#NEXUS [written Mon Aug 24 00:16:40 BRT 2015 by Mesquite version 3.04 (build 725) at fernando-HP-Pavilion-15-Notebook-PC/127.0.1.1] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=10; TAXLABELS 'Thermococcus onnurineus TON_1021' 'Escherichia coli YP_006125568' 'Escherichia coli YP_006125370.1' 'Caldanaerobacter subterraneus tengcongensis_ NP_623302.1' 'Caldanaerobacter subterraneus yonseiensis_ERM92234.1' 'Thermoanaerobacter sp. YS13 THYS13_RS04690' 'Caldanaerobacter subterraneus pacificus_CDSM653_01586' 'Moorella thermoacetica YP_431023.1' 'Geobacillus sp. Y4.1MC1 YP_003989190.1' 'Geobacillus thermoglucosidasius YP_004587922.1' ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=695; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX 'Thermococcus onnurineus TON_1021' -MEV--IFLFIVIILSVASFIGV-FSRSAILTKLVNALSALGSLTIAYAGIVGLKESVELNITLLHLKSDSIINAFSTLTLKVDPLSGFFMIILGILGFCTSVYGIAYLDMYKGD-KRLYAFNYPLFLLFMFLVLVSWNLLWFVVFWELMTLFSQFLVAFER-NEKTLIATLKYFCMTKAAADFMLIAIVLVLITISGGGDYDILSSQLVNYFRSHPLEMYLVSAGFMIGLGVKAALVPFHVWLPDAYVEAPSNVSSLLSGAMEKMPVYMMFRFFLSFTPLTP---NIGLLIALFGTLTLFFGTMYALKQTDSKRLLAYHSVGQIGYVVFALGAGIYLLSKGYTTFGALALMASLFHALNHAFFKGLLFLTAGSILYRTGSRDLDHLGGLARFMPITAFAALIGSLSIAGMPPFNGFVSKWMIYVSTLPTPT----LVSLFGALALFI----SAVTTASFVKYFTSIFVRPP--AKEITVKEVPVSMWASQLILAVLCVIFGV-YPALPLEAISKAVDSVGVTTPSIT----VFPGLIVSDGIGNIAPLALLVFSGALTAV-LLAIF-------PYKISLPVWTTGTRRSLAMRLPASSYYASFEEEFEDVYSW-------GEWCVCTTKRL------------WDA--TKAVLSNFEEVSFDLDKMMTGAWLMLLILLTILGGVLL-------- 'Escherichia coli YP_006125568' -MSAISLINSGVAWFVAAAVLAFLFSFQK---ALSGWIAGIGGAVGSLYTAAAGFTVLTGAVGV----SGALS--LVSYDVQISPLNAIWLITLGLCGLFVSLYNIDWHRHAQVKCNG---LQINMLMAAAVCAVIASNLGMFVVMAEVMALCAVFLTSNSK-------EGKLWFALGRLGTLLLAIACWLLWQRY-GTLDLRLLDMRMQQLP--LGSDIWLLG---VIGFGLLAGIIPLHGWVPQAHANASAPAAALFSTVVMKIGLLGMLT--LSLLGGNA-PLWWGIALLVLGMITAFVGGLYALMEHNIQRLLAYHTLENIGIILLGLGAGVTGIALEQPALIALGLVGGLYHLLNHSLFKSVLFLGAGSVWFRTGHRDIEKLGGIGKKMPVISIAMLVGLMAMAALPPLNGFAGEWVIYQSFFKLSNSGAFVARLLGPLLAVGLAITGALAVMCMAKVYGVTFLGAPRTKEAENATCAPLLMSVSVVALAICCVIGGVAAPWLL---------------PMLSAAVPL-PLEPANTTVS--QPMITLLLIACPLLP-FIIMAICKGDRLPSRSRGAAWVCGYDHEKSMVITAHGFAMPVKQAFAPVLKLRK------------------WLNPVSLVPGWQC---------------------EGSALLFRRMALVELAVLVVIIVSRGA 'Escherichia coli