#NEXUS [written Sat Aug 23 19:59:20 IST 2014 by Mesquite version 2.75 (build 564) at Subha_PC/192.168.204.48] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=26; TAXLABELS Rhizoctonia_solani_endornavirus_RS002 Rhizoctonia_cerealis_endornavirus_1 Helicobasidium_mompa_endornavirus_1_670 Chalara_elegans_endornavirus Gremmeniella_abietina_type_B_RNA_virus_XL1 Gremmeniella_abietina_type_B_RNA_virus_XL2 Phytophthora_endornavirus_1_OR Bell_pepper_endornavirus_KS Bell_pepper_endornavirus_YW Bell_pepper_endornavirus_KY Bell_pepper_endornavirus_Is Phaseolus_vulgaris_endornavirus_1 Phaseolus_vulgaris_endornavirus_2 Persea_americana_endornavirus Oryza_sativa_endornavirus Oryza_rufipogon_endornavirus Vicia_faba_endornavirus Grapevine_endophyte_endornavirus Brome_mosaic_virus Cherry_green_ring_mottle_virus Shallot_virus_X Garlic_latent_virus Turnip_vein_clearing_virus Beet_soil_borne_virus_Ahl Tobacco_rattle_virus_SYM Pea_early_browning_virus ; END; BEGIN CHARACTERS; TITLE 'Matrix in file "Hel1 alignment.nexus"'; DIMENSIONS NCHAR=308; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX Rhizoctonia_solani_endornavirus_RS002 GCGKSTKIKQMIK-EGEIATAMTSGALDSLSI--KLGKSK-------------------------------------VISVEKLLSIQHNY----------DVIYIDEATSMTP--FDVTL-IAQKAKKIHMFGDTDQIGLSDMHSAPGDRSKVMAMAYAGR---KDVNPYSLRVGNPLA-AEIGK---VIERFKTKADHETNFNTLWEESFIASKVVDLAKENSIDVIFVFYKKHYEDITNQL-NLRSRTERTKIKVYKVHANQGREGDNVMVVQG-GVSDDFRGIHLD------KHYTYSAATRAK Rhizoctonia_cerealis_endornavirus_1 GAGKSTFIKSKFK-SGDIACATTGGAIQSIRD--KGIKS--------------------------------------AMSIERLTYTRPQC----------KTLFIDEASSLSL--ASFAICLPESVESVHLLGDLDQVVYVDMYETFGTRKQALVMQLAGT---TVPMYKSYRIGNPLA-AELKY---IKPAFEP-AAHETKVTLLNVASFDSLDIQKLVTDYEVDMIWVFYDAMQKALK----------KVVTIPINKVHADQGKEASCVLVIQGTNRSDGTGSIHLD------RNYCYSAASRAK Helicobasidium_mompa_endornavirus_1_670 GAGKSTRIAEAYK-KGDIVVSATRGSIASLKNKIKVKDKK-------------------------------------IISFENLASGVTTIEAT------VNTIFFDECTLLDPV-LLAFAIESPYMPEIRFYGDNTQIANKDFVDCPGTRMEISLLDFCKAT---ETTNVQYRIGEGLATEIDLVR--PGGYKSSPGHKGTTFATMDVVMVDAKEVINAIKEHNISTVLVFYKKHAKIMKEALAG---DASLTKVVIETVHKFQGLEAKRGMIIQARMGDRVYIENDPT--------YCMSAVTRFS Chalara_elegans_endornavirus GSGKTTMIQALPGLQNATIIAKTRAALSGLSSTPCHK----------------------------------------LMSLESASYTKINS----------PTIVVEEAGMVLP--TELLSVLDQPNMRIHLFGDSQQIGLVDMHTTPGLRGFESILQRFKT----ETLTKTFRFGNPLARDWISK---FYPTIETVETNQTTYGYSRLDS--IEETVSVAINSKVDAIYCFLSHTQRVIQD-----ELAARSVDIPVFKVHSGQGAEFDKVLVAHIGGGASHS-GVMYQ------KSYVVTAMTRAR Gremmeniella_abietina_type_B_RNA_virus_XL1 GIGAIQLYKDAPKQDENATWVLPTYRTAQLQDDMRLLNSANSNIKIVDYLHNCTLYAGPPGSGKTHSMLNTYGNIPIVTTSETQLKLHNDWTTPSGVVNYVPIIGVDEAGLITL---STLLTLIAKADKLIFTCDVGQIINKQEQNIQELTGIDSVAHLLMKFCNVITFNESYRLGKNICQVVSKL----GTKLSSKREQDDEIVGISCVIGNNPEFSNAIINSNPDLIICATNNLARQLRS----------FIDINITTITRCQGADVKRVLLVISGIDYRNIGNETLYVALTRHSQHITIVVDRPN