MesquiteProject/MesquiteCore

Project: MesquiteCore (GitHub Link)

MesquiteCore-master
- Additional Files
  - classpaths.txt
  - Mesquite_Start_Script java 1.8.command
  - execsToStartUnderWindows
    - Mesquite.jar
    - Mesquite_Start_Script.bat
    - Mesquite.exe
  - receipts.xml
  - menuSquares.txt
  - Mesquite_Start_Script java 1.7.command
  - jarFileMaking.txt
  - Mesquite.exe
  - preparingMesquite.html
- pom.xml
- Mesquite_Folder
  - lib
    - libjri.jnilib
  - jars
- Resources
  - mesquite.sh
  - images
    - new.gif
    - colors
      - 2
      - 1parametersTab.gif
      - infoBarBase copy 2.gif
      - 0graphicsTab.gif
      - 1modulesTab.gif
      - 1infoBarBase.gif
      - 3
      - 0blank-on copy.gif
      - 2citationsTab.gif
      - infoBarBase copy.gif
      - 3modulesTab.gif
      - 3textTab.gif
      - 0modulesTab.gif
      - 3infoBarBase.gif
      - 0
      - 2graphicsTab.gif
      - 1blank-off.gif
      - 1citationsTab.gif
      - blank-offClear.gif
      - 3citationsTab.gif
      - 1blank-on.gif
      - infoBarBase.gif
      - 2blank-on.gif
      - 2infoBarBase.gif
      - blank-off.gif
      - 2blank-off.gif
      - 2textTab.gif
      - 3graphicsTab.gif
      - 1
      - 0parametersTab.gif
      - 1graphicsTab.gif
      - 3blank-off.gif
      - 1textTab.gif
      - 0blank-off.gif
      - blank-offBordered.gif
      - 0blank-on.gif
      - 0textTab.gif
      - 2parametersTab.gif
      - 0citationsTab.gif
      - 3blank-on.gif
      - 2modulesTab.gif
      - 3parametersTab.gif
      - 0infoBarBase.gif
    - windowIcons
      - matrixSequence.gif
      - matrix.gif
      - goAway.gif
      - goAway old.gif
      - listC.gif
      - tree.gif
      - listT.gif
    - showTransparent.gif
    - mesquiteIcon128.gif
    - blank-on.gif
    - 64disabled.gif
    - closeTriangleUp.gif
    - pointer.gif
    - dropper.gif
    - rightarrow-red.gif
    - how.gif
    - 32zoomIn.gif
    - sitetositetab.gif
    - or.gif
    - explanationPlus.gif
    - maximizeTransparent.gif
    - leftarrow-blue.gif
    - and.gif
    - mesquiteIcon48.gif
    - bannerBeta.gif
    - minimize.gif
    - matrix.gif
    - release.gif
    - tabRight.gif
    - enterHorizDisabled.gif
    - uparrow-blue.gif
    - 64bucket.gif
    - taxon.gif
    - ratematrixtabOff.gif
    - triangleDown.gif
    - 64pointer.gif
    - disabled.gif
    - explanationMinus.gif
    - mesquitesmall.gif
    - 32wandMinus.gif
    - decrease.gif
    - 32arrow.gif
    - pause.gif
    - help.gif
    - zoomOut.gif
    - miniscrollHoriz.gif
    - 32notesTool.gif
    - 64wand.gif
    - revSort.gif
    - dataSearch.gif
    - rightarrowPressed.gif
    - 64sort.gif
    - increase.gif
    - small.top.arrow.gif
    - 32bucket.gif
    - subtractGray.gif
    - goawayTransparent.gif
    - 64dropper.gif
    - ratematrixtab.gif
    - rightarrowDisabled.gif
    - 64ibeam.gif
    - triangleRightOff.gif
    - rightarrow-blue.gif
    - triangleDownOn.gif
    - leftarrow.gif
    - rightarrow-green.gif
    - 32disabled.gif
    - enterVert.gif
    - subtract.gif
    - empty.gif
    - arrow.gif
    - listS.gif
    - ant_logo_large.gif
    - back.gif
    - addGray.gif
    - compactTransparent.gif
    - construction.gif
    - rootstatestabOff.gif
    - bucket.gif
    - wandMinus.gif
    - wandPlus.gif
    - infoBarBase.gif
    - uparrowDisabled.gif
    - list.gif
    - spot.gif
    - infoBarTriangle.gif
    - blue-ball-small.gif
    - listP.GIF
    - triangleDownOff.gif
    - wand.gif
    - buttons.gif
    - sliderVert.gif
    - substantiveBug.gif
    - manual.gif
    - listC.gif
    - tabLeft.gif
    - infoBarIcons.gif
    - downarrow-red.gif
    - minimizeTransparent.gif
    - blank-on22.gif
    - 32ibeam.gif
    - 64wandMinus.gif
    - helpPressed.gif
    - blank-off.gif
    - 32wand.gif
    - enterVertPressed.gif
    - ok.gif
    - showInfo.gif
    - mediumizeTransparent.gif
    - backDim.gif
    - sort.gif
    - mesquite.gif
    - prerelease.gif
    - downarrow-blue.gif
    - downarrowDisabled.gif
    - 32wandPlus.gif
    - download.gif
    - functionIcons
      - matrixSource.gif
      - treeSource.gif
      - fileInterpret.gif
      - matrixEditor.gif
      - matrixNumber.gif
      - charSource.gif
      - treeNumber.gif
      - treeWindow.gif
      - simulate.gif
      - matrixEditorUtil.gif
      - chart.gif
      - treeCharNumber.gif
      - characterNumber.gif
      - treeWindowUtil.gif
    - triangleUpOn.gif
    - miniScroll.jpg
    - blank-off22.gif
    - spotgreen.gif
    - decompactTransparent.gif
    - 32info.gif
    - enterHoriz.gif
    - link.gif
    - manualPressed.gif
    - rootstatestab.gif
    - 64revSort.gif
    - checkMark.gif
    - blackPixel3.gif
    - addRemote.gif
    - annot.gif
    - mesquiteBeta.gif
    - 64info.gif
    - colorLegend.gif
    - 32sort.gif
    - enterVertDisabled.gif
    - leftarrow-gray.gif
    - notesTool.gif
    - 32zoomOut.gif
    - sitetositetabOff.gif
    - explanationMinusOff.gif
    - mesquitePlain.gif
    - uparrow-green.gif
    - 32pointer.gif
    - 64zoomIn.gif
    - banner.gif
    - search.gif
    - 32revSort.gif
    - add.gif
    - downarrow.gif
    - downarrowPressed.gif
    - leftarrow-red.gif
    - replaceLeft.gif
    - uparrow.gif
    - showInfoOld.gif
    - trashcan.gif
    - miniscrollVert.gif
    - uparrow-red.gif
    - triangleRightOn.gif
    - sliderHoriz.gif
    - equilstatestabOff.gif
    - blackPixel.gif
    - 64wandPlus.gif
    - 64zoomOut.gif
    - menuDropArrow.gif
    - menus.gif
    - zoomIn.gif
    - queryGray.gif
    - leftarrowDisabled.gif
    - leftarrowPressed.gif
    - 64notesTool.gif
    - ibeam.gif
    - tabOn.gif
    - mesquiteIcon16.gif
    - listT.gif
    - goaway.gif
    - 32dropper.gif
    - uparrowPressed.gif
    - info.gif
    - 64arrow.gif
    - equilstatestab.gif
    - green-ball-small.gif
    - enterHorizPressed.gif
    - play.gif
    - tabOff.gif
    - simplification
      - simple.gif
      - redRing.gif
      - power.gif
      - blueRing.gif
      - load.gif
    - mesquiteIcon.gif
    - equivocal.gif
    - rightarrow.gif
    - downarrow-green.gif
    - leftarrow-green.gif
  - examples
    - Ancestral_States
      - 15-Mk1AsymmCompare.nex
      - 15a-estimatingParameters.nex
      - 16b-BranchLengths.nex
      - 15ab-xiphStochCharMap.nex
      - 11b-TextView.nex
      - 03b-LiveUpdate.nex
      - 03-TraceCharPars.nex
      - 04-Equivocal.nex
      - 13-AsymmLikelihood.nex
      - 02-TreeWindow.nex
      - 10-PlotTree.nex
      - 17-TraceOverTrees.nex
      - 12-Mk1Likelihood.nex
      - 15b1-estimatingParameters.nex
      - 07-EditingParsModels.nex
      - 11-TraceCharMLE.nex
      - 09-Continuous.nex
      - 20-likelihoodToT.nex
      - 05-TreeForm.nex
      - 14-AsymmEstLikelihood.nex
      - 01-DataMatrix.nex
      - 08-ParsimonyMacClade.nex
      - 15aa-xiphLikelihood.nex
      - 21-likelihoodTot.nex
      - 15b-estimatingParameters.nex
      - 16c-TraceAllChars.nex
      - 19-likelihoodTot.nex
      - 18-TraceOverResolutions.nex
      - 15b2-estimatingParameters.nex
      - 06-ParsimonyModels.nex
    - Correlation
      - 00-introduction.nex
      - 01-pairwise.nex
      - 07-pairwiseFig3-6(3).nex
      - 02-pairwiseFig2(1).nex
      - 00a-FelsensteinsContrasts.nex
      - 00b-pagel94Hominids.nex
      - 00c-pairwiseIntro.nex
      - 05-pairwiseFig3-6(1).nex
      - 03-pairwiseFig2(2).nex
      - 06-pairwiseFig3-6(2).nex
      - 04-pairwiseFig2(3).nex
    - Diversification
      - 00-introduction.nex
      - 05-BiSSENetViewer.nex
      - 06-BiSSEtrees.nex
      - 01-lineagesThroughTime.nex
      - 03-sisterDiversification.nex
      - 04-BiSSEViewer.nex
      - 02-speciationExtinctionRates.nex
      - 08-binaryTreeSim.nex
      - 07-contTreeSim.nex
    - Coalescence
      - 06-twoPopulations2.nex
      - 00-introduction.nex
      - 11-geneInSpecies2.nex
      - tutorial
        02b-associationsHow2.nex
        03-associationsHow3.nex
        01-associationsHow1.nex
        04-associationsHow4.nex
        02-associationsHow2.nex
      - 05-twoPopulations.nex
      - 03-coalescenceDepth.nex
      - 08-fluctuating.nex
      - 10-speciesTreeSearch.nex
      - 09-genesInSpecies.nex
      - 02-coalescence2.nex
      - 04-associations.nex
      - 01-coalescence.nex
      - outOfAfrica
        03-outOfAfrica.nex
        01-outOfAfrica.nex
        02-outOfAfrica.nex
        04-outOfAfrica.nex
    - Multivariate_Continuous
      - 17-landmarks.nex
      - 06-anoles.nex
      - 00-introduction.nex
      - epca
        Image2.gif
        Image1.gif
      - 14-epca.nex
      - 13-epca.nex
      - 08-anoles.nex
      - 19-landmarks.nex
      - 10-pcaLiveSim.nex
      - 16-epcaLiveSim.nex
      - 05-anoles.nex
      - 04-anoles.nex
      - 02-wingsPCA.nex
      - 03-wingsCVA.nex
      - 07-anoles.nex
      - 01-wingsPlot.nex
      - 15-epca.nex
      - 18-landmarks.nex
      - 12-epca.nex
      - 20-landmarks.nex
      - 09-pcaSim.nex
      - 11-cvaLiveSim.nex
      - fish
        one.gif
        blue.gif
        two.gif
        red.gif
    - Introduction.nex
    - Basic_Examples
      - taxa
        08-multipleBlocks.nex
        03-partitions.nex
        07-selecting.nex
        06-selecting.nex
        02-addingDeleting.nex
        01-taxa.nex
        04-partitions.nex
        05-selecting.nex
      - charts
        02-histogram.nex
        01-charts.nex
        04-scattergram.nex
        03-scattergram.nex
      - characters
        fubonidianImages
        snorolopaKnobble.gif
        zorabynyxGizmoid.gif
        quidnubiaGizmoid.gif
        zorabynyxZibinator.gif
        fubonidiaKnobble.gif
        zorabynyxKnobble.gif
        snorolopaGizmoid.gif
        fubonidiaGizmoid.gif
        quidnubiaKnobble.gif
        quidnubiaZibinator.gif
        fubonidiaZibinator.gif
        snorolopaZibinator.gif
        07-dataEditing.nex
        10-names.nex
        03-newMatrix.nex
        12-continuous.nex
        08-addDelete.nex
        05-dataEditing.nex
        16-charSources.nex
        11-viewingStyles.nex
        14-partitions.nex
        11a-annotations.nex
        15-selecting.nex
        06-fill.nex
        01-characters.nex
        09-copyPaste.nex
        02-newMatrix.nex
        04-characterLists.nex
        13-continuousItems.nex
        17-charSources.nex
      - introduction.nex
      - continuous
        06-sim.nex
        07-mirrorTree.nex
        05-treeSearch.nex
        08-plotTree.nex
        09-plotTreeSim.nex
        03-trace.nex
        01-editContinuous.nex
        04-branchLengths.nex
      - basic_operation
        13-blockOfTaxa.nex
        fubonidianImages
        snorolopaKnobble.gif
        zorabynyxGizmoid.gif
        quidnubiaGizmoid.gif
        zorabynyxZibinator.gif
        fubonidiaKnobble.gif
        zorabynyxKnobble.gif
        snorolopaGizmoid.gif
        fubonidiaGizmoid.gif
        quidnubiaKnobble.gif
        quidnubiaZibinator.gif
        fubonidiaZibinator.gif
        snorolopaZibinator.gif
        07-moreHelp.nex
        15-annotations.nex
        11-newFile.nex
        05-windowModes.nex
        01-basics.nex
        12-fileFormats.nex
        06-helpMenu.nex
        13-matrix.nex
        14-included.nex
        02-standardMenus.nex
        08-logFile.nex
        04a-windowTabs.nex
        16-webLinks.nex
        04-treeWindow.nex
        10-scripting.nex
        03-characterMatrices.nex
        09-windowFonts.nex
        13-trees.nex
      - tree_manipulation
        09-treeBlocks.nex
        03-editingTrees.nex
        10-externalTrees.nex
        06-branchSelection.nex
        01-editingTrees.nex
        11-treeSources.nex
        02-editingTrees.nex
        12-treeSources.nex
