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Viewing all changes in revision 1.

Committer: Bazaar Package Importer
Author(s): Julien Dutheil
Date: 2011-06-09 11:00:00 UTC
Revision ID: james.westby@ubuntu.com-20110609110000-yvx78svv6w7xxgph

Tags: upstream-2.0.2

Import upstream version 2.0.2

files added:

AUTHORS.txt

CMakeLists.txt

COPYING.txt

ChangeLog

Doxyfile

INSTALL.txt

Phyl.spec

debian

debian/changelog

debian/compat

debian/control

debian/copyright

debian/docs

debian/libbpp-phyl-dev.install

debian/libbpp-phyl9.install

debian/rules

debian/source

debian/source/format

src

src/Bpp

src/Bpp/Phyl

src/Bpp/Phyl.all

src/Bpp/Phyl/AncestralStateReconstruction.h

src/Bpp/Phyl/App

src/Bpp/Phyl/App.all

src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp

src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h

src/Bpp/Phyl/BipartitionList.cpp

src/Bpp/Phyl/BipartitionList.h

src/Bpp/Phyl/BipartitionTools.cpp

src/Bpp/Phyl/BipartitionTools.h

src/Bpp/Phyl/Distance

src/Bpp/Phyl/Distance.all

src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp

src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h

src/Bpp/Phyl/Distance/AgglomerativeDistanceMethod.h

src/Bpp/Phyl/Distance/BioNJ.cpp

src/Bpp/Phyl/Distance/BioNJ.h

src/Bpp/Phyl/Distance/DistanceEstimation.cpp

src/Bpp/Phyl/Distance/DistanceEstimation.h

src/Bpp/Phyl/Distance/HierarchicalClustering.cpp

src/Bpp/Phyl/Distance/HierarchicalClustering.h

src/Bpp/Phyl/Distance/NeighborJoining.cpp

src/Bpp/Phyl/Distance/NeighborJoining.h

src/Bpp/Phyl/Distance/PGMA.cpp

src/Bpp/Phyl/Distance/PGMA.h

src/Bpp/Phyl/Graphics

src/Bpp/Phyl/Graphics.all

src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp

src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h

src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp

src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h

src/Bpp/Phyl/Graphics/CladogramPlot.cpp

src/Bpp/Phyl/Graphics/CladogramPlot.h

src/Bpp/Phyl/Graphics/PhylogramPlot.cpp

src/Bpp/Phyl/Graphics/PhylogramPlot.h

src/Bpp/Phyl/Graphics/TreeDrawing.h

src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp

src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h

src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp

src/Bpp/Phyl/Graphics/TreeDrawingListener.h

src/Bpp/Phyl/Io

src/Bpp/Phyl/Io.all

src/Bpp/Phyl/Io/IoDistanceMatrix.h

src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp

src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h

src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp

src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h

src/Bpp/Phyl/Io/IoTree.h

src/Bpp/Phyl/Io/IoTreeFactory.cpp

src/Bpp/Phyl/Io/IoTreeFactory.h

src/Bpp/Phyl/Io/Newick.cpp

src/Bpp/Phyl/Io/Newick.h

src/Bpp/Phyl/Io/NexusIoTree.cpp

src/Bpp/Phyl/Io/NexusIoTree.h

src/Bpp/Phyl/Io/Nhx.cpp

src/Bpp/Phyl/Io/Nhx.h

src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp

src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h

src/Bpp/Phyl/Likelihood

src/Bpp/Phyl/Likelihood.all

src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h

src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h

src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h

src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h

src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp

src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h

src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp

src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h

src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h

src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h

src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp

src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h

src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h

src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp

src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h

src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp

src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h

src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp

src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h

src/Bpp/Phyl/Likelihood/RASTools.cpp

src/Bpp/Phyl/Likelihood/RASTools.h

src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h

src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h

src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h

src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/SitePartitionTreeLikelihood.h

