequenceEvolution.h
ProcessComputationTree.cpp
ProcessComputationTree.h
RateAcrossSitesSubstitutionProcess.cpp
RateAcrossSitesSubstitutionProcess.h
SequenceEvolution.h
SimpleSubstitutionProcess.cpp
SimpleSubstitutionProcess.h
SitePartition.h
SubstitutionProcess.h
SubstitutionProcessCollection.cpp
SubstitutionProcessCollection.h
SubstitutionProcessCollectionMember.cpp
SubstitutionProcessCollectionMember.h
► Mapping
► PhyloMappings
AbstractSinglePhyloSubstitutionMapping.cpp
AbstractSinglePhyloSubstitutionMapping.h
OneProcessSequenceSubstitutionMapping.cpp
OneProcessSequenceSubstitutionMapping.h
PhyloSubstitutionMapping.h
SingleProcessSubstitutionMapping.cpp
SingleProcessSubstitutionMapping.h
BranchedModelSet.h
CategorySubstitutionRegister.h
DecompositionMethods.cpp
DecompositionMethods.h
DecompositionReward.cpp
DecompositionReward.h
DecompositionSubstitutionCount.cpp
DecompositionSubstitutionCount.h
LaplaceSubstitutionCount.cpp
LaplaceSubstitutionCount.h
Mapping.h
NaiveSubstitutionCount.cpp
NaiveSubstitutionCount.h
OneJumpSubstitutionCount.cpp
OneJumpSubstitutionCount.h
PhyloBranchMapping.h
PhyloBranchReward.h
ProbabilisticRewardMapping.cpp
ProbabilisticRewardMapping.h
ProbabilisticSubstitutionMapping.cpp
ProbabilisticSubstitutionMapping.h
Reward.h
RewardMapping.h
RewardMappingTools.cpp
RewardMappingTools.h
StochasticMapping.cpp
StochasticMapping.h
SubstitutionCount.h
SubstitutionDistance.cpp
SubstitutionDistance.h
SubstitutionMapping.h
SubstitutionMappingTools.cpp
SubstitutionMappingTools.h
SubstitutionRegister.cpp
SubstitutionRegister.h
UniformizationSubstitutionCount.cpp
UniformizationSubstitutionCount.h
WeightedSubstitutionCount.cpp
WeightedSubstitutionCount.h
► Model
► Codon
AbstractCodonAAFitnessSubstitutionModel.cpp
AbstractCodonAAFitnessSubstitutionModel.h
AbstractCodonAARateSubstitutionModel.cpp
AbstractCodonAARateSubstitutionModel.h
AbstractCodonBGCSubstitutionModel.cpp
AbstractCodonBGCSubstitutionModel.h
AbstractCodonClusterAASubstitutionModel.cpp
AbstractCodonClusterAASubstitutionModel.h
AbstractCodonCpGSubstitutionModel.cpp
AbstractCodonCpGSubstitutionModel.h
AbstractCodonDistanceSubstitutionModel.cpp
AbstractCodonDistanceSubstitutionModel.h
AbstractCodonFitnessSubstitutionModel.cpp
AbstractCodonFitnessSubstitutionModel.h
AbstractCodonFrequenciesSubstitutionModel.cpp
AbstractCodonFrequenciesSubstitutionModel.h
AbstractCodonPhaseFrequenciesSubstitutionModel.cpp
AbstractCodonPhaseFrequenciesSubstitutionModel.h
AbstractCodonSubstitutionModel.cpp
AbstractCodonSubstitutionModel.h
AbstractDFPSubstitutionModel.cpp
AbstractDFPSubstitutionModel.h
AbstractKroneckerCodonSubstitutionModel.cpp
AbstractKroneckerCodonSubstitutionModel.h
CodonAdHocSubstitutionModel.cpp
