#NEXUS [written Mon Feb 20 12:32:10 EST 2012 by Mesquite version 2.75 (build 566) at M100/49.127.7.76] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=12; TAXLABELS Homo_sapiens_PRF1 Mus_musculus_PRF1 Anolis_carolinensis_PRF1 Takifugu_rubripes_PRF1.2 Homo_sapiens_C6 Mus_musculus_C6 Anolis_carolinensis_C6 Takifugu_rubripes_C6 Homo_sapiens_MPEG1 Mus_musculus_MPEG1 Anolis_carolinensis_MPEG1 Takifugu_rubripes_MPEG1 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=269; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX Homo_sapiens_PRF1 ARSECKRHKPGAWLAGEGVDVTSLRRSGPVDTQRFLRCTLCENALQRLPLALTRAQGCQRHVTRAKVSSTEAVARDHSVAGSHKTHQDQYSFSTDTVECRFYSFHVVHTPPLHPDFKRALGDLPHHFNAPAYLRLISNYGTHFIRAVELGTALRTCELALEGLTDNEVEDCLEAQVNIHGSAEAKACEEKKKKHKMTSFHQTYRERHSEVVGGTSINDLLFGIQEQYSAWVNSLPGSPGLVDYTLEPLHVLLDSQDPRREALRRALSQY Mus_musculus_PRF1 TRSECKQHKPGVWMAGEGMDVTTLRRSGPVNTQRFLRCTLCKNSTQRLPVAITRPHHCQRNVAAAKVHSTEGVARERSVAGSHKTYQDQYNFNSDTVECRMYSFRLVQKPPLHLDFKKALRALPRNFNSHAYHRLISSYGTHFITAVDLGTALRTCQLTLNGLTADEVGDCLEAQVSIQASSEYKACEEKKKQHKMASFHQTYRERHVEVLGGDSTHDLLFGNQEQFSTWTASLPSNPGLVDYSLEPLHTLLEEQNPKREALRQAISHY Anolis_carolinensis_PRF1 TEDECQDQHPGHGLAGVGFDITKLERKAVLDMSQWQKCTLCQNPLQRLPLAIAEAKACQKNLRSSIQVSGISAVQAQALAGSHKSSQDQYTFVSHEVSCSYYSLRIGHRRKLAEHFRHALKTLPLKYNRLEYHQLIGTYGTHWITHLRLGTATRVCETVLDGVTADEVKDCLEASASIRNSSSYKMCQELKKKQNFKSFHNTYNERHTEVVGGASHVDLLFSNDESFKEWLEGLKSLPDLLSYSLEPIHTLVRKGHPKRESLRQAVSEY Takifugu_rubripes_PRF1.2 SFTECQNAPPGHNLVGEGFDVVTMKTSGVVDVKTFMVCTMCHNSAQKLPVSVLRVKNCQRSLSSKIFESSQAVMKEGSVGGSHHSRQDKFSFTSYEMKCRYYTFRLHARPPLSKEFEVSLKNLPPTYDHSAFRQFISVYGTHFIRRVHLGTAIRTCQASISQMSVHTVSNCLEAEATIKGVAASRFCQSKSKSLKTGTFSQAFSDRTTDVLGGESVGDILFQPNAAFKKWLISLKKVPGLVSYQLSPLHLLVPDNPVLQESLRSAISDY Homo_sapiens_C6 TKAVCTRYNPSVQLMGNGFHFLAGEPRGEVLDNSFTGCKTVKSSPYRVPANLEGFETAEDDLKTDFYKDLTSLGHNKSENINHASHKKDSSFIRIHKVMKVLNFTTKAKDHLSDVFLKALNHLPLEYNSALYSRIFDDFGTHYFTSGSLGYQFSSEELKNSGLTEEEAKHCVETKKRVAKKVEHRCTTNKLSEKHEGSFIQGAEKSISLIRGGEYGAALAWEKGKTFSEWLESVKENPAVIDFELAPIVDLVRCAVTKRNNLRKALQEY Mus_musculus_C6 TKPVCTRYTPSVQLMGTGFHFLAGEPRGEVLDNSFTGCKLVKTSPYRVSANLENFETIEDDLKTEFYKNLISFEKNENEHSHYASHKKDSSFIRIHKLIKVLNFTMKATDQLSDVFLKALVHLPLEYNSAVYSRIFDDFGTHYFTSGSLGYQFSRQELQNSGLTEEEAQNCVETKKLKYMEKEDTCTKNKLSEKYGGSFLQGSEKSISLVQGGQQAAALAWEKGNVYSEWLESVKENPAVVDYKLAPITDLVRCAVTKRNNLRRALQEY Anolis_carolinensis_C6 INRVCKRFIPSAQLMGLGYHILADESRGEVLDYSFHGCVRVKSETYRVPANLENFQNQEDDVKAHYYTDLTPIMQTGNSMVSSSSHKMSSNFIRVHKVIAVSNFTVKQSDQVSRVFLNALNSLPLEYNYALYSRIFDDFGTHYYTSGSLGYQFNEEETKNSGLTQEEITNCVETTFYIIPIRHEECTRSKMTERYEGSVLKSSERSISLVKGGQYAAALAFEKKNIFNNWLESTKENPGVIEFEVASILDLVKCAVTKRYNLRKAFFEY Takifugu_rubripes_C6 FKTVCPAKRPGADLVGNGFDAMAEEPRGAVLDNMFMGCNIKRPQYHRIPHNFANFDDHYERLEVTFLPSLAGSEPESSPYAENLFRDKDSKFLRVHQVLPVSTFKMMDSEVLSQPFLQFLHALPLEYNYALYREIFQRFGTHYYHSGVLGYQYSREELKSSGTTEEHIRGCSSTAQIPQEGPLLEVVSNQIQIQFNTSYIQAAEKSYSMVRGGREAAALAWERQVSFKNWAKSVLDNPAVVESTVNPIIDLVRCAVTKRRHLRKALLQY Homo_sapiens_MPEG1 GVQKCKNLKLPVLEVLPGGGWDNLRNVDRVMELTYSNCRTTEDGQYIIPDEIFPQKQSNLEMNSEILESWANYQSSSFSKVNGKTLQVKDQAITTRVQVRNLVYTVKINPELSSGFRKELLDISDRLENYLAELLVLNYGTHVTTSVDAGAALIQEDHLRASFLQDSQSSRSTASAGLQNTVNFKFEENYTSQNVLTSYLSNRTNSRVQSIGGPFYPGITLQAWQGITNHLVAIDRSGLPLHFFINPNMLPDLLVKKVSKTVETAVKRY Mus_musculus_MPEG1 GFQICKNLKLPVLEVLPGGGWDNLRNVDRVMDLTYTNCKTTEDGQYIIPDEVYPQKESNLEMNSEVLESWMNYQSTAFSRVNGKTLQVKDQAVTTRVQVRNRIYTVKTTPELSLGFTKALMDICDQLEKYLAELLILNYGTHVITSVDAGAALVQEDHVRSSFLLDNQNSQNTASAGILNIVNFKVETDYISQTSLTDYLSNRTNSRVQSFGGPFYPGITLETWKGITNHLVAIDRAGLPLHFFIKPDKLPGLLVKKLSKTVETAVRHY Anolis_carolinensis_MPEG1 