Menu
▾
▴
[Treebase-guts] SF.net SVN: treebase:[378] trunk/treebase-core/lib/examples
|
From: <rv...@us...> - 2009-12-15 18:16:38
|
Revision: 378
http://treebase.svn.sourceforge.net/treebase/?rev=378&view=rev
Author: rvos
Date: 2009-12-15 18:16:21 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/examples/Diversification/
trunk/treebase-core/lib/examples/Diversification/00-introduction.nex
trunk/treebase-core/lib/examples/Diversification/01-lineagesThroughTime.nex
trunk/treebase-core/lib/examples/Diversification/02-speciationExtinctionRates.nex
trunk/treebase-core/lib/examples/Diversification/03-sisterDiversification.nex
trunk/treebase-core/lib/examples/Diversification/04-BiSSEViewer.nex
trunk/treebase-core/lib/examples/Diversification/05-BiSSENetViewer.nex
trunk/treebase-core/lib/examples/Diversification/06-BiSSEtrees.nex
trunk/treebase-core/lib/examples/Diversification/07-contTreeSim.nex
trunk/treebase-core/lib/examples/Diversification/08-binaryTreeSim.nex
trunk/treebase-core/lib/examples/Introduction.nex
trunk/treebase-core/lib/examples/Molecular/
trunk/treebase-core/lib/examples/Molecular/00-introduction.nex
trunk/treebase-core/lib/examples/Molecular/01-gcContentChart.nex
trunk/treebase-core/lib/examples/Molecular/02-gcContentMatrix.nex
trunk/treebase-core/lib/examples/Molecular/03-gcContentBirdsEye.nex
trunk/treebase-core/lib/examples/Molecular/03a-cytochromeB.nex
trunk/treebase-core/lib/examples/Molecular/04-gcContentTaxa.nex
trunk/treebase-core/lib/examples/Molecular/05-gcContentTaxaExons.nex
trunk/treebase-core/lib/examples/Molecular/06-cytochromeB.nex
trunk/treebase-core/lib/examples/Molecular/07-cytochromeBHydro.nex
trunk/treebase-core/lib/examples/Molecular/08-cytochromeBlinked.nex
trunk/treebase-core/lib/examples/Molecular/09-cytochromeBscatter.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/
trunk/treebase-core/lib/examples/Multivariate_Continuous/00-introduction.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/01-wingsPlot.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/02-wingsPCA.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/03-wingsCVA.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/04-anoles.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/05-anoles.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/06-anoles.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/07-anoles.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/08-anoles.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/09-pcaSim.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/10-pcaLiveSim.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/11-cvaLiveSim.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/12-epca.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/13-epca.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/14-epca.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/15-epca.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/16-epcaLiveSim.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/17-landmarks.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/18-landmarks.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/19-landmarks.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/20-landmarks.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/epca/
trunk/treebase-core/lib/examples/Multivariate_Continuous/epca/Image1.gif
trunk/treebase-core/lib/examples/Multivariate_Continuous/epca/Image2.gif
trunk/treebase-core/lib/examples/Multivariate_Continuous/fish/
trunk/treebase-core/lib/examples/Multivariate_Continuous/fish/blue.gif
trunk/treebase-core/lib/examples/Multivariate_Continuous/fish/one.gif
trunk/treebase-core/lib/examples/Multivariate_Continuous/fish/red.gif
trunk/treebase-core/lib/examples/Multivariate_Continuous/fish/two.gif
trunk/treebase-core/lib/examples/Other_Examples/
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/01.concatenatingMatrices.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/02.concatenatingMatrices.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/03.concatenatingMatrices.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/04.concatenatingMatrices.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/05.concatenatingMatrices.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/06.concatenatingMatrices.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/07.mergedMatrix.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/otherGeneMatrix.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreTheSame/
