#NEXUS [written Wed Feb 19 14:47:04 SGT 2014 by Mesquite version 2.75 (build 566) at 199-156.priv23.nus.edu.sg/172.23.199.156] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=8; TAXLABELS Helicobacter_bizzozeronii Campylobacter_jejuni_CstII Campylobacter_jejuni_CstIII Campylobacter_jejuni_CstI Campylobacter_coli_76330_CstI Haemophilus_influenzae Campylobacter_coli_202.94_CstIV Campylobacter_coli_76339_CstV ; END; BEGIN CHARACTERS; TITLE GoodSialyTr_PRANKTxwoHAY_fna; DIMENSIONS NCHAR=1836; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Helicobacter_bizzozeronii ---------------------------------------------ATG------------------------TGTGATTTACCCCCTCTGCAAACCATGAAGCCC------------------------------------------------------------------------------------------------------------CTCATCATCGCC---------GGCAATGGCCCGAGCATTAAAAACCTCGATTATAGTTTATTCCCCCCGAATTTTGATGTTTTTAGGTGTAATCAGTTTTATTTTGAGGACAAATATTATTTAGGCAAAGAAGTTAAGGGGGTGTTTTTTAACGCTCAAGTCTTTGATATGCAGATGAAAACGGCTAGAGAGTTGAGTTTGCGTCAAGAATATTATTTTGAAGACCTTTTTTGTTCGACTATTGCGCCTTTTATGAATTTT---GGGAATCACTAT------------ACGCACGCCCAAGATTACCTAGACAAACATTAT---------CCGGGGGCACGCAACACTTACGCA---CTATTACAAAGCCTAGAGCCTTTTTATAAACTCTACACCACTAGGCGTAATTTTTAC---CAACAA---CACTTTACCACTGGTGTAATGATGATTATTGTGGCAATTGTCTTAGGGTATAAAGAAATTTATTGTGCTGGATTGGATTTTTACCTAGAGGGA------TTA---GGGCATTTTTACCATGCT---AAAAGC---CCGCATTTTACCCTCGCCCCCGATTGCCAG---------------------------------CACACAAAAGACCTTGATATCAAGGGAATTGAA---GTAGCCAAACAATAC---GCCCAGCTTTATGCGCTTGTTCCTAATAGTGCGCTCTCTGCAATTTTACCCCTAAGCCCGCATAAAAATGCC---CTGTCTCAAGAAAAAATGCAAGCC------CTAAAATTAGGAGATCCTAAACCGAATGGCTATATTGATGATGTTTGCGTTGAT------------CCTGTTGAATTTTCCATG------------CGC---------GCAACTTTG---ATACAGGCTATTCAGAGTGTGGGCATCACC------------------------------------------------CCTGACAATCTCATTTACAAAGGTTTGAAC------------------------------------------ATGGTTTGGCGTTGTGCTAGC---------------------------GATCTGTATCGTGTTGTGAGGGGTTTATACAGACTCAGCCTAAAAGCCCTTTATTTTTTGAGGGCA---------------------------------------------------------------------------------------------TGGTTT------AAACGCCATAGGGCTACGGGAGGGTAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Campylobacter_jejuni_CstII ---------------------------------------------ATG---------------------------------------------------AAAAAA------------------------------------------------------------------------------------------------------------GTTATTATTGCT---------GGAAATGGACCAAGTTTAAAAGAAATTGATTATTCAAGACTACCAAATGATTTTGATGTATTTAGATGTAATCAATTTTATTTTGAAGATAAATACTATCTTGGTAAAAAATGCAAGGCAGTATTTTACAATCCTATTCTTTTTTTTGAACAATACTACACTTTAAAACATTTAATCCAAAATCAAGAATATGAGACCGAACTAATTATGTGTTCTAAT------------------TAC---AACCAAGCTCAT------------CTAGAAAATGAAAATTTTGTAAAAACTTTTTACGATTATTTTCCTGATGCTCATTTGGGATATGAT---TTTTTCAAACAACTTAAAGATTTTAATGCTTATTTTAAATTTCACGAAATTTATTTC---AATCAA---AGAATTACCTCAGGGGTCTATATGTGTGCAGTAGCCATAGCCCTAGGATACAAAGAAATTTATCTTTCGGGAATTGATTTTTATCAAAAT---GGGTCATCT---TATGCTTTTGATACTAAA---CAAAAA---AATCTTTTAAAATTGGCTCCTAATTTTAAAAATGATAAT---TCA------CACTATATCGGACATAGTAAAAATACAGATATAAAAGCTTTAGAATTTCTAGAAAAAACTTACAAAATAAAACTATATTGCTTATGTCCTAACAGTCTTTTAGCAAATTTTATAGAACTAGCGCCAAATTTAAATTCA------------------------AAT------TTTATCATA---CAAGAAAAA---AATAACTACACTAAAGATATACTCATACCTTCTAGTGAGGCTTATGGAAAATTTTCAAAAAATATTAATTTTAAA---------------AAA---ATAAAA---------------------ATT------------------------------------------------AAAGAAAATATTTATTACAAGTTGATAAAA------------------------------------------GATCTATTAAGATTACCTAGT---------------------------GATATA------------------------------------------------------AAGCAT---------------------------------------------------------------------------------------------TATTTCAAAGGAAAATAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Campylobacter_jejuni_CstIII ---------------------------------------------ATG---------------------------------------------------AGTATG------------------------------------------------------------------------------------------------------------AATATTAATGCTTTGGTATGCGGTAATGGACCTAGTTTAAAAAATATAGATTATAAAAGGTTACCAAAACAATTTGATGTATTTAGATGCAATCAGTTTTATTTTGAAGATAGATATTTTGTGGGTAAAGATGTAAAATATGTTTTTTTTAATCCTTTTGTGTTTTTTGAACAATACTATACTAGTAAAAAACTTATACAAAACGAAGAATATAACATAGAAAATATAGTTTGTTCTACT------------------ATT---AATTTAGAATAC------------ATAGATGGATTTCAATTTGTTGATAATTTTGAATTATACTTTAGTGATGCTTTTTTAGGTCATGAG---ATTATAAAAAAGCTTAAAGATTTTTTTGCCTATATTAAATATAATGAAATATACAAT---AGGCAA---AGAATTACTAGTGGAGTTTATATGTGTGCTACAGCTGTGGCTCTGGGATATAAAAGTATATATATAAGTGGTATTGATTTTTATCAAGAT---ACAAATAATTTATATGCCTTCGATAATAAT---AAAAAA---AATTTATTAAATAAATGCACTGGTTTTAAAAATCAAAAA---TTC------AAATTTATCAATCATTCAATGGCATGTGATTTACAAGCTTTAGATTATCTAATGAAAAGGTATGATGTGAATATTTATAGTTTAAATTCAGAT------------GAGTATTTTAAATTGGCTCCGGATATTGGAAGT------------------------GAT------TTTGTATTG---AGTAAAAAACCAAAAAAATATATAAATGATATATTGATACCAGATAAGTATGCACAAGAAAGATATTATGGA------------AAA---------------AAA---AGTAGG---------------------TTA------------------------------------------------AAAGAAAATCTCCATTATAAGCTAATAAAA------------------------------------------GATCTAATTAGACTTCCAAGT---------------------------GACATA------------------------------------------------------AAACAC---------------------------------------------------------------------------------------------TACTTAAAGGAAAAATATGCAAATAAAAATAGA---TAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Campylobacter_jejuni_CstI ATGACAAGGACTAGAATGGAAAATGAACTCATTGTTAGTAAAAATATG---------------------------------------------------CAAAAT------------------------------------------------------------------------------------------------------------ATAATCATAGCA---------GGAAATGGACCTAGCCTAAAAAATATTAATTATAAAAGACTGCCTAGAGAATATGATGTTTTTAGGTGTAACCAGTTTTATTTTGAAGATAAGTATTATTTAGGAAAAAAGATTAAAGCAGTATTTTTTAATCCTGGTGTCTTTTTACAACAGTATCACACTGCAAAACAACTTATACTAAAAAATGAGTATGAAATAAAAAATATTTTTTGCTCTACA------------------TTT---AATTTACCTTTT------------ATTGAAAGCAATGATTTTTTACATCAATTTTATAATTTTTTCCCCGATGCAAAACTTGGCTATGAA---GTTATTGAAAACCTTAAAGAATTTTATGCTTATATAAAATACAATGAAATTTATTTC---AATAAA---AGAATTACTTCGGGCGTCTATATGTGTGCAATTGCTATTGCATTAGGATATAAAACCATCTATTTATGTGGCATTGATTTTTATGAAGGA---GATGTTATT---TATCCTTTTGAAGCTATG---AGTACA---AATATAAAAACAATCTTTCCTGGAATAAAAGATTTCAAACCTTCA------AATTGT------CATTCTAAGGAATACGATATAGAAGCATTAAAATTGTTAAAATCAATATACAAAGTTAATATCTACGCATTGTGTGATGATTCTATTTTGGCAAATCATTTTCCTTTATCAATTAATATTAATAAC------------------------AAT------TTCACTTTA---GAAAATAAGCATAATAATTCTATAAATGATATTTTATTGACTGATAATACTCCTGGCGTAAGTTTTTATAAA------------AAT---------------CAA---CTTAAA---------------------GCTGATAATAAA------ATTATGCTTAATTTTTATAATATTCTTCATTCTAAAGATAATTTAATTAAATTTTTAAACAAA------------------------------------------GAAATTGCGGTATTAAAAAAA---------------------------CAAACC------------------------------------------------------ACTCAA---------------------------------------------------------------------------------------------------CGAGCTAAAGCAAGAATCCAAAACCAT---CTATCCTATAAACTAGGACAAGCTTTGATTATAAATTCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Campylobacter_coli_76330_CstI ---------------------------------------------ATG---------------------------------------------------CAAAAT------------------------------------------------------------------------------------------------------------GTAATTATAGCA---------GGAAATGGGCCTAGTCTTCAAAGTATTAACTATCAAAGACTACCGAAAGAATATGATATTTTTAGATGCAATCAGTTCTATTTTGAAGATAAATATTATTTAGGAAAAAATATCAAAGCTGCATTTTTTAATCCATACCCTTTCTTACAGCAATATCACACAGCTAAGCAATTGGTGTTTAACAATGAATACAAGATAGAAAATATTTTTTGCTCCACA------------------TTC---AATTTGCCTTTT------------ATCGAAAAGGATAATTTTATAAATAAATTTTATGATTTTTTTCCTGATGCAAAACTTGGCCATAAG---ATCATTGAAAATCTTAAAGAGTTTTATGCCTATATAAAATATAATGAAATTTATTTA---AATAAG---AGAATTACTTCTGGTATTTATATGTGCGCCATAGCAATTGCATTGGGATATAAAAATATATATTTATGTGGAATTGATTTTTATGAAGGA---GAAACCATT---TATCCTTTTAAGGCTATG---AGTAAA---AATATAAAAAAAATATTTCCTTGGATAAAAGATTTTAATCCATCA------AATTTT------CATTCTAAAGAATATGATATAGAAATATTAAAATTGCTAGAATCAATATACAAGGTTAACATCTACGCATTATGTGATAATTCTGCTTTGGCAAATTATTTTCCTCTATTAGTGAATACTGATAAT------------------------AGT------TTTGTTTTG---GAAAATAAGAGTGATGATTGTATAAATGATATTTTATTAACCAATAATACACCGGGAATAAATTTTTACAAA------------AGT---------------CAA---ATACAA---------------------GTTAATAATACTGAAATTCTATTACTCAATTTTCAAAATATGATTAGCGCTAAAGAAAATGAAATTTCTAATTTAAATAAGATTTTACAAGACAGTTATAAAACTATCAATACTAAAGAAAATGAAATTTCTAATTTAAATAAGATTTTACAAGACAGTTATAAAACTATCAATACT------------------------------------------------------AAAGAAAATGAAATTTCTAATTTAAATAAGATTTTACAAGATAAGGACAAGCTGCTAATTGTGAAAGAAAACTTGCTAAACTTCAAAAGTCGCCATGGA------AAAGCCAAATTCCGTATTCAAAACCAA---CTTTCCTATAAACTAGGACAAGCTATGATGGTAAATTCTAAATCTTTACTAGGTTATATAAGAATGCCTTTTGTATTATCTTATATAAAAGACAAACATAAACAAGAGCAAAAAATCTATCAAGAAAAAATAAAAAAAGATCCATCTTTAACACTACCTCCTTTGGAAGACTATCCTGATTATAAAGAAGCTCTAAAAGAAAAAGAATGTTTAACTTATAGATTAGGACAAACTTTAATTAAGGCTGATCAAGAATGGTATAAGGGAGGGTATGTTAAGATGTGGTTCGAGATCAAGAAATTAAAGAAGGAATATAAAAAGAAATAA Haemophilus_influenzae ---------------------------------------------ATG---------------------------------------------------CCCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAAAGCCTGTCATTATTGCA---------GGTAATGGAACAAGTTTAAAATCAATTGACTATAGTTTATTACCTAAAGATTATGATGTTTTCCGTTGCAATCAATTTTATTTTGAGGATCATTATTTTCTTGGTAAGAAAATAAAAAAGGTATTTTTTAATTGTTCTGTAATTTTTGAACAATACTATACGTTTATGCAATTAATTAAAAATAATGAATATGAATATGCTGATATTATTCTATCATCT------------------TTTCTGAATTTAGGGGAT------------TCAGAATTAAAGAAA---ATCCAGCGTTTAGAAAAATTACTACCACAAATCGATCTTGGTCATAGC---TATTTAAAAAAACTACGAGCTTTTGATGCTCATTTACAATATCACGAACTATATGAG---AATAAG---AGGATTACATCAGGCGTTTATATGTGTGCAGTGGCAACTGCTATGGGTTATAAAGATCTTTATTTGACAGGCATTGATTTTTATCAAGAAAAAGGGAATCCT---TACGCATTTCATCATCAA---AAAGAA---AATATTATTAAATTATTACCTTCTTTTTCACAAAATAAA---AGTCAAAATGATATC------CATTCTATGGAATATGATTTAAATGCACTTTATTTCTTACAAAAACATTATGGTGTAAATATTTACTGTATTTCGCCAGAAAGTCCTCTATGTAATTATTTTCCTTTATCACCACTGAATAACCCATTT---------------------ACT------TTTATTCCC---GAAGAAAAG---AAAAATTACACACAAGATATTTTAATTCCG------------CCAGAGTCAGTGTATAAA------------AAAATTGGTATATATTCCAAA---CCAAGA---------------------ATT------------------------------------------------TACCAAAATCTGGTTTTTCGGTTGATCTGG------------------------------------------GATATATTACGTTTACCTAAT---------------------------GATATA------------------------------------------------------AAAAAA---------------------------------------------------------------------------------------------GCTTTGAAAGCAAAGAAAATGAGACTACGCAAA---TAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Campylobacter_coli_202.94_CstIV ---------------------------------------------ATGAATAAAAATTTAAATTTTACAAAA---------------------------AAATCT------------------------------------------------------------------------------------------------------------GTATTAATAGCA---------GGGAATGGGCCTAGTTTGAAAGAAATTGATTATTCTCTACTTCCGAAAGAATATGATGTATTCCGTTGCAATCATTTTTACGCAGAAGATAAATATTATACAGGAAAAAAAATAAAAGCTGCATTTTTTGTTATTCCTTATTTTTTTAATGAGTATTATACTATGCAAAAAATGCTCCAAAATGGTGATTATGAATGTGAAAATATAGTCTGTAAAATG------------------TAT---AATTTTCAAGAT------------AGAAAAGAGAAAATTTTTCGTGAAAATTTCAAATATTTTTTCCCAGCAGCTATAAATGGATATGATGCTTTCTTTTATAAGCTAAAAGAATTAAGTAACATGATAGATTTTGACTTTTGCTATGAATATAACACAACAGAAATGCTTACTGGCACTTATGTTATATGTTGCGCTGTTGCATGTGGCTATAAAGAAATTTATTTAGCTGGCATGGATTTTGGAGATGAAAAA------TAT---AACTATTTTAGCGAAAAAATTGAAAAAATA------------------AAAGAAAGCAAAAAACGAACT---ACC------AAAATG------CATCATAAAAGTATTGATTTAAAAATTTTGGATTTTCTACAACAGCAGTATAATGTAAAAATTTTTTCAATTTGTCCAAATAGCTCTATAAATGCATTTATACCTCTACATCCAATACAAAACAAT------------------------GAAAATATTTTTAAACCC---ATAGAACGTCCAAAAGATGCTATTAAAACCCAGCTTACTCCA------------CCAATTAAAGCTGTAAGA------------AGA---------TATAAACGA---CTTTAT---------------------TTG------------------------------------------------GAATCCAATATAATTATTAAGTTTTTTCAC------------------------------------------GAACTTGTGCAAGTTCCAAGA---------------------------CGCATA------------------------------------------------------AGACAT---------------------------------------------------------------------------------------------TATTAC------TCAAAAACAAGATATACAAGA---TAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Campylobacter_coli_76339_CstV ---------------------------------------------ATGATAGAAAAC------------------------------------------AATGCA------------------------------------------------------------------------------------------------------------GTTGTTGTTGCA---------GGAAATGGGACTAGTTTAAAAGAGATCGATTATTCAAGACTACCTAAAGAATTTGATGTGTTTAGATGTAATCAATTCTATTTTGAAGATAAATACTATCTTGGAAGAAAAGTTAAAGCTGCGTTTTCTTTTCCTGGAGTTTTTTTTGAGCAATATTACACTTTAAATACTCTTATGCAAAATAAAGAATACTATTGCGAAAATATTGTATGCAAACTA------------------TTT---CCTTTGCAACACGAAATAAACCAAAAATCATTAAGGAATTTTAAAAAGATTTTTCCATTATTTTTTCCTTATGCATTAGATGGCAATGAGCATTATTTTAATAAATTAAAAGAGTTAAATTCTTTTATAAATTTTAACTTCTTGTATGAT---GAAGGATTGCAAATAACTACCGGAATGTATGCTATCGCCTGTGCTGTTGCTTGCGGATATAAAGAAATATATATTACAGGAATAGATTTTTATTCAACGCAA------GAG---TATGCATTTGATATTAAA---GATAAGATAGGATTATATGCTTTAAATCCTTCATTTAAAATTCAATAT---TTA------AAATCT------CATAGTAAGGAAACGGATCTTGAAATTTTATCTTTTTTGAAACAAACTTATAATGCTAATTTTTTCTCTATATCCCCTAAAAGTCCTATGACAAAATATATTCCGCTAGCTCCAAAACAAAATTAT------------------------AGT------TTTGATATT---GAAGAAAAATCTTCAGAATCCATTAAAGATTTTCTTATCCCT------------TCAAAAAAAGCATATCGA------------AAT---------TATTCTAGAGCTCTATAT---------------------TTA------------------------------------------------CAGAACAATATGTTTTACAATTTTATACAC------------------------------------------GATTGCTTAAAATTTCCAAGT---------------------------GCTTTA------------------------------------------------------AAAAAT---------------------------------------------------------------------------------------------TATTTT------AAAAATATAAAAAAGGCAAAA---TAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ; END; BEGIN TREES; Title GoodSialyTr_PRANKTxwoHAY_fna; LINK Taxa = Taxa; TRANSLATE 1 Helicobacter_bizzozeronii, 2 Campylobacter_jejuni_CstII, 3 Campylobacter_jejuni_CstIII, 4 Campylobacter_jejuni_CstI, 5 Campylobacter_coli_76330_CstI, 6 Haemophilus_influenzae, 7 Campylobacter_coli_202.94_CstIV, 8 Campylobacter_coli_76339_CstV; TREE con_50_majrule = (1:1.01610314818692,6:0.4840224149753866,(3:0.3910505466834145,(4:0.1406550906468848,5:0.1474923131495429):0.3410973676098185):0.06057806626725476,(2:0.2104083824689487,(7:0.6234340879612911,8:0.2504783661969658):0.3084626896789976):0.05964878214107379); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 1836; END; BEGIN mrbayes; lset nucmodel = 4by4 nst = 6 rates = gamma ngammacat = 6; mcmc ngen = 10000000 printfreq = 5000 samplefreq = 10000 nruns = 2; sumt burnin = 250; sump burnin = 250; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 1836; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 1836; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1392792424180; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 6669433820045792442; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 6424912274816124699; mqVersion 275; checksumv 0 3 1365044519 null getNumChars 1836 numChars 1836 getNumTaxa 8 numTaxa 8 short true bits 15 states 15 sumSquaresStatesOnly 196707.0 sumSquares 196707.0 longCompressibleToShort false usingShortMatrix true 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 1046 604; setLocation 65 24; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #6424912274816124699 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 203; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 65 24; 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; getWindow; tell It; forceAutosize; endTell; hideWindow; 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 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;