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usr/share/
usr/share/mesquite/
usr/share/mesquite/examples/
usr/share/mesquite/examples/Ancestral_States/
usr/share/mesquite/examples/Ancestral_States/01-DataMatrix.nex
usr/share/mesquite/examples/Ancestral_States/02-TreeWindow.nex
usr/share/mesquite/examples/Ancestral_States/03-TraceCharPars.nex
usr/share/mesquite/examples/Ancestral_States/03b-LiveUpdate.nex
usr/share/mesquite/examples/Ancestral_States/04-Equivocal.nex
usr/share/mesquite/examples/Ancestral_States/05-TreeForm.nex
usr/share/mesquite/examples/Ancestral_States/06-ParsimonyModels.nex
usr/share/mesquite/examples/Ancestral_States/07-EditingParsModels.nex
usr/share/mesquite/examples/Ancestral_States/08-ParsimonyMacClade.nex
usr/share/mesquite/examples/Ancestral_States/09-Continuous.nex
usr/share/mesquite/examples/Ancestral_States/10-PlotTree.nex
usr/share/mesquite/examples/Ancestral_States/11-TraceCharMLE.nex
usr/share/mesquite/examples/Ancestral_States/11b-TextView.nex
usr/share/mesquite/examples/Ancestral_States/12-Mk1Likelihood.nex
usr/share/mesquite/examples/Ancestral_States/13-AsymmLikelihood.nex
usr/share/mesquite/examples/Ancestral_States/14-AsymmEstLikelihood.nex
usr/share/mesquite/examples/Ancestral_States/15-Mk1AsymmCompare.nex
usr/share/mesquite/examples/Ancestral_States/15a-estimatingParameters.nex
usr/share/mesquite/examples/Ancestral_States/15aa-xiphLikelihood.nex
usr/share/mesquite/examples/Ancestral_States/15ab-xiphStochCharMap.nex
usr/share/mesquite/examples/Ancestral_States/15b-estimatingParameters.nex
usr/share/mesquite/examples/Ancestral_States/15b1-estimatingParameters.nex
usr/share/mesquite/examples/Ancestral_States/15b2-estimatingParameters.nex
usr/share/mesquite/examples/Ancestral_States/16b-BranchLengths.nex
usr/share/mesquite/examples/Ancestral_States/16c-TraceAllChars.nex
usr/share/mesquite/examples/Ancestral_States/17-TraceOverTrees.nex
usr/share/mesquite/examples/Ancestral_States/17a-TraceOverTrees.nex
usr/share/mesquite/examples/Ancestral_States/18-TraceOverResolutions.nex
usr/share/mesquite/examples/Ancestral_States/19-likelihoodTot.nex
usr/share/mesquite/examples/Ancestral_States/20-likelihoodToT.nex
usr/share/mesquite/examples/Ancestral_States/21-likelihoodTot.nex
usr/share/mesquite/examples/Basic_Examples/
usr/share/mesquite/examples/Basic_Examples/basic_operation/
usr/share/mesquite/examples/Basic_Examples/basic_operation/01-basics.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/02-standardMenus.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/03-characterMatrices.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/04-treeWindow.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/04a-windowTabs.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/05-windowModes.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/06-helpMenu.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/07-moreHelp.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/08-logFile.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/09-windowFonts.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/10-scripting.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/11-newFile.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/12-fileFormats.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/13-blockOfTaxa.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/13-matrix.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/13-trees.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/14-included.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/15-annotations.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/16-webLinks.nex
usr/share/mesquite/examples/Basic_Examples/basic_operation/fubonidianImages/
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usr/share/mesquite/examples/Basic_Examples/basic_operation/fubonidianImages/fubonidiaKnobble.gif
usr/share/mesquite/examples/Basic_Examples/basic_operation/fubonidianImages/fubonidiaZibinator.gif
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usr/share/mesquite/examples/Basic_Examples/basic_operation/fubonidianImages/zorabynyxZibinator.gif
usr/share/mesquite/examples/Basic_Examples/characters/
usr/share/mesquite/examples/Basic_Examples/characters/01-characters.nex
