#NEXUS [written Mon Mar 04 11:50:47 EST 2013 by Mesquite version 2.75 (build 566) at d-i191-19-46.student.eduroam.uq.edu.au/10.191.19.46] BEGIN TAXA; TITLE Taxa2; DIMENSIONS NTAX=46; TAXLABELS Branchiostoma_floridae_tyrh Branchiostoma_floridae_tyrg Branchiostoma_floridae_tyrf Branchiostoma_floridae_tyre Branchiostoma_floridae_tyri Branchiostoma_floridae_tyrd Branchiostoma_floridae_tyrc Branchiostoma_floridae_tyra Branchiostoma_floridae_tyrb Branchiostoma_floridae_tyrl Branchiostoma_floridae_tyrk Branchiostoma_floridae_tyrj Branchiostoma_floridae_tyrm Saccoglossus_kowalevskii_tyrd Saccoglossus_kowalevskii_tyrc Saccoglossus_kowalevskii_tyrb Saccoglossus_kowalevskii_tyra Suberites_domuncula_tyr Branchiostoma_floridae_tyrC1 Branchiostoma_floridae_tyrB1 Branchiostoma_floridae_tyrA1 Ciona_intestinalis_tyr Mus_musculus_Tyr Homo_sapiens_TYR Homo_sapiens_TYRP2a Homo_sapiens_TYRP2b Mus_musculus_Tyrp2 'Branchiostoma floridae tyr1/2b' 'Branchiostoma floridae tyr1/2a' Mus_musculus_Tyrp1 Homo_sapiens_TYRP1 'Ciona intestinalis tyr1/2b' 'Ciona intestinalis tyr1/2a' Capitella_teleta_tyr2 Capitella_teleta_tyr1 Clonorhis_sinensis_tyr1 Schmidtea_mediterranea_tyr Schistosoma_mansoni_tyr1 Clonorchis_sinensis_tyr2 Clonorchis_sinensis_tyr5 Clonorchis_sinensis_tyr4 Clonorchis_sinensis_tyr3 Schistosoma_japonicum_tyr Schistosoma_mansoni_try2 Schistosoma_mansoni_tyr4 Schistosoma_mansoni_tyr3 ; END; BEGIN CHARACTERS; TITLE 'Matrix in file "alignment_gammatype.nex"'; DIMENSIONS NCHAR=149; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX Branchiostoma_floridae_tyrh HNFIARDGTQHSGPSFPVWHRRYMLTVEKEFQRIMGNDTFGFPYWQWEENDMTPEYFGVPASVSGSLVQDWNTICCNPALARPVQRGGGSYLPNTVEVMISLSFRSRLEGWHMHNNVHVWVGGQMDVVPAAVNDPIFNLHHCNVDRIFW Branchiostoma_floridae_tyrg HYYVSRDNIRHGGPGFPTWHRYFMLLWERALQKVSNNEEFALPYWDWAGELNTDTYFGKSTDTVTGTFANWPAICCSNTNTPRIQRNPGGVLPSKEAVYYALSFRNVLEGFQLHNQVHIYLNGTMSDVPIAPNDPIFILHHSNVDRIFW Branchiostoma_floridae_tyrf HYYSVWDNIVHSGPGFPTWHRSFIQLWEMALQKVSNNEEFALPYWDWAGEPNTDTYFGKSTDTVTGTFANWPAICCSNTNTPRIQRNPGGVLPSKEAVYYALSFRNVLEGYQLHNQVHLYFNGTISVIANAPSDPIFILHHVNVDRILW Branchiostoma_floridae_tyre HYYAARENIRHAGPAFLTWHRAYLLLFERMIQQVNNDDDFAIPYWDWSGAPNTEEYMGKNSSNILGEFSGWKDLCCSNNNLPSITRNPGGELPSLEALYYTLSFRNILEGFQSHNQVHSYMNGTMGVVETSPNDPMFWLHHSNVDRIMW Branchiostoma_floridae_tyri