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreTheSame/01.concatenatingMatricesSimple.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreTheSame/02.concatenatingMatricesSimple.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreTheSame/03.concatenatingMatricesSimple.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreTheSame/otherGeneMatrix.nex
Added: trunk/treebase-core/lib/examples/Diversification/00-introduction.nex
===================================================================
--- trunk/treebase-core/lib/examples/Diversification/00-introduction.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Diversification/00-introduction.nex 2009-12-15 18:16:21 UTC (rev 378)
@@ -0,0 +1,33 @@
+#NEXUS
+[written Thu Sep 20 14:35:29 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium.local/192.168.0.3 (David Maddison)]
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '01-lineagesThroughTime.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 429 288;
+ setLocation 7 29;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'Phylogeny can be used to explore species diversification, speciation and extinction. Here are some example files of relevant Mesquite features.^n^nTo go from one file to another, hit the "Next" button';
+ setTitle Species_Diversification;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ addFileLink Return_to_main_Introduction '../Introduction.nex';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Diversification/01-lineagesThroughTime.nex
===================================================================
--- trunk/treebase-core/lib/examples/Diversification/01-lineagesThroughTime.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Diversification/01-lineagesThroughTime.nex 2009-12-15 18:16:21 UTC (rev 378)
@@ -0,0 +1,329 @@
+#NEXUS
+[written Thu Sep 20 16:42:25 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium/192.168.0.3 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=32;
+ TAXLABELS
+ 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 taxon_16 taxon_17 taxon_18 taxon_19 taxon_20 taxon_21 taxon_22 taxon_23 taxon_24 taxon_25 taxon_26 taxon_27 taxon_28 taxon_29 taxon_30 taxon_31 taxon_32
+ ;
+ IDS WM1148f47d2061 WM1148f47d2072 WM1148f47d2073 WM1148f47d2074 WM1148f47d2075 WM1148f47d2076 WM1148f47d2077 WM1148f47d2078 WM1148f47d2079 WM1148f47d20710 WM1148f47d20711 WM1148f47d20712 WM1148f47d20713 WM1148f47d20714 WM1148f47d20715 WM1148f47d20716 WM1148f47d20717 WM1148f47d20718 WM1148f47d20719 WM1148f47d20720 WM1148f47d20721 WM1148f47d20722 WM1148f47d20723 WM1148f47d20724 WM1148f47d20725 WM1148f47d20726 WM1148f47d20727 WM1148f47d20728 WM1148f47d20729 WM1148f47d20830 WM1148f47d20831 WM1148f47d20832 ;
+ BLOCKID WM1148f47d2081;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "01-lineagesThroughTime.nex"';
+ DIMENSIONS NCHAR=1;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ taxon_1 0
+ taxon_2 1
+ taxon_3 0
+ taxon_4 0
+ taxon_5 0
+ taxon_6 1
+ taxon_7 0
+ taxon_8 1
+ taxon_9 1
+ taxon_10 1
+ taxon_11 1
+ taxon_12 1
+ taxon_13 1
+ taxon_14 1
+ taxon_15 1
+ taxon_16 1
+ taxon_17 1
+ taxon_18 0
+ taxon_19 1
+ taxon_20 0
+ taxon_21 0
+ taxon_22 0
+ taxon_23 1
+ taxon_24 1
+ taxon_25 1
+ taxon_26 1
+ taxon_27 1
+ taxon_28 1
+ taxon_29 1
+ taxon_30 1
+ taxon_31 1
+ taxon_32 0
+
+;
+ IDS WM1148f4828fe0 ;
+ BLOCKID WM114911738c20;
+
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1;
+
+
+END;
+
+BEGIN TREES;
+ Title 'Trees from "01-lineagesThroughTime.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 taxon_1,
+ 2 taxon_2,
+ 3 taxon_3,
+ 4 taxon_4,
+ 5 taxon_5,
+ 6 taxon_6,
+ 7 taxon_7,
+ 8 taxon_8,
+ 9 taxon_9,
+ 10 taxon_10,
+ 11 taxon_11,
+ 12 taxon_12,
+ 13 taxon_13,
+ 14 taxon_14,
+ 15 taxon_15,
+ 16 taxon_16,
+ 17 taxon_17,
+ 18 taxon_18,
+ 19 taxon_19,
+ 20 taxon_20,
+ 21 taxon_21,
+ 22 taxon_22,
+ 23 taxon_23,
+ 24 taxon_24,
+ 25 taxon_25,
+ 26 taxon_26,
+ 27 taxon_27,
+ 28 taxon_28,
+ 29 taxon_29,
+ 30 taxon_30,
+ 31 taxon_31,
+ 32 taxon_32;
+ TREE Tree = (((((7:5.187000000000067,22:5.186999999999937):2.4919999999998366,(2:5.19600000000007,((31:2.6009999999998246,14:2.6009999999998246):2.269999999999861,26:4.870999999999961):0.32500000000000023):2.4829999999999215):0.6730000000000005,((((6:0.8290000000000006,9:0.8290000000000006):0.3140000000000002,16:1.142999999999985):2.6749999999998164,(((15:0.20300000000000015,12:0.20300000000000015):0.2490000000000002,8:0.45200000000000035):1.360999999999961,32:1.8129999999999111):2.00499999999989):3.5429999999998403,((23:0.8660000000000007,(17:0.0010,24:0.0010):0.8650000000000007):1.0020000000000004,(18:1.059999999999994,4:1.059999999999994):0.8080000000000006):5.4930000000000865):0.9910000000000008):2.2739999999998606,((((10:0.21500000000000016,29:0.21500000000000016):1.1809999999999807,21:1.395999999999957):6.895000000000504,27:8.291000000000466):2.2449999999998638,((11:0.5600000000000004,19:0.5600000000000004):7.632000000000883,3:8.192000000000526):2.343999999999853):0.09000000000000007):2.389999999999848,((5:3.7479999999996982,(20:0.03300000000000002,1:0.03300000000000002):3.714999999999702):5.209999999999916,((28:0.5840000000000004,13:0.5840000000000004):7.191000000000736,(25:1.5889999999999358,30:1.5889999999999358):6.185999999999934):1.1829999999999805):4.0579999999997804):0.0;
