#NEXUS [written Sun May 04 15:13:30 PDT 2008 by Mesquite version 2.01+ (build j65) at Thrandina.local/10.0.1.8 (Wayne Maddison)] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=16; TAXLABELS taxon_0 taxon_1 taxon_2 taxon_3 taxon_4 taxon_5 taxon_6 taxon_7 taxon_8 taxon_9 taxon_10 taxon_11 taxon_12 taxon_13 taxon_14 taxon_15 ; BLOCKID WM114891ff7d559; END; BEGIN CHARACTERS; TITLE 'Matrix in file "05-treeSearch.nex"'; DIMENSIONS NCHAR=5; FORMAT DATATYPE = CONTINUOUS; CHARSTATELABELS 1 length, 2 width, 3 speed, 4 temperature, 5 personality ; MATRIX taxon_0 9.367 5.022 2.763 38.57 1.723 taxon_1 8.793 3.244 4.664 38.81 0.296 taxon_2 8.576 6.245 2.528 38.5 -0.0239 taxon_3 11.54 8.718 5.862 40.54 -2.039 taxon_4 9.977 6.082 5.984 38.32 0.7256 taxon_5 9.381 5.468 4.398 38.48 1.213 taxon_6 8.162 5.782 4.894 39.69 0.8212 taxon_7 8.676 4.86 4.186 39.61 0.5508 taxon_8 9.356 6.75 4.649 38.01 0.795 taxon_9 8.107 5.989 2.975 40.13 -1.686 taxon_10 9.692 7.227 5.747 39.52 -0.8719 taxon_11 8.902 6.05 4.337 37.5 -0.9571 taxon_12 9.055 6.575 4.896 40.48 -0.293 taxon_13 10.11 4.199 3.327 38.94 -0.1349 taxon_14 10.2 3.975 4.623 37.1 -0.4575 taxon_15 7.604 5.438 2.809 37.69 -2.129 ; BLOCKID WM114891ff8060; END; BEGIN TREES; Title 'Trees from "05-treeSearch.nex"'; LINK Taxa = Taxa; TRANSLATE 1 taxon_0, 2 taxon_1, 3 taxon_2, 4 taxon_3, 5 taxon_4, 6 taxon_5, 7 taxon_6, 8 taxon_7, 9 taxon_8, 10 taxon_9, 11 taxon_10, 12 taxon_11, 13 taxon_12, 14 taxon_13, 15 taxon_14, 16 taxon_15; TREE one_tree = ((((1,4),13),5),(11,(((3,10),9),(((6,14),15),((((7,12),16),8),2))))); END; BEGIN NOTES; TEXT FILE TEXT = 'Reconstruction of phylogenetic trees has been dominated (in practice) by categorical data. Mesquite allows other criteria for tree search, including parsimony searches using continuous valued data.^n^nMesquite has a general concept of "a number for a tree". Examples could be the treelength, the number of steps in a character, the likelihood of the tree, its symmetry, and so on. Each of these is a number that applies to the tree. For any given number for a tree, one might seek that tree which maximizes or minimizes it (e.g., minimizing treelength in a standard parsimony search). The Tree Search modules allow one to search for a tree optimizing any such number for a tree available. Here, we''d like to search for a species tree minimizing treelength for continuous-valued data. ^n^nTo do that, go to the Taxa&Trees menu and select "Heuristic" under "Tree Search" under the "Make trees block from" submenu. Indicate you want to use the criterion "Treelength". The tree search modules currently do a simple addition sequence followed by branch rearrangements, and are much much much much slower than PAUP* (for instance). But, after humming for a while, they should indicate that the trees are ready, and ask if you want to see the tree in a tree window. Say "yes". You''ll see the tree found by the search. You can also return to the '; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = Squared: 1 - 5; TYPESET Current_Parsimony_Models = Squared: 1 - 5; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = Brownian_default: 1 - 5; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 9019647525474091584 WM114891ff7d559; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 8548924366163732821 WM114891ff8060; checksum 0 3542125815 WM114891ff8060; endTell; getWindow; tell It; setResourcesState false true 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 515 353; setLocation 7 22; setFont SanSerif; setFontSize 10; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #9019647525474091584 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 6039.975479485824.5658383844903825957; getTreeWindow; tell It; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 527 461; setLocation 595 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle on; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientRight; toggleCorners off; endTell; setBackground Green; setBranchColor Blue; 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 Serif; setFontSize 18; setColor Black; toggleColorPartition on; toggleShadePartition on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; useSuggestedSize off; toggleSizeToFit on; toggleTextOnTree off; showWindow; newAssistant #mesquite.trees.TreeLegendMaker.TreeLegendMaker; tell It; setOffsetsX 6; setOffsetsY 294; getLegendsVector; tell It; distributeCommands; setBounds 6 294 137 39; setOffsetX 6; setOffsetY 294; endDistributeCommands; endTell; newLegendItemNoCalc #mesquite.parsimony.Treelength.Treelength; tell It; getEmployee #mesquite.parsimony.TreelengthForMatrix.TreelengthForMatrix; tell It; getEmployee #mesquite.parsimony.ParsCharSteps.ParsCharSteps; tell It; setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels; getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared; tell It; toggleWeight on; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.CharMatrixCoordIndep.CharMatrixCoordIndep; tell It; setCharacterSource #mesquite.charMatrices.StoredMatrices.StoredMatrices; tell It; setDataSet #8548924366163732821; endTell; endTell; endTell; calculate; endTell; 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; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #8548924366163732821 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 572 425; setLocation 277 468; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleShowChanges on; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames on; toggleShowDefaultCharNames off; toggleConstrainCW on; setColumnWidth 66; toggleBirdsEye off; toggleAllowAutosize on; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; endTell; endTell; newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator; tell It; setNextFileName '06-sim.nex'; setPrevFileName '04-branchLengths.nex'; getWindow; tell It; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 515 336; setLocation 7 22; setFont SanSerif; setFontSize 10; setActive; setExplanation 'Reconstruction of phylogenetic trees has been dominated (in practice) by categorical data. Mesquite allows other criteria for tree search, including parsimony searches using continuous valued data.^n^nMesquite has a general concept of "a number for a tree". Examples could be the treelength, the number of steps in a character, the likelihood of the tree, its symmetry, and so on. Each of these is a number that applies to the tree. For any given number for a tree, one might seek that tree which maximizes or minimizes it (e.g., minimizing treelength in a standard parsimony search). The Tree Search modules allow one to search for a tree optimizing any such number for a tree available. Here, we''d like to search for a species tree minimizing treelength for continuous-valued data. Notice that the tree in the green window has a treelength of 57.104^n^nTo do that, go to the Taxa&Trees menu and select "Heuristic" under "Tree Search" under the "Make New Trees Block from" submenu. Indicate you want to use the criterion "Treelength". The tree search modules currently do a simple addition sequence followed by branch rearrangements, and are much much much much slower than PAUP* (for instance). But, after humming for a while, they should indicate that the trees are ready, and ask if you want to see the tree in a tree window. Say "yes". You''ll see the tree found by the search. ^n^nTree searches don''t currently adjust branch lengths.^n^nYou can also return to the green tree window and you''ll see a Tree Block submenu in the Tree menu. Choose the new tree block created by the search, and you''ll see it.'; setTitle Tree_search; toggleFileNames off; setPrevButtonName Previous; setNextButtonName Next; endTell; showWindow; endTell; endTell; end;