#NEXUS [written Mon Dec 05 10:59:49 MST 2016 by Mesquite version 3.03 (build 702) at Macintosh-2.local/10.0.1.3] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=20; TAXLABELS CraImm_GavImm AquSp_PolPol 462AnaSp_BraBer ArdGer_GerCal 493AnaCra_AnaStr 464AnaRhe_BraBer 1546CarZon_CalPus 1486CarZon_CalMau 1482CarZon_CalMin 345CarZon_CalMin 170CarZon_CalFer 224CarMei_CalAlp 19CarMei_CalAlp 375ColBac_StrDec 471DegFul_ButLag 350DegNis_AccNic 276QuaAur_HaeOst 69QuaObt_TriTot 216SaeSte_SteHir 215SaeLoc_StePar ; END; BEGIN CHARACTERS; TITLE 'Matrix in file "Carduiceps phylogeny 12S.nex"'; DIMENSIONS NCHAR=539; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX CraImm_GavImm ACACTTCTCATTACCA--ATTCAGCCCTTTATG----ATAAAAGG-------------GGCTTACTTTCAAATTTGATCCCACCAGTT--------------------------------------------------GTTTCAATTCCATTGTGTGAG----------TTATCTCCTCTAAACTAAAGTACATC--CGATCACTTCCCATAGTCTGCACCTTGACCTGACTTAT------------------------------------------------GTCCCAAAGCAGGGACCTGTAACAGAAGATTTTTAGTCCCAGATGGGCCAAGGGCTAAGATCTCTCAATCTAGCCTTCCGACGGCGATGTACAAAATGT--TTGATTGCGAGGGATAAGGTAAGATATTCGTGCATCTTCGAT---TAAGAACATACTCCTCTG-AATAGTTGATGAAGCCGCCATATACTGTTTAATTTTGGGGAATTATATAACCGTACTCCTTTGTTTTCT---------------------- AquSp_PolPol ACACTAAAAAGAGCCT-TGTTCGATTAAACTTT----ATTATTTT-------------AATCTACTGTTAAATTTTACTTCATATTTT--------------------------------------------------ATTTCAAAAATAAT-----------------TTGAAATTTTTATACTAAAACACATT--TCATC-CAAACTATTATCCGTACCTTGACCTGACTTAA------------------------------------------------CATTTATTAATAATTCAAGAAATAAA-----------------------------------AATTAATCTATTTCTTCCGACGGCGGTGTGCGAAATAA-------ACAAAGTT---TGGTAAGATTTTCGTGCACCATCGATT--ACTAAACATGTCTCTCTA-ATTGGGATTCATAACCGCCATATG--ACTTAATTTTCAATTATT-TAAATCTAATCTATACAATTTTATTACA------------------ 462AnaSp_BraBer ACATAATAAAGAGCCA--ATTCATATATATATT----ATTAAATA--------------TATTACTTTTAAATTTTCCTTCATTAATA--------------------------------------------------ATTTCATATTTAAT-----------------CTGTAATTTTTATTATAAAATACATT--TAATC-TTAAATATTGTCCGTGCCTAGACCTGACTTAT------------------------------------------------AAC--CAACAAGGTTATAGAATAATT-----------------------------------TATTAAAATTATTCTTCAGACGGTGGTGTAAGAAATTT-----------AAAATTTAAGTAAGATAATCGTGCATCATCGGTTT-AATAAACATATTTCTCTA--ATTGGATTTAAAATTGCCATACA--GTTTCAATTTTGAAGAAATTAATCTTTACTCCTTACGTTTTTATATAATATTT------------ ArdGer_GerCal -------------------------------------------------------------TTACTATTAAATTTATACATATATTT----------------------------------------------------------------------------------CATTCACAATTATAAAATAACACATT--AAAAC-TTATTCATATCTTGCACCTTTACCTGACTTAT------------------------------------------------TAT-AAATATTATTAAAGATACAAAC-----------------------------------TTTTCAAAATTATCTTCAGACGGCGGTGTACAAAGTGA--AAATTACAAGAAA---AAGTAAGATATTCGTGTCCTTCGATTT--TATTAACATGTCCCTCTA--ATCAGATATCAAACCGCCATGCA--ACTTAGCTTTTCAAGATTAATAATCTATACTC--------------------------------- 493AnaCra_AnaStr