HYYAARENIRHAGPAFLTWHRAYLLLFERMIQQVNNDDDFAIPYWDWSGAPNTEEYMGENSSNILGEFSGWKDLCCSNVNLPSITRHPGSELPSLDALYYTLSFRNILEGFQSQNRVHSYLNGTMGIVASSPNDPMFWLHHSNVDRIMW Branchiostoma_floridae_tyrd HYYASRATTPHEGAGFPTWHRAYLLEFDRAVQEVNNDPDWTLPYWDWGAAEDTNEYVGANDDDSRSVFASWGTICCNVTVLGKLKRNPGKRLPLATEVDFALSFRNLLEGTTMHNQVHIYLNGTMSHVPSAANDPTFFLHHCNVDRLLW Branchiostoma_floridae_tyrc HYYASRDTMPHEGVGFPTWHRAYLLEFERAVQEVNDDPDWTVPYWDWSAAEDTNEYVGKNDDEPESVFASWWTICCNVTVTGTLKRNPGKHLPLATEVDFALTFRNLLEGYTLHNHVHLYLDGTMSNVPSAANDPTFFLHHCNVDRLLW Branchiostoma_floridae_tyra HYYASRDTMPHEGVGFPTWHRAYVLEIERALQEVNNDPDWTLPYWDWSAAAKTNEYVGSNDNDSESAFTSWGTICCDVTVLGKLKRNPGKRLPLATEVDFALSFRNLLEGFTVHNQVHIYLNGTMSSVPSAANDPTFFLHHCNVDRLLW Branchiostoma_floridae_tyrb HYYASRATMPHKGPAFTTWHRAYLLEFERAVQVVNNDPDWTLPYWDWSAAEDTNEYVGANDDDSGSVFASWGIICCDVTVLGKLNRNPGQHLPLVTEVDFALSFRNLLEGYSMHNQVHIYLNGTMSHVPSAPNDPMFFLHHCNVDRLFW Branchiostoma_floridae_tyrl HYYASRETMPHDGSGFLTWHRAYVLEVERALQEVNGDPDWTMPYWDWGAAEKTNEYVGANNHDTGSLFASWRTICCNVTASGKLKRNPGHHLPLATEVDFALSFRNLLEGNTLHDEVHIYLNGTMSNVPTAPNDPMFFLHHCNVDRLLW Branchiostoma_floridae_tyrk HYYASRETMPHDGSGFLTWHRAYVLEVERALQEVNGDPDWTMPYWDWGAAEKTNEYVGANNHDTGSLFASWRTICCNVTASGKLKRNPGHHLPLATEVDFALSFRNLLEGNTLHDEVHIYLNGTMSNVPTAPNDPMFFLHHCNVDRLLW Branchiostoma_floridae_tyrj HYYASRETLPHEGAGFPTWHRAFLLEAERALQEVNGDPDWTLPYWDWSAAEQTNEYVGTNDHDSESIFATWRTICCDVTPTGRLKRNPGHRLPLATEVDFALSFRNLLDGFTLHNHVHLYLNGTMSTVITAANDPIFLLHHSNVDRLFW Branchiostoma_floridae_tyrm HYYASRETLPHEGAGFPTWHRAFLQEAERALQEVNGDPDWTIPYWDWSAAEQTNEYVGANDGDSESSFATWRTLCCDVTPTGRLKRNPGHRLPLATEVDFALNFRNLLEGFTLHNHVHLYLNGTMSTVITAANDPIFLLHHANVDRLFW Saccoglossus_kowalevskii_tyrd HYYASRATMPHEGVGFPTWHRAYVLEFERAVQEVNDDSDWTLPYWDWSAAEDTNDYVGKNDDDTGSVFANWETICCNVTGTGKLKRNPGNRLPYTTEVDFALSFRNLLEGYTLHNHVHIYLDGTMSDVPSAANDPIFFLHHCNVDRLFW Saccoglossus_kowalevskii_tyrc HYYASRATMPHEGSGFPTWHRAFLLDLERALQEVNNDPDFTIPYWDWTEAENTNDYVGANYDDPRSLFATWETICCNVTRDGHVMRNPGHRLPTAAEVDFGLTFRNLLEGFTLHNHVHLYLDGTMSAVPSSANDPIFFLHHCFVDRIFW Saccoglossus_kowalevskii_tyrb HYYASRETILHDAVGFLTWHRGYLLEMERSIQEVNNDPDWAIPYWDWTVSEQTNDFVGANDNDSGSAFAGWEALCCDPNPPEKLKRNPGTELPRKEEVDFALVFRNLVEGYTLHNHVHLYLNGTMSDVPSSANDPIFWLHHAFIDRIFW Saccoglossus_kowalevskii_tyra HYYASRETILHDAVGFLTWHRGYLLEMERLIQEVNNDPDWALPYWDWTVSEQTNDFVGANDNDSGSAFAGWEVLCCDPNPPEKLKRNPGTELPRKEEVDFALVFRNLVEGYTLHNHVHLYLNGTMSDVPSSANDPIFWLHHAFIDRIFW