#NEXUS [written Mon Mar 04 19:01:54 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 Taxa; DIMENSIONS NTAX=46; TAXLABELS Suberites_domuncula_tyr Saccoglossus_kowalevskii_tyrd Saccoglossus_kowalevskii_tyrc Saccoglossus_kowalevskii_tyrb Saccoglossus_kowalevskii_tyra Branchiostoma_floridae_tyrh Branchiostoma_floridae_tyre Branchiostoma_floridae_tyrf Branchiostoma_floridae_tyrg Branchiostoma_floridae_tyrd Branchiostoma_floridae_tyrc Branchiostoma_floridae_tyra Branchiostoma_floridae_tyrb Branchiostoma_floridae_tyri Branchiostoma_floridae_tyrl Branchiostoma_floridae_tyrk Branchiostoma_floridae_tyrj Branchiostoma_floridae_tyrm Mus_musculus_Tyr Homo_sapiens_TYR Branchiostoma_floridae_tyrA1 Branchiostoma_floridae_tyrC1 Branchiostoma_floridae_tyrB1 Mus_musculus_Tyrp1 Homo_sapiens_TYRP1 Mus_musculus_Tyrp2 Homo_sapiens_TYRP2a Homo_sapiens_TYRP2b 'Ciona intestinalis tyr1/2b' 'Ciona intestinalis tyr1/2a' 'Branchiostoma floridae tyr1/2b' 'Branchiostoma floridae tyr1/2a' Ciona_intestinalis_tyr Capitella_teleta_tyr2 Capitella_teleta_tyr1 Clonorchis_sinensis_tyr5 Clonorchis_sinensis_tyr4 Clonorchis_sinensis_tyr3 Schistosoma_japonicum_tyr Schistosoma_mansoni_tyr4 Schistosoma_mansoni_tyr2 Schistosoma_mansoni_tyr3 Schistosoma_mansoni_tyr1 Clonorchis_sinensis_tyr2 Clonorhis_sinensis_tyr1 Schmidtea_mediterranea_tyr ; END; BEGIN CHARACTERS; TITLE 'gamma alignment_BI'; DIMENSIONS NCHAR=149; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX Suberites_domuncula_tyr HNFIARDGTQHSGPSFPVWHRRYMLTVEKEFQRIMGNDTFGFPYWQWEENDMTPEYFGVPASVSGSLVQDWNTICCNPALARPVQRGGGSYLPNTVEVMISLSFRSRLEGWHMHNNVHVWVGGQMDVVPAAVNDPIFNLHHCNVDRIFW Saccoglossus_kowalevskii_tyrd HYYVSRDNIRHGGPGFPTWHRYFMLLWERALQKVSNNEEFALPYWDWAGELNTDTYFGKSTDTVTGTFANWPAICCSNTNTPRIQRNPGGVLPSKEAVYYALSFRNVLEGFQLHNQVHIYLNGTMSDVPIAPNDPIFILHHSNVDRIFW Saccoglossus_kowalevskii_tyrc HYYSVWDNIVHSGPGFPTWHRSFIQLWEMALQKVSNNEEFALPYWDWAGEPNTDTYFGKSTDTVTGTFANWPAICCSNTNTPRIQRNPGGVLPSKEAVYYALSFRNVLEGYQLHNQVHLYFNGTISVIANAPSDPIFILHHVNVDRILW Saccoglossus_kowalevskii_tyrb HYYAARENIRHAGPAFLTWHRAYLLLFERMIQQVNNDDDFAIPYWDWSGAPNTEEYMGKNSSNILGEFSGWKDLCCSNNNLPSITRNPGGELPSLEALYYTLSFRNILEGFQSHNQVHSYMNGTMGVVETSPNDPMFWLHHSNVDRIMW Saccoglossus_kowalevskii_tyra HYYAARENIRHAGPAFLTWHRAYLLLFERMIQQVNNDDDFAIPYWDWSGAPNTEEYMGENSSNILGEFSGWKDLCCSNVNLPSITRHPGSELPSLDALYYTLSFRNILEGFQSQNRVHSYLNGTMGIVASSPNDPMFWLHHSNVDRIMW Branchiostoma_floridae_tyrh