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Viewing all changes in revision 1.

Committer: Package Import Robot
Author(s): Andreas Tille
Date: 2012-01-27 13:57:54 UTC
Revision ID: package-import@ubuntu.com-20120127135754-d63l3581f65fw9pk

Tags: upstream-1.5.1

Import upstream version 1.5.1

files added:

General Notes.txt

README.html

doc

doc/acknowledgements.html

doc/contributing.html

doc/download.html

doc/features.html

doc/history.html

doc/index.html

doc/license.html

doc/online.html

doc/pal.gif

doc/people.html

doc/related.html

doc/user_interfaces.html

src

src/build.xml

src/makeclean.bat

src/makefile

src/makejar-signed.bat

src/makejar.bat

src/makejike.bat

src/newmake.bat

src/pal

src/pal/algorithmics

src/pal/algorithmics/Assessor.java

src/pal/algorithmics/GeneralObjectState.java

src/pal/algorithmics/Markable.java

src/pal/algorithmics/ObjectState.java

src/pal/algorithmics/ProbabilityIterator.java

src/pal/algorithmics/Ranker.java

src/pal/algorithmics/SearchEngine.java

src/pal/algorithmics/StateProvider.java

src/pal/algorithmics/StoppingCriteria.java

src/pal/algorithmics/UndoableAction.java

src/pal/alignment

src/pal/alignment/AbstractAlignment.java

src/pal/alignment/Alignment.java

src/pal/alignment/AlignmentBuilder.java

src/pal/alignment/AlignmentGenerator.java

src/pal/alignment/AlignmentParseException.java

src/pal/alignment/AlignmentReaders.java

src/pal/alignment/AlignmentReceiver.java

src/pal/alignment/AlignmentTool.java

src/pal/alignment/AlignmentUtils.java

src/pal/alignment/AnnotationAlignment.java

src/pal/alignment/BootstrappedAlignment.java

src/pal/alignment/CharacterAlignment.java

src/pal/alignment/ConcatenatedAlignment.java

src/pal/alignment/ConcatenatedAnnotatedAlignment.java

src/pal/alignment/DataTranslator.java

src/pal/alignment/GapBalancedAlignment.java

src/pal/alignment/Genotype.java

src/pal/alignment/IndelAlignment.java

src/pal/alignment/IndelAnnotatedAlignment.java

src/pal/alignment/JumbledAlignment.java

src/pal/alignment/MultiLocusAnnotatedAlignment.java

src/pal/alignment/ReadAlignment.java

src/pal/alignment/ReadAlignmentOld.java

src/pal/alignment/SimpleAlignment.java

src/pal/alignment/SimpleAnnotatedAlignment.java

src/pal/alignment/SimpleCharacterAlignment.java

src/pal/alignment/SitePattern.java

src/pal/alignment/StrippedAlignment.java

src/pal/alignment/StrippedAnnotatedAlignment.java

src/pal/alignment/makefile

src/pal/alignment/package.html

src/pal/coalescent

src/pal/coalescent/CoalescentException.java

src/pal/coalescent/CoalescentIntervals.java

src/pal/coalescent/CoalescentSimulator.java

src/pal/coalescent/CoalescentTree.java

src/pal/coalescent/ConstExpConst.java

src/pal/coalescent/ConstExpGrowth.java

src/pal/coalescent/ConstantPopulation.java

src/pal/coalescent/DemographicClockTree.java

src/pal/coalescent/DemographicModel.java

src/pal/coalescent/DemographicTree.java

src/pal/coalescent/ExpandingPopulation.java

src/pal/coalescent/ExponentialGrowth.java

src/pal/coalescent/IntervalsExtractor.java

src/pal/coalescent/SerialCoalescentGenerator.java

src/pal/coalescent/SerialCoalescentSimulator.java

src/pal/coalescent/SkylinePlot.java

src/pal/coalescent/makefile

src/pal/coalescent/package.html

src/pal/datatype

src/pal/datatype/.#SpecificAminoAcids.java.1.6

src/pal/datatype/AmbiguousDataType.java

src/pal/datatype/AminoAcids.java

src/pal/datatype/CodonTable.java

src/pal/datatype/CodonTableFactory.java

src/pal/datatype/CodonTableUtils.java

src/pal/datatype/Codons.java

src/pal/datatype/DataType.java

src/pal/datatype/DataTypeTool.java

src/pal/datatype/GapBalanced.java

src/pal/datatype/IUPACNucleotides.java

src/pal/datatype/IUPACPenaltyTable.java

src/pal/datatype/MolecularDataType.java

src/pal/datatype/Nucleotides.java

src/pal/datatype/NumericDataType.java

