├── .github └── workflows │ └── main.yml ├── .gitignore ├── COPYING ├── Dockerfile ├── README.md ├── action.yml ├── examples ├── ACGsimulations │ ├── simulateACGs2taxon.xml │ ├── simulateACGs2taxon_fixedCF.xml │ ├── simulateACGs5taxon.xml │ ├── simulateACGs5taxonDynamicPopSize.xml │ ├── simulateACGs5taxonMultiLocus.xml │ ├── simulateACGs5taxonSerialSampling.xml │ ├── simulateACGs5taxonShortSSML.xml │ └── simulateACGsShortSequence5taxon.xml ├── CFOperatorTests │ ├── CFConversionSwapTest5taxon.xml │ ├── CFSubtreeExchangeTest5taxon.xml │ ├── CFSubtreeSlideTest5taxon.xml │ ├── CFUniformTest5taxon.xml │ └── CFWilsonBaldingTest5taxon.xml ├── Validation.ipynb ├── addRemoveDetourTests │ └── addRemoveDetourTest5taxon.xml ├── addRemoveTests │ ├── addRemoveDynamicPopSize5taxon.xml │ ├── addRemoveRedundantTest5taxon.xml │ ├── addRemoveSerialSamplingTest5taxon.xml │ ├── addRemoveShortSequenceTest5taxon.xml │ ├── addRemoveTest2taxon.xml │ └── addRemoveTest5taxon.xml ├── allOperatorTests │ ├── allOperatorTestSSMultiLocus.xml │ ├── allOperatorTestSeriallySampled.xml │ └── allOperatorTestShortSSML.xml ├── cumulativePairwiseDistance │ └── simulatePairwiseDistances.xml ├── inferenceSimulatedData │ ├── BSP │ │ ├── inferenceSimulatedDataEvenLinear.xml │ │ └── plotBSP.R │ ├── approx │ │ └── inferenceSimulatedDataApprox.xml │ ├── basic │ │ ├── inferenceSimulatedData.xml │ │ ├── inferenceSimulatedData2taxon.xml │ │ ├── inferenceSimulatedDataMultiLocus.xml │ │ └── inferenceSimulatedDataMultiLocusSerial.xml │ ├── plotConvertedRegions.R │ └── popModelFit │ │ ├── popModelFit.xml │ │ └── popModelFitMultiLocus.xml ├── mergeSplitTests │ └── mergeSplitTest5taxon.xml ├── regionShiftTests │ ├── boundaryShiftTest5taxon.xml │ └── regionShiftTest5taxon.xml ├── simulated_data_A.fasta └── simulated_data_B.fasta ├── fxtemplates ├── Bacter.xml └── BacterACGPriors.xml ├── lib └── guava-17.0.jar ├── src └── bacter │ ├── ACGEventList.java │ ├── AffectedSiteList.java │ ├── CFEventList.java │ ├── Coalescence.java │ ├── Conversion.java │ ├── ConversionEvent.java │ ├── ConversionGraph.java │ ├── Locus.java │ ├── MarginalNode.java │ ├── MarginalTree.java │ ├── Region.java │ ├── RegionList.java │ ├── SiteAncestry.java │ ├── acgannotator │ ├── ACGAnnotator.java │ ├── ACGCladeSystem.java │ └── icon.png │ ├── beauti │ └── CustomConnectors.java │ ├── devutils │ ├── CFConvSwapExperiment.java │ ├── ComputeCPDMatrix.java │ ├── DensityCalculator.java │ ├── DifferenceFromTrueACG.java │ ├── MCMCTrace.java │ └── OperatorTester.java │ ├── model │ ├── ACGCoalescent.java │ ├── ACGLikelihood.java │ ├── ACGLikelihoodApprox.java │ ├── ACGLikelihoodBeagle.java │ ├── ACGLikelihoodSlow.java │ ├── ACGSimulator.java │ ├── AlignmentSimulator.java │ ├── SimulatedACG.java │ ├── SimulatedAlignment.java │ └── pop │ │ ├── PiecewisePopulationFunction.java │ │ └── SkylinePopulationFunction.java │ ├── operators │ ├── ACGOperator.java │ ├── ACGScaler.java │ ├── ACGValidityWrapper.java │ ├── AddRemoveConversion.java │ ├── AddRemoveDetour.java │ ├── AddRemoveRedundantConversion.java │ ├── CFConversionSwap.java │ ├── CFOperator.java │ ├── CFSubtreeExchange.java │ ├── CFSubtreeSlide.java │ ├── CFUniform.java │ ├── CFWilsonBalding.java │ ├── ConversionCreationOperator.java │ ├── ConvertedEdgeFlip.java │ ├── ConvertedEdgeHop.java │ ├── ConvertedEdgeHopContemp.java │ ├── ConvertedEdgeSlide.java │ ├── ConvertedRegionBoundaryShift.java │ ├── ConvertedRegionShift.java │ ├── ConvertedRegionSwap.java │ ├── EdgeCreationOperator.java │ ├── MergeSplitConversion.java │ └── ReplaceConversion.java │ └── util │ ├── ACGLogReader.java │ ├── BacterACGLogReader.java │ ├── COACGLogFileReader.java │ ├── ClonalFrameLogger.java │ ├── ConversionCount.java │ ├── ConversionCountBounds.java │ ├── ConversionGraphStatsLogger.java │ ├── ConvertedRegionLogger.java │ ├── IntRanges.java │ ├── TrimmedACGLogger.java │ └── parsers │ ├── ExtendedNewick.g4 │ ├── ExtendedNewickBaseListener.java │ ├── ExtendedNewickBaseVisitor.java │ ├── ExtendedNewickLexer.java │ ├── ExtendedNewickListener.java │ ├── ExtendedNewickParser.java │ └── ExtendedNewickVisitor.java ├── test └── bacter │ ├── MarginalTreeTest.java │ ├── SerializationDeserializationTest.java │ ├── SiteAncestryTest.java │ ├── TestBase.java │ ├── model │ ├── ACGLikelihoodApproxTest.java │ ├── ACGLikelihoodTest.java │ ├── SimulatedAlignmentTest.java │ └── pop │ │ └── SkylinePopulationFunctionTest.java │ ├── operators │ └── AddRemoveConversionTest.java │ ├── util │ ├── BacterACGLogReaderTest.java │ └── IntRangesTest.java │ └── xmltests │ ├── AddRemoveDetourTest.java │ ├── AddRemoveRedundantTest.java │ ├── AddRemoveTest.java │ ├── AllOperatorTest.java │ ├── CFOperatorTest.java │ ├── MergeSplitTest.java │ ├── RegionShiftTest.java │ └── SimulatedACGTest.java └── version.xml /.github/workflows/main.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/.github/workflows/main.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/.gitignore -------------------------------------------------------------------------------- /COPYING: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/COPYING -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/Dockerfile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/README.md -------------------------------------------------------------------------------- /action.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/action.yml -------------------------------------------------------------------------------- /examples/ACGsimulations/simulateACGs2taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/ACGsimulations/simulateACGs2taxon.xml -------------------------------------------------------------------------------- /examples/ACGsimulations/simulateACGs2taxon_fixedCF.