CHANGELOG.rst
LICENSE.txt
MANIFEST.in
README.rst
setup.py
docs/ExpCM.rst
docs/Makefile
docs/README.rst
docs/acknowledgments.rst
docs/api.rst
docs/auxiliary_progs.rst
docs/conf.py
docs/example1_omega_violinplot.pdf
docs/example2_omega_violinplot.pdf
docs/example3_stringency_violinplot.pdf
docs/example4_diffprefs_violinplot.pdf
docs/example_modelcomparison.txt
docs/example_phydms_plotselection_plot.pdf
docs/index.rst
docs/indices_and_tables.rst
docs/installation.rst
docs/modules.rst
docs/phydms_analyzeselection_prog.rst
docs/phydms_comprehensive_prog.rst
docs/phydms_plotselection_prog.rst
docs/phydms_prepalignment.rst
docs/phydms_prog.rst
docs/phydms_renumber_prog.rst
docs/phydmslib.rst
docs/plot_diffprefs_prior.py
docs/quick_example.rst
docs/weblinks.txt
phydms.egg-info/PKG-INFO
phydms.egg-info/SOURCES.txt
phydms.egg-info/dependency_links.txt
phydms.egg-info/requires.txt
phydms.egg-info/top_level.txt
phydmslib/__init__.py
phydmslib/_metadata.py
phydmslib/diffpref.py
phydmslib/file_io.py
phydmslib/parsearguments.py
phydmslib/plot.py
phydmslib/pybpp.cpp
phydmslib/pybpp.pyx
phydmslib/pylsd.cpp
phydmslib/pylsd.pyx
phydmslib/utils.py
phydmslib/Bpp/README.rst
phydmslib/Bpp/bpp-core/src/Bpp/BppBoolean.h
phydmslib/Bpp/bpp-core/src/Bpp/BppString.cpp
phydmslib/Bpp/bpp-core/src/Bpp/BppString.h
phydmslib/Bpp/bpp-core/src/Bpp/BppVector.h
phydmslib/Bpp/bpp-core/src/Bpp/Clonable.h
phydmslib/Bpp/bpp-core/src/Bpp/Exceptions.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Exceptions.h
phydmslib/Bpp/bpp-core/src/Bpp/App/ApplicationTools.cpp
phydmslib/Bpp/bpp-core/src/Bpp/App/ApplicationTools.h
phydmslib/Bpp/bpp-core/src/Bpp/App/BppApplication.cpp
phydmslib/Bpp/bpp-core/src/Bpp/App/BppApplication.h
phydmslib/Bpp/bpp-core/src/Bpp/App/NumCalcApplicationTools.cpp
phydmslib/Bpp/bpp-core/src/Bpp/App/NumCalcApplicationTools.h
phydmslib/Bpp/bpp-core/src/Bpp/Graph/AssociationGraphObserver.h
phydmslib/Bpp/bpp-core/src/Bpp/Graph/AssociationTreeGraphObserver.h
phydmslib/Bpp/bpp-core/src/Bpp/Graph/BasicONode.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Graph/BasicONode.h
phydmslib/Bpp/bpp-core/src/Bpp/Graph/BasicTNode.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Graph/BasicTNode.h
phydmslib/Bpp/bpp-core/src/Bpp/Graph/Graph.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Graph/Graph.h
phydmslib/Bpp/bpp-core/src/Bpp/Graph/GraphObserver.h
phydmslib/Bpp/bpp-core/src/Bpp/Graph/ONode.h
phydmslib/Bpp/bpp-core/src/Bpp/Graph/TNode.h
phydmslib/Bpp/bpp-core/src/Bpp/Graph/TreeGraph.h
phydmslib/Bpp/bpp-core/src/Bpp/Graph/UNode.h
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/AbstractGraphicDevice.h
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/ColorManager.h
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/ColorSet.h
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/ColorTools.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/ColorTools.h
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/DefaultColorSet.h
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/GraphicDevice.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/GraphicDevice.h
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/Point2D.h
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/Point2DTools.h
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/RgbColor.h
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/Fig/XFigGraphicDevice.cpp
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phydmslib/Bpp/bpp-core/src/Bpp/Graphics/Font/Font.cpp
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phydmslib/Bpp/bpp-core/src/Bpp/Graphics/Font/FontManager.h
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/Latex/DvipsColorSet.cpp
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phydmslib/Bpp/bpp-core/src/Bpp/Graphics/Latex/PgfGraphicDevice.cpp
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phydmslib/Bpp/bpp-core/src/Bpp/Graphics/Molscript/MolscriptColorSet.cpp
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phydmslib/Bpp/bpp-core/src/Bpp/Graphics/R/RColorSet.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/R/RColorSet.h
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/Svg/SvgGraphicDevice.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Graphics/Svg/SvgGraphicDevice.h
phydmslib/Bpp/bpp-core/src/Bpp/Io/BppODiscreteDistributionFormat.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Io/BppODiscreteDistributionFormat.h
phydmslib/Bpp/bpp-core/src/Bpp/Io/BppOParametrizableFormat.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Io/BppOParametrizableFormat.h
phydmslib/Bpp/bpp-core/src/Bpp/Io/FileTools.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Io/FileTools.h
phydmslib/Bpp/bpp-core/src/Bpp/Io/IoDiscreteDistribution.h
phydmslib/Bpp/bpp-core/src/Bpp/Io/IoDiscreteDistributionFactory.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Io/IoDiscreteDistributionFactory.h
phydmslib/Bpp/bpp-core/src/Bpp/Io/IoFormat.h
phydmslib/Bpp/bpp-core/src/Bpp/Io/IoParametrizable.h
phydmslib/Bpp/bpp-core/src/Bpp/Io/OutputStream.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/AbstractParameterAliasable.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/AbstractParameterAliasable.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/AbstractParametrizable.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/AbstractParametrizable.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/AdaptiveKernelDensityEstimation.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/AdaptiveKernelDensityEstimation.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/AutoParameter.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/AutoParameter.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Constraints.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/DataTable.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/DataTable.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/DataTableExceptions.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/NumConstants.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/NumTools.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/NumTools.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Number.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Parameter.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Parameter.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/ParameterAliasable.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/ParameterExceptions.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/ParameterExceptions.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/ParameterList.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/ParameterList.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Parametrizable.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/ParametrizableCollection.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Range.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/TransformedParameter.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/VectorExceptions.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/VectorTools.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/VectorTools.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/AbstractNumericalDerivative.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/AbstractOptimizer.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/AbstractOptimizer.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/BfgsMultiDimensions.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/BfgsMultiDimensions.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/BrentOneDimension.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/BrentOneDimension.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/ConjugateGradientMultiDimensions.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/ConjugateGradientMultiDimensions.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/DirectionFunction.