src/Bpp/Phyl/Likelihood/TreeLikelihood.h

src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h

src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp

src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h

src/Bpp/Phyl/Mapping

src/Bpp/Phyl/Mapping.all

src/Bpp/Phyl/Mapping/AnalyticalSubstitutionCount.cpp

src/Bpp/Phyl/Mapping/AnalyticalSubstitutionCount.h

src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp

src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h

src/Bpp/Phyl/Mapping/IndexToCount.cpp

src/Bpp/Phyl/Mapping/IndexToCount.h

src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp

src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h

src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp

src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h

src/Bpp/Phyl/Mapping/SimpleSubstitutionCount.cpp

src/Bpp/Phyl/Mapping/SimpleSubstitutionCount.h

src/Bpp/Phyl/Mapping/SubstitutionCount.h

src/Bpp/Phyl/Mapping/SubstitutionMapping.h

src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp

src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h

src/Bpp/Phyl/Mapping/SubstitutionRegister.h

src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp

src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h

src/Bpp/Phyl/Model

src/Bpp/Phyl/Model.all

src/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractCodonReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractCodonReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractWordReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractWordReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/CodonAsynonymousFrequenciesReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonAsynonymousFrequenciesReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/CodonAsynonymousReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonAsynonymousReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/CodonNeutralFrequenciesReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonNeutralFrequenciesReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/CodonNeutralReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonNeutralReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/DSO78.cpp

