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[Treebase-guts] SF.net SVN: treebase:[356] trunk/treebase-core/lib
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From: <rv...@us...> - 2009-12-15 17:16:46
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Revision: 356
http://treebase.svn.sourceforge.net/treebase/?rev=356&view=rev
Author: rvos
Date: 2009-12-15 17:16:33 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/docs/
trunk/treebase-core/lib/docs/mesquite/
trunk/treebase-core/lib/docs/mesquite/BeanTree/
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTree.class
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTreeControls.class
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/Branch.class
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/TreeCanvas.class
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/TreeClass.class
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/com/
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/com/metrowerks/
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/com/metrowerks/AppletFrame.class
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.html
trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/AncestralStates.html
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/Pagel94.html
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/ProcessCharEvol.html
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/charEvolution.html
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/ancStates.gif
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/anceStates.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/anolesPlot2D.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/anolesPlot3D.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/mirrorTree.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/p94Table1.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/p94Table2.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/pagel94.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/pairwise.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/pdapFelsContrH.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/scm.jpg
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/tcot.gif
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/traceAll.gif
trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/images/traceOverTrees.gif
trunk/treebase-core/lib/docs/mesquite/Diversification/
trunk/treebase-core/lib/docs/mesquite/Diversification/BiSSESimParams.gif
trunk/treebase-core/lib/docs/mesquite/Diversification/diversification.html
trunk/treebase-core/lib/docs/mesquite/Help/
trunk/treebase-core/lib/docs/mesquite/Help/MesquiteFAQ.html
trunk/treebase-core/lib/docs/mesquite/Help/QualityTrees.html
trunk/treebase-core/lib/docs/mesquite/Help/images/
trunk/treebase-core/lib/docs/mesquite/Help/images/Thumbs.db
trunk/treebase-core/lib/docs/mesquite/Help/images/abcTree.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/ballsNSticksTree.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/branchesCollapsed.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/branchesToCollapse.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/collapseBranchTool.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/curvogramTree.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/diagonalTree.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/fourTreeForms.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/fragModelScaled.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/fragModelSim.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/fragModelSim.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/fragModelText.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/fragModelWindow.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/nodeNamer.GIF
trunk/treebase-core/lib/docs/mesquite/Help/images/observedStatistic.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/refugiaModel.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/refugiaModelScaled.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/refugiaModelSim.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/refugiaModelText.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/refugiaModelWindow.JPG
trunk/treebase-core/lib/docs/mesquite/Help/images/squareTree.GIF
trunk/treebase-core/lib/docs/mesquite/Help/slatkinMaddisonS.html
trunk/treebase-core/lib/docs/mesquite/Library/
trunk/treebase-core/lib/docs/mesquite/Library/MesquiteVersionNumber.lbi
trunk/treebase-core/lib/docs/mesquite/Library/Untitled.lbi
trunk/treebase-core/lib/docs/mesquite/Library/_notes/
trunk/treebase-core/lib/docs/mesquite/Library/styles.xml
trunk/treebase-core/lib/docs/mesquite/RandomSimul/
trunk/treebase-core/lib/docs/mesquite/RandomSimul/RandomSimul.html
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/chalceum.jpg
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/codeSnippet.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/exportMatrixBatch.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/fullmodel.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/gamma10reps.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/gamma15.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/gamma15dlog.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/gammaTest.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/sim1.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/simMatrix.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/snippetEg.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/templateEditor2.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/templateManager.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/textViewTab.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/images/treeCode.gif
trunk/treebase-core/lib/docs/mesquite/RandomSimul/simChars.html
trunk/treebase-core/lib/docs/mesquite/RandomSimul/simDNA.html
trunk/treebase-core/lib/docs/mesquite/RandomSimul/simTrees.html
trunk/treebase-core/lib/docs/mesquite/Templates/
trunk/treebase-core/lib/docs/mesquite/Templates/Template.dwt
trunk/treebase-core/lib/docs/mesquite/Templates/TemplateBlank.dwt
trunk/treebase-core/lib/docs/mesquite/Templates/mesq.ico
trunk/treebase-core/lib/docs/mesquite/changes.html
trunk/treebase-core/lib/docs/mesquite/characters.html
trunk/treebase-core/lib/docs/mesquite/charts.html
trunk/treebase-core/lib/docs/mesquite/continuous/
trunk/treebase-core/lib/docs/mesquite/continuous/continuous.html
trunk/treebase-core/lib/docs/mesquite/continuous/images/
trunk/treebase-core/lib/docs/mesquite/continuous/images/cvaflies.jpg
trunk/treebase-core/lib/docs/mesquite/continuous/images/landmarks.jpg
trunk/treebase-core/lib/docs/mesquite/credits.html
trunk/treebase-core/lib/docs/mesquite/glossary.html
trunk/treebase-core/lib/docs/mesquite/help.html
trunk/treebase-core/lib/docs/mesquite/howMesquiteWorks.html
trunk/treebase-core/lib/docs/mesquite/images/
trunk/treebase-core/lib/docs/mesquite/images/BembMatrix.gif
trunk/treebase-core/lib/docs/mesquite/images/DNAMatrix.gif
trunk/treebase-core/lib/docs/mesquite/images/DNAMatrix.jpg
trunk/treebase-core/lib/docs/mesquite/images/NSERClogo.jpg
trunk/treebase-core/lib/docs/mesquite/images/a_logo.gif
trunk/treebase-core/lib/docs/mesquite/images/addCharsTool.gif
trunk/treebase-core/lib/docs/mesquite/images/addTaxaTool.gif
trunk/treebase-core/lib/docs/mesquite/images/analyses.gif