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6732219986260810463 WM1148f47d2081;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 444104661901299517 WM114911738c20;
+ checksum 0 909469476 WM114911738c20;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #6732219986260810463 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 786.1187814845004.4817563795317733133;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 833 341;
+ setLocation 386 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.trees.SelectTaxaInClade.SelectTaxaToolExtra.SelectTaxa;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.ArcTree.ArcTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 2;
+ 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;
+ setFontSize 9;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize on;
+ toggleTextOnTree off;
+ newWindowAssistant #mesquite.diverse.LineagesThroughTime.LineagesThroughTime;
+ tell It;
+ makeWindow;
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 682 344;
+ setLocation 500 510;
+ setFont SanSerif;
+ setFontSize 10;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.charts.Histogram.Histogram;
+ tell It;
+ showAverageToggle on;
+ setCumulativeMode 0;
+ showAsBarChartToggle off;
+ showRawToggle off;
+ setNumberIntervals 20;
+ setIntervalSize 1.0;
+ setMovingWindowSize 5.0 1.0;
+ setMode 0;
+ endTell;
+ endTell;
+ endTell;
+ showWindow;
+ 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;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #444104661901299517 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 833 341;
+ setLocation 386 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ hideWindow;
+ 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.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '02-speciationExtinctionRates.nex';
+ setPrevFileName '00-introduction.nex';
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 375 333;
+ setLocation 1 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'Availabe in the Analysis menu of the Tree Window is Lineages Through Time, which plots the logarithm of the number of lineages in a tree through time. With a pure birth process, one expects the plot to be a straight line.';
+ setTitle Lineages_Through_Time;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Diversification/02-speciationExtinctionRates.nex
===================================================================
--- trunk/treebase-core/lib/examples/Diversification/02-speciationExtinctionRates.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Diversification/02-speciationExtinctionRates.nex 2009-12-15 18:16:21 UTC (rev 378)
@@ -0,0 +1,315 @@
+#NEXUS
+[written Thu Sep 20 16:42:34 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium/192.168.0.3 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=32;
+ TAXLABELS
+ 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 taxon_16 taxon_17 taxon_18 taxon_19 taxon_20 taxon_21 taxon_22 taxon_23 taxon_24 taxon_25 taxon_26 taxon_27 taxon_28 taxon_29 taxon_30 taxon_31 taxon_32
+ ;
+ IDS WM1148f47d2061 WM1148f47d2072 WM1148f47d2073 WM1148f47d2074 WM1148f47d2075 WM1148f47d2076 WM1148f47d2077 WM1148f47d2078 WM1148f47d2079 WM1148f47d20710 WM1148f47d20711 WM1148f47d20712 WM1148f47d20713 WM1148f47d20714 WM1148f47d20715 WM1148f47d20716 WM1148f47d20717 WM1148f47d20718 WM1148f47d20719 WM1148f47d20720 WM1148f47d20721 WM1148f47d20722 WM1148f47d20723 WM1148f47d20724 WM1148f47d20725 WM1148f47d20726 WM1148f47d20727 WM1148f47d20728 WM1148f47d20729 WM1148f47d20830 WM1148f47d20831 WM1148f47d20832 ;
+ BLOCKID WM1148f47d2081;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "02-speciationExtinctionRates.nex"';
+ DIMENSIONS NCHAR=1;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ taxon_1 0
+ taxon_2 1
+ taxon_3 0
+ taxon_4 0
+ taxon_5 0
+ taxon_6 1
+ taxon_7 0
+ taxon_8 1
+ taxon_9 1
+ taxon_10 1
+ taxon_11 1
+ taxon_12 1
+ taxon_13 1
+ taxon_14 1