src/Bpp/Phyl/Model/DSO78.h

src/Bpp/Phyl/Model/F84.cpp

src/Bpp/Phyl/Model/F84.h

src/Bpp/Phyl/Model/FrequenciesSet.cpp

src/Bpp/Phyl/Model/FrequenciesSet.h

src/Bpp/Phyl/Model/G2001.h

src/Bpp/Phyl/Model/GTR.cpp

src/Bpp/Phyl/Model/GTR.h

src/Bpp/Phyl/Model/GY94.cpp

src/Bpp/Phyl/Model/GY94.h

src/Bpp/Phyl/Model/HKY85.cpp

src/Bpp/Phyl/Model/HKY85.h

src/Bpp/Phyl/Model/JCnuc.cpp

src/Bpp/Phyl/Model/JCnuc.h

src/Bpp/Phyl/Model/JCprot.cpp

src/Bpp/Phyl/Model/JCprot.h

src/Bpp/Phyl/Model/JTT92.cpp

src/Bpp/Phyl/Model/JTT92.h

src/Bpp/Phyl/Model/K80.cpp

src/Bpp/Phyl/Model/K80.h

src/Bpp/Phyl/Model/L95.cpp

src/Bpp/Phyl/Model/L95.h

src/Bpp/Phyl/Model/LG08.cpp

src/Bpp/Phyl/Model/LG08.h

src/Bpp/Phyl/Model/LLG08_EHO.cpp

src/Bpp/Phyl/Model/LLG08_EHO.h

src/Bpp/Phyl/Model/LLG08_EX2.cpp

src/Bpp/Phyl/Model/LLG08_EX2.h

src/Bpp/Phyl/Model/LLG08_EX3.cpp

src/Bpp/Phyl/Model/LLG08_EX3.h

src/Bpp/Phyl/Model/LLG08_UL2.cpp

src/Bpp/Phyl/Model/LLG08_UL2.h

src/Bpp/Phyl/Model/LLG08_UL3.cpp

src/Bpp/Phyl/Model/LLG08_UL3.h

src/Bpp/Phyl/Model/MG94.cpp

src/Bpp/Phyl/Model/MG94.h

src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp

src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h

src/Bpp/Phyl/Model/MixedSubstitutionModel.h

src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp

src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h

src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp

src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h

src/Bpp/Phyl/Model/NucleotideSubstitutionModel.h

src/Bpp/Phyl/Model/ProteinSubstitutionModel.h

src/Bpp/Phyl/Model/RE08.cpp

src/Bpp/Phyl/Model/RE08.h

src/Bpp/Phyl/Model/RN95.cpp

src/Bpp/Phyl/Model/RN95.h

src/Bpp/Phyl/Model/RN95s.cpp

src/Bpp/Phyl/Model/RN95s.h

src/Bpp/Phyl/Model/RateDistributionFactory.cpp

src/Bpp/Phyl/Model/RateDistributionFactory.h

src/Bpp/Phyl/Model/SSR.cpp

src/Bpp/Phyl/Model/SSR.h

src/Bpp/Phyl/Model/SubstitutionModel.h

src/Bpp/Phyl/Model/SubstitutionModelFactory.cpp

src/Bpp/Phyl/Model/SubstitutionModelFactory.h

src/Bpp/Phyl/Model/SubstitutionModelSet.cpp

src/Bpp/Phyl/Model/SubstitutionModelSet.h

src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp

src/Bpp/Phyl/Model/SubstitutionModelSetTools.h

src/Bpp/Phyl/Model/T92.cpp

src/Bpp/Phyl/Model/T92.h

src/Bpp/Phyl/Model/TN93.cpp

src/Bpp/Phyl/Model/TN93.h

src/Bpp/Phyl/Model/TS98.h

src/Bpp/Phyl/Model/TripletReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/TripletReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/UserProteinSubstitutionModel.cpp

src/Bpp/Phyl/Model/UserProteinSubstitutionModel.h

src/Bpp/Phyl/Model/WAG01.cpp

src/Bpp/Phyl/Model/WAG01.h

src/Bpp/Phyl/Model/WordReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/WordReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/YN98.cpp

src/Bpp/Phyl/Model/YN98.h

src/Bpp/Phyl/Model/YNGKP_M1.cpp

src/Bpp/Phyl/Model/YNGKP_M1.h

src/Bpp/Phyl/Model/YNGKP_M2.cpp

src/Bpp/Phyl/Model/YNGKP_M2.h

src/Bpp/Phyl/Model/YNGKP_M3.cpp

src/Bpp/Phyl/Model/YNGKP_M3.h

src/Bpp/Phyl/Model/YNGKP_M7.cpp

src/Bpp/Phyl/Model/YNGKP_M7.h

src/Bpp/Phyl/Model/YNGKP_M8.cpp

src/Bpp/Phyl/Model/YNGKP_M8.h

src/Bpp/Phyl/Model/__DSO78ExchangeabilityCode

src/Bpp/Phyl/Model/__DSO78FrequenciesCode

src/Bpp/Phyl/Model/__JTT92ExchangeabilityCode

src/Bpp/Phyl/Model/__JTT92FrequenciesCode

src/Bpp/Phyl/Model/__LG08ExchangeabilityCode

src/Bpp/Phyl/Model/__LG08FrequenciesCode

src/Bpp/Phyl/Model/__LLG08_EHOExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_EHOFrequenciesCode

src/Bpp/Phyl/Model/__LLG08_EHORatesProps

src/Bpp/Phyl/Model/__LLG08_EX2ExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_EX2FrequenciesCode

src/Bpp/Phyl/Model/__LLG08_EX2RatesProps

src/Bpp/Phyl/Model/__LLG08_EX3ExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_EX3FrequenciesCode

src/Bpp/Phyl/Model/__LLG08_EX3RatesProps

src/Bpp/Phyl/Model/__LLG08_UL2ExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_UL2FrequenciesCode

src/Bpp/Phyl/Model/__LLG08_UL2RatesProps

src/Bpp/Phyl/Model/__LLG08_UL3ExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_UL3FrequenciesCode