src/pal/datatype/SimpleDataType.java

src/pal/datatype/SpecificAminoAcids.java

src/pal/datatype/StateRemover.java

src/pal/datatype/TransitionPenaltyTable.java

src/pal/datatype/TwoStates.java

src/pal/datatype/makefile

src/pal/datatype/package.html

src/pal/distance

src/pal/distance/AlignmentDistanceMatrix.java

src/pal/distance/DistanceMatrix.java

src/pal/distance/DistanceMatrixAccess.java

src/pal/distance/DistanceMatrixGenerator.java

src/pal/distance/DistanceMatrixUtils.java

src/pal/distance/DistanceParseException.java

src/pal/distance/DistanceTool.java

src/pal/distance/JukesCantorDistanceMatrix.java

src/pal/distance/PairwiseDistance.java

src/pal/distance/ReadDistanceMatrix.java

src/pal/distance/SequencePairLikelihood.java

src/pal/distance/makefile

src/pal/distance/package.html

src/pal/eval

src/pal/eval/ChiSquareValue.java

src/pal/eval/ConditionalProbabilityStore.java

src/pal/eval/DemographicLikelihoodValue.java

src/pal/eval/DemographicValue.java

src/pal/eval/FastFourStateLHCalculator.java

src/pal/eval/FastLikelihoodCalculator.java

src/pal/eval/GeneralLikelihoodCalculator.java

src/pal/eval/LHCalculator.java

src/pal/eval/LikelihoodCalculator.java

src/pal/eval/LikelihoodOptimiser.java

src/pal/eval/LikelihoodSummary.java

src/pal/eval/LikelihoodTool.java

src/pal/eval/LikelihoodValue.java

src/pal/eval/ModelParameters.java

src/pal/eval/MolecularClockLikelihoodModel.java

src/pal/eval/PatternInfo.java

src/pal/eval/SimpleLHCalculator.java

src/pal/eval/SimpleLeafCalculator.java

src/pal/eval/SimpleLikelihoodCalculator.java

src/pal/eval/SimpleModelFastFourStateLHCalculator.java

src/pal/eval/SimpleMolecularClockLikelihoodModel.java

src/pal/eval/SimpleUnconstrainedLikelihoodModel.java

src/pal/eval/SingleSplitMolecularClockLikelihoodModel.java

src/pal/eval/SiteDetails.java

src/pal/eval/UnconstrainedLikelihoodModel.java

src/pal/eval/makefile

src/pal/eval/package.html

src/pal/gui

src/pal/gui/CircularGraphics.java

src/pal/gui/LabelDisplayer.java

src/pal/gui/LayoutTracker.java

src/pal/gui/LinkageDisequilibriumComponent.java

src/pal/gui/NameColouriser.java

src/pal/gui/Painter.java

src/pal/gui/PositionedNode.java

src/pal/gui/TreeComponent.java

src/pal/gui/TreePainter.java

src/pal/gui/TreePainterCircular.java

src/pal/gui/TreePainterNormal.java

src/pal/gui/makefile

src/pal/gui/package.html

src/pal/io

src/pal/io/FormattedInput.java

src/pal/io/FormattedOutput.java

src/pal/io/InputSource.java

src/pal/io/NexusParseException.java

src/pal/io/NexusTokenizer.java

src/pal/io/OutputTarget.java

src/pal/io/makefile

src/pal/io/package.html

src/pal/makefile

src/pal/math

src/pal/math/Binomial.java

src/pal/math/BoundsCheckedFunction.java

src/pal/math/ConjugateDirectionSearch.java

src/pal/math/ConjugateGradientSearch.java

src/pal/math/DifferentialEvolution.java

src/pal/math/ErrorFunction.java

src/pal/math/EvaluationCounter.java

src/pal/math/GammaFunction.java

src/pal/math/GeneralizedDEOptimizer.java

src/pal/math/LMSSolver.java

src/pal/math/LineFunction.java

src/pal/math/MFWithGradient.java

src/pal/math/MachineAccuracy.java

src/pal/math/MathUtils.java

src/pal/math/Matrix.java

src/pal/math/MersenneTwisterFast.java

src/pal/math/MinimiserMonitor.java

src/pal/math/MultivariateFunction.java

src/pal/math/MultivariateMinimum.java

src/pal/math/NumericalDerivative.java

src/pal/math/OrderEnumerator.java

src/pal/math/OrthogonalHints.java

src/pal/math/OrthogonalLineFunction.java

src/pal/math/OrthogonalSearch.java

src/pal/math/UnivariateFunction.java

src/pal/math/UnivariateMinimum.java

src/pal/math/UrnModel.java

src/pal/math/makefile

src/pal/math/package.html

src/pal/mep

src/pal/mep/ConstantMutationRate.java

src/pal/mep/DeltaModel.java

src/pal/mep/MutationRateModel.java

src/pal/mep/SteppedMutationRate.java

src/pal/mep/WindowedMutationRate.java