Gremmeniella_abietina_type_B_RNA_virus_XL2 GIGAIQLYKDAPKQDENATWVLPTYRTAQLQDDMRLLNSANSNIKIVDYLHNCTLYAGPPGSGKTHSMLNTYGNIPIVTTSETQLKLHNDWTTPSGVVNYVPIIGVDEAGLITL---STLLTLIAKADKLVFTCDVGQIINKQEQNIQELTGIDSVAHLLMKFCNVVTFNESYRLGKNICQVVSKL----GTKLSSKREQDDEIVGISCVIGNNPEFSNAIINSNPDLIICATNNLARQLRS----------FIDINITTITRCQGADVKRVLLVISGIDYRDIGNETLYVALTRHSQHITIVVDRPN Phytophthora_endornavirus_1_OR GWGKSTKIVKEFD-TDTTVTCVTSEAVKNLVAMGLPRNK--------------------------------------VTSVERAVESKIHT----------KKLAIDECTQVDW--LMVHMMCGDEVEIITLAGDSFQIGAVDFSASTGERTITSCNMFSLHQN---TYNNSHRFGQPLCSQLTVL----NPRLTTDALHQTSYSVHNLSSLDLNVLGSVIAQERPGVILTFHQITKSQIQRAF-GRTIKTSLTTGDVKTVHSYQGKESSRVMVIQDFLSPAG---VHTD------RRYLMSAASRAS Bell_pepper_endornavirus_KS GSGKSTMIANNWV-DGTIAIAKTTSAVKNLQLKIGGPKN-------------------------------------LVMSHEKYAFTQTPI----------HDLVIDECSMFTW--FDLYFSLTELPRTLTMYGDPHQISTIDTFMLGGERILDNITDYVVE---KTNLRSTFRYGASVC-ALLSP---LVGELSSKAKHDTKVVDVNLALWDNVELKAIINEHNPDVVLTHHNITKQRLMA--------LCPN-KRVETIHSFQSMEANSVLIVQYNEGGNS--KIYMD------KKYAISAITRAK Bell_pepper_endornavirus_YW GSGKSTMIANNWA-DGTIAIAKTTSAVKNLQLKVGGPKN-------------------------------------LVMSHEKYAFTQTPI----------HDLVIDECSMFTW--FDLYFSLIELPRTLTMYGDPHQISTIDTFMLGGERILDNITDYVME---KTNLRSTFRYGASVC-ALLSP---LVGELSSKAKHDTKVVDVNLVLWDNVELKTIIDEHNPDVILTHHNITKQRLLA--------LCPN-KRVETIHSFQSMEANSVLIVQYNEGGNS--KIYMD------KKYAISAITRAK Bell_pepper_endornavirus_KY GSGKSTMIANNWV-DGTIAIAKTTSAVKNLQLKIGGPKN-------------------------------------LVMSHEKYAFTQTPI----------HDLVIDECSMFTW--FDLYFSLTELPRTLTMYGDPHQISTIDTFMLGGERILDNITDYVVE---KTNLRSTFRYGASVC-ALLSP---LVGELSSKAKHDTKVVDVNLALWDNVELKAIINEHNPDVVLTHHNITKQRLMA--------LCPN-KRVETIHSFQSMEANSVLIVQYNEGGNS--KIYMD------KKYAISAITRAK Bell_pepper_endornavirus_Is GSGKSTMIANNWV-DGTIAIAKTTSAVKNLQLKIGGPKN-------------------------------------LVMSHEKYAFTQTPI----------HDLVIDECSMFTW--FDLYFSLTELPRTLTMYGDPHQISTIDTFMLGGERILDNITDYVVE---KTNLRSTFRYGASVC-ALLSP---LVGELSSKAKHDTKVVDVNLALWDNVELKAIINEHNPDVVLTHHNITKQRLMA--------LCPN-KRVETIHSFQSMEANSVLIVQYNEGGNS--KIYMD------KKYAISAITRAK Phaseolus_vulgaris_endornavirus_1 GFGKSTAIAAKCS-DNDLCVAMTSTSVESLKSKIKNK-VR-------------------------------------VMTVEKALYSHATT----------ASTLYIDEAMLVP--WQVILLLCAKGTTLGMFGAKNQIANVDMSSSPGIRHVVNIDKLIKASNITEQFT-TYRIGTGLF-EFIKP---LEPGLLQGSDHRTSFSVTILDPEQFGTLSNIYNRKQYDVVITPYNYNKMAITN--------LLGSASPVVTAHSFQGQEVNSSLVVLKADKTG-KWDLNSD------PRYLNAALTRAK Phaseolus_vulgaris_endornavirus_2 GSGKTTKIARDWT-TDDLAIARTTVAVTSLREKLNSPKQ-------------------------------------LVMSHEKYSFTQPPT----------HRLVIDECTMFPW--YELYFSLTTLPTSLVMYGDPNQISTIDTYMLGGERILDNIADYVPN---KTLLKSTYRYGPKLC-GILNS---IVGEIVSNAPHDTMVLDLNLPTWDDSKLISIIRDAKPDVVLVHHNVTKRRIGK--------LLTT-IKVETIHSYQSKEANAVLVVQYNEGGNS--QIYMN------RNYAVSAATRCK