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data/beast-mcmc-1.10.4+dfsg/src/dr/app/bss/icons/stop.png: PNG image data, 24 x 24, 8-bit/color RGBA, non-interlaced data/beast-mcmc-1.10.4+dfsg/src/dr/app/bss/test/AncestralSequenceTrait.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/bss/test/BeagleSeqSimTest.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/checkpoint/BeastCheckpointer.java: Java source, UTF-8 Unicode text data/beast-mcmc-1.10.4+dfsg/src/dr/app/checkpoint/DebugTreeImporter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/checkpoint/checkpointing.md: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/coalgen/CoalGenApp.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/coalgen/CoalGenData.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/coalgen/CoalGenFrame.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/coalgen/CoalGenMenuFactory.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/coalgen/DataPanel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/coalgen/InputsPanel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/coalgen/ModelPanel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/coalgen/SimulationsPanel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/coalgen/images/CoalGen.png: PNG image data, 128 x 128, 8-bit/color RGBA, non-interlaced data/beast-mcmc-1.10.4+dfsg/src/dr/app/coalgen/images/add.png: PNG image data, 12 x 12, 8-bit/color RGBA, non-interlaced data/beast-mcmc-1.10.4+dfsg/src/dr/app/coalgen/images/exclude.png: PNG image data, 12 x 12, 8-bit/color RGBA, non-interlaced data/beast-mcmc-1.10.4+dfsg/src/dr/app/coalgen/images/include.png: PNG image data, 12 x 12, 8-bit/color RGBA, non-interlaced data/beast-mcmc-1.10.4+dfsg/src/dr/app/coalgen/images/minus.png: PNG image data, 12 x 12, 8-bit/color RGBA, non-interlaced data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/ColorFunction.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/DeleteActionResponder.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/FileDrop.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/SelectAllActionResponder.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/AreaPlot.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/Axis.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/BlankAxis.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/BoxPlot.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/ChartException.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/ChartLayout.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/ChartRuntimeException.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/ChartSelector.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/ChartSetupDialog.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/ColumnPlot.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/CorrelationPlot.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/CustomAxis.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/DiscreteAxis.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/ErrorBarPlot.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/HistogramPlot.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/IntegerViolinPlot.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/JChart.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/JChartPanel.java: Java source, ASCII 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data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/RegressionPlot.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/ScatterPlot.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/TangHuLuPlot.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/ViolinPlot.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/chart/XY.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/components/ColorWellButton.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/components/JVerticalLabel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/components/RealNumberField.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/components/WholeNumberField.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/table/DateCellEditor.java: Java source, ASCII text 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data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/tree/CoordinateTransform.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/tree/JTreeDisplay.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/tree/JTreePanel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/tree/NodeDecorator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/tree/NodeHeightBoxPlot.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/tree/SquareTreePainter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/tree/TreePainter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/util/CorrelationData.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/util/LongTask.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/util/LongTaskMonitor.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/gui/util/SimpleLongTask.java: ASCII text 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data/beast-mcmc-1.10.4+dfsg/src/dr/app/pathogen/images/include.png: PNG image data, 12 x 12, 8-bit/color RGBA, non-interlaced data/beast-mcmc-1.10.4+dfsg/src/dr/app/pathogen/images/pathogen.png: PNG image data, 128 x 128, 8-bit/color RGBA, non-interlaced data/beast-mcmc-1.10.4+dfsg/src/dr/app/phylogeography/tools/ContinuousKML.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/phylogeography/tools/ContinuousTreeToKML.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/phylogeography/tools/DiscreteKMLString.java: Java source, ASCII text, with very long lines data/beast-mcmc-1.10.4+dfsg/src/dr/app/phylogeography/tools/DiscreteRatePriorGenerator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/app/phylogeography/tools/DiscreteTreeToKML.java: C source, ASCII text, with very long lines data/beast-mcmc-1.10.4+dfsg/src/dr/app/phylogeography/tools/RateIndicatorBF.java: Java source, ASCII text, with very long lines 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text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/parsers/MulMSCoalescentParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/parsers/MulSpeciesBindingsParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/parsers/MulSpeciesTreeModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/parsers/MulSpeciesTreePriorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/parsers/MulTreeNodeSlideParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/parsers/MulTreeSequenceReassignmentParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/AlloppDiploidHistory.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/AlloppLeggedTree.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/AlloppMSCoalescent.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/AlloppMulLabTree.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/AlloppNetworkPrior.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/AlloppNetworkPriorModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/AlloppNode.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/AlloppNumHybsStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/AlloppSpeciesBindings.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/AlloppSpeciesNetworkModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/BirthDeathCollapseModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/BirthDeathCollapseNClustersStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/MulMSCoalescent.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/MulSpeciesBindings.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/MulSpeciesTreeModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/speciation/MulSpeciesTreePrior.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/tree/SlidableTree.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/alloppnet/util/AlloppMisc.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/AntigenicDriftPrior.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/AntigenicLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/AntigenicSplitPrior.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/AntigenicTraitLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/CRPClusterRandomWalkOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/ClusterSingleMoveOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/ClusterSplitMergeOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/ContinuousAntigenicTraitLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/DirichletProcessGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/DiscreteAntigenicTraitLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/DistanceDependentCRPGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/DriftedLocationsStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/DriftedTraitsLogger.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/MultidimensionalScalingLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/NPAntigenicLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/TreeClusteringSharedRoutines.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/TreeClusteringVirusesPrior.java: Java source, ASCII text, with very long lines data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/mergeAdjacencyMatrixPlots.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/obsolete/AGLikelihoodCluster.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/obsolete/AGLikelihoodTreeCluster.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/obsolete/ClusterAlgorithmOperator.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/obsolete/ClusterComparison.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/obsolete/ClusterOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/obsolete/ClusterViruses.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/obsolete/ClusterWalkOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/obsolete/ClusterWalkOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/obsolete/OrderDouble.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/obsolete/TiterImporter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/obsolete/TreeClusterGibbsOperator.java: Java source, ASCII text, with very long lines data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/obsolete/TreeClusterSequentialSampling.java: Java source, ASCII text, with very long lines data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/obsolete/serumDriftScalingMuOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/misc/simulateClusters.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/operators/Mu1ScaleActiveScaledMu1IntactOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/operators/Mu2ScaleActiveScaledMu2IntactOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/operators/ProbGenericSiteGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/operators/ProbSitesGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/operators/RandomWalkOnActiveMu.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/operators/TreeClusterAlgorithmOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/operators/muMeanTranslateInactiveMu1Operator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/operators/muPrecisionInactiveMuOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/operators/randomWalkSerumDriftAndMu.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/operators/serumDriftActiveScaledMu1Operator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/operators/serumPrecisionSerumLocOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/ActiveIndicatorsStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/AnnotateLocationParameterTreeTrait.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/AnnotateMuTreeTrait.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/CausalMutationsLogger.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/ClusterLabelsVirusesStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/ClusterLabelsVirusesTreeTrait.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/DriftedMuStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/DriftedTreeClusterLocationsStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/DriverCountStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/KStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/MutationsTreeTrait.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/NodeNumberTreeTrait.