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/ACGsimulations/simulateACGs2taxon_fixedCF.xml -------------------------------------------------------------------------------- /examples/ACGsimulations/simulateACGs5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/ACGsimulations/simulateACGs5taxon.xml -------------------------------------------------------------------------------- /examples/ACGsimulations/simulateACGs5taxonDynamicPopSize.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/ACGsimulations/simulateACGs5taxonDynamicPopSize.xml -------------------------------------------------------------------------------- /examples/ACGsimulations/simulateACGs5taxonMultiLocus.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/ACGsimulations/simulateACGs5taxonMultiLocus.xml -------------------------------------------------------------------------------- /examples/ACGsimulations/simulateACGs5taxonSerialSampling.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/ACGsimulations/simulateACGs5taxonSerialSampling.xml -------------------------------------------------------------------------------- /examples/ACGsimulations/simulateACGs5taxonShortSSML.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/ACGsimulations/simulateACGs5taxonShortSSML.xml -------------------------------------------------------------------------------- /examples/ACGsimulations/simulateACGsShortSequence5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/ACGsimulations/simulateACGsShortSequence5taxon.xml -------------------------------------------------------------------------------- /examples/CFOperatorTests/CFConversionSwapTest5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/CFOperatorTests/CFConversionSwapTest5taxon.xml -------------------------------------------------------------------------------- /examples/CFOperatorTests/CFSubtreeExchangeTest5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/CFOperatorTests/CFSubtreeExchangeTest5taxon.xml -------------------------------------------------------------------------------- /examples/CFOperatorTests/CFSubtreeSlideTest5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/CFOperatorTests/CFSubtreeSlideTest5taxon.xml -------------------------------------------------------------------------------- /examples/CFOperatorTests/CFUniformTest5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/CFOperatorTests/CFUniformTest5taxon.xml -------------------------------------------------------------------------------- /examples/CFOperatorTests/CFWilsonBaldingTest5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/CFOperatorTests/CFWilsonBaldingTest5taxon.xml -------------------------------------------------------------------------------- /examples/Validation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/Validation.ipynb -------------------------------------------------------------------------------- /examples/addRemoveDetourTests/addRemoveDetourTest5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/addRemoveDetourTests/addRemoveDetourTest5taxon.xml -------------------------------------------------------------------------------- /examples/addRemoveTests/addRemoveDynamicPopSize5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/addRemoveTests/addRemoveDynamicPopSize5taxon.xml -------------------------------------------------------------------------------- /examples/addRemoveTests/addRemoveRedundantTest5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/addRemoveTests/addRemoveRedundantTest5taxon.xml -------------------------------------------------------------------------------- /examples/addRemoveTests/addRemoveSerialSamplingTest5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/addRemoveTests/addRemoveSerialSamplingTest5taxon.xml -------------------------------------------------------------------------------- /examples/addRemoveTests/addRemoveShortSequenceTest5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/addRemoveTests/addRemoveShortSequenceTest5taxon.xml -------------------------------------------------------------------------------- /examples/addRemoveTests/addRemoveTest2taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/addRemoveTests/addRemoveTest2taxon.xml -------------------------------------------------------------------------------- /examples/addRemoveTests/addRemoveTest5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/addRemoveTests/addRemoveTest5taxon.xml -------------------------------------------------------------------------------- /examples/allOperatorTests/allOperatorTestSSMultiLocus.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/allOperatorTests/allOperatorTestSSMultiLocus.xml -------------------------------------------------------------------------------- /examples/allOperatorTests/allOperatorTestSeriallySampled.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/allOperatorTests/allOperatorTestSeriallySampled.xml -------------------------------------------------------------------------------- /examples/allOperatorTests/allOperatorTestShortSSML.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/allOperatorTests/allOperatorTestShortSSML.xml -------------------------------------------------------------------------------- /examples/cumulativePairwiseDistance/simulatePairwiseDistances.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/cumulativePairwiseDistance/simulatePairwiseDistances.xml -------------------------------------------------------------------------------- /examples/inferenceSimulatedData/BSP/inferenceSimulatedDataEvenLinear.