trunk/treebase-core/lib/docs/mesquite/images/annot.gif
trunk/treebase-core/lib/docs/mesquite/images/annot.jpg
trunk/treebase-core/lib/docs/mesquite/images/annotation.gif
trunk/treebase-core/lib/docs/mesquite/images/arrow.gif
trunk/treebase-core/lib/docs/mesquite/images/babyMesquite.jpg
trunk/treebase-core/lib/docs/mesquite/images/basics.gif
trunk/treebase-core/lib/docs/mesquite/images/bigModularity.gif
trunk/treebase-core/lib/docs/mesquite/images/blue-ball-small.gif
trunk/treebase-core/lib/docs/mesquite/images/bruchine.jpg
trunk/treebase-core/lib/docs/mesquite/images/cellPictures.gif
trunk/treebase-core/lib/docs/mesquite/images/cellPictures.jpg
trunk/treebase-core/lib/docs/mesquite/images/charList.jpg
trunk/treebase-core/lib/docs/mesquite/images/charWand.gif
trunk/treebase-core/lib/docs/mesquite/images/closeTab.jpg
trunk/treebase-core/lib/docs/mesquite/images/color.gif
trunk/treebase-core/lib/docs/mesquite/images/colorLegend.gif
trunk/treebase-core/lib/docs/mesquite/images/construction.gif
trunk/treebase-core/lib/docs/mesquite/images/dataWindow.gif
trunk/treebase-core/lib/docs/mesquite/images/demail.jpg
trunk/treebase-core/lib/docs/mesquite/images/depthVsImbalance.jpg
trunk/treebase-core/lib/docs/mesquite/images/email.jpg
trunk/treebase-core/lib/docs/mesquite/images/employeeTree.gif
trunk/treebase-core/lib/docs/mesquite/images/employees.jpg
trunk/treebase-core/lib/docs/mesquite/images/exampleWindow.jpg
trunk/treebase-core/lib/docs/mesquite/images/eyeDropper.gif
trunk/treebase-core/lib/docs/mesquite/images/fadeDown.gif
trunk/treebase-core/lib/docs/mesquite/images/fadeLeft.gif
trunk/treebase-core/lib/docs/mesquite/images/fadeRight.gif
trunk/treebase-core/lib/docs/mesquite/images/fadeUp.gif
trunk/treebase-core/lib/docs/mesquite/images/favicon.ico
trunk/treebase-core/lib/docs/mesquite/images/gcSequence.jpg
trunk/treebase-core/lib/docs/mesquite/images/green-ball-small.gif
trunk/treebase-core/lib/docs/mesquite/images/helpButton.gif
trunk/treebase-core/lib/docs/mesquite/images/iBeamTool.gif
trunk/treebase-core/lib/docs/mesquite/images/iemail.jpg
trunk/treebase-core/lib/docs/mesquite/images/infoBar.gif
trunk/treebase-core/lib/docs/mesquite/images/introduction.gif
trunk/treebase-core/lib/docs/mesquite/images/keySelector.gif
trunk/treebase-core/lib/docs/mesquite/images/listC.gif
trunk/treebase-core/lib/docs/mesquite/images/listT.gif
trunk/treebase-core/lib/docs/mesquite/images/littleModularity.gif
trunk/treebase-core/lib/docs/mesquite/images/logWindow.jpg
trunk/treebase-core/lib/docs/mesquite/images/logo_cipres.gif
trunk/treebase-core/lib/docs/mesquite/images/maintainTargetMatch.jpg
trunk/treebase-core/lib/docs/mesquite/images/manual.jpg
trunk/treebase-core/lib/docs/mesquite/images/matrix.gif
trunk/treebase-core/lib/docs/mesquite/images/mesquiteIcon.gif
trunk/treebase-core/lib/docs/mesquite/images/mesquiteLower.gif
trunk/treebase-core/lib/docs/mesquite/images/mesquiteLowerManual.GIF
trunk/treebase-core/lib/docs/mesquite/images/mesquitePlain.gif
trunk/treebase-core/lib/docs/mesquite/images/mesquitesmall.gif
trunk/treebase-core/lib/docs/mesquite/images/miniScroll.jpg
trunk/treebase-core/lib/docs/mesquite/images/miniscrollHoriz.gif
trunk/treebase-core/lib/docs/mesquite/images/miniscrollVert.gif
trunk/treebase-core/lib/docs/mesquite/images/notesTool.gif
trunk/treebase-core/lib/docs/mesquite/images/nsf4c.jpg
trunk/treebase-core/lib/docs/mesquite/images/objects.gif
trunk/treebase-core/lib/docs/mesquite/images/pFWindow.jpg
trunk/treebase-core/lib/docs/mesquite/images/paintBucket.gif
trunk/treebase-core/lib/docs/mesquite/images/pixel.gif
trunk/treebase-core/lib/docs/mesquite/images/popIn.jpg
trunk/treebase-core/lib/docs/mesquite/images/popOut.jpg
trunk/treebase-core/lib/docs/mesquite/images/prerelease.gif
trunk/treebase-core/lib/docs/mesquite/images/projFilesWindow.jpg
trunk/treebase-core/lib/docs/mesquite/images/project1.gif
trunk/treebase-core/lib/docs/mesquite/images/projector.gif
trunk/treebase-core/lib/docs/mesquite/images/projectsFiles.gif
trunk/treebase-core/lib/docs/mesquite/images/release.gif
trunk/treebase-core/lib/docs/mesquite/images/searchData.jpg
trunk/treebase-core/lib/docs/mesquite/images/searchDicon.jpg
trunk/treebase-core/lib/docs/mesquite/images/searchFeaturesAND.jpg
trunk/treebase-core/lib/docs/mesquite/images/searchFeaturesOR.jpg
trunk/treebase-core/lib/docs/mesquite/images/searchWindow.jpg
trunk/treebase-core/lib/docs/mesquite/images/selectTaxa.gif
trunk/treebase-core/lib/docs/mesquite/images/showPicture.gif
trunk/treebase-core/lib/docs/mesquite/images/small.top.arrow.gif
trunk/treebase-core/lib/docs/mesquite/images/sortTool.gif
trunk/treebase-core/lib/docs/mesquite/images/stepsVsHydro.jpg
trunk/treebase-core/lib/docs/mesquite/images/submenu.gif
trunk/treebase-core/lib/docs/mesquite/images/tabLeft.gif
trunk/treebase-core/lib/docs/mesquite/images/tabRight.gif
trunk/treebase-core/lib/docs/mesquite/images/tabs.jpg
trunk/treebase-core/lib/docs/mesquite/images/taxWand.gif
trunk/treebase-core/lib/docs/mesquite/images/thassus.jpg
trunk/treebase-core/lib/docs/mesquite/images/toc.GIF
trunk/treebase-core/lib/docs/mesquite/images/toolPalette.gif
trunk/treebase-core/lib/docs/mesquite/images/treeScroll.jpg
trunk/treebase-core/lib/docs/mesquite/images/treeTools/
trunk/treebase-core/lib/docs/mesquite/images/treeTools/adjustBranchLength.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/adjustNodePosition.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/annotateNode.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/assignLineageWidth.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/branchInfo.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/collapseAllBranches.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/collapseBranch.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/colorBranch.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/drawAsTriangle.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/hyperlink.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/insertUnbranchedNode.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/interchangeBranches.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/ladderizeClade.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/magnifyClade.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/nameNode.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/pruneClade.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/rerootAtBranch.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/searchBetterTool.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/searchTaxonInDBTool.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/selectBranch.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/selectBranchesInClade.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/selectTaxaInClade.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/showPicture.gif
trunk/treebase-core/lib/docs/mesquite/images/treeTools/stretchBranch.gif
trunk/treebase-core/lib/docs/mesquite/images/treeValues.jpg
trunk/treebase-core/lib/docs/mesquite/images/treeWindow.gif
trunk/treebase-core/lib/docs/mesquite/images/ubc_blue.gif
trunk/treebase-core/lib/docs/mesquite/images/using.gif
trunk/treebase-core/lib/docs/mesquite/images/wand.gif
trunk/treebase-core/lib/docs/mesquite/images/wiko_logo_grau.gif
trunk/treebase-core/lib/docs/mesquite/images/window.gif
trunk/treebase-core/lib/docs/mesquite/installation/