src/pal/mep/makefile

src/pal/mep/package.html

src/pal/misc

src/pal/misc/Attribute.java

src/pal/misc/BranchLimits.java

src/pal/misc/ExternalParameterListener.java

src/pal/misc/IdGenerator.java

src/pal/misc/IdGroup.java

src/pal/misc/Identifier.java

src/pal/misc/IndividualParameterHandler.java

src/pal/misc/LabelMapping.java

src/pal/misc/MultiParameterized.java

src/pal/misc/MutableDouble.java

src/pal/misc/Nameable.java

src/pal/misc/NamedParameterized.java

src/pal/misc/NeoParameterized.java

src/pal/misc/PalEventMulticaster.java

src/pal/misc/PalObjectEvent.java

src/pal/misc/PalObjectListener.java

src/pal/misc/ParameterEvent.java

src/pal/misc/Parameterized.java

src/pal/misc/ParameterizedDoubleBundle.java

src/pal/misc/ParameterizedNeoWrapper.java

src/pal/misc/ReleaseInfo.java

src/pal/misc/Report.java

src/pal/misc/SampleInformation.java

src/pal/misc/SimpleIdGroup.java

src/pal/misc/SimpleSummarizable.java

src/pal/misc/Summarizable.java

src/pal/misc/TOCDSampleInformation.java

src/pal/misc/TableReport.java

src/pal/misc/TimeOrderCharacterData.java

src/pal/misc/TimeStamp.java

src/pal/misc/Units.java

src/pal/misc/UnitsProvider.java

src/pal/misc/Utils.java

src/pal/misc/makefile

src/pal/misc/package.html

src/pal/popgen

src/pal/popgen/LinkageDisequilibrium.java

src/pal/popgen/makefile

src/pal/popgen/package.html

src/pal/statistics

src/pal/statistics/BootstrapStatistics.java

src/pal/statistics/ChiSquareDistribution.java

src/pal/statistics/ChiSquareTest.java

src/pal/statistics/ContigencyTable.java

src/pal/statistics/DiscreteStatistics.java

src/pal/statistics/ExponentialDistribution.java

src/pal/statistics/FisherExact.java

src/pal/statistics/GammaDistribution.java

src/pal/statistics/GeneralTopologyPool.java

src/pal/statistics/KishinoHasegawaTest.java

src/pal/statistics/LikelihoodEvaluator.java

src/pal/statistics/LikelihoodRatioTest.java

src/pal/statistics/ModelSupport.java

src/pal/statistics/NormalDistribution.java

src/pal/statistics/ParetoDistribution.java

src/pal/statistics/PenalizedLikelihood.java

src/pal/statistics/RELLTopologyPool.java

src/pal/statistics/ReplicateLikelihoodEvaluator.java

src/pal/statistics/ShimodairaHasegawaStatistics.java

src/pal/statistics/ShimodairaHasegawaTest.java

src/pal/statistics/TopologyTestEngine.java

src/pal/statistics/makefile

src/pal/statistics/package.html

src/pal/substmodel

src/pal/substmodel/AbstractRateMatrix.java

src/pal/substmodel/AminoAcidModel.java

src/pal/substmodel/AminoAcidModelID.java

src/pal/substmodel/BLOSUM62.java

src/pal/substmodel/CPREV.java

src/pal/substmodel/CachedRateMatrix.java

src/pal/substmodel/ClassDistribution.java

src/pal/substmodel/CodonModel.java

src/pal/substmodel/ConstantIndependentSingleSplitDistribution.java

src/pal/substmodel/Dayhoff.java

src/pal/substmodel/F81.java

src/pal/substmodel/F84.java

src/pal/substmodel/GTR.java

src/pal/substmodel/GammaRates.java

src/pal/substmodel/GeneralPoissonRateMatrix.java

src/pal/substmodel/GeneralREVRateMatrix.java

src/pal/substmodel/GeneralRateDistributionSubstitutionModel.java

src/pal/substmodel/HKY.java

src/pal/substmodel/InvariableSites.java

src/pal/substmodel/JTT.java

src/pal/substmodel/MTREV24.java

src/pal/substmodel/MatrixExponential.java

src/pal/substmodel/MultiRateMatrixHandler.java

src/pal/substmodel/NeoRateMatrix.java

src/pal/substmodel/NeutralSelectionRateMatrixGroup.java

src/pal/substmodel/NucleotideModel.java

src/pal/substmodel/NucleotideModelID.java

src/pal/substmodel/PositiveSelectionRateMatrixGroup.java

src/pal/substmodel/RateDistribution.java

src/pal/substmodel/RateMatrix.java

src/pal/substmodel/RateMatrixGroup.java

src/pal/substmodel/RateMatrixHandler.java

src/pal/substmodel/RateMatrixUtils.java

src/pal/substmodel/SaturatedSingleSplitDistribution.java

src/pal/substmodel/SequenceSimulator.java

