#NEXUS [written Sat Aug 23 19:50:56 IST 2014 by Mesquite version 2.75 (build 564) at Subha_PC/192.168.204.48] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=17; TAXLABELS Rhizoctonia_solani_endornavirus_RS002 Rhizoctonia_cerealis_endornavirus_1 Gremmeniella_abietina_type_B_RNA_virus_XL1 Gremmeniella_abietina_type_B_RNA_virus_XL2 Bell_pepper_endornavirus_KS Bell_pepper_endornavirus_YW Bell_pepper_endornavirus_KY Bell_pepper_endornavirus_Is Phaseolus_vulgaris_endornavirus_2 Sunn_hemp_mosaic_virus Tobacco_mild_green_mosaic_virus Obuda_pepper_virus Tobacco_rattle_virus_CAM Beet_virus_Q Barley_stripe_mosaic_virus Alfalfa_mosaic_virus Tobacco_streak_virus_WC ; END; BEGIN CHARACTERS; TITLE 'Matrix in file "MTR.nexus"'; DIMENSIONS NCHAR=230; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX Rhizoctonia_solani_endornavirus_RS002 NPHAFLATCRKVARDFILR-LHKN-RPMVDIGGS-PDKYR----PQDFTVRPLLDVSDKVR---------------------------------------------QLVK-PTINGCAHRVGGCTCMW--------PENHGTMLIDSIYDITADELLNTLATRKVETFYYTSSLYGVNFDKATIQELDLDQGYVQIL--------GDITTTVLTGESVSYENHTPTARMW Rhizoctonia_cerealis_endornavirus_1 NPHAMIAVTRKMIYKSLKN-IYKG-RPIIDVGGD-PTQGA----DNVHTMRPNLDVHDGLR---------------------------------------------KITK-KNELGCDHLLSECNCKF--------KPNSGLIFVDSIYDIQPKDVVKFCRENKIETFYYAISTHGIQVDKN-LNALPFSSGTAIRD--------QESMVTFLTGESNPYLNSENLTQFW Gremmeniella_abietina_type_B_RNA_virus_XL1 HSHIYHHANRLMLTEMLASRHPRN-ALLYDIGGNINRHLD-HGRLNVHCVYTTSTPADLSRHTLWVKKATQWAHANLKNK--------------SVHGATYSSIAASMIKEDNSMWCTNGIANCSHAP--------ISVGFAMSIDTLVHLDPSDLIKFYIDNNVAHASHAMTIPDNYAYAT-KGVLRHNEGHWYRTN------NGTWVIEFVGES-LSYEQKVSYTDAY Gremmeniella_abietina_type_B_RNA_virus_XL2 HSHIYHHANRLMLTEMLASRHPRN-ALLYDIGGNINRHLD-HGRLNVHCVYTTSTPADLSRHTLWVKKATQWAHANLKNK--------------SVHGATYSSIAASMIKEDNSMWCTNGIANCSHAP--------ISVGFAMSIDTLVHLDPSDLIKFYIDNNVAHASHAMTIPDNYAYAT-KGVLRHNEGHWYRTN------NGTWVIEFVGES-LSYEQKVSYTDAY Bell_pepper_endornavirus_KS NPHAMLAAERRICAVTMGDKVKKG-KKILDIGTRINLTGN----DSWHGMGPCLDWRDVER---------------------------------------------YHNRPLTANTCDHTVKECGCMD--------GQNPLLISVDAMYDIDPTDVISLMHRTGTNQLFFCLSTAEVDFENT-NGKLAHGQGEWMRH--------DDKLVTVLRGDDRPYVNNWKLTKLW Bell_pepper_endornavirus_YW NPHAMLAAERRICAVTMGDKVRRD-KKILDIGTRINLTGN----DNWHGMGPCLDWRDVER---------------------------------------------YHNRPLTANTCDHTVKECGCLD--------GQNPLLISVDAMYDIDPTDVISLMQRTGTNQLFFCLSTAEVDFDNT-NGKLAHGQGEWMRH--------DDKLITVLRGDDRPYVNNWKLTKLW Bell_pepper_endornavirus_KY