trunk/treebase-core/lib/docs/mesquite/installation/images/
trunk/treebase-core/lib/docs/mesquite/installation/images/installWin1.gif
trunk/treebase-core/lib/docs/mesquite/installation/images/installWin2.gif
trunk/treebase-core/lib/docs/mesquite/installation/images/installWin3.GIF
trunk/treebase-core/lib/docs/mesquite/installation/images/osXinstall.jpg
trunk/treebase-core/lib/docs/mesquite/installation/images/wc.gif
trunk/treebase-core/lib/docs/mesquite/installation/installation.html
trunk/treebase-core/lib/docs/mesquite/installation/installationMacOS.html
trunk/treebase-core/lib/docs/mesquite/installation/installationUNIX.html
trunk/treebase-core/lib/docs/mesquite/installation/installationWindows.html
trunk/treebase-core/lib/docs/mesquite/managingFiles.html
trunk/treebase-core/lib/docs/mesquite/manual.html
trunk/treebase-core/lib/docs/mesquite/menus.html
trunk/treebase-core/lib/docs/mesquite/moduleIndex.html
trunk/treebase-core/lib/docs/mesquite/modules.html
trunk/treebase-core/lib/docs/mesquite/molecular/
trunk/treebase-core/lib/docs/mesquite/molecular/images/
trunk/treebase-core/lib/docs/mesquite/molecular/images/aahydroColorMatrix.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/assocBeforeFusedExport.gif
trunk/treebase-core/lib/docs/mesquite/molecular/images/becomesArrow.gif
trunk/treebase-core/lib/docs/mesquite/molecular/images/consensus.gif
trunk/treebase-core/lib/docs/mesquite/molecular/images/consensusAA.gif
trunk/treebase-core/lib/docs/mesquite/molecular/images/cytStructure.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/gcBiasColorMatrix.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/gcBiasTaxa.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/gene1beforeConcat.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/gene1beforeConcat2.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/gene2beforeConcat.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/gene2beforeInclude.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/genePQRBeforeInclude.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/genesAfterConcat.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/images/genesAfterInclude.jpg
trunk/treebase-core/lib/docs/mesquite/molecular/molecular.html
trunk/treebase-core/lib/docs/mesquite/otherPrograms.html
trunk/treebase-core/lib/docs/mesquite/popGen/
trunk/treebase-core/lib/docs/mesquite/popGen/images/
trunk/treebase-core/lib/docs/mesquite/popGen/images/assoc.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/assoc2.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/assocEditing.jpg
trunk/treebase-core/lib/docs/mesquite/popGen/images/assocEst.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/assocList.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/createNewPop.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/depths.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/depths10000.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/geneTree.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/mbfChart.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/mbfFiles.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/mbfFiles2.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/mbfMBF.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/mbfModel.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/mbfTree.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/sDivergence.gif
trunk/treebase-core/lib/docs/mesquite/popGen/images/tree.gif
trunk/treebase-core/lib/docs/mesquite/popGen/popGen.html
trunk/treebase-core/lib/docs/mesquite/publication.html
trunk/treebase-core/lib/docs/mesquite/scripting.html
trunk/treebase-core/lib/docs/mesquite/studies/
trunk/treebase-core/lib/docs/mesquite/studies/index.html
trunk/treebase-core/lib/docs/mesquite/studies/study001/
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trunk/treebase-core/lib/docs/mesquite/studies/study001/images/histogramAsText.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/noterid.jpg
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/showPercentile.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/showPercentileText.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/tdtree.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/templateEditor1.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/testStructure1.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/trachypachid.jpg
trunk/treebase-core/lib/docs/mesquite/studies/study001/images/treeTestDialog.gif
trunk/treebase-core/lib/docs/mesquite/studies/study001/index.html
trunk/treebase-core/lib/docs/mesquite/studies/study001/study001.nex
trunk/treebase-core/lib/docs/mesquite/studies/study002/
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/
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trunk/treebase-core/lib/docs/mesquite/studies/study002/images/gamma.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/model.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/modelTree.gif
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trunk/treebase-core/lib/docs/mesquite/studies/study002/images/parsimony.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/parsimonyLB.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/paupEnd.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/paupStart.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/result.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/images/titv.gif
trunk/treebase-core/lib/docs/mesquite/studies/study002/index.html
trunk/treebase-core/lib/docs/mesquite/studies/study002/study002.nex
trunk/treebase-core/lib/docs/mesquite/support.html
trunk/treebase-core/lib/docs/mesquite/taxa.html
trunk/treebase-core/lib/docs/mesquite/toc.html
trunk/treebase-core/lib/docs/mesquite/trees.html
trunk/treebase-core/lib/docs/mesquite/whyMesquite.html
trunk/treebase-core/lib/docs/mesquite/windows.html
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTree.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTree.class
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTreeControls.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTreeControls.class
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/Branch.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/Branch.class
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/TreeCanvas.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/TreeCanvas.class
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/TreeClass.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/TreeClass.class
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/com/metrowerks/AppletFrame.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/com/metrowerks/AppletFrame.class
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.html
===================================================================
--- trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.html (rev 0)
+++ trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.html 2009-12-15 17:16:33 UTC (rev 356)
@@ -0,0 +1,9 @@
+<title>BeanTree</title>
+<h2>BeanTree</h2>
+It all started yesterday because I thought that perhaps I should try out some object oriented programming in case I wanted to teach an object oriented language to the students in my class next spring....
+<p>Much faster as stand alone application.
+<p>Taxon names must be one character only (actually, they can all be the same character).