HYYASRATTPHEGAGFPTWHRAYLLEFDRAVQEVNNDPDWTLPYWDWGAAEDTNEYVGANDDDSRSVFASWGTICCNVTVLGKLKRNPGKRLPLATEVDFALSFRNLLEGTTMHNQVHIYLNGTMSHVPSAANDPTFFLHHCNVDRLLW Branchiostoma_floridae_tyre HYYASRDTMPHEGVGFPTWHRAYLLEFERAVQEVNDDPDWTVPYWDWSAAEDTNEYVGKNDDEPESVFASWWTICCNVTVTGTLKRNPGKHLPLATEVDFALTFRNLLEGYTLHNHVHLYLDGTMSNVPSAANDPTFFLHHCNVDRLLW Branchiostoma_floridae_tyrf HYYASRDTMPHEGVGFPTWHRAYVLEIERALQEVNNDPDWTLPYWDWSAAAKTNEYVGSNDNDSESAFTSWGTICCDVTVLGKLKRNPGKRLPLATEVDFALSFRNLLEGFTVHNQVHIYLNGTMSSVPSAANDPTFFLHHCNVDRLLW Branchiostoma_floridae_tyrg HYYASRATMPHKGPAFTTWHRAYLLEFERAVQVVNNDPDWTLPYWDWSAAEDTNEYVGANDDDSGSVFASWGIICCDVTVLGKLNRNPGQHLPLVTEVDFALSFRNLLEGYSMHNQVHIYLNGTMSHVPSAPNDPMFFLHHCNVDRLFW Branchiostoma_floridae_tyrd HYYASRETMPHDGSGFLTWHRAYVLEVERALQEVNGDPDWTMPYWDWGAAEKTNEYVGANNHDTGSLFASWRTICCNVTASGKLKRNPGHHLPLATEVDFALSFRNLLEGNTLHDEVHIYLNGTMSNVPTAPNDPMFFLHHCNVDRLLW Branchiostoma_floridae_tyrc HYYASRETMPHDGSGFLTWHRAYVLEVERALQEVNGDPDWTMPYWDWGAAEKTNEYVGANNHDTGSLFASWRTICCNVTASGKLKRNPGHHLPLATEVDFALSFRNLLEGNTLHDEVHIYLNGTMSNVPTAPNDPMFFLHHCNVDRLLW Branchiostoma_floridae_tyra HYYASRETLPHEGAGFPTWHRAFLLEAERALQEVNGDPDWTLPYWDWSAAEQTNEYVGTNDHDSESIFATWRTICCDVTPTGRLKRNPGHRLPLATEVDFALSFRNLLDGFTLHNHVHLYLNGTMSTVITAANDPIFLLHHSNVDRLFW Branchiostoma_floridae_tyrb HYYASRETLPHEGAGFPTWHRAFLQEAERALQEVNGDPDWTIPYWDWSAAEQTNEYVGANDGDSESSFATWRTLCCDVTPTGRLKRNPGHRLPLATEVDFALNFRNLLEGFTLHNHVHLYLNGTMSTVITAANDPIFLLHHANVDRLFW Branchiostoma_floridae_tyri HYYASRATMPHEGVGFPTWHRAYVLEFERAVQEVNDDSDWTLPYWDWSAAEDTNDYVGKNDDDTGSVFANWETICCNVTGTGKLKRNPGNRLPYTTEVDFALSFRNLLEGYTLHNHVHIYLDGTMSDVPSAANDPIFFLHHCNVDRLFW Branchiostoma_floridae_tyrl HYYASRATMPHEGSGFPTWHRAFLLDLERALQEVNNDPDFTIPYWDWTEAENTNDYVGANYDDPRSLFATWETICCNVTRDGHVMRNPGHRLPTAAEVDFGLTFRNLLEGFTLHNHVHLYLDGTMSAVPSSANDPIFFLHHCFVDRIFW Branchiostoma_floridae_tyrk HYYASRETILHDAVGFLTWHRGYLLEMERSIQEVNNDPDWAIPYWDWTVSEQTNDFVGANDNDSGSAFAGWEALCCDPNPPEKLKRNPGTELPRKEEVDFALVFRNLVEGYTLHNHVHLYLNGTMSDVPSSANDPIFWLHHAFIDRIFW Branchiostoma_floridae_tyrj HYYASRETILHDAVGFLTWHRGYLLEMERLIQEVNNDPDWALPYWDWTVSEQTNDFVGANDNDSGSAFAGWEVLCCDPNPPEKLKRNPGTELPRKEEVDFALVFRNLVEGYTLHNHVHLYLNGTMSDVPSSANDPIFWLHHAFIDRIFW Branchiostoma_floridae_tyrm QYYAGVHSFPQGSAGFATWNRAFLVAFELAVQVVNADYDFALPYYDWTESSSSNDLVGANNSDDMSVFSRWNTVCCDVNDTGPIIRKADGSLPAKKEVNFAQSFRNLLEGFYLNEQVHQSLGGTMSQLWQASNDPIFYLHRCFMDRIFW Mus_musculus_Tyr HYYVSRDTLLHEAPGFLPWHRLFLLLWEQEIRELTGDENFTVPYWDWRDAENTDEYLGGRHESPASFFSSWQIICCDGTPEGPLLRNPGNRLPSSADVEFCLSFRNTLEGFSMHNALHIFMNGTMSQVQGSANDPIFLLHHAFVDSIFW