#NEXUS [written Mon Apr 24 10:03:23 CEST 2017 by Mesquite version 3.2 (build 801) at HG17209/172.30.18.79] BEGIN TAXA; TITLE 16S; DIMENSIONS NTAX=7; TAXLABELS Homonota_spa_LJAMMCNP_10495 Homonota_spa_LJAMMCNP_10576 Homonota_spa_LJAMMCNP_5047 Homonota_spb_MNHNP_12238 Homonota_spb_SMF_101984 Homonota_spb_MNHNP_11873 Phyllopezus_przewalskii_GK_3688 ; END; BEGIN CHARACTERS; TITLE 16S_Matrix; DIMENSIONS NCHAR=528; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Homonota_spa_LJAMMCNP_10495 GTGA-CTCACTTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTTCTCCAAATAGGAACTAGTATGAACGGCTAAATGAGGGCCCAACTGTCTCCTTTAGCAAGCCAATGAAACTGATCTTTCAGTACAAAAGCTGAGATAAACACATAAGACGAGAAGACCCTGTGGAGCTTTCAAACTACCACTAGACCAC-------CCACCCTA--ACTAGCCAGCAG-----------------TTTTAAGTTGGGGCGACTACGGGACCAAAAAAACACCCGCGAGCCAGGGCCTACAGCCCGCTACTGGCCAACATGCCAAAAGCACAATAACACTCGACCCAGCCACCACTGAGCAACGAACCCAGTTACCCCAGGGATAACAGCGCCATCCTCTTAAAGAGTCCATATCGCTAAGAGGGCTTACGACCTCGATGTTGGATCGGGACACCCAGGCGGTGCAGCCGTAGCC-AAAGGTTCGTTTGTTCAACGACTAATGTCCCACGTGATCTGAG- Homonota_spa_LJAMMCNP_10576 GTGA-CTCACTTAA-CGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTTCTCCAAATAGGAACTAGTATGAACGGCTAAATGAGGGCCCAACTGTCTCCTTTAGCAAGCCAATGAAACTGATCTTTCAGTACAAAAGCTGAGATAAACACATAAGACGAGAAGACCCTGTGGAGCTTTCAAACTACCACTAGACCAC-------CCACCCTA--ACTAGTCAACAG-----------------TTTTAAGTTGGGGCGACTACGGGACCAAAAAAACACCCGCGAGCCAGGGCCTACAGCCCGCTACTGGCCAACATGCCAAAAGCACAATAACACTCGACCCAGCTACCACTGAGCAACGAACCCAGTTACCCCAGGGATAACAGCGCCATCCTCTTAAAGAGTCCATATCGCTAAGAGGGCTTACGA?CTCGATGTTGGATCGGGACACCCAGGCGGTGCAGCCGCTGCC-AAAGGTTCGTTTGTTCAACGACTAATGTCCCACGTGATCT???- Homonota_spa_LJAMMCNP_5047 GTGAACTCACTTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTTCTCCAAATAGGAACTAGTATGAACGGCTAAATGAGGGCCCAACTGTCTCCTTTAGCAAGCCAATGAAACTGATCTTTCAGTACAAAAGCTGAGATAAACACATAAGACGAGAAGACCCTGTGGAGCTTTCAAACTACCACTAGACCAC-------CCACCCTA--ACTAGCCAGCAG-----------------TTTTAAGTTGGGGCGACTACGGGACCAAAAAAACACCCGCGAGCCAGGGCCTACAGCCCGCTACTGGCCAACATGCCAAAAGCACAATAACACTCGACCCAGCCACCACTGAGCAACGAACCCAGTTACCCCAGGGATAACAGCGCCATCCTCTTAAAGAGTCCATATCGCTAAGAGGGCTTACGACCTCGATGTTGGATCGGGACACCCAGGCGGTGCAGCCGCTGCCCAAAGGTTCGTTTGTTCAACGACTAATGTCCCACGTGATCTGAG- Homonota_spb_MNHNP_12238 GTGAGCCCACTTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTTCTCCAAATAGGAACTAGTATGAACGGCTAAATGAGGGCCCAACTGTCTCCTTTAGCAAGCCAATGAAACTGATCTTTCAGTACAAAAGCTGAAATAAACACATAAGACGAGAAGACCCTGTGGAGCTTT-AAACTACCACTAGACCAC-------CCACCCCAG-ACTAGCCAGCAG-----------------TTTTAAGTTGGGGCGACTACGGGACCAAAAAAACACCCGCGAGCCAGGGCCCACAGCCCGCTACTGGCCCACATGCCAAAAGCACACTAACACTCGACCCAGCCATCACTGAGCAACGAACCCAGTTACCCCAGGGATAACAGCGCCATCCTCTTAAAGAGTCCATATCGCCAAGAGGGCTTACGACCTCGATGTTGGATCGGGACACCCAGGCGGTGCAGCCGCTGCC-AAAGGTTCGTTTGTTCAACGACTAACGTCCCACGTGATCTGAG- Homonota_spb_SMF_101984 GTGAGCCCACTTAAACGGCCGCGGTATCCTAACCGTGCAAAGGTAGCGTAATCACTTGTTCTCCAAATAGGAACTAGTATGAACGGCTAAATGAGGGCCCAACTGTCTCCTTTAGCAAGCCAATGAAACTGATCTTTCAGTACAAAAGCTGAAATAAACACATAAGACGAGAAGACCCTGTGGAGCTTT-AAACTACCACTAGACCAC-------CCACCCCAG-ACTAGCCAGCAG-----------------TTTTAAGTTGGGGCGACTACGGGACCAAAAAAACACCCGCGAGCCAGGGCCCACAGCCCGCTACTGGCCCACATGCCAAAAGCACACTAACACTCGACCCAGCCATCACTGAGCAACGAACCCAGTTACCCCAGGGATAACAGCGCCATCCTCTTAAAGAGTCCATATCGCCAAGAGGGCTTACGACCTCGATGTTGGATCGGGACACCCAGGCGGTGCAGCCGCTGCC-AAAGGTTCGTTTGTTCAACGACTAACGTCCCACGTGATCTGAG- Homonota_spb_MNHNP_11873 ???????????????????????????????????????????????????????TTGTTCTCCAAATAGGAACTAGTATGAACGGCTAAATGAGGGCCCAACTGTCTCCTTTAGCAAGCCAATGAAACTGATCTTTCAGTACAAAAGCTGAAATAAACACATAAGACGAGAAGACCCTGTGGAGCTTT-AAACTACCACTAGACCAC-------CCACCCCAG-ACTAGCCAGCAG-----------------TTTTAAGTTGGGGCGACTACGGGACCAAAAAAACACCCGCGAGCCAGGGCCCACAGCCCGCTACTGGCCCACATGCCAAAAGCACACTAACACTCGACCCAGCCATCACTGAGCAACGAACCCAGTTACCCCAGGGATAACAGCGCCATCCTCTTAAAGAGTCCATATCGCCAAGAGGGCTTACGACCTCGATGTTGGATCGGGACACCCAGGCGGTGCAGCCG-TGCC-AAAGGTTCGTTTGTTCAACGACTAACGTCCCACGTGATCTGAG- Phyllopezus_przewalskii_GK_3688 