+<hr>
+<applet codebase="BeanTree" code="BeanTree.class" width="500" height="400">
+</applet>
+<hr>
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.html
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java
===================================================================
--- trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java (rev 0)
+++ trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java 2009-12-15 17:16:33 UTC (rev 356)
@@ -0,0 +1,492 @@
+//package wpm;
+
+import java.awt.*;
+import java.applet.Applet;
+
+
+public class BeanTree extends Applet
+{
+ static TreeCanvas TreeDisplay;
+ static BeanTreeControls controls;
+
+
+ public void init()
+ {
+ setLayout( new BorderLayout() );
+ resize(300, 300);
+ TreeDisplay = new TreeCanvas(10, 10, 400, 400);
+ add( "Center", TreeDisplay );
+ add("North", controls = new BeanTreeControls(TreeDisplay));
+ TreeDisplay.Tree = new TreeClass();
+ TreeDisplay.controls = controls;
+ TreeDisplay.Tree.SubRoot = new Branch(null, false);
+ TreeDisplay.Tree.Root = new Branch(TreeDisplay.Tree.SubRoot, false);
+ TreeDisplay.edgewidth = 10;
+ TreeDisplay.needsUpdating = false;
+ TreeDisplay.highlightedBranch = null;
+ TreeDisplay.Tree.exists = false;
+ repaint();
+ }
+
+ public void start() {
+ controls.enable();
+ }
+
+ public void stop() {
+ controls.disable();
+ }
+ public static void main(String args[])
+ {
+ com.metrowerks.AppletFrame.startApplet("BeanTree", "BeanTree", args);
+ }
+
+}
+/** ======================================================================== */
+class TreeCanvas extends Canvas {
+ TreeClass Tree;
+
+ int x_max, y_max;
+ int edgewidth;
+ Branch highlightedBranch, branchFrom;
+ int xFrom, yFrom, xTo, yTo;
+ boolean needsUpdating;
+ String treeDescription;
+ BeanTreeControls controls;
+ private int lastleft;
+ private int taxspacing;
+ private Branch foundBranch;
+
+
+ public TreeCanvas( int x_max, int y_max, int x_size, int y_size )
+ {
+ this.x_max = x_max;
+ this.y_max = y_max;
+
+ resize( x_size, y_size );
+ repaint();
+ }
+
+
+ /*_________________________________________________*/
+ private void WriteTreeDescription(Branch N) {
+ if (N.left!=null)
+ {
+ treeDescription+='(';
+ WriteTreeDescription(N.left);
+ treeDescription+=',';
+ WriteTreeDescription(N.right);
+ treeDescription+=')';
+ }
+ else
+ {
+ treeDescription+='*';
+ }
+ }
+ public String Describe() {
+ treeDescription="";
+ WriteTreeDescription(Tree.Root);
+ treeDescription+=';';
+ return treeDescription;
+ }
+ /*_________________________________________________*/
+ private void CalcInternalLocs(Branch N)
+ {
+ if (N.left != null) //internal
+ {
+ CalcInternalLocs(N.left);
+ CalcInternalLocs(N.right);
+
+ N.y = (-N.left.x + N.right.x+N.left.y + N.right.y) / 2;
+ N.x =(N.left.x + N.right.x - N.left.y + N.right.y) / 2;
+ }
+ }
+
+ /*_________________________________________________*/
+ private void CalcTerminalLocs(Branch N)
+ {
+ if (N.left == null) //terminal
+ {
+ lastleft+= taxspacing;
+ N.y = 90;
+ N.x = lastleft;
+ }
+ else
+ {
+ CalcTerminalLocs(N.left);
+ CalcTerminalLocs(N.right);
+ }
+ }
+
+ /*_________________________________________________*/
+ private void CalcBranchPolys(Branch N)
+ {
+ if (N.left != null) //terminal
+ {
+ CalcBranchPolys(N.left);
+ CalcBranchPolys(N.right);
+ N.branchPoly.npoints=0;
+ N.branchPoly.addPoint(N.x, N.y);
+ N.branchPoly.addPoint(N.x+edgewidth/2, N.y-edgewidth/2);
+ N.branchPoly.addPoint(N.x+edgewidth, N.y);
+ N.branchPoly.addPoint(N.ancestor.x+edgewidth, N.ancestor.y);
+ N.branchPoly.addPoint(N.ancestor.x, N.ancestor.y);
+ N.branchPoly.npoints=5;
+ }
+ else
+ {
+ N.branchPoly.npoints=0;
+ N.branchPoly.addPoint(N.x, N.y);
+ N.branchPoly.addPoint(N.x+edgewidth, N.y);
+ N.branchPoly.addPoint(N.ancestor.x+edgewidth, N.ancestor.y);
+ N.branchPoly.addPoint(N.ancestor.x, N.ancestor.y);
+ N.branchPoly.npoints=4;
+ }
+ }
+ /*_________________________________________________*/
+ private void calcBranches() {
+ lastleft = 0;
+ taxspacing = (bounds().width - 10) / Tree.numTaxa;
+ CalcTerminalLocs(Tree.Root);
+ CalcInternalLocs(Tree.Root);
+ Tree.SubRoot.y = (Tree.Root.y)+20;
+ Tree.SubRoot.x = (Tree.Root.x)-20;
+ CalcBranchPolys(Tree.Root);
+ }
+
+ /*_________________________________________________*/
+ private void drawBranch(Graphics g, Branch N) {
+ g.setColor(N.color);
+ g.fillPolygon(N.branchPoly);
+ if (N.left != null)
+ drawBranch(g, N.left);
+ if (N.right != null)
+ drawBranch(g, N.right);
+ }
+ /*_________________________________________________*/
+ public void drawTree(Graphics g) {
+ if (Tree.exists)
+ {
+ calcBranches();
+ drawBranch(g, Tree.Root);
+ }
+ }
+ /*_________________________________________________*/
+ public void paint(Graphics g) {
+ drawTree(g);
+ needsUpdating = false;
+ }
+ /*_________________________________________________*/
+
+ public void InvertBranch(Graphics g, Branch N) {
+ // N.color=Color.white;
+ highlightedBranch=N;
+ g.setColor(Color.white);
+ g.fillPolygon(N.branchPoly);
+ // needsUpdating=true;
+ }
+
+ /*_________________________________________________*/
+ public void RevertBranch(Graphics g, Branch N) {
+ // N.color=Color.black;
+ highlightedBranch=null;
+ g.setColor(Color.black);
+ g.fillPolygon(N.branchPoly);
+ // needsUpdating=true;
+ }
+ /*_________________________________________________*/
+ private void ScanBranches(Branch N, int x, int y)
+ {
+ if (foundBranch==null) {
+ if (N.branchPoly.inside(x, y))
+ foundBranch = N;
+ if (N.left != null) //terminal
+ {
+ ScanBranches(N.left, x, y);
+ ScanBranches(N.right, x, y);
+ }
+ }
+ }
+ /*_________________________________________________*/