        13-instability.nex
        04-branchLengths.nex
        05-branchColorNames.nex
        08-listOfTrees.nex
        07-storedTrees.nex
        10-treeFile.nex
      - tree_viewing
        06-printingTrees.nex
        01-treeWindow.nex
        04-moreTreeForms.nex
        03-drawingSize.nex
        05-moreTreeForms.nex
        07-dependentWindow.nex
        09-multiTrees.nex
        02-treeForm.nex
        08-mirrorTree.nex
        10-multiTrees.nex
    - Character_Simulations
      - 00-introduction.nex
      - 02-gammaTest.nex
      - templates
        GammaInvarTest.template
        TiTvTest.template
        GammaTest.template
        GTRTest.template
        GIGTRTest.template
      - 01-modelTree.nex
      - 03-TestingTreeStructure.nex
    - Molecular
      - 00-introduction.nex
      - 05-gcContentTaxaExons.nex
      - 07-cytochromeBHydro.nex
      - 06-cytochromeB.nex
      - 08-cytochromeBlinked.nex
      - 04-gcContentTaxa.nex
      - 09-cytochromeBscatter.nex
      - 01-gcContentChart.nex
      - 03a-cytochromeB.nex
      - 03-gcContentBirdsEye.nex
      - 02-gcContentMatrix.nex
    - Other_Examples
      - ConcatenatingMatrices
        TaxonNamesAreDifferent
        06.concatenatingMatrices.nex
        07.mergedMatrix.nex
        03.concatenatingMatrices.nex
        01.concatenatingMatrices.nex
        02.concatenatingMatrices.nex
        05.concatenatingMatrices.nex
        otherGeneMatrix.nex
        04.concatenatingMatrices.nex
  - startingMesquiteAndMemoryAllocation.txt
  - documentation.html
  - Mesquite.exe
  - com
    - apple
      - mrj
        datatransfer
        FlaggedTransferable.class
        Transfer.class
        OSTypeFlavor.class
        MRJMenuUtils.class
        MRJOpenDocumentHandler.class
        MRJAboutHandler.class
        MRJOpenApplicationHandler.class
        MRJPrintDocumentHandler.class
        MRJOSType.class
        MRJPriv.class
        MRJApplicationUtils.class
        MRJCoercionHandler.class
        dnd
        DragListener.class
        DragAdapter.class
        DragInitiatorAdapter.class
        DragInitiatorListener.class
        MRJPrefsHandler.class
        MRJQuitHandler.class
        MRJFileUtils.class
      - eawt
        ApplicationListener.class
        CocoaComponent.class
        ApplicationAdapter.class
        ApplicationBeanInfo.class
        Application.class
        ApplicationEvent.class
      - eio
        FileManager.class
  - settings
    - minimal
      - Simplicity
        note.txt
  - Mesquite.app
    - Contents
      - _CodeSignature
        CodeResources
      - Info.plist
      - Resources
        Mesquite.icns
        en.lproj
        Localizable.strings
      - PkgInfo
      - Java
        mesquite.jar
      - MacOS
        JavaAppLauncher
  - lesser.txt
- LibrarySource
  - JSci
    - Version.java
    - maths
      - statistics
        ParetoDistribution.java
        BetaDistribution.java
        BinomialDistribution.java
        ProbabilityDistribution.java
        CauchyDistribution.java
        ChiSqrDistribution.java
        ExponentialDistribution.java
        PoissonDistribution.java
        WeibullDistribution.java
        NormalDistribution.java
        LognormalDistribution.java
        FDistribution.java
        OutOfRangeException.java
        TDistribution.java
        GeometricDistribution.java
        GammaDistribution.java
      - NumericalConstants.java
      - ExtraMath.java
      - SpecialMath.java
      - AbstractMath.java
    - GlobalSettings.java
  - Jama
    - CholeskyDecomposition.java
    - LUDecomposition.java
    - examples
      - MagicSquareExample.java
    - test
      - TestMatrix.java
    - EigenvalueDecomposition.java
    - util
      - Maths.java
    - Matrix.java
    - SingularValueDecomposition.java
    - QRDecomposition.java
  - pal
    - statistics
      - ParetoDistribution.java
      - ChiSquareDistribution.java
      - ChiSquareTest.java
      - BootstrapStatistics.java
      - ExponentialDistribution.java
      - DiscreteStatistics.java
      - PenalizedLikelihood.java
      - makefile
      - LikelihoodRatioTest.java
      - NormalDistribution.java
      - KishinoHasegawaTest.java
      - package.html
      - ModelSupport.java
      - GammaDistribution.java
      - ShimodairaHasegawaTest.java
    - substmodel
      - RateMatrix.java
      - NucleotideModelID.java
      - UniformRate.java
      - GTR.java
      - JTT.java
      - F84.java
      - AminoAcidModel.java
      - TN.java
      - MatrixExponential.java
      - WAG.java
      - AbstractRateMatrix.java
      - BLOSUM62.java
      - MTREV24.java
      - makefile
      - CodonModel.java
      - InvariableSites.java
      - TwoStateModel.java
      - NucleotideModel.java
      - VT.java
      - YangCodonModel.java
      - RateMatrixUtils.java
      - GammaRates.java
      - CPREV.java
      - Dayhoff.java
      - AminoAcidModelID.java
      - package.html
      - F81.java
      - RateDistribution.java
      - TransitionProbability.java
      - HKY.java
      - SubstitutionModel.java
    - mep
      - WindowedMutationRate.java
      - MutationRateModel.java
      - SteppedMutationRate.java
      - makefile
      - ConstantMutationRate.java
      - package.html
    - util
      - ThreeNumberSort.java
      - Log.java
      - makefile
      - ComparableDouble.java
      - Comparable.java
      - HeapSort.java
      - Logger.java
      - Comparator.java
      - package.html
    - datatype
      - StateRemover.java
      - DataType.java
      - CodonTableUtils.java
      - AminoAcids.java
      - IUPACNucleotides.java
      - Codons.java
      - makefile
      - IUPACPenaltyTable.java
      - CodonTable.java
      - CodonTableFactory.java
      - Nucleotides.java
      - DataTypeUtils.java
      - GeneralizedCodons.java
      - TwoStates.java
      - package.html
      - TransitionPenaltyTable.java
      - SimpleDataType.java
    - alignment
      - ConcatenatedAlignment.java
      - StrippedAlignment.java
      - AminoAcidAlignment.java
      - AbstractAlignment.java
      - JumbledAlignment.java
      - GapBalancedAlignment.java
      - Alignment.java
      - ReadAlignment.java
      - BootstrappedAlignment.java
      - makefile
      - CodonAlignment.java
      - AlignmentUtils.java
      - AlignmentParseException.java
      - SitePattern.java
      - package.html
      - SimpleAlignment.java
    - eval
      - DemographicValue.java
      - ChiSquareValue.java
      - makefile
      - DemographicLikelihoodValue.java
      - ModelParameters.java
      - LikelihoodValue.java
      - package.html
    - gui
      - Painter.java
      - makefile
      - CircularGraphics.java
      - PositionedNode.java
      - TreePainterCircular.java
      - TreeComponent.java
      - TreePainter.java
      - package.html
      - TreePainterNormal.java
    - misc
      - Product.java
      - WeightedFunction.java
      - TimeStamp.java
      - BranchLimits.java
      - Utils.java
      - ReleaseInfo.java
      - Nameable.java
      - Identifier.java
      - SimpleIdGroup.java
      - Summarizable.java
      - Weighting.java
      - Parameterized.java
      - SimpleSummarizable.java
      - TimeOrderCharacterData.java
      - makefile
      - Units.java
      - Report.java
      - UniformWeighting.java
      - SumToOneWeighting.java
      - IdGroup.java
      - Sum.java
      - package.html
      - ParameterizedDouble.java
      - IdGenerator.java
      - GeneralFunction.java
    - makefile
    - coalescent
      - ExponentialGrowth.java
      - ConstantPopulation.java
      - ExpandingPopulation.java
      - IntervalsExtractor.java
      - SkylinePlot.java
      - CoalescentTree.java
      - CoalescentSimulator.java
      - CoalescentIntervals.java
      - makefile
      - DemographicTree.java
      - CoalescentException.java
      - DemographicModel.java
      - DemographicClockTree.java
      - package.html
      - ConstExpGrowth.java
    - io
      - FormattedOutput.java
      - makefile
      - OutputTarget.java
      - FormattedInput.java
      - InputSource.java
      - package.html
    - tree
      - UPGMATree.java
      - MutationRateModelTree.java
      - ClockTree.java
      - ReadTree.java
      - ParameterizedTree.java
      - SplitSystem.java
      - Node.java
      - Tree.java
      - SimulatedAlignment.java
      - makefile
      - TreeParseException.java
      - UnconstrainedTree.java
      - NodeUtils.java
      - SimpleNode.java
      - SplitUtils.java
      - SimpleTree.java
      - SUPGMATree.java
      - NodeFactory.java
      - NeighborJoiningTree.java
      - TreeUtils.java
      - package.html
      - DatedTipsClockTree.java
      - LogParameterizedTree.java
      - TreeDistanceMatrix.java
    - math
      - UnivariateMinimum.java
      - UrnModel.java
      - MFWithGradient.java
      - UnivariateFunction.java
      - GeneralizedDEOptimizer.java
      - GammaFunction.java
      - MultivariateMinimum.java
      - DifferentialEvolution.java
      - MultivariateFunction.java
      - makefile
      - OrthogonalLineFunction.java
      - MathUtils.java
      - Binomial.java
      - MersenneTwisterFast.java
      - LineFunction.java
      - ConjugateDirectionSearch.java
      - ErrorFunction.java
      - OrthogonalSearch.java
      - MachineAccuracy.java
      - package.html
      - ConjugateGradientSearch.java
      - BoundsCheckedFunction.java
      - NumericalDerivative.java
    - distance
      - DistanceMatrix.java
      - DistanceMatrixUtils.java
      - JukesCantorDistanceMatrix.java
      - makefile
      - SequencePairLikelihood.java
      - PairwiseDistance.java
      - DistanceParseException.java
      - SUPGMADistanceMatrix.java
      - ReadDistanceMatrix.java
      - AlignmentDistanceMatrix.java
      - package.html
  - com
    - lowagie
      - text
        ImgPostscript.java
        Rectangle.java
        pdf
        PdfGState.java
        GlyphList.java
        PdfPageEvent.java
        ByteBuffer.java
        ArabicLigaturizer.java
        PdfTextArray.java
        PdfOCProperties.java
        PdfPSXObject.java
        PdfBorderDictionary.java
        PdfPTableEvent.java
        PdfArray.java
        TrueTypeFontUnicode.java
        PdfPages.java
        PdfLayerMembership.java
        PdfPage.java
        ColorDetails.java
        PdfFormXObject.java
        PdfTransparencyGroup.java
        PdfResources.java
        PdfRectangle.java
        PdfGraphics2D.java
        FontDetails.java
        TextField.java
        PdfAcroForm.java
        PatternColor.java
        codec
        BmpImage.java
        CCITTG4Encoder.java
        GifImage.java
        TIFFFaxDecoder.java
        TIFFConstants.java
        TiffImage.java
        PngImage.java
        TIFFLZWDecoder.java
        wmf
        MetaBrush.java
        MetaObject.java
        MetaPen.java
        InputMeta.java
        MetaState.java
        MetaDo.java
        MetaFont.java
        postscript
        PACommand.java
        PAEngine.java
        Token.java
        PAPencil.java
        PAToken.java
        PAParser.java
        MetaDoPS.java
        PAContext.java
        PAParserConstants.java
        TokenMgrError.java
        PAParserTokenManager.java
        PainterException.java
        JavaCharStream.java
        paparser.jj
        ParseException.java
        TIFFField.java
        TIFFDirectory.java
        PdfMediaClipData.java
        PdfAppearance.java
        PdfObject.java
        ExtraEncoding.java
        PdfDocument.java
        PushbuttonField.java
        TrueTypeFontSubSet.java
        CMYKColor.java
        PdfTransition.java
        RandomAccessFileOrArray.java
