#NEXUS [written Fri Jun 21 15:22:39 MDT 2013 by Mesquite version 2.75 (build 564) at Lindsay-PC/129.82.37.188] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=37; TAXLABELS Burkholderia_pseudomallei_T6SS1 Burkholderai_pseudomallei_T6SS3 Burkholderia_pseudomallei_T6SS2 Burkholderia_pseudomallei_T6SS6 Burkholderia_pseudomallei_T6SS4 Burkholderai_pseudomallei_T6SS5 Burkholderia_thailandensis_T6SS1 Burkholderia_thailandensis_T6SS6 Burkholderia_thailandensis_T6SS2 Burkholderia_thailandensis_T6SS4 Burkholderai_thailandensis_T6SS5 Burkholderia_glumae_BGR1_YP_002910292 Burkholderia_glumae_BGR1_YP_002907865 Burkholderia_glumae_BGR1_YP_002908402 Burkholderia_glumae_BGR1_YP_002908734 Burkholderia_glumae_BGR1_YP_002907919 Burkholderia_gladioli_BSR3_YP_004359059 Burkholderia_gladioli_BSR3_YP_004362835 Burkholderia_gladioli_BSR3_YP_004348376 Burkholderia_glumae32525_contig64 Burkholderia_glumae32525_contig36 Burkholderia_glumae32525_contig300 Burkholderia_glumae32525_contig468 Burkholderia_gladioli3848s_contig16 Burkholderia_gladioli3848s_contig265 Ralstonia_eutropha_YP_841946 Ralstonia_eutropha_YP_725168 Agrobacterium_tumefaciens_C5A Vibrio_cholerae_O1 Burkholderia_glumae_AU6208_1 Burkholderia_glumae_AU6208_2 Burkholderia_glumae_AU6208_3 Burkholderia_glumae_AU6208_4 Burkholderia_glumae_LMG2196_1_Contig156 Burkholderia_glumae_LMG2196_2_Contig4 Burkholderia_glumae_LMG2196_3_Contig26 Burkholderia_glumae_LMG2196_4_Contig199 ; END; BEGIN CHARACTERS; TITLE 'Matrix in file "BurkholderiaT6SS.nexus"'; DIMENSIONS NCHAR=217; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX Burkholderia_pseudomallei_T6SS1 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEIKELPFVVGVVGDLAG--Q-SEIEQPKLRDRKFVNIDRDNFDDVMKAIEPRATFQVENRLSEA---GGKFAVDLK--------FRSINDFNPDEVVGQVEPLRRLLEARSKLADLRNKLAGNDKLEDLLSEVLSNTQQLE----------------ALKKSADGGDKQGE----------- Burkholderai_pseudomallei_T6SS3 MSAS----SSSQKFIARNRAPRVQIEYDVEVYGSEKKVELPFVMGVLADLSGK---PVAPLPAVADRRFLDIDIDNFDERMKAIKPRVAFAVDNTLSGD---GQLM-VDMT--------FESIEDFSPAAIARMVGPLRQLLEARTQLANLQTYMDGKSGAETLVNQLLQDPALLRS------LAAAPKPQLAGGPDAGNARGAKDAPDTANHDSDA Burkholderia_pseudomallei_T6SS2 MAIS----NSSQKFIARNRAPRVQIEYDVEIYGSEKKVELPFVMGVLADLSGK---PLEPLPAVGDRKFFSIDIDNFDERMKAMKPRVAFSVPNTLSGD---GQLM-VDIT--------FESMDDFSPAAIAKKVDALSQLLDARTQLANLQTYMDGKSGAENLVSKVLKDPALLSA------LAKAPKPVAEQAENRESKEKH------------- Burkholderia_pseudomallei_T6SS6 MTSKYKASASGQKFIARNRAPRVQIEYDVETYGAERKVQLPFVMGVIADLAGK---RAEPLPDLPERKFLEIDVDNFDERMKSIAPRVAFQVPNTLSGD---GMLS-VDMT--------FESIDDFSPAAIARNVDALRRLLDARTELSNLLSYMDGKHGAEQLIENAINDPALLAS------LVRQPLAADAEGGARQPV-TGTEDDPEIRHE--- Burkholderia_pseudomallei_T6SS4 