src/Bpp/Phyl/Model/__LLG08_UL3RatesProps

src/Bpp/Phyl/Model/__WAG01ExchangeabilityCode

src/Bpp/Phyl/Model/__WAG01FrequenciesCode

src/Bpp/Phyl/NNISearchable.h

src/Bpp/Phyl/NNITopologySearch.cpp

src/Bpp/Phyl/NNITopologySearch.h

src/Bpp/Phyl/Node.cpp

src/Bpp/Phyl/Node.h

src/Bpp/Phyl/NodeTemplate.h

src/Bpp/Phyl/OptimizationTools.cpp

src/Bpp/Phyl/OptimizationTools.h

src/Bpp/Phyl/Parsimony

src/Bpp/Phyl/Parsimony.all

src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h

src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp

src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h

src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp

src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h

src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp

src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h

src/Bpp/Phyl/Parsimony/TreeParsimonyData.h

src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h

src/Bpp/Phyl/PatternTools.cpp

src/Bpp/Phyl/PatternTools.h

src/Bpp/Phyl/PhyloStatistics.cpp

src/Bpp/Phyl/PhyloStatistics.h

src/Bpp/Phyl/Simulation

src/Bpp/Phyl/Simulation.all

src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h

src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h

src/Bpp/Phyl/Simulation/MutationProcess.cpp

src/Bpp/Phyl/Simulation/MutationProcess.h

src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp

src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h

src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp

src/Bpp/Phyl/Simulation/SequenceSimulationTools.h

src/Bpp/Phyl/Simulation/SequenceSimulator.h

src/Bpp/Phyl/Simulation/SiteSimulator.h

src/Bpp/Phyl/SitePatterns.cpp

src/Bpp/Phyl/SitePatterns.h

src/Bpp/Phyl/TopologySearch.h

src/Bpp/Phyl/Tree.h

src/Bpp/Phyl/TreeExceptions.cpp

src/Bpp/Phyl/TreeExceptions.h

src/Bpp/Phyl/TreeTemplate.h

src/Bpp/Phyl/TreeTemplateTools.cpp

src/Bpp/Phyl/TreeTemplateTools.h

src/Bpp/Phyl/TreeTools.cpp

src/Bpp/Phyl/TreeTools.h

src/CMakeLists.txt

test

test/CMakeLists.txt

test/test_bowker.cpp

test/test_detailed_simulations.cpp

test/test_likelihood.cpp

test/test_mapping.cpp

test/test_mapping_codon.cpp

test/test_nhx.cpp

test/test_simulations.cpp

test/test_tree.cpp

Show diffs side-by-side

added added

removed removed

debian/changelog

debian/copyright

debian/libbpp-phyl-dev.install

debian/libbpp-phyl9.install

debian/source/format

src/Bpp/Phyl.all

src/Bpp/Phyl/AncestralStateReconstruction.h

src/Bpp/Phyl/App.all

src/Bpp/Phyl/App/

src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp

src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h

src/Bpp/Phyl/BipartitionList.cpp

src/Bpp/Phyl/BipartitionList.h

src/Bpp/Phyl/BipartitionTools.cpp

src/Bpp/Phyl/BipartitionTools.h

src/Bpp/Phyl/Distance.all

src/Bpp/Phyl/Distance/

src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp

src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h

src/Bpp/Phyl/Distance/AgglomerativeDistanceMethod.h

src/Bpp/Phyl/Distance/BioNJ.cpp

src/Bpp/Phyl/Distance/BioNJ.h

src/Bpp/Phyl/Distance/DistanceEstimation.cpp

src/Bpp/Phyl/Distance/DistanceEstimation.h

src/Bpp/Phyl/Distance/HierarchicalClustering.cpp

src/Bpp/Phyl/Distance/HierarchicalClustering.h

src/Bpp/Phyl/Distance/NeighborJoining.cpp

src/Bpp/Phyl/Distance/NeighborJoining.h

src/Bpp/Phyl/Distance/PGMA.cpp

src/Bpp/Phyl/Distance/PGMA.h

src/Bpp/Phyl/Graphics.all

src/Bpp/Phyl/Graphics/

src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp

src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h

src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp

src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h

src/Bpp/Phyl/Graphics/CladogramPlot.cpp

src/Bpp/Phyl/Graphics/CladogramPlot.h

src/Bpp/Phyl/Graphics/PhylogramPlot.cpp

src/Bpp/Phyl/Graphics/PhylogramPlot.h

src/Bpp/Phyl/Graphics/TreeDrawing.h

src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp

src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h

src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp

src/Bpp/Phyl/Graphics/TreeDrawingListener.h

src/Bpp/Phyl/Io.all

src/Bpp/Phyl/Io/

src/Bpp/Phyl/Io/IoDistanceMatrix.h

src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp

src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h

