[Phylobase-commits] r748 - pkg/inst/nexusfiles
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Mar 11 03:35:46 CET 2010
Author: francois
Date: 2010-03-11 03:35:45 +0100 (Thu, 11 Mar 2010)
New Revision: 748
Added:
pkg/inst/nexusfiles/treepluscharV02.nex
Log:
additional NEXUS file with polymorphic and excluded characters
Added: pkg/inst/nexusfiles/treepluscharV02.nex
===================================================================
--- pkg/inst/nexusfiles/treepluscharV02.nex (rev 0)
+++ pkg/inst/nexusfiles/treepluscharV02.nex 2010-03-11 02:35:45 UTC (rev 748)
@@ -0,0 +1,465 @@
+#NEXUS
+[written Wed Mar 10 11:51:23 EST 2010 by Mesquite version 2.72 (build 527) at francois-laptop/127.0.1.1]
+
+BEGIN TAXA;
+ TITLE Taxa;
+ DIMENSIONS NTAX=18;
+ TAXLABELS
+ Myrmecocystuscfnavajo Myrmecocystuscreightoni Myrmecocystusdepilis Myrmecocystuskathjuli Myrmecocystuskennedyi Myrmecocystusmendax Myrmecocystusmexicanus Myrmecocystusmimicus Myrmecocystusnavajo Myrmecocystusnequazcatl Myrmecocystusplacodops Myrmecocystusromainei Myrmecocystussemirufus Myrmecocystussnellingi Myrmecocystustenuinodis Myrmecocystustestaceus Myrmecocystuswheeleri Myrmecocystusyuma
+ ;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE testIncomplete;
+ DIMENSIONS NCHAR=3;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2";
+ CHARSTATELABELS
+ 1 Test1 / test1A test1B, 2 Test2 / test2A test2B, 3 Test3 / test3A test3B test3C ;
+ MATRIX
+ Myrmecocystuscfnavajo 1(0 1)(0 1 2)
+ Myrmecocystuscreightoni ?(0 1)(0 1)
+ Myrmecocystusdepilis 102
+ Myrmecocystuskathjuli 100
+ Myrmecocystuskennedyi 010
+ Myrmecocystusmendax 101
+ Myrmecocystusmexicanus 000
+ Myrmecocystusmimicus ??0
+ Myrmecocystusnavajo ?11
+ Myrmecocystusnequazcatl 100
+ Myrmecocystusplacodops 001
+ Myrmecocystusromainei 11(0 1 2)
+ Myrmecocystussemirufus 001
+ Myrmecocystussnellingi 1?0
+ Myrmecocystustenuinodis 101
+ Myrmecocystustestaceus ??0
+ Myrmecocystuswheeleri 000
+ Myrmecocystusyuma 01?
+
+;
+
+END;
+BEGIN TREES;
+ Title 'Trees from "treepluscharV01.nex"';
+ LINK Taxa = Taxa;
+ TRANSLATE
+ 1 Myrmecocystuscfnavajo,
+ 2 Myrmecocystuscreightoni,
+ 3 Myrmecocystusdepilis,
+ 4 Myrmecocystuskathjuli,
+ 5 Myrmecocystuskennedyi,
+ 6 Myrmecocystusmendax,
+ 7 Myrmecocystusmexicanus,
+ 8 Myrmecocystusmimicus,
+ 9 Myrmecocystusnavajo,
+ 10 Myrmecocystusnequazcatl,
+ 11 Myrmecocystusplacodops,
+ 12 Myrmecocystusromainei,
+ 13 Myrmecocystussemirufus,
+ 14 Myrmecocystussnellingi,
+ 15 Myrmecocystustenuinodis,
+ 16 Myrmecocystustestaceus,
+ 17 Myrmecocystuswheeleri,
+ 18 Myrmecocystusyuma;
+ TREE bestML = (((((((((13:1.724765,11:1.724765):2.926053,6:4.650818):0.689044,(4:1.08387,17:1.08387):4.255993):0.198842,((8:2.708942,3:2.708942):2.027251,((12:2.193845,10:2.193845):2.257581,18:4.451425):0.284767):0.802512):0.506099,5:6.044804):4.524387,2:10.569191):0.836689,(14:2.770378,15:2.770378):8.635503):0.89482,16:12.300701):1.699299,(7:5.724923,(1:2.869547,9:2.869547):2.855375):8.275077);
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1 - 3;
+
+ EXSET * UNTITLED = 3;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 3;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ timeSaved 1268239884091;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 9015005506118934442;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 2565950173085067248;
+ checksumv 0 2 4144740407 null numChars 3 short true bits 7 states 7 sumSquaresStatesOnly 220.0 NumFiles 1 NumMatrices 1;
+ endTell;
+ getWindow;
+ tell It;
+ suppress;
+ setResourcesState false false 155;
+ setPopoutState 400;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1278 934;
+ setLocation 1440 0;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ desuppress;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #9015005506118934442 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ suppressEPCResponse;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 630.1180487973731.4514395117633566598;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1123 867;
+ setLocation 1440 0;
+ 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;
+ inhibitStretchToggle on;
+ 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;
+ toggleShowFootnotes on;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ namesAngle ?;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ setDrawingSizeMode 0;