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/PathStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/indicatorsStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/antigenic/phyloclustering/statistics/muStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/ARGDistinctTreeCountStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/ARGLogger.java: Java source, ASCII text, with very long lines data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/ARGModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/ARGPartitionLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/ARGRatePrior.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/ARGReassortmentNodeCountStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/ARGReassortmentTimingStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/ARGRelaxedClock.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/ARGTotalLengthStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/ARGTrace.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/ARGTraceAnalysis.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/ARGTraceAnalysisParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/ARGTree.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/ARGTreeLogger.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/HierarchicalPartitionLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/OldTreeLogger.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/PoissonPartitionLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/RecombinationPartitionStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/UniformPartitionLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/beast.properties: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/branchratemodel/ARGDiscretizedBranchRates.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/coalescent/ARGCoalescentLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/coalescent/ARGUniformPrior.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/coalescent/VeryOldCoalescentLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/likelihood/ARGLikelihood.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/likelihood/AbstractARGLikelihood.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/operators/ARGAddRemoveEventOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/operators/ARGExchangeOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/operators/ARGOperatorFailedException.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/operators/ARGPartitioningOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/operators/ARGReassortmentOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/operators/ARGSubtreeSlideOperator.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/operators/ARGSwapOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/operators/NonContiguousPartitionsException.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/operators/ObsoleteARGAddRemoveEventOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/operators/ObsoleteARGNewEventOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/operators/SlidingPatternsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/arg/parsers.txt: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchmodel/BranchAssignmentModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchmodel/BranchModel.java: Java source, ASCII text 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data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/AbstractBranchRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/ArbitraryBranchRates.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/AttributeBranchRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/BranchRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/CompoundBranchRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/ContinuousBranchRates.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/ContinuousEpochBranchRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/ContinuousTraitBranchRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/CountableBranchCategoryProvider.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/CountableMixtureBranchRates.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/CountableModelMixtureBranchRates.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/DecayingRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/DefaultBranchRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/DiscreteTraitBranchRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/DiscretizedBranchRates.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/FixedDriftModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/LatentStateBranchRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/LocalClockModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/MixtureModelBranchRates.java: ASCII text, with very long lines, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/PassageBranchRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/RandomLocalClockModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/RateEpochBranchRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/RelaxedDriftModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/ScaledTreeLengthRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/SericolaLatentStateBranchRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/StrictClockBranchRates.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/branchratemodel/TipBranchRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/AbstractCoalescentLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/AsymptoticGrowthModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/BMPriorLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/BNPRSamplingLikelihood.java: Java source, ASCII text, with very long lines data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/BayesianSkylineLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/BayesianSkylinePopSizeStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/CataclysmicDemographicModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/CoalescentConstantLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/CoalescentEventsStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/CoalescentIntervalProvider.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/CoalescentIntervalStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/CoalescentLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/CoalescentSimulator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/CoalescentTreeIntervalStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ConstExpConstModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ConstantExponentialModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ConstantLogisticModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ConstantPopulationModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/CovariateGMRFSkylineLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/DemographicModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/EBSPAnalysis.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/EmergingEpidemicModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/EmpiricalPiecewiseModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ExpConstExpDemographicModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ExpansionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ExponentialConstantModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ExponentialExponentialModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ExponentialGrowthModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ExponentialLogisticModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ExponentialProductLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ExponentialProductPosteriorMeansLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ExponentialProductSufficientStatisticsLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ExponentialSawtoothModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ExponentialSkythingLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/GMRFBivariateCurveAnalysis.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/GMRFDensityComponent.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/GMRFFixedGridLikelihood.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/GMRFIntervalHeightsStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/GMRFMultilocusSkyrideLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/GMRFPopSizeStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/GMRFSkyrideLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/GMRFTestLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/GPSkytrackAnalysis.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/GammaProductLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/GaussianProcessMultilocusSkytrackLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/GaussianProcessSkytrackLikelihood.java: Java source, ASCII text, with very long lines data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/GaussianProcessSkytrackParser.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/LineageCountStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/LinearGrowthModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/LogisticGrowthModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/MultiEpochExponentialModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/MultiLociTreeSet.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/OldAbstractCoalescentLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/OrnsteinUhlenbeckPriorLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/PeakAndDeclineModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/PiecewisePopulationModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/PopSizeStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/PopulationSizeGraph.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/PowerLawGrowthModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/ScaledPiecewiseModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/SkylineLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/TwoEpochDemographicModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/VDdemographicFunction.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/VariableDemographicModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/VariableSkylineLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/operators/BayesianSkylineGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/operators/GMRFMultilocusSkyrideBlockUpdateOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/operators/GMRFSkyrideBlockUpdateOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/operators/GMRFSkyrideFixedEffectsGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/operators/GaussianProcessSkytrackBlockUpdateOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/operators/GaussianProcessSkytrackTreeOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/operators/SampleNonActiveGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/structure/ColourSamplerModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/structure/ConstantMigrationModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/structure/MetaPopulationModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/structure/MigrationModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/structure/StructuredCoalescentLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/coalescent/structure/TreeColouringOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/AbstractMultivariateTraitLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/AncestralTaxonInTree.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/ApproximateFactorAnalysisPrecisionMatrix.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/BiasedMultivariateDiffusionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/BifractionalDiffusionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/BinaryLatentLiabilityLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/BivariateDiscreteDiffusionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/BivariateTraitBranchAttributeProvider.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/BranchDirectionAttributeProvider.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/BranchMagnitudeAttributeProvider.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/CartogramDiffusionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/ConstrainedGaussianProcessRandomGenerator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/ContinuousDiffusionStatistic.java: Java source, ASCII text, with very long lines data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/ContinuousLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/DebugableIntegratedMultivariateTraitLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/DiffusionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/DiffusionRateCovarianceStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/DiffusionRateStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/FullyConjugateMultivariateTraitLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/GaussianProcessFromTree.