usr/share/mesquite/examples/Basic_Examples/characters/02-newMatrix.nex
usr/share/mesquite/examples/Basic_Examples/characters/03-newMatrix.nex
usr/share/mesquite/examples/Basic_Examples/characters/04-characterLists.nex
usr/share/mesquite/examples/Basic_Examples/characters/05-dataEditing.nex
usr/share/mesquite/examples/Basic_Examples/characters/06-fill.nex
usr/share/mesquite/examples/Basic_Examples/characters/07-dataEditing.nex
usr/share/mesquite/examples/Basic_Examples/characters/08-addDelete.nex
usr/share/mesquite/examples/Basic_Examples/characters/09-copyPaste.nex
usr/share/mesquite/examples/Basic_Examples/characters/10-names.nex
usr/share/mesquite/examples/Basic_Examples/characters/11-viewingStyles.nex
usr/share/mesquite/examples/Basic_Examples/characters/11a-annotations.nex
usr/share/mesquite/examples/Basic_Examples/characters/12-continuous.nex
usr/share/mesquite/examples/Basic_Examples/characters/13-continuousItems.nex
usr/share/mesquite/examples/Basic_Examples/characters/14-partitions.nex
usr/share/mesquite/examples/Basic_Examples/characters/15-selecting.nex
usr/share/mesquite/examples/Basic_Examples/characters/16-charSources.nex
usr/share/mesquite/examples/Basic_Examples/characters/17-charSources.nex
usr/share/mesquite/examples/Basic_Examples/characters/fubonidianImages/
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usr/share/mesquite/examples/Basic_Examples/characters/fubonidianImages/fubonidiaZibinator.gif
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usr/share/mesquite/examples/Basic_Examples/characters/fubonidianImages/snorolopaKnobble.gif
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usr/share/mesquite/examples/Basic_Examples/characters/fubonidianImages/zorabynyxGizmoid.gif
usr/share/mesquite/examples/Basic_Examples/characters/fubonidianImages/zorabynyxKnobble.gif
usr/share/mesquite/examples/Basic_Examples/characters/fubonidianImages/zorabynyxZibinator.gif
usr/share/mesquite/examples/Basic_Examples/charts/
usr/share/mesquite/examples/Basic_Examples/charts/01-charts.nex
usr/share/mesquite/examples/Basic_Examples/charts/02-histogram.nex
usr/share/mesquite/examples/Basic_Examples/charts/03-scattergram.nex
usr/share/mesquite/examples/Basic_Examples/charts/04-scattergram.nex
usr/share/mesquite/examples/Basic_Examples/continuous/
usr/share/mesquite/examples/Basic_Examples/continuous/01-editContinuous.nex
usr/share/mesquite/examples/Basic_Examples/continuous/03-trace.nex
usr/share/mesquite/examples/Basic_Examples/continuous/04-branchLengths.nex
usr/share/mesquite/examples/Basic_Examples/continuous/05-treeSearch.nex
usr/share/mesquite/examples/Basic_Examples/continuous/06-sim.nex
usr/share/mesquite/examples/Basic_Examples/continuous/07-mirrorTree.nex
usr/share/mesquite/examples/Basic_Examples/continuous/08-plotTree.nex
usr/share/mesquite/examples/Basic_Examples/continuous/09-plotTreeSim.nex
usr/share/mesquite/examples/Basic_Examples/introduction.nex
usr/share/mesquite/examples/Basic_Examples/taxa/
usr/share/mesquite/examples/Basic_Examples/taxa/01-taxa.nex
usr/share/mesquite/examples/Basic_Examples/taxa/02-addingDeleting.nex
usr/share/mesquite/examples/Basic_Examples/taxa/03-partitions.nex
usr/share/mesquite/examples/Basic_Examples/taxa/04-partitions.nex
usr/share/mesquite/examples/Basic_Examples/taxa/05-selecting.nex
usr/share/mesquite/examples/Basic_Examples/taxa/06-selecting.nex
usr/share/mesquite/examples/Basic_Examples/taxa/07-selecting.nex
usr/share/mesquite/examples/Basic_Examples/taxa/08-multipleBlocks.nex
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/01-editingTrees.nex
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/02-editingTrees.nex
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/03-editingTrees.nex
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/04-branchLengths.nex
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/05-branchColorNames.nex
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/06-branchSelection.nex
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/07-storedTrees.nex
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/08-listOfTrees.nex
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/09-treeBlocks.nex
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/10-externalTrees.nex