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/inferenceSimulatedData/BSP/inferenceSimulatedDataEvenLinear.xml -------------------------------------------------------------------------------- /examples/inferenceSimulatedData/BSP/plotBSP.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/inferenceSimulatedData/BSP/plotBSP.R -------------------------------------------------------------------------------- /examples/inferenceSimulatedData/approx/inferenceSimulatedDataApprox.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/inferenceSimulatedData/approx/inferenceSimulatedDataApprox.xml -------------------------------------------------------------------------------- /examples/inferenceSimulatedData/basic/inferenceSimulatedData.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/inferenceSimulatedData/basic/inferenceSimulatedData.xml -------------------------------------------------------------------------------- /examples/inferenceSimulatedData/basic/inferenceSimulatedData2taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/inferenceSimulatedData/basic/inferenceSimulatedData2taxon.xml -------------------------------------------------------------------------------- /examples/inferenceSimulatedData/basic/inferenceSimulatedDataMultiLocus.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/inferenceSimulatedData/basic/inferenceSimulatedDataMultiLocus.xml -------------------------------------------------------------------------------- /examples/inferenceSimulatedData/basic/inferenceSimulatedDataMultiLocusSerial.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/inferenceSimulatedData/basic/inferenceSimulatedDataMultiLocusSerial.xml -------------------------------------------------------------------------------- /examples/inferenceSimulatedData/plotConvertedRegions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/inferenceSimulatedData/plotConvertedRegions.R -------------------------------------------------------------------------------- /examples/inferenceSimulatedData/popModelFit/popModelFit.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/inferenceSimulatedData/popModelFit/popModelFit.xml -------------------------------------------------------------------------------- /examples/inferenceSimulatedData/popModelFit/popModelFitMultiLocus.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/inferenceSimulatedData/popModelFit/popModelFitMultiLocus.xml -------------------------------------------------------------------------------- /examples/mergeSplitTests/mergeSplitTest5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/mergeSplitTests/mergeSplitTest5taxon.xml -------------------------------------------------------------------------------- /examples/regionShiftTests/boundaryShiftTest5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/regionShiftTests/boundaryShiftTest5taxon.xml -------------------------------------------------------------------------------- /examples/regionShiftTests/regionShiftTest5taxon.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/regionShiftTests/regionShiftTest5taxon.xml -------------------------------------------------------------------------------- /examples/simulated_data_A.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/simulated_data_A.fasta -------------------------------------------------------------------------------- /examples/simulated_data_B.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/examples/simulated_data_B.fasta -------------------------------------------------------------------------------- /fxtemplates/Bacter.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/fxtemplates/Bacter.xml -------------------------------------------------------------------------------- /fxtemplates/BacterACGPriors.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/fxtemplates/BacterACGPriors.xml -------------------------------------------------------------------------------- /lib/guava-17.0.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/lib/guava-17.0.jar -------------------------------------------------------------------------------- /src/bacter/ACGEventList.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/ACGEventList.java -------------------------------------------------------------------------------- /src/bacter/AffectedSiteList.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/AffectedSiteList.java -------------------------------------------------------------------------------- /src/bacter/CFEventList.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/CFEventList.java -------------------------------------------------------------------------------- /src/bacter/Coalescence.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/Coalescence.java -------------------------------------------------------------------------------- /src/bacter/Conversion.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/Conversion.java -------------------------------------------------------------------------------- /src/bacter/ConversionEvent.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/ConversionEvent.java -------------------------------------------------------------------------------- /src/bacter/ConversionGraph.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/ConversionGraph.java -------------------------------------------------------------------------------- /src/bacter/Locus.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/Locus.java -------------------------------------------------------------------------------- /src/bacter/MarginalNode.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/MarginalNode.java -------------------------------------------------------------------------------- /src/bacter/MarginalTree.