forester/test_data/gsdi_test_gene_tree_ids.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">
   4   <clade>
   5     <clade>
   6       <clade>
   7         <clade>
   8           <clade>
   9             <clade>
  10               <clade>
  11                 <clade>
  12                   <clade>
  13                     <clade>
  14                       <clade>
  15                         <clade>
  16                           <clade>
  17                             <taxonomy>
  18                               <id provider="uniprot">5833</id>
  19                             </taxonomy>
  20                             <sequence>
  21                               <name>A</name>
  22                             </sequence>
  23                           </clade>
  24                           <clade>
  25                             <taxonomy>
  26                               <id provider="uniprot">73239</id>
  27                               <scientific_name>Plasmodium yoelii yoelii</scientific_name>
  28                             </taxonomy>
  29                             <sequence>
  30                               <name>A</name>
  31                             </sequence>
  32                           </clade>
  33                         </clade>
  34                         <clade>
  35                           <taxonomy>
  36                             <id provider="uniprot">5825</id>
  37                             <scientific_name>Plasmodium chabaudi</scientific_name>
  38                           </taxonomy>
  39                           <sequence>
  40                             <name>A</name>
  41                           </sequence>
  42                         </clade>
  43                       </clade>
  44                       <clade>
  45                         <taxonomy>
  46                           <id provider="uniprot">73239</id>
  47                           <scientific_name>Plasmodium yoelii yoelii</scientific_name>
  48                         </taxonomy>
  49                         <sequence>
  50                           <name>B</name>
  51                         </sequence>
  52                       </clade>
  53                     </clade>
  54                     <clade>
  55                       <name>i have no species</name>
  56                     </clade>
  57                   </clade>
  58                   <clade>
  59                     <taxonomy>
  60                       <id provider="uniprot">9606</id>
  61                       <code>HUMAN</code>
  62                       <scientific_name>Homo sapiens</scientific_name>
  63                       <common_name>Human</common_name>
  64                       <rank>species</rank>
  65                     </taxonomy>
  66                     <sequence>
  67                       <name>X</name>
  68                     </sequence>
  69                   </clade>
  70                 </clade>
  71                 <clade>
  72                   <taxonomy>
  73                     <code>XXXXX</code>
  74                   </taxonomy>
  75                   <sequence>
  76                     <name>X</name>
  77                   </sequence>
  78                 </clade>
  79               </clade>
  80               <clade>
  81                 <taxonomy>
  82                   <id provider="ncbi">3093</id>
  83                   <scientific_name>Characium perforatum</scientific_name>
  84                   <rank>species</rank>
  85                 </taxonomy>
  86                 <sequence>
  87                   <name>X</name>
  88                 </sequence>
  89               </clade>
  90             </clade>
  91             <clade>
  92               <clade>
  93                 <clade>
  94                   <clade>
  95                     <taxonomy>
  96                       <id provider="uniprot">9606</id>
  97                       <code>HUMAN</code>
  98                       <scientific_name>Homo sapiens</scientific_name>
  99                       <common_name>Human</common_name>
 100                       <rank>species</rank>
 101                     </taxonomy>
 102                     <sequence>
 103                       <name>A</name>
 104                     </sequence>
 105                   </clade>
 106                   <clade>
 107                     <taxonomy>
 108                       <id provider="uniprot">10090</id>
 109                       <code>MOUSE</code>
 110                       <scientific_name>Mus musculus</scientific_name>
 111                       <common_name>Mouse</common_name>
 112                       <rank>species</rank>
 113                     </taxonomy>
 114                     <sequence>
 115                       <name>A</name>
 116                     </sequence>
 117                   </clade>
 118                 </clade>
 119                 <clade>
 120                   <taxonomy>
 121                     <id provider="uniprot">559292</id>
 122                     <code>YEAST</code>
 123                     <scientific_name>Saccharomyces cerevisiae (strain ATCC 204508 / S288c)</scientific_name>