Homo_sapiens_TYR HYYVSMDALLHEAPAFLPWHRLFLLRWEQEIQKLTGDENFTIPYWDWRDAEKTDEYMGGQHTSPASFFSSWQIVCCNGTPEGPLRRNPGNRLPSSADVEFCLSFRNTLEGFSMHNALHIYMNGTMSQVQGSANDPIFLLHHAFVDSIFW Branchiostoma_floridae_tyrA1 HYYVVRNVLLHEGPAFLPWHRLYLLLLERELAKIIGDENFALPYWDWRDLADTNDFFGASLDSSGSFLSGWQIVCCDGTPEGPLQRNPGKSLPTWEEVQGALSFRNSLEGFYLHAAVHVWMNGTVSLPAASPNDPVFFLHHAFVDSIYW Branchiostoma_floridae_tyrC1 HYYVSRNVLLHEGPVFLPWHRLFLLLWERELARFVDDENFAIPYWDWRGLDGTDDFLGATPNSNETVFSDWQVICCDGSPEGPLLRNPGTTLPTWQDVLDVLSFVNSLEGFYLHNAVHRFMNGTLSSVGSSANDPIFIIHHAYVDSIYW Branchiostoma_floridae_tyrB1 HYYVSRNVLLHEGPVFLPWHRLFLLLWERELARFVDDENFAIPYWDWRGLDGTDDFLGATPNSNETVFSDWQVICCDGSPEGPLLRNPGTSLPTWQDVRDVLSFVNTLEGFYLHNAVHRFMNGTLSSVGSSANDPIFIIHHAYVDSIYW Mus_musculus_Tyrp1 HYYSVKKTFLHEGPAFLTWHRYHLLQLERDMQEMLQEPSFSLPYWNFATGKNTDDLMGSRSFSPNSVFSQWRVVCCNSTEGGPIRRNPAGRLPEPQDVTQCLSFRNTVEGYSLHNLAHLFLNGTGGQTHLSPNDPIFVLLHTFTDAVFW Homo_sapiens_TYRP1 HYYSVKKTFLHEGPAFLTWHRYHLLRLEKDMQEMLQEPSFSLPYWNFATGKNTDDLMGSRSFSPNSVFSQWRVVCCNSTEDGPIRRNPAGRLPEPQDVAQCLSFRNTVEGYSLHNLAHLFLNGTGGQTHLSPNDPIFVLLHTFTDAVFW Mus_musculus_Tyrp2 HYYSVRDTLLHQGPAFVTWHRYHLLWLERELQRLTGNESFALPYWNFATGKNTDELLGAARDSRNSRFSTWEIVCCNGTYEGLLRRNKVGKLPTLKNVQDCLSFRNALEGFNLHNLAHSFLNGTNALPHSAANDPVFVVLHSFTDAIFW Homo_sapiens_TYRP2a HYYSVRDTLLHQGPAFVTWHRYHLLCLERDLQRLIGNESFALPYWNFATGRNTDQLFGAARDSRNSRFSSWETVCCNGTYEGLLRRNQMGKLPTLKDIRDCLSFRNALEGFSLHNLVHSFLNGTNALPHSAANDPIFVVLHSFTDAIFW Homo_sapiens_TYRP2b HYYSVRDTLLHQGPAFVTWHRYHLLCLERDLQRLIGNESFALPYWNFATGRNTDQLFGAARDSRNSRFSSWETVCCNGTYEGLLRRNQMGKLPTLKDIRDCLSFRNALEGFSLHNLVHSFLNGTNALPHSAANDPIFVVLHSFTDAIFW 'Ciona intestinalis tyr1/2b' HYYSVRDTLLHEGPAFLTWHRMHLLGLENDLQDLSGDPTFALPYWDFAIGGTTDELLGGQETGSNSRFADWEVVCCNGTNEGPIRRNPGGSLPVPEDVAECLSFRNALEGYTLHNLAHLFLNGTGGMTHASANDPIFVLLHTFTDAIFW 'Ciona intestinalis tyr1/2a' HYYSVRDTLLHEGPAFLTWHRMHLMGLENDLQVLSNDPTFALPYWDFAIGGSTDDILGGQNNGPNSTFADWEVVCCNGTFEGPIRRNPGGTLPATEDVIKCLSFRNALEGYTLHNLAHLFLNGTGGMTHASANDPVFVLLHTFTDAIFW 'Branchiostoma floridae tyr1/2b' HYYAVRDTLLHEGPAYNTWHRMHLLWLEREMQKMLGDETFALHYWDWAVGGTTDDMMGARHLSPGSPFSRWQSVCCNGTDEGPIFRNPGGVLPRPEDVGRCLSFRNSLEGYSLHNLAHLFLNGTGGITHASANDPIFVLLHSYSDAIFW 'Branchiostoma floridae tyr1/2a' HYYAVRDTLLHEGPAYNTWHRMHLLWLEREIQKMLGDETFALHYWDWAVGGTTDDMMGARHLSPGSPFSRWQSVCCNGTDEGPIFRNPGGVLPRGRDVGRCLSFRNTLEGFSLHNLAHLFLNGTASITHASANDPIFVLLHSYSDAIFW Ciona_intestinalis_tyr HAYVSRDNLVHEGPAFLPWHRYYLLKWEQELRDVVNDVTFTIPYWDWRDNQDNDVMMGGNDDSQGSPISKWEIICCTGASEGPLLRSPGNGLPTSQEVDDVISFRNLVEGFYLHNAVHLFMNGTMSEVATSANDPIFVLHHAYVDSLYW