src/pal/substmodel/SimpleRateMatrixGroup.java

src/pal/substmodel/SingleClassSubstitutionModel.java

src/pal/substmodel/SingleSplitDistribution.java

src/pal/substmodel/SubstitutionModel.java

src/pal/substmodel/SubstitutionTool.java

src/pal/substmodel/TN.java

src/pal/substmodel/TemporalModelChange.java

src/pal/substmodel/TwoStateModel.java

src/pal/substmodel/UniformRate.java

src/pal/substmodel/VT.java

src/pal/substmodel/VariableIndependentSingleSplitDistribution.java

src/pal/substmodel/WAG.java

src/pal/substmodel/YangCodonModel.java

src/pal/substmodel/makefile

src/pal/substmodel/package.html

src/pal/supgma

src/pal/supgma/RateHandler.java

src/pal/supgma/SUPGMABase.java

src/pal/supgma/SUPGMADistanceMatrix.java

src/pal/supgma/SUPGMATree.java

src/pal/supgma/ThetaHandler.java

src/pal/tree

src/pal/tree/AttributeNode.java

src/pal/tree/CladeSystem.java

src/pal/tree/ClockTree.java

src/pal/tree/ClusterTree.java

src/pal/tree/Local.java

src/pal/tree/LogParameterizedTree.java

src/pal/tree/MutationRateModelTree.java

src/pal/tree/NeighborJoiningTree.java

src/pal/tree/Node.java

src/pal/tree/NodeFactory.java

src/pal/tree/NodeUtils.java

src/pal/tree/ParameterizedTree.java

src/pal/tree/ReadTree.java

src/pal/tree/RootedTreeInterface.java

src/pal/tree/RootedTreeUtils.java

src/pal/tree/SimpleNode.java

src/pal/tree/SimpleTree.java

src/pal/tree/SimulatedAlignment.java

src/pal/tree/SplitSystem.java

src/pal/tree/SplitUtils.java

src/pal/tree/Tree.java

src/pal/tree/TreeDistanceMatrix.java

src/pal/tree/TreeGenerator.java

src/pal/tree/TreeIterator.java

src/pal/tree/TreeManipulator.java

src/pal/tree/TreeOperation.java

src/pal/tree/TreeParseException.java

src/pal/tree/TreeRestricter.java

src/pal/tree/TreeTool.java

src/pal/tree/TreeUtils.java

src/pal/tree/UPGMATree.java

src/pal/tree/UnconstrainedTree.java

src/pal/tree/UnrootedTreeInterface.java

src/pal/tree/makefile

src/pal/tree/package.html

src/pal/treesearch

src/pal/treesearch/AbstractLeafNode.java

src/pal/treesearch/AbstractParentableConstrainedNode.java

src/pal/treesearch/BranchAccess.java

src/pal/treesearch/Constants.java

src/pal/treesearch/ConstrainedInternalNode.java

src/pal/treesearch/ConstrainedLeafNode.java

src/pal/treesearch/ConstrainedNode.java

src/pal/treesearch/ConstraintModel.java

src/pal/treesearch/FixedBSRDTGlobalClockModel.java

src/pal/treesearch/FixedSRDTGlobalClockModel.java

src/pal/treesearch/FreeBranch.java

src/pal/treesearch/FreeInternalNode.java

src/pal/treesearch/FreeLeafNode.java

src/pal/treesearch/FreeNode.java

src/pal/treesearch/GeneralConstraintGroupManager.java

src/pal/treesearch/GeneralConstructionTool.java

src/pal/treesearch/GeneralLikelihoodSearcher.java

src/pal/treesearch/GeneralOptimisable.java

src/pal/treesearch/GeneralTreeComponent.java

src/pal/treesearch/GlobalClockModel.java

src/pal/treesearch/GroupLeader.java

src/pal/treesearch/HeightInformationUser.java

src/pal/treesearch/MRDTGlobalClockModel.java

src/pal/treesearch/NodeAccess.java

src/pal/treesearch/ParentableConstrainedNode.java

src/pal/treesearch/PivotNode.java

src/pal/treesearch/RootAccess.java

src/pal/treesearch/SRDTGlobalClockModel.java

src/pal/treesearch/SearchMonitor.java

src/pal/treesearch/SearcherUtils.java

src/pal/treesearch/TreeSearchTool.java

src/pal/treesearch/UnconstrainedModel.java

src/pal/treesearch/UnrootedMLSearcher.java

src/pal/util

src/pal/util/AlgorithmCallback.java

src/pal/util/Comparable.java

src/pal/util/ComparableDouble.java

src/pal/util/Comparator.java

src/pal/util/DefaultCache.java

src/pal/util/DoubleKey.java

src/pal/util/DoubleKeyCache.java

src/pal/util/HeapSort.java

src/pal/util/Log.java

src/pal/util/Logger.java

src/pal/util/ThreeNumberSort.java

src/pal/util/Version.java

src/pal/util/XMLConstants.java

src/pal/util/makefile