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/DirectionFunction.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/DownhillSimplexMethod.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/DownhillSimplexMethod.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/FivePointsNumericalDerivative.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/FivePointsNumericalDerivative.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/FunctionTools.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/FunctionTools.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/Functions.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/GoldenSectionSearch.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/GoldenSectionSearch.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/MetaOptimizer.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/MetaOptimizer.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/NewtonBacktrackOneDimension.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/NewtonBacktrackOneDimension.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/NewtonOneDimension.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/NewtonOneDimension.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/OneDimensionOptimizationTools.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/OneDimensionOptimizationTools.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/OptimizationStopCondition.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/OptimizationStopCondition.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/Optimizer.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/PowellMultiDimensions.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/PowellMultiDimensions.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/SimpleMultiDimensions.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/SimpleMultiDimensions.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/SimpleNewtonMultiDimensions.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/SimpleNewtonMultiDimensions.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/TwoPointsNumericalDerivative.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Function/TwoPointsNumericalDerivative.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/AutoCorrelationTransitionMatrix.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/AutoCorrelationTransitionMatrix.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/HmmEmissionProbabilities.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/HmmExceptions.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/HmmLikelihood.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/HmmLikelihood.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/HmmStateAlphabet.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/HmmTransitionMatrix.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Matrix/EigenValue.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Matrix/LUDecomposition.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Matrix/Matrix.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Matrix/MatrixTools.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/BetaDiscreteDistribution.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/BetaDiscreteDistribution.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/ConstantDistribution.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/ConstantDistribution.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/DirichletDiscreteDistribution.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/DirichletDiscreteDistribution.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/DiscreteDistribution.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/GammaDiscreteDistribution.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/GammaDiscreteDistribution.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/GaussianDiscreteDistribution.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/GaussianDiscreteDistribution.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/MixtureOfDiscreteDistributions.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/MixtureOfDiscreteDistributions.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/MultipleDiscreteDistribution.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/Simplex.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/Simplex.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/UniformDiscreteDistribution.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Prob/UniformDiscreteDistribution.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Random/ContingencyTableGenerator.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Random/ContingencyTableGenerator.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Random/RandomFactory.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Random/RandomTools.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Random/RandomTools.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Random/Uniform01K.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Random/Uniform01K.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Random/Uniform01QD.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Random/Uniform01QD.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Random/Uniform01WH.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Random/Uniform01WH.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Stat/ContingencyTableTest.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Stat/ContingencyTableTest.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Stat/StatTest.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Stat/StatTools.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Stat/StatTools.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Stat/Mva/CorrespondenceAnalysis.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Stat/Mva/CorrespondenceAnalysis.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Stat/Mva/DualityDiagram.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Stat/Mva/DualityDiagram.h
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Stat/Mva/PrincipalComponentAnalysis.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Numeric/Stat/Mva/PrincipalComponentAnalysis.h
phydmslib/Bpp/bpp-core/src/Bpp/Text/KeyvalTools.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Text/KeyvalTools.h
phydmslib/Bpp/bpp-core/src/Bpp/Text/NestedStringTokenizer.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Text/NestedStringTokenizer.h
phydmslib/Bpp/bpp-core/src/Bpp/Text/StringTokenizer.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Text/StringTokenizer.h
phydmslib/Bpp/bpp-core/src/Bpp/Text/TextTools.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Text/TextTools.h
phydmslib/Bpp/bpp-core/src/Bpp/Utils/AttributesTools.cpp
phydmslib/Bpp/bpp-core/src/Bpp/Utils/AttributesTools.h
phydmslib/Bpp/bpp-core/src/Bpp/Utils/MapTools.h
