forester/aptx/aptx_example_files/visual_styles.xml

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" xmlns="http://www.phyloxml.org">
   3 <phylogeny rooted="true" rerootable="true">
   4   <clade>
   5     <branch_length>0.30159</branch_length>
   6     <confidence type="bootstrap">97</confidence>
   7     <events>
   8       <duplications>1</duplications>
   9     </events>
  10     <clade>
  11       <branch_length>0.15021</branch_length>
  12       <confidence type="bootstrap">69</confidence>
  13       <events>
  14         <duplications>1</duplications>
  15       </events>
  16       <property ref="style:node_shape" datatype="xsd:token" applies_to="node">rectangle</property>
  17       <property ref="style:node_size" datatype="xsd:float" applies_to="node">12.0</property>
  18       <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ff00ff</property>
  19       <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
  20       <clade>
  21         <branch_length>0.04885</branch_length>
  22         <confidence type="bootstrap">68</confidence>
  23         <events>
  24           <speciations>1</speciations>
  25         </events>
  26         <property ref="style:node_shape" datatype="xsd:token" applies_to="node">rectangle</property>
  27         <property ref="style:node_size" datatype="xsd:float" applies_to="node">11.0</property>
  28         <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ff00ee</property>
  29         <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
  30         <clade>
  31           <branch_length>0.04633</branch_length>
  32           <confidence type="bootstrap">59</confidence>
  33           <events>
  34             <speciations>1</speciations>
  35           </events>
  36           <property ref="style:node_shape" datatype="xsd:token" applies_to="node">rectangle</property>
  37           <property ref="style:node_size" datatype="xsd:float" applies_to="node">10.0</property>
  38           <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ff00dd</property>
  39           <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
  40           <clade>
  41             <branch_length>0.18918</branch_length>
  42             <confidence type="bootstrap">100</confidence>
  43             <events>
  44               <speciations>1</speciations>
  45             </events>
  46             <property ref="style:node_shape" datatype="xsd:token" applies_to="node">rectangle</property>
  47             <property ref="style:node_size" datatype="xsd:float" applies_to="node">9.0</property>
  48             <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ff00cc</property>
  49             <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
  50             <clade>
  51               <branch_length>0.07518</branch_length>
  52               <confidence type="bootstrap">97</confidence>
  53               <events>
  54                 <speciations>1</speciations>
  55               </events>
  56               <property ref="style:node_shape" datatype="xsd:token" applies_to="node">rectangle</property>
  57               <property ref="style:node_size" datatype="xsd:float" applies_to="node">8.0</property>
  58               <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ff00bb</property>
  59               <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
  60               <clade>
  61                 <branch_length>0.0073</branch_length>
  62                 <confidence type="bootstrap">100</confidence>
  63                 <events>
  64                   <speciations>1</speciations>
  65                 </events>
  66                 <property ref="style:node_shape" datatype="xsd:token" applies_to="node">rectangle</property>
  67                 <property ref="style:node_size" datatype="xsd:float" applies_to="node">7.0</property>
  68                 <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ff0099</property>
  69                 <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
  70                 <clade>
  71                   <branch_length>0.0036</branch_length>
  72                   <confidence type="bootstrap">91</confidence>
  73                   <events>
  74                     <speciations>1</speciations>
  75                   </events>
  76                   <property ref="style:node_shape" datatype="xsd:token" applies_to="node">rectangle</property>
  77                   <property ref="style:node_size" datatype="xsd:float" applies_to="node">6.0</property>
  78                   <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ff0088</property>
  79                   <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
  80                   <clade>
  81                     <name>NP_001025424.1</name>
  82                     <branch_length>1.0E-5</branch_length>
  83                     <taxonomy>
  84                       <id provider="uniprot">7955</id>
  85                       <code>DANRE</code>
  86                       <scientific_name>Danio rerio</scientific_name>
  87                       <common_name>Zebrafish</common_name>
  88                       <synonym>Brachydanio rerio</synonym>
  89                       <rank>species</rank>
