/usr/lib/R/site-library/phylobase/nexusfiles/treeWithUnderscoreLabels.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 | #NEXUS
[written Tue May 29 18:24:39 PDT 2007 by Mesquite version 1.06 (build g97) at cnidaria-1347.ucdavis.edu/169.237.66.185]
BEGIN TAXA;
DIMENSIONS NTAX=18;
TAXLABELS
Myrmecocystuscfnavajo Myrmecocystus_creightoni Myrmecocystusdepilis Myrmecocystuskathjuli Myrmecocystuskennedyi Myrmecocystusmendax Myrmecocystusmexicanus Myrmecocystusmimicus Myrmecocystusnavajo Myrmecocystusnequazcatl Myrmecocystusplacodops Myrmecocystusromainei Myrmecocystussemirufus Myrmecocystussnellingi Myrmecocystustenuinodis Myrmecocystustestaceus Myrmecocystuswheeleri Myrmecocystusyuma
;
END;
BEGIN CHARACTERS;
TITLE Foraging;
DIMENSIONS NCHAR=2;
FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2";
CHARSTATELABELS
1 time_period / diurnal crepuscular nocturnal, 2 subgenus / Endiodioctes Eremnocystus Myrmecocystus ;
MATRIX
Myrmecocystuscfnavajo 22
Myrmecocystus_creightoni 11
Myrmecocystusdepilis 00
Myrmecocystuskathjuli 00
Myrmecocystuskennedyi 00
Myrmecocystusmendax 00
Myrmecocystusmexicanus 22
Myrmecocystusmimicus 00
Myrmecocystusnavajo 22
Myrmecocystusnequazcatl 00
Myrmecocystusplacodops 00
Myrmecocystusromainei 00
Myrmecocystussemirufus 00
Myrmecocystussnellingi 11
Myrmecocystustenuinodis 11
Myrmecocystustestaceus 12
Myrmecocystuswheeleri 00
Myrmecocystusyuma 11
;
END;
BEGIN TREES;
TRANSLATE
1 Myrmecocystuscfnavajo,
2 Myrmecocystus_creightoni,
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 (CHARACTERS = Foraging) = unord: 1 - 2;
END;
BEGIN MESQUITECHARMODELS;
ProbModelSet * UNTITLED (CHARACTERS = 'Matrix in file "treepluscharV01.nex"') = Browniandefault: 1 - 32;
ProbModelSet * UNTITLED (CHARACTERS = Foraging) = 'Mk1 (est.)': 1 - 2;
END;
Begin MESQUITE;
MESQUITESCRIPTVERSION 2;
TITLE AUTO;
tell ProjectCoordinator;
getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
tell It;
setID 0 9015005506118934442;
endTell;
getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
tell It;
setID 0 2565950173085067248;
checksum 0 389122022;
setID 1 1161953040649633474;
checksum 1 3582198254;
endTell;
getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
tell It;
showDataWindow #2565950173085067248 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
tell It;
getWindow;
tell It;
setSize 420 280;
setLocation 400 156;
setFont SanSerif;
setFontSize 10;
onInfoBar;
setExplanationSize 30;
setAnnotationSize 20;
setFontIncAnnot 0;
setFontIncExp 0;
getToolPalette;
tell It;
endTell;
setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
colorCells #mesquite.charMatrices.NoColor.NoColor;
setBackground White;
toggleShowNames on;
toggleTight off;
toggleShowChanges on;
toggleSeparateLines off;
toggleShowStates on;
toggleAutoWithCharNames on;
toggleShowDefaultCharNames off;
toggleConstrainCW on;
toggleBirdsEye off;
toggleColorsPanel off;
birdsEyeWidth 2;
toggleLinkedScrolling on;
toggleScrollLinkedTables off;
endTell;
showWindow;
getWindow;
tell It;
forceAutosize;
endTell;
getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
tell It;
togglePanel off;
endTell;
getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
tell It;
setColor Red;
removeColor off;
endTell;
endTell;
showDataWindow #1161953040649633474 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
tell It;
getWindow;
tell It;
getTable;
tell It;
rowNamesWidth 232;
endTell;
setSize 798 748;
setLocation 348 22;
setFont SanSerif;
setFontSize 10;
onInfoBar;
setExplanationSize 30;
setAnnotationSize 20;
setFontIncAnnot 0;
setFontIncExp 0;
getToolPalette;
tell It;
setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
endTell;
setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
colorCells #mesquite.charMatrices.NoColor.NoColor;
setBackground White;
toggleShowNames on;
toggleTight off;
toggleShowChanges on;
toggleSeparateLines off;
toggleShowStates on;
toggleAutoWithCharNames on;
toggleShowDefaultCharNames off;
toggleConstrainCW on;
toggleBirdsEye off;
toggleColorsPanel off;
birdsEyeWidth 2;
toggleLinkedScrolling on;
toggleScrollLinkedTables off;
endTell;
showWindow;
getWindow;
tell It;
forceAutosize;
endTell;
getEmployee #mesquite.categ.StateNamesEditor.StateNamesEditor;
tell It;
makeWindow;
tell It;
setSize 314 400;
setLocation 60 10;
setFont SanSerif;
setFontSize 10;
onInfoBar;
setExplanationSize 30;
setAnnotationSize 20;
setFontIncAnnot 0;
setFontIncExp 0;
getToolPalette;
tell It;
setTool mesquite.categ.StateNamesEditor.StateNamesWindow.ibeam;
endTell;
rowsAreCharacters on;
toggleConstrainChar on;
toggleConstrainCharNum 3;
togglePanel 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.ColorCells.ColorCells;
tell It;
setColor Red;
removeColor off;
endTell;
getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
tell It;
autotabOff;
endTell;
endTell;
endTell;
getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
tell It;
makeTreeWindow #9015005506118934442 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
tell It;
setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
tell It;
setTreeBlock 1;
toggleUseWeights off;
endTell;
setAssignedID 630.1180487973731.4514395117633566598;
getTreeWindow;
tell It;
setSize 520 400;
setLocation 60 10;
setFont SanSerif;
setFontSize 10;
onInfoBar;
setExplanationSize 30;
setAnnotationSize 20;
setFontIncAnnot 0;
setFontIncExp 0;
getToolPalette;
tell It;
endTell;
setActive;
getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
tell It;
suppress;
setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
tell It;
setEdgeWidth 12;
orientUp;
getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
tell It;
stretchToggle off;
branchLengthsToggle off;
toggleScale on;
toggleCenter off;
toggleEven off;
namesAngle ?;
endTell;
endTell;
setBackground White;
setBranchColor Black;
showNodeNumbers off;
labelBranchLengths off;
desuppress;
getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
tell It;
setColor Black;
toggleColorPartition on;
toggleShadePartition off;
toggleNodeLabels on;
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;
endTell;
setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
tell It;
getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
tell It;
setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
tell It;
setDataSet #1161953040649633474;
endTell;
endTell;
setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
tell It;
setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
endTell;
endTell;
setCharacter 1;
toggleShowLegend on;
toggleGray off;
toggleWeights on;
setInitialOffsetX -162;
setInitialOffsetY -177;
setLegendWidth 142;
setLegendHeight 177;
resume ;
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;
endTell;
end;
begin brownie;
taxset all=1-18;
end;
|