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/GibbsIndependentCoalescentOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/GibbsSampleFromTreeInterface.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/GibbsSampleMissingTraitsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/GreatCircleDiffusionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/IndependentCoalescentSampler.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/InhibitionAssayLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/IntegratedMultivariateTraitLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/IntervalLatentLiabilityLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/LatentFactorModelSimulator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/LatentTruncation.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/MapDiffusionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/MissingTraits.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/MixtureCartogramDiffusionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/MultinomialLatentLiabilityLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/MultivariateDiffusionModel.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/MultivariateTDiffusionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/MultivariateTraitUtils.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/NonPhylogeneticMultivariateTraitLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/OrderedLatentLiabilityLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/RestrictedPartials.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/RestrictedPartialsModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/RootTraitMLE.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/RootTraitStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/SampledMultivariateTraitLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/SemiConjugateMultivariateTraitLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/SimulateTrait.java: Java source, ASCII 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data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/hmc/FullyConjugateTreeTipsPotentialDerivative.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/continuous/plink/PlinkImporter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/DynamicalForce.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/DynamicalSystem.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/DynamicalVariable.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/LambertW.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/LogisticGrowthN0.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/LogisticGrowthN0Model.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/LogisticGrowthN0ModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/ODEDemographicFunction.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/SIRModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/SIRModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/SIRepidemic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/SIRepidemicModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/SIRepidemicModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/AbstractCase.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/AbstractOutbreak.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/BadPartitionException.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/BranchMapModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/CaseToCaseTransmissionLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/CaseToCaseTreeLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/CategoryOutbreak.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/PartitionedTreeLogger.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/PartitionedTreeLoggerParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/PartitionedTreeModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/PartitionedTreeModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/SpatialKernel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/WithinCaseCoalescent.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/operators/InfectionBranchMovementOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/operators/TransmissionExchangeOperatorA.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/operators/TransmissionExchangeOperatorB.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/operators/TransmissionSubtreeSlideA.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/operators/TransmissionSubtreeSlideB.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/operators/TransmissionTreeOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/operators/TransmissionWilsonBaldingA.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/operators/TransmissionWilsonBaldingB.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/periodpriors/AbstractPeriodPriorDistribution.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/periodpriors/IndividualPrior.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/periodpriors/KnownVarianceNormalPeriodPriorDistribution.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/periodpriors/NormalPeriodPriorDistribution.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/epidemiology/casetocase/periodpriors/OneOverStDevPeriodPriorDistribution.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/AbstractImportanceDistributionOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/AbstractTreeOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/BitFlipInSubstitutionModelOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/CCPImportanceDistributionOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/CategoryOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/DiscretizedLocationOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/EmpiricalTreeDistributionOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/ExchangeOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/FNPR.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/FixedHeightSubtreePruneRegraftOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/FunkyPriorMixerOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/GibbsPruneAndRegraft.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/GibbsSubtreeSwap.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/ImportanceNarrowExchange.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/ImportancePruneAndRegraft.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/ImportanceSubtreeSwap.java: ASCII text, with CRLF line 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data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/RateExchangeOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/RateSampleOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/RateScaleOperator.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/RateVarianceScaleOperator.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/SubtreeJumpOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/SubtreeLeapOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/SubtreeSlideOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/TipLeapOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/TipStateSwapOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/TipTraitSwapOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/TraitGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/TraitRateGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/TreeBitMoveOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/TreeBitRandomWalkOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/TreeNodeSlide.java: HTML document, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/TreeUniform.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/operators/WilsonBalding.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/siteratemodel/GammaSiteRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/siteratemodel/SiteRateModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/speciation/BetaSplittingModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/speciation/BirthDeathGernhard08Model.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/speciation/BirthDeathSerialSamplingModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/speciation/BirthDeathSerialSkylineModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/speciation/BranchingLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/speciation/BranchingModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/speciation/CalibrationLineagesIterator.java: C++ source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/speciation/CalibrationPoints.java: Java source, ASCII text 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data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/speciation/SpeciesTreeSimplePrior.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/speciation/TaxonRichnessBirthDeathModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/speciation/UltrametricSpeciationModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/speciation/YuleModel.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/AbstractCovarionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/AbstractPCARateMatrix.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/BaseSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/BinaryCovarionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/CodonLabeling.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/CodonPartitionedRobustCounting.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/ColtEigenSystem.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/ComplexColtEigenSystem.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/ComplexSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/CovarionFrequencyModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/DefaultEigenSystem.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/DependentProductChainSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/EigenDecomposition.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/EigenSystem.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/EmpiricalRateMatrix.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/EmpiricalRateMatrixReader.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/ExposeRateCategoriesWrapper.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/FrequencyModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/GLMSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/GeneralSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/MarkovJumpsSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/MarkovModulatedFrequencyModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/MarkovModulatedSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/MutationDeathModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/OldGLMSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/PCARateMatrixMammalia.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/ProductChainFrequencyModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/ProductChainSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/SVSComplexSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/SVSGeneralSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/StratifiedTraitOutputFormat.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/SubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/SubstitutionProcess.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/UniformizedSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/aminoacid/AminoAcidModelType.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/aminoacid/Blosum62.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/aminoacid/CPREV.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/aminoacid/Dayhoff.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/aminoacid/EmpiricalAminoAcidModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/aminoacid/FLU.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/aminoacid/JTT.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/aminoacid/LG.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/aminoacid/MTREV.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/aminoacid/WAG.