ACATACAGAGTTACAG--ATTCACAAAATTATA----ATAAAAAT-------------TTGTTACTTGTAAATTTTTCTTATTTATT---------------------------------------------------CTTTGCAAGAATAA-----------------AGCTGACTTGAAAAATAAGATACATT--CAACC-CTTCCAATCATTCATGCCTTGACCTGACTTAA------------------------------------------------GAC--------TATATAAGTTAAGGA-----------------------------------GTTTATACAAACTCTTCAGACGGAGGTGTATGAAATGA---AGATTCAATAGA---AGGTAAGATTTTCGTGTAGTATCGATT--AATGAACATACCCCTCTA-CTAGGGCTCATGAATTGCCACTCA--GTTTTATTTTTAGAATTATATAAGTTCTAGTCCATATGTAATAAGTATCCGTAT----------- 464AnaRhe_BraBer ACATGTTAAGTGAACT--ATTCATACAACTATT----CTTAAGAA-------------GTATTACTTGTAAATTTTCCTTACTTACT---------------------------------------------------TTATTGCAAAGTAA-----------------TTCTGTCTTTAATAATAAAGTACATT--CAACC-CTCTTAATAGTCCACGCCTTGACCTGACTTAC------------------------------------------------AAC--------CTCAAAGGTTCAAGA-----------------------------------GCTCTAACGAACTCTTCAGACGGAGGTGTGTGAAATGA---AATTTCAATAAA---AGGTAAGATTCTCGTGAAGTATCGATT--AATAAACATACCTCTCTA--CTATTACTTAAAATTGCCACCCA--ATTTAACTTTTAAACATT-AAAAAGTATAATCCGTATATCTTCTATATCCGTAT----------- 1546CarZon_CalPus ACACTCTTAATATCAC--ATTCAAATCAGTATG----ATAAACTTATAAATTTTG---ATTTTACTTTCAAATTCTTTTTTGGAAATTTT------------------------------------------------TTTCAATTATCCAT-----------------ATTCAATAACATTATTGAAGAACATT--TTCAC-TTAACTATGACCTGCACCTTGACCTGACTTTC------------------------------------------------TCC------TATTTTATTTGAGGACT-------------------------CGATCGATATTTTTTAATTTGACCTATGGACGGTGGTGTACAAAGTTC-------TATAAATT---AAGAAAGATTCTCGCGCACTTTCGAT---TATGGACATTCCTATCTG-AGTTGTTAGAAGAGCCGCCATATT--ATTTGGTTTTTATATAATTTATTAATATCCCGGAGCAAATAATTTTAAAAGA------------- 1486CarZon_CalMau ACACTCTTAATATCAC--ATTCAAATCAGTATG----ATAAACTTATAAATTTTG---ATTTTACTTTCAAATTCTTTTTTGGAAATTTT------------------------------------------------TTTCAATTATCCAT-----------------ATTCAATAACATTATTGAAGAACATT--TTCAC-TTAACTATGACCTGCACCTTGACCTGACTTTC------------------------------------------------TCC------TATTTTATTTGAGGACT-------------------------CGATCGATATTTTTTAATTTGACCTATGGACGGTGGTGTACAAAGTTC-------TATAAATT---AAGAAAGATTCTCGCGCACTTTCGAT---TATGGACATTCCTATCTG-AGTTGTTAGAAGAGCCGCCATATT--ATTTGGTTTTTATATAATTTATTAATATCCCGGAGCAAATAATTTTAAAAGA------------- 1482CarZon_CalMin ACACTCTTAATATCAC--ATTCAAATCAGTATG----ATAAACTTATAAATTTTG---ATTTTACTTTCAAATTCTTTTTTGGAAATTTT------------------------------------------------TTTCAATTATCCAT-----------------ATTCAATAACATTATTGAAGAACATT--TTCAC-TTAACTATGACCTGCACCTTGACCTGACTTTC------------------------------------------------TCC------TATTTTATTTGAGGACT-------------------------CGATCGATATTTTTTAATTTGACCTATGGACGGTGGTGTACAAAGTTC-------TATAAATT---AAGAAAGATTCTCGCGCACTTTCGAT---TATGGACATTCCTATCTG-AGTTGTTAGAAGAGCCGCCATATT--ATTTGGTTTTTATATAATTTATTAATATCCCGGAGCAAATAATTTTAAAAGA------------- 345CarZon_CalMin ACACTCTTAATATCAT--ATTCAAATCAGTATG----ATAAACTTATAAGTTTTG---ATTTTACTTTCAAATTCTTTTTTGGAAATTTT------------------------------------------------TTTCAATTATCCAT-----------------ATTCAATAACATTATTGAAGAACATT--TTCAC-TTAACTATAACCTGCACCTTGACCTGACTTTC------------------------------------------------TCC------TATTTGATTTGAGGACT-------------------------CGATCGATATTTTTTAATTTGACCTATGGACGGTGGTGTACAAAGTTC-------TATAAATT---AAGAAAGATTCTCGCGCACTTTCGAT---TATGGACATTCCTATCTG-AGTTGTTAGAAGAGCCGCCATATT--ATTTGGTTTTTATATAATTTATTAATATCCCGGAGCATATAATTTTAAAAGA------------- 