Capitella_teleta_tyr2 HFFSVKTPIKHNGPGFPTWHRRFLLEFERELQRASGDEQMGIPYWDWTDHAHTNDLVGEMVDDRGSDFWNWTMRCCNMSPPSQIWRLPTGNLPILEDISFALSFRNCLEGFSLHGQGHTFFSGSVNAVPISPSDPLFYLHHAYVDKILW Capitella_teleta_tyr1 HYFSTKNAEVHNGPGFLTWHRLYLMMMEREMGRVAGDPFFALPYWNWSGAGVTDDLAGSINSSTGSPFSRWESACCDLRPRGPVIRDPEAFLPPMEDVIFTLSFRNCIEGFTMHIQVHSFFRGTISQVSSSPDDPLFFFHHTYIDKLFW Clonorchis_sinensis_tyr5 HNYSSRTTLYHDGPEFPTWHRYLMLIWERLLAEIAGIKDFTLPYWDWVGLLKDNKYVGAPGKDSESIFYNVTNYCCQAGRAGKLVRRFVSVFPTQADVAFVLSFHMALEGFWMHNKVHNMIDGAMRSTATATNDPFFILHHNFVDKLLW Clonorchis_sinensis_tyr4 NSYGSRTTLYHDGPTFPTWHRYLMLIWERMLAEIAGIKNFALPYWDWVGLLKDNKYVGAPGRDSRSIFYNATNYCCQAGRVGKLVRKFVSVFPNQADIAFILSFHMALEGFWTNNKVHNMIEGSMQRTATATNDPIYILHQVFIDKLLW Clonorchis_sinensis_tyr3 HRYGARPTLYHDGVTFPTWHRYFQLIWERMLSNIAGIHNFAVPYWDMIGLEKTDDYVGGPGRSPNSAFTGFQEYCCQGTPNTTITRQFLTAFPNQEDLYFTLSFHMALEGYWMHNRLHRMINGSMCCTSTATNDPIFIVLHNFVDKIFW Schistosoma_japonicum_tyr HRYGSRSTLYHDGVCFPTWHRYYILLWERLMSRITGITDYATPYWDWVGLKHTNRYIGAPGESTGSPFHNLTEYCCQRGNRGTITRNFYRDLPDIDDLKFVLSFHMALEGFWFHNKVHVLIDGSMCCTGTASNDPIFVLHHALTDKIFW Schistosoma_mansoni_tyr4 HRYGSRSTLYHDGVCFPTWHRYYGLLWERLMSKIAGITDFATPYWDWTGLTYTNRYIGAPGDSSRSPFSNLTEFCCQKSKRLTITREFKKNLPDVEDLKYVLSFNIALEGFWFHNKLHVLVDGSMCCTGTASNDPLFILHHTFIDKIFW Schistosoma_mansoni_tyr2 HRYGSRSTLYHDGVCFPTWHRYYGLLWERLMSKIAGITDFATPYWDWTGLTYTNRYIGAPGDSSRSPFSNLTEFCCQKSKRLTITREFKKNLPDVEDLKYVLSFNIALEGFWFHNKLHVLVDGSMCCTGTASNDPLFILHHTFIDKIFW Schistosoma_mansoni_tyr3 HRYGSRSTLYHDGVCFPTWHRYYGLLWERLMSKIAGITDFATPYWDWTGLTYTNRYIGAPGDSSRSPFSNLTEFCCQKSKRLTITREFKKNLPDVEDLKYVLSFNIALEGFWFHNKLHVLVDGSMCCTGTASNDPLFILHHTFIDKIFV Schistosoma_mansoni_tyr1 HRYASRATLFHEVVGFLTWHRYYMLFWERHLRKIAGWTDFTIPYWDWVDSTRVNSLLGGYGGDPRSPFYMWPEYCCHAGNFRVLTRYFESAFPTTHNLLFTLGFHQALEGFFMHNKVHNVVSGTFCCAATSPNDPLFLVHHTQIDRIFW Clonorchis_sinensis_tyr2 HEYASRGTLYHHVLGFATWHRYFMLVWERQLRKIAGWKDFAVPYWDWIDADKVNSLVGAPGDHRDSPFSNWTEQCCHSANFKPLNRHYKQAFPTTKDLQFTLGFHQALEGFFMHNKVHNMVHGSFCCASTAANDPLFLLHHSQIDRIMW Clonorhis_sinensis_tyr1 HVYASRSTLTHKGPGFPTWHRAYVLFVEEELGRLTDGDNFALPYWDWTGQTGTTDLVGAFLNLDSSPFADWVTFCCDPGLTSNGRKSPMARLPDQLDVDITLSFRDLLEGFHMHNLVHSYFNGSWFDVATSPNDPIFFLHHTFVDKLFW Schmidtea_mediterranea_tyr HFYASRSTMSHKGPAFFTWHRHYLLMFEDLLRSIAGYFNFTLPYWDWTNQTTTNDLLGDIPEESNSTFFKWKPICCDPSEEPFLWRKYSSRLPNQNEIDELFSFRNFAEGYMMHNMVHSFINGTWMDFTTSPNDPLFLLHHTFMDKIFW ; END; BEGIN TREES; Title 'gamma tree_BI'; LINK Taxa = Taxa; TRANSLATE 