        PdfDestination.java
        PdfPRow.java
        BadPdfFormatException.java
        PdfColor.java
        FontSelector.java
        CFFFont.java
        PdfFormField.java
        PdfNameTree.java
        ExtendedColor.java
        SimpleXMLDocHandler.java
        PdfCell.java
        hyphenation
        Hyphen.java
        ByteVector.java
        HyphenationException.java
        Hyphenator.java
        TernaryTree.java
        Hyphenation.java
        HyphenationTree.java
        SimplePatternParser.java
        PatternConsumer.java
        CharVector.java
        PdfPatternPainter.java
        PdfReaderInstance.java
        FdfReader.java
        PdfDictionary.java
        DocumentFont.java
        PdfEncodings.java
        LZWDecoder.java
        PdfPageEventHelper.java
        PdfAction.java
        PdfString.java
        PdfName.java
        HyphenationEvent.java
        CFFFontSubset.java
        CJKFont.java
        PRIndirectReference.java
        ColumnText.java
        PdfOutline.java
        PdfOCG.java
        ShadingColor.java
        PdfIndirectReference.java
        PRTokeniser.java
        PdfPTable.java
        PdfNumber.java
        PdfLayer.java
        PdfRendition.java
        PdfFunction.java
        BidiOrder.java
        PdfImage.java
        PdfLine.java
        PdfAnnotation.java
        Pfm2afm.java
        PdfFont.java
        PdfTable.java
        SimpleBookmark.java
        BaseFont.java
        PdfShading.java
        PdfPrinterGraphics2D.java
        OutputStreamCounter.java
        fonts
        Helvetica-BoldOblique.afm
        Times-Roman.afm
        Courier-BoldOblique.afm
        Helvetica.afm
        Times-Italic.afm
        Helvetica-Bold.afm
        Times-BoldItalic.afm
        Symbol.afm
        Courier.afm
        Helvetica-Oblique.afm
        FontsResourceAnchor.java
        Courier-Bold.afm
        ZapfDingbats.afm
        Courier-Oblique.afm
        Times-Bold.afm
        VerticalText.java
        PdfFileSpecification.java
        SequenceList.java
        IntHashtable.java
        GrayColor.java
        PdfPCellEvent.java
        XfdfReader.java
        PdfContentByte.java
        PdfException.java
        PdfICCBased.java
        PdfWriter.java
        HyphenationAuto.java
        PdfPageLabels.java
        PdfStream.java
        SimpleXMLParser.java
        PdfTemplate.java
        PdfEncryptionStream.java
        PdfNull.java
        PdfShadingPattern.java
        PdfSpotColor.java
        PdfLiteral.java
        PdfImportedPage.java
        PdfContents.java
        SimpleNamedDestination.java
        EnumerateTTC.java
        PdfPCell.java
        PageResources.java
        PdfDate.java
        BidiLine.java
        FontMapper.java
        PdfBoolean.java
        PdfXConformanceException.java
        DefaultFontMapper.java
        PdfBorderArray.java
        PdfDashPattern.java
        PdfIndirectObject.java
        MultiColumnText.java
        AsianFontMapper.java
        PdfPattern.java
        PdfChunk.java
        SimpleXMLDocHandlerComment.java
        PRStream.java
        Type1Font.java
        PdfReader.java
        SpotColor.java
        BaseField.java
        PdfEncryption.java
        PdfLister.java
        TrueTypeFont.java
        RadioCheckField.java
        PdfPageElement.java
        ElementTags.java
        markup
        MarkupParser.java
        MarkupTags.java
        ImgCCITT.java
        SplitCharacter.java
        GreekList.java
        Watermark.java
        ImgTemplate.java
        Header.java
        StringCompare.java
        Image.java
        PageSize.java
        html
        HtmlTags.java
        HtmlWriter.java
        HtmlEncoder.java
        simpleparser
        IncTable.java
        IncCell.java
        HTMLWorker.java
        ChainedProperties.java
        StyleSheet.java
        FactoryProperties.java
        MarkupAttributes.java
        Phrase.java
        Chapter.java
        BadElementException.java
        ElementListener.java
        Graphic.java
        HeaderFooter.java
        DocumentException.java
        Cell.java
        Annotation.java
        ZapfDingbatsList.java
        Entities.java
        RomanList.java
        SpecialSymbol.java
        Row.java
        ListItem.java
        ImgWMF.java
        Anchor.java
        Section.java
        Element.java
        Chunk.java
        ZapfDingbatsNumberList.java
        DocListener.java
        Document.java
        TextElementArray.java
        Font.java
        Meta.java
        Paragraph.java
        Table.java
        FontFactory.java
        List.java
        ImgRaw.java
        DocWriter.java
        Jpeg.java
        ExceptionConverter.java
- LICENSE
- .settings
  - org.eclipse.jdt.ui.prefs
  - org.eclipse.ltk.core.refactoring.prefs
  - org.eclipse.jdt.core.prefs
- README.md
- distributionBuildFiles
  - build.xml
  - build.properties
  - Windows XP.properties
  - serverinfo.properties.sample
  - jsch-0.1.28.jar
  - buildInstructions.html
- Source
  - start
    - Mesquite.java
  - corejava
    - Format.java
  - edu
    - stanford
      - ejalbert
        BrowserLauncher.java
  - mesquite
    - iText
      - explanation.txt
      - aiTextIntro
        splash.gif
        aiTextIntro.java
        splash.ai
        index.html
    - ornamental
      - NodeLocsOval
        NodeLocsOval.java
      - ManageHyperlinks
        ManageHyperlinks.java
      - Projector
        64projector.gif
        projector.gif
        Projector.java
        32projector.gif
      - NodePositionAdjust
        NodePositionAdjust.java
        32adjustPosition.gif
        64adjustPosition.gif
        adjustPosition.gif
      - Constellation
        Constellation.java
      - explanation.txt
      - NodeLocsCircular
        NodeLocsCircular.java
      - BranchNotes
        asteriskTool.gif
        64asteriskTool.gif
        asteriskBIGTool.gif
        32asteriskTool.gif
        BranchNotes.java
      - PictureWindowMaker
        PictureWindowMaker.java
      - ColorTreeByPartition
        ColorTreeByPartition.java
      - UnrootedTree
        UnrootedTree.java
      - aOrnamentalIntro
        aOrnamentalIntro.java
      - CircularTree
        CircularTree.java
      - ManagePictures
        ManagePictures.java
      - DrawTreeAssocDoubles
        DrawTreeAssocDoubles.java
      - NodeLocsUnrootedBasic
        NodeLocsUnrootedBasic.java
      - DrawTreeAssocStrings
        DrawTreeAssocStrings.java
      - ManageAttachedNotes
        ManageAttachedNotes.java
      - NodeNumbers
        NodeNumbers.java
      - TaxonLink
        TaxonLink.java
        64link.gif
        32link.gif
        link.gif
    - opentree
      - ExemplarTaxonAssistant
        ExemplarTaxonAssistant.java
      - ExportTreeForOpenTree
        ExportTreeForOpenTree.java
      - lib
        OpenTreeUtil.java
      - CopyNewickForOpenTree
        CopyNewickForOpenTree.java
      - OpenTreeLabeller
        openTree.gif
        32openTree.gif
        OpenTreeLabeller.java
        64openTree.gif
    - mb
      - TreesFromMrBayes
        TreesFromMrBayes.java
      - lib
        ExportForMrBayesLib.java
      - aMBIntro
        aMBIntro.java
      - BestBayesTree
        BestBayesTree.java
      - SimplifyTaxonNames
        SimplifyTaxonNames.java
      - ExportForMrBayes
        ExportForMrBayes.java
      - MrBayesScore
        MrBayesScore.java
    - charts
      - TaxonValuesChart
        TaxonValuesChart.java
      - ItemValuesChart
        ItemValuesChart.java
      - ItemsBiplot
        ItemsBiplot.java
      - TreeBlockValues
        TreeBlockValues.java
      - TaxonPairsScattergram
        TaxonPairsScattergram.java
      - ShowYEqualsX
        ShowYEqualsX.java
      - explanation.txt
      - TreesScattergram
        TreesScattergram.java
      - Scattergram
        Scattergram.java
      - aChartsIntro
        aChartsIntro.java
      - CharsScattergram
        CharsScattergram.java
      - TreeValuesChart
        TreeValuesChart.java
      - TaxonPairValuesChart
        TaxonPairValuesChart.java
      - CharacterValuesChart
        CharacterValuesChart.java
      - TaxaScattergram
        TaxaScattergram.java
      - NodesScattergram
        NodesScattergram.java
      - ShowMean
        ShowMean.java
      - Histogram
        Histogram.java
      - ShowPercentile
        05.gif
        01.gif
        ShowPercentile.java
        manual.html
        001.gif
      - MatrixValuesChart
        MatrixValuesChart.java
      - Notes
        Chart Notes.txt
    - tol
      - aTolIntro
        aTolIntro.java
      - CatalogueOfLifeURLServer
        CatalogueOfLifeURLServer.java
      - TaxonOnWebDB
        TaxonOnWeb.gif
        32TaxonOnWeb.gif
        TaxonOnWebDB.java
        64TaxonOnWeb.gif
      - uBioURLServer
        uBioURLServer.java
      - TreeBaseURLServer
        TreeBaseURLServer.java
      - lib
        TaxonOnWebServer.java
        MesquiteXMLToLUtilities.java
        BaseHttpRequestMaker.java
        ToLUtil.java
        BaseSearchToLTaxon.java
        ToLRequestParameters.java
        ToLProjectOpener.java
        XMLConstants.java
        BaseSearchToLToolTaxonExtra.java
      - SearchToLTaxon
        SearchToLTaxon.java
        32ToL.gif
        ToL.gif
        64ToL.gif
      - GetToLTree
        GetToLTree.java
      - ToLURLServer
        ToLURLServer.java
      - iSpeciesURLServer
        iSpeciesURLServer.java
      - GoogleURLServer
        GoogleURLServer.java
      - GenBankTaxonURLServer
        GenBankTaxonURLServer.java
    - trees
      - SquareTree
        SquareTree.java
      - RatioLongestBranches
        RatioLongestBranches.java
      - SelectTaxaInClade
        64selectTaxa.gif
        32selectTaxa.gif
        SelectTaxaInClade.java
        64selectTaxaInClade.gif
        32selectTaxaInClade.gif
        selectTaxaInClade.gif
        selectTaxa.gif
      - ClearBranchNames
        ClearBranchNames.java
      - DependentTreeWindow
        DependentTreeWindow.java
      - ColorTaxonByPartition
        ColorTaxonByPartition.java
      - BLFromNodeAgeConstraints
        BLFromNodeAgeConstraints.java
      - SetAssumptionDefault
        SetAssumptionDefault.java
      - NumForNodesWithChar
        NumForNodesWithChar.java
      - OtherTreeBlocks
        OtherTreeBlocks.java
      - LabelBranchLengths
        LabelBranchLengths.java
      - ScaleSelBranchLengths
        ScaleSelBranchLengths.java
      - BasicTreeDrawCoordinator
        BasicTreeDrawCoordinator.java
      - ArcTree
        ArcTree.java
      - ResolvePolytomiesToZero
        ResolvePolytomiesToZero.java
      - BasicDrawTaxonNames
        BasicDrawTaxonNames.java
      - SetAssumptionSoft
        SetAssumptionSoft.java
      - explanation.txt
      - NumsForNodesBrLengths
        NumsForNodesBrLengths.java
      - SetToLadderized
        SetToLadderized.java
      - DiagonalDrawTree
        DiagonalDrawTree.java
      - NumForCharRespTree
        NumForCharRespTree.java
      - NumForTreeWithChar
        NumForTreeWithChar.java
      - BooleanTreeValue
        BooleanTreeValue.java
      - SearchTreeToolAssistant
        searchTree.gif
        64searchTree.gif
        32searchTree.gif
        SearchTreeToolAssistant.java
      - NumForCharOnTree
        NumForCharOnTree.java
      - NegativeToZeroBL
        NegativeToZeroBL.java
      - ConstrainNodeAge
        anchor.gif
        32anchorTool.gif
        anchorWide.gif
        64anchorTool.gif
        ConstrainNodeAge.java
        anchorTool.gif
      - AverageTreeValue
        AverageTreeValue.java
      - TreeValueUsingMatrix
        TreeValueUsingMatrix.java
      - MirrorTreeWindowMaker