src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp

src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h

src/Bpp/Phyl/Io/IoTree.h

src/Bpp/Phyl/Io/IoTreeFactory.cpp

src/Bpp/Phyl/Io/IoTreeFactory.h

src/Bpp/Phyl/Io/Newick.cpp

src/Bpp/Phyl/Io/Newick.h

src/Bpp/Phyl/Io/NexusIoTree.cpp

src/Bpp/Phyl/Io/NexusIoTree.h

src/Bpp/Phyl/Io/Nhx.cpp

src/Bpp/Phyl/Io/Nhx.h

src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp

src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h

src/Bpp/Phyl/Likelihood.all

src/Bpp/Phyl/Likelihood/

src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h

src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h

src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h

src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h

src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp

src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h

src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp

src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h

src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h

src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h

src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp

src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h

src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h

src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp

src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h

src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp

src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h

src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp

src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h

src/Bpp/Phyl/Likelihood/RASTools.cpp

src/Bpp/Phyl/Likelihood/RASTools.h

src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h

src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h

src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h

src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/SitePartitionTreeLikelihood.h

src/Bpp/Phyl/Likelihood/TreeLikelihood.h

src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h

src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp

src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h

src/Bpp/Phyl/Mapping.all

src/Bpp/Phyl/Mapping/

src/Bpp/Phyl/Mapping/AnalyticalSubstitutionCount.cpp

src/Bpp/Phyl/Mapping/AnalyticalSubstitutionCount.h

src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp

src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h

src/Bpp/Phyl/Mapping/IndexToCount.cpp

src/Bpp/Phyl/Mapping/IndexToCount.h

src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp

src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h

src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp

src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h

src/Bpp/Phyl/Mapping/SimpleSubstitutionCount.cpp

src/Bpp/Phyl/Mapping/SimpleSubstitutionCount.h

src/Bpp/Phyl/Mapping/SubstitutionCount.h

src/Bpp/Phyl/Mapping/SubstitutionMapping.h

src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp

src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h

src/Bpp/Phyl/Mapping/SubstitutionRegister.h

src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp

src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h

src/Bpp/Phyl/Model.all

src/Bpp/Phyl/Model/

src/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractCodonReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractCodonReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractWordReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractWordReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/CodonAsynonymousFrequenciesReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonAsynonymousFrequenciesReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/CodonAsynonymousReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonAsynonymousReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/CodonNeutralFrequenciesReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonNeutralFrequenciesReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/CodonNeutralReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonNeutralReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/DSO78.cpp

