#NEXUS [written Fri Dec 22 11:58:47 CET 2017 by Mesquite version 3.31 (build 859) at 228net115.unica.it/193.206.228.115] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=55; TAXLABELS callithrix_jacchus_ERV1_1_proviral_consensus ERV1_1CJaLTR_ERV1_1CJaInt_ERV1_1_RepBase HERVW_subgroup1_consensus HERVW_subgroup2_consensus homo_sapiens_hg19_chr10_99049848_99051021 homo_sapiens_hg19_chr11_114217924_114220414 homo_sapiens_hg19_chr11_18840552_18842462 homo_sapiens_hg19_chr12_14369478_14374042 homo_sapiens_hg19_chr12_18220942_18223574 homo_sapiens_hg19_chr14_38573435_38576501 homo_sapiens_hg19_chr1_47412274_47413748 homo_sapiens_hg19_chr147595486_47596960 homo_sapiens_hg19_chr15_51649330_51653005 homo_sapiens_hg19_chr16_18124951_18125497 homo_sapiens_hg19_chr16_20656274_20658178 homo_sapiens_hg19_chr18_1729227_1730327 homo_sapiens_hg19_chr19_24350451_24353078 homo_sapiens_hg19_chr2_180922439_180924977 homo_sapiens_hg19_chr3_109693465_109693986 homo_sapiens_hg19_chr3_88935018_88936153 homo_sapiens_hg19_chr5_18742581_18746140 homo_sapiens_hg19_chr5_34062285_34064918 homo_sapiens_hg19_chr5_74600280_74602253 homo_sapiens_hg19_chr6_115319550_115323003 homo_sapiens_hg19_chr6_166759559_166760142 homo_sapiens_hg19_chr6_86683575_86685615 homo_sapiens_hg19_chr7_9057073_9059465 homo_sapiens_hg19_chr8_124422873_124424005 homo_sapiens_hg19_chr8_129390098_129394380 homo_sapiens_hg19_chr9_29776755_29779436 homo_sapiens_hg19_chrX_105794494_105796487 homo_sapiens_hg19_chrY_16452922_16456884 homo_sapiens_hg19_chrY_19244538_19249067 homo_sapiens_hg19_chrY19246861_19247702 LTR10F_HERVIP10FH_LTR10F LTR10F_HERVIP10F_int_LTR10F LTR12_HERV9int_LTR12 LTR17_HERV17int_LTR17 LTR21A_HERVFH21I_LTR21A LTR2_HARLEQUIN_LTR2 LTR2_HERVEint_LTR2 LTR30_HERV30I_LTR30 LTR35A_HERV1_I_int_LTR35A LTR46_HERVFc1_LTR46 LTR4_HERV3int_LTR4 LTR6A_HERVTint_LTR6A LTR71A_HERVP71Aint_LTR71A LTR7C_HERVHint_LTR7C MER41C_PRIMA41_MER41C MER48_HERVH48I_MER48 MER50_MER50I_MER50 MER57A_MER57A_I_MER57A MER57_MER57A_I_MER57 MTL2A1_HERVLint_MTL2A1 PABL_AI ; END; BEGIN TREES; Title Imported_trees; ID 015fed68dad51; LINK Taxa = Taxa; TRANSLATE [0] 1 callithrix_jacchus_ERV1_1_proviral_consensus, [1] 2 ERV1_1CJaLTR_ERV1_1CJaInt_ERV1_1_RepBase, [2] 3 HERVW_subgroup1_consensus, [3] 4 HERVW_subgroup2_consensus, [4] 5 homo_sapiens_hg19_chr10_99049848_99051021, [5] 6 homo_sapiens_hg19_chr11_114217924_114220414, [6] 7 homo_sapiens_hg19_chr11_18840552_18842462, [7] 8 homo_sapiens_hg19_chr12_14369478_14374042, [8] 9 homo_sapiens_hg19_chr12_18220942_18223574, [9] 10 homo_sapiens_hg19_chr14_38573435_38576501, [10] 11 homo_sapiens_hg19_chr1_47412274_47413748, [11] 12 homo_sapiens_hg19_chr147595486_47596960, [12] 13 homo_sapiens_hg19_chr15_51649330_51653005, [13] 14 homo_sapiens_hg19_chr16_18124951_18125497, [14] 15 homo_sapiens_hg19_chr16_20656274_20658178, [15] 16 homo_sapiens_hg19_chr18_1729227_1730327, [16] 17 homo_sapiens_hg19_chr19_24350451_24353078, [17] 18 homo_sapiens_hg19_chr2_180922439_180924977, [18] 19 homo_sapiens_hg19_chr3_109693465_109693986, [19] 20 homo_sapiens_hg19_chr3_88935018_88936153, [20] 21 homo_sapiens_hg19_chr5_18742581_18746140, [21] 22 homo_sapiens_hg19_chr5_34062285_34064918, [22] 23 homo_sapiens_hg19_chr5_74600280_74602253, [23] 24 homo_sapiens_hg19_chr6_115319550_115323003, [24] 25 homo_sapiens_hg19_chr6_166759559_166760142, [25] 26 homo_sapiens_hg19_chr6_86683575_86685615, [26] 27 homo_sapiens_hg19_chr7_9057073_9059465, [27] 28 homo_sapiens_hg19_chr8_124422873_124424005, [28] 29 homo_sapiens_hg19_chr8_129390098_129394380, [29] 30 homo_sapiens_hg19_chr9_29776755_29779436, [30] 31 homo_sapiens_hg19_chrX_105794494_105796487, [31] 32 