+ public Branch FindBranch(int x, int y) {
+ foundBranch=null;
+ ScanBranches(Tree.Root, x, y);
+ return foundBranch;
+ }
+
+ /*_________________________________________________*/
+ public void ScanTouch(Graphics g, int x, int y) {
+ Branch branchFound=FindBranch( x, y);
+ if (branchFound!=null)
+ {
+ branchFrom=branchFound;
+ xFrom=x;
+ yFrom=y;
+ xTo=x;
+ yTo=y;
+ g.setXORMode(Color.gray);
+ g.setColor(Color.black);
+ g.drawLine(xFrom,yFrom,xTo,yTo);
+ }
+
+ }
+ /*_________________________________________________*/
+ public void ScanFlash(Graphics g, int x, int y) {
+ Branch branchFound=FindBranch( x, y);
+ if (highlightedBranch != null)
+ {if (branchFound==null)
+ RevertBranch(g, highlightedBranch);
+ else if (branchFound!=highlightedBranch)
+ {
+ RevertBranch(g, highlightedBranch);
+ InvertBranch(g, branchFound);
+ }
+ }
+ else if (branchFound!=null)
+ InvertBranch(g, branchFound);
+ }
+ /*_________________________________________________*/
+ public void ScanDrop(Graphics g, int x, int y) {
+ Branch branchTo=FindBranch( x, y);
+ if (branchTo != null)
+ {if (branchFrom==branchTo)
+ {
+ }
+ else
+ {
+ Tree.MoveBranch(branchFrom, branchTo);
+ controls.RedescribeTree();
+ }
+ };
+ needsUpdating=true;
+ branchFrom = null;
+
+ }
+ /*_________________________________________________*/
+ public boolean mouseMove(Event e, int x, int y) {
+ Graphics g = getGraphics();
+ ScanFlash(g, x, y);
+ return true;
+ }
+ /*_________________________________________________*/
+ public boolean mouseDown(Event e, int x, int y) {
+ Graphics g = getGraphics();
+ ScanTouch(g, x, y);
+ if (needsUpdating)
+ repaint();
+ return true;
+ }
+
+ /*_________________________________________________*/
+ public boolean mouseDrag(Event e, int x, int y) {
+ if (branchFrom!=null)
+ {
+ Graphics g = getGraphics();
+ g.setColor(Color.black);
+ g.setXORMode(Color.gray);
+ g.drawLine(xFrom,yFrom,xTo,yTo);
+ xTo=x;
+ yTo=y;
+ g.drawLine(xFrom,yFrom,xTo,yTo);
+ }
+ return true;
+ }
+ /*_________________________________________________*/
+ public boolean mouseUp(Event e, int x, int y) {
+ Graphics g = getGraphics();
+ if (branchFrom!=null) {
+ ScanDrop( g, x, y);
+ repaint();
+ }
+ branchFrom=null;
+ g.setXORMode(g.getColor());
+ return true;
+ }
+ }
+
+
+
+/** ======================================================================== */
+public class TreeClass {
+ Branch Root, SubRoot;
+ int numTaxa;
+ boolean exists;
+
+ private int stringloc;
+
+ /** ________________ read tree ________________ */
+ private void ParseTreeDescription(String TreeDescription, Branch Ancestor) {
+ if (TreeDescription.charAt(stringloc) == '(')
+ {
+ stringloc++;
+ Ancestor.sprout();
+ ParseTreeDescription(TreeDescription, Ancestor.left);
+ stringloc++; //skip comma
+ ParseTreeDescription(TreeDescription, Ancestor.right);
+ stringloc++; //skip parensu
+ }
+ else
+ {
+ stringloc++; //skip tt name
+ numTaxa++;
+ }
+ }
+ public void ReadTree(String TreeDescription) {
+ stringloc=0;
+ numTaxa=0;
+ ParseTreeDescription(TreeDescription, Root);
+ exists=true;
+ }
+
+ /** ______________________________________________ */
+
+ private boolean DescendantOf(Branch branchD, Branch branchA) {
+ return false;
+ }
+
+ private boolean NodeSlantsRight(Branch N) {
+ if (N.ancestor.right==N)
+ return true;
+ else
+ return false;
+ }
+ private Branch Sister(Branch N) {
+ if (N.ancestor.right==N)
+ return N.ancestor.left;
+ else
+ return N.ancestor.right;
+ }
+ /** ______________________________________________ */
+ public void MoveBranch(Branch branchFrom, Branch branchTo) {
+
+ Branch sideN,C, G, F, H, NCAnc;
+ boolean fromancslantRight, fromslantRight, toslantRight, NCslantRight, fromroot, toroot;
+
+ if ((branchFrom.ancestor.ancestor == branchTo) & (branchTo == Root))
+ {
+ branchFrom = Sister(branchFrom);
+ branchTo = Sister(branchFrom.ancestor);
+ }
+ if ((branchFrom.ancestor == Root) & (branchTo.ancestor.ancestor == Root))
+ {
+ sideN = branchFrom;
+ branchFrom = branchTo;
+ branchTo = sideN;
+ }
+
+ fromroot = false;
+ toroot = false;
+ fromslantRight = NodeSlantsRight(branchFrom);
+ fromancslantRight = NodeSlantsRight(branchFrom.ancestor);
+ toslantRight = NodeSlantsRight(branchTo);
+ G = Sister(branchFrom);
+ H = branchFrom.ancestor.ancestor;
+ C = branchTo.ancestor;
+ F = branchFrom.ancestor;
+
+ if (F == Root)
+ fromroot = true;
+ else if (branchTo == Root )
+ toroot = true;
+
+ if (fromslantRight == toslantRight)
+ {
+ sideN = F.left;
+ F.left = F.right;
+ F.right = sideN;
+ }
+
+ G.ancestor = H;
+ F.ancestor = C;
+ branchTo.ancestor = F;
+ if (fromancslantRight)
+ H.right = G;
+ else
+ H.left = G;
+ if (toslantRight)
+ {
+ F.right = branchTo;
+ C.right = F;
+ }
+ else
+ {
+ F.left = branchTo;
+ C.left = F;
+ }
+ sideN = Sister(G);
+
+ if (fromroot)
+ {
+ sideN = Root;
+ Root = G;
+ G = sideN;
+ }
+ if (toroot)
+ {
+ sideN = Root;
+ Root = F;
+ F = sideN;
+ }
+ if (!NodeSlantsRight(Root))
+ {
+ SubRoot.right = Root;
+ }
+
+ }
+
+}
+/** ======================================================================== */
+public class Branch {
+ Branch left, right, ancestor;
+ int x;
+ int y;
+ Polygon branchPoly;
+ Color color;
+
+ Branch(Branch Ancestor, boolean isFirstDescendant) {
+ this.ancestor = Ancestor;
+ this.color=Color.black;
+ branchPoly= new Polygon();
+ branchPoly.xpoints = new int[5];
+ branchPoly.ypoints = new int[5];
+ branchPoly.npoints=5;
+ }
+
+ public boolean sprout() {
+ this.left = new Branch(this, true);
+ this.right = new Branch(this, false);
+ return true;
+ }
+}
+
+class BeanTreeControls extends Panel {