src/pal/util/package.html

src/pal/xml

src/pal/xml/ElementFactory.java

src/pal/xml/ElementParser.java

src/pal/xml/XmlParseException.java

src/pal/xml/make.bat

src/pal/xml/makefile

src/pal/xml/package.html

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added added

removed removed

General Notes.txt

doc/acknowledgements.html

doc/contributing.html

doc/download.html

doc/features.html

doc/history.html

doc/license.html

doc/online.html

doc/people.html

doc/user_interfaces.html

src/makeclean.bat

src/makejar-signed.bat

src/makejar.bat

src/makejike.bat

src/newmake.bat

src/pal/algorithmics/

src/pal/algorithmics/Assessor.java

src/pal/algorithmics/GeneralObjectState.java

src/pal/algorithmics/Markable.java

src/pal/algorithmics/ObjectState.java

src/pal/algorithmics/ProbabilityIterator.java

src/pal/algorithmics/Ranker.java

src/pal/algorithmics/SearchEngine.java

src/pal/algorithmics/StateProvider.java

src/pal/algorithmics/StoppingCriteria.java

src/pal/algorithmics/UndoableAction.java

src/pal/alignment/

src/pal/alignment/AbstractAlignment.java

src/pal/alignment/Alignment.java

src/pal/alignment/AlignmentBuilder.java

src/pal/alignment/AlignmentGenerator.java

src/pal/alignment/AlignmentParseException.java

src/pal/alignment/AlignmentReaders.java

src/pal/alignment/AlignmentReceiver.java

src/pal/alignment/AlignmentTool.java

src/pal/alignment/AlignmentUtils.java

src/pal/alignment/AnnotationAlignment.java

src/pal/alignment/BootstrappedAlignment.java

src/pal/alignment/CharacterAlignment.java

src/pal/alignment/ConcatenatedAlignment.java

src/pal/alignment/ConcatenatedAnnotatedAlignment.java

src/pal/alignment/DataTranslator.java

src/pal/alignment/GapBalancedAlignment.java

src/pal/alignment/Genotype.java

src/pal/alignment/IndelAlignment.java

src/pal/alignment/IndelAnnotatedAlignment.java

src/pal/alignment/JumbledAlignment.java

src/pal/alignment/MultiLocusAnnotatedAlignment.java

src/pal/alignment/ReadAlignment.java

src/pal/alignment/ReadAlignmentOld.java

src/pal/alignment/SimpleAlignment.java

src/pal/alignment/SimpleAnnotatedAlignment.java

src/pal/alignment/SimpleCharacterAlignment.java

src/pal/alignment/SitePattern.java

src/pal/alignment/StrippedAlignment.java

src/pal/alignment/StrippedAnnotatedAlignment.java

src/pal/alignment/makefile

src/pal/alignment/package.html

src/pal/coalescent/

src/pal/coalescent/CoalescentException.java

src/pal/coalescent/CoalescentIntervals.java

src/pal/coalescent/CoalescentSimulator.java

src/pal/coalescent/CoalescentTree.java

src/pal/coalescent/ConstExpConst.java

src/pal/coalescent/ConstExpGrowth.java

src/pal/coalescent/ConstantPopulation.java

src/pal/coalescent/DemographicClockTree.java

src/pal/coalescent/DemographicModel.java

src/pal/coalescent/DemographicTree.java

src/pal/coalescent/ExpandingPopulation.java

src/pal/coalescent/ExponentialGrowth.java

src/pal/coalescent/IntervalsExtractor.java

src/pal/coalescent/SerialCoalescentGenerator.java

src/pal/coalescent/SerialCoalescentSimulator.java

src/pal/coalescent/SkylinePlot.java

src/pal/coalescent/makefile

src/pal/coalescent/package.html

src/pal/datatype/

src/pal/datatype/.#SpecificAminoAcids.java.1.6

src/pal/datatype/AmbiguousDataType.java

src/pal/datatype/AminoAcids.java

src/pal/datatype/CodonTable.java

src/pal/datatype/CodonTableFactory.java

src/pal/datatype/CodonTableUtils.java

src/pal/datatype/Codons.java

src/pal/datatype/DataType.java

src/pal/datatype/DataTypeTool.java

src/pal/datatype/GapBalanced.java

src/pal/datatype/IUPACNucleotides.java

src/pal/datatype/IUPACPenaltyTable.java

src/pal/datatype/MolecularDataType.java

src/pal/datatype/Nucleotides.java

src/pal/datatype/NumericDataType.java

src/pal/datatype/SimpleDataType.java

src/pal/datatype/SpecificAminoAcids.java

src/pal/datatype/StateRemover.java

src/pal/datatype/TransitionPenaltyTable.java