  90                     </taxonomy>
  91                     <property ref="style:font" datatype="xsd:token" applies_to="node">Courier</property>
  92                     <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">12</property>
  93                     <property ref="style:font_color" datatype="xsd:token" applies_to="node">#00ffff</property>
  94                     <property ref="style:node_size" datatype="xsd:float" applies_to="node">6.0</property>
  95                     <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ff0000</property>
  96                     <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
  97                   </clade>
  98                   <clade>
  99                     <branch_length>0.00327</branch_length>
 100                     <taxonomy>
 101                       <id provider="uniprot">9685</id>
 102                       <code>FELCA</code>
 103                       <scientific_name>Felis catus</scientific_name>
 104                       <common_name>Cat</common_name>
 105                       <synonym>Felis silvestris catus</synonym>
 106                       <rank>species</rank>
 107                     </taxonomy>
 108                     <sequence>
 109                       <accession source="ncbi">ABJ16409.1</accession>
 110                       <name>BCL2</name>
 111                     </sequence>
 112                     <property ref="style:font" datatype="xsd:token" applies_to="node">Monospaced</property>
 113                     <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">12</property>
 114                     <property ref="style:font_style" datatype="xsd:token" applies_to="node">bold</property>
 115                     <property ref="style:font_color" datatype="xsd:token" applies_to="node">#00ccff</property>
 116                     <property ref="style:node_size" datatype="xsd:float" applies_to="node">5.0</property>
 117                     <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ff00ff</property>
 118                     <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">solid</property>
 119                   </clade>
 120                 </clade>
 121                 <clade>
 122                   <branch_length>0.00962</branch_length>
 123                   <taxonomy>
 124                     <id provider="uniprot">8355</id>
 125                     <code>XENLA</code>
 126                     <scientific_name>Xenopus laevis</scientific_name>
 127                     <common_name>African clawed frog</common_name>
 128                     <rank>species</rank>
 129                   </taxonomy>
 130                   <sequence>
 131                     <name>AB427203</name>
 132                   </sequence>
 133                   <property ref="style:font" datatype="xsd:token" applies_to="node">Century Schoolbook L</property>
 134                   <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">6</property>
 135                   <property ref="style:font_style" datatype="xsd:token" applies_to="node">bold</property>
 136                   <property ref="style:font_color" datatype="xsd:token" applies_to="node">#0099ff</property>
 137                   <property ref="style:node_size" datatype="xsd:float" applies_to="node">7.0</property>
 138                   <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ffffff</property>
 139                   <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">none</property>
 140                 </clade>
 141               </clade>
 142               <clade>
 143                 <name>BAH28834</name>
 144                 <branch_length>0.28745</branch_length>
 145                 <taxonomy>
 146                   <id provider="uniprot">8355</id>
 147                   <code>XENLA</code>
 148                   <scientific_name>Xenopus laevis</scientific_name>
 149                   <common_name>African clawed frog</common_name>
 150                   <rank>species</rank>
 151                 </taxonomy>
 152                 <property ref="style:font" datatype="xsd:token" applies_to="node">Dialog</property>
 153                 <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">14</property>
 154                 <property ref="style:font_color" datatype="xsd:token" applies_to="node">#0033ff</property>
 155                 <property ref="style:node_size" datatype="xsd:float" applies_to="node">6.0</property>
 156                 <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ffffff</property>
 157                 <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
 158               </clade>
 159             </clade>
 160             <clade>
 161               <branch_length>0.12824</branch_length>
 162               <sequence>
 163                 <name>BCL2_CRIGR</name>
 164               </sequence>
 165               <property ref="style:font" datatype="xsd:token" applies_to="node">Dialog</property>
 166               <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">10</property>
 167               <property ref="style:font_style" datatype="xsd:token" applies_to="node">italic</property>
 168               <property ref="style:font_color" datatype="xsd:token" applies_to="node">#3300ff</property>
