forester/aptx/aptx_example_files/seq_colors_with_species_and_annotations.xml

   1 <?xml version="1.0" encoding="UTF-8"?>\r
   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">\r
   3 <phylogeny rooted="true" rerootable="true">\r
   4   <name>seq name colors example</name>\r
   5   <clade>\r
   6     <clade>\r
   7       <branch_length>0.07475587</branch_length>\r
   8       <clade>\r
   9         <branch_length>0.10234752</branch_length>\r
  10         <clade>\r
  11           <name>Gnetum_gnemon_GGM15</name>\r
  12           <branch_length>0.4191439</branch_length>\r
  13           <taxonomy>\r
  14             <id provider="uniprot">3382</id>\r
  15             <code>GNEGN</code>\r
  16             <scientific_name>Gnetum gnemon</scientific_name>\r
  17             <common_name>Bago</common_name>\r
  18             <synonym>Gnetum acutatum</synonym>\r
  19             <rank>species</rank>\r
  20           </taxonomy>\r
  21           <sequence>\r
  22             <name>Tubulin-alpha</name>\r
  23             <annotation ref="subtree:one"></annotation>\r
  24           </sequence>\r
  25         </clade>\r
  26         <clade>\r
  27           <name>Picea_abies_DAL12</name>\r
  28           <branch_length>0.37097505</branch_length>\r
  29           <taxonomy>\r
  30             <id provider="uniprot">3329</id>\r
  31             <code>PICAB</code>\r
  32             <scientific_name>Picea abies</scientific_name>\r
  33             <common_name>Norway spruce</common_name>\r
  34             <synonym>Picea excelsa</synonym>\r
  35             <rank>species</rank>\r
  36           </taxonomy>\r
  37           <sequence>\r
  38             <name>Tubulin-beta</name>\r
  39             <annotation ref="subtree:one"></annotation>\r
  40           </sequence>\r
  41         </clade>\r
  42       </clade>\r
  43       <clade>\r
  44         <branch_length>0.07836347</branch_length>\r
  45         <clade>\r
  46           <name>Gnetum_gnemon_GGM2</name>\r
  47           <branch_length>0.32192346</branch_length>\r
  48           <taxonomy>\r
  49             <id provider="uniprot">3382</id>\r
  50             <code>GNEGN</code>\r
  51             <scientific_name>Gnetum gnemon</scientific_name>\r
  52             <common_name>Bago</common_name>\r
  53             <synonym>Gnetum acutatum</synonym>\r
  54             <rank>species</rank>\r
  55           </taxonomy>\r
  56           <sequence>\r
  57             <name>Tubulin-beta</name>\r
  58             <annotation ref="subtree:one"></annotation>\r
  59           </sequence>\r
  60         </clade>\r
  61         <clade>\r
  62           <branch_length>0.13691099</branch_length>\r
  63           <clade>\r
  64             <name>Picea_abies_DAL13</name>\r
  65             <branch_length>0.17518067</branch_length>\r
  66             <taxonomy>\r
  67               <id provider="uniprot">3329</id>\r
  68               <code>PICAB</code>\r
  69               <scientific_name>Picea abies</scientific_name>\r
  70               <common_name>Norway spruce</common_name>\r
  71               <synonym>Picea excelsa</synonym>\r
  72               <rank>species</rank>\r
  73             </taxonomy>\r
  74             <sequence>\r
  75               <name>Tubulin-alpha</name>\r
  76               <annotation ref="subtree:one"></annotation>\r
  77             </sequence>\r
  78           </clade>\r
  79           <clade>\r
  80             <name>Picea_abies_DAL11</name>\r
  81             <branch_length>0.22006623</branch_length>\r
  82             <taxonomy>\r
  83               <id provider="uniprot">3329</id>\r
  84               <code>PICAB</code>\r
  85               <scientific_name>Picea abies</scientific_name>\r
  86               <common_name>Norway spruce</common_name>\r
  87               <synonym>Picea excelsa</synonym>\r
  88               <rank>species</rank>\r
  89             </taxonomy>\r
  90             <sequence>\r