CodonAdHocSubstitutionModel.h
CodonDistanceFrequenciesSubstitutionModel.cpp
CodonDistanceFrequenciesSubstitutionModel.h
CodonDistancePhaseFrequenciesSubstitutionModel.cpp
CodonDistancePhaseFrequenciesSubstitutionModel.h
CodonDistanceSubstitutionModel.cpp
CodonDistanceSubstitutionModel.h
CodonSameAARateSubstitutionModel.cpp
CodonSameAARateSubstitutionModel.h
CodonSubstitutionModel.h
DFP07.cpp
DFP07.h
DFPDistanceFrequenciesSubstitutionModel.cpp
DFPDistanceFrequenciesSubstitutionModel.h
GY94.cpp
GY94.h
KCM.cpp
KCM.h
KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp
KroneckerCodonDistanceFrequenciesSubstitutionModel.h
KroneckerCodonDistanceSubstitutionModel.cpp
KroneckerCodonDistanceSubstitutionModel.h
MG94.cpp
MG94.h
RELAX.cpp
RELAX.h
SENCA.cpp
SENCA.h
TripletSubstitutionModel.cpp
TripletSubstitutionModel.h
YN98.cpp
YN98.h
YNGP_M.h
YNGP_M1.cpp
YNGP_M1.h
YNGP_M10.cpp
YNGP_M10.h
YNGP_M2.cpp
YNGP_M2.h
YNGP_M3.cpp
YNGP_M3.h
YNGP_M7.cpp
YNGP_M7.h
YNGP_M8.cpp
YNGP_M8.h
YNGP_M9.cpp
YNGP_M9.h
► FrequencySet
CodonFrequencySet.cpp
CodonFrequencySet.h
FrequencySet.cpp
FrequencySet.h
MvaFrequencySet.cpp
MvaFrequencySet.h
NucleotideFrequencySet.cpp
NucleotideFrequencySet.h
ProteinFrequencySet.h
WordFrequencySet.cpp
WordFrequencySet.h
► Nucleotide
F81.cpp
F81.h
F84.cpp
F84.h
gBGC.cpp
gBGC.h
GTR.cpp
GTR.h
HKY85.cpp
HKY85.h
JCnuc.cpp
JCnuc.h
K80.cpp
K80.h
L95.cpp
L95.h
NucleotideSubstitutionModel.h
RN95.cpp
RN95.h
RN95s.cpp
RN95s.h
SSR.cpp
SSR.h
T92.cpp
T92.h
TN93.cpp
TN93.h
YpR.cpp
YpR.h
► Protein
Coala.cpp
Coala.h
CoalaCore.cpp
CoalaCore.h
DSO78.cpp
DSO78.h
JCprot.cpp
JCprot.h
JTT92.cpp
JTT92.h
LG08.cpp
LG08.h
LG10_EX_EHO.cpp
LG10_EX_EHO.h
LGL08_CAT.cpp
LGL08_CAT.h
LLG08_EHO.cpp
LLG08_EHO.h
LLG08_EX2.cpp
LLG08_EX2.h
LLG08_EX3.cpp
LLG08_EX3.h
LLG08_UL2.cpp
LLG08_UL2.h
LLG08_UL3.cpp
LLG08_UL3.h
ProteinSubstitutionModel.h
UserProteinSubstitutionModel.cpp
UserProteinSubstitutionModel.h
WAG01.cpp
WAG01.h
► RateDistribution
ConstantRateDistribution.h
ExponentialDiscreteRateDistribution.h
GammaDiscreteRateDistribution.h
GaussianDiscreteRateDistribution.h
AbstractBiblioMixedTransitionModel.cpp
AbstractBiblioMixedTransitionModel.h
AbstractBiblioSubstitutionModel.cpp
AbstractBiblioSubstitutionModel.h
AbstractFromSubstitutionModelTransitionModel.cpp
AbstractFromSubstitutionModelTransitionModel.h
AbstractKroneckerWordSubstitutionModel.cpp
AbstractKroneckerWordSubstitutionModel.h
AbstractMixedTransitionModel.cpp
AbstractMixedTransitionModel.h
AbstractSubstitutionModel.cpp
AbstractSubstitutionModel.h
AbstractWordSubstitutionModel.cpp
AbstractWordSubstitutionModel.h
AbstractWrappedModel.h
AnonymousSubstitutionModel.h
BinarySubstitutionModel.cpp
BinarySubstitutionModel.h
D1WalkSubstitutionModel.cpp
