#NEXUS [written Sun May 04 15:09:34 PDT 2008 by Mesquite version 2.01+ (build j65) at Thrandina.local/10.0.1.8 (Wayne Maddison)] BEGIN TAXA; TITLE Fubonidians; DIMENSIONS NTAX=9; TAXLABELS Aus Fubonidia Ibbinidibe Snorolopa Quidnubia Suinon Zorabynyx Huichoros Jotinupa ; BLOCKID WM11489100a4832; END; BEGIN TAXA; TITLE Niconaceae; DIMENSIONS NTAX=8; TAXLABELS Niconus Saraplisia Conotypinium Snariolus Phybunica Ytuna Lapicorea Salipunta ; BLOCKID WM11489100a6533; END; BEGIN CHARACTERS; TITLE 'Matrix in file "08-multipleBlocks.nex"'; LINK TAXA = Fubonidians; DIMENSIONS NCHAR=2; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1"; CHARSTATELABELS 1 number_of_eyes / one two, 2 tail_color / blue red ; MATRIX Aus 11 Fubonidia 11 Ibbinidibe 11 Snorolopa 1(0 1) Quidnubia 00 Suinon 00 Zorabynyx 00 Huichoros 00 Jotinupa 00 ; BLOCKID WM11489100a780; END; BEGIN TREES; Title 'Trees block 2 from 08-multipleBlocks.nex'; LINK Taxa = Fubonidians; TRANSLATE 1 Aus, 2 Fubonidia, 3 Ibbinidibe, 4 Snorolopa, 5 Quidnubia, 6 Suinon, 7 Zorabynyx, 8 Huichoros, 9 Jotinupa; TREE First_Tree = ((((1,5),4),((7,6),2)),((9,8),3)); TREE Second_Tree = ((((9,((4,1),2)),6),3),((8,7),5)); TREE Third_Tree = ((8,((2,6),1)),((((3,9),7),4),5)); TREE Polytomous = ((1,5),(7,6,2),4,((9,8),3)); TREE Partial_tree = (((9,(1,2)),(8,7)),(3,5)); END; BEGIN TREES; Title 'Trees block 2 from 08-multipleBlocks.nex'; LINK Taxa = Niconaceae; TRANSLATE 1 Niconus, 2 Saraplisia, 3 Conotypinium, 4 Snariolus, 5 Phybunica, 6 Ytuna, 7 Lapicorea, 8 Salipunta; TREE Smith_1998 = (1,(((2,5),3),((4,7),(6,8)))); END; BEGIN NOTES; TEXT TAXA = Fubonidians TAXON = 5 TEXT = Lives_deep_in_dark_caves; CHARACTERS = 'Matrix in file "08-multipleBlocks.nex"' TAXA = Fubonidians; TEXT TAXON = 4 CHARACTER = 2 TEXT = 'Some individuals are blue, others are red. Why, no one knows.'; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 2; END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS; TYPESET * UNTITLED = unord: 1 - 2; TYPESET Current_Parsimony_Models = unord: 1 - 2; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8476784597994698209 WM11489100a4832; setID 1 6050503871130632551 WM11489100a6533; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 974864624972105434 WM11489100a780; checksum 0 4129971366 WM11489100a780; endTell; getWindow; tell It; setResourcesState false true 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 449 358; setLocation 4 24; setFont SanSerif; setFontSize 10; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #8476784597994698209 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #8476784597994698209; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 315 316; setLocation 442 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; showTaxa #6050503871130632551 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #6050503871130632551; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 365 225; setLocation 13 455; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #8476784597994698209 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTaxa #8476784597994698209; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 679.984013351205.6490942559320754920; getTreeWindow; tell It; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 486 307; setLocation 761 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle off; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter off; toggleEven off; endTell; setEdgeWidth 12; 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 on; toggleShadePartition off; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; useSuggestedSize off; toggleSizeToFit on; toggleTextOnTree off; showWindow; endTell; 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.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; makeTreeWindow #6050503871130632551 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTaxa #6050503871130632551; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 691.984013362206.425371040947643172; getTreeWindow; tell It; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 500 299; setLocation 392 431; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle off; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter off; toggleEven off; endTell; setEdgeWidth 12; 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 on; toggleShadePartition off; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; useSuggestedSize off; toggleSizeToFit on; toggleTextOnTree off; showWindow; endTell; 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.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator; tell It; setNextFileName '../introduction.nex'; setPrevFileName '07-selecting.nex'; getWindow; tell It; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 449 341; setLocation 4 24; setFont SanSerif; setFontSize 10; setActive; setExplanation 'Mesquite allows more than one block of taxa in a file. Here is a file with two blocks of taxa, the Fubonidians, and the Noconaceae (these are both fictitious, but you can image the former to be herbivores that eat the latter).^n^nYou can create additional blocks of taxa by choosing New Block of Taxa from the Taxa&Trees menu.^n'; setTitle Multiple_taxa_blocks; toggleFileNames off; setPrevButtonName Previous; setNextButtonName Return_to_intro; endTell; showWindow; endTell; endTell; end;