+ toggleLegendFloat on;
+ scale 0;
+ toggleTextOnTree off;
+ showWindow;
+ 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 #2565950173085067248;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ toggleMPRsMode off;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend on;
+ toggleGray off;
+ toggleWeights on;
+ setInitialOffsetX 4;
+ setInitialOffsetY -191;
+ setLegendWidth 142;
+ setLegendHeight 191;
+ resume ;
+ endTell;
+ 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;
+ setDigits 4;
+ writeAsPercentage off;
+ toggleCentred on;
+ toggleHorizontal on;
+ setFontSize 10;
+ setOffset 0 0;
+ endTell;
+ getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues;
+ tell It;
+ panelOpen false;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #2565950173085067248 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1123 867;
+ setLocation 1440 0;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor;
+ colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor;
+ colorText #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleShowTaxonNames on;
+ toggleTight off;
+ toggleThinRows off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleAutoTaxonNames off;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 70;
+ toggleBirdsEye off;
+ toggleAllowAutosize on;
+ toggleColorsPanel off;
+ toggleDiagonal on;
+ setDiagonalHeight 80;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ hideWindow;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ 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.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ getEmployee #mesquite.categ.SmallStateNamesEditor.SmallStateNamesEditor;
+ tell It;
+ panelOpen true;
+ endTell;
+ endTell;
+ showExtraDataWindow #2565950173085067248 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1123 867;
+ setLocation 1440 0;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor;
+ colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor;
+ colorText #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleShowTaxonNames on;
+ toggleTight off;
+ toggleThinRows off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleAutoTaxonNames off;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ toggleBirdsEye off;
+ toggleAllowAutosize on;
+ toggleColorsPanel off;
+ toggleDiagonal on;
+ setDiagonalHeight 80;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ getInfoPanel;
+ tell It;
+ btspOpen true;
+ apOpen true;
+ fpOpen true;
+ endTell;
+ toggleInfoPanel off;
+ endTell;
+ showWindow;
+ getWindow;
+ tell It;
+ forceAutosize;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.categ.StateNamesEditor.StateNamesEditor;
+ tell It;
+ makeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1123 867;
+ setLocation 1440 0;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.categ.StateNamesEditor.StateNamesWindow.ibeam;
+ endTell;
+ setActive;
+ rowsAreCharacters on;
+ toggleConstrainChar on;
+ toggleConstrainCharNum 3;
+ togglePanel off;
+ toggleSummaryPanel off;
+ endTell;
+ showWindow;
+ endTell;
+ 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.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ getEmployee #mesquite.categ.SmallStateNamesEditor.SmallStateNamesEditor;
+ tell It;
+ panelOpen true;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ showCharacters #2565950173085067248 #mesquite.lists.CharacterList.CharacterList;
+ tell It;
+ setData 0;
+ getWindow;
+ tell It;
+ newAssistant #mesquite.lists.DefaultCharOrder.DefaultCharOrder;
+ newAssistant #mesquite.lists.CharListInclusion.CharListInclusion;
+ newAssistant #mesquite.lists.CharListPartition.CharListPartition;
+ newAssistant #mesquite.stochchar.CharListProbModels.CharListProbModels;
+ getTable;
+ tell It;
+ columnWidth 1 101;
+ endTell;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1123 867;
+ setLocation 1440 0;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.lists.CharacterList.CharacterListWindow.arrow;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.lists.CharListAnnotPanel.CharListAnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ endTell;
+ endTell;
+ endTell;
+end;
+
+begin brownie;
+taxset all = 1 -18;
+
+END;
+
More information about the Phylobase-commits
mailing list