170CarZon_CalFer ACACTCTTAATATCAT--ATTCAAATCAGTATG----ATAAACTTATAAGTTTTG---ATTTTACTTTCAAATTCTTTTTTGGAAATTTT------------------------------------------------TTTCAATTATCCAT-----------------ATTCAATAACATTATTGAAGAACATT--TTCAC-TTAACTATAACCTGCACCTTGACCTGACTTTC------------------------------------------------TCC------TATTTGATTTGAGGACT-------------------------CGATCGATATTTTTCAATTTGACCTATGGACGGTGGTGTACAAAGTTC-------TATAAATT---AAGAAAGATTCTCGCGCACTTTCGAT---TATGGACATTCCTATCTG-AGTTGTTAGAAGAGCCGCCATATT--ATTTGGTTTTTATATAATTTATTAATATCCCGGAGCATATAATTTTAAAAGA------------- 224CarMei_CalAlp ACACTCTGAATATCAT--ATTCAAACCAGTATA----ATAAACTT-----TTTTG---ATTTTACTTTCAAATTCTTTTTTGAATCTTTTTCAAT-------------------------------------------TTTTTTTTACTCAT-----------------ATTCAATAACATTATTGAAGAACATCAACACAC-TTAATTATAACCTGCACCTTGACCTGACTTCC------------------------------------------------CCCTAAAATTATATCAATAAAGGACT-------------------------AGACCGATATTTTTAAATCCGATCTTTGGACGGTGGTGTACAAAGTAA-------TATAAATT---AAGAAAGATTTTCGCGCACCTTCGAT---TACGAACATTCCTATCTG-AGATGTTAGTAGAGCCGCCATATT--ATTTGGTTTATAATTAAATTATTAGTGTCCCGGAGTCACAAAATTAATACTAAAAGA-------- 19CarMei_CalAlp ACACTCTGAATATCAT--ATTCAAACCAGTATA----ATAAACTT-----TTTTG---ATTTTACTTTCAAATTCTTTTTTGAATCTTTTTCAAT-------------------------------------------TTTTTTTTACTCAT-----------------ATTCAATAACATTATTGAAGAACATCAACACAC-TTAATTATAACCTGCACCTTGACCTGACTTCC------------------------------------------------CCCTAAAATTATATTAATAAAGGACT-------------------------AGACCGATATTTTTAAATCCGATCTTTGGACGGTGGTGTACAAAGTAA-------TATAAATT---AAGAAAGATTTTCGCGCACCTTCGAT---TACGAACATTCCTATCTG-AGATGTTAGTAGAGCCGCCATATT--ATTTGGTTTATAATTAAATTATTAGTGTCCCGGAGTCACAAAATTAATACTAAAAGA-------- 375ColBac_StrDec ACATTTTTTTGGTATA-AATTCAGATTTTTTTT----ATTAAAAA-------------TTCTTACTTTCAAATTCTTCTTCTAGAGAGTA------------------------------------------------TTTCAACCCCCTTT-----------------CCGTTTTGTTTTTAGGGAAATGCATT--TTTTC-CAACCCATTGTCTGCACCTT-ACCTGACTTAT------------------------------------------------TTTCGCAAGATGAGGGGGAAATAAGA----------------------------GTTCATTTTTTACAATGACCCTTCAGACGGCGGTGTACAGGATGG----GTTTCCAGAGT---TGGAAAGATCTTCGTGTGGTTTCGTTT--TAAAAACACATTTTTCTG--AAAATAAAAAAAACCGCCATTCT--GGATAGTTTTCAACTGTACTCTACTCCCAAACTGTTTATTTACTCCTA----------------- 471DegFul_ButLag ACGTCTGTCGTTGCAG--GCTCGATTACTTTCA----AGCAGGGATTGAATTCTAACTCCTTTACTTATAAATTCTATCTACCAAAGGCACCTTTTGTACTACTCTGGAGCCATGTCTCTATCCATTAGTACTTGAGCATACATATAGTATA-----------------ATGACTTACTTACATAGGAATACACT--ACTAC-TGTCCTATAGTCTGCACCTAAACTTAACTTATAGGTCTATAGTTATAAAGATTGGTACATCAAAGATGCTATTA------TACCTTACACATTTATTACAACCAAC-----AACGATATTACCTTGAGAGAAAACGGATCATCTACCTCCGTATATTCAGATAGCGGTGTACAAGATGGTCCTATATCTAAAGA---CAGTAAGAAGTCTGTGCTGCTTCACT---CACGTGCATATCCCTCTA--TCTTGCCGACTGACCGCCATGTT--CTATATTTATTCAGCTCACTATATTTTACCTACTGTACCTACATCTACTCCTCT----------- 350DegNis_AccNic