+ taxon_15 1
+ taxon_16 1
+ taxon_17 1
+ taxon_18 0
+ taxon_19 1
+ taxon_20 0
+ taxon_21 0
+ taxon_22 0
+ taxon_23 1
+ taxon_24 1
+ taxon_25 1
+ taxon_26 1
+ taxon_27 1
+ taxon_28 1
+ taxon_29 1
+ taxon_30 1
+ taxon_31 1
+ taxon_32 0
+
+;
+ IDS WM1148f4828fe0 ;
+ BLOCKID WM114910e80a10;
+
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1;
+
+
+END;
+
+BEGIN TREES;
+ Title 'Trees from "02-speciationExtinctionRates.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 taxon_1,
+ 2 taxon_2,
+ 3 taxon_3,
+ 4 taxon_4,
+ 5 taxon_5,
+ 6 taxon_6,
+ 7 taxon_7,
+ 8 taxon_8,
+ 9 taxon_9,
+ 10 taxon_10,
+ 11 taxon_11,
+ 12 taxon_12,
+ 13 taxon_13,
+ 14 taxon_14,
+ 15 taxon_15,
+ 16 taxon_16,
+ 17 taxon_17,
+ 18 taxon_18,
+ 19 taxon_19,
+ 20 taxon_20,
+ 21 taxon_21,
+ 22 taxon_22,
+ 23 taxon_23,
+ 24 taxon_24,
+ 25 taxon_25,
+ 26 taxon_26,
+ 27 taxon_27,
+ 28 taxon_28,
+ 29 taxon_29,
+ 30 taxon_30,
+ 31 taxon_31,
+ 32 taxon_32;
+ TREE Tree = (((((7:5.187000000000067,22:5.186999999999937):2.4919999999998366,(2:5.19600000000007,((31:2.6009999999998246,14:2.6009999999998246):2.269999999999861,26:4.870999999999961):0.32500000000000023):2.4829999999999215):0.6730000000000005,((((6:0.8290000000000006,9:0.8290000000000006):0.3140000000000002,16:1.142999999999985):2.6749999999998164,(((15:0.20300000000000015,12:0.20300000000000015):0.2490000000000002,8:0.45200000000000035):1.360999999999961,32:1.8129999999999111):2.00499999999989):3.5429999999998403,((23:0.8660000000000007,(17:0.0010,24:0.0010):0.8650000000000007):1.0020000000000004,(18:1.059999999999994,4:1.059999999999994):0.8080000000000006):5.4930000000000865):0.9910000000000008):2.2739999999998606,((((10:0.21500000000000016,29:0.21500000000000016):1.1809999999999807,21:1.395999999999957):6.895000000000504,27:8.291000000000466):2.2449999999998638,((11:0.5600000000000004,19:0.5600000000000004):7.632000000000883,3:8.192000000000526):2.343999999999853):0.09000000000000007):2.389999999999848,((5:3.7479999999996982,(20:0.03300000000000002,1:0.03300000000000002):3.714999999999702):5.209999999999916,((28:0.5840000000000004,13:0.5840000000000004):7.191000000000736,(25:1.5889999999999358,30:1.5889999999999358):6.185999999999934):1.1829999999999805):4.0579999999997804):0.0;
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6732219986260810463 WM1148f47d2081;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 444104661901299517 WM114910e80a10;
+ checksum 0 909469476 WM114910e80a10;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #6732219986260810463 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 786.1187814845004.4817563795317733133;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1019 626;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.trees.SelectTaxaInClade.SelectTaxaToolExtra.SelectTaxa;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.ArcTree.ArcTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 8;
+ 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;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize on;
+ toggleTextOnTree off;
+ newWindowAssistant #mesquite.diverse.CharIndepDivViewer.CharIndepDivViewer;
+ tell It;
+ setCalculator #mesquite.diverse.SpecExtincLikelihood.SpecExtincLikelihood;
+ tell It;
+ getIntegTask #mesquite.diverse.SpecExtincMLCalculator.SpecExtincMLCalculator;
+ tell It;
+ setUnderflowCheckFreq -1;
+ setStepCount 1000.0;
+ conditionOnSurvival off;
+ endTell;
+ setS ?;
+ setE ?;
+ endTell;
+ doCounts;
+ endTell;
+ endTell;
+ showWindow;
+ 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;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #444104661901299517 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1019 626;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ hideWindow;
+ 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.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '03-sisterDiversification.nex';
+ setPrevFileName '01-lineagesThroughTime.nex';
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 623 267;
+ setLocation 33 631;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'A likelihood analysis can give estimates of speciation and extinction rates. Here a method reduced from Maddison, Midford & Otto''s BiSSE method is used to calculate likelihoods for a simple birth/death model, where lambda = birth = speciation rate, and mu = death = extinction rate.^n^nThis calculation is available as Diversification (Char. Indep.) in the Analysis menu of the Tree Window.';
+ setTitle Speciation_and_Extinction_Rates;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Diversification/03-sisterDiversification.nex