MVRQ----KDGQKFIGESRAPRVQIEYDVEVYGSQKKVELPFVAGVMADLSGD---NVEPLGPVEDRRFQEIDVENFDERMAQIAPSLSYHVKNVLTND---GTLIPIDLT--------FTSMESFEPADVVKRIPELSTLLEARNRLKELLTYMDGKAAAEDVIQELLKSPQWANE------ADAA-EQSGGAGEGGDHQPEEGAK---------- Burkholderai_pseudomallei_T6SS5 ----------MTTNGSVAPKERVNIVYRPATGDAQAEVELPLKVLVLGEFSTA-----ADKPPLEELSPVNVDKDDFNDVMRAQNLQLTLSVPNLLDDQAGEDDRLSVTLG--------FDSVHDFSPDAIVEKVPELKQLIALRDALKALKSPIGNIPGFRRRIQEIVADKGARKQ------------LLDEL----GLDEQ-------------- Burkholderia_thailandensis_T6SS1 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEIKELPFVVGVVGDLAG--Q-SEVEQPKLRDRKFVNIDRDNFDDVMKAIEPRATFQVENRLSDA---GGKFAVDLK--------FRSINDFNPDEVVGQVEPLRRLLEARSKLADLRNKLAGNDKLEDLLSEVLSNTQQLE----------------ALKKGADGGDKQGE----------- Burkholderia_thailandensis_T6SS6 MTSKYKASASGQKFIARNRAPRVQIEYDVETYGAERRVQLPFVMGVIADLAGK---RAEPLPDLPERKFLEVDVDNFDERMKSIAPRVAFQVPNTLSGD---GMLS-VDMT--------FESIDDFSPAAIARNVDALRRLLEARTELSNLLSYMDGKHGAEQLIENAINDPELLKT------LVRQPLAASADGGAPAVADTGTADDSEIRHE--- Burkholderia_thailandensis_T6SS2 MAIS----NSSQKFIARNRAPRVQIEYDVEIYGSEKKVELPFVMGVLADLSGK---PIEPLPAVGDRKFFSIDIDNFDERMKAMKPRVAFSVPNTLSGD---GQLM-VDIT--------FESMDDFSPAAIAKKVDALSQLLDARTQLANLQTYMDGKSGAENLVSKVLKDPALLSA------LAKAPKPAAQQAENRESKEKH------------- Burkholderia_thailandensis_T6SS4 MVRQ----KDGQKFIGESRAPRVQIEYDVEVYGSQKKVELPFVAGVMADLSGD---NTEPLGPVEDRRFQEVDVENFDERMAQIAPSLSYHVKNVLTND---GTLIPIDLT--------FTSMESFEPAAVVKRIPELSTLLEARNRLKELLTYMDGKAAAEDVIQELLKSPQWANE------ADAAPEQSGGAGEGADHQPEEGAK---------- Burkholderai_thailandensis_T6SS5 ----------MTTNGSVAPKERVNIVYRPATGDAKAEVELPLKVLVLGEFSTA-----DDKPPIEELAPVNVDKDDFNDVMKAQRLTLALSVPNLLDDQAGEDDRLSVALG--------FESIADFSPDAIVETVPELKQLVALRDALKALKGPLGNIPGFRKRIQEIVADKGARKQ------------LLDEL----GLDEQ-------------- Burkholderia_glumae_BGR1_YP_002910292 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEVKELPFVVGVVGDLAG--Q-SEVEMPKLRDRKFVNIDRDNFDDVMKAIEPRAAYQVENKLSED---GGKFAVDLK--------FRSLDDFDPDQVVNQIEPLRRLIEARSKLADLRNKMAGNDKLEDLLSEVLSNTQQLE----------------ALAKQSGEADGKPDDGKNSGE---- Burkholderia_glumae_BGR1_YP_002907865 MSVS----NNSQKFIARNRAPRVQIEYDVEIYGSEKKVELPFVMGVLADLSGK---PIEALPAVAERKFFNIDIDNFDERMKAMKPRVAFSVPNTLTNQ---GELM-VDMT--------FESMDDFSPAAVARKVDALAQLLDARTQLANLQTYMDGKAGAESLVSKVLRDPALLEA------LAKAPKPRSASSDDATAGE--------------- Burkholderia_glumae_BGR1_YP_002908402 