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/MarginalTree.java -------------------------------------------------------------------------------- /src/bacter/Region.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/Region.java -------------------------------------------------------------------------------- /src/bacter/RegionList.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/RegionList.java -------------------------------------------------------------------------------- /src/bacter/SiteAncestry.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/SiteAncestry.java -------------------------------------------------------------------------------- /src/bacter/acgannotator/ACGAnnotator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/acgannotator/ACGAnnotator.java -------------------------------------------------------------------------------- /src/bacter/acgannotator/ACGCladeSystem.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/acgannotator/ACGCladeSystem.java -------------------------------------------------------------------------------- /src/bacter/acgannotator/icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/acgannotator/icon.png -------------------------------------------------------------------------------- /src/bacter/beauti/CustomConnectors.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/beauti/CustomConnectors.java -------------------------------------------------------------------------------- /src/bacter/devutils/CFConvSwapExperiment.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/devutils/CFConvSwapExperiment.java -------------------------------------------------------------------------------- /src/bacter/devutils/ComputeCPDMatrix.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/devutils/ComputeCPDMatrix.java -------------------------------------------------------------------------------- /src/bacter/devutils/DensityCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/devutils/DensityCalculator.java -------------------------------------------------------------------------------- /src/bacter/devutils/DifferenceFromTrueACG.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/devutils/DifferenceFromTrueACG.java -------------------------------------------------------------------------------- /src/bacter/devutils/MCMCTrace.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/devutils/MCMCTrace.java -------------------------------------------------------------------------------- /src/bacter/devutils/OperatorTester.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/devutils/OperatorTester.java -------------------------------------------------------------------------------- /src/bacter/model/ACGCoalescent.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/model/ACGCoalescent.java -------------------------------------------------------------------------------- /src/bacter/model/ACGLikelihood.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/model/ACGLikelihood.java -------------------------------------------------------------------------------- /src/bacter/model/ACGLikelihoodApprox.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/model/ACGLikelihoodApprox.java -------------------------------------------------------------------------------- /src/bacter/model/ACGLikelihoodBeagle.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/model/ACGLikelihoodBeagle.java -------------------------------------------------------------------------------- /src/bacter/model/ACGLikelihoodSlow.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/model/ACGLikelihoodSlow.java -------------------------------------------------------------------------------- /src/bacter/model/ACGSimulator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/model/ACGSimulator.java -------------------------------------------------------------------------------- /src/bacter/model/AlignmentSimulator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/model/AlignmentSimulator.java -------------------------------------------------------------------------------- /src/bacter/model/SimulatedACG.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/model/SimulatedACG.java -------------------------------------------------------------------------------- /src/bacter/model/SimulatedAlignment.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/model/SimulatedAlignment.java -------------------------------------------------------------------------------- /src/bacter/model/pop/PiecewisePopulationFunction.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/model/pop/PiecewisePopulationFunction.java -------------------------------------------------------------------------------- /src/bacter/model/pop/SkylinePopulationFunction.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/model/pop/SkylinePopulationFunction.java -------------------------------------------------------------------------------- /src/bacter/operators/ACGOperator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/ACGOperator.java -------------------------------------------------------------------------------- /src/bacter/operators/ACGScaler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/ACGScaler.java -------------------------------------------------------------------------------- /src/bacter/operators/ACGValidityWrapper.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/ACGValidityWrapper.java -------------------------------------------------------------------------------- /src/bacter/operators/AddRemoveConversion.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/AddRemoveConversion.java -------------------------------------------------------------------------------- /src/bacter/operators/AddRemoveDetour.