phydmslib/Bpp/bpp-core/test/PolynomialFunction.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/AncestralStateReconstruction.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/OptimizationTools.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/OptimizationTools.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/PatternTools.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/PatternTools.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/PhyloStatistics.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/PhyloStatistics.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/SitePatterns.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/SitePatterns.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Distance/BioNJ.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Distance/BioNJ.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Distance/DistanceEstimation.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Distance/DistanceEstimation.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Distance/DistanceMethod.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Distance/HierarchicalClustering.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Distance/NeighborJoining.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Distance/NeighborJoining.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Distance/PGMA.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Distance/PGMA.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Graphics/CladogramPlot.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Graphics/CladogramPlot.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Graphics/PhylogramPlot.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Graphics/TreeDrawing.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Graphics/TreeDrawingListener.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/BppORateDistributionFormat.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/IoDistanceMatrix.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/IoFrequenciesSet.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/IoSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/IoTree.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/IoTreeFactory.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/IoTreeFactory.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/Newick.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/Newick.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/NexusIoTree.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/NexusIoTree.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/Nhx.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/Nhx.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/RASTools.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/RASTools.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/SitePartitionTreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/TreeLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/CategorySubstitutionRegister.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/DecompositionReward.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/DecompositionReward.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/Mapping.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/Reward.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/RewardMapping.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/RewardMappingTools.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/SubstitutionCount.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/SubstitutionMapping.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/SubstitutionRegister.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/BinarySubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/G2001.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/MixedSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/RE08.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/RE08.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/StateMap.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/StateMap.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/SubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/SubstitutionModelSet.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/SubstitutionModelSetTools.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/TS98.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/WordSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/WordSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/GY94.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/GY94.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/MG94.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/MG94.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/SENCA.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/SENCA.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YN98.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YN98.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YNGKP_M1.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YNGKP_M1.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YNGKP_M10.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YNGKP_M10.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YNGKP_M2.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YNGKP_M2.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YNGKP_M3.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YNGKP_M3.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YNGKP_M7.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YNGKP_M7.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YNGKP_M8.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YNGKP_M8.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YNGKP_M9.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Codon/YNGKP_M9.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/FrequenciesSet/ProteinFrequenciesSet.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/F81.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/F81.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/F84.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/F84.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/GTR.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/HKY85.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/JCnuc.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/K80.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/K80.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/L95.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/L95.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/RN95.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/RN95s.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/SSR.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/T92.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/T92.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/TN93.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/YpR.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Nucleotide/gBGC.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/Coala.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/Coala.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/CoalaCore.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/DSO78.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/DSO78.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/JCprot.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/JCprot.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/JTT92.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/JTT92.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LG08.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LG08.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LGL08_CAT.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LLG08_EHO.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LLG08_EX2.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LLG08_EX3.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LLG08_UL2.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/LLG08_UL3.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/WAG01.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/WAG01.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__CATC10FrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__CATC10RatesProps
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__CATC20FrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__CATC20RatesProps
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__CATC30FrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__CATC30RatesProps
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__CATC40FrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__CATC40RatesProps
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__CATC50FrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__CATC50RatesProps