MS------ESVQKKLLRIRPPRVRITYDVETGGAIEKTELPFIVGILADLKGERE-DAEHYPSLKERSMIEIDRDNFDDVMKKIQPRATFTQLK---QD---DAALKALLVQDGDNALIFPNMEAFEPLKVIKALPSLNDIYVNRGKIRDLQARAETSDPVSKVLDAMIQGAVLGQAAVAAQPAVPDQPEVPAVPAVPADGDKPAVEAVPGKPAVKG Burkholderia_glumae_BGR1_YP_002908734 ----------MDSFQREIPKSRVSITLDLHTGGARKKVELPLKLLVAGDFSAG-----REQAPLAERKKINIDKNNFDAVLADYAPDLKISAENTLAGD---GSALPVNLS--------FRSMKDFEPEQVARQIPELQAMLAMRNLLRDLKSNLLDNGTFRREFEKILKDKHLSDK------------LRSELAQVATAATQPEGQA--------- Burkholderia_glumae_BGR1_YP_002907919 ----------------------------MHTGGARKKVELPLKLLVAGDFSAG-----REQAPLAERKKINIDKNNFDAVLADYAPDLKISAENTLAGD---GSALPVNLS--------FRSMKDFEPEQVARQIPELQAMLAMRNLLRDLKSNLLDNGTFRREFEKILKDKHLSDK------------LRSELAQVATAATQPEGQA--------- Burkholderia_gladioli_BSR3_YP_004359059 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEVKELPFVVGVVGDLAG--Q-SEVEMPKLRDRKFVNIDRDNFDDVMKAIEPRAAYQVENKLSEE---GGKFAVDLK--------FRSLDDFDPDQVVNQIEPLRRLIEARSKLADLRNKLAGNDKLEDLLSEVLSNTQQLQ----------------ALAKQSGGGDKEGE----------- Burkholderia_gladioli_BSR3_YP_004362835 MSAS----SSSQKFIARNRAPRVQIEYDVEVYGSEKKVELPFVMGVLADLSGK--HPSEPLPAVTDRRFLEIDIDNFDERMKAIRPRVAFAVPNTLTGE---GQMM-VDMT--------FESMEDFSPAAIARKVEPLRQLLEARTQLANLQTYMDGKSGAEALVTQLLQDPALLKS------LAAAPKPERH---DAGAAD-----PSEAN----- Burkholderia_gladioli_BSR3_YP_004348376 MATR----QSSQKFIARNRAPRVQIEYDVELYGAQKKVQIPFVMGVMSDLSGA---NAGELPPIEERKALEIDVDNFDSRMQSMKPRVNFTVPNTLTGE---GNLE-VDIS--------FESMDDFSPAAVARKVDSLARLLEARTQLANLGTYLDGKVGAEKLIAQALKDPALLQS------LSSAPKAADTEPGQE------------------- Burkholderia_glumae32525_contig64 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEVKELPFVVGVVGDLAG--Q-SEVEMPKLRDRKFVNIDRDNFDDVMKAIEPRAAYQVENKLSED---GGKFAVDLK--------FRSLDDFDPDQVVNQIEPLRRLIEARSKLADLRNKMAGNDKLEDLLSEVLSNTQQLE----------------ALAKQSGEADGKPDDGKNSGE---- Burkholderia_glumae32525_contig36 MSVS----NNSQKFIARNRAPRVQIEYDVEIYGSEKKVELPFVMGVLADLSGK---PLEALPAVAERKFFNIDIDNFDERMKAMKPRVAFSVPNTLTNQ---GELM-VDMT--------FESMDDFSPAAVARKVDALAQLLDARTQLANLQTYMDGKAGAESLVSKVLRDPALLEA------LAKAPKPRSASSDDATAGE--------------- Burkholderia_glumae32525_contig300 MS------ESVQKKLLRIRPPRVRITYDVETGGAIEKTELPFIVGILADLKGERE-DAEHYPSLKERSMIEIDRDNFDDVMKKIQPRATFTQLK---QD---DAALKALLVQDGDNALIFPNMEAFEPLKVIKALPSLNDIYVNRGKIRDLQARAETSDPVSKVLDAMIQGAVLGQAAVAAQPAVPDQPEVPAVPAVPADGDKPAVEAVPGKPAVKG Burkholderia_glumae32525_contig468 ----------MDSFQREIPKSRVSITLDLHTGGARKKVELPLKLLVAGDFSAG-----REQAPLAERKKINIDKNNFDAVLADYAPDLKISAENTLAGD---GSALPVNLS--------FRSMKDFEPEQVARQIPELQAMLAMRNLLRDLKSNLLDNGTFRREFEKILKDKHLSDK------------LRSELAQVATAATQPEGQA--------- Burkholderia_gladioli3848s_contig16 