NPHAMLAAERRICAVTMGDKVKKG-KKILDIGTRINLTGN----DSWHGMGPCLDWRDVER---------------------------------------------YHNRPLTANTCDHTVKECGCMD--------GQNPLLISVDAMYDIDPTDVISLMHRTGTNQLFFCLSTAEVDFENT-NGKLAHGQGEWMRH--------DDKLVTVLRGDDRPYVNNWKLTKLW Bell_pepper_endornavirus_Is NPHAMLAAERRICAVTMGDKVKKG-KKILDIGTRINLTGN----DSWHGMGPCLDWRDVER---------------------------------------------YHNRPLTANTCDHTVKECGCMD--------GQNPLLISVDAMYDIDPTDVISLMHRTGTNQLFFCLSTAEVDFENT-NGKLAHGQGEWMRH--------DDKLVTVLRGDDRPYVNNWKLTKLW Phaseolus_vulgaris_endornavirus_2 NPHAMLAAERRIATIMFADKRGPG-QTILDVGSRKNLTGL----KEWHGMGPIMDWRDVER---------------------------------------------YNDKPLNTNICDHTVRTCECMQ--------GKKPMVMCIDSIYDIDPCDVLKLMHTVQTNQLFFCVSTAEVDFEST-SGLLAHGQGMWSRH--------KDKLVTSLRGDDRPYVNSWKLTKLW Sunn_hemp_mosaic_virus TSHAMAAGLRGLELEYLYTLVPYG-AVSYDIGGNFPAHMM-KGRSYVHCCNPALDARDLARNENYRISIENYLSRFEDKSGDYCQWQRKKPKVSKPLPRYQKACFDRYNEDPEHVTCSETFEKCRISP-----PAERDDIYATSLHSLYDIPYQNLGPALARKRIKVLHAAFHFSEDLLLGASEGLLTQIGGTFQRN-------GDVLTFSFLDESSLIYTHSFRNVFEY Tobacco_mild_green_mosaic_virus AVHSLAGGLRALELEYLMLQVPYG-SPTYDIGGNFAAHLF-KGRDYVHCCMPNLDIRDIMRHEGQKDSIEMYLSRLSRSN--------------KVIPEFQREAFNRYAEAPNEVCCSKTFQDCRIHP-----PENSGRRYAVALHSLYDIPVHEFGAALISKNIHVCYAASILAEALLLDQTEVTLNEIGATFKRE-------GDDVSFFFADESTLNYSHKYKNILHY Obuda_pepper_virus AVHSLAAGLRSLELEYLMMQVPYG-SLTYDIGGNFAAHLF-KGRDYVHCCMPNLDLRDIMRHENQKDSVATYLSRLKARN--------------KVLPAFQQEAFQRYSERSDEVVCNNTFQCCESNR-----YSSGGRVYAISLHSLYDIPADELGAALLRKNVHTLYAAFHFAEELLLEVSTVELPTIGGIFSRD-------GDKINFCFSNESTLNYSHSYSNLLKY Tobacco_rattle_virus_CAM MVHGFAAAERKLQALLLLARVPK-LEEVDDIGGQWSYWLT-RGEKRVHSSCPILDVRDKQREMQRQSFLKSFRDNATTSDSVVTDAQYEMYN-----------AFKNGVDKPNFVRCNNTFQDCNCRGYTKDGLRRG-AEHAIALHSLYDFELDSVADAMIEKKTKFLHAAMLFAPEAIMIE-EGPLPDVNGYYHRVQKNLGTRPERIMFGFHDDPSYNYIHTWSEYKKY Beet_virus_Q GTHSMAAAMRKIETDLVLSSFPS--EVIYDVGGNWATHAMRSDKRFVHCCCPILDFRDAQRKMTRMINYTKFIESSKELDPATAERAERIRDDTKRIKDQVDAGLLSHHDLNGKWYCQNRFEDCVFEPFSDDTLKKDALVCGMAIHSIYDIHLVDLVAAMQRKGIRVLTGTFLFAVDMLLGKKEGELPTVNGFYRVN-------GNKVKYGFYDDPNCGYEHDLDSLLLY Barley_stripe_mosaic_virus GTHSMAACFRFLETEYLLDMVPMKETFVYDIGGNWFSHMKFRADREIHCCCPILSMRDSERLETRMMAMQKYMRGSKDKPLRLLSRYQNILREQAARTTAFMAGEVNAGVLDGDVFCENTFQDCVRR------VPEGFLKTAIAVHSIYDIKVEEFASALKRKGITQAYGCFLFPPAVLIGQKEGILPSVDGHYLVE-------NGRIKFFFANDPNAGYSHDLKDYLKY Alfalfa_mosaic_virus SSHCFAAAHRLLETDFVYRCFGNTVDSIIDLGGNFVSHMK-VKRHNVHCCCPILDARDGARLTERILSLKSYVR-------------------------------KHPEIVGEADYCMDTFQKCSRR-----------ADYAFAIHSTSDLDVGELACSLDQKGVMKFICTMMVDADMLIHN-EGEIPNFNVRWEID-----RKKDLIHFDFIDEPNLGYSHRFSLLKHY Tobacco_streak_virus_WC