#NEXUS [written Fri Oct 23 14:58:36 EDT 2015 by Mesquite version 3.03 (build 702) at Thomas-MacBook-Air.local/10.217.195.155] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=45; TAXLABELS Anchiornis Anchiornis_huxleyi Caudipteryx Caudipteryx__dongi Protoarchaeopteryx 'Similicaudipteryx STM4-1 ' 'Similicaudipteryx STM22-6' 'NGMC-91A' Sinornithosaurus Tianyuraptor_ Sinocalliopteryx Yixianosaurus_ Sinosauropteryx_1 Sinosauropteryx_2 Microrpator_gui_1 Microrpator_gui_2 Archaeopteryx_Berlin Archaeopteryx_Thermopolis Archaeopteryx_Munich Archaeopteryx_Eichstatt Archaeopteryx_London Archaeopteryx_11th Sapeornis_1 Eoconfuciusornis Jeholornis_1 Confuciusornis Mei_long_1 Mei_long_2 Mahakala Jinfengopteryx Xiaotingia Aurornis Sinovenator Microraptor_hanqingi Jianchangosaurus Sapeornis_2 Yulong_mini Jeholornis_2 Changyuraptor_ Eosinopteryx Zhenyuanlog Sinornithodes 'MOR 246-1 ' 'MPC-D100/971 ' 'MPC-D100/1018 ' ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=9; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2"; CHARSTATELABELS 1 All_90 / NO WAIR_1 WAIR_2, 2 All_70 / NO WAIR_1 WAIR_2, 3 All_50 / NO WAIR_1 WAIR_2, 4 GF_90 / NO WAIR_1 WAIR_2, 5 GF_70 / NO WAIR_1 WAIR_2, 6 GF_50 / NO WAIR_1 WAIR_2, 7 Mod_90 / NO WAIR_1 WAIR_2, 8 Mod_70 / NO WAIR_1 WAIR_2, 9 Mod_50 / NO WAIR_1 WAIR_2 ; MATRIX Anchiornis 110110110 Anchiornis_huxleyi 111111111 Caudipteryx 000000000 Caudipteryx__dongi 000000000 Protoarchaeopteryx 000000000 'Similicaudipteryx STM4-1 '000000000 'Similicaudipteryx STM22-6'000000000 'NGMC-91A' 000000000 Sinornithosaurus 000000100 Tianyuraptor_ 000000000 Sinocalliopteryx 000000000 Yixianosaurus_ 000000000 Sinosauropteryx_1 000000000 Sinosauropteryx_2 000000000 Microrpator_gui_1 111111111 Microrpator_gui_2 111111111 Archaeopteryx_Berlin {1 2}{1 2}1{1 2}{1 2}12{1 2}1 Archaeopteryx_Thermopolis {1 2}{1 2}1{1 2}{1 2}1{1 2}{1 2}1 Archaeopteryx_Munich {1 2}{1 2}1{1 2}{1 2}1{1 2}{1 2}1 Archaeopteryx_Eichstatt {1 2}{1 2}1{1 2}{1 2}1{1 2}{1 2}1 Archaeopteryx_London {1 2}11111{1 2}11 Archaeopteryx_11th {1 2}{1 2}1{1 2}{1 2}12{1 2}1 Sapeornis_1 221{1 2}{1 2}122{1 2} Eoconfuciusornis 22{1 2}221222 Jeholornis_1 22{1 2}221222 Confuciusornis 222222222 Mei_long_1 000000000 Mei_long_2 000000000 Mahakala 000000000 Jinfengopteryx 000100000 Xiaotingia 000000000 Aurornis 110111111 Sinovenator 000000000 Microraptor_hanqingi 111111111 Jianchangosaurus 000000000 Sapeornis_2 2{1 2}1{1 2}{1 2}1{1 2}{1 2}{1 2} Yulong_mini 000000000 Jeholornis_2 22{1 2}2{1 2}{1 2}222 Changyuraptor_ 111100111 Eosinopteryx 111111111 Zhenyuanlog 000000000 Sinornithodes 000000000 'MOR 246-1 ' 000000000 'MPC-D100/971 ' 000000000 'MPC-D100/1018 ' 000000000 ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 9; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 9; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1445626716414; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 4895326335237637358; tell It; setDefaultOrder 0 1 2 3 4 5 6 7 8 9 10 11 12 27 13 14 15 16 17 18 19 20 21 22 23 24 25 26 28 29 30 31 32 33 34 35 37 38 47 39 40 41 42 43 44; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 9141692538799259154; mqVersion 303; checksumv 0 3 889539640 null getNumChars 9 numChars 9 getNumTaxa 45 numTaxa 45 short true bits 2305843009213693959 states 7 sumSquaresStatesOnly 2773.0 sumSquares -4.0582836962161014E20 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1153 689; setLocation 84 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #4895326335237637358 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.DefaultTrees.DefaultTrees; setAssignedID 1159.1405456967358.2911311637813817009; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1053 617; setLocation 84 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; setFixedTaxonDistance 0; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; toggleColorPartition on; toggleColorAssigned off; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setTree '(((((((22,17,20,21,18,19),((23,36),((24,26),(25,38)))),(((((15,16),34),8,10,41,39),29),((1,2),31,40,32,((43,42),(30,((27,28),33)))))),12),(5,((7,6),((3,4),((44,45),37))))),35),((13,14),11));'; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory; tell It; suspend ; setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree; tell It; toggleLabels off; togglePredictions off; toggleGray off; endTell; setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates; tell It; getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed; tell It; setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters; tell It; setDataSet #9141692538799259154; endTell; endTell; setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates; tell It; setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels; toggleMPRsMode off; endTell; toggleShowSelectedOnly off; endTell; setCharacter 8; setMapping 1; toggleShowLegend on; setColorMode 0; toggleWeights on; setInitialOffsetX 4; setInitialOffsetY -224; setLegendWidth 142; setLegendHeight 177; resume ; endTell; endTell; desuppressEPCResponse; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; toggleShow consensusFrequency; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal on; toggleWhiteEdges on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings; tell It; setOn on; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #9141692538799259154 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1053 617; setLocation 84 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.NoColor.NoColor; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges on; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames on; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; toggleShowPaleExcluded off; togglePaleInapplicable on; toggleShowBoldCellText off; toggleAllowAutosize on; toggleColorsPanel off; toggleDiagonal on; setDiagonalHeight 80; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesEditor.StateNamesEditor; tell It; makeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1053 617; setLocation 84 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.categ.StateNamesEditor.StateNamesWindow.ibeam; endTell; rowsAreCharacters on; toggleConstrainChar on; toggleConstrainCharNum 3; togglePanel off; toggleSummaryPanel off; endTell; showWindow; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.charMatrices.SelSummaryStrip.SelSummaryStrip; tell It; showStrip off; endTell; getEmployee #mesquite.categ.SmallStateNamesEditor.SmallStateNamesEditor; tell It; panelOpen true; endTell; endTell; endTell; endTell; end;