YP_006125370.1' -MDALQLLTWSLILYLFASLASLFLLGLD---RLAIKLSGITSLVGGVIGIISGITQLHAGVTLVARFATPFD--FADFTLRMDSLSAFMVLVISLLVVVCSLYSLTYMREYEGKGAAAMGFFMNLFIASMVALLVMDNAFWFIVLFEMMSLSSWFLVIARQ-DKTSINAGMLYFFIAHAGSVLIMIAFLLMGRES-GSLDFA--SFRTLSLSPGLASAVFLLA---FFGFGAKAGMMPLHSWLPRAHPAAPSHASALMSGVMVKIGIFGILKVAMDLLAQTGLPLWWGILVMAIGAISALLGVLYALAEQDIKRLLAWSTVENVGIILLAVGVAMVGLSLHDPLLTVVGLLGALFHLLNHALFKGLLFLGAGAIISRLHTHDMEKMGALAKRMPWTAAACLIGCLAISAIPPLNGFISEWYTWQSLFSLSRVEAVALQLAGPIAMVMLAVTGGLAVMCFVKMYGITFCGAPRSTHAEEAQEVPNTMIVAMLLLAALCVLIALSASWLAPKIMHIAHAFTNTPPVTVASGIALVPGT-FHTQVT--PSLLLLLLLAMPLLPGLYWLW-CRSRRAAFRRTGDAWACGYGWENAMAPSGNGVMQPLRVVFSALFRLRQQL-DPTLRLNKGFAHVTARAQSTEPF--WDERVIRPIVSATQRLAKEIQHLQSGDFRLYCLYVVAALVVLLIAIAV--- 'Caldanaerobacter subterraneus tengcongensis_ NP_623302.1' MMTVQQLFLLSIFLYVVGALISLGLNRDG---KIANYVSGTTAFLAGCTGVASAVPVLIEGKGFILEGMEFIP--FGRFTINVDPLSAFMTLVISLLSIATGVYSISYQEEYIGKGTGVMGFLNNIFIVSMILVVTSDNAFYFLVFWELMTLVSYFLVCFEQENREAIKAGFVYFVMAHVGTVLIMISFILFYVYT-GTFDFA--AFRNANLSPVIKNLAFLLA---FLGFGVKAGIVPFHFWLPQAHPAAPSNVSALMSGVMIKTAIYGIIRVGVDFLGAAT--WWWGLTVLAFGAISAVFGVLYAVSENDLKRLLAYSSIENVGIILMGVGAGMMGIATGYVSVGILGILAGLYHLINHAVFKGLLFLGAGSVVYRLHTRNMEEMGGLARYMPWTGLTFFIGALSISALPPLNGFVSKWFTYHTLFAVSTKGSVLIRMAFPLAAVALALTGALTSLCFVKAYGVTFTGPFRGGNELKIKEVPVTMLIGMGLLAIGCFVLGLGAPVGAGYIANVASALLHVSSPKVSDGLSIFPASSEQAMLS--TPLVLVFVVGLAILP-LLIIG-TGGKRAGRRVDFEPWACGYKYSSRMAWTSTAFAHSLYPLFSPVYLLRTAFTEAGRFIILLFKKAMAYISQIELM--WERYIYYPLLHFMVYIGKRAQTFQTGNVRMYCLYIILTLGVLLIATVR--- 'Caldanaerobacter subterraneus yonseiensis_ERM92234.1' -MIVQQLFLLSIFLYVVGALISLGLNRDG---KIANYVSGTTAFLAGCTGVASAVPVLIEGKGFILEGMEFIP--FGRFTINVDPLSAFMTLVISLLSIATGVYSISYQEEYIGKGTGVMGFLNNIFIVSMILVVTSDNAFYFLVFWELMTLVSYFLVCFEQENREAIKAGFVYFVMAHVGTVLIMISFILFYVYT-GTFDFA--AFRNANLSPVIKNLAFLLA---FLGFGVKAGIVPFHFWLPQAHPAAPSNVSALMSGVMIKTAIYGIIRVGVDFLGAAT--WWWGLTVLAFGAISAVFGVLYAVSENDLKRLLAYSSIENVGIILMGVGAGMMGIATGYVSVGILGILAGLYHLINHAVFKGLLFLGAGSVVYRLHTRNMEEMGGLARYMPWTGLTFFIGALSISALPPLNGFVSKWFTYHTLFAVSTKGSVLIRMAFPLAAVALALTGALTSLCFVKAYGVTFTGPFRGGNELKIKEVPVTMLIGMGLLAIGCFVLGLGAPVGAGYIANVASALLHVSSPKVSDGLSIFPASSEQAMLS--TPLVLVFVVGLAILP-LLIIG-TGGKRAGRRVDFEPWACGYKYSSRMAWTSTAFAHSLYPLFSPVYLLRTAFTEAGRFIILLFKKAMAYISQIELM--WERYIYYPLFHFMVYIGKRAQTFQTGNVRIYCLYIILTLGVLLIATVR--- 'Thermoanaerobacter sp. YS13 