 169               <property ref="style:node_shape" datatype="xsd:token" applies_to="node">circle</property>
 170               <property ref="style:node_size" datatype="xsd:float" applies_to="node">6.0</property>
 171               <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ffffff</property>
 172               <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">none</property>
 173             </clade>
 174           </clade>
 175           <clade>
 176             <branch_length>0.38499</branch_length>
 177             <taxonomy>
 178               <id provider="uniprot">10029</id>
 179               <code>CRIGR</code>
 180               <scientific_name>Cricetulus griseus</scientific_name>
 181               <common_name>Chinese hamster</common_name>
 182               <synonym>Cricetulus barabensis griseus</synonym>
 183               <rank>species</rank>
 184             </taxonomy>
 185             <sequence>
 186               <mol_seq is_aligned="false">-maqagrtgydnreivmkyihyklsqrgyewdvgdvdaaplgaaptpgifsfqpesnptpavhrdmaartsplrpivattgptlspvppvvhltlrragddfsrryrrdfaemssqlhltpftargrfatvveelfrdgvnwgrivaffefggvmcvesvnremsplvdnialwmteylnrhlhtwiqdnggwdafvelygpsvrplfdfswlslktllslalvgacitlgtylghk</mol_seq>
 187             </sequence>
 188             <property ref="style:font" datatype="xsd:token" applies_to="node">SansSerif</property>
 189             <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">10</property>
 190             <property ref="style:font_color" datatype="xsd:token" applies_to="node">#6600ff</property>
 191             <property ref="style:node_shape" datatype="xsd:token" applies_to="node">circle</property>
 192             <property ref="style:node_size" datatype="xsd:float" applies_to="node">5.5</property>
 193             <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ff00ff</property>
 194             <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">solid</property>
 195           </clade>
 196         </clade>
 197         <clade>
 198           <branch_length>0.37118</branch_length>
 199           <confidence type="bootstrap">100</confidence>
 200           <events>
 201             <speciations>1</speciations>
 202           </events>
 203           <clade>
 204             <branch_length>0.29315</branch_length>
 205             <taxonomy>
 206               <id provider="uniprot">9606</id>
 207               <code>HUMAN</code>
 208               <scientific_name>Homo sapiens</scientific_name>
 209               <common_name>Human</common_name>
 210               <rank>species</rank>
 211             </taxonomy>
 212             <sequence>
 213               <accession source="bootstrap">_O95417_</accession>
 214               <name>neuroendocrine-specific Golgi protein p55</name>
 215             </sequence>
 216             <property ref="style:font" datatype="xsd:token" applies_to="node">Serif</property>
 217             <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">12</property>
 218             <property ref="style:font_color" datatype="xsd:token" applies_to="node">#ff00ff</property>
 219             <property ref="style:node_shape" datatype="xsd:token" applies_to="node">circle</property>
 220             <property ref="style:node_size" datatype="xsd:float" applies_to="node">6.0</property>
 221             <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ff00ff</property>
 222             <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">solid</property>
 223           </clade>
 224           <clade>
 225             <branch_length>0.18816</branch_length>
 226             <taxonomy>
 227               <id provider="uniprot">9606</id>
 228               <code>HUMAN</code>
 229               <scientific_name>Homo sapiens</scientific_name>
 230               <common_name>Human</common_name>
 231               <rank>species</rank>
 232             </taxonomy>
 233             <sequence>
 234               <accession source="bootstrap">AAD11804</accession>
 235               <name>neuroendocrine-specific Golgi protein p55</name>
 236             </sequence>
 237             <property ref="style:font" datatype="xsd:token" applies_to="node">Dialog</property>
 238             <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">12</property>
 239             <property ref="style:font_color" datatype="xsd:token" applies_to="node">#ff0099</property>
 240             <property ref="style:node_shape" datatype="xsd:token" applies_to="node">rectangle</property>
 241             <property ref="style:node_size" datatype="xsd:float" applies_to="node">6.0</property>
 242             <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ff00ff</property>
 243             <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">solid</property>
 244           </clade>
 245         </clade>
 246       </clade>
 247       <clade>
 248         <branch_length>0.4337</branch_length>
 249         <confidence type="bootstrap">100</confidence>
 250         <events>
 251           <speciations>1</speciations>
 252         </events>
 253         <clade>
 254           <branch_length>0.02104</branch_length>
 255           <taxonomy>