1 Suberites_domuncula_tyr, 2 Saccoglossus_kowalevskii_tyrd, 3 Saccoglossus_kowalevskii_tyrc, 4 Saccoglossus_kowalevskii_tyrb, 5 Saccoglossus_kowalevskii_tyra, 6 Branchiostoma_floridae_tyrh, 7 Branchiostoma_floridae_tyre, 8 Branchiostoma_floridae_tyrf, 9 Branchiostoma_floridae_tyrg, 10 Branchiostoma_floridae_tyrd, 11 Branchiostoma_floridae_tyrc, 12 Branchiostoma_floridae_tyra, 13 Branchiostoma_floridae_tyrb, 14 Branchiostoma_floridae_tyri, 15 Branchiostoma_floridae_tyrl, 16 Branchiostoma_floridae_tyrk, 17 Branchiostoma_floridae_tyrj, 18 Branchiostoma_floridae_tyrm, 19 Mus_musculus_Tyr, 20 Homo_sapiens_TYR, 21 Branchiostoma_floridae_tyrA1, 22 Branchiostoma_floridae_tyrC1, 23 Branchiostoma_floridae_tyrB1, 24 Mus_musculus_Tyrp1, 25 Homo_sapiens_TYRP1, 26 Mus_musculus_Tyrp2, 27 Homo_sapiens_TYRP2a, 28 Homo_sapiens_TYRP2b, 29 'Ciona intestinalis tyr1/2b', 30 'Ciona intestinalis tyr1/2a', 31 'Branchiostoma floridae tyr1/2b', 32 'Branchiostoma floridae tyr1/2a', 33 Ciona_intestinalis_tyr, 34 Capitella_teleta_tyr2, 35 Capitella_teleta_tyr1, 36 Clonorchis_sinensis_tyr5, 37 Clonorchis_sinensis_tyr4, 38 Clonorchis_sinensis_tyr3, 39 Schistosoma_japonicum_tyr, 40 Schistosoma_mansoni_tyr4, 41 Schistosoma_mansoni_tyr2, 42 Schistosoma_mansoni_tyr3, 43 Schistosoma_mansoni_tyr1, 44 Clonorchis_sinensis_tyr2, 45 Clonorhis_sinensis_tyr1, 46 Schmidtea_mediterranea_tyr; TREE con_50_majrule = (1:0.3708553011784541,(((2:0.03280018437247154,3:0.1114269283404914):0.1231623965269222,(4:0.013077874481502,5:0.04784298080369961):0.2894851627445335):0.1962201718600934,((18:0.5386259144445545,(15:0.126105091515733,((16:0.00841684608390134,17:0.01009183664557641):0.2458497304845762,(14:0.07004601832254358,((7:0.07384055675845247,8:0.08180654393762092,(6:0.03650122880483223,9:0.08011499956467841):0.02285651461387047):0.03686537215881946,((10:0.003815653298890852,11:0.003730610194693925):0.1035817893171057,(12:0.01707726311356271,13:0.04350377733590937):0.09407171646789983):0.05530919216338462):0.03209580958437435):0.05911019888167272):0.06688536727770075):0.05330118135518978):0.0970434239725149,((((34:0.4580419588222356,35:0.441288114403087):0.1325215025411661,(45:0.3668757129417114,46:0.4270849137798134):0.1490998501294593):0.09898346093566986,((43:0.2454908965878471,44:0.140988669705198):0.2000415728846868,(38:0.254639822077458,((36:0.07521639802166952,37:0.09651156662554232):0.2421743157376172