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/codon/AbstractCodonModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/codon/EmpiricalCodonModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/codon/GY94CodonModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/codon/MG94CodonModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/codon/MG94HKYCodonModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/codon/MarkovModulatedGY94CodonModel.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/codon/PCACodonModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/nucleotide/GTR.java: Java source, UTF-8 Unicode text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/nucleotide/HKY.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/nucleotide/NucModelType.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/substmodel/nucleotide/TN93.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/tipstatesmodel/HypermutantErrorModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/tipstatesmodel/SequenceErrorModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/tipstatesmodel/TipStatesModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/trace/CnCsPerSiteAnalysis.java: Java source, ASCII text 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data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/treelikelihood/LikelihoodPartialsProvider.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/treelikelihood/LikelihoodScalingProvider.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/treelikelihood/MarkovJumpsBeagleTreeLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/treelikelihood/MarkovJumpsTraitProvider.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/treelikelihood/MultiPartitionTreeLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/treelikelihood/PartialsRescalingScheme.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/treelikelihood/SplitBySiteTraitLogger.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/treelikelihood/SubstitutionModelDelegate.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/treelikelihood/utilities/CompleteHistoryLogger.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/treelikelihood/utilities/DnDsLogger.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/treelikelihood/utilities/HistoryFilter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodel/treelikelihood/utilities/TreeTraitLogger.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/CSVExporterParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/ConditionalCladeFrequencyParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/TreeTraceAnalysisParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/TreeWorkingPriorParsers.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/WanderingTaxonLoggerParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchmodel/BranchAssignmentModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchmodel/BranchSpecificBranchModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchmodel/EpochBranchModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchmodel/ExternalInternalBranchModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchmodel/RandomBranchAssignmentModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchmodel/RandomBranchModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/ArbitraryBranchRatesParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/AttributeBranchRateModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/BranchCategoriesParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/CompoundBranchRateModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/ContinuousBranchRatesParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/ContinuousTraitBranchRateModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/CountableMixtureBranchRatesParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/DiscreteTraitBranchRateModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/DiscretizedBranchRatesParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/FixedDriftModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/LatentStateBranchRateModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/LocalClockModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/MixtureModelBranchRatesParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/RandomLocalClockModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/RateEpochBranchRateModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/RelaxedDriftModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/ScaledTreeLengthRateModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/branchratemodel/StrictClockBranchRatesParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/AsymptoticGrowthModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/BMPriorLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/BNPRSamplingLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/BayesianSkylineLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/BayesianSkylinePopSizeStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/CataclysmicDemographicModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/CoalescentEventsStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/CoalescentIntervalStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/CoalescentLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/CoalescentSimulatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/CoalescentTreeIntervalStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/ConstExpConstModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/ConstantExponentialModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/ConstantLogisticModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/ConstantPopulationModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/EBSPAnalysisParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/EmergingEpidemicModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/EmpiricalPiecewiseModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/ExpConstExpDemographicModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/ExpansionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/ExponentialConstantModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/ExponentialExponentialModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/ExponentialGrowthModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/ExponentialLogisticModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/ExponentialSawtoothModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/GMRFBivariateCurveAnalysisParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/GMRFIntervalHeightsStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/GMRFPopSizeStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/GMRFSkyrideLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/GMRFTestLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/GPSkytrackAnalysisParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/GaussianProcessSkytrackLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/LineageCountStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/LinearGrowthModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/LogisticGrowthModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/MultiEpochExponentialModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/OldCoalescentSimulatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/OrnsteinUhlenbeckPriorLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/PeakAndDeclineModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/PiecewisePopulationModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/PopulationSizeGraphParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/PowerLawGrowthModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/ScaledPiecewiseModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/TwoEpochDemographicModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/VariableDemographicModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/VariableSkylineLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/operators/BayesianSkylineGibbsOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/operators/GMRFSkyrideBlockUpdateOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/operators/GMRFSkyrideFixedEffectsGibbsOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/operators/GaussianProcessSkytrackBlockUpdateOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/operators/GaussianProcessSkytrackTreeOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/coalescent/operators/SampleNonActiveGibbsOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/continuous/BuildCompoundSymmetricMatrix.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/continuous/DataFromTreeTipsParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/continuous/GaussianProcessFromTreeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/continuous/LeafTraitExtractorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/continuous/OrderedLatentLiabilityTransformParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/continuous/RestrictedPartialsParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/continuous/hmc/FullyConjugateTreeTipsPotentialDerivativeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/EmpiricalTreeDistributionOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/ExchangeOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/FNPRParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/FixedHeightSubtreePruneRegraftOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/FunkyPriorMixerOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/GibbsPruneAndRegraftParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/GibbsSubtreeSwapParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/ImportanceNarrowExchangeParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/ImportancePruneAndRegraftParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/ImportanceSubtreeSwapParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/MicrosatelliteBitFlipOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/MicrosatelliteFullAncestryImportanceSamplingOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/MicrosatelliteModelSelectOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/MicrosatelliteSingleAncestralStateGibbsOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/MicrosatelliteUpDownOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/MoveLinkageGroupParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/NNIParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/PatternWeightIncrementOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/RandomWalkIntegerNodeHeightWeightedOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/RandomWalkIntegerSetSizeWeightedOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/RateExchangeOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/RateSampleOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/RateScaleOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/RateVarianceScaleOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/SubtreeJumpOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/SubtreeLeapOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/SubtreeSlideOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/TipLeapOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/TipStateSwapOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/TreeBitMoveOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/TreeBitRandomWalkOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/TreeNodeSlideParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/TreeUniformParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/operators/WilsonBaldingParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/siteratemodel/GammaSiteModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/BetaSplittingModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/BirthDeathEpidemiologyModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/BirthDeathModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/BirthDeathSerialSamplingModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/BirthDeathSerialSkylineModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/BranchingLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/ModelAveragingSpeciationLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/MultiSpeciesCoalescentParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/RLTVLoggerParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/RandomLocalYuleModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/SpeciationLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/SpeciesBindingsParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/SpeciesBindingsSPinfoParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/SpeciesTreeBMPriorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/SpeciesTreeModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/SpeciesTreeSimplePriorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/TaxonRichnessBirthDeathModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/speciation/YuleModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/BinaryCovarionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/BinarySubstitutionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/CodonPartitionedRobustCountingParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/ComplexSubstitutionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/EmpiricalAminoAcidModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/EmpiricalCodonModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/FrequencyModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/GLMSubstitutionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/GTRParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/GY94CodonModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/GeneralSubstitutionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/HKYParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/LewisMkSubstitutionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/MG94CodonModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/MarkovModulatedGY94CodonModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/MarkovModulatedHiddenClassRewardParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/MarkovModulatedSubstitutionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/MutationDeathModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/OldGLMSubstitutionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/PCACodonModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/substmodel/TN93Parser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/tipstatesmodel/SequenceErrorModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/tree/AncestralTraitParser.java: ASCII text, with CRLF line terminators 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data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/tree/TreeLoggerParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/tree/TreeMetricStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/tree/TreeModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/tree/TreeShapeStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/tree/UniformNodeHeightPriorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treedatalikelihood/ContinuousDataLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treedatalikelihood/MultiPartitionDataLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treedatalikelihood/TreeDataLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/ALSTreeLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/AncestralStateTreeLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/ApproximatePoissonTreeLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/BalancedBeagleTreeLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/BeagleOperationParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/BeagleTreeLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/CompleteHistoryLoggerParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/DnDsLoggerParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/HistoryFilterParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/MarkovJumpsLikelihoodLoggerParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/MarkovJumpsTreeLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/OptimizedBeagleTreeLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/StratifiedTraitLoggerParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/TraitLoggerParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evomodelxml/treelikelihood/TreeTraitParserUtilities.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/AlignmentParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/AscertainedSitePatternsParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/AttributePatternsParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/BifractionalDiffusionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/CompositeDataTypeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/ConstantPatternsParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/ConvertAlignmentParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/DateParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/DistanceMatrixParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/GeneralDataTypeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/HypermutantAlignmentParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/KStateDataTypeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/LineageCountThroughTimeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/LinkageConstraintsParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/LinkedGroupParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/LocationParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/MaskedPatternsParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/MergePatternsParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/MetagenomeDataParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/MicrosatelliteParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/MicrosatellitePatternParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/MicrosatellitePatternStatisticParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/MicrosatelliteSimulatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/MultiLociDistanceParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/MutationDeathTypeParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/NeighborJoiningParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/NewickParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/OldHiddenNucleotideParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/PatternSubSetParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/PearsonCorrelationParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/PolarCoordinatesParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/RandomSubsetTaxaParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/RandomTaxaSampleParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/RescaledTreeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/SequenceParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/SimpleNodeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/SimpleTreeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/SitePatternsParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/TaxaParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/TaxonParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/UPGMATreeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/UncertainAttributePatternsParser.java: C++ source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/util/DataTypeUtils.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/util/DateUnitsType.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/util/GraphMLUtils.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/evoxml/util/XMLUnits.java: C++ source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/AbstractPolygon2D.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/BrownianBridge1D.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/GTOPO30Browser.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/GTOPO30Panel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/GTOPO30RandomWalk.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/GTOPO30Tile.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/GeoSpatialCollectionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/GeoSpatialDistribution.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/GreatCircleDistances.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/InhomogeneousRandomWalk.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/IslandLattice.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/KMLCoordinates.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/KMLRenderer.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/KMLViewer.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/KernelDensityEstimator2D.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/Lattice.java: C++ source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/Location.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/ManyUniformGeoDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/ManyUniformGeoDistributionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/MultiRegionGeoSpatialDistribution.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/MultivariateBrownianBridge.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/NewPolygon2D.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/NumericalSpaceTimeProbs2D.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/Polygon.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/Polygon2D.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/Polygon2DFactory.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/Polygon2DSampling.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/RateMatrix.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/Reject.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/SpaceTime.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/SpaceTimeRejector.java: C++ source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/SpaceTimeRejector1D.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/SpaceTimeSimulator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/ViewTransform.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/VisualizeBrownianBridge2D.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/VisualizeKMLBrownianBridge.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/VisualizeKMLJointProb.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/VisualizeKMLNumericalProbs.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/VisualizeSpaceTimeSim2D.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/cartogram/CartogramMapping.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/color/ChannelColorScheme.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/color/ColorScheme.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/contouring/ContourAttrib.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/contouring/ContourGenerator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/contouring/ContourMaker.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/contouring/ContourMode.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/contouring/ContourPath.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/contouring/ContourWithR.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/contouring/ContourWithSynder.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/contouring/SnyderContour.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/distributions/FisherBinghamKentDistribution.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/distributions/HyperSphereDistribution.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/distributions/VonMisesDistribution.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/distributions/VonMisesFisherDistribution.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/math/Space.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/math/SphericalPolarCoordinates.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/math/Vector3D.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/operators/UniformGeoSpatialOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/operators/UniformGeoSpatialOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/geo/testGreatCircleDistances.xml: exported SGML document, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/geo/testLocations.xml: exported SGML document, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/AbstractDistributionLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/BetaDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/BinomialLikelihood.java: C++ source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/CachedDistributionLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/CauchyDistribution.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/DensityModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/DeterminentalPointProcessPrior.