src/Bpp/Phyl/Model/DSO78.h

src/Bpp/Phyl/Model/F84.cpp

src/Bpp/Phyl/Model/F84.h

src/Bpp/Phyl/Model/FrequenciesSet.cpp

src/Bpp/Phyl/Model/FrequenciesSet.h

src/Bpp/Phyl/Model/G2001.h

src/Bpp/Phyl/Model/GTR.cpp

src/Bpp/Phyl/Model/GTR.h

src/Bpp/Phyl/Model/GY94.cpp

src/Bpp/Phyl/Model/GY94.h

src/Bpp/Phyl/Model/HKY85.cpp

src/Bpp/Phyl/Model/HKY85.h

src/Bpp/Phyl/Model/JCnuc.cpp

src/Bpp/Phyl/Model/JCnuc.h

src/Bpp/Phyl/Model/JCprot.cpp

src/Bpp/Phyl/Model/JCprot.h

src/Bpp/Phyl/Model/JTT92.cpp

src/Bpp/Phyl/Model/JTT92.h

src/Bpp/Phyl/Model/K80.cpp

src/Bpp/Phyl/Model/K80.h

src/Bpp/Phyl/Model/L95.cpp

src/Bpp/Phyl/Model/L95.h

src/Bpp/Phyl/Model/LG08.cpp

src/Bpp/Phyl/Model/LG08.h

src/Bpp/Phyl/Model/LLG08_EHO.cpp

src/Bpp/Phyl/Model/LLG08_EHO.h

src/Bpp/Phyl/Model/LLG08_EX2.cpp

src/Bpp/Phyl/Model/LLG08_EX2.h

src/Bpp/Phyl/Model/LLG08_EX3.cpp

src/Bpp/Phyl/Model/LLG08_EX3.h

src/Bpp/Phyl/Model/LLG08_UL2.cpp

src/Bpp/Phyl/Model/LLG08_UL2.h

src/Bpp/Phyl/Model/LLG08_UL3.cpp

src/Bpp/Phyl/Model/LLG08_UL3.h

src/Bpp/Phyl/Model/MG94.cpp

src/Bpp/Phyl/Model/MG94.h

src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp

src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h

src/Bpp/Phyl/Model/MixedSubstitutionModel.h

src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp

src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h

src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp

src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h

src/Bpp/Phyl/Model/NucleotideSubstitutionModel.h

src/Bpp/Phyl/Model/ProteinSubstitutionModel.h

src/Bpp/Phyl/Model/RE08.cpp

src/Bpp/Phyl/Model/RE08.h

src/Bpp/Phyl/Model/RN95.cpp

src/Bpp/Phyl/Model/RN95.h

src/Bpp/Phyl/Model/RN95s.cpp

src/Bpp/Phyl/Model/RN95s.h

src/Bpp/Phyl/Model/RateDistributionFactory.cpp

src/Bpp/Phyl/Model/RateDistributionFactory.h

src/Bpp/Phyl/Model/SSR.cpp

src/Bpp/Phyl/Model/SSR.h

src/Bpp/Phyl/Model/SubstitutionModel.h

src/Bpp/Phyl/Model/SubstitutionModelFactory.cpp

src/Bpp/Phyl/Model/SubstitutionModelFactory.h

src/Bpp/Phyl/Model/SubstitutionModelSet.cpp

src/Bpp/Phyl/Model/SubstitutionModelSet.h

src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp

src/Bpp/Phyl/Model/SubstitutionModelSetTools.h

src/Bpp/Phyl/Model/T92.cpp

src/Bpp/Phyl/Model/T92.h

src/Bpp/Phyl/Model/TN93.cpp

src/Bpp/Phyl/Model/TN93.h

src/Bpp/Phyl/Model/TS98.h

src/Bpp/Phyl/Model/TripletReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/TripletReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/UserProteinSubstitutionModel.cpp

src/Bpp/Phyl/Model/UserProteinSubstitutionModel.h

src/Bpp/Phyl/Model/WAG01.cpp

src/Bpp/Phyl/Model/WAG01.h

src/Bpp/Phyl/Model/WordReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/WordReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/YN98.cpp