THYS13_RS04690' -MTVQQLFLLSIFLYVVGALISLGLNRDG---KIANYVSGTTAFLAGCTGVASAIPVLIEGKGFILEGMEFIT--FGRFTINVDPLSAFMILVISLLSIATGIYSISYQEEYIGKGTGVMGFLNNIFIVSMILVVTIENAFYFLVFWELMTLVSYFLVCFEQENREAIKAGFVYFVMAHVGTVLIMISFILFYVYT-GTFDFA--AFRNANLLPVIKNLAFLLA---FLGFGVKAGIVPFHFWLPQAHPAAPSNVSALMSGVMIKTAIYGIIRVGVDFLGASA--WWWGLTVLAFGAISAVFGVLYAVSENDLKRLLAYSSIENLGIILMGVGAGMMGIATGQVSVGILGILAGLYHLINHAVFKGLLFLGAGSVVYRLHTRNMEEMGGLARYMPWTGLTFFIGALSISALPPLNGFVSKWFIYHTLFVASTKGSVPIRMAFPLAAVALALTGALTSLCFVKAYGVPFTGPFRGGNELKIKEVPVTMLIGMGLLAICCFVLGLGVPIGPGHIVNMASALLHVSSPQLSDGLSIFPASSEQAMLS--TPLVLVFVVGLAILP-LLIIG-TGGKRAGRRVDFEPWACGYKYSSRMAWTSTAFAHSLYLLFSPAYLLRTAFTKVGCFIILLFKKAMAYIAQIELM--WERYIYYPLLHFMVYIGKRAQTFQTGNVRMYCLYIILTLGVLLIATVR--- 'Caldanaerobacter subterraneus pacificus_CDSM653_01586' -MTVQQLFLLSIFLYVVGALISLGLNRDG---KIANYVSGTTAFLAGCTGVASAVPVLIEGKGFILEGMEFIP--FGRFTINVDPLSAFMTLVISLLSIATGIYSISYQEEYIGKGTGVMGFLNNIFIVSMILVVTIDNAFYFLVFWELMTLVSYFLVCFEQENREAIKAGFVYFVMAHVGTVLIMISFILFYVYT-GTFDFA--AFRNANLLPVIKNLAFLLA---FLGFGVKAGIVPFHFWLPQAHPAAPSNVSALMSGVMIKTAIYGIIRVGVDFLGASA--WWWGLTVLAFGAISAVFGVLYAVSENDLKRLLAYSSIENVGIILMGVGAGMMGIATGQVSVGILGILAGLYHLINHAVFKGLLFLGAGSVVYRLHTRNMEEMGGLARYMPWTGLTFFIGALSISALPPLNGFVSKWFTYHTLFAASTKGSALIRMAFPLAAVALALTGALTSLCFVKAYGVTFTGPFRGGNELKIKEVPVTMLIGMGLLAIGCFVLGLGVPIGAGYIANVASALLHVSSPQLSDGLSIFPASSEQAMLS--TLLVLVFVVGLAILP-LLIIG-TGGKRAGRRVDFEPWACGYKYSSRMAWTSTAFAHSLYLLFSPAYLLRTAFTKAGCFIILLFKKAMAYISQIELM--WERYIYYPLLHFMVYIGKRAQTFQTGNVRMYCLYIILTLGVLLIATVR--- 'Moorella thermoacetica YP_431023.1' -MLTQQLLLLSVLLYVAGALASLALNRAG---KIANYASGISALAAAGTGMASAVQVLAGGAAFTWEAAGFIP--FAKFIIKVDPLSAFMLLVISLLTGATALYSLSYLDEYTGKGAGVMGFFNNLFIASMVLVVISGNAFYFLIFWELMTLASYFLVSFDQEDSEAVKAGFIYLFMAHAGTALIMLAFILFFVYT-GTFDFA--SFRGANLPVFTKSLIFLLA---FLGFGAKAGIIPLHIWLPKAHPAAPSNASALMSGVMIKTAIYGILRVSVDFLGASV--WWWGFIVLASGAISAVLGVLYALGEHDIKRLLAYHSVENVGIILMGAGAGMIGIAAGQPVLGVLGILAGLYHLLNHAVFKGLLFLGAGSVIYRTHTKHMEELGGLARRMPWTALAFLVGAVAISAIPPLNGFVSEWFTYQSLFIASTSSILAVRVFAPLFVVMLALTGALAAMCFVKAYGVTFGGPCRSGHAREAREVPIPMLAGMAILAISCIILGVGAPVVAPYIGKVASALLAITAVQVSDGLLVFPANSMQAMLS--TPLIAILLVGLATLP-LLIIGIQGGFQAGRRIDAEPWACGYKYSPRMAYTATAFAQPLRVLFRPVYSLRTTLDGPGYTVASYFKGAVVYIASVESL--WERYIYAPLARGTVYLGKKLQAFQIGNVRLYCLYIIITLVVLLLATVR--- 'Geobacillus sp. Y4.1MC1 