D1WalkSubstitutionModel.h
EquiprobableSubstitutionModel.cpp
EquiprobableSubstitutionModel.h
FromMixtureSubstitutionModel.cpp
FromMixtureSubstitutionModel.h
G2001.h
InMixedSubstitutionModel.cpp
InMixedSubstitutionModel.h
KroneckerWordSubstitutionModel.cpp
KroneckerWordSubstitutionModel.h
MarkovModulatedSubstitutionModel.cpp
MarkovModulatedSubstitutionModel.h
MixedTransitionModel.h
MixtureOfASubstitutionModel.h
MixtureOfATransitionModel.cpp
MixtureOfATransitionModel.h
MixtureOfSubstitutionModels.h
MixtureOfTransitionModels.cpp
MixtureOfTransitionModels.h
MultinomialFromTransitionModel.cpp
MultinomialFromTransitionModel.h
OneChangeRegisterTransitionModel.cpp
OneChangeRegisterTransitionModel.h
OneChangeTransitionModel.cpp
OneChangeTransitionModel.h
POMO.cpp
POMO.h
RE08.cpp
RE08.h
RegisterRatesSubstitutionModel.cpp
RegisterRatesSubstitutionModel.h
StateMap.cpp
StateMap.h
SubstitutionModel.h
TransitionFromTransitionModel.cpp
TransitionFromTransitionModel.h
TS98.h
TwoParameterBinarySubstitutionModel.cpp
TwoParameterBinarySubstitutionModel.h
WordSubstitutionModel.cpp
WordSubstitutionModel.h
WrappedModel.h
► Parsimony
AbstractTreeParsimonyData.h
AbstractTreeParsimonyScore.cpp
AbstractTreeParsimonyScore.h
DRTreeParsimonyData.cpp
DRTreeParsimonyData.h
DRTreeParsimonyScore.cpp
DRTreeParsimonyScore.h
TreeParsimonyData.h
TreeParsimonyScore.h
► Simulation
DetailedSiteSimulator.h
EvolutionSequenceSimulator.cpp
EvolutionSequenceSimulator.h
GivenDataSubstitutionProcessSequenceSimulator.cpp
GivenDataSubstitutionProcessSequenceSimulator.h
GivenDataSubstitutionProcessSiteSimulator.cpp
GivenDataSubstitutionProcessSiteSimulator.h
MutationProcess.cpp
MutationProcess.h
SequenceSimulationTools.cpp
SequenceSimulationTools.h
SequenceSimulator.h
SimpleSubstitutionProcessSequenceSimulator.cpp
SimpleSubstitutionProcessSequenceSimulator.h
SimpleSubstitutionProcessSiteSimulator.cpp
SimpleSubstitutionProcessSiteSimulator.h
SiteSimulator.h
SubstitutionProcessSequenceSimulator.cpp
SubstitutionProcessSequenceSimulator.h
► Tree
BipartitionList.cpp
BipartitionList.h
BipartitionTools.cpp
BipartitionTools.h
NNISearchable.h
Node.cpp
Node.h
NodeTemplate.h
PhyloBranch.cpp
PhyloBranch.h
PhyloBranchParam.cpp
PhyloBranchParam.h
PhyloNode.cpp
PhyloNode.h
PhyloTree.cpp
PhyloTree.h
PhyloTreeExceptions.cpp
PhyloTreeExceptions.h
PhyloTreeTools.cpp
PhyloTreeTools.h
TopologySearch.h
Tree.h
TreeExceptions.cpp
TreeExceptions.h
TreeTemplate.h
TreeTemplateTools.cpp
TreeTemplateTools.h
TreeTools.cpp
TreeTools.h
AncestralStateReconstruction.h
OptimizationTools.cpp
OptimizationTools.h
PatternTools.cpp
PatternTools.h
PhyloStatistics.cpp
PhyloStatistics.h
PseudoNewtonOptimizer.cpp
PseudoNewtonOptimizer.h
SitePatterns.cpp
SitePatterns.h