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/DirichletProcessLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/DistributionLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/EmpiricalDistributionLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/ExponentialDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/ExponentialMarkovModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/GammaDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/GeneralizedLinearModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/HierarchicalGraphLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/IndependentInverseGammaDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/IndependentNormalDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/InverseGammaDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/InverseGaussianDistributionModel.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/LatentFactorModelInterface.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/LinearRegression.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/LocationScaleJeffreysPrior.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/LogLinearModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/LogNormalDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/LogisticRegression.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/MixedDistributionLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/ModelSpecificPseudoPriorLikelihood.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/MomentDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/MultivariateDistributionLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/MultivariateNormalDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/NegativeBinomialDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/NormalDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/ParametricDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/ParametricMultivariateDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/PoissonDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/RandomWalkGenerator.java: C source, ASCII text, with very long lines data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/RandomWalkModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/RowDimensionMultinomialPrior.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/RowDimensionPoissonPrior.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/ShrinkageGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/SkewNormalDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/SplineInterpolatedLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/TDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/TruncatedNormalDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/TwoPartsDistributionLikelihood.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/TwoPieceLocationScaleDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/UniformDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/distribution/WishartGammalDistributionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/glm/GeneralizedLinearModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/hmc/CompoundGradient.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/hmc/GradientWrtParameterProvider.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/hmc/LFMFactorPotentialDerivative.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/hmc/LFMLoadingsPotentialDerivative.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/hmc/MaskedGradient.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/hmc/NormalPotentialDerivative.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/hmc/SumDerivative.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/loggers/ArrayLogFormatter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/loggers/BooleanColumn.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/loggers/Columns.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/loggers/LogColumn.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/loggers/LogFormatter.java: ASCII text 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data/beast-mcmc-1.10.4+dfsg/src/dr/inference/markovjumps/TwoStateOccupancyMarkovReward.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/markovjumps/TwoStateSericolaSeriesMarkovReward.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/markovjumps/UniformizedStateHistory.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/mcmc/MCMC.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/mcmc/MCMCCriterion.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/mcmc/MCMCOptions.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/mcmc/MarginalLikelihoodEstimator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/mcmcmc/MCMCMC.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/mcmcmc/MCMCMCOptions.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/mcmcmc/MCMCMCRunner.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/ml/GreatDelugeCriterion.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/ml/HillClimbingCriterion.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/ml/MLOptimizer.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/AbstractAlgebraStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/AbstractModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/AbstractModelLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/AdaptableSizeFastMatrixParameter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/BayesianStochasticSearchVariableSelection.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/BlockDiagonalMatrixParameter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/BlockUpperTriangularMatrixParameter.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/BooleanLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/BooleanStatistic.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/Bounds.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/ComplementParameter.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/CompoundFastMatrixParameter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/CompoundLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/CompoundMatrixParameter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/CompoundModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/CompoundParameter.java: Java source, ASCII text 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data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/ParameterIntegerParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/ParameterParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/PathLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/PearsonCorrelation.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/ProductParameter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/ProductStatistic.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/RPNcalculatorStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/RPNexpressionCalculator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/RatioStatistic.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/ReciprocalStatistic.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/SplineBasis.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/Statistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/StatisticList.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/StatisticParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/SubStatistic.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/SumParameter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/SumStatistic.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/TestStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/TestThreadedCompoundLikelihood.java: C++ source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/ThreadAwareLikelihood.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/ThreadedCompoundLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/ThresholdStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/TransformedParameter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/TransposedBlockUpperTriangularMatrixParameter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/TransposedMatrixParameter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/TruncatedDistributionLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/ValuesPool.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/ValuesPoolParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/Variable.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/VariableListener.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/VarianceStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/VectorSliceParameter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/model/WeightedMixtureModel.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/multidimensionalscaling/MassivelyParallelMDSImpl.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/multidimensionalscaling/MultiDimensionalScalingCore.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/multidimensionalscaling/MultiDimensionalScalingCoreImpl.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/multidimensionalscaling/MultiDimensionalScalingLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/multidimensionalscaling/NativeMDSSingleton.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/multidimensionalscaling/mm/MMAlgorithm.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/multidimensionalscaling/mm/MultiDimensionalScalingMM.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/AbstractAdaptableOperator.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/AdaptableMCMCOperator.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/AdaptableVarianceMultivariateNormalOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/AdaptationMode.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/AlternatingOperatorSchedule.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/BitFlipOperator.java: C++ source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/BitMoveOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/BitSwapOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/CenteredScaleOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/CombinedOperatorSchedule.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/DeltaExchangeOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/DeltaMixOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/DirtyLikelihoodOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/EllipticalSliceOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/FactorGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/FactorIndependenceOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/FactorOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/FactorRJMCMCOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/FactorTreeGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/FireParameterOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/GaussianProcessDrawOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/GeneralOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/GenericIndependentSampler.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/GibbsIndependentGammaOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/GibbsIndependentJointNormalGammaOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/GibbsIndependentNormalDistributionOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/GibbsOperator.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/HierarchicalBitFlipOperator.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/IBPBitFlipOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/IndependentGammaSampler.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/IndependentNormalDistributionSampler.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/InvariantOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/JointGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/JointOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/LFMSplitMergeOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/LFMTargetedSearchOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/LatentFactorLiabilityGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/LatentFactorModelPrecisionGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/LoadingsGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/LoadingsGibbsTruncatedOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/LoadingsIndependenceOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/LoadingsSparsityOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/MCMCOperator.java: C++ source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/MVOUCovarianceOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/MaskMoveOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/ModeFindOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/ModeIndependenceOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/MultipleRandomWalkIntegerOperator.