src/pal/datatype/TwoStates.java

src/pal/datatype/makefile

src/pal/datatype/package.html

src/pal/distance/

src/pal/distance/AlignmentDistanceMatrix.java

src/pal/distance/DistanceMatrix.java

src/pal/distance/DistanceMatrixAccess.java

src/pal/distance/DistanceMatrixGenerator.java

src/pal/distance/DistanceMatrixUtils.java

src/pal/distance/DistanceParseException.java

src/pal/distance/DistanceTool.java

src/pal/distance/JukesCantorDistanceMatrix.java

src/pal/distance/PairwiseDistance.java

src/pal/distance/ReadDistanceMatrix.java

src/pal/distance/SequencePairLikelihood.java

src/pal/distance/makefile

src/pal/distance/package.html

src/pal/eval/ChiSquareValue.java

src/pal/eval/ConditionalProbabilityStore.java

src/pal/eval/DemographicLikelihoodValue.java

src/pal/eval/DemographicValue.java

src/pal/eval/FastFourStateLHCalculator.java

src/pal/eval/FastLikelihoodCalculator.java

src/pal/eval/GeneralLikelihoodCalculator.java

src/pal/eval/LHCalculator.java

src/pal/eval/LikelihoodCalculator.java

src/pal/eval/LikelihoodOptimiser.java

src/pal/eval/LikelihoodSummary.java

src/pal/eval/LikelihoodTool.java

src/pal/eval/LikelihoodValue.java

src/pal/eval/ModelParameters.java

src/pal/eval/MolecularClockLikelihoodModel.java

src/pal/eval/PatternInfo.java

src/pal/eval/SimpleLHCalculator.java

src/pal/eval/SimpleLeafCalculator.java

src/pal/eval/SimpleLikelihoodCalculator.java

src/pal/eval/SimpleModelFastFourStateLHCalculator.java

src/pal/eval/SimpleMolecularClockLikelihoodModel.java

src/pal/eval/SimpleUnconstrainedLikelihoodModel.java

src/pal/eval/SingleSplitMolecularClockLikelihoodModel.java

src/pal/eval/SiteDetails.java

src/pal/eval/UnconstrainedLikelihoodModel.java

src/pal/eval/makefile

src/pal/eval/package.html

src/pal/gui/CircularGraphics.java

src/pal/gui/LabelDisplayer.java

src/pal/gui/LayoutTracker.java

src/pal/gui/LinkageDisequilibriumComponent.java

src/pal/gui/NameColouriser.java

src/pal/gui/Painter.java

src/pal/gui/PositionedNode.java

src/pal/gui/TreeComponent.java

src/pal/gui/TreePainter.java

src/pal/gui/TreePainterCircular.java

src/pal/gui/TreePainterNormal.java

src/pal/gui/makefile

src/pal/gui/package.html

src/pal/io/FormattedInput.java

src/pal/io/FormattedOutput.java

src/pal/io/InputSource.java

src/pal/io/NexusParseException.java

src/pal/io/NexusTokenizer.java

src/pal/io/OutputTarget.java

src/pal/io/makefile

src/pal/io/package.html

src/pal/makefile

src/pal/math/Binomial.java

src/pal/math/BoundsCheckedFunction.java

src/pal/math/ConjugateDirectionSearch.java

src/pal/math/ConjugateGradientSearch.java

src/pal/math/DifferentialEvolution.java

src/pal/math/ErrorFunction.java

src/pal/math/EvaluationCounter.java

src/pal/math/GammaFunction.java

src/pal/math/GeneralizedDEOptimizer.java

src/pal/math/LMSSolver.java

src/pal/math/LineFunction.java

src/pal/math/MFWithGradient.java

src/pal/math/MachineAccuracy.java

src/pal/math/MathUtils.java

src/pal/math/Matrix.java

src/pal/math/MersenneTwisterFast.java

src/pal/math/MinimiserMonitor.java

src/pal/math/MultivariateFunction.java

src/pal/math/MultivariateMinimum.java

src/pal/math/NumericalDerivative.java

src/pal/math/OrderEnumerator.java

src/pal/math/OrthogonalHints.java

src/pal/math/OrthogonalLineFunction.java

src/pal/math/OrthogonalSearch.java

src/pal/math/UnivariateFunction.java

src/pal/math/UnivariateMinimum.java

src/pal/math/UrnModel.java

src/pal/math/makefile

src/pal/math/package.html

src/pal/mep/ConstantMutationRate.java

src/pal/mep/DeltaModel.java

src/pal/mep/MutationRateModel.java

src/pal/mep/SteppedMutationRate.java

src/pal/mep/WindowedMutationRate.java

src/pal/mep/makefile

src/pal/mep/package.html

src/pal/misc/Attribute.java

src/pal/misc/BranchLimits.java

src/pal/misc/ExternalParameterListener.java

src/pal/misc/IdGenerator.java

src/pal/misc/IdGroup.java