GFQECRQLGRPALEVLPGGGWDNLQNRARVIHLNYSLCRTTEDGAYLIPNDVFPLKETYLELNSEIIESWMDYQSASTSFINGKTHQVKDQTVTTRVQVRNRMYTVKFDPRFDEGFQQQLVAIASHLENYLAEILVLNYGTHVITGVDAGASLIQEDQVRSTFVKDSKFMRSTAAAGVHKVVNFQSSLSVGIDDSFIQYEANRTNSRVESIGGPFYPGITLKTWESIPNRLVAIDRFGLPLEFFITPEKLPGLIVKRLSKTVASAITRY Takifugu_rubripes_MPEG1 WLRQCRETNITALEVLPGGGWDNLRNMDRVMNISYFQCQTTEDGLYLIPDEVFPHKETGVETNSEIISSWLEQKSCSFSVLNGKTHQVKDSSITTRVQIRNFIYKVKAFPALDVRFAQQAKEIADAIENYLSEKMVLEFGTHVITSVDAGATLVEEDYLTAKYVSDATSKSSTAQAGLFDKLKFDISSQTSTQSSILGYQSNITYSIIQSHGGPFYPGMTLQKWESTRNNLVAIDRSGMPLQYFINPNTFPDLTVRKVSRSVRQAIDRY ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 269; END; BEGIN TREES; Title 'Trees from "mpc6.tre"'; LINK Taxa = Taxa; TRANSLATE 1 Homo_sapiens_PRF1, 2 Mus_musculus_PRF1, 3 Anolis_carolinensis_PRF1, 4 Takifugu_rubripes_PRF1.2, 5 Homo_sapiens_C6, 6 Mus_musculus_C6, 7 Anolis_carolinensis_C6, 8 Takifugu_rubripes_C6, 9 Homo_sapiens_MPEG1, 10 Mus_musculus_MPEG1, 11 Anolis_carolinensis_MPEG1, 12 Takifugu_rubripes_MPEG1; TREE con_50_majrule = (1:0.2182058881928563,2:0.1135144373896666,((3:0.434490372214341,4:0.5968679091159527):0.08996341315032971,(((5:0.08804900181605667,6:0.1360188446115988):0.088993829417424,(7:0.3260618880834291,8:0.7249791289248632):0.1147805744707456):0.9263745148458866,(((9:0.07351530013815946,10:0.1446294552332519):0.1477984618646638,11:0.2838862053433839):0.1894372751243247,12:0.2782843600436303):1.681453800550064):0.5087466468811458):0.2349182466549733); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 269; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 269; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1329701530953; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 6039757037272141433; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 6695596724988640187; mqVersion 275; checksumv 0 3 4209586524 null getNumChars 269 numChars 269 getNumTaxa 12 numTaxa 12 short false bits 1048575 states 1048575 sumSquaresStatesOnly 4.2079359592635E13 sumSquares 4.2079359592635E13 longCompressibleToShort false usingShortMatrix false NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 326; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 948 590; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #6039757037272141433 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #6039757037272141433; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; getTable; tell It; rowNamesWidth 143; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 622 523; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.arrow; 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 #6039757037272141433 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 878.1329701340859.2916258475367208634; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 622 523; setLocation 8 8; 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 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; setTree '((12:0.2782843600436303,(11:0.2838862053433839,(9:0.07351530013815946,10:0.1446294552332519):0.1477984618646638):0.1894372751243247):0.840726900275032,(((1:0.2182058881928563,2:0.1135144373896666):0.2349182466549733,(3:0.434490372214341,4:0.5968679091159527):0.08996341315032971):0.5087466468811458,((5:0.08804900181605667,6:0.1360188446115988):0.088993829417424,(7:0.3260618880834291,8:0.7249791289248632):0.1147805744707456):0.9263745148458866):0.840726900275032);'; 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; 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 #6695596724988640187 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 622 523; setLocation 8 8; 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; 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;