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__CATC60FrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__CATC60RatesProps
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__DSO78ExchangeabilityCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__DSO78FrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__JTT92ExchangeabilityCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__JTT92FrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LG08ExchangeabilityCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LG08FrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LG10_EX_EHOExchangeabilityCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LG10_EX_EHOFrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LG10_EX_EHORatesProps
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_EHOExchangeabilityCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_EHOFrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_EHORatesProps
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_EX2ExchangeabilityCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_EX2FrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_EX2RatesProps
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_EX3ExchangeabilityCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_EX3FrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_EX3RatesProps
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_UL2ExchangeabilityCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_UL2FrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_UL2RatesProps
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_UL3ExchangeabilityCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_UL3FrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__LLG08_UL3RatesProps
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__WAG01ExchangeabilityCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/Protein/__WAG01FrequenciesCode
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/AbstractLikelihoodNode.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/AbstractLikelihoodNode.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/AbstractLikelihoodTree.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/AbstractLikelihoodTree.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/AbstractLikelihoodTreeCalculation.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/AbstractLikelihoodTreeCalculation.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/AbstractSubstitutionProcess.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/AbstractSubstitutionProcess.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/AutoCorrelationSequenceEvolution.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/AutoCorrelationSequenceEvolution.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/ComputingNode.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/ComputingNode.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/ComputingTree.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/ComputingTree.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/HmmProcessAlphabet.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/HmmProcessEmissionProbabilities.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/HmmProcessEmissionProbabilities.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/HmmSequenceEvolution.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/HmmSequenceEvolution.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/LikelihoodNode.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/LikelihoodTree.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/LikelihoodTreeCalculation.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/MarginalAncestralReconstruction.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/MarginalAncestralReconstruction.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/MixtureSequenceEvolution.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/MixtureSequenceEvolution.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/ModelIterator.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/MultiProcessSequenceEvolution.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/MultiProcessSequenceEvolution.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/NonHomogeneousSubstitutionProcess.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/NonHomogeneousSubstitutionProcess.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/OneProcessSequenceEvolution.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/OneProcessSequenceEvolution.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/ParametrizableTree.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/ParametrizableTree.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PartitionSequenceEvolution.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PartitionSequenceEvolution.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/RateAcrossSitesSubstitutionProcess.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/RateAcrossSitesSubstitutionProcess.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/RecursiveLikelihoodNode.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/RecursiveLikelihoodTree.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/RecursiveLikelihoodTree.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/RecursiveLikelihoodTreeCalculation.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/RecursiveLikelihoodTreeCalculation.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/SequenceEvolution.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/SimpleSubstitutionProcess.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/SimpleSubstitutionProcess.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/SitePartition.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/SubstitutionProcess.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/SubstitutionProcessCollection.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/SubstitutionProcessCollection.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/SubstitutionProcessCollectionMember.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/SubstitutionProcessCollectionMember.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/AlignedPhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/AutoCorrelationOfAlignedPhyloLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/AutoCorrelationOfAlignedPhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/AutoCorrelationProcessPhyloLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/AutoCorrelationProcessPhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/HmmOfAlignedPhyloLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/HmmOfAlignedPhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/HmmPhyloAlphabet.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/HmmPhyloEmissionProbabilities.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/HmmPhyloEmissionProbabilities.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/HmmProcessPhyloLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/HmmProcessPhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/MixtureOfAlignedPhyloLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/MixtureOfAlignedPhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/MixtureProcessPhyloLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/MixtureProcessPhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/MultiProcessSequencePhyloLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/MultiProcessSequencePhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/OneProcessSequencePhyloLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/OneProcessSequencePhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/PartitionProcessPhyloLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/PartitionProcessPhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/PhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/PhyloLikelihoodContainer.