+ TextField tf;
+ TreeCanvas TreeDisplay;
+
+ public BeanTreeControls(TreeCanvas TreeDisplay) {
+ this.TreeDisplay = TreeDisplay;
+ add(tf = new TextField("(((*,*),(*,*)),(((*,*),*),*));", 40));
+ add(new Button("Show"));
+ }
+
+ public boolean action(Event ev, Object arg) {
+ if (ev.target instanceof Button) {
+ /* destroy current tree if present */
+ /*Display.startApplet("BeanTree.html", "BeanTree.html", args);*/
+
+
+ TreeDisplay.treeDescription=tf.getText();
+ TreeDisplay.Tree.ReadTree(TreeDisplay.treeDescription);
+ TreeDisplay.repaint();
+ return true;
+ }
+ return false;
+ }
+
+ public void RedescribeTree() {
+ TreeDisplay.treeDescription = TreeDisplay.Describe();
+ tf.setText(TreeDisplay.treeDescription);
+ repaint();
+ }
+
+}
+
Property changes on: trunk/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/AncestralStates.html
===================================================================
--- trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/AncestralStates.html (rev 0)
+++ trunk/treebase-core/lib/docs/mesquite/CharacterEvolution/AncestralStates.html 2009-12-15 17:16:33 UTC (rev 356)
@@ -0,0 +1,802 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><!-- #BeginTemplate "/Templates/Template.dwt" --><!-- DW6 -->
+<head>
+<!--LINK REL="SHORTCUT ICON" HREF="images/mesq.ico"-->
+<!-- #BeginEditable "doctitle" -->
+<title>Ancestral States</title>
+<!-- #EndEditable -->
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+</head>
+
+<body bgcolor="#FFFFFF">
+<div id="Page" style="position:absolute; left:0px; top:0px; z-index:1; visibility: visible; width: 100%; height: 100%">
+ <table border="0" cellspacing="0" cellpadding="0" width="100%">
+ <tr>
+ <td align="left" valign="top" height="60">
+ <table border="0" cellspacing="0" cellpadding="0" height="60" width="300">
+ <tr>
+ <td width="10" height="60" align="left" valign="top"> <font face="Trebuchet MS"><img src="../images/pixel.gif" width="1" height="1" alt=" " border="0"></font></td>
+ <td bgcolor="#FFFFFF">
+ <div align="left"><font face="Trebuchet MS"><a href="../manual.html"><img src="../images/mesquitesmall.gif" width="268" height="92" border="0" alt="Mesquite"></a></font></div>
+ </td>
+ </tr>
+ <tr>
+ <td height="42" align="left" valign="top"></td>
+ <td height="42" align="left" valign="top"><font face="Trebuchet MS"><a href="../manual.html"><img src="../images/mesquiteLowerManual.gif" border="0"></a></font></td>
+ </tr>
+<!-- <tr>
+ <td colspan="2" height="10"></td>
+ </tr>
+ <tr>
+ <td colspan="2" height="15" align="center" valign="middle">
+ <!-- Google CSE Search Box Begins
+ <form id="searchbox_016202157087875381635:khljhzi-ps8" action="http://www.google.com/cse">
+ <input type="hidden" name="cx" value="016202157087875381635:khljhzi-ps8" />
+ <input type="hidden" name="cof" value="FORID:0" />
+ <input name="q" type="text" size="20" />
+ <input type="submit" name="sa" value="Search Mesquite" />
+ <!--<img src="http://www.google.com/coop/images/google_custom_search_smnar.gif" alt="Google Custom Search" />
+ </form>
+ <!-- Google CSE Search Box Ends
+ </td>
+ </tr> -->
+ </table>
+ </td>
+ <td>
+ <table border="0" cellspacing="0" cellpadding="0" height="134" width="550">
+ <tr valign="top" height="92">
+ <td width="72" align="center" height="92" valign="top" bgcolor="#FFFFFF"><font face="Trebuchet MS"><img src="../images/fadeRight.gif" width="72" height="160"></font></td>
+ <td bgcolor="#99FF99"><img src="../images/introduction.gif" valign="bottom"></td>
+ <td align="left" valign="top" height="92" width = "160" bgcolor="#99FF99">
+ <p><font face="Trebuchet MS"><span class="smallplain"><a href="../manual.html">
+ Introduction</a><br>
+ </span><a href="../whyMesquite.html">Why?</a><br>
+ <a href="../publication.html#howToCite">How to Cite</a> <br>
+ <a href="../publication.html">Publication</a><br>
+ <a href="../support.html">Support</a><br>
+ <a href="../credits.html">Credits</a> </font><br>
+ <font face="Trebuchet MS"><span class="smallplain"><a href="../help.html">Help</a></span></font><br>
+ <a href="../Help/MesquiteFAQ.html"><font face="Trebuchet MS">FAQ</font></a><br>
+ <a href="http://mesquiteproject.org"><font face="Trebuchet MS">Web Site</font></a><br>
+ </td>
+ <td bgcolor="#99FF99"><img src="../images/basics.gif" valign="bottom"></td>
+ <td align="left" valign="top" height="92" width="220" bgcolor="#99FF99">
+ <p><font face="Trebuchet MS"><span class="smallplain"><a href="../help.html"></a>
+ <a href="../managingFiles.html">Files</a></span> <br>
+ <span class="smallplain"><a href="../menus.html">Menus</a><br>
+ <a href="../windows.html">Windows</a><br>
+ <a href="../charts.html">Charts</a><br>
+ <a href="../scripting.html">Scripts/Macros</a> <br>
+ <a href="../modules.html">Modules</a><br>
+ <a href="../howMesquiteWorks.html">How</a></span></font>
+ </td>
+ <td bgcolor="#99FF99"><img src="../images/objects.gif" valign="bottom"></td>
+ <td align="left" valign="top" height="92" width="260" bgcolor="#99FF99">
+ <p><font face="Trebuchet MS">
+ <span class="smallplain"><a href="../characters.html">Characters</a></span></font><font face="Trebuchet MS"><span class="smallplain"><a href="../Taxa.html"><br>
+ Taxa<br>
+ </a></span></font><font face="Trebuchet MS"><a href="../trees.html">Trees</a><br>
+ <a href="../glossary.html">Glossary</a> </font></p>
+ <p><font face="Trebuchet MS"><em><font face="Trebuchet MS"><a href="../changes.html">New</a><br>
+ <a href="../changes.html">Features</a></font></em></font></p>
+ </td>
+ <td align="left" valign="top" height="92" width="92"><font face="Trebuchet MS"><img src="../images/fadeLeft.gif" width="92" height="160"></font></td>