        MirrorTreeWindowMaker.java
      - ScaleBranchLengths
        ScaleBranchLengths.java
      - AddTaxaToTree
        AddTaxaToTree.java
      - CollapseZeroToPolys
        CollapseZeroToPolys.java
      - lib
        TreeOptimizer.java
        ManyTreesFromFileLib.java
        SimpleTreeWindowMaker.java
        DrawTreeUtil.java
        SimpleTreeWindow.java
        TreeInfoExtraPanel.java
        TaxonPolygon.java
      - ListedTreeBlocks
        ListedTreeBlocks.java
      - SetToUnrooted
        SetToUnrooted.java
      - TreeOfContext
        TreeOfContext.java
      - TreeInfoValues
        TreeInfoValues.java
      - BranchLengthsAdjust
        64adjustLengths.gif
        adjustLengths.gif
        dragLengths.gif
        64dragLengths.gif
        BranchLengthsAdjust.java
        32adjustLengths.gif
        32dragLengths.gif
      - NumForTreeSelNodeValue
        NumForTreeSelNodeValue.java
      - NumFor2CharCurrentTree
        NumFor2CharCurrentTree.java
      - BranchLengthFromRoot
        BranchLengthFromRoot.java
      - SearchForBetterTree
        SearchForBetterTree.java
      - NodeNamer
        32nodeNamer.gif
        64nodeNamer.gif
        NodeNamer.java
        nodeNamer.gif
      - Ultrametricize
        Ultrametricize.java
      - AlterTrees
        AlterTrees.java
      - ManyTreesFromFile
        ManyTreesFromFile.java
      - NoColorForTaxon
        NoColorForTaxon.java
      - NumForCharCurrentTree
        NumForCharCurrentTree.java
      - SetAssumptionHard
        SetAssumptionHard.java
      - NumForNodesWithCharHist
        NumForNodesWithCharHist.java
      - StoredTreeBlocks
        StoredTreeBlocks.java
      - NumForMatCurrentTree
        NumForMatCurrentTree.java
      - DefaultTrees
        DefaultTrees.java
      - ObedientTreeWindow
        ObedientTreeWindow.java
      - DefiniteTreeSource
        DefiniteTreeSource.java
      - NumForTreeWith2Chars
        NumForTreeWith2Chars.java
      - TreeNotesMaker
        TreeNotesMaker.java
      - SetToRooted
        SetToRooted.java
      - NumAttachedToTree
        NumAttachedToTree.java
      - SimulateTree
        SimulateTree.java
      - EqualRatesMarkovSp
        EqualRatesMarkovSp.java
      - ColorTaxonByAssigned
        ColorTaxonByAssigned.java
      - SquareLineTree
        SquareLineTree.java
      - UtilityCoordinator
        UtilityCoordinator.java
      - BasicTreeWindowMaker
        32interchange.gif
        32collapse.gif
        32zoom.gif
        triangle.gif
        reverseLadderize.gif
        64magnify.gif
        64triangle.gif
        zoomOut.gif
        32reverseLadderize.gif
        interchange.gif
        recent
        recent2.gif
        recent5.gif
        recent8.gif
        recent10.gif
        recent9.gif
        recent1.gif
        recent3.gif
        recent0.gif
        recent4.gif
        recent7.gif
        recent6.gif
        collapseAllBelow.gif
        64ladderize.gif
        64collapse.gif
        32magnify.gif
        64reroot.gif
        collapse.gif
        64scissors.gif
        reroot.gif
        32reroot.gif
        magnify.gif
        32ladderize.gif
        32zoomOut.gif
        32collapseall.gif
        collapseall.gif
        32scissors.gif
        64collapseAllBelow.gif
        64zoom.gif
        64interchange.gif
        64reverseLadderize.gif
        64collapseall.gif
        32collapseAllBelow.gif
        64zoomOut.gif
        zoom.gif
        32triangle.gif
        ladderize.gif
        scissors.gif
      - BasicTreeWindowCoord
        BasicTreeWindowCoord.java
      - ValuesAtNodes
        ValuesAtNodes.java
      - ShowTreeInList
        64showTree.gif
        showTree.gif
        32showTree.gif
        ShowTreeInList.java
      - EquiprobableTrees
        EquiprobableTrees.java
      - ShadeNumbersOnTree
        ShadeNumbersOnTree.java
      - MultiTreeWindowMaker
        MultiTreeWindowMaker.java
      - AllUnassignBrLengths1
        AllUnassignBrLengths1.java
      - SetToArbitrarySymmetrical
        SetToArbitrarySymmetrical.java
      - aTreesIntro
        aTreesIntro.java
      - DifferenceInNumsForTree
        DifferenceInNumsForTree.java
      - SimulatedTreeBlocks
        SimulatedTreeBlocks.java
      - StoredTrees
        StoredTrees.java
      - SetBranchLengthsFromNames
        SetBranchLengthsFromNames.java
      - ColorBranches
        ColorBranches.java
        32color.gif
        64color.gif
        color.gif
      - SetBranchLengthsIfLessThan
        SetBranchLengthsIfLessThan.java
      - SetTreeDefaults
        SetTreeDefaults.java
      - BallsNSticks
        BallsNSticks.java
      - SelectBranches
        32select.gif
        32selectClade.gif
        select.gif
        64selectClade.gif
        64select.gif
        selectClade.gif
        SelectBranches.java
      - TreeLegendMaker
        TreeLegendMaker.java
      - SetSelBranchLengths
        SetSelBranchLengths.java
      - NodeLocsStandard
        32expand.gif
        NodeLocsStandard.java
        64expand.gif
        expand.gif
      - BranchInfo
        branchInfo.gif
        BranchInfo.java
        32branchInfo.gif
        64branchInfo.gif
      - NumForNodesWithMat
        NumForNodesWithMat.java
      - NumForTreeCladeValue
        NumForTreeCladeValue.java
      - DeassignBranchLengths
        DeassignBranchLengths.java
      - ManageTrees
        ManageTrees.java
      - AlterLengths
        AlterLengths.java
      - NumberOfTaxa
        NumberOfTaxa.java
      - SampleManyTreesFromFile
        SampleManyTreesFromFile.java
      - SetBranchLengths
        SetBranchLengths.java
      - AllBranchLengthsOne
        AllBranchLengthsOne.java
    - jsci
      - aJSciIntro
        splash.gif
        index.html
        aJSciIntro.java
      - explanation.txt
    - stochchar
      - SimCharsOnTrees
        SimCharsOnTrees.java
      - StoredProbModelSim
        StoredProbModelSim.java
      - CharListProbModels
        CharListProbModels.java
      - zMargLikeCateg
        zMargLikeCateg.java
      - MargProbAncStates
        MargProbAncStates.java
      - explanation.txt
      - MkModelCurator
        MkModelCurator.java
      - SimMatricesOnTrees
        SimMatricesOnTrees.java
      - Mk1Rate
        Mk1Rate.java
      - EvolveCategChars
        EvolveCategChars.java
      - Brownian
        Brownian.java
      - CharLikelihood
        CharLikelihood.java
      - GainLossRates
        GainLossRates.java
      - lib
        CharacterLikelihood.java
        AsymmModel.java
        JointLikeAncStForModel.java
        MargLikeAncStCLForModel.java
        ProbModelSource.java
        BrownianMotionModel.java
        SimModelCompatInfo.java
        MargLikeAncStForModel.java
        ProbabilityContCharModel.java
        TreeDataModelBundle.java
        PagelFormatI.java
        ProbPhenCategCharModel.java
        MargLikelihoodForModel.java
        MkModel.java
        CategProbModelCurator.java
        PagNodeRecord.java
        ProbModelSourceLike.java
        ProbabilityCategCharModel.java
        ProbModelSourceSim.java
      - AsymmModelCurator
        AsymmModelCurator.java
      - LikelihoodInCharacter
        LikelihoodInCharacter.java
      - CurrentProbModelsSim
        CurrentProbModelsSim.java
      - ManageProbModelSets
        ManageProbModelSets.java
      - SimAncestralStates
        SimAncestralStates.java
      - SimulatedCharacters
        SimulatedCharacters.java
      - StoredProbModel
        StoredProbModel.java
      - SimulatedMatrix
        SimulatedMatrix.java
      - aStochCharIntro
        aStochCharIntro.java
      - AsymmMkExplorer
        AsymmMkExplorer.java
      - ManageCharModelsBlock
        ManageCharModelsBlock.java
      - EvolveContinuous
        EvolveContinuous.java
      - ProbModelSetList
        ProbModelSetList.java
      - InterpretPagelFormat
        InterpretPagelFormat.java
      - AsymmetryLR
        AsymmetryLR.java
      - CurrentProbModels
        CurrentProbModels.java
      - InterpretPagelFormatM
        InterpretPagelFormatM.java
      - StochCharMapper
        StochCharMapper.java
    - trunk
      - AboutWindow.java
      - FileOpener.java
      - ModuleLoader.java
      - ConfigFileRecord.java
      - WelcomeDialog.java
      - EAWTHandler.java
      - AboutPanel.java
      - JarLoader.java
      - PhoneHomeThread.java
      - ClockWatcherThread.java
      - ProjectTreeWindow.java
    - thinkTrees
      - examples
        02.treeThinking.nex
      - RandomRotateToolAssistant
        32randomRotate.gif
        RandomRotateToolAssistant.java
        64randomRotate.gif
        randomRotate.gif
      - RandomlyRotate
        RandomlyRotate.java
      - InformCharBoolean
        InformCharBoolean.java
      - AlphabeticTaxonNames
        AlphabeticTaxonNames.java
      - Notes
        ThinkTrees notes
    - consensus
      - ConsensusTree
        ConsensusTree.java
      - SemistrictConsensusTree
        SemistrictConsensusTree.java
      - aConsensusIntro
        aConsensusIntro.java
      - lib
        BasicTreeConsenser.java
        Bipartition.java
        StrictConsenser.java
        BipartitionVector.java
      - MajRuleTree
        MajRuleTree.java
      - StrictConsensusTree
        StrictConsensusTree.java
      - Notes
        Examples
        BembidionWithTrees
        Consensus Notes
    - lists
      - TaxonGroupList
        TaxonGroupList.java
      - TaxaSetListNum
        TaxaSetListNum.java
      - TreeblocksListNumber
        TreeblocksListNumber.java
      - TaxablockListNumber
        TaxablockListNumber.java
      - TaxonGroupListColor
        TaxonGroupListColor.java
      - BooleanForCharList
        BooleanForCharList.java
      - DatasetsListConcatenate
        DatasetsListConcatenate.java
      - CharacterStats
        CharacterStats.java
      - CharListWeights
        CharListWeights.java
      - CharGroupList
        CharGroupList.java
      - CharacterList
        CharacterList.java
      - NumForCharMatrixList
        NumForCharMatrixList.java
      - DatasetsListClass
        DatasetsListClass.java
      - TreeListRooted
        TreeListRooted.java
      - explanation.txt
      - CharListAnnotPanel
        CharListAnnotPanel.java
      - DefaultTaxaOrder
        DefaultTaxaOrder.java
      - TaxonListVoucherCode
        TaxonListVoucherCode.java
      - ModelsListDatatype
        ModelsListDatatype.java
      - TaxaListUniqueID
        TaxaListUniqueID.java
      - NumForTaxaList
        NumForTaxaList.java
      - TreesList
        TreesList.java
      - TaxonGroupListNumTaxa
        TaxonGroupListNumTaxa.java
      - TaxaPartitionList
        TaxaPartitionList.java
      - TreeListPolyAssumption
        TreeListPolyAssumption.java
      - NumForTreeblockList
        NumForTreeblockList.java
      - WeightSetList
        WeightSetList.java
      - lib
        TaxaSpecsListWindow.java
        TreeListInit.java
        TaxaListPartitionUtil.java
        CharSetListAsst.java
        TaxaPartListAssistant.java
        TaxonListAssistant.java
        TaxaListAssistantI.java
        ListLVModule.java
        CharListPartitionUtil.java
        ModelsListAssistant.java
        TaxonGroupListAssistant.java
        TreeBlockListUtility.java
        GroupDialog.java
        CharListAssistantI.java
        TaxaBlocksListAssistant.java
        ListWindow.java
        ArchivedTaxonNamesListAssistant.java
        TaxaSetListAssistant.java
        TaxaSpecssetList.java
        DatasetsListUtility.java
        DataSpecssetList.java
        TreeblocksListAssistant.java
        ListableVectorWindow.java
        DataSetsListAssistant.java
        CharGroupListAssistant.java
