#NEXUS [written Fri Nov 12 13:44:21 CET 2010 by Mesquite version 2.74 (build 550) at AG-Hausdorf-5/134.100.201.176] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=48; TAXLABELS Acropora_millepora Alcyonidium_diaphanum Anopheles_gambiae Apis_mellifera Aplysia_californica Arenicola_marina Argopecten_irradians Ascaris_suum Barentsia_elongata Bugula_neritina Capitella_sp. Cerebratulus_lacteus Ciona_intestinalis Crassostrea_gigas Cristatella_mucedo Daphnia_pulex Echinococcus_granulosus Euprymna_scolopes Eurythoe_complanata Flaccisagitta_enflata Flustra_foliacea Helobdella_robusta Homarus_americanus Homo_sapiens Hydra_magnipapillata Hypsibius_dujardini Idiosepius_paradoxus Ixodes_scapularis Lineus_viridis Lumbricus_rubellus Macrostomum_lagnano Nematostella_vectensis Novocrania_anomala Paraplanocera_sp. Pedicellina_cernua Philodina_roseola Phoronis_muelleri Phoronis_ijimai Pomphorhynchus_laevis Priapulus_caudatus Schistosoma_mansoni Sipunculus_nudus Spadella_cephaloptera Strongylocentrotus_purpuratus Takifugu_rubripes Terebratalia_transversa Tubulipora_sp. Xiphinema_index ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=6482; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX Acropora_millepora 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Alcyonidium_diaphanum 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Anopheles_gambiae 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Apis_mellifera 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Arenicola_marina 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Argopecten_irradians 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Ascaris_suum 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Barentsia_elongata 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Bugula_neritina 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Capitella_sp. 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Cerebratulus_lacteus 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Ciona_intestinalis 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Crassostrea_gigas 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Cristatella_mucedo 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Daphnia_pulex 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Euprymna_scolopes 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Eurythoe_complanata 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Helobdella_robusta 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Homarus_americanus 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Homo_sapiens 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Hydra_magnipapillata 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Hypsibius_dujardini 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Lineus_viridis 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Lumbricus_rubellus 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Macrostomum_lagnano 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Nematostella_vectensis 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Novocrania_anomala 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Paraplanocera_sp. 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Pedicellina_cernua 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Philodina_roseola 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Phoronis_muelleri 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Phoronis_ijimai 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Pomphorhynchus_laevis 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Priapulus_caudatus 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Schistosoma_mansoni 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Sipunculus_nudus 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Spadella_cephaloptera 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Strongylocentrotus_purpuratus 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Takifugu_rubripes 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Terebratalia_transversa 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Tubulipora_sp. 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Xiphinema_index 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; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 6482; END; BEGIN TREES; Title Imported_trees; LINK Taxa = Taxa; TRANSLATE 1 Acropora_millepora, 2 Alcyonidium_diaphanum, 3 Anopheles_gambiae, 4 Apis_mellifera, 5 Aplysia_californica, 6 Arenicola_marina, 7 Argopecten_irradians, 8 Ascaris_suum, 9 Barentsia_elongata, 10 Bugula_neritina, 11 Capitella_sp., 12 Cerebratulus_lacteus, 13 Ciona_intestinalis, 14 Crassostrea_gigas, 15 Cristatella_mucedo, 16 Daphnia_pulex, 17 Echinococcus_granulosus, 18 Euprymna_scolopes, 19 Eurythoe_complanata, 20 Flaccisagitta_enflata, 21 Flustra_foliacea, 22 Helobdella_robusta, 23 Homarus_americanus, 24 Homo_sapiens, 25 Hydra_magnipapillata, 26 Hypsibius_dujardini, 27 Idiosepius_paradoxus, 28 Ixodes_scapularis, 29 Lineus_viridis, 30 Lumbricus_rubellus, 31 Macrostomum_lagnano, 32 Nematostella_vectensis, 33 Novocrania_anomala, 34 Paraplanocera_sp., 35 Pedicellina_cernua, 36 Philodina_roseola, 37 Phoronis_muelleri, 38 Phoronis_ijimai, 39 Pomphorhynchus_laevis, 40 Priapulus_caudatus, 41 Schistosoma_mansoni, 42 Sipunculus_nudus, 43 Spadella_cephaloptera, 44 Strongylocentrotus_purpuratus, 45 Takifugu_rubripes, 46 Terebratalia_transversa, 47 Tubulipora_sp., 48 Xiphinema_index; TREE Imported_tree_0 = ((1:0.13955069,32:0.08123452):0.0398634,25:0.3149534,((44:0.19443103,(13:0.24110796,(45:0.02990334,24:0.02463221):0.08501121):0.01894813):0.01378849,(((((20:0.06270981,43:0.03392175):0.20455496,(36:0.23509,39:0.56402102):0.07745347):0.00555287,40:0.14950848):0.0104143,(((8:0.24328424,48:0.13725681):0.05752544,26:0.29698467):0.02350183,(28:0.15027218,(23:0.21022635,(16:0.14559361,(4:0.08617028,3:0.23111798):0.04838487):0.02619184):0.03034846):0.0274145):0.0098711):0.0131319,((((34:0.19519303,(31:0.27167245,(41:0.15149887,17:0.19024478):0.21792198):0.01420418):0.08450538,(9:0.04751236,35:0.05279814):0.1233504):0.01183447,(15:0.11058596,(47:0.1966248,(2:0.35383246,(10:0.03941104,21:0.02970813):0.05891945):0.07762693):0.01446467):0.04216192):0.01027936,(((((38:0.05861588,37:0.05712038):0.06863323,(33:0.07304206,46:0.08179426):0.01239465):0.01411916,(12:0.02332678,29:0.03099176):0.08962351):0.00878423,(((7:0.0720893,14:0.07330024):0.02312926,5:0.13504099):0.02085558,(18:0.05426764,27:0.0146718):0.14680985):0.02405249):0.00797166,(42:0.10360223,(19:0.07465407,(6:0.08801234,(11:0.12512254,(30:0.09160963,22:0.07997325):0.04398295):0.00815289):0.01830586):0.0053364):0.00819378):0.01370825):0.02078689):0.02624751):0.0677022); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 6482; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 6482; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1289565864973; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 849083200218301521; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 722122112227613472; mqVersion 274; checksumv 0 2 1846663232 null getNumChars 6482 numChars 6482 getNumTaxa 48 numTaxa 48 short false bits 4611686018458845184 states 31457280 sumSquaresStatesOnly 1.6617134734857732E19 sumSquares 1.6617134734857732E19 NumFiles 1 NumMatrices 1 errorReportedDuringRun errorDuringImport; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 495; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1110 893; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #849083200218301521 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #849083200218301521; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 615 826; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; 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 #849083200218301521 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1989.1289565636558.3231957906455683515; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 615 826; 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 #722122112227613472 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 615 826; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; 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 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;