Suberites_domuncula_tyr QYYAGVHSFPQGSAGFATWNRAFLVAFELAVQVVNADYDFALPYYDWTESSSSNDLVGANNSDDMSVFSRWNTVCCDVNDTGPIIRKADGSLPAKKEVNFAQSFRNLLEGFYLNEQVHQSLGGTMSQLWQASNDPIFYLHRCFMDRIFW Branchiostoma_floridae_tyrC1 HYYVSRDTLLHEAPGFLPWHRLFLLLWEQEIRELTGDENFTVPYWDWRDAENTDEYLGGRHESPASFFSSWQIICCDGTPEGPLLRNPGNRLPSSADVEFCLSFRNTLEGFSMHNALHIFMNGTMSQVQGSANDPIFLLHHAFVDSIFW Branchiostoma_floridae_tyrB1 HYYVSMDALLHEAPAFLPWHRLFLLRWEQEIQKLTGDENFTIPYWDWRDAEKTDEYMGGQHTSPASFFSSWQIVCCNGTPEGPLRRNPGNRLPSSADVEFCLSFRNTLEGFSMHNALHIYMNGTMSQVQGSANDPIFLLHHAFVDSIFW Branchiostoma_floridae_tyrA1 HYYVVRNVLLHEGPAFLPWHRLYLLLLERELAKIIGDENFALPYWDWRDLADTNDFFGASLDSSGSFLSGWQIVCCDGTPEGPLQRNPGKSLPTWEEVQGALSFRNSLEGFYLHAAVHVWMNGTVSLPAASPNDPVFFLHHAFVDSIYW Ciona_intestinalis_tyr HYYVSRNVLLHEGPVFLPWHRLFLLLWERELARFVDDENFAIPYWDWRGLDGTDDFLGATPNSNETVFSDWQVICCDGSPEGPLLRNPGTTLPTWQDVLDVLSFVNSLEGFYLHNAVHRFMNGTLSSVGSSANDPIFIIHHAYVDSIYW Mus_musculus_Tyr HYYVSRNVLLHEGPVFLPWHRLFLLLWERELARFVDDENFAIPYWDWRGLDGTDDFLGATPNSNETVFSDWQVICCDGSPEGPLLRNPGTSLPTWQDVRDVLSFVNTLEGFYLHNAVHRFMNGTLSSVGSSANDPIFIIHHAYVDSIYW Homo_sapiens_TYR HYYSVKKTFLHEGPAFLTWHRYHLLQLERDMQEMLQEPSFSLPYWNFATGKNTDDLMGSRSFSPNSVFSQWRVVCCNSTEGGPIRRNPAGRLPEPQDVTQCLSFRNTVEGYSLHNLAHLFLNGTGGQTHLSPNDPIFVLLHTFTDAVFW Homo_sapiens_TYRP2a HYYSVKKTFLHEGPAFLTWHRYHLLRLEKDMQEMLQEPSFSLPYWNFATGKNTDDLMGSRSFSPNSVFSQWRVVCCNSTEDGPIRRNPAGRLPEPQDVAQCLSFRNTVEGYSLHNLAHLFLNGTGGQTHLSPNDPIFVLLHTFTDAVFW Homo_sapiens_TYRP2b HYYSVRDTLLHQGPAFVTWHRYHLLWLERELQRLTGNESFALPYWNFATGKNTDELLGAARDSRNSRFSTWEIVCCNGTYEGLLRRNKVGKLPTLKNVQDCLSFRNALEGFNLHNLAHSFLNGTNALPHSAANDPVFVVLHSFTDAIFW Mus_musculus_Tyrp2 HYYSVRDTLLHQGPAFVTWHRYHLLCLERDLQRLIGNESFALPYWNFATGRNTDQLFGAARDSRNSRFSSWETVCCNGTYEGLLRRNQMGKLPTLKDIRDCLSFRNALEGFSLHNLVHSFLNGTNALPHSAANDPIFVVLHSFTDAIFW 'Branchiostoma floridae tyr1/2b' HYYSVRDTLLHQGPAFVTWHRYHLLCLERDLQRLIGNESFALPYWNFATGRNTDQLFGAARDSRNSRFSSWETVCCNGTYEGLLRRNQMGKLPTLKDIRDCLSFRNALEGFSLHNLVHSFLNGTNALPHSAANDPIFVVLHSFTDAIFW 'Branchiostoma floridae tyr1/2a' HYYAVRDTLLHEGPAYNTWHRMHLLWLEREIQKMLGDETFALHYWDWAVGGTTDDMMGARHLSPGSPFSRWQSVCCNGTDEGPIFRNPGGVLPRGRDVGRCLSFRNTLEGFSLHNLAHLFLNGTASITHASANDPIFVLLHSYSDAIFW Mus_musculus_Tyrp1 HYYSVKKTFLHEGPAFLTWHRYHLLQLERDMQEMLQEPSFSLPYWNFATGKNTDDLMGSRSFSPNSVFSQWRVVCCNSTEGGPIRRNPAGRLPEPQDVTQCLSFRNTVEGYSLHNLAHLFLNGTGGQTHLSPNDPIFVLLHTFTDAVFW