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/AddRemoveDetour.java -------------------------------------------------------------------------------- /src/bacter/operators/AddRemoveRedundantConversion.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/AddRemoveRedundantConversion.java -------------------------------------------------------------------------------- /src/bacter/operators/CFConversionSwap.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/CFConversionSwap.java -------------------------------------------------------------------------------- /src/bacter/operators/CFOperator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/CFOperator.java -------------------------------------------------------------------------------- /src/bacter/operators/CFSubtreeExchange.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/CFSubtreeExchange.java -------------------------------------------------------------------------------- /src/bacter/operators/CFSubtreeSlide.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/CFSubtreeSlide.java -------------------------------------------------------------------------------- /src/bacter/operators/CFUniform.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/CFUniform.java -------------------------------------------------------------------------------- /src/bacter/operators/CFWilsonBalding.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/CFWilsonBalding.java -------------------------------------------------------------------------------- /src/bacter/operators/ConversionCreationOperator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/ConversionCreationOperator.java -------------------------------------------------------------------------------- /src/bacter/operators/ConvertedEdgeFlip.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/ConvertedEdgeFlip.java -------------------------------------------------------------------------------- /src/bacter/operators/ConvertedEdgeHop.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/ConvertedEdgeHop.java -------------------------------------------------------------------------------- /src/bacter/operators/ConvertedEdgeHopContemp.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/ConvertedEdgeHopContemp.java -------------------------------------------------------------------------------- /src/bacter/operators/ConvertedEdgeSlide.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/ConvertedEdgeSlide.java -------------------------------------------------------------------------------- /src/bacter/operators/ConvertedRegionBoundaryShift.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/ConvertedRegionBoundaryShift.java -------------------------------------------------------------------------------- /src/bacter/operators/ConvertedRegionShift.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/ConvertedRegionShift.java -------------------------------------------------------------------------------- /src/bacter/operators/ConvertedRegionSwap.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/ConvertedRegionSwap.java -------------------------------------------------------------------------------- /src/bacter/operators/EdgeCreationOperator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/EdgeCreationOperator.java -------------------------------------------------------------------------------- /src/bacter/operators/MergeSplitConversion.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/MergeSplitConversion.java -------------------------------------------------------------------------------- /src/bacter/operators/ReplaceConversion.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/operators/ReplaceConversion.java -------------------------------------------------------------------------------- /src/bacter/util/ACGLogReader.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/ACGLogReader.java -------------------------------------------------------------------------------- /src/bacter/util/BacterACGLogReader.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/BacterACGLogReader.java -------------------------------------------------------------------------------- /src/bacter/util/COACGLogFileReader.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/COACGLogFileReader.java -------------------------------------------------------------------------------- /src/bacter/util/ClonalFrameLogger.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/ClonalFrameLogger.java -------------------------------------------------------------------------------- /src/bacter/util/ConversionCount.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/ConversionCount.java -------------------------------------------------------------------------------- /src/bacter/util/ConversionCountBounds.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/ConversionCountBounds.java -------------------------------------------------------------------------------- /src/bacter/util/ConversionGraphStatsLogger.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/ConversionGraphStatsLogger.java -------------------------------------------------------------------------------- /src/bacter/util/ConvertedRegionLogger.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/ConvertedRegionLogger.java -------------------------------------------------------------------------------- /src/bacter/util/IntRanges.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/IntRanges.java -------------------------------------------------------------------------------- /src/bacter/util/TrimmedACGLogger.