#NEXUS [written Sun Mar 07 17:17:52 PST 2004 by Mesquite version 1.01+ (build e89)] BEGIN TAXA; TITLE species; 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 ; END; BEGIN CHARACTERS; TITLE measurements; 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 ; END; BEGIN TREES; Title stored_trees; LINK Taxa = species; 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 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; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 8548924366163732821; checksum 0 3542125815; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #8548924366163732821 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setSize 524 441; setLocation 7 11; setFont SanSerif; setFontSize 10; offInfoBar; setExplanationSize 20; setAnnotationSize 20; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; toggleShowNames on; toggleTight off; toggleShowChanges on; toggleShowStates on; toggleAutoWithCharNames on; setColumnWidth 66; endTell; showWindow; getEmployee #mesquite.ornamental.CellPictures.CellPictures; tell It; toggleSeparate off; toggleAA off; endTell; endTell; 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; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setEdgeWidth 6; orientRight; getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle on; branchLengthsToggle off; toggleScale on; toggleCenter on; toggleEven on; namesAngle ?; endTell; endTell; setBackground Green; setBranchColor Blue; showNodeNumbers off; labelBranchLengths off; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setFont Serif; setFontSize 18; setColor Black; toggleColorPartition on; toggleShadePartition on; toggleNodeLabels on; toggleShowNames on; endTell; endTell; getTreeWindow; tell It; setSize 527 372; setLocation 389 16; setFont SanSerif; setFontSize 10; onInfoBar; setExplanationSize 20; setAnnotationSize 20; getToolPalette; tell It; endTell; setTreeNumber 1; toggleSizeToFit on; toggleTextOnTree off; newAssistant #mesquite.trees.TreeLegendMaker.TreeLegendMaker; tell It; setOffsetsX 6; setOffsetsY 294; getLegendsVector; tell It; distributeCommands; setBounds 6 294 137 37; setOffsetX 6; setOffsetY 294; endDistributeCommands; endTell; newLegendItem #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; endTell; endTell; showWindow; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.trees.ColorBranches.ColorBranches; 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; setSize 461 461; setLocation 22 166; setFont SanSerif; setFontSize 10; offInfoBar; setExplanationSize 0; setAnnotationSize 0; 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;