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/10-treeFile.nex
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/11-treeSources.nex
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/12-treeSources.nex
usr/share/mesquite/examples/Basic_Examples/tree_manipulation/13-instability.nex
usr/share/mesquite/examples/Basic_Examples/tree_viewing/
usr/share/mesquite/examples/Basic_Examples/tree_viewing/01-treeWindow.nex
usr/share/mesquite/examples/Basic_Examples/tree_viewing/02-treeForm.nex
usr/share/mesquite/examples/Basic_Examples/tree_viewing/03-drawingSize.nex
usr/share/mesquite/examples/Basic_Examples/tree_viewing/04-moreTreeForms.nex
usr/share/mesquite/examples/Basic_Examples/tree_viewing/05-moreTreeForms.nex
usr/share/mesquite/examples/Basic_Examples/tree_viewing/06-printingTrees.nex
usr/share/mesquite/examples/Basic_Examples/tree_viewing/07-dependentWindow.nex
usr/share/mesquite/examples/Basic_Examples/tree_viewing/08-mirrorTree.nex
usr/share/mesquite/examples/Basic_Examples/tree_viewing/09-multiTrees.nex
usr/share/mesquite/examples/Basic_Examples/tree_viewing/10-multiTrees.nex
usr/share/mesquite/examples/Character_Simulations/
usr/share/mesquite/examples/Character_Simulations/00-introduction.nex
usr/share/mesquite/examples/Character_Simulations/01-modelTree.nex
usr/share/mesquite/examples/Character_Simulations/02-gammaTest.nex
usr/share/mesquite/examples/Character_Simulations/03-TestingTreeStructure.nex
usr/share/mesquite/examples/Character_Simulations/templates/
usr/share/mesquite/examples/Character_Simulations/templates/GIGTRTest.template
usr/share/mesquite/examples/Character_Simulations/templates/GTRTest.template
usr/share/mesquite/examples/Character_Simulations/templates/GammaInvarTest.template
usr/share/mesquite/examples/Character_Simulations/templates/GammaTest.template
usr/share/mesquite/examples/Character_Simulations/templates/TiTvTest.template
usr/share/mesquite/examples/Coalescence/
usr/share/mesquite/examples/Coalescence/00-introduction.nex
usr/share/mesquite/examples/Coalescence/01-coalescence.nex
usr/share/mesquite/examples/Coalescence/02-coalescence2.nex
usr/share/mesquite/examples/Coalescence/03-coalescenceDepth.nex
usr/share/mesquite/examples/Coalescence/04-associations.nex
usr/share/mesquite/examples/Coalescence/05-twoPopulations.nex
usr/share/mesquite/examples/Coalescence/06-twoPopulations2.nex
usr/share/mesquite/examples/Coalescence/08-fluctuating.nex
usr/share/mesquite/examples/Coalescence/09-genesInSpecies.nex
usr/share/mesquite/examples/Coalescence/10-speciesTreeSearch.nex
usr/share/mesquite/examples/Coalescence/11-geneInSpecies2.nex
usr/share/mesquite/examples/Coalescence/outOfAfrica/
usr/share/mesquite/examples/Coalescence/outOfAfrica/01-outOfAfrica.nex
usr/share/mesquite/examples/Coalescence/outOfAfrica/02-outOfAfrica.nex
usr/share/mesquite/examples/Coalescence/outOfAfrica/03-outOfAfrica.nex
usr/share/mesquite/examples/Coalescence/outOfAfrica/04-outOfAfrica.nex
usr/share/mesquite/examples/Coalescence/tutorial/
usr/share/mesquite/examples/Coalescence/tutorial/01-associationsHow1.nex
usr/share/mesquite/examples/Coalescence/tutorial/02-associationsHow2.nex
usr/share/mesquite/examples/Coalescence/tutorial/02b-associationsHow2.nex
usr/share/mesquite/examples/Coalescence/tutorial/03-associationsHow3.nex
usr/share/mesquite/examples/Coalescence/tutorial/04-associationsHow4.nex
usr/share/mesquite/examples/Correlation/
usr/share/mesquite/examples/Correlation/00-introduction.nex
usr/share/mesquite/examples/Correlation/00a-FelsensteinsContrasts.nex
usr/share/mesquite/examples/Correlation/00b-pagel94Hominids.nex
usr/share/mesquite/examples/Correlation/00c-pairwiseIntro.nex
usr/share/mesquite/examples/Correlation/01-pairwise.nex
usr/share/mesquite/examples/Correlation/02-pairwiseFig2(1).nex
usr/share/mesquite/examples/Correlation/03-pairwiseFig2(2).nex
usr/share/mesquite/examples/Correlation/04-pairwiseFig2(3).nex
usr/share/mesquite/examples/Correlation/05-pairwiseFig3-6(1).nex
usr/share/mesquite/examples/Correlation/06-pairwiseFig3-6(2).nex
usr/share/mesquite/examples/Correlation/07-pairwiseFig3-6(3).nex
usr/share/mesquite/examples/Diversification/
usr/share/mesquite/examples/Diversification/00-introduction.nex