 256             <id provider="uniprot">9606</id>
 257             <code>HUMAN</code>
 258             <scientific_name>Homo sapiens</scientific_name>
 259             <common_name>Human</common_name>
 260             <rank>species</rank>
 261           </taxonomy>
 262           <sequence>
 263             <accession source="bootstrap">4206780</accession>
 264             <name>neuroendocrine-specific Golgi protein p55</name>
 265           </sequence>
 266           <reference>
 267             <desc>Molecular characterization of XL2, a neuroendocrine-specific luminal Golgi-resident protein</desc>
 268           </reference>
 269           <property ref="style:font" datatype="xsd:token" applies_to="node">Dialog</property>
 270           <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">13</property>
 271           <property ref="style:font_color" datatype="xsd:token" applies_to="node">#ff0000</property>
 272           <property ref="style:node_shape" datatype="xsd:token" applies_to="node">rectangle</property>
 273           <property ref="style:node_size" datatype="xsd:float" applies_to="node">6.0</property>
 274           <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ffff00</property>
 275           <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
 276         </clade>
 277         <clade>
 278           <name>ceClcn_CE29336</name>
 279           <branch_length>0.00466</branch_length>
 280           <taxonomy>
 281             <scientific_name>CAEEL</scientific_name>
 282           </taxonomy>
 283           <property ref="style:font" datatype="xsd:token" applies_to="node">Dialog</property>
 284           <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">14</property>
 285           <property ref="style:font_color" datatype="xsd:token" applies_to="node">#ff6600</property>
 286           <property ref="style:node_shape" datatype="xsd:token" applies_to="node">rectangle</property>
 287           <property ref="style:node_size" datatype="xsd:float" applies_to="node">6.0</property>
 288           <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ff00ff</property>
 289           <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">none</property>
 290         </clade>
 291       </clade>
 292     </clade>
 293     <clade>
 294       <branch_length>0.27675</branch_length>
 295       <confidence type="bootstrap">100</confidence>
 296       <width>1.0</width>
 297       <events>
 298         <speciations>1</speciations>
 299       </events>
 300       <property ref="style:node_shape" datatype="xsd:token" applies_to="node">circle</property>
 301       <property ref="style:node_size" datatype="xsd:float" applies_to="node">12.0</property>
 302       <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ffff00</property>
 303       <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
 304       <clade>
 305         <branch_length>0.16193</branch_length>
 306         <confidence type="bootstrap">100</confidence>
 307         <width>6.0</width>
 308         <events>
 309           <speciations>1</speciations>
 310         </events>
 311         <property ref="style:node_shape" datatype="xsd:token" applies_to="node">circle</property>
 312         <property ref="style:node_size" datatype="xsd:float" applies_to="node">10.0</property>
 313         <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ffee00</property>
 314         <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
 315         <clade>
 316           <branch_length>0.06936</branch_length>
 317           <confidence type="bootstrap">98</confidence>
 318           <width>4.0</width>
 319           <color>
 320             <red>255</red>
 321             <green>51</green>
 322             <blue>0</blue>
 323           </color>
 324           <events>
 325             <speciations>1</speciations>
 326           </events>
 327           <property ref="style:node_shape" datatype="xsd:token" applies_to="node">circle</property>
 328           <property ref="style:node_size" datatype="xsd:float" applies_to="node">8.0</property>
 329           <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ffdd00</property>
 330           <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
 331           <clade>
 332             <branch_length>0.03192</branch_length>
 333             <confidence type="bootstrap">100</confidence>
 334             <width>3.0</width>
 335             <color>
 336               <red>255</red>
 337               <green>51</green>
 338               <blue>0</blue>
 339             </color>
 340             <events>
 341               <speciations>1</speciations>
 342             </events>
 343             <property ref="style:node_shape" datatype="xsd:token" applies_to="node">circle</property>
 344             <property ref="style:node_size" datatype="xsd:float" applies_to="node">6.0</property>
 345             <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ffdd00</property>
 346             <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
 347             <clade>
 348               <branch_length>0.02482</branch_length>
 349               <confidence type="bootstrap">99</confidence>
 350               <width>2.0</width>
 351               <color>