===================================================================
--- trunk/treebase-core/lib/examples/Diversification/03-sisterDiversification.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Diversification/03-sisterDiversification.nex 2009-12-15 18:16:21 UTC (rev 378)
@@ -0,0 +1,346 @@
+#NEXUS
+[written Thu Sep 20 16:44:06 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium/192.168.0.3 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=32;
+ TAXLABELS
+ 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 taxon_16 taxon_17 taxon_18 taxon_19 taxon_20 taxon_21 taxon_22 taxon_23 taxon_24 taxon_25 taxon_26 taxon_27 taxon_28 taxon_29 taxon_30 taxon_31 taxon_32
+ ;
+ IDS WM1148f47d2061 WM1148f47d2072 WM1148f47d2073 WM1148f47d2074 WM1148f47d2075 WM1148f47d2076 WM1148f47d2077 WM1148f47d2078 WM1148f47d2079 WM1148f47d20710 WM1148f47d20711 WM1148f47d20712 WM1148f47d20713 WM1148f47d20714 WM1148f47d20715 WM1148f47d20716 WM1148f47d20717 WM1148f47d20718 WM1148f47d20719 WM1148f47d20720 WM1148f47d20721 WM1148f47d20722 WM1148f47d20723 WM1148f47d20724 WM1148f47d20725 WM1148f47d20726 WM1148f47d20727 WM1148f47d20728 WM1148f47d20729 WM1148f47d20830 WM1148f47d20831 WM1148f47d20832 ;
+ BLOCKID WM1148f47d2081;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "03-sisterDiversification.nex"';
+ DIMENSIONS NCHAR=1;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ taxon_1 0
+ taxon_2 1
+ taxon_3 0
+ taxon_4 0
+ taxon_5 0
+ taxon_6 1
+ taxon_7 0
+ taxon_8 1
+ taxon_9 1
+ taxon_10 1
+ taxon_11 1
+ taxon_12 1
+ taxon_13 1
+ taxon_14 1
+ taxon_15 1
+ taxon_16 1
+ taxon_17 1
+ taxon_18 0
+ taxon_19 1
+ taxon_20 0
+ taxon_21 0
+ taxon_22 0
+ taxon_23 1
+ taxon_24 1
+ taxon_25 1
+ taxon_26 1
+ taxon_27 1
+ taxon_28 1
+ taxon_29 1
+ taxon_30 1
+ taxon_31 1
+ taxon_32 0
+
+;
+ IDS WM1148f4828fe0 ;
+ BLOCKID WM1149106b2f00;
+
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1;
+
+
+END;
+
+BEGIN TREES;
+ Title 'Trees from "03-sisterDiversification.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 taxon_1,
+ 2 taxon_2,
+ 3 taxon_3,
+ 4 taxon_4,
+ 5 taxon_5,
+ 6 taxon_6,
+ 7 taxon_7,
+ 8 taxon_8,
+ 9 taxon_9,
+ 10 taxon_10,
+ 11 taxon_11,
+ 12 taxon_12,
+ 13 taxon_13,
+ 14 taxon_14,
+ 15 taxon_15,
+ 16 taxon_16,
+ 17 taxon_17,
+ 18 taxon_18,
+ 19 taxon_19,
+ 20 taxon_20,
+ 21 taxon_21,
+ 22 taxon_22,
+ 23 taxon_23,
+ 24 taxon_24,
+ 25 taxon_25,
+ 26 taxon_26,
+ 27 taxon_27,
+ 28 taxon_28,
+ 29 taxon_29,
+ 30 taxon_30,
+ 31 taxon_31,
+ 32 taxon_32;
+ TREE Tree = (((((7:5.187000000000067,22:5.186999999999937):2.4919999999998366,(2:5.19600000000007,((31:2.6009999999998246,14:2.6009999999998246):2.269999999999861,26:4.870999999999961):0.32500000000000023):2.4829999999999215):0.6730000000000005,((((6:0.8290000000000006,9:0.8290000000000006):0.3140000000000002,16:1.142999999999985):2.6749999999998164,(((15:0.20300000000000015,12:0.20300000000000015):0.2490000000000002,8:0.45200000000000035):1.360999999999961,32:1.8129999999999111):2.00499999999989):3.5429999999998403,((23:0.8660000000000007,(17:0.0010,24:0.0010):0.8650000000000007):1.0020000000000004,(18:1.059999999999994,4:1.059999999999994):0.8080000000000006):5.4930000000000865):0.9910000000000008):2.2739999999998606,((((10:0.21500000000000016,29:0.21500000000000016):1.1809999999999807,21:1.395999999999957):6.895000000000504,27:8.291000000000466):2.2449999999998638,((11:0.5600000000000004,19:0.5600000000000004):7.632000000000883,3:8.192000000000526):2.343999999999853):0.09000000000000007):2.389999999999848,((5:3.7479999999996982,(20:0.03300000000000002,1:0.03300000000000002):3.714999999999702):5.209999999999916,((28:0.5840000000000004,13:0.5840000000000004):7.191000000000736,(25:1.5889999999999358,30:1.5889999999999358):6.185999999999934):1.1829999999999805):4.0579999999997804):0.0;
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6732219986260810463 WM1148f47d2081;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 444104661901299517 WM1149106b2f00;
+ checksum 0 909469476 WM1149106b2f00;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #6732219986260810463 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 786.1187814845004.4817563795317733133;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1141 555;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.ArcTree.ArcTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 8;
+ 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;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #444104661901299517;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend on;