ACGTCTGTCGTTGCAATGTTTTACACGATTATTTCAAGCAAGGATTGAGATCTCAATAGCTTTACTTATAAATTCTATGTACCTTGGACACTTTTGCACCCTTAGTCCCTAAAAACGATCTGAAAGACATCTATAAGGATTTTACTCACATTCTAAGACACCCCTCGTATTGTCACACTTACACTGGAATACACT--ACTAC-TCCCCTATCATCTGCACCTAAACTTAACTTACAGGCCCTATACGATATAATTGCTCTAGCCAGAGGTTATTTTCCCTACCGCCTTTACATTTTTACATCCATGATACAACATTTACGGTGTAACTTAGGACAGGTAGAACGATCTCCTTCTACATTTCAGATAGCGGTGTACAAGATGGGCATGATTCGAAAGA---GAGTAAGAAATATGTGCAGTTTCATT---CACGTGCATATCCCTCTA-T-CCTGCCGACAGACCGCCATGTT--CTCTGTTTGCTCGGCTCAAGACACCTTTTACCTACTAGACCTTTCCTGTATTTTGGCCCTCCTCT 276QuaAur_HaeOst ACATCTCTCAGAGCTT--TTTCCCCCAAGCTCCCTTAACTAACAA---------------GGTACTTCTAAATTCTTTTTCCCCCTTCTCCT----------------------------------------------ACTCGAAGGGGTCC-----------------ACACAACATCCAACTAGAAACACATC--TTTTC-TCTCCCTTCTCCTGCACCTTTACTTGCCTTAC------------------------------------------------TTC------CTTATCAAGAAATCAGA-----------------------------------GAGACACTCCCCCTTTCAGACAGCAGTGGACAAAGTTTCCTCCTTTCGGAAAGGAGAGAAGAGTAAATTGTGCATCTTCATTTTCCAAACACATGTTTCTCTAGAAAGAGATAAGAGACCGCCAGGAA--TAGTTCTTTCAGAAGAATCCTAATCCGACCATTTTCGAGA------------------------- 69QuaObt_TriTot ACGTACCTCAGAGCCC-CATTCAATAGGGGCTT----GTAAACCC-------------CATTTACTTCTAAATTCTCTCCCCTTACCTC-------------------------------------------------ATTTAAAAAGGTAA-----------------ATGAATCCTTCTGATTGGAGCACACA--CTTTCAACACCCATAGCCTACACGTGTGCTTGCCTTAC------------------------------------------------TCC------CTTCTGAGGGGGTAAGA-----------------------------------AGTCCACGACTTCTTTCAGACAGTGGTGTGCAAAGTGG-GTTATTCCAGGGTG---TGAAGGGTAATTCGTGCAGATTCGATAT-ACAGGGCATGCCCCTCTA--GTTAGGTGAGGTACCGCCAGAGA--CTATTCTTTCCAAAATTAATTTATCTCCGTAAGAAGTTTTTACTCCTTC---------------- 216SaeSte_SteHir ACATCCTCTAGAGCGGTGGTTCAGGTGAGTATT---AGTAAACCC-------------CCCTTACTTCTAAATTCTCTAAAAGGGAAAA-------------------------------------------------ATTTTCACTAATCC-----------------AAGAATCAATTAGACTGGCCTACAC---CATTC-CTCTCCATATCCTACACTTTTACTTGCCTTAA------------------------------------------------GTC------CTTTTGAGGGAGTAGGA----------------------------------ATAATTCTCTATTTCTTCAGACAGCAGTGGGTAGGGTGAAATATATCTTAGAGA---GGACTAATCTGGCGCGCAGATTCGTT---TAGAGGCATAGGTCTCTA--GTTAGATAGAGGACCGCCAGTAG--AAATGTTTTTCC---TTTCGTACTCTAAATGTCTTACTTGTTTTCTTT----------------- 215SaeLoc_StePar ACATCTTCTAGAGCTT-AATTCAGACAAGTATG----GTAAACTT------------AGACTTACTTCTAAATTCTCTCTGAGAAAGA--------------------------------------------------AATTTCATTTCTCT-----------------TTAAATTAATTAAATTGGCCTACACG--TTTTC-CTTTCCATTCCCTACACTTTTACTTGCCTTAT------------------------------------------------CTC--------TTCAAGAGAGGAGGA-----------------------------------GGTAATTTTACCTCTTCAGACAGTGGTGGGTAAAGTGAAATATATCTTTTAAA---GGAGAAATCTAGCGCGCAGATTCGTT---TAGAGGCATAGGCCTCTA--GGCAGGTAGAAGACCGCCAGTAA--AAATCCTTTTCCCAAAAG-GTACTCTGAATGTCCGATTACGTTTCCTT----------------- ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED (CHARACTERS = 'Matrix in file "Carduiceps phylogeny 12S.nex"') = unord: 1 - 539; END; BEGIN CODONS; CODESET * UNTITLED (CHARACTERS = 'Matrix in file "Carduiceps phylogeny 