src/pal/misc/Identifier.java

src/pal/misc/IndividualParameterHandler.java

src/pal/misc/LabelMapping.java

src/pal/misc/MultiParameterized.java

src/pal/misc/MutableDouble.java

src/pal/misc/Nameable.java

src/pal/misc/NamedParameterized.java

src/pal/misc/NeoParameterized.java

src/pal/misc/PalEventMulticaster.java

src/pal/misc/PalObjectEvent.java

src/pal/misc/PalObjectListener.java

src/pal/misc/ParameterEvent.java

src/pal/misc/Parameterized.java

src/pal/misc/ParameterizedDoubleBundle.java

src/pal/misc/ParameterizedNeoWrapper.java

src/pal/misc/ReleaseInfo.java

src/pal/misc/Report.java

src/pal/misc/SampleInformation.java

src/pal/misc/SimpleIdGroup.java

src/pal/misc/SimpleSummarizable.java

src/pal/misc/Summarizable.java

src/pal/misc/TOCDSampleInformation.java

src/pal/misc/TableReport.java

src/pal/misc/TimeOrderCharacterData.java

src/pal/misc/TimeStamp.java

src/pal/misc/Units.java

src/pal/misc/UnitsProvider.java

src/pal/misc/Utils.java

src/pal/misc/makefile

src/pal/misc/package.html

src/pal/popgen/

src/pal/popgen/LinkageDisequilibrium.java

src/pal/popgen/makefile

src/pal/popgen/package.html

src/pal/statistics/

src/pal/statistics/BootstrapStatistics.java

src/pal/statistics/ChiSquareDistribution.java

src/pal/statistics/ChiSquareTest.java

src/pal/statistics/ContigencyTable.java

src/pal/statistics/DiscreteStatistics.java

src/pal/statistics/ExponentialDistribution.java

src/pal/statistics/FisherExact.java

src/pal/statistics/GammaDistribution.java

src/pal/statistics/GeneralTopologyPool.java

src/pal/statistics/KishinoHasegawaTest.java

src/pal/statistics/LikelihoodEvaluator.java

src/pal/statistics/LikelihoodRatioTest.java

src/pal/statistics/ModelSupport.java

src/pal/statistics/NormalDistribution.java

src/pal/statistics/ParetoDistribution.java

src/pal/statistics/PenalizedLikelihood.java

src/pal/statistics/RELLTopologyPool.java

src/pal/statistics/ReplicateLikelihoodEvaluator.java

src/pal/statistics/ShimodairaHasegawaStatistics.java

src/pal/statistics/ShimodairaHasegawaTest.java

src/pal/statistics/TopologyTestEngine.java

src/pal/statistics/makefile

src/pal/statistics/package.html

src/pal/substmodel/

src/pal/substmodel/AbstractRateMatrix.java

src/pal/substmodel/AminoAcidModel.java

src/pal/substmodel/AminoAcidModelID.java

src/pal/substmodel/BLOSUM62.java

src/pal/substmodel/CPREV.java

src/pal/substmodel/CachedRateMatrix.java

src/pal/substmodel/ClassDistribution.java

src/pal/substmodel/CodonModel.java

src/pal/substmodel/ConstantIndependentSingleSplitDistribution.java

src/pal/substmodel/Dayhoff.java

src/pal/substmodel/F81.java

src/pal/substmodel/F84.java

src/pal/substmodel/GTR.java

src/pal/substmodel/GammaRates.java

src/pal/substmodel/GeneralPoissonRateMatrix.java

src/pal/substmodel/GeneralREVRateMatrix.java

src/pal/substmodel/GeneralRateDistributionSubstitutionModel.java

src/pal/substmodel/HKY.java

src/pal/substmodel/InvariableSites.java

src/pal/substmodel/JTT.java

src/pal/substmodel/MTREV24.java

src/pal/substmodel/MatrixExponential.java

src/pal/substmodel/MultiRateMatrixHandler.java

src/pal/substmodel/NeoRateMatrix.java

src/pal/substmodel/NeutralSelectionRateMatrixGroup.java

src/pal/substmodel/NucleotideModel.java

src/pal/substmodel/NucleotideModelID.java

src/pal/substmodel/PositiveSelectionRateMatrixGroup.java

src/pal/substmodel/RateDistribution.java

src/pal/substmodel/RateMatrix.java

src/pal/substmodel/RateMatrixGroup.java

src/pal/substmodel/RateMatrixHandler.java

src/pal/substmodel/RateMatrixUtils.java

src/pal/substmodel/SaturatedSingleSplitDistribution.java

src/pal/substmodel/SequenceSimulator.java

src/pal/substmodel/SimpleRateMatrixGroup.java

src/pal/substmodel/SingleClassSubstitutionModel.java

src/pal/substmodel/SingleSplitDistribution.java

src/pal/substmodel/SubstitutionModel.java