+ toggleGray off;
+ toggleWeights on;
+ setInitialOffsetX -162;
+ setInitialOffsetY -163;
+ setLegendWidth 142;
+ setLegendHeight 161;
+ resume ;
+ endTell;
+ newWindowAssistant #mesquite.diverse.CharAssocDivViewer.CharAssocDivViewer;
+ tell It;
+ getCharSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #444104661901299517;
+ endTell;
+ endTell;
+ setCalculator #mesquite.diverse.SisterDiversification.SisterDiversification;
+ setCharacter -1;
+ doCounts;
+ endTell;
+ endTell;
+ showWindow;
+ 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;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #444104661901299517 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1141 555;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ hideWindow;
+ 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.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '04-BiSSEViewer.nex';
+ setPrevFileName '02-speciationExtinctionRates.nex';
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 522 211;
+ setLocation 28 594;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'This and the following two example files answer the question: are rates of diversification (speciation and extinction) associated with the state of a binary character?^n^nThis analysis, available by chosing Character-Associated Diversification from the Analysis menu of the Tree window, uses the simple sign test analysis for independent sister clade pairs in the style of Mitter, Farrell and Wiegmann 1988. The analysis automatically finds sister clade pairs that contrast in the character state of the binary character. Each clade must be completely uniform in state. The number of pairs favoring state 1 (i.e. the clade with state 1 is larger) and favoring state 0 are counted and used as the basis for the sign test.';
+ setTitle Sister_Clade_comparison;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Diversification/04-BiSSEViewer.nex
===================================================================
--- trunk/treebase-core/lib/examples/Diversification/04-BiSSEViewer.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Diversification/04-BiSSEViewer.nex 2009-12-15 18:16:21 UTC (rev 378)
@@ -0,0 +1,361 @@
+#NEXUS
+[written Thu Sep 20 16:44:18 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium/192.168.0.3 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=32;
+ TAXLABELS
+ 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 taxon_16 taxon_17 taxon_18 taxon_19 taxon_20 taxon_21 taxon_22 taxon_23 taxon_24 taxon_25 taxon_26 taxon_27 taxon_28 taxon_29 taxon_30 taxon_31 taxon_32
+ ;
+ IDS WM1148f47d2061 WM1148f47d2072 WM1148f47d2073 WM1148f47d2074 WM1148f47d2075 WM1148f47d2076 WM1148f47d2077 WM1148f47d2078 WM1148f47d2079 WM1148f47d20710 WM1148f47d20711 WM1148f47d20712 WM1148f47d20713 WM1148f47d20714 WM1148f47d20715 WM1148f47d20716 WM1148f47d20717 WM1148f47d20718 WM1148f47d20719 WM1148f47d20720 WM1148f47d20721 WM1148f47d20722 WM1148f47d20723 WM1148f47d20724 WM1148f47d20725 WM1148f47d20726 WM1148f47d20727 WM1148f47d20728 WM1148f47d20729 WM1148f47d20830 WM1148f47d20831 WM1148f47d20832 ;
+ BLOCKID WM1148f47d2081;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "04-BiSSEViewer.nex"';
+ DIMENSIONS NCHAR=1;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ taxon_1 0
+ taxon_2 1
+ taxon_3 0
+ taxon_4 0
+ taxon_5 0
+ taxon_6 1
+ taxon_7 0
+ taxon_8 1
+ taxon_9 1
+ taxon_10 1
+ taxon_11 1
+ taxon_12 1
+ taxon_13 1
+ taxon_14 1
+ taxon_15 1
+ taxon_16 1
+ taxon_17 1
+ taxon_18 0
+ taxon_19 1
+ taxon_20 0
+ taxon_21 0
+ taxon_22 0
+ taxon_23 1
+ taxon_24 1
+ taxon_25 1
+ taxon_26 1
+ taxon_27 1
+ taxon_28 1
+ taxon_29 1
+ taxon_30 1
+ taxon_31 1
+ taxon_32 0
+
+;
+ IDS WM1148f4828fe0 ;
+ BLOCKID WM11490f84ae00;
+
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1;
+
+
+END;
+
+BEGIN TREES;
+ Title 'Trees from "04-BiSSEViewer.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 taxon_1,
+ 2 taxon_2,
+ 3 taxon_3,
+ 4 taxon_4,
+ 5 taxon_5,
+ 6 taxon_6,
+ 7 taxon_7,
+ 8 taxon_8,
+ 9 taxon_9,
+ 10 taxon_10,
+ 11 taxon_11,
+ 12 taxon_12,
+ 13 taxon_13,
+ 14 taxon_14,
+ 15 taxon_15,
+ 16 taxon_16,
+ 17 taxon_17,
+ 18 taxon_18,
+ 19 taxon_19,
+ 20 taxon_20,
+ 21 taxon_21,
+ 22 taxon_22,
+ 23 taxon_23,
+ 24 taxon_24,
+ 25 taxon_25,
+ 26 taxon_26,
+ 27 taxon_27,
+ 28 taxon_28,
+ 29 taxon_29,
+ 30 taxon_30,
+ 31 taxon_31,
+ 32 taxon_32;