12S.nex"') = universal: 1 - 539; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED (CHARACTERS = 'Matrix in file "Carduiceps phylogeny 12S.nex"') = 'Jukes-Cantor': 1 - 539; END; BEGIN TREES; Title NJ; LINK Taxa = Taxa; TRANSLATE [0] 1 CraImm_GavImm, [1] 2 AquSp_PolPol, [2] 3 462AnaSp_BraBer, [3] 4 ArdGer_GerCal, [4] 5 493AnaCra_AnaStr, [5] 6 464AnaRhe_BraBer, [6] 7 1546CarZon_CalPus, [7] 8 1486CarZon_CalMau, [8] 9 1482CarZon_CalMin, [9] 10 345CarZon_CalMin, [10] 11 170CarZon_CalFer, [11] 12 224CarMei_CalAlp, [12] 13 19CarMei_CalAlp, [13] 14 375ColBac_StrDec, [14] 15 471DegFul_ButLag, [15] 16 350DegNis_AccNic, [16] 17 276QuaAur_HaeOst, [17] 18 69QuaObt_TriTot, [18] 19 216SaeSte_SteHir, [19] 20 215SaeLoc_StePar; TREE NJ = (19:0.27944809,20:0.18231266,(18:0.61252971,(17:0.88899563,((15:0.9745486,16:0.26979836)0.993000:1.17885796,((4:1.16080447,(((5:0.43069393,6:0.26490484)0.999000:0.70671844,3:0.45441285)0.796000:0.12239144,2:0.76647881)0.904000:0.39176156)0.636000:0.12430305,(14:1.01743117,(1:0.41859008,((12:0.0031894,13:0.00000052)0.730000:0.10690729,((10:0.00000021,11:0.00333909)0.791000:0.01598483,(7:0.00000001,(8:0.00000001,9:0.00000001)0.000000:0.00000001)0.000000:0.00113237)0.854000:0.14320973)1.000000:1.42710625)0.745000:0.29718719)0.733000:0.25285858)0.936000:0.55965034)0.928000:0.57551184)0.332000:0.17534583)0.996000:0.86331813); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1480960789540; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3035729544840539793; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 1698411072966784172; mqVersion 303; checksumv 0 3 922487426 null getNumChars 539 numChars 539 getNumTaxa 20 numTaxa 20 short true bits 15 states 15 sumSquaresStatesOnly 187938.0 sumSquares 187938.0 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 1382 719; setLocation 8 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #3035729544840539793 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 3434.1480960740041.5463684712004115063; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1282 647; setLocation 8 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareLineTree.SquareLineTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; setFixedTaxonDistance 0; endTell; setEdgeWidth 4; showEdgeLines on; orientUp; 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 off; toggleColorAssigned on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; 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 off; 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 #1698411072966784172 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1282 647; setLocation 8 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; 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 off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; toggleShowPaleExcluded off; togglePaleInapplicable on; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; 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.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;