  91               <name>Tubulin-alpha</name>\r
  92               <annotation ref="subtree:one"></annotation>\r
  93             </sequence>\r
  94           </clade>\r
  95         </clade>\r
  96       </clade>\r
  97     </clade>\r
  98     <clade>\r
  99       <branch_length>0.065986283</branch_length>\r
 100       <clade>\r
 101         <branch_length>0.065986283</branch_length>\r
 102         <clade>\r
 103           <name>Amborella_trichopoda_AmAP3</name>\r
 104           <branch_length>0.16098303</branch_length>\r
 105           <taxonomy>\r
 106             <id provider="uniprot">13333</id>\r
 107             <code>AMBTC</code>\r
 108             <scientific_name>Amborella trichopoda</scientific_name>\r
 109             <rank>species</rank>\r
 110           </taxonomy>\r
 111           <sequence>\r
 112             <name>Tubulin-alpha</name>\r
 113             <annotation ref="subtree:two"></annotation>\r
 114           </sequence>\r
 115         </clade>\r
 116         <clade>\r
 117           <branch_length>0.1882019</branch_length>\r
 118           <clade>\r
 119             <name>Nuphar_advena_Nu.ad.AP3.1</name>\r
 120             <branch_length>0.076055825</branch_length>\r
 121             <taxonomy>\r
 122               <id provider="uniprot">77108</id>\r
 123               <code>NUPAD</code>\r
 124               <scientific_name>Nuphar advena</scientific_name>\r
 125               <common_name>Common spatterdock</common_name>\r
 126               <synonym>Nuphar lutea subsp. advena</synonym>\r
 127               <rank>species</rank>\r
 128             </taxonomy>\r
 129             <sequence>\r
 130               <name>Tubulin-alpha</name>\r
 131               <annotation ref="subtree:two"></annotation>\r
 132             </sequence>\r
 133           </clade>\r
 134           <clade>\r
 135             <name>Nuphar_advena_Nu.ad.AP3.2</name>\r
 136             <branch_length>0.045621026</branch_length>\r
 137             <taxonomy>\r
 138               <id provider="uniprot">77108</id>\r
 139               <code>NUPAD</code>\r
 140               <scientific_name>Nuphar advena</scientific_name>\r
 141               <common_name>Common spatterdock</common_name>\r
 142               <synonym>Nuphar lutea subsp. advena</synonym>\r
 143               <rank>species</rank>\r
 144             </taxonomy>\r
 145             <sequence>\r
 146               <name>Tubulin-alpha</name>\r
 147               <annotation ref="subtree:two"></annotation>\r
 148             </sequence>\r
 149           </clade>\r
 150         </clade>\r
 151       </clade>\r
 152       <clade>\r
 153         <branch_length>0.07475587</branch_length>\r
 154         <clade>\r
 155           <branch_length>0.10234752</branch_length>\r
 156           <clade>\r
 157             <name>Gnetum_gnemon_GGM15</name>\r
 158             <branch_length>0.4191439</branch_length>\r
 159             <taxonomy>\r
 160               <id provider="uniprot">3382</id>\r
 161               <code>GNEGN</code>\r
 162               <scientific_name>Gnetum gnemon</scientific_name>\r
 163               <common_name>Bago</common_name>\r
 164               <synonym>Gnetum acutatum</synonym>\r
 165               <rank>species</rank>\r
 166             </taxonomy>\r
 167             <sequence>\r
 168               <name>Tubulin-alpha</name>\r
 169               <annotation ref="subtree:two"></annotation>\r
 170             </sequence>\r
 171           </clade>\r
 172           <clade>\r
 173             <name>Picea_abies_DAL12</name>\r
 174             <branch_length>0.37097505</branch_length>\r
 175             <taxonomy>\r
 176               <id provider="uniprot">3329</id>\r
 177               <code>PICAB</code>\r
 178               <scientific_name>Picea abies</scientific_name>\r
 179               <common_name>Norway spruce</common_name>\r
 180               <synonym>Picea excelsa</synonym>\r
 181               <rank>species</rank>\r