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEVKELPFVVGVVGDLAG--Q-SEVEMPKLRDRKFVNIDRDNFDDVMKAMEPRAAYQVENKLSEE---GGKFAVDLK--------FRSLDDFDPDQVVNQIEPLRRLIEARSKLADLRNKLAGNDKLEDLLSEVLSNTQQLQ----------------ALAKQSGGGDKEGE----------- Burkholderia_gladioli3848s_contig265 MATR----QSSQKFIARNRAPRVQIEYDVELYGAQKKVQIPFVMGVMSDLSGA---NAGELPPIEERKALEIDVDNFDSRMQSMKPRVNFTVPNTLTGE---GNLE-VDIS--------FESMDDFSPAAVARKVDSLARLLEARTQLANLGTYLDGKVGAEKLIAQALKDPALLQS------LSSAPKAADTEPGQE------------------- Ralstonia_eutropha_YP_841946 MS------NSLQKWVGRNRPPRVQISYDVEVGDAVEKRELPMVVGLLADLSG--Q-PAVPPPKLKERRFIEIDRDNFDGIMGKIAPRLELSVPDTM-KG---DTNLKVELR--------FDKFSDFHPESLVAQVPRLAKLLEARQQLRDLLGKLDGNDELDVLLERIVNNADELK-------LVRSEADSGAAAAQPETGDATPA----------- Ralstonia_eutropha_YP_725168 MSVV----NSSQKFIARNRAPRVQIEYDVEVYGSEKRIELPFVMGVLADLSGR---PAEPLPAVADRKFLEIDIDNFDERMKAMKPRVAFAVPNTLSGD---GQLM-VDMT--------FESIEDFSPAAVAGKVDALRQLLEARTQLANLQTYMDGKSGAESLINQLLQDPALLQS------LAKAPKPR------AGDDE-----PQSPQS---- Agrobacterium_tumefaciens_C5A MA-------SVHEKLERVRKPRVHIKYEVETEGAMVVKELPFVVGVLGDFSGN---PTQPLKPFGERKFVQIDRDNFDEVMRRMTPGLNISVANTLQKD---GTDMQVNLK--------FESMDDFEPGAVVQQVPALKALLDARNELRDLLSKADRSEDLERMLEGILQNKTDLAT------------LVSELKEKSGAGE--------------- Vibrio_cholerae_O1 ----------MSKEGSVAPKERINIKYIPATGDAQAEVELPLKTLVVGDFKGH-----AEQTPLEERATVTVDKNNFEAVMRESELKITATVKNKLTDD--ENAELPVELN--------FKSLADFAPDAVASQVPELKKLIELREALVALKGPLGNIPAFRERLQSLLNSEESREK------------LLAELNLLSGQEEPQA------------ Burkholderia_glumae_AU6208_1 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEVKELPFVVGVVGDLAG--Q-SEVEMPKLRDRKFVNIDRDNFDDVMKAIEPRAAYQVENKLSED---GGKFAVDLK--------FRSLDDFDPDQVVNQIEPLRRLIEARSKLADLRNKMAGNDKLEDLLSEVLSNTQQLE----------------ALAKQSGEADG-------------- Burkholderia_glumae_AU6208_2 -S------ESVQKKLLRIRPPRVRITYDVETGGAIEKTELPFIVGILADLKGERE-DAEHYPSLKERSMIEIDRDNFDDVMKKIQPRATFTQLK---QD---DAALKALLVQDGDNALIFPNMEAFEPLKVIKALPSLNDIYVNRGKIRDLQARAETSDPVSKVLDAMIQGAVL------------------------------------------- Burkholderia_glumae_AU6208_3 MSVS----NNSQKFIARNRAPRVQIEYDVEIYGSEKKVELPFVMGVLADLSGK---PLEALPAVAERKFFNIDIDNFDERMKAMKPRVAFSVPNTLTNQ---GELM-VDMT--------FESMDDFSPAAVARKVDALAQLLDARTQLANLQTYMDGKAGAESLVSKVLRDPALLEA------LAKAPKPRSASSDDA------------------- Burkholderia_glumae_AU6208_4 ------------------PKSRVSITLDLHTGGARKKVELPLKLLVAGDFSAG-----REQAPLAERKKINIDKNNFDAVLADYAPDLKISAENTLAGD---GSALPVNLS--------FRSMKDFEPEQVARQIPELQAMLAMRNLLRDLKSNLLDNGTFRREFEKILKDKHLSDK------------LRSELA---------------------- Burkholderia_glumae_LMG2196_1_Contig156 