        ModelSetListAsst.java
        CharMatricesListWindow.java
        CharListAssistant.java
        TreeListAssistant.java
        CharListModel.java
        DataSpecsListWindow.java
        TreeListUtility.java
        ListAssistant.java
        ListTable.java
        ListModule.java
        CharInclSetListAsst.java
        TaxaBlocksListUtility.java
        GroupSymbolsDialog.java
      - ModelsList
        ModelsList.java
      - CharSetMembershipListAsst
        CharSetMembershipListAsst.java
      - CharPartitionList
        CharPartitionList.java
      - TreeblockList
        TreeblockList.java
      - CharListInclusion
        CharListInclusion.java
      - aListsIntro
        aListsIntro.java
      - CharSetListNum
        CharSetListNum.java
      - BooleanForTaxaList
        BooleanForTaxaList.java
      - CharNumForList
        CharNumForList.java
      - TaxonSetList
        TaxonSetList.java
      - TaxonGroupListVisibility
        TaxonGroupListVisibility.java
      - TaxonListShowAllHasData
        TaxonListShowAllHasData.java
      - CharInclSetList
        CharInclSetList.java
      - ModelsListType
        ModelsListType.java
      - CharListUniqueID
        CharListUniqueID.java
      - TaxablockList
        TaxablockList.java
      - ModelsListWhole
        ModelsListWhole.java
      - CodePosSetsList
        CodePosSetsList.java
      - CharListCodonPos
        CharListCodonPos.java
      - CharGroupListColor
        CharGroupListColor.java
      - TaxonGroupListSymbolSize
        TaxonGroupListSymbolSize.java
      - MatrixListEditable
        MatrixListEditable.java
      - TaxonListCurrPartition
        TaxonListCurrPartition.java
      - NumForTreeList
        NumForTreeList.java
      - ColorTaxon
        32color.gif
        64color.gif
        color.gif
        ColorTaxon.java
      - ModelsListParadigm
        ModelsListParadigm.java
      - TaxonListVoucherDB
        TaxonListVoucherDB.java
      - DatasetsListTaxa
        DatasetsListTaxa.java
      - TaxonListArchivedName
        TaxonListArchivedName.java
      - BooleanForTreeList
        BooleanForTreeList.java
      - NexusBlockList
        NexusBlockList.java
      - DatasetsListDuplicate
        DatasetsListDuplicate.java
      - TaxaPartListNumGroups
        TaxaPartListNumGroups.java
      - TreeblocksListTaxa
        TreeblocksListTaxa.java
      - TaxonGroupListSymbol
        TaxonGroupListSymbol.java
      - DatasetList
        DatasetList.java
      - DefaultCharOrder
        DefaultCharOrder.java
      - MarkTaxonInList
        MarkTaxonInList.java
      - TreeListPolys
        TreeListPolys.java
      - TaxonListAnnotPanel
        TaxonListAnnotPanel.java
      - MatrixListVisible
        MatrixListVisible.java
      - CharSetList
        CharSetList.java
      - DatasetsListNumChars
        DatasetsListNumChars.java
      - TreeListAttachment
        TreeListAttachment.java
      - CharListPartition
        CharListPartition.java
      - CharInclSetListNum
        CharInclSetListNum.java
      - TaxonList
        TaxonList.java
    - search
      - LikelihoodTreeSearch
        LikelihoodTreeSearch.java
      - SPRRearranger
        SPRRearranger.java
      - explanation.txt
      - DistanceTreeSearch
        DistanceTreeSearch.java
      - ParsimonyTreeSearch
        ParsimonyTreeSearch.java
      - aSearchIntro
        aSearchIntro.java
      - InvariantsTreeSearch
        InvariantsTreeSearch.java
      - AddAndRearrange
        AddAndRearrange.java
      - lib
        TreeSearch.java
      - NNIRearranger
        NNIRearranger.java
      - OtherTreeSearch
        OtherTreeSearch.java
      - OldStyleTreeSearch
        OldStyleTreeSearch.java
    - jama
      - explanation.txt
      - aJamaIntro
        splash.gif
        aJamaIntro.java
        index.html
    - rhetenor
      - wPCA
        wPCA.java
      - PlotTree3D
        PlotTree3D.java
      - ShowCharLoadings
        ShowCharLoadings.java
      - explanation.txt
      - MatricesFromOrdinations
        MatricesFromOrdinations.java
      - LandmarkDrawings
        32landmark.gif
        landmark.gif
        64landmark.gif
        LandmarkDrawings.java
      - CharsFromMatrices
        CharsFromMatrices.java
      - lib
        PCACorrelOrdination.java
        OrdinationAssistant.java
        Ordinator.java
        MatrixUtil.java
        CVAOrdination.java
        wPCAOrdination.java
        CharacterLoadings.java
        PCAOrdination.java
        NodeLocsPlot3D.java
        aPCAOrdination.java
        CharsFromMatrixSource.java
        Ordination.java
        EPCAOrdination.java
      - aPCA
        aPCA.java
      - CharFromOrdinations
        CharFromOrdinations.java
      - PrincipalComponents
        PrincipalComponents.java
      - CharLoadings
        CharLoadings.java
      - aRhetenorIntro
        splash.gif
        splash.gif copy
        aRhetenorIntro.java
        splashSmall.gif
        index.html
      - CanonicalVariates
        CanonicalVariates.java
      - NodeLocs3DPlot
        NodeLocs3DPlot.java
      - EvolutionaryPCA
        EvolutionaryPCA.java
    - diverse
      - BiSSELikelihood
        BiSSELikelihood.java
      - ContCharSpeciation
        ContCharSpeciation.java
      - BiSSETreeCharSim
        BiSSETreeCharSim.java
      - CharAssocDivViewer
        CharAssocDivViewer.java
      - SpecExtincLikelihood
        SpecExtincLikelihood.java
      - SisterDiversification
        SisterDiversification.java
      - lib
        TreeCharSimulate.java
        RK4Solver.java
        RKF45Solver.java
        DESystem.java
        NumberForTreeDivers.java
        DEQNumSolver.java
        NumForCharAndTreeDivers.java
      - BiSSELikelihoodCalculator
        BiSSELikelihoodCalculator.java
      - DiversCategCharLikelihood
        DiversCategCharLikelihood.java
      - SpecExtincMLCalculator
        SpecExtincMLCalculator.java
      - EvolveTreesDiversChars
        EvolveTreesDiversChars.java
      - BirthDeathTrees
        BirthDeathTrees.java
      - LineagesThroughTime
        LineagesThroughTime.java
      - CharIndepDivViewer
        CharIndepDivViewer.java
      - BiSSELikelihoodRatio
        BiSSELikelihoodRatio.java
      - aDiverseIntro
        splash.gif
        aDiverseIntro.java
      - DivCategCharMLCalculator
        DivCategCharMLCalculator.java
    - assoc
      - ManageAssociations
        ManageAssociations.java
      - DepContTreeWindow
        DepContTreeWindow.java
      - explanation.txt
      - StoredAssociations
        StoredAssociations.java
      - TaxaAssociationSpecs.txt
      - PartitionFromAssociation
        PartitionFromAssociation.java
      - lib
        AssociationsManager.java
        AssociationSource.java
        ReconstructAssociation.java
        NumberForAssociation.java
        NumberForAssocAndTree.java
        TaxaAssociation.java
        AssociationHistory.java
        SimpleTaxaList.java
      - aAssocIntro
        aAssocIntro.java
      - TaxonListAssoc
        TaxonListAssoc.java
      - ContainedAssociates
        ContainedAssociates.java
      - ManageDistributionBlock
        ManageDistributionBlock.java
      - macros
        setupAssocMacro
    - cont
      - AddToStates
        AddToStates.java
      - RemoveItem
        RemoveItem.java
      - explanation.txt
      - MeanValue
        MeanValue.java
      - ManageContChars
        ManageContChars.java
      - MapContinuous
        MapContinuous.java
      - InverseContState
        InverseContState.java
      - ArcSineTransform
        ArcSineTransform.java
      - XYMatrixToItems
        XYMatrixToItems.java
      - lib
        ContinuousDistribution.java
        ManageContCharsA.java
        MContinuousDistribution.java
        MGeographicStates.java
        EigenAnalysis.java
        ContinuousState.java
        GeographicData.java
        ContinuousData.java
        ContDataUtility.java
        MContinuousEmbedded.java
        SquaredReconstructor.java
        GeogDataUtility.java
        MContinuousHistory.java
        MContinuousStates.java
        ContDataAlterer.java
        BasicStatPak.java
        GeographicState.java
        ContColorTable.java
        ContinuousHistory.java
        ContinuousEmbedded.java
        GeographicAdjustable.java
        ContinuousStates.java
        ContinuousStateTest.java
        ContDataSearcher.java
        GeographicStateTest.java
        ItemContainer.java
        GeographicStates.java
        MContinuousAdjustable.java
        ContinuousAdjustable.java
        GeogDataSearcher.java
      - MultiplyStates
        MultiplyStates.java
      - ContCharFrTaxonValue
        ContCharFrTaxonValue.java
      - Standardize
        Standardize.java
      - ManageGeogChars
        ManageGeogChars.java
      - ContinuousStatesT
        ContinuousStatesT.java
      - PlotTree
        PlotTree.java
      - AddItem
        AddItem.java
      - LogTransform
        LogTransform.java
      - RenameItem
        RenameItem.java
      - SquareRootTransform
        SquareRootTransform.java
      - ItemsEditorForInfoPanel
        ItemsEditorForInfoPanel.java
      - aContIntro
        aContIntro.java
      - AddNoise
        AddNoise.java
      - RandomFillCont
        RandomFillCont.java
      - DiscretizeContinuousCharacters
        DiscretizeContinuousCharacters.java
      - NodeLocs2DPlot
        NodeLocs2DPlot.java
      - RandomFillUniform
        RandomFillUniform.java
      - MultiplyByCharacter
        MultiplyByCharacter.java
      - AddCharacter
        AddCharacter.java
      - ItemValueInTaxon
        ItemValueInTaxon.java
    - treefarm
      - ConcatTreeBlocks
        ConcatTreeBlocks.java
      - FractionCladesShared2Trees
        FractionCladesShared2Trees.java
      - TopologyCongruent
        TopologyCongruent.java
      - RandomModifTree
        RandomModifTree.java
      - SharedPartitions2Trees
        SharedPartitions2Trees.java
      - EmailTree
        EmailTree.java
      - aTreeFarmIntro
        splash.gif
        splash.psd
        aTreeFarmIntro.java
      - SelectTaxaInSameClade
        SelectTaxaInSameClade.java
      - CollessImbalance
        CollessImbalance.java
      - TreeSatisfiesValue
        TreeSatisfiesValue.java
      - TreeTotalPathLength
        TreeTotalPathLength.java
      - CopyTreesToSimpleFile
        CopyTreesToSimpleFile.java
      - DuplicateTreeBlocks
        DuplicateTreeBlocks.java
      - RearrangedTree
        RearrangedTree.java
      - AvgTaxonValueAmgTrees
        AvgTaxonValueAmgTrees.java
      - CutSelectedTaxa
        CutSelectedTaxa.java
      - explanation.txt
      - CladeMatch
        CladeMatch.java
      - BlockDirectlyFromFile
        BlockDirectlyFromFile.java
      - NumTopologyCongruent
        NumTopologyCongruent.java
      - GraftTree
        GraftTree.java
      - ReinterpretBranchLabels
        ReinterpretBranchLabels.java
      - RandomResolve
        RandomResolve.java
      - CladeInTree
        CladeInTree.java
      - TaxonValueFromTree
        TaxonValueFromTree.java
      - TerminalInstability
        TerminalInstability.java
      - SortTaxaByTree
        SortTaxaByTree.java
      - CurrentTree
        CurrentTree.java
      - lib
        LiveTreeBlocks.java
        RndTreeModifier.java
        BlockFromTreeSource.java
        SourceFromTreeSource.java
        NForTaxonWithTree.java
        NForTaxonWithTrees.java
        PatristicDistances.java
        DetTreeModifier.java
        SourceModifiedTree.java
      - ReshuffleTaxa
        ReshuffleTaxa.java
      - AllTrees
        AllTrees.java
      - RandomlyModifiedTrees