 182             </taxonomy>\r
 183             <sequence>\r
 184               <name>Tubulin-beta</name>\r
 185               <annotation ref="subtree:two"></annotation>\r
 186             </sequence>\r
 187           </clade>\r
 188         </clade>\r
 189         <clade>\r
 190           <branch_length>0.07836347</branch_length>\r
 191           <clade>\r
 192             <name>Gnetum_gnemon_GGM2</name>\r
 193             <branch_length>0.32192346</branch_length>\r
 194             <taxonomy>\r
 195               <id provider="uniprot">3382</id>\r
 196               <code>GNEGN</code>\r
 197               <scientific_name>Gnetum gnemon</scientific_name>\r
 198               <common_name>Bago</common_name>\r
 199               <synonym>Gnetum acutatum</synonym>\r
 200               <rank>species</rank>\r
 201             </taxonomy>\r
 202             <sequence>\r
 203               <name>Tubulin-beta</name>\r
 204               <annotation ref="subtree:two"></annotation>\r
 205             </sequence>\r
 206           </clade>\r
 207           <clade>\r
 208             <branch_length>0.13691099</branch_length>\r
 209             <clade>\r
 210               <name>Picea_abies_DAL13</name>\r
 211               <branch_length>0.17518067</branch_length>\r
 212               <taxonomy>\r
 213                 <id provider="uniprot">3329</id>\r
 214                 <code>PICAB</code>\r
 215                 <scientific_name>Picea abies</scientific_name>\r
 216                 <common_name>Norway spruce</common_name>\r
 217                 <synonym>Picea excelsa</synonym>\r
 218                 <rank>species</rank>\r
 219               </taxonomy>\r
 220               <sequence>\r
 221                 <name>Tubulin-delta</name>\r
 222                 <annotation ref="subtree:two"></annotation>\r
 223               </sequence>\r
 224             </clade>\r
 225             <clade>\r
 226               <name>Picea_abies_DAL11</name>\r
 227               <branch_length>0.22006623</branch_length>\r
 228               <taxonomy>\r
 229                 <id provider="uniprot">3329</id>\r
 230                 <code>PICAB</code>\r
 231                 <scientific_name>Picea abies</scientific_name>\r
 232                 <common_name>Norway spruce</common_name>\r
 233                 <synonym>Picea excelsa</synonym>\r
 234                 <rank>species</rank>\r
 235               </taxonomy>\r
 236               <sequence>\r
 237                 <name>Tubulin-delta</name>\r
 238                 <annotation ref="subtree:two"></annotation>\r
 239               </sequence>\r
 240             </clade>\r
 241           </clade>\r
 242         </clade>\r
 243       </clade>\r
 244     </clade>\r
 245     <clade>\r
 246       <branch_length>0.13691099</branch_length>\r
 247       <clade>\r
 248         <name>Picea_abies_DAL13</name>\r
 249         <branch_length>0.17518067</branch_length>\r
 250         <taxonomy>\r
 251           <id provider="uniprot">3329</id>\r
 252           <code>PICAB</code>\r
 253           <scientific_name>Picea abies</scientific_name>\r
 254           <common_name>Norway spruce</common_name>\r
 255           <synonym>Picea excelsa</synonym>\r
 256           <rank>species</rank>\r
 257         </taxonomy>\r
 258         <sequence>\r
 259           <name>Tubulin-epsilon</name>\r
 260         </sequence>\r
 261       </clade>\r
 262       <clade>\r
 263         <name>Picea_abies_DAL11</name>\r
 264         <branch_length>0.22006623</branch_length>\r
 265         <taxonomy>\r
 266           <id provider="uniprot">3329</id>\r
 267           <code>PICAB</code>\r
 268           <scientific_name>Picea abies</scientific_name>\r
 269           <common_name>Norway spruce</common_name>\r
 270           <synonym>Picea excelsa</synonym>\r
 271           <rank>species</rank>\r
 272         </taxonomy>\r
 273       </clade>\r
 274     </clade>\r
 275   </clade>\r
 276 </phylogeny>\r
 277 </phyloxml>