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/MultivariateNormalGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/MultivariateNormalIndependenceSampler.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/MultivariateNormalOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/NegationOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/NormalGammaPrecisionGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/NormalNormalMeanGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/OperatorAnalysisPrinter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/OperatorSchedule.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/OperatorUtils.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/PathDependentOperator.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/RandomWalkGammaPrecisionGibbsOperator.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/RandomWalkIntegerOperator.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/RandomWalkOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/RateBitExchangeOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/RegressionGibbsEffectOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/RegressionGibbsPrecisionOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/RegressionMetropolizedIndicatorOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/Scalable.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/ScaleOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/SelectorOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/SetOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/ShrinkageAugmentedGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/SimpleMCMCOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/SimpleMetropolizedGibbsOperator.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/SimpleOperator.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/SimpleOperatorSchedule.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/SliceInterval.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/SliceOperator.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/SwapOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/SwapParameterGibbsOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/SwapParameterOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/TeamOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/TransformedRandomWalkOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/TwoPhaseOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/UniformIntegerOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/UniformOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/UpDownOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/ValuesPoolSwapOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/hmc/BouncyParticleOperator.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/hmc/HamiltonianMonteCarloOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/hmc/NewBouncyParticleOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/hmc/NoUTurnOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/hmc/deprecated/AbstractHamiltonianMCOperator.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/hmc/deprecated/LatentFactorHamiltonianMC.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/hmc/deprecated/LatentFactorHamiltonianMCParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/hmc/deprecated/LoadingsHamiltonianMC.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/operators/hmc/deprecated/LoadingsHamiltonianMCParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/parallel/MPILikelihoodRunner.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/parallel/MPISerializable.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/parallel/MPIServices.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/parallel/ServiceRequest.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/regression/RegressionJNIWrapper.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/regression/SelfControlledCaseSeries.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/smc/SMC.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/smc/SMCOptions.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/state/Factory.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/state/StateLoader.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/state/StateLoaderSaver.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/state/StateSaver.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/state/StateSaverChainListener.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/AbstractTraceList.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/ArrayTraceList.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/DensityEstimate.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/DensityRectangle.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/Filter.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/FilteredTraceList.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/GeneralizedSteppingStoneSamplingAnalysis.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/KernelDensityEstimate.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/LogFileTraceExporter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/LogFileTraces.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/MarginalLikelihoodAnalysis.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/NumberUtils.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/PathSamplingAnalysis.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/SteppingStoneSamplingAnalysis.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/Trace.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/TraceAnalysis.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/TraceCorrelation.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/TraceDistribution.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/TraceException.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/TraceList.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/TraceType.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/TraceTypeUtils.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/TracesListener.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/trace/TracesReader.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inference/tutorial/Tutorial1.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/MCMCParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/MLOptimizerParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/SignTransformParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/BetaDistributionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/BinomialLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/CachedDistributionLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/CompoundGaussianProcessParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/DeterminentalPointProcessPriorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/DirichletProcessLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/DistributionLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/DistributionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/EmpiricalDistributionLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/ExponentialDistributionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/ExponentialMarkovModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/FactorTreeGibbsOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/GammaDistributionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/GeneralizedLinearModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/HierarchicalGraphLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/IndependentInverseGammaDistributionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/IndependentNormalDistributionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/InverseGammaDistributionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/InverseGaussianDistributionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/LocationScaleJeffreysPriorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/LogNormalDistributionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/MixedDistributionLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/ModelSpecificPseudoPriorLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/MomentDistributionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/MultivariateNormalDistributionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/MultivariateOUModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/MultivariateOUModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/NegativeBinomialDistributionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/NormalDistributionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/OnePGammaDistributionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/PoissonDistributionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/PriorParsers.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/RandomWalkGeneratorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/RandomWalkModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/RowDimensionMultinomialPriorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/RowDimensionPoissonPriorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/ScaledBetaDistributionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/SkewNormalDistributionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/TDistributionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/TruncatedDistributionLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/TruncatedNormalDistributionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/TwoPartsDistributionLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/TwoPieceLocationScaleDistributionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/UniformDistributionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/WishartGammaDistributionModelParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/distribution/WorkingPriorParsers.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/glm/GeneralizedLinearModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/glm/MultivariateOUModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/hmc/AppendedPotentialDerivativeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/hmc/GradientWrapperParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/hmc/LFMFactorPotentialDerivativeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/hmc/LFMLoadingsPotentialDerivativeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/hmc/MaskedGradientParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/hmc/NormalPotentialDerivativeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/hmc/RotationTranslationMaskParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/hmc/SumDerivativeParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/loggers/ColumnsParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/loggers/LoggerParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/loggers/MLLoggerParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/AdaptableSizeFastMatrixParameterParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/BlockUpperTriangularMatrixParameterParser.java: Java source, 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data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/DiagonalMatrixParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/DifferenceMatrixParameterParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/DifferenceParameterParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/DifferenceStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/DummyLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/DuplicatedParameterParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/ElementWiseMatrixMultiplicationParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/ExponentialStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/ExpressionStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/FastBlockUpperTriangularMatrixParameterParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/ImmutableParameterParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/IndianBuffetProcessPriorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/JointParameterParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/LatentFactorModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/LikelihoodBenchmarkerParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/LogarithmStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/MarkovRandomFieldMatrixParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/MaskedMatrixParameterParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/MaskedParameterParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/MatrixMatrixProductParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/MatrixVectorProductParameterParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/MeanStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/NegativeStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/NotBooleanStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/NotStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/OneOnX3PriorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/OneOnXPriorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/ProductParameterParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/ProductStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/RPNcalculatorStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/RatioStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/ReciprocalStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/ScaleData.