        RandomlyModifiedTrees.java
      - FilterTreesOtherSrc
        FilterTreesOtherSrc.java
      - RemoveAllBranchLabels
        RemoveAllBranchLabels.java
      - ProbRndTreeModifier
        ProbRndTreeModifier.java
      - CompareOtherTrees
        CompareOtherTrees.java
      - NodeDepth
        NodeDepth.java
      - NumSPRRearrangements
        NumSPRRearrangements.java
      - AllRerootings
        AllRerootings.java
      - NumTreesMatchingCriterion
        NumTreesMatchingCriterion.java
      - ModTreesOtherSource
        ModTreesOtherSource.java
      - DetermModifTree
        DetermModifTree.java
      - EqualRatesSpSampled
        EqualRatesSpSampled.java
      - ConcatMultTreeSources
        ConcatMultTreeSources.java
      - FAFillTreeBlock
        FAFillTreeBlock.java
      - SplitFrequencies
        SplitFrequencies.java
      - OutgroupRoot
        OutgroupRoot.java
      - Concat2TreeSources
        Concat2TreeSources.java
      - AverageNodeAssociatedDifference
        AverageNodeAssociatedDifference.java
      - MRPMatrices
        MRPMatrices.java
      - NNAssocValues
        NNAssocValues.java
      - Correlation2Trees
        Correlation2Trees.java
      - DeleteReticulations
        DeleteReticulations.java
      - CopyTreesToNexusBlock
        CopyTreesToNexusBlock.java
      - ConvexInTree
        ConvexInTree.java
      - RandomBranchMoves
        RandomBranchMoves.java
      - CondensedTreeSource
        CondensedTreeSource.java
      - AugmentTreeRandomly
        AugmentTreeRandomly.java
      - CompareOtherTree
        CompareOtherTree.java
      - ExtractTreeBlock
        ExtractTreeBlock.java
      - ConsensusTreesFromBlocks
        ConsensusTreesFromBlocks.java
      - MakeRerootings
        MakeRerootings.java
        32allRerootings.gif
        allRerootings.gif
        64allRerootings.gif
      - RarefyTree
        RarefyTree.java
      - NoiseToBranchLengths
        NoiseToBranchLengths.java
      - SharedClades2Trees
        SharedClades2Trees.java
      - AddSelectedTaxaToTree
        AddSelectedTaxaToTree.java
      - BLfromDivergenceTimes
        BLfromDivergenceTimes.java
    - coalesce
      - DeepCoalescencesG
        DeepCoalescencesG.java
      - DeepCoalescencesSp
        DeepCoalescencesSp.java
      - ContainedCoalescence
        ContainedCoalescence.java
      - ContainedCoalescSim
        ContainedCoalescSim.java
      - TreeDepth
        TreeDepth.java
      - DuplicationsExtinctionsSp
        DuplicationsExtinctionsSp.java
      - aCoalescencePkgIntro
        aCoalescencePkgIntro.java
        splash.gif
        splash.gif copy
        splashSmall.gif
        index.html
      - DuplicationsExtinctionsG
        DuplicationsExtinctionsG.java
      - explanation.txt
      - CoalescentTrees
        CoalescentTrees.java
      - lib
        SpeciesTreeFit.java
        CoalescerObed.java
        CoalescedNode.java
        NumForGeneTInSpeciesT.java
        ContainedTreeSim.java
        GeneTreeFit.java
        Coalescer.java
      - RecCoalescenceHistory
        RecCoalescenceHistory.java
      - NeutralCoalescence
        NeutralCoalescence.java
      - InsertNode
        32insertNode.gif
        64insertNode.gif
        insertNode.gif
        InsertNode.java
      - LineageWidth
        LineageWidth.java
        adjustWidths.gif
        64adjustWidths.gif
        32adjustWidths.gif
      - CoalescenceWMigration
        CoalescenceWMigration.java
      - DeepCoalMultLoci
        DeepCoalMultLoci.java
      - SlatkinMaddisonS
        SlatkinMaddisonS.java
      - AverageTreeDepth
        AverageTreeDepth.java
      - macros
        s_by_depth
    - categ
      - StateConsistencyInWindowStrip
        StateConsistencyInWindowStrip.java
      - MultistateToMissing
        MultistateToMissing.java
      - ResolveStateAmbiguity
        ResolveStateAmbiguity.java
      - CategVariable
        CategVariable.java
      - ManageProteinChars
        ManageProteinChars.java
      - explanation.txt
      - StateFrequency
        StateFrequency.java
      - NumberOfStates
        NumberOfStates.java
      - aCategIntro
        aCategIntro.java
      - ManageCategoricalChars
        ManageCategoricalChars.java
      - lib
        RNACharacterHistory.java
        DNAData.java
        CategoricalEmbedded.java
        MProteinHistory.java
        ProteinData.java
        DNAState.java
        CategTModel.java
        CategStateForCharacter.java
        DNADataSearcher.java
        MolecularState.java
        MDNAHistory.java
        CategStateChanges.java
        RNAState.java
        CategMatrixManager.java
        MProteinEmbedded.java
        MesquiteSequence.java
        RequiresAnyCategoricalData.java
        MolecularData.java
        DNAColorTable.java
        CategColorTable.java
        MCategoricalStates.java
        ProteinState.java
        OffersDNAData.java
        MDNAEmbedded.java
        ProteinColorTable.java
        DNACharacterHistory.java
        DNADataAltererCon.java
        DNACharacterAdjustable.java
        RequiresExactlyCategoricalData.java
        CategDataEditorInit.java
        CategDataSearcher.java
        CategDataEditorInitD.java
        CategDataUtility.java
        RNAData.java
        RequiresAnyDNAData.java
        MCategoricalHistory.java
        ProteinAdjustable.java
        CategInternodeEvent.java
        CategoricalHistory.java
        OffersCategoricalData.java
        MProteinAdjustable.java
        CategDataAlterer.java
        MCategoricalDistribution.java
        ProteinCharacterHistory.java
        DNAEmbedded.java
        CategoricalDistribution.java
        CategoricalState.java
        CategoricalStates.java
        CategDataMatcher.java
        CategoricalAdjustable.java
        DNADataAlterer.java
        CategTModelEditWindow.java
        MDNAAdjustable.java
        MCategoricalEmbedded.java
        MolecDataEditorInit.java
        OffersProteinData.java
        RNACharacterAdjustable.java
        CategoricalData.java
        MCategoricalAdjustable.java
        ProteinEmbedded.java
        RequiresProteinData.java
        RequiresAnyMolecularData.java
        MolecularDataAlterer.java
        MolecularDataUtil.java
        DNADataUtility.java
      - StateNamesStrip
        StateNamesStrip.java
      - StateNamesEditor
        StateNamesEditor.java
        transpose.gif
      - ManageDNARNAChars
        ManageDNARNAChars.java
      - ConsensusSequenceStrip
        consensus.gif
        ConsensusSequenceStrip.java
      - PolymToAmbiguity
        PolymToAmbiguity.java
      - SmallStateNamesEditor
        SmallStateNamesEditor.java
      - StateConsistencyStrip
        StateConsistencyStrip.java
      - ProportionUniqueStates
        ProportionUniqueStates.java
      - RemoveInvariant
        RemoveInvariant.java
      - ConsensusStateForChar
        ConsensusStateForChar.java
      - AmbiguityToPolym
        AmbiguityToPolym.java
    - lib
      - EnglishDecimalFormatSymbols.java
      - MesquiteTabbedPanel.java
      - ExternalProcessManager.java
      - TaxaPartition.java
      - ProjPanelCommand.java
      - FunctionExplanation.java
      - PendingCommand.java
      - ZipUtil.java
      - MesquiteCheckMenuItem.java
      - Abortable.java
      - EmployeeVector.java
      - Short2DArray.java
      - OtherAnalysis.java
      - MesquiteButton.java
      - MesquitePanel.java
      - ShellScriptWatcher.java
      - Explainable.java
      - ListableVector.java
      - TreeDisplayDrawnExtra.java
      - MiniControl.java
      - TwoStringsDialog.java
      - DialogListener.java
      - MesquiteParameter.java
      - PanelsAtNodes.java
      - ParametersDialog.java
      - ETContentArea.java
      - StringUtil.java
      - MesquitePrintJob.java
      - CommandRecord.java
      - NumberArray.java
      - MesquiteDropListener.java
      - TreeDisplayExtra.java
      - StringLister.java
      - TaxaTreeDisplay.java
      - MesquiteDialogParent.java
      - SymbolGraphicsPanel.java
      - ChartField.java
      - ColorTheme.java
      - Integer2DArray.java
      - Listened.java
      - AssociableWithSpecs.java
      - IntegerField.java
      - ExtensibleDialog.java
      - ClosablePanelContainer.java
      - Charter.java
      - Debugg.java
      - AnnotPanelOwner.java
      - OTUIDCodeInfoCoord.java
      - AttachedNote.java
      - Reconnectable.java
      - TaxaDisplayBkgdExtra.java
      - VoucherInfoFromOTUIDDB.java
      - ColorDialog.java
      - StringIntegerDialog.java
      - PhoneHomeRecord.java
      - FileDirtier.java
      - MesquiteExternalProcess.java
      - Listable.java
      - MesquiteMacro.java
      - RadioButtons.java
      - TreeDisplay.java
      - BitsSpecsSet.java
      - Parser.java
      - MesquiteDouble.java
      - DoubleSqMatrixFields.java
      - Arguments.java
      - Taxa.java
      - HelpSearchManager.java
      - Clade.java
      - ScrollTextField.java
      - MiniScroll.java
      - TreeReference.java
      - characters
        CharactersBlock.java
        WholeCharacterModel.java
        CharacterStateTest.java
        ProbabilityModelSet.java
        MCharactersHistory.java
        CharSort.java
        AltererDNACell.java
        AltererRandomizations.java
        CellBlock.java
        MCharactersStatesHolder.java
        AltererContinuousTransformations.java
        CharWeightSet.java
        CharacterStatesHolder.java
        CharInclusionSet.java
        CentralModelListener.java
        AltererConvertGapMissPolyUncert.java
        MCharactersDistribution.java
        CModelEstimator.java
        CharNumSet.java
        CharSelectionSet.java
        AlteredDataParameters.java
        CharHistoryContainer.java
        AltererWholeCharacterAddRemove.java
        CharacterState.java
        ModelSet.java
        CLikelihoodCalculator.java
        ProbabilityModel.java
        AltererSimpleCell.java
        MCharactersStates.java
        CharacterSubmodel.java
        CharacterHistory.java
        CharacterDistribution.java
        AltererAlignShift.java
        DefaultReference.java
        TaxaInfo.java
        MAdjustableDistribution.java
        SlicedCharacterHistory.java
        CharacterModel.java
        CharactersGroup.java
        CharacterPartition.java
        CharacterData.java
        CharBitsSet.java
        CodonPositionsSet.java
        ModelVector.java
        ModelCompatibilityInfo.java
        CharSpecsSet.java
        CharacterStates.java
        StoredCharacterHistory.java
        CharObjectSpecsSet.java
        AdjustableDistribution.java
        CharactersGroupVector.java
      - SliderWindow.java
      - MesquiteEvent.java
      - MesquiteSubmenuSpec.java
      - CommandChecker.java
      - LowLevelListener.java
      - NexusBlockEditableRaw.java
      - HelpSearchStrip.java
      - Incrementable.java
      - MenuVisibility.java
      - MiniStringEditor.java
      - ContentArea.java
      - TaxaDisplayDrawnExtra.java
      - ProgressWindow.java
      - NexusCommandTest.java
      - FunctionExplainable.java
      - OuterContentArea.java
      - MesquiteCollator.java
      - StdOutWatcher.java
      - ShellScriptRunner.java
      - MesquiteDialog.java
      - MesquiteMenuItemSpec.java
      - ParsimonyAnalysis.java
      - Notification.java
      - MesquiteException.java
      - MesquiteString.java
      - FileBlock.java
      - CanRetrieveTreeBlock.java
      - ImageLabel.java
      - Projects.java
      - Evaluator.java
      - TaxaBlock.java
      - BooleanUtil.java
      - Snapshot.java
      - DoubleArray.java
      - ThermoPanel.java
      - ChartListener.java
      - CompatibilityChecker.java
