#NEXUS [written Mon Jun 27 16:57:56 EST 2011 by Mesquite version 2.74 (build 550) at RBG-HERB2-001/203.55.15.173] BEGIN TAXA; TITLE 'Figure 3 - ITS Taxa for calibration'; DIMENSIONS NTAX=87; TAXLABELS Macrolepiota_turbinata_JF495071 Macrolepiota_turbinata_JF495076 Macrolepiota_detersa Macrolepiota_detersa_AF482851 Macrolepiota_dolichaula Macrolepiota_dolichaula_AY085193 Macrolepiota_vinaceofibrillosa Macrolepiota_procera Macrolepiota_rhodosperma Macrolepiota_fuliginosa Macrolepiota_colombiana Macrolepiota_clelandii Macrolepiota_excoriata Macrolepiota_heimii Macrolepiota_konradii_ Macrolepiota_subsquarrosa Macrolepiota_velosa Macrolepiota_eucharis Barcheria_willisiana_JF495035 Barcheria_willisiana_JF495036 Agaricus_melanosporus_JF495042 Agaricus_curcumans_JF495048 Agaricus_curcumans_JF495047 Agaricus_wariatodes_JF495053 Agaricus_wariatodes Agaricus_sp.D_JF495057 Agaricus_dimunitivus Agaricus_semotus Agaricus_abruptibulbus Agaricus_subrufescens Agaricus_arvensis Agaricus_augustus Agaricus_fissuratus Agaricus_nivescens Agaricus_albolutescens Agaricus_inapertus Agaricus_macrosporus Agaricus_sp.B_JF495060 Agaricus_eburneocanus_JF495062 Agaricus_comtulus Agaricus_subrutilescens Agaricus_bresadolianus Agaricus_fuscofibrillosus_AY484684 Agaricus_californicus Agaricus_campestris Agaricus_inilleasper Agaricus_langei Agaricus_sp.A_JF495044 Agaricus_sp.A_JF495045 Agaricus_lilaceps Agaricus_erythrosarx_JF495069 Agaricus_sp.C_JF495066 Agaricus_pattersonae Agaricus_fuscovelatus Agaricus_boisseletii Agaricus_gennadii Agaricus_bernardii Agaricus_phaeolepidotus Agaricus_freirei Agaricus_hondensis Agaricus_pseudopratensis Agaricus_endoxanthus Agaricus_iodosmus Agaricus_placomyces Agaricus_xanthodermus Agaricus_pocillator Agaricus_bisporus Agaricus_subfloccosus Agaricus_bitorquis Agaricus_impudicus Agaricus_devoniensis Agaricus_cupressicola Agaricus_silvaticus Clarkeinda_trachodes Heinemannomyces_splendissimUS Coniolepiota_spongodes Eriocybe_chionea Chlorophyllum_brunneum Chlorophllum_olivieri Chlorophyllum_rachodes Chlorophyllum_hortense Chlorophyllum_alborubescens Chlorophyllum_molybdites Chlorophyllum_globosum Chlorophyllum_agaricoides Chlorophllum_nothorachodes Macrolepiota_neomastoidea ; END; BEGIN CHARACTERS; TITLE ITS_taxa_for_calibration; DIMENSIONS NCHAR=2; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Macrolepiota_turbinata_JF495071 -- Macrolepiota_turbinata_JF495076 -- Macrolepiota_detersa -- Macrolepiota_detersa_AF482851 -- Macrolepiota_dolichaula -- Macrolepiota_dolichaula_AY085193 -- Macrolepiota_vinaceofibrillosa -- Macrolepiota_procera -- Macrolepiota_rhodosperma -- Macrolepiota_fuliginosa -- Macrolepiota_colombiana -- Macrolepiota_clelandii -- Macrolepiota_excoriata -- Macrolepiota_heimii -- Macrolepiota_konradii_ -- Macrolepiota_subsquarrosa -- Macrolepiota_velosa -- Macrolepiota_eucharis -- Barcheria_willisiana_JF495035 -- Barcheria_willisiana_JF495036 -- Agaricus_melanosporus_JF495042 -- Agaricus_curcumans_JF495048 -- Agaricus_curcumans_JF495047 -- Agaricus_wariatodes_JF495053 -- Agaricus_wariatodes -- Agaricus_sp.D_JF495057 -- Agaricus_dimunitivus -- Agaricus_semotus -- Agaricus_abruptibulbus -- Agaricus_subrufescens -- Agaricus_arvensis -- Agaricus_augustus -- Agaricus_fissuratus -- Agaricus_nivescens -- Agaricus_albolutescens -- Agaricus_inapertus -- Agaricus_macrosporus -- Agaricus_sp.B_JF495060 -- Agaricus_eburneocanus_JF495062 -- Agaricus_comtulus -- Agaricus_subrutilescens -- Agaricus_bresadolianus -- Agaricus_fuscofibrillosus_AY484684 -- Agaricus_californicus -- Agaricus_campestris -- Agaricus_inilleasper -- Agaricus_langei -- Agaricus_sp.A_JF495044 -- Agaricus_sp.A_JF495045 -- Agaricus_lilaceps -- Agaricus_erythrosarx_JF495069 -- Agaricus_sp.C_JF495066 -- Agaricus_pattersonae -- Agaricus_fuscovelatus -- Agaricus_boisseletii -- Agaricus_gennadii -- Agaricus_bernardii -- Agaricus_phaeolepidotus -- Agaricus_freirei -- Agaricus_hondensis -- Agaricus_pseudopratensis -- Agaricus_endoxanthus -- Agaricus_iodosmus -- Agaricus_placomyces -- Agaricus_xanthodermus -- Agaricus_pocillator -- Agaricus_bisporus -- Agaricus_subfloccosus -- Agaricus_bitorquis -- Agaricus_impudicus -- Agaricus_devoniensis -- Agaricus_cupressicola -- Agaricus_silvaticus -- Clarkeinda_trachodes -- Heinemannomyces_splendissimUS -- Coniolepiota_spongodes -- Eriocybe_chionea -- Chlorophyllum_brunneum -- Chlorophllum_olivieri -- Chlorophyllum_rachodes -- Chlorophyllum_hortense -- Chlorophyllum_alborubescens -- Chlorophyllum_molybdites -- Chlorophyllum_globosum -- Chlorophyllum_agaricoides -- Chlorophllum_nothorachodes -- Macrolepiota_neomastoidea -- ; END; BEGIN TREES; Title 'Figure 3 - ITS calibrated tree'; LINK Taxa = 'Figure 3 - ITS Taxa for calibration'; TRANSLATE 1 Macrolepiota_turbinata_JF495071, 2 Macrolepiota_turbinata_JF495076, 3 Macrolepiota_detersa, 4 Macrolepiota_detersa_AF482851, 5 Macrolepiota_dolichaula, 6 Macrolepiota_dolichaula_AY085193, 7 Macrolepiota_vinaceofibrillosa, 8 Macrolepiota_procera, 9 Macrolepiota_rhodosperma, 10 Macrolepiota_fuliginosa, 11 Macrolepiota_colombiana, 12 Macrolepiota_clelandii, 13 Macrolepiota_excoriata, 14 Macrolepiota_heimii, 15 Macrolepiota_konradii_, 16 Macrolepiota_subsquarrosa, 17 Macrolepiota_velosa, 18 Macrolepiota_eucharis, 19 Barcheria_willisiana_JF495035, 20 Barcheria_willisiana_JF495036, 21 Agaricus_melanosporus_JF495042, 22 Agaricus_curcumans_JF495048, 23 Agaricus_curcumans_JF495047, 24 Agaricus_wariatodes_JF495053, 25 Agaricus_wariatodes, 26 Agaricus_sp.D_JF495057, 27 Agaricus_dimunitivus, 28 Agaricus_semotus, 29 Agaricus_abruptibulbus, 30 Agaricus_subrufescens, 31 Agaricus_arvensis, 32 Agaricus_augustus, 33 Agaricus_fissuratus, 34 Agaricus_nivescens, 35 Agaricus_albolutescens, 36 Agaricus_inapertus, 37 Agaricus_macrosporus, 38 Agaricus_sp.B_JF495060, 39 Agaricus_eburneocanus_JF495062, 40 Agaricus_comtulus, 41 Agaricus_subrutilescens, 42 Agaricus_bresadolianus, 43 Agaricus_fuscofibrillosus_AY484684, 44 Agaricus_californicus, 45 Agaricus_campestris, 46 Agaricus_inilleasper, 47 Agaricus_langei, 48 Agaricus_sp.A_JF495044, 49 Agaricus_sp.A_JF495045, 50 Agaricus_lilaceps, 51 Agaricus_erythrosarx_JF495069, 52 Agaricus_sp.C_JF495066, 53 Agaricus_pattersonae, 54 Agaricus_fuscovelatus, 55 Agaricus_boisseletii, 56 Agaricus_gennadii, 57 Agaricus_bernardii, 58 Agaricus_phaeolepidotus, 59 Agaricus_freirei, 60 Agaricus_hondensis, 61 Agaricus_pseudopratensis, 62 Agaricus_endoxanthus, 63 Agaricus_iodosmus, 64 Agaricus_placomyces, 65 Agaricus_xanthodermus, 66 Agaricus_pocillator, 67 Agaricus_bisporus, 68 Agaricus_subfloccosus, 69 Agaricus_bitorquis, 70 Agaricus_impudicus, 71 Agaricus_devoniensis, 72 Agaricus_cupressicola, 73 Agaricus_silvaticus, 74 Clarkeinda_trachodes, 75 Heinemannomyces_splendissimUS, 76 Coniolepiota_spongodes, 77 Eriocybe_chionea, 78 Chlorophyllum_brunneum, 79 Chlorophllum_olivieri, 80 Chlorophyllum_rachodes, 81 Chlorophyllum_hortense, 82 Chlorophyllum_alborubescens, 83 Chlorophyllum_molybdites, 84 Chlorophyllum_globosum, 85 Chlorophyllum_agaricoides, 86 Chlorophllum_nothorachodes, 87 Macrolepiota_neomastoidea; TREE TREE1 = ((((((((((1:1.7893990458545947,2:1.7893990458545947):3.9371023937037024,(3:1.006509840598078,4:1.006509840598078):4.71999159896022):3.3580151065856896,(5:0.8783596144109265,6:0.8783596144109265):8.20615693173307):3.087522587372904,7:12.172039133516913):5.338469736359471,8:17.51050886987636):1.9099022090161561,((9:1.6170271560971454,10:1.6170271560971454):12.181399789762276,11:13.798426945859426):5.62198413303312):4.430039279749373,12:23.85045035864188):4.802047583696087,((13:0.9680272829281689,14:0.9680272829281689):5.195895324774791,(15:0.720243679399756,16:0.720243679399756):5.443678928303196):22.488575334635):6.146731153871556,(17:9.15417107145535,18:9.15417107145535):25.645058024754213):47.747165023481905,(((19:2.6646273590033873,20:2.6646273590033873):62.69867019789018,(((21:34.257763005223765,(((((((((22:3.7512455758860517,23:3.7512455758860517):3.5504318745367205,(24:1.1074972645198737,25:1.1074972645198737):6.194180185902901):2.8134528774032814,(26:5.393004976672821,27:5.39300497667282):4.7221253511532275):3.0551581316882395,28:13.170288459514293):3.9588634916904937,(((29:3.8189580895595268,30:3.8189580895595268):3.154693225878949,31:6.9736513154384765):3.314897911808546,(32:7.861097994156622,((33:4.739867501891081,(34:3.047161330686713,(35:1.7375260757038524,36:1.7375260757038524):1.3096352549828616):1.6927061712043718):2.0613780414378278,(37:5.475732332751244,(38:3.4822444100682577,39:3.4822444100682572):1.99348792268299):1.325513210577662):1.0598524508277238):2.427451233090399):6.840602723957762):2.33900815670842,40:19.46816010791324):3.7877444942982734,(41:17.492750924535606,42:17.492750924535628):5.763153677675817):4.097933876152716,43:27.353838478364192):3.0864246385425247,((((44:10.236574914196192,45:10.236574914196192):5.30377267507882,(46:9.793285359644955,47:9.793285359644955):5.747062229630069):5.191977136195733,(48:0.6542143684996431,49:0.6542143684996431):20.07811035697111):6.666289018433574,(((50:12.956245907152503,((51:5.884647590953465,52:5.884647590953465):3.8341531545442535,(53:5.593221526707124,54:5.593221526707123):4.125579218790603):3.237445161654785):6.184982557506672,55:19.14122846465919):5.756118531163512,(((56:11.875449354103322,57:11.875449354103322):8.852585718655408,(((58:10.37094362548177,(59:6.458731938828066,60:6.458731938828068):3.91221168665371):4.892594949779674,(61:12.508771852027744,((62:5.081391752686322,(63:3.2262334576561673,(64:2.1997952011615958,65:2.199795201161595):1.0264382564945738):1.8551582950301593):2.854485497246108,66:7.935877249932431):4.572894602095337):2.754766723233688):3.306515584676763,(((67:4.178779655226083,68:4.178779655226083):6.464394353620836,(69:8.580502507171715,(70:6.316017197322809,71:6.31601719732281):2.264485309848914):2.062671501675199):1.7411674272898754,72:12.384341436136788):6.185712723801428):2.1579809128205305):0.8748860556072025,73:21.602921128365946):3.2944258674567237):2.501266748081658):3.0416493730023717):3.817499888317027):12.216106170495287,(74:40.475105491192814,75:40.475105491192814):5.998763684526189):4.544324869393435,(76:29.397583896846378,77:29.397583896846378):21.62061014826604):14.34510351178109):7.902112986713163,(((78:19.76949995158656,(79:11.878066402070536,80:11.878066402070537):7.891433549516044):11.361512361292895,(81:1.5093688883789498,82:1.5093688883789498):29.62164342450052):10.379378548230616,(((83:5.383173134558537,84:5.383173134558537):8.500329642832444,85:13.88350277739099):17.212034308533365,(86:19.993390441399818,87:19.993390441399825):11.102146644524588):10.414853775185676):31.75501968249666):9.28098357608475); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 2; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 2; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 2; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1309157876437; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8941924786569957019; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4056081508678574395; mqVersion 274; checksumv 0 2 2750894845 null getNumChars 2 numChars 2 getNumTaxa 87 numTaxa 87 short true bits 0 states 0 sumSquaresStatesOnly 0.0 sumSquares 0.0 NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 304; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1070 709; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #8941924786569957019 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #8941924786569957019; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 766 642; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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 #8941924786569957019 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 827.1308803879175.2054630223289392455; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 766 642; setLocation 8 8; 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 off; 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.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; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal 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 #4056081508678574395 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 766 642; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; 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; 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;