src/Bpp/Phyl/Model/YN98.h

src/Bpp/Phyl/Model/YNGKP_M1.cpp

src/Bpp/Phyl/Model/YNGKP_M1.h

src/Bpp/Phyl/Model/YNGKP_M2.cpp

src/Bpp/Phyl/Model/YNGKP_M2.h

src/Bpp/Phyl/Model/YNGKP_M3.cpp

src/Bpp/Phyl/Model/YNGKP_M3.h

src/Bpp/Phyl/Model/YNGKP_M7.cpp

src/Bpp/Phyl/Model/YNGKP_M7.h

src/Bpp/Phyl/Model/YNGKP_M8.cpp

src/Bpp/Phyl/Model/YNGKP_M8.h

src/Bpp/Phyl/Model/__DSO78ExchangeabilityCode

src/Bpp/Phyl/Model/__DSO78FrequenciesCode

src/Bpp/Phyl/Model/__JTT92ExchangeabilityCode

src/Bpp/Phyl/Model/__JTT92FrequenciesCode

src/Bpp/Phyl/Model/__LG08ExchangeabilityCode

src/Bpp/Phyl/Model/__LG08FrequenciesCode

src/Bpp/Phyl/Model/__LLG08_EHOExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_EHOFrequenciesCode

src/Bpp/Phyl/Model/__LLG08_EHORatesProps

src/Bpp/Phyl/Model/__LLG08_EX2ExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_EX2FrequenciesCode

src/Bpp/Phyl/Model/__LLG08_EX2RatesProps

src/Bpp/Phyl/Model/__LLG08_EX3ExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_EX3FrequenciesCode

src/Bpp/Phyl/Model/__LLG08_EX3RatesProps

src/Bpp/Phyl/Model/__LLG08_UL2ExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_UL2FrequenciesCode

src/Bpp/Phyl/Model/__LLG08_UL2RatesProps

src/Bpp/Phyl/Model/__LLG08_UL3ExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_UL3FrequenciesCode

src/Bpp/Phyl/Model/__LLG08_UL3RatesProps

src/Bpp/Phyl/Model/__WAG01ExchangeabilityCode

src/Bpp/Phyl/Model/__WAG01FrequenciesCode

src/Bpp/Phyl/NNISearchable.h

src/Bpp/Phyl/NNITopologySearch.cpp

src/Bpp/Phyl/NNITopologySearch.h

src/Bpp/Phyl/Node.cpp

src/Bpp/Phyl/Node.h

src/Bpp/Phyl/NodeTemplate.h

src/Bpp/Phyl/OptimizationTools.cpp

src/Bpp/Phyl/OptimizationTools.h

src/Bpp/Phyl/Parsimony.all

src/Bpp/Phyl/Parsimony/

src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h

src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp

src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h

src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp

src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h

src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp

src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h

src/Bpp/Phyl/Parsimony/TreeParsimonyData.h

src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h

src/Bpp/Phyl/PatternTools.cpp

src/Bpp/Phyl/PatternTools.h

src/Bpp/Phyl/PhyloStatistics.cpp

src/Bpp/Phyl/PhyloStatistics.h

src/Bpp/Phyl/Simulation.all

src/Bpp/Phyl/Simulation/

src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h

src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h

src/Bpp/Phyl/Simulation/MutationProcess.cpp

src/Bpp/Phyl/Simulation/MutationProcess.h

src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp

src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h

src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp

src/Bpp/Phyl/Simulation/SequenceSimulationTools.h

src/Bpp/Phyl/Simulation/SequenceSimulator.h

src/Bpp/Phyl/Simulation/SiteSimulator.h

src/Bpp/Phyl/SitePatterns.cpp

src/Bpp/Phyl/SitePatterns.h

src/Bpp/Phyl/TopologySearch.h

src/Bpp/Phyl/Tree.h

src/Bpp/Phyl/TreeExceptions.cpp

src/Bpp/Phyl/TreeExceptions.h

src/Bpp/Phyl/TreeTemplate.h

src/Bpp/Phyl/TreeTemplateTools.cpp

src/Bpp/Phyl/TreeTemplateTools.h

src/Bpp/Phyl/TreeTools.cpp

src/Bpp/Phyl/TreeTools.h

src/CMakeLists.txt

test/CMakeLists.txt

test/test_bowker.cpp

test/test_detailed_simulations.cpp

test/test_likelihood.cpp

test/test_mapping.cpp

test/test_mapping_codon.cpp

test/test_nhx.cpp

test/test_simulations.cpp

test/test_tree.cpp

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