+ TREE Tree = (((((7:5.187000000000067,22:5.186999999999937):2.4919999999998366,(2:5.19600000000007,((31:2.6009999999998246,14:2.6009999999998246):2.269999999999861,26:4.870999999999961):0.32500000000000023):2.4829999999999215):0.6730000000000005,((((6:0.8290000000000006,9:0.8290000000000006):0.3140000000000002,16:1.142999999999985):2.6749999999998164,(((15:0.20300000000000015,12:0.20300000000000015):0.2490000000000002,8:0.45200000000000035):1.360999999999961,32:1.8129999999999111):2.00499999999989):3.5429999999998403,((23:0.8660000000000007,(17:0.0010,24:0.0010):0.8650000000000007):1.0020000000000004,(18:1.059999999999994,4:1.059999999999994):0.8080000000000006):5.4930000000000865):0.9910000000000008):2.2739999999998606,((((10:0.21500000000000016,29:0.21500000000000016):1.1809999999999807,21:1.395999999999957):6.895000000000504,27:8.291000000000466):2.2449999999998638,((11:0.5600000000000004,19:0.5600000000000004):7.632000000000883,3:8.192000000000526):2.343999999999853):0.09000000000000007):2.389999999999848,((5:3.7479999999996982,(20:0.03300000000000002,1:0.03300000000000002):3.714999999999702):5.209999999999916,((28:0.5840000000000004,13:0.5840000000000004):7.191000000000736,(25:1.5889999999999358,30:1.5889999999999358):6.185999999999934):1.1829999999999805):4.0579999999997804):0.0;
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6732219986260810463 WM1148f47d2081;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 444104661901299517 WM11490f84ae00;
+ checksum 0 909469476 WM11490f84ae00;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #6732219986260810463 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 786.1187814845004.4817563795317733133;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1141 555;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.ArcTree.ArcTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 8;
+ 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;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #444104661901299517;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend on;
+ toggleGray off;
+ toggleWeights on;
+ setInitialOffsetX -162;
+ setInitialOffsetY -163;
+ setLegendWidth 142;
+ setLegendHeight 161;
+ resume ;
+ endTell;
+ newWindowAssistant #mesquite.diverse.CharAssocDivViewer.CharAssocDivViewer;
+ tell It;
+ getCharSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #444104661901299517;
+ endTell;
+ endTell;
+ setCalculator #mesquite.diverse.BiSSELikelihood.BiSSELikelihood;
+ tell It;
+ suspend ;
+ setParameters ? ? ? ? =2 ? ? =4;
+ setReportMode Likelihood;
+ getIntegTask #mesquite.diverse.BiSSELikelihoodCalculator.BiSSELikelihoodCalculator;
+ tell It;
+ suspend ;
+ setUnderflowCheckFreq 2;
+ setStepCount 1000.0;
+ setIterations 2;
+ conditionOnSurvival off;
+ resume ;
+ endTell;
+ resume ;
+ endTell;
+ setCharacter -1;
+ doCounts;
+ endTell;
+ endTell;
+ showWindow;
+ 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;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #444104661901299517 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1141 555;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ hideWindow;
+ 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.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '05-BiSSENetViewer.nex';
+ setPrevFileName '03-sisterDiversification.nex';
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 531 336;
+ setLocation 28 594;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'Here the BiSSE likelihood calculations are done. When you have a tree and a binary character (here stored in a matrix), you can select Character-Associated Diversification from the Analysis menu of the Tree window, and indicate you want BiSSE Speciation/Extinction likelihood to be calculated. The BiSSE method is described by Maddison, Midford and Otto 2007.^n^nIn the panel are shown the estimated values of the speciation (lambda) and extinction (mu) rates for states 0 and 1, and the transition rates between states 0 and 1 (q''s). In the Parameters dialog box (in the Diversification(Ch) menu) you can set and constrain parameters. Here, mu1 is constrainted equal to mu0 and q10 is constrained equal to q01.^n^nTo do a likelihood ratio test, change the parameters to an alternative set of constaints, and compare the likelihood. ^n^nA chi-square approximation appears reasonable for significance of the likelihood ratio, but you can also generate a null distribution of log likelihood differences using simulations. The manual outlines the procedure.';
+ setTitle BiSSE_Diversification;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Diversification/05-BiSSENetViewer.nex
===================================================================