Homo_sapiens_TYRP1 HYYAVRDTLLHEGPAYNTWHRMHLLWLEREMQKMLGDETFALHYWDWAVGGTTDDMMGARHLSPGSPFSRWQSVCCNGTDEGPIFRNPGGVLPRPEDVGRCLSFRNSLEGYSLHNLAHLFLNGTGGITHASANDPIFVLLHSYSDAIFW 'Ciona intestinalis tyr1/2b' HYYAVRDTLLHEGPAYNTWHRMHLLWLEREIQKMLGDETFALHYWDWAVGGTTDDMMGARHLSPGSPFSRWQSVCCNGTDEGPIFRNPGGVLPRGRDVGRCLSFRNTLEGFSLHNLAHLFLNGTASITHASANDPIFVLLHSYSDAIFW 'Ciona intestinalis tyr1/2a' HAYVSRDNLVHEGPAFLPWHRYYLLKWEQELRDVVNDVTFTIPYWDWRDNQDNDVMMGGNDDSQGSPISKWEIICCTGASEGPLLRSPGNGLPTSQEVDDVISFRNLVEGFYLHNAVHLFMNGTMSEVATSANDPIFVLHHAYVDSLYW Capitella_teleta_tyr2 HFFSVKTPIKHNGPGFPTWHRRFLLEFERELQRASGDEQMGIPYWDWTDHAHTNDLVGEMVDDRGSDFWNWTMRCCNMSPPSQIWRLPTGNLPILEDISFALSFRNCLEGFSLHGQGHTFFSGSVNAVPISPSDPLFYLHHAYVDKILW Capitella_teleta_tyr1 HYFSTKNAEVHNGPGFLTWHRLYLMMMEREMGRVAGDPFFALPYWNWSGAGVTDDLAGSINSSTGSPFSRWESACCDLRPRGPVIRDPEAFLPPMEDVIFTLSFRNCIEGFTMHIQVHSFFRGTISQVSSSPDDPLFFFHHTYIDKLFW Clonorhis_sinensis_tyr1 HNYSSRTTLYHDGPEFPTWHRYLMLIWERLLAEIAGIKDFTLPYWDWVGLLKDNKYVGAPGKDSESIFYNVTNYCCQAGRAGKLVRRFVSVFPTQADVAFVLSFHMALEGFWMHNKVHNMIDGAMRSTATATNDPFFILHHNFVDKLLW Schmidtea_mediterranea_tyr NSYGSRTTLYHDGPTFPTWHRYLMLIWERMLAEIAGIKNFALPYWDWVGLLKDNKYVGAPGRDSRSIFYNATNYCCQAGRVGKLVRKFVSVFPNQADIAFILSFHMALEGFWTNNKVHNMIEGSMQRTATATNDPIYILHQVFIDKLLW Schistosoma_mansoni_tyr1 HRYGARPTLYHDGVTFPTWHRYFQLIWERMLSNIAGIHNFAVPYWDMIGLEKTDDYVGGPGRSPNSAFTGFQEYCCQGTPNTTITRQFLTAFPNQEDLYFTLSFHMALEGYWMHNRLHRMINGSMCCTSTATNDPIFIVLHNFVDKIFW Clonorchis_sinensis_tyr2 HRYGSRSTLYHDGVCFPTWHRYYILLWERLMSRITGITDYATPYWDWVGLKHTNRYIGAPGESTGSPFHNLTEYCCQRGNRGTITRNFYRDLPDIDDLKFVLSFHMALEGFWFHNKVHVLIDGSMCCTGTASNDPIFVLHHALTDKIFW Clonorchis_sinensis_tyr5 HRYGSRSTLYHDGVCFPTWHRYYGLLWERLMSKIAGITDFATPYWDWTGLTYTNRYIGAPGDSSRSPFSNLTEFCCQKSKRLTITREFKKNLPDVEDLKYVLSFNIALEGFWFHNKLHVLVDGSMCCTGTASNDPLFILHHTFIDKIFW Clonorchis_sinensis_tyr4 HRYGSRSTLYHDGVCFPTWHRYYGLLWERLMSKIAGITDFATPYWDWTGLTYTNRYIGAPGDSSRSPFSNLTEFCCQKSKRLTITREFKKNLPDVEDLKYVLSFNIALEGFWFHNKLHVLVDGSMCCTGTASNDPLFILHHTFIDKIFW Clonorchis_sinensis_tyr3 HRYGSRSTLYHDGVCFPTWHRYYGLLWERLMSKIAGITDFATPYWDWTGLTYTNRYIGAPGDSSRSPFSNLTEFCCQKSKRLTITREFKKNLPDVEDLKYVLSFNIALEGFWFHNKLHVLVDGSMCCTGTASNDPLFILHHTFIDKIFV Schistosoma_japonicum_tyr HRYASRATLFHEVVGFLTWHRYYMLFWERHLRKIAGWTDFTIPYWDWVDSTRVNSLLGGYGGDPRSPFYMWPEYCCHAGNFRVLTRYFESAFPTTHNLLFTLGFHQALEGFFMHNKVHNVVSGTFCCAATSPNDPLFLVHHTQIDRIFW