SSHSFAAAHRVCETLNIYNRFKTKTERIIDLGGNYVTHAK-QGRSNVHSCCPILDVRDGARHTDRYISLAASVEN------------------------------RHRELP--VDFCCHKFEECDVK-----------APFAMAIHSISDIPISTVATHCVRRGVRKLIASVMMDPLMMLYD-KGHIPLLNVDWEKEDVEE-TGKTLIHFHFVDAPGLSYSHDFDTLSQY ; END; BEGIN TREES; Title MTR_ML_tree; LINK Taxa = Taxa; TRANSLATE 1 Rhizoctonia_solani_endornavirus_RS002, 2 Rhizoctonia_cerealis_endornavirus_1, 3 Gremmeniella_abietina_type_B_RNA_virus_XL1, 4 Gremmeniella_abietina_type_B_RNA_virus_XL2, 5 Bell_pepper_endornavirus_KS, 6 Bell_pepper_endornavirus_YW, 7 Bell_pepper_endornavirus_KY, 8 Bell_pepper_endornavirus_Is, 9 Phaseolus_vulgaris_endornavirus_2, 10 Sunn_hemp_mosaic_virus, 11 Tobacco_mild_green_mosaic_virus, 12 Obuda_pepper_virus, 13 Tobacco_rattle_virus_CAM, 14 Beet_virus_Q, 15 Barley_stripe_mosaic_virus, 16 Alfalfa_mosaic_virus, 17 Tobacco_streak_virus_WC; TREE UNTITLED = ((((((11:0.28628813,12:0.16222987)0.9980:0.16206292,10:0.49703674)0.9990:0.60108953,(13:0.96465017,(14:0.52720479,15:0.56799945)0.7390:0.15966736)0.4010:0.0)0.5020:0.24970092,(16:0.35629837,17:0.50933755)1.0000:0.54267676)0.9740:0.80476217,(3:0.0,4:0.0)1.0000:1.76432001)1.0000:0.56124416,((1:1.42893105,2:0.31158271)0.8650:0.6739896,(9:0.39190054,(6:0.04704782,(5:0.0,(7:0.0,8:0.0)0.3260:0.0)0.9990:0.0)0.9960:0.08271945)1.0000:0.72734727)1.0000:0.61091288); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 230; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 230; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 230; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1408803656175; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 4444890172392308368; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 8418362624119213277; mqVersion 275; checksumv 0 3 4116535318 null getNumChars 230 numChars 230 getNumTaxa 17 numTaxa 17 short false bits 1048575 states 1048575 sumSquaresStatesOnly 4.3727950793942E13 sumSquares 4.3727950793942E13 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 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #4444890172392308368 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #4444890172392308368; 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 -8; 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 #4444890172392308368 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 831.1408772252468.2401814451962186020; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1035 582; setLocation -8 -8; 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 #8418362624119213277 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1035 582; 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;