File List

Here is a list of all files with brief descriptions:

[detail level 12345]

Bpp
Phyl
App
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
BppOFrequenciesSetFormat.cpp
BppOFrequenciesSetFormat.h
BppORateDistributionFormat.cpp
BppORateDistributionFormat.h
BppOSubstitutionModelFormat.cpp
BppOSubstitutionModelFormat.h
IoDistanceMatrix.h
IoDistanceMatrixFactory.cpp
IoDistanceMatrixFactory.h
IoFrequenciesSet.h
IoFrequenciesSetFactory.cpp
IoFrequenciesSetFactory.h
IoPairedSiteLikelihoods.cpp
IoPairedSiteLikelihoods.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
PhylipDistanceMatrixFormat.cpp
PhylipDistanceMatrixFormat.h
Likelihood
AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp
AbstractDiscreteRatesAcrossSitesTreeLikelihood.h
AbstractHomogeneousTreeLikelihood.cpp
AbstractHomogeneousTreeLikelihood.h
AbstractNonHomogeneousTreeLikelihood.cpp
AbstractNonHomogeneousTreeLikelihood.h
AbstractTreeLikelihood.cpp
AbstractTreeLikelihood.h
AbstractTreeLikelihoodData.h
ClockTreeLikelihood.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
PseudoNewtonOptimizer.cpp
PseudoNewtonOptimizer.h
RASTools.cpp
RASTools.h
RHomogeneousClockTreeLikelihood.cpp
RHomogeneousClockTreeLikelihood.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
DecompositionSubstitutionCount.cpp
DecompositionSubstitutionCount.h
LaplaceSubstitutionCount.cpp
LaplaceSubstitutionCount.h
NaiveSubstitutionCount.cpp
NaiveSubstitutionCount.h
OneJumpSubstitutionCount.cpp
OneJumpSubstitutionCount.h
ProbabilisticSubstitutionMapping.cpp
ProbabilisticSubstitutionMapping.h
SubstitutionCount.h
SubstitutionMapping.h
SubstitutionMappingTools.cpp
SubstitutionMappingTools.h
SubstitutionRegister.h
UniformizationSubstitutionCount.cpp
UniformizationSubstitutionCount.h
WeightedSubstitutionCount.cpp
WeightedSubstitutionCount.h
Model
Codon
AbstractCodonDistanceSubstitutionModel.cpp
AbstractCodonDistanceSubstitutionModel.h
AbstractCodonFitnessSubstitutionModel.cpp
AbstractCodonFitnessSubstitutionModel.h
AbstractCodonFrequenciesSubstitutionModel.cpp
AbstractCodonFrequenciesSubstitutionModel.h
AbstractCodonPhaseFrequenciesSubstitutionModel.cpp
AbstractCodonPhaseFrequenciesSubstitutionModel.h
AbstractCodonSubstitutionModel.cpp
AbstractCodonSubstitutionModel.h
CodonDistanceFitnessPhaseFrequenciesSubstitutionModel.cpp
CodonDistanceFitnessPhaseFrequenciesSubstitutionModel.h
CodonDistanceFrequenciesSubstitutionModel.cpp
CodonDistanceFrequenciesSubstitutionModel.h
CodonDistancePhaseFrequenciesSubstitutionModel.cpp
CodonDistancePhaseFrequenciesSubstitutionModel.h
CodonDistanceSubstitutionModel.cpp
CodonDistanceSubstitutionModel.h
CodonRateFrequenciesSubstitutionModel.cpp
CodonRateFrequenciesSubstitutionModel.h
CodonRateSubstitutionModel.cpp
CodonRateSubstitutionModel.h
CodonSubstitutionModel.h
GY94.cpp
GY94.h
MG94.cpp
MG94.h
TripletSubstitutionModel.cpp
TripletSubstitutionModel.h
YN98.cpp
YN98.h
YNGKP_M1.cpp
YNGKP_M1.h
YNGKP_M2.cpp
YNGKP_M2.h
YNGKP_M3.cpp
YNGKP_M3.h
YNGKP_M7.cpp
YNGKP_M7.h
YNGKP_M8.cpp
YNGKP_M8.h
FrequenciesSet
CodonFrequenciesSet.cpp
CodonFrequenciesSet.h
FrequenciesSet.cpp
FrequenciesSet.h
MvaFrequenciesSet.cpp
MvaFrequenciesSet.h
NucleotideFrequenciesSet.cpp
NucleotideFrequenciesSet.h
ProteinFrequenciesSet.h
WordFrequenciesSet.cpp
WordFrequenciesSet.h
Nucleotide
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
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
AbstractBiblioMixedSubstitutionModel.cpp
AbstractBiblioMixedSubstitutionModel.h
AbstractBiblioSubstitutionModel.cpp
AbstractBiblioSubstitutionModel.h
AbstractMixedSubstitutionModel.cpp
AbstractMixedSubstitutionModel.h
AbstractSubstitutionModel.cpp
AbstractSubstitutionModel.h
AbstractWordSubstitutionModel.cpp
AbstractWordSubstitutionModel.h
BinarySubstitutionModel.cpp
BinarySubstitutionModel.h
G2001.h
MarkovModulatedSubstitutionModel.cpp
MarkovModulatedSubstitutionModel.h
MixedSubstitutionModel.h
MixedSubstitutionModelSet.cpp
MixedSubstitutionModelSet.h
MixtureOfASubstitutionModel.cpp
MixtureOfASubstitutionModel.h
MixtureOfSubstitutionModels.cpp
MixtureOfSubstitutionModels.h
RateDistributionFactory.cpp
RateDistributionFactory.h
RE08.cpp
RE08.h
StateMap.cpp
StateMap.h
SubstitutionModel.h
SubstitutionModelFactory.cpp
SubstitutionModelFactory.h
SubstitutionModelSet.cpp
SubstitutionModelSet.h
SubstitutionModelSetTools.cpp
SubstitutionModelSetTools.h
TS98.h
WordSubstitutionModel.cpp
WordSubstitutionModel.h
Parsimony
AbstractTreeParsimonyData.h
AbstractTreeParsimonyScore.cpp
AbstractTreeParsimonyScore.h
DRTreeParsimonyData.cpp
DRTreeParsimonyData.h
DRTreeParsimonyScore.cpp
DRTreeParsimonyScore.h
TreeParsimonyData.h
TreeParsimonyScore.h
Simulation
DetailedSiteSimulator.h
HomogeneousSequenceSimulator.h
MutationProcess.cpp
MutationProcess.h
NonHomogeneousSequenceSimulator.cpp
NonHomogeneousSequenceSimulator.h
SequenceSimulationTools.cpp
SequenceSimulationTools.h
SequenceSimulator.h
SiteSimulator.h
AncestralStateReconstruction.h
BipartitionList.cpp
BipartitionList.h
BipartitionTools.cpp
BipartitionTools.h
NNISearchable.h
NNITopologySearch.cpp
NNITopologySearch.h
Node.cpp
Node.h
NodeTemplate.h
OptimizationTools.cpp
OptimizationTools.h
PatternTools.cpp
PatternTools.h
PhyloStatistics.cpp
PhyloStatistics.h
SitePatterns.cpp
SitePatterns.h
TopologySearch.h
Tree.h
TreeExceptions.cpp
TreeExceptions.h
TreeTemplate.h
TreeTemplateTools.cpp
TreeTemplateTools.h
TreeTools.cpp
TreeTools.h