src/pal/substmodel/SubstitutionTool.java

src/pal/substmodel/TN.java

src/pal/substmodel/TemporalModelChange.java

src/pal/substmodel/TwoStateModel.java

src/pal/substmodel/UniformRate.java

src/pal/substmodel/VT.java

src/pal/substmodel/VariableIndependentSingleSplitDistribution.java

src/pal/substmodel/WAG.java

src/pal/substmodel/YangCodonModel.java

src/pal/substmodel/makefile

src/pal/substmodel/package.html

src/pal/supgma/

src/pal/supgma/RateHandler.java

src/pal/supgma/SUPGMABase.java

src/pal/supgma/SUPGMADistanceMatrix.java

src/pal/supgma/SUPGMATree.java

src/pal/supgma/ThetaHandler.java

src/pal/tree/AttributeNode.java

src/pal/tree/CladeSystem.java

src/pal/tree/ClockTree.java

src/pal/tree/ClusterTree.java

src/pal/tree/Local.java

src/pal/tree/LogParameterizedTree.java

src/pal/tree/MutationRateModelTree.java

src/pal/tree/NeighborJoiningTree.java

src/pal/tree/Node.java

src/pal/tree/NodeFactory.java

src/pal/tree/NodeUtils.java

src/pal/tree/ParameterizedTree.java

src/pal/tree/ReadTree.java

src/pal/tree/RootedTreeInterface.java

src/pal/tree/RootedTreeUtils.java

src/pal/tree/SimpleNode.java

src/pal/tree/SimpleTree.java

src/pal/tree/SimulatedAlignment.java

src/pal/tree/SplitSystem.java

src/pal/tree/SplitUtils.java

src/pal/tree/Tree.java

src/pal/tree/TreeDistanceMatrix.java

src/pal/tree/TreeGenerator.java

src/pal/tree/TreeIterator.java

src/pal/tree/TreeManipulator.java

src/pal/tree/TreeOperation.java

src/pal/tree/TreeParseException.java

src/pal/tree/TreeRestricter.java

src/pal/tree/TreeTool.java

src/pal/tree/TreeUtils.java

src/pal/tree/UPGMATree.java

src/pal/tree/UnconstrainedTree.java

src/pal/tree/UnrootedTreeInterface.java

src/pal/tree/makefile

src/pal/tree/package.html

src/pal/treesearch/

src/pal/treesearch/AbstractLeafNode.java

src/pal/treesearch/AbstractParentableConstrainedNode.java

src/pal/treesearch/BranchAccess.java

src/pal/treesearch/Constants.java

src/pal/treesearch/ConstrainedInternalNode.java

src/pal/treesearch/ConstrainedLeafNode.java

src/pal/treesearch/ConstrainedNode.java

src/pal/treesearch/ConstraintModel.java

src/pal/treesearch/FixedBSRDTGlobalClockModel.java

src/pal/treesearch/FixedSRDTGlobalClockModel.java

src/pal/treesearch/FreeBranch.java

src/pal/treesearch/FreeInternalNode.java

src/pal/treesearch/FreeLeafNode.java

src/pal/treesearch/FreeNode.java

src/pal/treesearch/GeneralConstraintGroupManager.java

src/pal/treesearch/GeneralConstructionTool.java

src/pal/treesearch/GeneralLikelihoodSearcher.java

src/pal/treesearch/GeneralOptimisable.java

src/pal/treesearch/GeneralTreeComponent.java

src/pal/treesearch/GlobalClockModel.java

src/pal/treesearch/GroupLeader.java

src/pal/treesearch/HeightInformationUser.java

src/pal/treesearch/MRDTGlobalClockModel.java

src/pal/treesearch/NodeAccess.java

src/pal/treesearch/ParentableConstrainedNode.java

src/pal/treesearch/PivotNode.java

src/pal/treesearch/RootAccess.java

src/pal/treesearch/SRDTGlobalClockModel.java

src/pal/treesearch/SearchMonitor.java

src/pal/treesearch/SearcherUtils.java

src/pal/treesearch/TreeSearchTool.java

src/pal/treesearch/UnconstrainedModel.java

src/pal/treesearch/UnrootedMLSearcher.java

src/pal/util/AlgorithmCallback.java

src/pal/util/Comparable.java

src/pal/util/ComparableDouble.java

src/pal/util/Comparator.java

src/pal/util/DefaultCache.java

src/pal/util/DoubleKey.java

src/pal/util/DoubleKeyCache.java

src/pal/util/HeapSort.java

src/pal/util/Log.java

src/pal/util/Logger.java

src/pal/util/ThreeNumberSort.java

src/pal/util/Version.java

src/pal/util/XMLConstants.java

src/pal/util/makefile

src/pal/util/package.html

src/pal/xml/ElementFactory.java

src/pal/xml/ElementParser.java

src/pal/xml/XmlParseException.java

src/pal/xml/make.bat

src/pal/xml/makefile

src/pal/xml/package.html

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