--- trunk/treebase-core/lib/examples/Diversification/05-BiSSENetViewer.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Diversification/05-BiSSENetViewer.nex 2009-12-15 18:16:21 UTC (rev 378)
@@ -0,0 +1,358 @@
+#NEXUS
+[written Thu Sep 20 16:44:38 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium/192.168.0.3 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=32;
+ TAXLABELS
+ 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 taxon_16 taxon_17 taxon_18 taxon_19 taxon_20 taxon_21 taxon_22 taxon_23 taxon_24 taxon_25 taxon_26 taxon_27 taxon_28 taxon_29 taxon_30 taxon_31 taxon_32
+ ;
+ IDS WM1148f47d2061 WM1148f47d2072 WM1148f47d2073 WM1148f47d2074 WM1148f47d2075 WM1148f47d2076 WM1148f47d2077 WM1148f47d2078 WM1148f47d2079 WM1148f47d20710 WM1148f47d20711 WM1148f47d20712 WM1148f47d20713 WM1148f47d20714 WM1148f47d20715 WM1148f47d20716 WM1148f47d20717 WM1148f47d20718 WM1148f47d20719 WM1148f47d20720 WM1148f47d20721 WM1148f47d20722 WM1148f47d20723 WM1148f47d20724 WM1148f47d20725 WM1148f47d20726 WM1148f47d20727 WM1148f47d20728 WM1148f47d20729 WM1148f47d20830 WM1148f47d20831 WM1148f47d20832 ;
+ BLOCKID WM1148f47d2081;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "05-BiSSENetViewer.nex"';
+ DIMENSIONS NCHAR=1;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ taxon_1 0
+ taxon_2 1
+ taxon_3 0
+ taxon_4 0
+ taxon_5 0
+ taxon_6 1
+ taxon_7 0
+ taxon_8 1
+ taxon_9 1
+ taxon_10 1
+ taxon_11 1
+ taxon_12 1
+ taxon_13 1
+ taxon_14 1
+ taxon_15 1
+ taxon_16 1
+ taxon_17 1
+ taxon_18 0
+ taxon_19 1
+ taxon_20 0
+ taxon_21 0
+ taxon_22 0
+ taxon_23 1
+ taxon_24 1
+ taxon_25 1
+ taxon_26 1
+ taxon_27 1
+ taxon_28 1
+ taxon_29 1
+ taxon_30 1
+ taxon_31 1
+ taxon_32 0
+
+;
+ IDS WM1148f4828fe0 ;
+ BLOCKID WM11493c252d50;
+
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1;
+
+
+END;
+
+BEGIN TREES;
+ Title 'Trees from "05-BiSSENetViewer.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 taxon_1,
+ 2 taxon_2,
+ 3 taxon_3,
+ 4 taxon_4,
+ 5 taxon_5,
+ 6 taxon_6,
+ 7 taxon_7,
+ 8 taxon_8,
+ 9 taxon_9,
+ 10 taxon_10,
+ 11 taxon_11,
+ 12 taxon_12,
+ 13 taxon_13,
+ 14 taxon_14,
+ 15 taxon_15,
+ 16 taxon_16,
+ 17 taxon_17,
+ 18 taxon_18,
+ 19 taxon_19,
+ 20 taxon_20,
+ 21 taxon_21,
+ 22 taxon_22,
+ 23 taxon_23,
+ 24 taxon_24,
+ 25 taxon_25,
+ 26 taxon_26,
+ 27 taxon_27,
+ 28 taxon_28,
+ 29 taxon_29,
+ 30 taxon_30,
+ 31 taxon_31,
+ 32 taxon_32;
+ TREE Tree = (((((7:5.187000000000067,22:5.186999999999937):2.4919999999998366,(2:5.19600000000007,((31:2.6009999999998246,14:2.6009999999998246):2.269999999999861,26:4.870999999999961):0.32500000000000023):2.4829999999999215):0.6730000000000005,((((6:0.8290000000000006,9:0.8290000000000006):0.3140000000000002,16:1.142999999999985):2.6749999999998164,(((15:0.20300000000000015,12:0.20300000000000015):0.2490000000000002,8:0.45200000000000035):1.360999999999961,32:1.8129999999999111):2.00499999999989):3.5429999999998403,((23:0.8660000000000007,(17:0.0010,24:0.0010):0.8650000000000007):1.0020000000000004,(18:1.059999999999994,4:1.059999999999994):0.8080000000000006):5.4930000000000865):0.9910000000000008):2.2739999999998606,((((10:0.21500000000000016,29:0.21500000000000016):1.1809999999999807,21:1.395999999999957):6.895000000000504,27:8.291000000000466):2.2449999999998638,((11:0.5600000000000004,19:0.5600000000000004):7.632000000000883,3:8.192000000000526):2.343999999999853):0.09000000000000007):2.389999999999848,((5:3.7479999999996982,(20:0.03300000000000002,1:0.03300000000000002):3.714999999999702):5.209999999999916,((28:0.5840000000000004,13:0.5840000000000004):7.191000000000736,(25:1.5889999999999358,30:1.5889999999999358):6.185999999999934):1.1829999999999805):4.0579999999997804):0.0;
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6732219986260810463 WM1148f47d2081;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 444104661901299517 WM11493c252d50;
+ checksum 0 909469476 WM11493c252d50;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #6732219986260810463 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 786.1187814845004.4817563795317733133;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1141 555;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.ArcTree.ArcTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 8;
+ 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;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #444104661901299517;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend on;
+ toggleGray off;
+ toggleWeights on;
+ setInitialOffsetX -162;
+ setInitialOffsetY -163;
+ setLegendWidth 142;
+ setLegendHeight 161;
+ ...
[truncated message content] |