Persea_americana_endornavirus GFGKSTMIGNQAK-AGDLCVAMTSTSVRSLQAKVTAS-AR-------------------------------------VMSIEKANYTHQKT----------KTNLFVDEALMVD--WLSIILLCTKDTKIKMFGAEHQIGLLDMSLTPGIRTIEPIIKHVSDNNIKRSKI-SYRIGEPLR-TFIEP---LEPGIVSGGTHKTTYTVTCLNDEQIENIGQAITRSRPDVIITPYQYNKAKIMS--------IDNR-VPVETTHSFQGQEVMRSMVVLRSDVTG-KWDLNGK------PDYLNSALTRAK Oryza_sativa_endornavirus GYGKSTMISKAIT-HGDLCVAMTRSSVMSIEEKTKDKHIT-------------------------------------VCSLEKASSSMMKC----------PNTIFVDEATMID--WLKLALLCEPTTTLRMYGSESQVGAVDMSPTPGLRHITRIQDLLLENQISRFYS-TYRIGESLA-TFIRP---IEPKLVSLADHKTTYNVTVLEDAEFEKLPVIVHRCKPDVIITPYNYNRQRIEN--------MTDVTIPVVTTHSYQGQEVNKSLVILRADRTG-KWDLNGN------ALYLNSALTRAK Oryza_rufipogon_endornavirus GYGKSTMISQEIT-SGDLCVAMTRSSVMSIEEKIKDKHVT-------------------------------------VCSLEKASCSMMKC----------ANTIFVDEATMVD--WLRLALLCERPTTLKLYGSESQVGAVDMSPTPGMRHVMRIQDLLLDHQVNRFNTTTNRIGEELA-TFIRP---MELKLVSLAKHKTTYNVTVLEDADFERLPIMVNRCNPDVIITPYNYNRQRIEA--------MHGISVPVVTTHSYQGQEVNKSLVILRADRTG-KWDLNGN------ELYLNSALTRAK Vicia_faba_endornavirus GWGKSTEIVKLVN-QDCTVVAQTSAAVSNILEKLEQGGKKNM------------------------------C---KVMSIEKCMTQQVNT----------PTLVLDEASMITW--ETLSLITGPQVENVYLYGNTLQICVLDMYRTGGSRATKSILEQAGI---IRRHYTTHRIGNPLA-RELSL---VTKELTTNAKHETNFCTKSWDAVRWAELTSIAGSLEEPVILCFYNNAVRAVMN--------YLKVGCRVDTIHKFQGLEADNVIVLQWCPTGQTPGRITLD------KHQCLSAATRAK Grapevine_endophyte_endornavirus GSGKTTLLRNLTNRDKATLVCKTRSAIESHYDSSFHT----------------------------------------LMTMEAAGMSHIVT----------NILVIDEASMITN--VELLCCLDNPNMLVHMMGDSMQIGVKDMSNVLGNRKENSLLAQLAN----TKLYHTYRFGQPLVDKMLKQ---FVPNITCEPNVHTELTQVTASS--YDEIVQLTNNYKVDAVYVFMDADYVQLLE-----ILGDK---IAVNKVHASQGKEFDNVLVVHWGNFQVET-SIVKS------SKFLFTAATRAR Brome_mosaic_virus GCGKTTAIKDAFRMGEDLIVTANRKSAEDVRMALFPDTFNSK------------------------------VALDIVRTADSAIMHGVPS---------CHRLLVDEAGLLHYG-QLLVVAALSKCSQVLAFGDTEQISFKSR--DAGFKLLHGNLKYDRRD----VVHKTYRCPQDVIAAVNLLKRKCGNRDTKYQSWTSESKVSRSLAKRRITSVLQVTIDPNRTYLTMTQADKAALQTRAKDFPVSKDWIDGHIKTVHEAQGISVDNVTLVRLKSTKCDLFKH---------EEYCLVALTRHK Cherry_green_ring_mottle_virus GCGKSTLVRKFLDLEDFHAQTFGVSKPTNLSG----------------------------------------------RGVEKAPVPLQSG-----------FNILDEYLSGPYS-EGFDLFLSDPYQNFRKPLTAHYIN-----------------------------SCTHRFGPSVCQFLNKLG----FEIESAKEEDTEL-----------IFGKVFGGTIRGEIICFEKEIEELLRS-----------HSASFHHPCDLRGAEFDDVTFISAHTDLQEIVGP-----------DLYVALTRAK Shallot_virus_X GSGKSTLVRALVTYRSTVACTLGAPYGSNLAFPGVTS-----------------------------------------PGLTQSLTDHETR-------------ILDEYQLGTESDLKPFNVLVGDPFQGNLHLKAHYVK-----------------------------SFSHRVPRIICNFLQSLG----YEIAGSKPGELAQLP----------IYGPNPSGPTGQVLHLGPLSRRLTQS-----------HGVCSKLPSEVQGLEFEEVTLVYHSSEFERN------------RVGFYIAATRAL