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/ProductOfAlignedPhyloLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/ProductOfAlignedPhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/ProductOfPhyloLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/ProductOfPhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/SequencePhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/SetOfAbstractPhyloLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/SetOfAbstractPhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/SetOfAlignedPhyloLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/SetOfAlignedPhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/SingleDataPhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/SingleProcessPhyloLikelihood.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/NewLikelihood/PhyloLikelihoods/SingleProcessPhyloLikelihood.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Parsimony/TreeParsimonyData.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Simulation/EvolutionSequenceSimulator.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Simulation/EvolutionSequenceSimulator.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Simulation/MutationProcess.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Simulation/MutationProcess.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Simulation/SequenceSimulationTools.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Simulation/SequenceSimulator.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Simulation/SiteSimulator.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Simulation/SubstitutionProcessSequenceSimulator.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Simulation/SubstitutionProcessSequenceSimulator.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/BipartitionList.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/BipartitionList.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/BipartitionTools.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/BipartitionTools.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/NNISearchable.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/NNITopologySearch.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/NNITopologySearch.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/Node.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/Node.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/NodeTemplate.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/TopologySearch.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/Tree.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/TreeExceptions.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/TreeExceptions.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/TreeTemplate.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/TreeTemplateTools.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/TreeTemplateTools.h
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/TreeTools.cpp
phydmslib/Bpp/bpp-phyl/src/Bpp/Phyl/Tree/TreeTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/CodonSiteTools.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/CodonSiteTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/CoreSequence.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/CoreSite.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/DNAToRNA.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/DNAToRNA.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/DistanceMatrix.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/DistanceMatrix.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/NucleicAcidsReplication.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/NucleicAcidsReplication.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/ProbabilisticSequence.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/ProbabilisticSequence.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/ProbabilisticSite.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/ProbabilisticSite.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/ProbabilisticSymbolList.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/ProbabilisticSymbolList.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/ProbabilisticSymbolListTools.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/ProbabilisticSymbolListTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Sequence.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Sequence.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceExceptions.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceExceptions.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceIterator.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequencePositionIterators.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequencePositionIterators.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceTools.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceWalker.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceWalker.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceWithAnnotation.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceWithAnnotation.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceWithAnnotationTools.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceWithAnnotationTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceWithQuality.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceWithQuality.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceWithQualityTools.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SequenceWithQualityTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Site.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Site.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SiteExceptions.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SiteExceptions.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SiteIterator.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SiteTools.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SiteTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/StringSequenceTools.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/StringSequenceTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SymbolList.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SymbolList.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SymbolListTools.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/SymbolListTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Transliterator.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Transliterator.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/AbstractAlphabet.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/Alphabet.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/AlphabetExceptions.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/AlphabetNumericState.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/AlphabetState.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/AlphabetTools.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/AlphabetTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/BinaryAlphabet.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/CodonAlphabet.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/DNA.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/DNA.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/DefaultAlphabet.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/IntegerAlphabet.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/IntegerAlphabet.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/LetterAlphabet.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/LetterAlphabet.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/LexicalAlphabet.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/NucleicAlphabet.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/NucleicAlphabetState.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/NumericAlphabet.