MAKK----ESIQKRLQKVRPPRVQLTYEVERGDAIEVKELPFVVGVVGDLAG--Q-SEVEMPKLRDRKFVNIDRDNFDDVMKAIEPRAAYQVENKLSED---GGKFAVDLK--------FRSLDDFDPDQVVNQIEPLRRLIEARSKLADLRNKMAGNDKLEDLLSEVLSNTQQLE----------------ALAKQSGEAD--------------- Burkholderia_glumae_LMG2196_2_Contig4 MSVS----NNSQKFIARNRAPRVQIEYDVEIYGSEKKVELPFVMGVLADLSGK---PIEALPAVAERKFFNIDIDNFDERMKAMKPRVAFSVPNTLTNQ---GELM-VDMT--------FESMDDFSPAAVARKVDALAQLLDARTQLANLQTYMDGKAGAESLVSKVLRDPALLEA------LAKAPKPRSASSDDA------------------- Burkholderia_glumae_LMG2196_3_Contig26 -----------DSFQREIPKSRVSITLDLHTGGARKKVELPLKLLVAGDFSAG-----REQAPLAERKKINIDKNNFDAVLADYAPDLKISAENTLAGD---GSALPVNLS--------FRSMKDFEPEQVARQIPELQAMLAMRNLLRDLKSNLLDNGTFRREFEKILKDKHLSDK------------LRSELA---------------------- Burkholderia_glumae_LMG2196_4_Contig199 MS------ESVQKKLLRIRPPRVRITYDVETGGAIEKTELPFIVGILADLKGERE-DAEHYPSLKERSMIEIDRDNFDDVMKKIQPRATFTQLK---QD---DAALKALLVQDGDNALIFPNMEAFEPLKVIKALPSLNDIYVNRGKIRDLQARAETSDPVSKVLDAMIQGAVL------------------------------------------- ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 217; END; BEGIN TREES; Title 'Trees from "T6SS.nex"'; LINK Taxa = Taxa; TRANSLATE 1 Burkholderia_pseudomallei_T6SS1, 2 Burkholderai_pseudomallei_T6SS3, 3 Burkholderia_pseudomallei_T6SS2, 4 Burkholderia_pseudomallei_T6SS6, 5 Burkholderia_pseudomallei_T6SS4, 6 Burkholderai_pseudomallei_T6SS5, 7 Burkholderia_thailandensis_T6SS1, 8 Burkholderia_thailandensis_T6SS6, 9 Burkholderia_thailandensis_T6SS2, 10 Burkholderia_thailandensis_T6SS4, 11 Burkholderai_thailandensis_T6SS5, 12 Burkholderia_glumae_BGR1_YP_002910292, 13 Burkholderia_glumae_BGR1_YP_002907865, 14 Burkholderia_glumae_BGR1_YP_002908402, 15 Burkholderia_glumae_BGR1_YP_002908734, 16 Burkholderia_glumae_BGR1_YP_002907919, 17 Burkholderia_gladioli_BSR3_YP_004359059, 18 Burkholderia_gladioli_BSR3_YP_004362835, 19 Burkholderia_gladioli_BSR3_YP_004348376, 20 Burkholderia_glumae32525_contig64, 21 Burkholderia_glumae32525_contig36, 22 Burkholderia_glumae32525_contig300, 23 Burkholderia_glumae32525_contig468, 24 Burkholderia_gladioli3848s_contig16, 25 Burkholderia_gladioli3848s_contig265, 26 Ralstonia_eutropha_YP_841946, 27 Ralstonia_eutropha_YP_725168, 28 Agrobacterium_tumefaciens_C5A, 29 Vibrio_cholerae_O1, 30 Burkholderia_glumae_AU6208_1, 31 Burkholderia_glumae_AU6208_2, 32 Burkholderia_glumae_AU6208_3, 33 Burkholderia_glumae_AU6208_4, 34 Burkholderia_glumae_LMG2196_1_Contig156, 35 Burkholderia_glumae_LMG2196_2_Contig4, 36 Burkholderia_glumae_LMG2196_3_Contig26, 37 Burkholderia_glumae_LMG2196_4_Contig199; TREE Tree1 = ((((((((32:0.0,35:0.0)0.1960:0.0,21:0.0)0.2110:0.0,13:0.0)1.0000:0.07476887,(3:0.0,9:0.0)1.0000:0.05135726)0.8920:0.04887383,(27:0.04595641,(2:0.0579834,18:0.04821129)0.8580:0.0374038)0.8740:0.04687678)0.7770:0.07183099,((4:-0.00664621,8:0.03970406)1.0000:0.22455707,(19:0.0,25:0.0)1.0000:0.26515674)0.4700:0.02322173)0.8790:0.19093476,(5:-3.9824E-4,10:0.0166584)1.0000:0.45854514)0.9930:0.41813477,(((((31:0.0,37:0.0)0.2010:0.0,22:0.0)0.1800:0.0,14:0.0)1.0000:1.04758659,26:0.45241341)0.8430:0.24409516,((1:0.00966818,7:0.00659198)0.8540:0.04814691,(12:-0.00102253,(20:-0.00193743,(30:-0.00368112,(34:-0.00701167,(17:0.00509382,24:0.0029707)0.8230:0.02340457)0.1850:0.00368112)0.1010:0.00193743)0.1570:0.00102253)0.8840:0.06825835)0.9980:0.36187448)0.4740:0.07181233,(28:0.23870194,(((6:0.09852436,11:0.05888305)0.9640:0.32127819,29:0.4119929)0.9960:0.58579135,(16:0.00403226,(15:0.0,(23:0.0,(33:0.0,36:0.0)0.2150:0.0)0.1360:0.0)0.6740:0.00403226)1.0000:0.56006869)0.9920:0.53676815)0.7350:0.1961246); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 217; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 217; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1371849759179; linkFile T6SS.nex; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 976545988373939769; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5382716589787486412; mqVersion 275; checksumv 0 3 996926539 null getNumChars 217 numChars 217 getNumTaxa 37 numTaxa 37 short false bits 1048573 states 1048573 sumSquaresStatesOnly 3.3350159318153E13 sumSquares 3.3350159318153E13 longCompressibleToShort false usingShortMatrix false NumFiles 2 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 297; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1310 784; setLocation 8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #976545988373939769 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #976545988373939769; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; getTable; tell It; rowNamesWidth 261; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1013 717; 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 #976545988373939769 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlockInt 0; toggleUseWeights off; endTell; setAssignedID 938.1371849663412.1768611151060635616; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1013 717; 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 #5382716589787486412 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1013 717; 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; endTell; end;