Garlic_latent_virus GCGKSRLHRKLIN-QDSRFIAPTFGAPDPLNVTGRR-----------------------------------------IRAVSELDTFDRTG----------KFLLLDEFQQGDF--EGLKPCPLWHVCQFFDSARPYPIADWYK-------------------------TLSHRVNKTTCDFLRNFG----FEITSSVQGNLTFG-------------GLYEEELQGVVITYCTQVSALVES-----------HRVEHYKLADCRGSEFNNVSLCLSDSVVHSED-----------LAKFYVCATRSR Turnip_vein_clearing_virus GCGKTKEIIEKVNFSEDLILVPGKEASKMIIRRANQAG-VIR------------------------------ADKDNVRTVDSFLMHPSRR--VF------KRLFIDEGLMLHTG-CVNFLLLLSQCDVAYVYGDTKQIPFICRVANFPYPAHFAKLVADEKE----VRRVTLRCPADVTYFLNK-----KYDGAVMCTSAVERSVKAEVVR-GKGALNPITLPLEGKILTFTQADKFELLE-----KGYK-----DVNTVHEVQGETYEKTAIVRLTSTPLEIISS---A-----SPHVLVALTRHT Beet_soil_borne_virus_Ahl GCGKSTHIVKEARLENQYVLTMGREAAAELRERFKTVRGSTE------------------------------EQLKRVRTVDSFLMNDKDS--RA------KILHFDEALMAHAG-MVYFCADNLSARTIICQGDSQQIPFINRVESITLEYAKLE--ITNVV----EKRLTYRSPLDVACFLTRKN--FYWHFHCYERKSNGRSISVVGPRDGMTSNYSIPKKKGAQYLTFTQSEKEDMVR-----YLGKGQWS--VNTVHESQGKTYDDVILVRLKPTDNEIYPGGRKS-----KPYVVVGTTRHR Tobacco_rattle_virus_SYM GCGKSTMIVNSANPCVDVVLSTGRAATDDLIERFASKG-FPC------------------------------KLKRRVKTVDSFLMHCVDGSLTG------DVLHFDEALMAHAG-MVYFCAQIAGAKRCICQGDQNQISFKPRVSQVDLRFSSLVGKFDIVT----EKRETYRSPADVAAVLNK-----YYTGDVRTHNATANSMTVRK----IVSKEQVSLKPGAQYITFLQSEKKELVN-----LLALRKVAAKVSTVHESQGETFKDVVLVRTKPTDDSIARG---------REYLIVALSRHT Pea_early_browning_virus GCGKSTMIVNTANPVFDVVLSTCKEATEDLLEKFAAKK-FGI------------------------------NLKKRVKTVDSFLMHCSDGNCVG------DLLHFDEALMAHAG-MVFFCAQIAKAKKVICQGDQKQIAYKPRVSQLTLRFTSLIGRFDEVE----EKRMSYRCPVDVALTLDR-----FYTGKVVTKNSVLRSMDVKR----IGSKEQVEMEHGIQYLTFLQSEKKDIAN-----LLCQRKVKSFVNTVHEAQGKTFKKVRLVRLKPTDDVLARG---------QEYQIVALSRHT ; END; BEGIN TREES; Title Hel_1_ML_Tree; LINK Taxa = Taxa; TRANSLATE 1 Rhizoctonia_solani_endornavirus_RS002, 2 Rhizoctonia_cerealis_endornavirus_1, 3 Helicobasidium_mompa_endornavirus_1_670, 4 Chalara_elegans_endornavirus, 5 Gremmeniella_abietina_type_B_RNA_virus_XL1, 6 Gremmeniella_abietina_type_B_RNA_virus_XL2, 7 Phytophthora_endornavirus_1_OR, 8 Bell_pepper_endornavirus_KS, 9 Bell_pepper_endornavirus_YW, 10 Bell_pepper_endornavirus_KY, 11 Bell_pepper_endornavirus_Is, 12 Phaseolus_vulgaris_endornavirus_1, 13 Phaseolus_vulgaris_endornavirus_2, 14 Persea_americana_endornavirus, 15 Oryza_sativa_endornavirus, 16 Oryza_rufipogon_endornavirus, 17 Vicia_faba_endornavirus, 18 Grapevine_endophyte_endornavirus, 19 Brome_mosaic_virus, 20 Cherry_green_ring_mottle_virus, 21 Shallot_virus_X, 22 Garlic_latent_virus, 23 Turnip_vein_clearing_virus, 24 Beet_soil_borne_virus_Ahl, 25 Tobacco_rattle_virus_SYM, 26 Pea_early_browning_virus; TREE UNTITLED = ((((((((((15:0.05157631,16:0.07172982)1.0000:0.31389411,14:0.25702491)0.4400:0.05558553,12:0.37583885)1.0000:0.64847195,(3:1.18778248,(1:0.48153419,2:0.55801401)0.8770:0.23509548)0.3460:0.12707127)0.1690:0.10411967,(13:0.27504565,(9:0.03566864,(8:0.0,(10:0.0,11:0.0)0.3270:0.0)0.5600:0.0)0.9690:0.19294835)0.9960:0.50477513)0.1190:0.08052721,(7:0.69637939,17:0.54223888)0.5240:0.16336695)0.3340:0.14941457,(4:0.50961762,18:0.54283667)0.9810:0.38186373)0.8220:0.40878114,(5:0.0,6:0.00578345)1.0000:1.8835024)0.4140:0.02806674,(19:0.56898466,(23:0.58738767,(24:0.46907433,(25:0.13834663,26:0.18976621)0.9350:0.16181087)0.9240:0.32577564)0.7880:0.29504351)0.9930:0.90069938)0.9980:0.39742225,(22:1.32438758,(20:0.6219313,21:1.53172036)0.3610:0.21258292)0.9980:0.73888205); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 308; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 308; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 308; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1408804160128; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 6314091461525006361; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 325135824047490504; mqVersion 275; checksumv 0 3 4146675599 null getNumChars 308 numChars 308 getNumTaxa 26 numTaxa 26 short false bits 1048575 states 1048575 sumSquaresStatesOnly 6.866826421964E13 sumSquares 6.866826421964E13 longCompressibleToShort false usingShortMatrix false NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 331; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1366 649; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #6314091461525006361 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #6314091461525006361; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1035 582; setLocation -8 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 #6314091461525006361 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 877.1408775873606.532764862594714290; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1035 582; setLocation -8 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 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; 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 #325135824047490504 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1035 582; setLocation -8 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; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; showCharacters #325135824047490504 #mesquite.lists.CharacterList.CharacterList; tell It; setData 0; getWindow; tell It; newAssistant #mesquite.lists.CharListInclusion.CharListInclusion; newAssistant #mesquite.stochchar.CharListProbModels.CharListProbModels; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1035 582; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.CharListAnnotPanel.CharListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; endTell; end;