+ </tr>
+ <tr>
+ <td width="72" height="20"></td>
+ <td></td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+ </table>
+ </td>
+ </tr>
+ </table>
+ <table border="0" cellspacing="0" cellpadding="0" width="100%" height="100%">
+ <tr>
+ <td valign="top" align="left" width="110" height="100%">
+ <table border="0" cellspacing="0" cellpadding="0" width="142">
+ <tr>
+ <td colspan="3" bgcolor="#99FF99"><p><font face="Trebuchet MS"><img src="../images/fadeDown.gif" width="100%" height="95" valign "top" border="0" alt=" "></font></p></td>
+ </tr>
+ <tr>
+ <td width="6" bgcolor="#99FF99" height="35"></td>
+ <td colspan="2" bgcolor="99FF99" valign="top" height="35"><p><font face="Trebuchet MS"><a href="../toc.html">Table of</a><br>
+ <a href="../toc.html">Contents</a></font></p></td>
+ </tr>
+ <tr>
+ <td width="6" bgcolor="#99FF99" height="35"></td>
+ <td colspan="2" bgcolor="#99FF99" height="35"><p><font face="Trebuchet MS"><img src="../images/analyses.gif"></font></p>
+ </td>
+ </tr>
+ <tr bgcolor="#99FF99">
+ <td height="35" align="left" valign="middle" bgcolor="#99FF99"> </td>
+ <td width="131" height="35" align="left" valign="middle"><p>
+ <font face="Trebuchet MS">
+ <a href="charEvolution.html">Character</a><br>
+ <a href="charEvolution.html">Evolution</a> <br> <br>
+ <a href="../Diversification/diversification.html">Diversification</a><br><br>
+ <a href="../molecular/molecular.html">Molecular</a><br>
+ <a href="../molecular/molecular.html">Data</a><br><br>
+ <a href="../popGen/popGen.html">Gene trees</a> <br> <br>
+ <a href="../RandomSimul/RandomSimul.html">Simulations &</a><br>
+ <a href="../RandomSimul/RandomSimul.html">Randomizations</a> <br> <br>
+ <a href="../continuous/continuous.html">Continuous</a><br>
+ <a href="../continuous/continuous.html">Characters</a><br> <br>
+ <a href="../otherPrograms.html">Use with</a><br>
+ <a href="../otherPrograms.html">Other Programs</a> <br><br>
+ <a href="../studies/index.html">Studies</a> </font></p></td>
+ <td width="5" height="35" align="left" valign="middle"> </td>
+ </tr>
+ <tr bgcolor="#99FF99">
+ <td height="35" align="left" valign="middle"> </td>
+ <td height="35" align="left" valign="middle"> </td>
+ <td height="35" align="left" valign="middle"> </td>
+ </tr>
+ <tr>
+ <td height="35" align="left" valign="middle"><font face="Trebuchet MS"><img src="../images/fadeUp.gif" width="5" height="92"></font></td>
+ <td height="35" align="left" valign="middle" colspan="2"><font face="Trebuchet MS"><img src="../images/fadeUp.gif" width="100%" height="92"></font></td>
+ </tr>
+ </table>
+ </td>
+ <td valign="top" width="100%" height="100%">
+ <table width="700" border="0" cellpadding="10" cellspacing="0">
+ <tr>
+ <td><font face="Trebuchet MS"><!-- #BeginEditable "body" -->
+ <h2><font face="Trebuchet MS">Studying the History of Character
+ Evolution</font></h2>
+ <p><font face="Trebuchet MS">With a phylogenetic tree and a distribution
+ of character states in the observed (terminal) taxa, Mesquite
+ can attempt to reconstruct the character states at ancestral nodes.
+ Two separate issues to consider are the method by which the reconstruction
+ is done, and how its results are displayed to the user. Mesquite
+ currently can use either parsimony, likelihood or Bayesian methods
+ to reconstruct ancestral states, and has several display methods,
+ including "Trace Character History" which paints the
+ branches of the tree to show the reconstruction. </font></p>
+ <p><font face="Trebuchet MS">We recommend highly that you examine
+ the <strong>example files</strong> provided in the folder "Ancestral
+ State Examples". The minimal configuration to use with these
+ examples is "Ancestral States" (indicate this configuration
+ under <u><font size="-1">File>Activate/Deactivate Packages>Choose
+ Configuration</font></u>), but you can also leave Mesquite in
+ its default All Installed Modules mode.</font></p>
+ <p align="center"><font face="Trebuchet MS"><img src="images/ancStates.gif"></font></p>
+ <h3><font face="Trebuchet MS"><a name="tch"></a>Trace Character
+ History</font></h3>
+ <p><font face="Trebuchet MS">The Trace Character History facility
+ graphically represents a history of character evolution on the
+ tree. It is available under the Analysis menu of a tree window
+ (e.g., the basic Tree Window, Dependent Tree Window, Mirror Tree
+ Window, Multitree Window). If you select this you will probably
+ be asked for a <strong>source of characters</strong> (e.g., stored
+ characters) and a <strong>reconstruction method</strong> (e.g.,
+ <a href="#parsimony">parsimony</a>, <a href="#likelihood">likelihood</a>,
+ <a href="#scm">stochastic character mapping</a>). (If you have "Use Stored Characters/Matrices by Default" turned on in the Defaults submenu if the File menu, Mesquite won't ask you and will simply use Stored Characters.) The tree will
+ be painted to show ancestral states, and a trace legend will appear.
+ The <strong>Trace Legend</strong> contains an important text area
+ that gives details of the current ancestral state tracing. You
+ can also see details of the reconstruction by switching the window
+ to Text mode using the tabs at its top.</font></p>
+ <p>For categorical and molecular data, you can <strong>change the
+ colors</strong> used in Trace Character by double clicking on
+ the color rectangle in the Trace Legend. Revert to Default Colors
+ is available in the Trace menu.</p>
+ <p>For parsimony reconstructions, any tree drawing style will suffice.