YP_003989190.1' -MNVQQLFLLSVFLYVAGALGSLAMNRVG---KAANYVSSGSAFLAACAGIALSIPAIAGGADFMMESAGVVP--FAKFVIKIDPLSAFMILVISLLTAASAVYSLAYQNEYVGRGNGVLGFLNNIFIASMILVVASDNAFYFLVFWELMTLASYFLVCFDQKNKEAIHAGFTYHVVAHAGTALIMISFILFFLQT-GTFDFA--AFRSANLSPVMKDLAFLLA---FFGFGAKAGIMPFHTWLPQAHPAAPSNVSSLMSGVMVKIAIYGIIRVGVDFLGASV--WWWGLTVLAFGAISALLGILYAASENDLKRLLAYSSIENVGIILMGIGVGMIGVASGQPVLGVLGILAGLYHLLNHAVFKGLLFLGTGSIIYRIGTKNMEEMGGLAKQMPWTGFAFLTGALAISAIPPLNGFVSEWFLYQSLFMAGKSDILTFKVLSPLFAVMLALTGALAAMCFVKAYGVTFVGPFRSDRVREAREVPVPMIAGMVILVAGCIVLGLGAPMIAPYIGIVASALLGTNPVWVSDDMMVFPGSNSQAMLS--TPLMFLLLIGLVMFS-LFIVWIQGGMKAGRRIDSVPWACGYAYSSRMAATANAFVQPLRILFHPIYLLRNALIGLGNKIASYSKQAVDYIDRLELI--WENNIYGLLARGMFHLGKRVQVIQVGNVQVYCMYIIITLVVLLITTVR--- 'Geobacillus thermoglucosidasius YP_004587922.1' -MNVQQLFLLSVFLYVAGALGSLAMNRVG---KAANYVSAISTFTAAIAGLISTIIVLVRETPIVTELSGFVP--FARFTIEMDHLSAFMILVISLLAAATAIFTLTYDDQYVGKNAGIFGFLNNSYILSMVLAVASSNAFYFLVFWEIMTLASYFLVVVKQ-DEEAIHSGFVYFAVAHAAATAIIISFVVLFLYT-GSFSFT--DFRSVEISQATKNLVFLLS---FIGFGTKAGIVPFHIWLPRTYSSAPSTVSALMS---TKVAIYGLIRVGVDFLGASV--WWWGLTVLTIGAISAFLGILYASGENDLNRQLAYSSTENVGIILMGIGVGMIGVASGQPVLGVLGILAGLYHLLNHAVFKGLLFLGTGSIIYRIGTKNMEEMGGLAKQMPWTGFAFLTGALAISAIPPLNGFVSEWFLYQSLFMAGKSDILTFKVLSPLFAVMLALTGALAAMCFVKAYGVTFVGPFRSDRVREAREVPVPMIAGMVILVAGCIVLGLGAPMIAPYIGIVASALLGTNPVWVSDDMMVFPGSNSQAMLS--TPLMFLLLIGLVMFS-LFIVWIQGGMKAGRRIDSVPWACGYAYSSRMAATANAFVQPLRILFHPIYLLRNALIGLGNKIASYSKQAVDYIDRLELI--WENNIYGLLARGMFHLGKRVQVIQVGNVQVYCMYIIITLVVLLITTVR--- ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 695; END; BEGIN NOTES; TAXABITS TAXA = Taxa NAME = newlyAddedTaxon on = 1 - 10; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 695; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 695; END; BEGIN TREES; Title 'Trees from "hyfB.tre"'; LINK Taxa = Taxa; TRANSLATE [0] 1 'Thermococcus onnurineus TON_1021', [1] 2 'Escherichia coli YP_006125568', [2] 3 'Escherichia coli YP_006125370.1', [3] 4 'Caldanaerobacter subterraneus tengcongensis_ NP_623302.1', [4] 5 'Caldanaerobacter subterraneus yonseiensis_ERM92234.1', [5] 6 'Thermoanaerobacter sp. YS13 THYS13_RS04690', [6] 7 'Caldanaerobacter subterraneus pacificus_CDSM653_01586', [7] 8 'Moorella thermoacetica YP_431023.1', [8] 9 'Geobacillus sp. Y4.1MC1 YP_003989190.1', [9] 10 'Geobacillus thermoglucosidasius YP_004587922.1'; TREE tree_1 = ((((((5:0.003787,4:0.000001)0.903000:0.011585,(7:0.00191,6:0.021044)0.921000:0.013368)1.000000:0.238237,(10:0.155964,9:0.04098)1.000000:0.152214)0.953000:0.085963,8:0.090643)0.944000:0.143417,1:1.287552)0.935000:0.197195,3:0.409023,2:1.002222)root; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1440386200323; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 2213585034471027822; tell It; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 446367995260553128; mqVersion 304; checksumv 0 3 2034738179 null getNumChars 695 numChars 695 getNumTaxa 10 numTaxa 10 short false bits 1048575 states 1048575 sumSquaresStatesOnly 8.7779115919785E13 sumSquares 8.7779115919785E13 longCompressibleToShort false usingShortMatrix false NumFiles 1 NumMatrices 1 errorReportedDuringRun; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 234; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1149 635; setLocation 217 44; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #2213585034471027822 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #2213585034471027822; getWindow; tell It; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 915 563; setLocation 217 44; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; 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 #2213585034471027822 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlockInt 0; toggleUseWeights off; endTell; setAssignedID 4009.1440383739292.2696674972240329640; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 915 563; setLocation 217 44; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; 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; setTree '((((((5:0.003787,4:0.000001)0.903000:0.011585,(7:0.00191,6:0.021044)0.921000:0.013368)1.000000:0.238237,(10:0.155964,9:0.04098)1.000000:0.152214)0.953000:0.085963,8:0.090643)0.944000:0.143417,(3:0.409023,2:1.002222)root:0.197195)0.935000:0.643776,1:0.643776);'; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; togglePrintName on; 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 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 #446367995260553128 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 915 563; setLocation 217 44; 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 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 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;