#NEXUS [written Thu Dec 19 10:45:59 CET 2013 by Mesquite version 2.75 (build 564) at wir-PC/192.168.178.22] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=8; TAXLABELS Allovahlkampfia_parasardiniensis_Sar37 Allovahlkampfia__neotibetensis_Tib191 Allovahlkampfia__sardiniensis_Sar9 Allovahlkampfia__tibetensis_Tib32 Allovahlkampfia__nederlandensis_Nl64 Allovahlkampfia__paratibetensis_Tib50 Allovahlkampfia__spelaea_EU696949_ '"Solumitrus palustris" JQ031196' ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=723; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Allovahlkampfia_parasardiniensis_Sar37 TGTCTTCGTAGGTGAACCTGCGTAGGGATCATTTTTGTGAGCGTTT--------------------------------------------------------------------------------------------------------------------------TATCCGAGGT--------------TAATA-ACTAAGGATATTTGTGCTCTAGCC-------------------------------------------------------------AAATTTTATTTGGCTTTTGT-------GCGCCTTAAAAAAGCGCCAAGCTGTTTTTTTTGTCTCTTCAAGTCTTCATAATGGATGACTTGGCTCTTGTATCGATGAAGAACGCAGTGAAAGGCGAAACGTAATGTGAATCGCAACTAACAGTGAATCATCGAATCTTTGAACGCAGGCCGCACCTTGTAATATCACTCTGTGATATTACAAGGTATCTACGTATGAGTGTCAGCCCAATATCATTTTGGTTCAAGAAGATGATTAAATTTTTTTTTCTC-----------------------------------------------GGATTCTTGAATACATAT-----CTATAACATGTAC--TTAACAT---ATTTTTAATATGTCTGGCCTCATATGTGGAAGGTTACCCGCTGGATTTAAGCATATCAGTAAGCGG Allovahlkampfia__neotibetensis_Tib191 TGTCTTCGTAGGTGAACCTGCGTAGGGATCATTTTTGTGAGCATTT------------------------------------------------------------------------------------------------------------------------ATTTTCCGAGGT--------------CAATAGACTAAGGATTACTGCTCTACAG----------------------------------------------------------------GTTGTTGGCTTTTTTTTAT-------GCGCCTTAAAAAAGCGCAAAGCTTT--------TTTTCTCAAGTCTTCATAATGGACGACTTGGCTCTTGTATCGATGAAGAACGCAGTGAAAGGCGAAACGTAATGTGAATCGCAACTAACAGTGAATCATCGAATCTTTGAACGCAGGCCGCACCTTGCAATATCACTCTGTGATATTACAAGGTATCTACGTATGAGTGTCAGCCCAATATTATTTTGGTTCAAGAACCTAATAACACTTACTCTTTTTTTAAAGGAGTGCCCCTCTTCCCATGTGGAAATAAGTGGTTAGTTATGAAACTCTTGAATACATTT-----TTATAATAGATATGTTAAATCATATTTTTTTAATATGTCTGGCCTCATATGTGGAAGGTTACCCGCTGGATTTAAGCATATCAGTAAGCGG Allovahlkampfia__sardiniensis_Sar9 TGTCTTCGTAGGTGAACCTGCGTAGGGATCATTTTTGTGGGTTTTT--------------------------------------------------------------------------------------------------------------------------GTATGGTAATATCATTTATGATATTATGTTGCCAAGTA---TTTATACTTAACCTTTAGTGTTT---CTGCAACAAACACAT-TCGCATAATAATTTATT---------TTTTTATGTGGTTGGTAATTTCCTA--------ATTATTTAGGAATGAGCCAT-------------AATTTTCAAGTCTTCATAATGGACGACTTGGCTCTTGTATCGATGAAGAACGCAGTGAAAGGCGAAACGTAATGTGAATCGCAACTAACAGTGAATCATCGAATCTTTGAACGCAGGCCGCGCCTTGC-ATATCACTC-GTGTTATCGCAAGGCATTTACGTATGAGTGTCAGCCTAATATACTTTTGGTTTAA-----TGGTA--ATTTATGTACTATTGAA-------------------------------------------TTCATTATGCGAATATCA----TTTTTGATATACGCGTTTAACAAAATTT-----GTATGTCTGGCCTCATATGTGAAAGGTTACCCGCTGGATTTAAGCATATCAGTAAGCGG Allovahlkampfia__tibetensis_Tib32 