+ For likelihood reconstructions, we recommend the Balls&Sticks
+ style (Drawing menu, Tree Form) with Line Style "Square".
+ This permits you to see the relative likelihoods and branch lengths.
+ For stochastic character mapping, we recommend the Square Tree
+ style in order to display the changes within a branch.</p>
+ <p><font face="Trebuchet MS">The Trace menu gives menu items to
+ control the character history and its display. Some important
+ ones are:</font></p>
+ <p><font face="Trebuchet MS"><strong>Character history source</strong>:
+ Typically you may use Trace Character History to reconstruct the
+ ancestral states of an observed character. Alternatively, you
+ can trace a simulated history ("Simulate Ancestral States").
+ The reconstructed states need not be based on actual data, but
+ could be based on simulated data. "Simulate Ancestral States"
+ shows the "actual" history of character evolution branch
+ by branch as it occured in the <a href="../RandomSimul/RandomSimul.html">simulation</a>,
+ not as it was reconstructed, and thus may show ancestral states
+ that would be unreconstructable, obliterated by subsequent changes.</font></p>
+ <p><font face="Trebuchet MS"><strong>Next, Previous, Choose Character
+ History</strong>: Usually, this will allow you to choose which
+ character to view. You can also scroll through characters using
+ the blue arrows in the trace legend.</font></p>
+ <p><font face="Trebuchet MS"><strong>Trace Display Mode</strong>:
+ With <u><font size="-1">Trace>Trace Display Mode>Shade States</font></u>
+ and <u><font size="-1">Trace>Trace Display Mode>Label States</font></u>
+ you choose whether to see the branches painted, or have the states
+ indicated in labels. If painted, you can also ask that states
+ be indicated by labels by choosing <u><font size="-1">Trace>Label
+ States</font></u>. </font></p>
+ <p><font face="Trebuchet MS">You can also see details of the reconstruction
+ at a node by holding the cursor over the branch. A description
+ of the reconstructed states will appear at the bottom part of
+ the Trace Character Legend. Another method is to use the Text
+ view of the window (touch on the Text tab at the top of the tree
+ window) and scroll down — a text version of the trace should
+ appear.</font></p>
+ <p><strong>Reconstruction Method</strong>: For more details on reconstruction
+ methods, see the sections on <a href="#parsimony">parsimony</a>,
+ <a href="#likelihood">likelihood</a>, and <a href="#scm">stochastic
+ character mapping</a>.</p>
+ <h3><a name="tac"></a>Trace All Characters</h3>
+ <p>Trace All Characters summarizes ancestral state reconstructions
+ of many characters simultaneously. To request it, choose Choose
+ <u><font size="-1">(Tree Window)Analysis>Trace All Characters</font></u>.
+ A text window like that shown below will appear, listing the ancestral
+ states reconstructed at each node for each character. Node numbers
+ show up in red on the tree. (Alternatively, spots showing node
+ numbers in the figure below can be turned on in the Tree Window's
+ Drawing menu by selecting Show Node Numbers.)</p>
+ <p align="center"><img src="images/traceAll.gif" width="630" height="299"></p>
+ <p align="left">By default only the selected nodes are listed. (Nodes
+ can be selected using tools in the Tree Window.) You can request
+ to show all nodes by turning off Show Selected Nodes Only in the
+ Trace_All menu. By default all characters are listed; this can
+ be changed using the Show Selected Characters Only menu item.</p>
+ <p align="left">The ancestral state reconstruction can be controlled
+ in the Trace_All menu of the tree window.</p>
+ <p align="left">The table is either listed by characters or by nodes;
+ you can switch from one to the other using the Rows are Characters
+ menu item</p>
+ <p align="left">Columns in the table in the text window may not
+ appear perfectly aligned, but it is presented as a tab-delimited
+ table, so you should be able to copy the text and paste it in
+ to a text file to read in to your favorite spreadsheet program.</p>
+ <h3><font face="Trebuchet MS"><a name="tcot"></a>Trace Character
+ Over Trees</font></h3>
+ <p>The Trace Character Over Trees facility summarizes<font face="Trebuchet MS">
+ ancestral state reconstructions over a series of trees. This is
+ useful to understand how ancestral state reconstructions vary
+ over a series of trees, for instance if there is uncertainty in
+ the tree. It works for <strong>categorical characters</strong>
+ only. Also, Trace Character Over Trees <strong>does NOT calculate
+ a consensus tree</strong> for you. As with all other analyses
+ in the Tree Window, it works with the tree that is given to it
+ by the Tree Window. If you want to make your summary on a consensus
+ tree, then you need to put the consensus tree into the Tree Window
+ first and then request Trace Character Over Trees.</font></p>
+ <p><font face="Trebuchet MS">Choose <u><font size="-1">(Tree Window)Analysis>Trace
+ Character Over Trees</font></u>. This examines a series of trees,
+ and for each examines a character's ancestral states on that tree.
+ For each node in the tree in the tree window, it attempts to summarize
+ what ancestral states are reconstructed for that same clade in
+ the series of trees (as long as the same clade exists in the other
+ trees). For example, imagine the tree in the tree window includes
+ the clade Tetrapoda. Each of the series of trees is examined,
+ and if that tree includes the clade Tetrapoda, then its reconstructed
+ ancestral states are examined. If the tree doesn't include Tetrapoda,
+ then it is ignored for the sake of summarizing the tetrapod ancestral
+ states. The tree in the tree window is then decorated to summarize
+ what ancestral states are reconstructed for each of the clades.</font></p>
+ <p>Here is an example of Trace Character Over Trees in action:</p>
+ <p align="center"><img src="images/tcot.gif" width="433" height="421"></p>
+ <p>The cursor is over a node (the most recent common ancestor of
+ carinatum and coxendix), and thus the legend shows a summary.
+ The node (i.e., the clade it
+ represents)
+ is
+ present
+ in only 445
+ of the 545 trees examined. For this reason, 100/545 or 18.3%
+ of the pie chart for that node is shown in red, as the node is
+ not present in that fraction of the trees. In addition, 100 of
+ the trees with that node have an equivocal reconstruction at
+ that node; those trees are shown in gray
+ in the pie chart.
+ Of the 345 trees with the node and an unequivocal reconstruction,
+ 321 trees have "isodiametric" reconstructed at the node (shown
+ in white), and in 24 trees have state "slightly trans." at that
+ node (shown as a very thin sliver of green). In this example,
+ "Count Trees with Un...
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