r-cran-phylobase 0.8.2-1 / usr / lib / R / site-library / phylobase / nexusfiles / treeWithPolyExcludedData.nex

This file is indexed.

/usr/lib/R/site-library/phylobase/nexusfiles/treeWithPolyExcludedData.nex is in r-cran-phylobase 0.8.2-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below. 

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
#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;

APT Browse - Built by Thomas Orozco.