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/ProteicAlphabet.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/ProteicAlphabetState.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/RNA.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/RNA.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/RNY.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/RNY.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/WordAlphabet.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Alphabet/WordAlphabet.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AAChargeIndex.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AAMassIndex.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AASEA1030Index.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AASEAInf10Index.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AASEASup30Index.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AASurfaceIndex.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AAVolumeIndex.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AlphabetIndex1.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/BLOSUM50.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/GranthamAAPolarityIndex.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/SimpleScore.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/UserAlphabetIndex1.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/__BLOSUM50MatrixCode
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/__GranthamMatrixCode
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/AlphabetIndex/__MiyataMatrixCode
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/App/SequenceApplicationTools.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/App/SequenceApplicationTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/AbstractSequenceContainer.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/AlignedSequenceContainer.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/MapSequenceContainer.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/MapSequenceContainer.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/OrderedSequenceContainer.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/SequenceContainer.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/SequenceContainerExceptions.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/SequenceContainerIterator.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/SequenceContainerIterator.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/SequenceContainerTools.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/SequenceContainerTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/SiteContainer.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/SiteContainerExceptions.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/SiteContainerExceptions.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/SiteContainerIterator.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/SiteContainerIterator.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/SiteContainerTools.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/SiteContainerTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/VectorSequenceContainer.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/VectorSequenceContainer.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/VectorSiteContainer.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Container/VectorSiteContainer.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/GeneticCode.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/GeneticCode.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/StandardGeneticCode.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/AbstractIAlignment.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/AbstractISequence.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/AbstractOAlignment.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/AbstractOSequence.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/Clustal.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/Clustal.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/Dcse.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/Dcse.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/Fasta.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/Fasta.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/GenBank.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/GenBank.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/ISequence.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/ISequenceStream.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/IoSequence.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/IoSequenceFactory.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/IoSequenceFactory.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/IoSequenceStream.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/Mase.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/Mase.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/MaseTools.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/MaseTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/NexusIoSequence.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/NexusIoSequence.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/NexusTools.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/NexusTools.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/OSequence.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/OSequenceStream.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/Pasta.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/Pasta.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/PhredPhd.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/PhredPhd.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/PhredPoly.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/PhredPoly.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/Phylip.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/Phylip.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/SequenceFileIndex.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/Stockholm.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/Stockholm.h
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/StreamSequenceIterator.cpp
phydmslib/Bpp/bpp-seq/src/Bpp/Seq/Io/StreamSequenceIterator.h
phydmslib/BppExtensions/BppTreeLikelihood.cpp
phydmslib/BppExtensions/BppTreeLikelihood.h
phydmslib/BppExtensions/ExperimentallyInformedCodonModel.cpp
phydmslib/BppExtensions/ExperimentallyInformedCodonModel.h
phydmslib/BppExtensions/README.rst
phydmslib/LSD/README.rst
phydmslib/LSD/lsd/src/dating.cpp
phydmslib/LSD/lsd/src/dating.h
phydmslib/LSD/lsd/src/dating_relative.cpp
phydmslib/LSD/lsd/src/dating_relative.h
phydmslib/LSD/lsd/src/estimate_root_relative_rooted.cpp
phydmslib/LSD/lsd/src/estimate_root_relative_rooted.h
phydmslib/LSD/lsd/src/estimate_root_relative_unrooted.cpp
phydmslib/LSD/lsd/src/estimate_root_relative_unrooted.h
phydmslib/LSD/lsd/src/estimate_root_rooted.cpp
phydmslib/LSD/lsd/src/estimate_root_rooted.h
phydmslib/LSD/lsd/src/estimate_root_unrooted.cpp
phydmslib/LSD/lsd/src/estimate_root_unrooted.h
phydmslib/LSD/lsd/src/options.cpp
phydmslib/LSD/lsd/src/options.h
phydmslib/LSD/lsd/src/readData.cpp
phydmslib/LSD/lsd/src/readData.h
phydmslib/LSD/lsd/src/utils.cpp
phydmslib/LSD/lsd/src/utils.h
phydmslib/LSDExtensions/README.rst
phydmslib/LSDExtensions/lsd.cpp
phydmslib/LSDExtensions/lsd.h
scripts/phydms
scripts/phydms_analyzeselection
scripts/phydms_comprehensive
scripts/phydms_plotselection
scripts/phydms_prepalignment
scripts/phydms_renumber
tests/Gal4_prefs.txt
tests/Gal4s.fasta
tests/NP_prefs.txt
tests/README.rst
tests/env_alignment.fasta
tests/env_prefs.txt
tests/run_Gal4test.py
tests/run_NPtest.py
tests/run_doctests.py
tests/run_envtest.py
tests/run_prepalignment_test.py
tests/seqdates.txt
tests/smallNPs.fasta