 352                 <red>255</red>
 353                 <green>51</green>
 354                 <blue>0</blue>
 355               </color>
 356               <events>
 357                 <speciations>1</speciations>
 358               </events>
 359               <property ref="style:node_shape" datatype="xsd:token" applies_to="node">circle</property>
 360               <property ref="style:node_size" datatype="xsd:float" applies_to="node">4.0</property>
 361               <property ref="style:node_color" datatype="xsd:token" applies_to="node">#ffdd00</property>
 362               <property ref="style:node_fill_type" datatype="xsd:token" applies_to="node">gradient</property>
 363               <clade>
 364                 <name>rnClcn6</name>
 365                 <branch_length>0.01157</branch_length>
 366                 <color>
 367                   <red>255</red>
 368                   <green>51</green>
 369                   <blue>0</blue>
 370                 </color>
 371                 <taxonomy>
 372                   <scientific_name>RAT</scientific_name>
 373                 </taxonomy>
 374                 <property ref="style:font" datatype="xsd:token" applies_to="node">Dialog</property>
 375                 <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">15</property>
 376                 <property ref="style:font_color" datatype="xsd:token" applies_to="node">#ffcc00</property>
 377               </clade>
 378               <clade>
 379                 <name>mmClcn6</name>
 380                 <branch_length>0.00537</branch_length>
 381                 <color>
 382                   <red>255</red>
 383                   <green>51</green>
 384                   <blue>0</blue>
 385                 </color>
 386                 <taxonomy>
 387                   <scientific_name>MOUSE</scientific_name>
 388                 </taxonomy>
 389                 <property ref="style:font" datatype="xsd:token" applies_to="node">Dialog</property>
 390                 <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">16</property>
 391                 <property ref="style:font_color" datatype="xsd:token" applies_to="node">#ffff00</property>
 392               </clade>
 393             </clade>
 394             <clade>
 395               <name>hsCLCN6</name>
 396               <branch_length>0.00234</branch_length>
 397               <color>
 398                 <red>255</red>
 399                 <green>51</green>
 400                 <blue>0</blue>
 401               </color>
 402               <taxonomy>
 403                 <scientific_name>HUMAN</scientific_name>
 404               </taxonomy>
 405               <property ref="style:font" datatype="xsd:token" applies_to="node">Dialog</property>
 406               <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">10</property>
 407               <property ref="style:font_style" datatype="xsd:token" applies_to="node">bold</property>
 408               <property ref="style:font_color" datatype="xsd:token" applies_to="node">#ccff00</property>
 409             </clade>
 410           </clade>
 411           <clade>
 412             <name>ggClcn6</name>
 413             <branch_length>0.08378</branch_length>
 414             <color>
 415               <red>255</red>
 416               <green>51</green>
 417               <blue>0</blue>
 418             </color>
 419             <taxonomy>
 420               <scientific_name>CHICK</scientific_name>
 421             </taxonomy>
 422             <property ref="style:font" datatype="xsd:token" applies_to="node">Dialog</property>
 423             <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">10</property>
 424             <property ref="style:font_style" datatype="xsd:token" applies_to="node">italic</property>
 425             <property ref="style:font_color" datatype="xsd:token" applies_to="node">#33ff00</property>
 426           </clade>
 427         </clade>
 428         <clade>
 429           <name>frClcn_g153343</name>
 430           <branch_length>0.23936</branch_length>
 431           <taxonomy>
 432             <scientific_name>FUGRU</scientific_name>
 433           </taxonomy>
 434           <property ref="style:font" datatype="xsd:token" applies_to="node">Dialog</property>
 435           <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">10</property>
 436           <property ref="style:font_style" datatype="xsd:token" applies_to="node">bold_italic</property>
 437           <property ref="style:font_color" datatype="xsd:token" applies_to="node">#00ff99</property>
 438         </clade>
 439       </clade>
 440       <clade>
 441         <name>ciClc_139586</name>
 442         <branch_length>0.35537</branch_length>
 443         <taxonomy>
 444           <scientific_name>CIOIN</scientific_name>
 445         </taxonomy>
 446         <property ref="style:font" datatype="xsd:token" applies_to="node">Utopia</property>
 447         <property ref="style:font_size" datatype="xsd:unsignedByte" applies_to="node">20</property>
 448         <property ref="style:font_color" datatype="xsd:token" applies_to="node">#33ffcc</property>
 449       </clade>
 450     </clade>
 451   </clade>
 452 </phylogeny>
 453 </phyloxml>