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/SubStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/SumParameterParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/SumStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/TestStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/ThreadedCompoundLikelihoodParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/ThresholdStatisticParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/TransformedParameterParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/model/VarianceStatisticParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/AlternatingOperatorScheduleParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/ApplyOperatorOnceParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/ApplyOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/BitFlipOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/BitMoveOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/BitSwapOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/CenteredScaleOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/DeltaExchangeOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/DeltaMixOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/DirtyLikelihoodOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/FactorGibbsOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/FactorIndependenceOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/FactorOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/FactorRJMCMCOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/FireParameterOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/HierarchicalBitFlipOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/InvariantOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/JointGibbsOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/JointOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/LFMSplitMergeOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/LFMTargetedSearchOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/LatentFactorLiabilityGibbsOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/LatentFactorModelPrecisionGibbsOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/LoadingsGibbsOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/LoadingsIndependenceOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/LoadingsSparsityOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/MVOUCovarianceOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/MaskMoveOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/MultipleRandomWalkIntegerOperatorParser.java: ASCII text, with CRLF line terminators data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/MultivariateNormalGibbsOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/inferencexml/operators/NegationOperatorParser.java: Java source, ASCII text 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data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/GeneralF81Model.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/GeneralSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/HKY.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/JTT.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/LG.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/LinearBiasModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/MTREV.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/MarginalVarianceStatistic.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/MicrosatelliteModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/MsatBMA.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/MutationDeathModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/NewMicrosatelliteModel.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/NtdBMA.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/NucModelType.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/OnePhaseModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/PCACodonModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/PCARateMatrixMammalia.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/PositiveDefiniteSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/PseudoCodonModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/SVSComplexSubstitutionModel.java: C source, ASCII text, with very long lines data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/SVSGeneralSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/SubstitutionEpochModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/SubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/SubstitutionModelUtils.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/TN93.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/TwoPhaseModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/TwoStateCovarionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/WAG.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/substmodel/YangCodonModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/AbstractLikelihoodCore.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/AbstractTreeLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/AdvancedTreeLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/AminoAcidLikelihoodCore.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/AncestralStateTreeLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/ArbitraryPrecisionLikelihoodCore.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/EpochTreeBranchSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/EpochTreeLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/GeneralLikelihoodCore.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/HiddenLinkageLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/LikelihoodCore.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/MicrosatelliteSamplerTreeLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/NativeAminoAcidLikelihoodCore.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/NativeCovarionLikelihoodCore.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/NativeGeneralLikelihoodCore.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/NativeNucleotideLikelihoodCore.java: C source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/NodePosteriorTreeLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/NucleotideLikelihoodCore.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/PrecisionTestTreeLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/PurifyingGammaTreeLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/PurifyingTreeLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/ScaleFactorsHelper.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/TreeBranchSubstitutionModel.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodel/treelikelihood/TreeLikelihood.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/MSSD/ALSSiteModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/MSSD/ALSTreeLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/MSSD/AnyTipObservationProcessParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/MSSD/ExponentialBranchLengthTreePriorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/MSSD/SingleTipObservationProcessParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/clock/ACLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/clock/UCLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/indel/IstvanOperatorParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/indel/TKF91LikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/indel/TKF91ModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/sitemodel/CategorySiteModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/sitemodel/DiscretizedLociRatesParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/sitemodel/GammaSiteBMAParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/sitemodel/GammaSiteModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/sitemodel/SampleQuantileLociRatesParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/sitemodel/SampleStateAndCategoryModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/sitemodel/SampleStateModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/AsymQuadModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/BinaryCovarionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/BinarySubstitutionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/ComplexSubstitutionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/CovarionGTRParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/CovarionHKYParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/EmpiricalAminoAcidModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/EmpiricalCodonModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/FrequencyModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/GLMSubstitutionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/GTRParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/GeneralF81ModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/GeneralSubstitutionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/HKYParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/LewisMkSubstitutionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/LinearBiasModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/MkModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/MsatBMAParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/MutationDeathModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/NewMicrosatelliteModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/NtdBMAParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/PCACodonModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/PositiveDefiniteSubstitutionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/SubstitutionEpochModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/TN93Parser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/TwoPhaseModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/TwoStateCovarionModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/substmodel/YangCodonModelParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/treelikelihood/AncestralStateTreeLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/treelikelihood/HiddenLinkageLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/treelikelihood/MarkovJumpsTreeLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/treelikelihood/MicrosatelliteSamplerTreeLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/oldevomodelxml/treelikelihood/TreeLikelihoodParser.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/stats/DiscreteStatistics.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/stats/FrequencyCounter.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/stats/Regression.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/stats/Variate.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/top-level-packages.txt: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/util/Attributable.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/util/Attribute.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/util/Author.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/util/Citable.java: C++ source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/util/Citation.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/util/CommonCitations.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/util/ComparableDouble.java: ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/util/DataTable.java: Java source, ASCII text data/beast-mcmc-1.10.4+dfsg/src/dr/util/ErrorLogHandler.java: Java source, ASCII 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