usr/share/mesquite/examples/Diversification/01-lineagesThroughTime.nex
usr/share/mesquite/examples/Diversification/02-speciationExtinctionRates.nex
usr/share/mesquite/examples/Diversification/03-sisterDiversification.nex
usr/share/mesquite/examples/Diversification/04-BiSSEViewer.nex
usr/share/mesquite/examples/Diversification/05-BiSSENetViewer.nex
usr/share/mesquite/examples/Diversification/06-BiSSEtrees.nex
usr/share/mesquite/examples/Diversification/07-contTreeSim.nex
usr/share/mesquite/examples/Diversification/08-binaryTreeSim.nex
usr/share/mesquite/examples/Introduction.nex
usr/share/mesquite/examples/Molecular/
usr/share/mesquite/examples/Molecular/00-introduction.nex
usr/share/mesquite/examples/Molecular/01-gcContentChart.nex
usr/share/mesquite/examples/Molecular/02-gcContentMatrix.nex
usr/share/mesquite/examples/Molecular/03-gcContentBirdsEye.nex
usr/share/mesquite/examples/Molecular/03a-cytochromeB.nex
usr/share/mesquite/examples/Molecular/04-gcContentTaxa.nex
usr/share/mesquite/examples/Molecular/05-gcContentTaxaExons.nex
usr/share/mesquite/examples/Molecular/06-cytochromeB.nex
usr/share/mesquite/examples/Molecular/07-cytochromeBHydro.nex
usr/share/mesquite/examples/Molecular/08-cytochromeBlinked.nex
usr/share/mesquite/examples/Molecular/09-cytochromeBscatter.nex
usr/share/mesquite/examples/Multivariate_Continuous/
usr/share/mesquite/examples/Multivariate_Continuous/00-introduction.nex
usr/share/mesquite/examples/Multivariate_Continuous/01-wingsPlot.nex
usr/share/mesquite/examples/Multivariate_Continuous/02-wingsPCA.nex
usr/share/mesquite/examples/Multivariate_Continuous/03-wingsCVA.nex
usr/share/mesquite/examples/Multivariate_Continuous/04-anoles.nex
usr/share/mesquite/examples/Multivariate_Continuous/05-anoles.nex
usr/share/mesquite/examples/Multivariate_Continuous/06-anoles.nex
usr/share/mesquite/examples/Multivariate_Continuous/07-anoles.nex
usr/share/mesquite/examples/Multivariate_Continuous/08-anoles.nex
usr/share/mesquite/examples/Multivariate_Continuous/09-pcaSim.nex
usr/share/mesquite/examples/Multivariate_Continuous/10-pcaLiveSim.nex
usr/share/mesquite/examples/Multivariate_Continuous/11-cvaLiveSim.nex
usr/share/mesquite/examples/Multivariate_Continuous/12-epca.nex
usr/share/mesquite/examples/Multivariate_Continuous/13-epca.nex
usr/share/mesquite/examples/Multivariate_Continuous/14-epca.nex
usr/share/mesquite/examples/Multivariate_Continuous/15-epca.nex
usr/share/mesquite/examples/Multivariate_Continuous/16-epcaLiveSim.nex
usr/share/mesquite/examples/Multivariate_Continuous/17-landmarks.nex
usr/share/mesquite/examples/Multivariate_Continuous/18-landmarks.nex
usr/share/mesquite/examples/Multivariate_Continuous/19-landmarks.nex
usr/share/mesquite/examples/Multivariate_Continuous/20-landmarks.nex
usr/share/mesquite/examples/Multivariate_Continuous/epca/
usr/share/mesquite/examples/Multivariate_Continuous/epca/Image1.gif
usr/share/mesquite/examples/Multivariate_Continuous/epca/Image2.gif
usr/share/mesquite/examples/Multivariate_Continuous/fish/
usr/share/mesquite/examples/Multivariate_Continuous/fish/blue.gif
usr/share/mesquite/examples/Multivariate_Continuous/fish/one.gif
usr/share/mesquite/examples/Multivariate_Continuous/fish/red.gif
usr/share/mesquite/examples/Multivariate_Continuous/fish/two.gif
usr/share/mesquite/examples/Other_Examples/
usr/share/mesquite/examples/Other_Examples/ConcatenatingMatrices/
usr/share/mesquite/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/
usr/share/mesquite/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/01.concatenatingMatrices.nex
usr/share/mesquite/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/02.concatenatingMatrices.nex
usr/share/mesquite/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/03.concatenatingMatrices.nex
usr/share/mesquite/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/04.concatenatingMatrices.nex
usr/share/mesquite/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/05.concatenatingMatrices.nex
usr/share/mesquite/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/06.concatenatingMatrices.nex
usr/share/mesquite/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/07.mergedMatrix.nex
usr/share/mesquite/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/otherGeneMatrix.nex