,(39:0.1048407829813983,(40:0.003844314313308133,41:0.003913925981411912,42:0.009346201668653902):0.1283644085948113):0.1899590005011199):0.04214844593796495):0.1531343488201746):0.4054387614519911):0.09301987033798506,(((19:0.03434367173943786,20:0.06179282610089001):0.1205729471145943,(33:0.3130238431985176,(21:0.1910755886576181,(22:0.01735044148302162,23:0.007182854617404231):0.1848696777960066):0.08898647680418134):0.08574920952269185):0.07707105146853871,((31:0.008005462987506214,32:0.04382229338044876):0.1238243860711432,((29:0.03982838274571782,30:0.08897140434397277):0.1274688456382839,((24:0.01890093769528196,25:0.01115386270382677):0.1956035253765875,(26:0.04269481223814361,(27:0.003931590618980988,28:0.003798511470410187):0.05196565109526435):0.2548882553972298):0.04942293921050411):0.07596766257451759):0.288144374665552):0.131364623178271):0.1028826325651615):0.135955801660977):0.3708553011784541); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 149; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 149; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 149; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1362387714219; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 4632691327686375404; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5810097476823593060; mqVersion 275; checksumv 0 3 59017723 null getNumChars 149 numChars 149 getNumTaxa 46 numTaxa 46 short false bits 1048575 states 1048575 sumSquaresStatesOnly 1.04693735562641E14 sumSquares 1.04693735562641E14 longCompressibleToShort false usingShortMatrix false NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState true false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1280 966; setLocation 0 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #4632691327686375404 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #4632691327686375404; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 0 22; 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 #4632691327686375404 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 8165.1362361747159.4950551841826997103; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 0 22; 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 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 #5810097476823593060 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 0 22; 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;