#NEXUS [written Thu Oct 13 15:43:19 CDT 2011 by Mesquite version 2.72 (build 528) at agustin-jimenezs-imac.local/131.230.62.194] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=29; TAXLABELS Ascaris_suum Toxocara_cati Anisakis_simplex Strongyluris_similis Heterakis_gallinarum Ascaridia_galli Aspidodera_scoleciformis_La_Pampa Aspidodera_scoleciformis__Limouy Aspidodera_binansata Paraspidodera_uncinata_La_Paz Paraspidodera_uncinata_Morelos Paraspidodera_uncinata_Tlaxcala Paraspidodera_uncinata_Cobo Paraspidodera_uncinata_Santa_Cruz Nematomystes_scapteromi_Balandra Nematomystes_scapteromi_La_Balandra Nematomystes_rodentiphilus Aspidodera_raillieti_Guatemala Aspidodera_raillieti_Apa2 Aspidodera_raillieti_Apa3 Aspidodera_raillieti_Apa5 Aspidodera_sogandaresi_Texas Aspidodera_sogandaresi_Nayarit Aspidodera_sp._Nayarit1 Aspidodera_sp._Nayarit Aspidodera_sp._Temazcal Lauroia_bolivari_El_Beni Lauroia_trinidadensis_Temazcal Lauroia_trinidadensis_Yucatan ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=52; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2"; MATRIX Ascaris_suum 00???00??????11?11000?100?0???????00??0????0????10?? Toxocara_cati 00???00??????11?11000?101?0???????00??0????0????00?? Anisakis_simplex 10??0000?????11?11000?100?0???????00??0????0????00?? Strongyluris_similis 00??0000???1110201000010011100?1?0?????????011000001 Heterakis_gallinarum 00??000?????110201001010000102111000100??01011010001 Ascaridia_galli 0000001101011112010110100000020100001001001011000001 Aspidodera_scoleciformis_La_Pampa 1100111111000102100100001010110011110010110000001110 Aspidodera_scoleciformis__Limouy 1100111111000102100100001010110011110010110000001110 Aspidodera_binansata 1111111110121102100101011001010011110000110000011110 Paraspidodera_uncinata_La_Paz 1100110000111102100101011111000011110110110000101110 Paraspidodera_uncinata_Morelos 1100110000111102100101011111000011110110110000101110 Paraspidodera_uncinata_Tlaxcala 1100110000111102100101011111000011110110110000101110 Paraspidodera_uncinata_Cobo 1100110000111102100101011111000011110110110000101110 Paraspidodera_uncinata_Santa_Cruz 1100110000111102100101011111000011110110110000101110 Nematomystes_scapteromi_Balandra 1111101001101102100101001101101100100101001111011101 Nematomystes_scapteromi_La_Balandra 1111101001101102100101001101101100100101001111011101 Nematomystes_rodentiphilus 1111101001111102101101001101101100100101001111011101 Aspidodera_raillieti_Guatemala 1111101111121102100101001000101100100101001111011101 Aspidodera_raillieti_Apa2 1111101111121102100101001000101100100101001111011101 Aspidodera_raillieti_Apa3 1111101111121102100101001000101100100101001111011101 Aspidodera_raillieti_Apa5 1111101111121102100101001000101100100101001111011101 Aspidodera_sogandaresi_Texas 111111111112210110010101101??01001100000110001111110 Aspidodera_sogandaresi_Nayarit 111111111112210110010101101??01001100000110001111110 Aspidodera_sp._Nayarit1 1111111111121102100101001001001101100000100000111110 Aspidodera_sp._Nayarit 1111111111121102100101001001001101100000100000111110 Aspidodera_sp._Temazcal 1111111111121102100101001001001101100000100000111110 Lauroia_bolivari_El_Beni 100010000011001?111011100000001100001101001011011101 Lauroia_trinidadensis_Temazcal 100010011100001?111011100000001100001101001011011101 Lauroia_trinidadensis_Yucatan 100010011100001?111011100000001100001101001011011101 ; END; BEGIN TREES; Title 'Trees from "AspidoMorphOCT.nex"'; LINK Taxa = Taxa; TRANSLATE 1 Ascaris_suum, 2 Toxocara_cati, 3 Anisakis_simplex, 4 Strongyluris_similis, 5 Heterakis_gallinarum, 6 Ascaridia_galli, 7 Aspidodera_scoleciformis_La_Pampa, 8 Aspidodera_scoleciformis__Limouy, 9 Aspidodera_binansata, 10 Paraspidodera_uncinata_La_Paz, 11 Paraspidodera_uncinata_Morelos, 12 Paraspidodera_uncinata_Tlaxcala, 13 Paraspidodera_uncinata_Cobo, 14 Paraspidodera_uncinata_Santa_Cruz, 15 Nematomystes_scapteromi_Balandra, 16 Nematomystes_scapteromi_La_Balandra, 17 Nematomystes_rodentiphilus, 18 Aspidodera_raillieti_Guatemala, 19 Aspidodera_raillieti_Apa2, 20 Aspidodera_raillieti_Apa3, 21 Aspidodera_raillieti_Apa5, 22 Aspidodera_sogandaresi_Texas, 23 Aspidodera_sogandaresi_Nayarit, 24 Aspidodera_sp._Nayarit1, 25 Aspidodera_sp._Nayarit, 26 Aspidodera_sp._Temazcal, 27 Lauroia_bolivari_El_Beni, 28 Lauroia_trinidadensis_Temazcal, 29 Lauroia_trinidadensis_Yucatan; TREE MORPH = (2:0.232281,((3:0.219003,4:0.258692):0.080462,((5:0.005139,6:0.123825):0.470381,(((((7:0.001209,8:0.001276):0.124917,(((10:0.12991,13:0.034997):0.016414,14:0.074253):0.016515,(11:0.032543,12:0.027794):0.026864):0.158719):0.070867,9:0.238827,(22:0.0146,23:0.004291):0.055573,((26:0.004993):0.007492,25:0.100165):0.041513):0.042176,((((15:0.050911,16:0.001477):0.021241,17:0.013477):0.024946,18:0.02537):0.013816,((20:0.001091):0.00425,21:0.012515):0.02854):0.019432):0.143515,((27:0.013824,28:0.024652):0.053927,29:0.012467):0.155767):0.205121):0.486846):0.075298); END; BEGIN MRBAYES; CHARSET morphology = 1 - 52; PARTITION FAVORED = 1 : morphology; SET PARTITION = favored; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 52; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 52; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1318538599334; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3260753200838271698; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 935488652111007692; checksumv 0 2 3446174716 null getNumChars 52 numChars 52 getNumTaxa 29 numTaxa 29 short true bits 7 states 7 sumSquaresStatesOnly 4037.0 sumSquares 4037.0 NumFiles 1 NumMatrices 1; endTell; getWindow; tell It; suppress; setResourcesState false false 240; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1691 949; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #3260753200838271698 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #3260753200838271698; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1451 882; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; endTell; showWindow; getEmployee #mesquite.lists.ColorTaxon.ColorTaxon; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #3260753200838271698 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 810.1318537680089.5627466277388640851; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1451 882; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; 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; 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.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; setDigits 4; writeAsPercentage off; 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 #935488652111007692 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 451; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1451 882; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setActive; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; 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; toggleAllowAutosize on; toggleColorsPanel off; toggleDiagonal on; setDiagonalHeight 80; 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.categ.SmallStateNamesEditor.SmallStateNamesEditor; tell It; panelOpen true; endTell; endTell; endTell; endTell; end;