      - Clades.java
      - OwnedByModule.java
      - OTUIDCodeInfoSource.java
      - ProgressPanel.java
      - ListDialog.java
      - ParseUtil.java
      - Context.java
      - MesquiteTextWindow.java
      - NexusWritable.java
      - TreeContextListener.java
      - ParametersExplorable.java
      - SystemWindow.java
      - ColorDistribution.java
      - MesquiteColorTable.java
      - Number2DArray.java
      - MesquiteFrame.java
      - MesquiteImage.java
      - ConsoleThread.java
      - Mesquite3DIntPoint.java
      - ValueToPixel.java
      - ShortArray.java
      - MesquitePDFFile.java
      - MesquiteFileUtil.java
      - TranslationTable.java
      - ProjectReadThread.java
      - TextCanvasWithButtons.java
      - EnterButton.java
      - MiniSliderWithText.java
      - InfoBar.java
      - MesquiteDroppedFileHandler.java
      - MesquiteInteger.java
      - DatabaseURLSource.java
      - ProgressIndicator.java
      - MesquiteListWindow.java
      - GraphicsUtil.java
      - TaxaInclusionSet.java
      - NexusBlock.java
      - UserNamePasswordDialog.java
      - TaxonNamer.java
      - TaxonFilterer.java
      - SpecsSet.java
      - MesquiteMenu.java
      - HTMLSidePanel.java
      - ChartExtra.java
      - ImageOwner.java
      - MesquiteCursor.java
      - TaxaSelectionSet.java
      - duties
        CharSubmodelCurator.java
        BranchNamesAltererMult.java
        DrawTaxaCoordinator.java
        CellColorerCharacters.java
        NumberFor2Characters.java
        ElementManager.java
        PackageIntro.java
        CellColorerMatrix.java
        CharacterSimulator.java
        CharacterObedSource.java
        DataMatcher.java
        TaxaSelectCoordinator.java
        NumberForTreeWContext.java
        TreeDisplayAssistantMA.java
        TaxaDisplayAssistantDI.java
        BooleanForItem.java
        NodeLocsUnrooted.java
        BranchLengthsAltererMult.java
        CellColorer.java
        TextDisplayer.java
        NumbersForNodesAndMatrix.java
        TreeDisplayAssistantD.java
        CharTableAssistantI.java
        TreeDisplayAssistantA.java
        DrawNamesTreeDisplay.java
        NEXUSInterpreter.java
        ManagerAssistant.java
        DataWindowAssistantA.java
        CharMapper.java
        TreeDisplayAssistantAD.java
        TaxaWindowAssistantN.java
        MatrixCharter.java
        TraceCharacterInit.java
        CharMatrixFiller.java
        NumberForCharacterIncr.java
        FileProcessor.java
        FileInitEarlyLoad.java
        ItemsBiplotter.java
        EmployeeTree.java
        CharacterSelector.java
        NumberForCharAndTaxon.java
        TaxonUtility.java
        FileInterpreter.java
        TreeWindowAssistant.java
        NumForCharHistAndTree.java
        TaxaTableAssistantI.java
        OneTreeSource.java
        DefaultsAssistant.java
        IncrementalConsenser.java
        CharSourceCoordObed.java
        ChartAssistant.java
        TreeDisplayAssistantDI.java
        CharsStatesForNodes.java
        TaxaWindowMaker.java
        DataWSelectionAssistant.java
        TreeWindowAssistantI.java
        MatrixSourceCoord.java
        CuratorWithSettings.java
        TaxonPairSource.java
        TreeAltererMult.java
        TreeSourceDefinite.java
        TreeDisplayAssistant.java
        TaxonNameStyler.java
        DataColumnNamesAssistant.java
        TreeTransformer.java
        NumbersForNodesIncr.java
        NumberForTaxaBlock.java
        TaxaDisplayAssistantMA.java
        CharSpecsSetManager.java
        FileInit.java
        DisplayNumbersAtNodes.java
        ReadFileFromString.java
        BooleanForTreeM.java
        MatrixSourceCoordObed.java
        TreeUtility.java
        NumberForTaxonIncr.java
        CharMatrixOneSource.java
        BrowseHierarchy.java
        NodeChooser.java
        Consenser.java
        TreeAlterer.java
        NodeLocs.java
        CharacterSource.java
        TreeDisplayAssistantAO.java
        ScriptingManager.java
        NodeLocsCircle.java
        DataUtility.java
        TreeWindowAssistantC.java
        CharSourceCoord.java
        PackageIntroInterface.java
        DataWindowMaker.java
        FileAssistantCP.java
        ItemsCharter.java
        WholeCharModelCurator.java
        TreeSearcher.java
        BooleanForTree.java
        CharacterModelSource.java
        NumberForCharAndTree.java
        TaxaWindowAssistantI.java
        NumberForTaxon.java
        NumbersForNodes.java
        WindowHolder.java
        BranchNamesAlterer.java
        CharactersManager.java
        MesquiteInit.java
        DataAlterer.java
        BooleanForTreeIncr.java
        DataWindowAssistant.java
        TaxaDisplayAssistantAD.java
        NumberFor2Taxa.java
        FileInterpreterITree.java
        TreeSwapper.java
        FileAssistant.java
        TreeInfoPanelAssistant.java
        FileAssistantN.java
        ExternalTreeSearcher.java
        DataSearcher.java
        NumbersForNodesWith2Char.java
        NumForCharTreeIndep.java
        CharStatesForNodes.java
        TreeTransformerMult.java
        TaxaDisplayAssistantA.java
        NumberForMatrix.java
        NodeLocsVH.java
        NumbersForNodesAndHistory.java
        TreeWindowAssistantOA.java
        NumberForCharAndTreeM.java
        NumberForCharacter.java
        TreeSource.java
        NumberForMatrixAndTree.java
        TreeWDIAssistant.java
        DisplayStatesAtNodes.java
        FileAssistantC.java
        ParametersExplorer.java
        NumberForNode.java
        NumberForTree.java
        NodeLocsPlot.java
        TreeWindowMaker.java
        DrawTaxa.java
        FileAssistantCS.java
        ManageModelSet.java
        NumberForItem.java
        NexusFileInterpreter.java
        NumberFor2CharAndTree.java
        TaxaManager.java
        MatrixInfoPanelAssistantI.java
        DataAltererCon.java
        DrawTreeCoordinator.java
        FileAssistantT.java
        TreeInferer.java
        CellColorerTaxa.java
        NumForCharTreeDep.java
        FileCoordinator.java
        AnalyticalDrawTree.java
        SpecsSetManager.java
        CharMatrixObedSource.java
        DrawNamesTaxaDisplay.java
        TaxaSource.java
        TreeWindowAssistantA.java
        TreeDisplayAssistantI.java
        FileInterpreterI.java
        DrawChart.java
        CharHistorySource.java
        TaxonNameAlterer.java
        TaxaDisplayAssistantI.java
        DisplayCharsStsAtNodes.java
        EditRawNexusBlock.java
        TreeSimulate.java
        CharacterOneSource.java
        ScattergramAssistantA.java
        NumberFor2TaxaIncr.java
        DataWindowAssistantI.java
        NumberForTreeBlock.java
        CharMatrixManager.java
        TaxaDisplayAssistant.java
        NumberFor2Trees.java
        TreeBlockFiller.java
        CharMatrixSource.java
        TreeWindowAssistantN.java
        GeneralFileMaker.java
        TaxaWindowAssistant.java
        TaxonSource.java
        EditingCurator.java
        BooleanForTaxon.java
        TaxaWindowAssistantC.java
        ItemsSource.java
        CharSelectCoordinator.java
        DistanceBetween2Trees.java
        FileElementManager.java
        StringMatcher.java
        NumberForTreeM.java
        DataWindowAssistantID.java
        TreeBlockSource.java
        TaxonSelector.java
        TreesManager.java
        TaxaPartitionSource.java
        FileAssistantCH.java
        TWindowMaker.java
        BooleanForCharacter.java
        NumFor2CharHistAndTree.java
        TaxaDisplayAssistantD.java
        BranchLengthsAlterer.java
        DrawTree.java
        NumberArrayForMatrix.java
        FileAssistantA.java
        FileAssistantM.java
        NumbersForNodesAndChar.java
        MatrixInfoPanelAssistant.java
        CharModelCurator.java
        UtilitiesAssistant.java
        HistogramAssistantA.java
        NodeLocsFree.java
        NumberForTreeIncr.java
      - MesquitePopup.java
      - Object2DArray.java
      - PathHolder.java
      - PropertyNamesProvider.java
      - NexusBlockTest.java
      - TreeDecorator.java
      - CleanUpJob.java
      - ExponentialDistribution.java
      - TaxaStringsSet.java
      - Tree.java
      - Priority.java
      - MainThread.java
      - Annotatable.java
      - table
        RowNamesPanel.java
        AutoScrollThread.java
        ColumnNamesPanel.java
        EditorPanel.java
        CMTable.java
        EditorTextField.java
        TableWindow.java
        TableTool.java
        MatrixPanel.java
        CornerPanel.java
        TableMarchingAnts.java
      - ToolKeyListener.java
      - WithStringDetails.java
      - CircleSymbol.java
      - Optimizer.java
      - PuppetThread.java
      - TDLegendWithColors.java
      - LegendHolder.java
      - InvariantsAnalysis.java
      - SeparateThreadStorage.java
      - ConsoleWindow.java
      - DoubleField.java
      - ExtensibleExplDialog.java
      - DistanceAnalysis.java
      - MesquiteTabbedPane.java
      - TaxaGroupVector.java
      - TwoIntegersDialog.java
      - UndoInstructions.java
      - ClassVector.java
      - ObjectCommenter.java
      - Fittable.java
      - MesquiteXMLPreferencesModule.java
      - MenuItemsSpecsVector.java
      - ChartWindow.java
      - OutputTextListener.java
      - ColorPickerPanel.java
      - MiniNumberEditor.java
      - SymbolsVector.java
      - Renamable.java
      - LinearValueToPixel.java
      - MenuOwner.java
      - ProjPanelPanel.java
      - MesquitePath2DFloat.java
      - MesquiteTrunk.java
      - HNode.java
      - simplicity
        SimplicityStrip.java
        InterfaceManager.java
        SimplicityManagerModule.java
      - MesquiteMenuSpec.java
      - CompatibilityTest.java
      - TaxaBitsSet.java
      - Identifiable.java
      - SimpleIntegerField.java
      - MesquiteLabel.java
      - MesquiteListTable.java
      - ObjectSpecsSet.java
      - AlertDialog.java
      - TreeDisplayBkgdExtra.java
      - ChartBkgdExtra.java
      - ObjectContainer.java
      - FillableMesquiteSymbol.java
      - Selectionable.java
      - IntegerSqMatrixFields.java
      - SimpleNamesTaxonNamer.java
      - Hyperlink.java
      - TreeDrawing.java
      - DoubleMiniScroll.java
      - MesquiteXMLUtilities.java
      - ToolPalette.java
      - MesquiteSymbol.java
      - ModuleInfoWindow.java
      - ChartTool.java
      - TextContentArea.java
      - ModulesInfoVector.java
      - ChecklistDialog.java
      - Binomial.java
      - LightLabel.java
      - MousePanel.java
      - MesquiteFile.java
      - DoubleSliderWindow.java
      - ExplanationArea.java
      - LongArray.java
      - FileElement.java
      - Bits.java
      - DragRectangle.java
      - NameReference.java
      - OutputFilePathModifier.java
      - ExtensibleListDialog.java
      - IntegerArray.java
      - Illustratable.java
      - CardPanel.java
      - MesquiteLong.java
      - CommandRecordHolder.java
      - LikelihoodAnalysis.java
      - Puppeteer.java
      - MesquiteMenuBar.java
      - SingleLineTextField.java
      - MesquiteDropManager.java
      - OutputFileProcessor.java
      - BasicTaxonNamer.java
      - EmployeeNeed.java
      - AlertWithLinkToDirectory.java
      - FontUtil.java
      - Author.java
      - MiniScrollButton.java
      - TaxaGroup.java
      - ColorRecord.java
      - MarchingAnts.java
      - TaxaDisplay.java
      - TaxaDrawing.java
      - KeyAdapterToConsumeKeys.java
      - StringArray.java
      - MesquiteHTMLWindow.java
      - MesquiteChart.java
      - MesquiteWindow.java
      - ChangeAuthority.java
      - DoubleClickList.java
      - MesquiteThread.java
      - LogWindow.java