TGTCTTCGTAGGTGAACCTGCGTAGGGATCATTTTTGTGGGTTTTT--------------------------------------------------------------------------------------------------------------------------GTATGGTAATATC--TTTTGATATTATGTTGCCAAGTA---TTTATACTTAACCTTTAGTGTTT---CTGCAACAAACACAT-TCGCAC-ATTATCTAGT---------ATTTTGTGTGGTTGGTAATTTCTC-------------TTTGAGAAAGAGCCA--------------CAATTTCAAGTCTTCATAATGGACGACTTGGCTCTTGTATCGATGAAGAACGCAGTGAAAGGCGAAACGTAATGTGAATCGCAACTAACAGTGAATCATCGAATCTTTGAACGCAGGCCGCGCCTTGC-ATATCACTC-GTGTTATCGCAAGGCATTTACGTATGAGTGTCAGCCTAATATACTTTTGGTTTAA-----TGGTA--ATTTATGTACTATTGAA-------------------------------------------TTCATTGTGCGAATATCA-----TTTTGATATACGCGTTTAACAAAATTT-----GTATGTCTGGCCTCATATGTGAAAGGTTACCCGCTGGATTTAAGCATATCAGTAAGCGG Allovahlkampfia__nederlandensis_Nl64 TGTCTTCGTAGGTGAACCTGCGTAGGGATCATTTTTGTGGGTTTTT--------------------------------------------------------------------------------------------------------------------------GTATGGTAATATC--TTTTGATATTATGTTGCCAAGTAT--TTTATACTTAACCTTTAGTGTTT---CTGCAACAAACACAT-TCGCAC-ATTATCTAGT---------ATTTTGTGTGGTTGGTAATTTCTC-------------TTTGAGAAAGAGCCA--------------CAATTTCAAGTCTTCATAATGGACGACTTGGCTCTTGTATCGATGAAGAACGCAGTGAAAGGCGAAACGTAATGTGAATCGCAACTAACAGTGAATCATCGAATCTTTGAACGCAGGCCGCGCTTTGC-ATATCACTC-GTGTTATCGCAAGGCATTTACGTATGAGTGTCAGCCTAATATACTTTTGGTTTAA-----TGGTA--ATTTATGTACTATTGAA-------------------------------------------TTCATTGTGCGAATATCA-----TTTTGATATACGCGTTTAAC-AAATTT-----GTATGTCTGGCCTCATATGTGAAAGGTTACCCGCTGGATTTAAGCATATCAGTAAGCGG Allovahlkampfia__paratibetensis_Tib50 TGTCTTCGTAGGTGAACCTGCGTAGGGATCATTTTTGTGGGGTTTT--------------------------------------------------------------------------------------------------------------------------TGACTGTCGCAA---------------------AAAGTGTAAAAACTTTTAACCCTTTGTGTT----TAGCGAC-AACACAA-TCGCATAATTTTATATTATGTGTTCGCTTCGGCGTGGTTAACTTTTTTCT----------TTATTGAAAAAGGTGCCAAACT----------TTTTTTCAAGTCTTCATAATGGACGACTTGGCTCTTGTATCGATGAAGAACGCAGTGAAAGGCGAAACGTAATGTGAATCGCAACTAACAGTGAATCATCGAATCTTTGAACGCAGGCCGCGCTTTGC-ATATCACTT-GTGTTATCGCAAAGCATCTACGTATGAGTGTCAGCCTAATATACTTTCGGTTTAA-----TGGTA--ATTTATTTACTATTAAA-------------------------------------------TACATTATGCGAGTATTT-----TTTAAATACACGCGTTTAACAGAAT-------TTATGTCTGGCCTCATATGTGGAAGATTACCCGCTGGATTTAAGCATATCAGTAAGCGG Allovahlkampfia__spelaea_EU696949_ -GTCTTCGTAGGTGAACCTGCGTAGGAGTCATTTTTGTGGGGTTTT--------------------------------------------------------------------------------------------------------------------------TGTCTGGAATATC-TTTAGAATATTGTGTCGCCAAAAGTACTTGACTTTTTACCCTTTGTGTT----CCGCGACAAACACAATTCGCATAACTTGATATTTTAT-TAGGTTATGTGGTTGC-------------------GTGCTTTTTTAAAAAGTGCCAAAC-----------TTTTTTCAAGTCTTCATAATGGACGACTTGGCTCTTGTATCGATGAAGAACGCAGTGAAAGGCGAAACGTAATGTGAATCGCAACTAACAGTGAATCATCGAATCTTTGAACGCAGGCCGCGCCTTGC-ATATCACTC-GTGTTATCGCAAGGCATCTACGTATGAGTGTCAGCCCAATATCCTTTTGGTTTAA-----TGGTA--ATATTTGTACTATTGAA--------------------------------------------CCATTATGCGAGATATT-----TTTTGATACACGCGTT-AACAAAGAAT-----ATGTGCCTGGCCCCATATGTGGAAGGTT-CCCGCTGGA-TTAAGCATATCAGTAAGCGG '"Solumitrus palustris" JQ031196' -GTCTTCGTAGGTGAACCTGCGTAGGGATCATTTTTGTGAGGTTTTTAATTTGTCTTGTGGTAAATCCGTTTTTTTAAAACTGGACGATGTCATTATAGGAAGTGATGACTTGGATTTGTTCAAACACTTTTTTGTGTTTAACCTGTGATATAACGTCGTAGGTTATGTTTTTAACATAACCGCAAGGCTGGCACGGTTCCAAGTTTCAAATACCTTCCGCCTTTTTCGTGTCCCCAATGACAGACACAA-AATCGTTAGTTTGGATT-TTTTCAAACATTAATACGATTAACCTCTTAGTTTTGGGTACATTTTCACAAAAAGTGCCAAA------------CTTTTTCAAGTCTTCATAATGGATGACTTGGCTCTTGTATCGATGAGGAACGCAGTGAAAGGCGAAACGTAATGTGAATCGCAACTAACAGTGAATCATCGAATCTTTGAACGCAGGCCGCGCCTTGC-ACGTCATTC-GTGATGTGGCAAGGCATCTATGTATGAGTGTCAGCCTAACATCCTTTTGGTTTAA-----TAATAATATTTTTTTATTATTAAA-------------------------------------------TCCATTATGCGAGTATCAATTTATTTCGTTACACGCTTTTAACAAGA--------ATGTGTCTGGCCTCATATATGGAAGGTTACCCGCTGGATTTAAGCATATCAGTAAGCGG ; END; BEGIN SETS; CHARSET Treepos = 2 - 46 315 - 329 344 - 471 473 - 481 483 - 537 612 - 627 633 - 645 665 - 723; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 723; END; BEGIN TREES; Title Imported_trees; LINK Taxa = Taxa; TRANSLATE 1 Allovahlkampfia_parasardiniensis_Sar37, 2 Allovahlkampfia__neotibetensis_Tib191, 3 Allovahlkampfia__sardiniensis_Sar9, 4 Allovahlkampfia__tibetensis_Tib32, 5 Allovahlkampfia__nederlandensis_Nl64, 6 Allovahlkampfia__paratibetensis_Tib50, 7 Allovahlkampfia__spelaea_EU696949_, 8 '"Solumitrus palustris" JQ031196'; TREE Imported_tree_0 = (1:0.03176,2:0.01642,((6:0.03589,(8:0.06967,7:0.02865)45:0.00677)42:0.00714,((5:0.00296,4:0.0)98:0.01039,3:0.00871)100:0.03359)100:0.10414); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 723; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 723; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1387446359314; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 214740564831750028; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4910717951395318026; mqVersion 275; checksumv 0 3 3487096121 null getNumChars 723 numChars 723 getNumTaxa 8 numTaxa 8 short true bits 15 states 15 sumSquaresStatesOnly 108712.0 sumSquares 108712.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1920 962; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #214740564831750028 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 833.1387445875865.2701538327343818115; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1820 895; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow; endTell; 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; setTree '((1:0.03176,2:0.01642):0.05207,((3:0.00871,(4:0.0,5:0.00296)98:0.01039)100:0.03359,(6:0.03589,(7:0.02865,8:0.06967)45:0.00677)42:0.00714)100:0.05207)<> <> < setBetweenBits = selected >;'; 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 #4910717951395318026 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1820 895; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setActive; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; 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 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;