GTGA-CCCACTTCA-CGGCCGCGGTACCCTAAC-GTGCAAAGGTAGCGTAATCACTTGTCCTCTAAATAGGGA?TAGTATGAACGGTTAAATGAGGGCCT?ACTGTCTCCTTCGGCCAATCAATGAA-CTGATCTTCCAGTAAAAAAGCTGGAATAAACCCACAAGACGAGAAGACCCTGTGGAGCTTT-AAACTACTACACCACCACATAAAACCCACCCC?ACACGGGCCAACAGCAAAAAGATGGTGTAAGTTTTAAGTTGGGGCGACTACGGAATAAAAAAATCTTCCATGCAC-AGGATACAACATCCATTAAAGACCAACAAACCAAAAATACCCTAAAAT--GAGCCAGTAAT-ACTGATCACCGGACCAAGTTACCCCAGGGATAACAGCGCAATCCTCTTCTAGAGTTCCTATCGCCAAGAGGG-TTACGACCTCGATGTTGGATCAGGACCCCCTGGCGGTGCAGCCGCTGCC-AACG???????????????????????????????????????- ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 528; END; BEGIN NOTES; TAXABITS NAME = newlyAddedTaxon on = 1 - 7; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 528; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 528; END; BEGIN TREES; Title 16S_ML; ID 015b81d9440820; LINK Taxa = 16S; TRANSLATE [0] 1 Homonota_spa_LJAMMCNP_10495, [1] 2 Homonota_spa_LJAMMCNP_10576, [2] 3 Homonota_spa_LJAMMCNP_5047, [3] 4 Homonota_spb_MNHNP_12238, [4] 5 Homonota_spb_SMF_101984, [5] 6 Homonota_spb_MNHNP_11873, [6] 7 Phyllopezus_przewalskii_GK_3688; TREE tree_1 = ((((1:0.00255471,3:0.0):0.00051495,2:0.00765412):0.01678243,(4:0.0,(5:0.0,6:0.0):0.0):0.00121716):0.0876392,7:0.11207575); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1493021003984; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3322710532186065101; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3154388791189695059; mqVersion 320; checksumv 0 3 3131303231 null getNumChars 528 numChars 528 getNumTaxa 7 numTaxa 7 short true bits 15 states 15 sumSquaresStatesOnly 57601.0 sumSquares 57601.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 198; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1052 653; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #3322710532186065101 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #3322710532186065101; getWindow; tell It; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; getTable; tell It; rowNamesWidth 252; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 854 581; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.arrow; 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 #3322710532186065101 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 015b81d9440820; toggleUseWeights off; endTell; setAssignedID 4223.1492532184720.3810580005595929136; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 854 581; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareLineTree.SquareLineTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; setFixedTaxonDistance 0; endTell; setEdgeWidth 4; showEdgeLines on; orientUp; 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 off; toggleColorAssigned on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; togglePrintName on; 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 off; toggleHorizontal on; toggleWhiteEdges on; toggleShowOnTerminals 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; toggleShowOnTerminals on; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #3154388791189695059 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 854 581; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; 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; toggleShowPaleExcluded off; togglePaleInapplicable on; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.AlterData.AlterData; tell It; toggleBySubmenus off; 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 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;