homo_sapiens_hg19_chrY_16452922_16456884, [32] 33 homo_sapiens_hg19_chrY_19244538_19249067, [33] 34 homo_sapiens_hg19_chrY19246861_19247702, [34] 35 LTR10F_HERVIP10FH_LTR10F, [35] 36 LTR10F_HERVIP10F_int_LTR10F, [36] 37 LTR12_HERV9int_LTR12, [37] 38 LTR17_HERV17int_LTR17, [38] 39 LTR21A_HERVFH21I_LTR21A, [39] 40 LTR2_HARLEQUIN_LTR2, [40] 41 LTR2_HERVEint_LTR2, [41] 42 LTR30_HERV30I_LTR30, [42] 43 LTR35A_HERV1_I_int_LTR35A, [43] 44 LTR46_HERVFc1_LTR46, [44] 45 LTR4_HERV3int_LTR4, [45] 46 LTR6A_HERVTint_LTR6A, [46] 47 LTR71A_HERVP71Aint_LTR71A, [47] 48 LTR7C_HERVHint_LTR7C, [48] 49 MER41C_PRIMA41_MER41C, [49] 50 MER48_HERVH48I_MER48, [50] 51 MER50_MER50I_MER50, [51] 52 MER57A_MER57A_I_MER57A, [52] 53 MER57_MER57A_I_MER57, [53] 54 MTL2A1_HERVLint_MTL2A1, [54] 55 PABL_AI; TREE Imported_tree_1 = (((((((((((25:0.03807916,30:0.06063089):0.00294792[%bootstrapFrequency = 0.08 ],(9:0.04954379,17:0.07648525):0.00431375[%bootstrapFrequency = 0.12 ]):0.00441014[%bootstrapFrequency = 0.02 ],(18:0.07599311,27:0.10311372):0.0046901[%bootstrapFrequency = 0.12 ]):0.01104453[%bootstrapFrequency = 0.1 ],7:0.04864224):0.01812873[%bootstrapFrequency = 0.2 ],(4:0.00610551,(38:0.00226204,3:0.0047053):0.0130681[%bootstrapFrequency = 1 ]):0.00766502[%bootstrapFrequency = 0.84 ]):0.01302278[%bootstrapFrequency = 0.46 ],15:0.04381302):0.07451037[%bootstrapFrequency = 0.96 ],33:0.4244297):0.16422459[%bootstrapFrequency = 0.66 ],(((42:0.25832265,37:0.34487218):0.10546492[%bootstrapFrequency = 1 ],(1:0.01625051,2:0.01365255):0.30444267[%bootstrapFrequency = 1 ]):0.05951427[%bootstrapFrequency = 0.84 ],(13:0.04975803,(((32:0.07433289,10:0.09005778):0.05352451[%bootstrapFrequency = 1 ],21:0.08953971):0.01275535[%bootstrapFrequency = 0.2 ],(29:0.05965855,(24:0.06269842,(6:0.04179097,8:0.04675602):0.00338285[%bootstrapFrequency = 0.24 ]):0.0034169[%bootstrapFrequency = 0.2 ]):0.00886812[%bootstrapFrequency = 0.22 ]):0.01180705[%bootstrapFrequency = 0.14 ]):0.21426999[%bootstrapFrequency = 1 ]):0.06428646[%bootstrapFrequency = 0.7 ]):0.25020863[%bootstrapFrequency = 1 ],((23:0.2572425,31:0.28920473):0.18334801[%bootstrapFrequency = 1 ],(((20:0.05105442,28:0.03555836):0.00855807[%bootstrapFrequency = 0.5 ],5:0.04797177):0.00201192[%bootstrapFrequency = 0.68 ],(19:0.05079625,(14:0.03365249,16:0.36480186):0.06065408[%bootstrapFrequency = 0.52 ]):0.05159373[%bootstrapFrequency = 0.34 ]):0.41993235[%bootstrapFrequency = 1 ]):0.45573723[%bootstrapFrequency = 0.7 ]):0.2704213[%bootstrapFrequency = 0.96 ],((26:1.08252459,22:1.02104542):0.17517293[%bootstrapFrequency = 0.44 ],((((50:0.41559019,39:0.40444494):0.09186515[%bootstrapFrequency = 1 ],48:0.65581786):0.08005005[%bootstrapFrequency = 0.98 ],44:0.97462882):0.24675691[%bootstrapFrequency = 0.98 ],(54:1.24590013,(49:0.71636537,(((36:0.02149872,35:0.22359601):0.31256564[%bootstrapFrequency = 1 ],47:0.31191774):0.56393191[%bootstrapFrequency = 1 ],(46:0.71125304,((43:0.24639223,45:0.21810525):0.19715093[%bootstrapFrequency = 1 ],(41:0.08153808,40:0.49788597):0.27151733[%bootstrapFrequency = 1 ]):0.3735164[%bootstrapFrequency = 1 ]):0.10602879[%bootstrapFrequency = 1 ]):0.08253244[%bootstrapFrequency = 0.26 ]):0.04237549[%bootstrapFrequency = 0.4 ]):0.05179416[%bootstrapFrequency = 0.18 ]):0.06323237[%bootstrapFrequency = 0.18 ]):0.03374321[%bootstrapFrequency = 0.06 ]):0.00850321[%bootstrapFrequency = 0.16 ],(51:1.01334631,(((11:0.0522822,12:0.01482356):0.78513545[%bootstrapFrequency = 1 ],34:0.43673865):0.26205678[%bootstrapFrequency = 1 ],(55:0.68936974,(53:0.0,52:0.0):0.79968156[%bootstrapFrequency = 1 ]):0.64457352[%bootstrapFrequency = 1 ]):0.08263203[%bootstrapFrequency = 0.14 ]):0.10475664[%bootstrapFrequency = 0.16 ]); END; BEGIN NOTES; SUT TAXON = 1 NAME = color INTEGER = 5; SUT TAXON = 2 NAME = color INTEGER = 5; SUT TAXON = 3 NAME = color INTEGER = 14; SUT TAXON = 4 NAME = color INTEGER = 14; SUT TAXON = 38 NAME = color INTEGER = 14; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1513940327030; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3832456652128010253; tell It; setDefaultOrder 14 15 9 7 28 22 6 23 2 18 49 50 16 30 10 31 3 4 29 26 19 33 24 21 0 32 5 27 20 1 25 17 11 51 41 40 13 8 35 47 46 12 44 37 45 43 42 36 39 34 48 54 53 38 52; attachments ; endTell; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1027 870; setLocation 771 77; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #3832456652128010253 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #3832456652128010253; getWindow; tell It; useTargetValue off; setTargetValue ; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 927 798; setLocation 771 77; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.arrow; endTell; setActive; 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 #3832456652128010253 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 015fed68dad51; toggleUseWeights off; endTell; setAssignedID 952.1511517194668.2489552797319494846; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 927 798; setLocation 771 77; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.ColorBranches.ColorToolExtra.ColorBranches; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareLineTree.SquareLineTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; setFixedTaxonDistance 0; endTell; setEdgeWidth 3; showEdgeLines on; orientRight; 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; setFont Helvetica; setFontSize 12; setColor Black; toggleColorPartition off; toggleColorAssigned on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setTree '(((((((((((25:0.03807916,30:0.06063089):0.00294792,(9:0.04954379,17:0.07648525):0.00431375):0.00441014,(18:0.07599311,27:0.10311372):0.0046901):0.01104453,7:0.04864224):0.01812873,(4:0.00610551,(38:0.00226204,3:0.0047053):0.0130681):0.00766502):0.01302278,15:0.04381302):0.07451037,33:0.4244297):0.16422459,(((42:0.25832265,37:0.34487218):0.10546492,(1:0.01625051,2:0.01365255):0.30444267):0.05951427,(13:0.04975803,(((32:0.07433289,10:0.09005778):0.05352451,21:0.08953971):0.01275535,(29:0.05965855,(24:0.06269842,(6:0.04179097,8:0.04675602):0.00338285):0.0034169):0.00886812):0.01180705):0.21426999):0.06428646):0.25020863,((23:0.2572425,31:0.28920473):0.18334801,(((20:0.05105442,28:0.03555836):0.00855807,5:0.04797177):0.00201192,(19:0.05079625,(14:0.03365249,16:0.36480186):0.06065408):0.05159373):0.41993235):0.45573723):0.2704213,((26:1.08252459,22:1.02104542):0.17517293,((((50:0.41559019,39:0.40444494):0.09186515,48:0.65581786):0.08005005,44:0.97462882):0.24675691,(54:1.24590013,(49:0.71636537,(((36:0.02149872,35:0.22359601):0.31256564,47:0.31191774):0.56393191,(46:0.71125304,((43:0.24639223,45:0.21810525):0.19715093,(41:0.08153808,40:0.49788597):0.27151733):0.3735164):0.10602879):0.08253244):0.04237549):0.05179416):0.06323237):0.03374321):0.00850321,(51:1.01334631,(((11:0.0522822,12:0.01482356):0.78513545,34:0.43673865):0.26205678,(55:0.68936974,(53:0.0,52:0.0):0.79968156):0.64457352):0.08263203):0.10475664);'; 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; toggleShow consensusFrequency; toggleShow posteriorProbability; toggleShow bootstrapFrequency; toggleShow consensusFrequency; toggleShow posteriorProbability; toggleShow bootstrapFrequency; setDigits 4; setThreshold ?; writeAsPercentage on; 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; endTell; end;