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/TrimmedACGLogger.java -------------------------------------------------------------------------------- /src/bacter/util/parsers/ExtendedNewick.g4: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/parsers/ExtendedNewick.g4 -------------------------------------------------------------------------------- /src/bacter/util/parsers/ExtendedNewickBaseListener.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/parsers/ExtendedNewickBaseListener.java -------------------------------------------------------------------------------- /src/bacter/util/parsers/ExtendedNewickBaseVisitor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/parsers/ExtendedNewickBaseVisitor.java -------------------------------------------------------------------------------- /src/bacter/util/parsers/ExtendedNewickLexer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/parsers/ExtendedNewickLexer.java -------------------------------------------------------------------------------- /src/bacter/util/parsers/ExtendedNewickListener.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/parsers/ExtendedNewickListener.java -------------------------------------------------------------------------------- /src/bacter/util/parsers/ExtendedNewickParser.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/parsers/ExtendedNewickParser.java -------------------------------------------------------------------------------- /src/bacter/util/parsers/ExtendedNewickVisitor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/src/bacter/util/parsers/ExtendedNewickVisitor.java -------------------------------------------------------------------------------- /test/bacter/MarginalTreeTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/MarginalTreeTest.java -------------------------------------------------------------------------------- /test/bacter/SerializationDeserializationTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/SerializationDeserializationTest.java -------------------------------------------------------------------------------- /test/bacter/SiteAncestryTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/SiteAncestryTest.java -------------------------------------------------------------------------------- /test/bacter/TestBase.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/TestBase.java -------------------------------------------------------------------------------- /test/bacter/model/ACGLikelihoodApproxTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/model/ACGLikelihoodApproxTest.java -------------------------------------------------------------------------------- /test/bacter/model/ACGLikelihoodTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/model/ACGLikelihoodTest.java -------------------------------------------------------------------------------- /test/bacter/model/SimulatedAlignmentTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/model/SimulatedAlignmentTest.java -------------------------------------------------------------------------------- /test/bacter/model/pop/SkylinePopulationFunctionTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/model/pop/SkylinePopulationFunctionTest.java -------------------------------------------------------------------------------- /test/bacter/operators/AddRemoveConversionTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/operators/AddRemoveConversionTest.java -------------------------------------------------------------------------------- /test/bacter/util/BacterACGLogReaderTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/util/BacterACGLogReaderTest.java -------------------------------------------------------------------------------- /test/bacter/util/IntRangesTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/util/IntRangesTest.java -------------------------------------------------------------------------------- /test/bacter/xmltests/AddRemoveDetourTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/xmltests/AddRemoveDetourTest.java -------------------------------------------------------------------------------- /test/bacter/xmltests/AddRemoveRedundantTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/xmltests/AddRemoveRedundantTest.java -------------------------------------------------------------------------------- /test/bacter/xmltests/AddRemoveTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/xmltests/AddRemoveTest.java -------------------------------------------------------------------------------- /test/bacter/xmltests/AllOperatorTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/xmltests/AllOperatorTest.java -------------------------------------------------------------------------------- /test/bacter/xmltests/CFOperatorTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/xmltests/CFOperatorTest.java -------------------------------------------------------------------------------- /test/bacter/xmltests/MergeSplitTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/xmltests/MergeSplitTest.java -------------------------------------------------------------------------------- /test/bacter/xmltests/RegionShiftTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/xmltests/RegionShiftTest.java -------------------------------------------------------------------------------- /test/bacter/xmltests/SimulatedACGTest.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/test/bacter/xmltests/SimulatedACGTest.java -------------------------------------------------------------------------------- /version.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tgvaughan/bacter/HEAD/version.xml --------------------------------------------------------------------------------