Schistosoma_mansoni_try2 HEYASRGTLYHHVLGFATWHRYFMLVWERQLRKIAGWKDFAVPYWDWIDADKVNSLVGAPGDHRDSPFSNWTEQCCHSANFKPLNRHYKQAFPTTKDLQFTLGFHQALEGFFMHNKVHNMVHGSFCCASTAANDPLFLLHHSQIDRIMW Schistosoma_mansoni_tyr4 HVYASRSTLTHKGPGFPTWHRAYVLFVEEELGRLTDGDNFALPYWDWTGQTGTTDLVGAFLNLDSSPFADWVTFCCDPGLTSNGRKSPMARLPDQLDVDITLSFRDLLEGFHMHNLVHSYFNGSWFDVATSPNDPIFFLHHTFVDKLFW Schistosoma_mansoni_tyr3 HFYASRSTMSHKGPAFFTWHRHYLLMFEDLLRSIAGYFNFTLPYWDWTNQTTTNDLLGDIPEESNSTFFKWKPICCDPSEEPFLWRKYSSRLPNQNEIDELFSFRNFAEGYMMHNMVHSFINGTWMDFTTSPNDPLFLLHHTFMDKIFW ; END; BEGIN TREES; Title Type_3_copper_gamma_subclass_Neighbor_Joining_tree; LINK Taxa = Taxa2; TRANSLATE 1 Branchiostoma_floridae_tyrh, 2 Branchiostoma_floridae_tyrg, 3 Branchiostoma_floridae_tyrf, 4 Branchiostoma_floridae_tyre, 5 Branchiostoma_floridae_tyri, 6 Branchiostoma_floridae_tyrd, 7 Branchiostoma_floridae_tyrc, 8 Branchiostoma_floridae_tyra, 9 Branchiostoma_floridae_tyrb, 10 Branchiostoma_floridae_tyrl, 11 Branchiostoma_floridae_tyrk, 12 Branchiostoma_floridae_tyrj, 13 Branchiostoma_floridae_tyrm, 14 Saccoglossus_kowalevskii_tyrd, 15 Saccoglossus_kowalevskii_tyrc, 16 Saccoglossus_kowalevskii_tyrb, 17 Saccoglossus_kowalevskii_tyra, 18 Suberites_domuncula_tyr, 19 Branchiostoma_floridae_tyrC1, 20 Branchiostoma_floridae_tyrB1, 21 Branchiostoma_floridae_tyrA1, 22 Ciona_intestinalis_tyr, 23 Mus_musculus_Tyr, 24 Homo_sapiens_TYR, 25 Homo_sapiens_TYRP2a, 26 Homo_sapiens_TYRP2b, 27 Mus_musculus_Tyrp2, 28 'Branchiostoma floridae tyr1/2b', 29 'Branchiostoma floridae tyr1/2a', 30 Mus_musculus_Tyrp1, 31 Homo_sapiens_TYRP1, 32 'Ciona intestinalis tyr1/2b', 33 'Ciona intestinalis tyr1/2a', 34 Capitella_teleta_tyr2, 35 Capitella_teleta_tyr1, 36 Clonorhis_sinensis_tyr1, 37 Schmidtea_mediterranea_tyr, 38 Schistosoma_mansoni_tyr1, 39 Clonorchis_sinensis_tyr2, 40 Clonorchis_sinensis_tyr5, 41 Clonorchis_sinensis_tyr4, 42 Clonorchis_sinensis_tyr3, 43 Schistosoma_japonicum_tyr, 44 Schistosoma_mansoni_try2, 45 Schistosoma_mansoni_tyr4, 46 Schistosoma_mansoni_tyr3; TREE tree_1 = (18:0.4093585,((((14:0.015356,15:0.150204):0.210048,(16:0.024127,17:0.054663):0.303809):0.147026,(13:0.654695,((11:0.011014,12:0.010017):0.240518,(10:0.132607,((8:0.025046,9:0.040085):0.090832,((6:1.0E-6,7:1.0E-6):0.138269,((4:0.1057,5:0.054588):0.027601,(3:0.084565,(1:0.084864,2:0.06425):0.026695):0.008586):0.015913):0.041157):0.075061):0.025366):0.045025):0.122036):0.037612,(((34:0.55833,35:0.492036):0.104517,((36:0.433646,37:0.489522):0.106003,((38:0.264712,39:0.210759):0.221774,((42:0.326621,(40:0.036723,41:0.166253):0.27665):0.017449,(43:0.106704,(44:0.0,(45:0.0,46:0.01773):0.005458):0.160301):0.211953):0.095254):0.343117):0.092196):0.004438,(((23:0.043994,24:0.068203):0.175262,(22:0.345373,(21:0.201658,(19:0.013587,20:0.007658):0.231828):0.075852):0.030293):0.073208,((27:0.063577,(25:1.0E-6,26:1.0E-6):0.052295):0.215784,((28:0.029886,29:0.021976):0.194567,((30:0.006799,31:0.021357):0.258472,(32:0.051062,33:0.08612):0.106496):0.036934):0.038062):0.252273):0.12314):0.022078):0.4093585); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 149; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 149; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 149; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1362361847800; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 544201959567539401; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 10223665458238507; mqVersion 275; checksumv 0 3 4137280340 null getNumChars 149 numChars 149 getNumTaxa 46 numTaxa 46 short false bits 1048575 states 1048575 sumSquaresStatesOnly 1.0538851484486E14 sumSquares 1.0538851484486E14 longCompressibleToShort false usingShortMatrix false NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1280 966; setLocation -1280 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #544201959567539401 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #544201959567539401; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1180 899; setLocation -1280 0; 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 #544201959567539401 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 8505.1362361826919.586793643690407176; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1180 899; setLocation -1280 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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; 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 #10223665458238507 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1180 899; setLocation -1280 0; 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;