      - Trees.java
      - PhoneHomeUtil.java
      - HPanel.java
      - MesquiteMenuItem.java
      - XMLUtil.java
      - StringIntegerListDlog.java
      - OutputFileTailer.java
      - SingleLineTextArea.java
      - ShellScriptUtil.java
      - MesquiteModuleInfo.java
      - Long2DArray.java
      - TaxaTool.java
      - ColorEventVector.java
      - LongField.java
      - TreeUtil.java
      - LabelsAtNodes.java
      - Attachable.java
      - PopUpPanelOfCards.java
      - TreeDisplayLegend.java
      - ChangeEvent.java
      - MesquitePackageRecord.java
      - Logger.java
      - ProjectRead.java
      - InterContentArea.java
      - MesquiteMessage.java
      - Prioritizable.java
      - CalculationMonitor.java
      - system
        SystemUtil.java
      - MesquiteListener.java
      - Double2DArray.java
      - ProcessUtil.java
      - Journal.java
      - CommandableOwner.java
      - Listenable.java
      - PanelOfCards.java
      - Commandable.java
      - GroupLabel.java
      - Taxon.java
      - AttachedNotesVector.java
      - LightLabelsAtNodes.java
      - SpecsSetVector.java
      - TaxonPair.java
      - EmployerEmployee.java
      - HTMLDescribable.java
      - ColorEvent.java
      - NumSpecsSet.java
      - MessagePanel.java
      - WindowButton.java
      - MesquiteNumber.java
      - ObjectArray.java
      - LeakFinder.java
      - MesquiteScrollbar.java
      - TreeTool.java
      - MRPopup.java
      - UndoReference.java
      - Undoer.java
      - TaxaSpecsSet.java
      - RotatedRectangle.java
      - MesquiteSubmenu.java
      - MesquiteFileDialog.java
      - TaxaDisplayActive.java
      - ChangeHistory.java
      - ClockPanel.java
      - MesquiteTextCanvas.java
      - AnnotationsPanel.java
      - ImagePanelListener.java
      - TreeVector.java
      - BayesianAnalysis.java
      - SelectionRectangle.java
      - Doomable.java
      - ImagePanel.java
      - MesqJEditorPane.java
      - ExporterDialog.java
      - MesquiteCMenuItemSpec.java
      - TreeDisplayActive.java
      - HorizontalLine.java
      - Legend.java
      - Associable.java
      - MiniSlider.java
      - CommandThread.java
      - Colorable.java
      - AdjustableTree.java
      - QueryDialogs.java
      - StringInABox.java
      - ClosablePanel.java
      - MesquiteModule.java
      - MesquitePasswordField.java
      - TreeContext.java
      - TextTree.java
      - NameHolder.java
      - DialogGraphicsPanel.java
      - ResizableLegend.java
      - LogValueToPixel.java
      - MesquiteTimer.java
      - MesquiteProject.java
      - MesquiteSet.java
      - TaxaDisplayExtra.java
      - Disposable.java
      - MesquiteCommand.java
      - QualificationsTest.java
      - MesquiteTool.java
      - XMLPreferencesProcessor.java
      - TextRotator.java
      - RandomBetween.java
      - MesquiteBoolean.java
      - DoubleClickListener.java
      - SpecialListName.java
      - CommandCommunicator.java
      - Showable.java
    - externalCommunication
      - lib
        RemoteJobFile.java
        UsernamePasswordKeeper.java
    - align
      - AlignToDroppedShift
        shiftToDropped.gif
        AlignToDroppedShift.java
        32shiftToDropped.gif
        64shiftToDropped.gif
      - SelectedBlockMover
        64SelectedBlockMover.gif
        64CrossHair.gif
        32SelectedBlockMover.gif
        CrossHair.gif
        32CrossHair.gif
        SelectedBlockMover.java
        SelectedBlockMover.gif
      - AlignScoreForTaxon
        AlignScoreForTaxon.java
      - ShiftOtherToMatch
        ShiftOtherToMatch.java
      - ColorGapsInCodingSequence
        ColorGapsInCodingSequence.java
      - SimpleBlockMover
        64BlockMover.gif
        64splitBlock.gif
        splitBlock.gif
        32Hand.gif
        32splitBlock.gif
        SimpleBlockMover.java
        BlockMover.gif
        Hand.gif
        32BlockMover.gif
        64Hand.gif
      - AlignDNAToProtein
        AlignDNAToProtein.java
      - ColorMisaligned
        ColorMisaligned.java
      - ColorForAlignment
        ColorForAlignment.java
      - MAFFTAlign
        MAFFTAlign.java
      - ZapGaps
        ZapGaps.java
      - lib
        TwoSequenceAlignerGaps.java
        AlignShiftToDroppedBase.java
        TwoSequenceAligner.java
        AlignmentHelperLinearSpace.java
        AlignTool.java
        AlignMatch.java
        AlignMultipleSequencesMachine.java
        AlignScoreForTaxonGen.java
        ExternalSequenceAligner.java
        AlignUtil.java
        MultipleSequenceAligner.java
        BlockMover.java
        MultiBlockMoveBase.java
        AlignmentHelper.java
        PairwiseAligner.java
        AlignmentHelperQuadraticSpace.java
      - AlignSequences
        AlignSequences.java
      - ShiftToMinimizeStops
        ShiftToMinimizeStops.java
      - AlignScoreForTaxonRC
        AlignScoreForTaxonRC.java
      - AlignToDropped
        alignToDropped.gif
        32alignToDropped.gif
        64alignToDropped.gif
        AlignToDropped.java
      - ScrollToData
        64scrollerLeft.gif
        32scrollerRight.gif
        scrollerRight.gif
        64scrollerRight.gif
        32scrollerLeft.gif
        ScrollToData.java
        scrollerLeft.gif
      - SidePusher
        splitBlockLeft.gif
        64leftGrab.gif
        32splitBlockRight.gif
        32leftGrab.gif
        SidePusher.java
        64rightGrab.gif
        rightGrab.gif
        splitBlockRight.gif
        64splitBlockRight.gif
        32rightGrab.gif
        32splitBlockLeft.gif
        leftGrab.gif
        64splitBlockLeft.gif
      - ClustalAlign
        ClustalAlign.java
      - MuscleAlign
        MuscleAlign.java
      - RemoveAllGaps
        RemoveAllGaps.java
      - aAlignIntro
        aAlignIntro.java
        statistics.html
        splash.gif
        acknowledgements.html
        visualization.html
        images
        multiSplitBefore.gif
        scrollToData.gif
        alignToDropped.gif
        rightGrab.gif
        multiBlockSpitter.gif
        multiBlockSplitterOther.gif
        multisplitAfter.gif
        BlockMover.gif
        email.jpg
        leftGrab.gif
        selectedBlockMover.gif
        mesquiteIcon.gif
        sourceCode.html
        citation.html
        _notes
        2col_leftNav.css.mno
        future.html
        faq.html
        Templates
        standard.dwt
        overview.html
        styles
        mesquitePackage.css
        manualAlignment.html
        automated.html
        colorMisaligned.jpg
        additions.html
      - ZapGapsRight
        ZapGapsRight.java
      - Notes
        coiLong.nex
        clustal Option List
        prot.nex
        Align Notes
        align.nex
        bugs
        bug.PairwiseAligner.nex
      - MultiBlockSplitter
        32MultiBlockSplitter.gif
        MultiBlockSplitterOption.gif
        64CrossHair.gif
        CrossHair.gif
        32CrossHair.gif
        64MultiBlockSplitter.gif
        64MultiBlockSplitterOption.gif
        MultiBlockSplitter.gif
        32MultiBlockSplitterOption.gif
        MultiBlockSplitter.java
    - dmanager
      - FuseTMSequences
        FuseTMSequences.java
      - ProcessDataFiles
        ProcessDataFiles.java
      - TaxaListImportSource
        TaxaListImportSource.java
      - ProcessFile
        ProcessFile.java
      - aDmanagerIntro
        aDmanagerIntro.java
      - lib
        ProcessDataFilesLib.java
      - InterchTaxonPrefixSuffix
        InterchTaxonPrefixSuffix.java
      - RandomizeTaxonOrder
        RandomizeTaxonOrder.java
      - KeepTaxonPrefixSuffix
        KeepTaxonPrefixSuffix.java
      - TaxonNamesFileProcessor
        TaxonNamesFileProcessor.java
      - RemoveTaxonPrefixSuffix
        RemoveTaxonPrefixSuffix.java
      - FuseTaxaMatrices
        FuseTaxaMatrices.java
      - TaxonNameFromSampleNamesFile
        TaxonNameFromSampleNamesFile.java
    - minimal
      - DrawHierarchy
        DrawHierarchy.java
      - ManageTaxa
        ManageTaxa.java
      - explanation.txt
      - IDsDefaults
        IDsDefaults.java
      - OpenSpecialNEXUS
        OpenSpecialNEXUS.java
      - Installer
        installExample.xml
        updateExample.xml
        noticeExample.xml
        Installer.java
        NoticesAndInstallationExplanation.xml
      - ManageForeignBlocks
        ManageForeignBlocks.java
      - OpenURL
        OpenURL.java
      - BasicFileCoordinator
        splash.gif
        splash.gif copy
        splashSmall.gif
        index.html
        ProjectWindow.java
        projectHTML
        matrixContSmallINREPOSITORY.gif
        fileLink.gif
        matrixContSmall.gif
        treesSmallUNCOMMITTED.gif
        taxaAssocSmall.gif
        taxaBlock.gif
        trees.gif
        matrixCont.gif
        matrixCategSmallINREPOSITORY.gif
        projectSimple.html
        fileSmall.gif
        baseTreesBlock.html
        matrixMolec.gif
        fileLinkTrees.gif
        baseTaxaBlock.html
        taxaBlockSmallINREPOSITORY.gif
        treeView.gif
        fileIncludeBasic.gif
        list.gif
        matrixCategSmall.gif
        fileIncludeTrees.gif
        projectPanel.jpg
        matrixCateg.gif
        matrixContSmallUNCOMMITTED.gif
        treesSmallINREPOSITORY.gif
        fileInclude.gif
        base.html
        fileLinkedSmall.gif
        fileMergeTM.gif
        rename.gif
        matrixMeristicSmallUNCOMMITTED.gif
        treesSmall.gif
        matrixMeristic.gif
        project.html
        baseMatrix.html
        chart.gif
        charModelSmall.gif
        matrixMolecSmallINREPOSITORY.gif
        matrixMolecSmall.gif
        taxaAssocSmallUNCOMMITTED.gif
        matrixMeristicSmall.gif
        delete.gif
        matrixMeristicSmallINREPOSITORY.gif
        taxaBlockSmall.gif
        matrixMolecSmallUNCOMMITTED.gif
        taxaAssocSmallINREPOSITORY.gif
        queryGray.gif
        matrixCategSmallUNCOMMITTED.gif
        taxaBlockSmallUNCOMMITTED.gif
        BasicFileCoordinator.java
      - ManageMesquiteBlock
        ManageMesquiteBlock.java
      - InterpretNEXUS
        InterpretNEXUS.java
      - Utilities
        Utilities.java
      - Defaults
        Defaults.java
      - WindowBabysitter
        WindowBabysitter.java
      - ShowEmployeeTree
        ShowEmployeeTree.java
      - NEXUSDefaults
        NEXUSDefaults.java
      - StoredTaxa
        StoredTaxa.java
      - Simplicity
        Simplicity.java
        SimplifyControlWindow.java
        instructions.html
        simplification.html
        simplifications
        acBasicPopGen.xml
        zzMinimal.xml
        zaNoneHidden.xml
        abMacclade.xml
        adMorphPhyl.xml
    - ancstates
      - TraceCharOverTrees
        TraceCharOverTrees.java
      - TraceCharacterHistory
        TraceCharacterOperator.java
        TraceCharacterHistory.java
      - LabelStatesOnTree
        LabelStatesOnTree.java
      - UnambigChangesAtNodes
        UnambigChangesAtNodes.java
      - explanation.txt
      - SummarizeChgOverTrees
        SummarizeChgOverTrees.java
      - aAncStatesIntro
        splash.gif
        aAncStatesIntro.java
        index.html
      - lib
        ChgSummarizerMultTrees.java
      - ExportAncRec
        ExportAncRec.java
      - SummarizeChanges
        SummarizeChanges.java
      - ShadeStatesOnTree
        ShadeStatesOnTree.java
      - AncestralStatesAll
        AncestralStatesAll.java
      - RecAncestralStates
        RecAncestralStates.java
      - TraceAllCharacters
        TraceAllCharacters.java
      - SummarizeChgOnBranches
        SummarizeChgOnBranches.java
    - parsimony
      - StepsInCharacter
        StepsInCharacter.java
      - CharListParsModels