 124                     <common_name>Baker&apos;s yeast</common_name>
 125                   </taxonomy>
 126                   <sequence>
 127                     <name>A</name>
 128                   </sequence>
 129                 </clade>
 130               </clade>
 131               <clade>
 132                 <clade>
 133                   <clade>
 134                     <taxonomy>
 135                       <id provider="uniprot">9606</id>
 136                       <code>HUMAN</code>
 137                       <scientific_name>Homo sapiens</scientific_name>
 138                       <common_name>Human</common_name>
 139                       <rank>species</rank>
 140                     </taxonomy>
 141                     <sequence>
 142                       <name>E</name>
 143                     </sequence>
 144                   </clade>
 145                   <clade>
 146                     <taxonomy>
 147                       <id provider="uniprot">559292</id>
 148                       <code>YEAST</code>
 149                       <scientific_name>Saccharomyces cerevisiae (strain ATCC 204508 / S288c)</scientific_name>
 150                       <common_name>Baker&apos;s yeast</common_name>
 151                     </taxonomy>
 152                     <sequence>
 153                       <name>E</name>
 154                     </sequence>
 155                   </clade>
 156                 </clade>
 157                 <clade>
 158                   <taxonomy>
 159                     <id provider="uniprot">10090</id>
 160                     <code>MOUSE</code>
 161                     <scientific_name>Mus musculus</scientific_name>
 162                     <common_name>Mouse</common_name>
 163                     <rank>species</rank>
 164                   </taxonomy>
 165                   <sequence>
 166                     <name>F</name>
 167                   </sequence>
 168                 </clade>
 169               </clade>
 170             </clade>
 171           </clade>
 172           <clade>
 173             <clade>
 174               <taxonomy>
 175                 <id provider="uniprot">45351</id>
 176                 <code>NEMVE</code>
 177                 <scientific_name>Nematostella vectensis</scientific_name>
 178                 <common_name>Starlet sea anemone</common_name>
 179                 <rank>species</rank>
 180               </taxonomy>
 181               <sequence>
 182                 <name>C</name>
 183               </sequence>
 184             </clade>
 185             <clade>
 186               <taxonomy>
 187                 <id provider="uniprot">7757</id>
 188                 <code>PETMA</code>
 189                 <scientific_name>Petromyzon marinus</scientific_name>
 190                 <common_name>Sea lamprey</common_name>
 191                 <rank>species</rank>
 192               </taxonomy>
 193               <sequence>
 194                 <name>C</name>
 195               </sequence>
 196             </clade>
 197           </clade>
 198         </clade>
 199         <clade>
 200           <clade>
 201             <clade>
 202               <taxonomy>
 203                 <id provider="uniprot">1047171</id>
 204                 <code>MYCGR</code>
 205                 <scientific_name>Mycosphaerella graminicola</scientific_name>
 206                 <common_name>Speckled leaf blotch fungus</common_name>
 207                 <synonym>Septoria tritici</synonym>
 208                 <rank>species</rank>
 209               </taxonomy>
 210               <sequence>
 211                 <name>D</name>
 212               </sequence>
 213             </clade>
 214             <clade>
 215               <taxonomy>
 216                 <id provider="uniprot">1047171</id>
 217                 <code>MYCGR</code>
 218                 <scientific_name>Mycosphaerella graminicola</scientific_name>
 219                 <common_name>Speckled leaf blotch fungus</common_name>
 220                 <synonym>Septoria tritici</synonym>
 221                 <rank>species</rank>
 222               </taxonomy>
 223               <sequence>
 224                 <name>D1</name>
 225               </sequence>
 226             </clade>
 227           </clade>
 228           <clade>
 229             <taxonomy>
 230               <id provider="uniprot">64363</id>
 231               <code>MYCPJ</code>
 232               <scientific_name>Mycosphaerella pini</scientific_name>
 233               <common_name>Red band needle blight disease fungus</common_name>
 234               <synonym>Dothistroma pini</synonym>
 235               <rank>species</rank>
 236             </taxonomy>
 237             <sequence>
 238               <name>D</name>
 239             </sequence>
 240           </clade>
 241         </clade>
 242       </clade>
 243       <clade>
 244         <taxonomy>
 245           <id provider="uniprot">70601</id>
 246           <code>PYRHO</code>
 247           <scientific_name>Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)</scientific_name>
 248         </taxonomy>
 249         <sequence>
 250           <name>A</name>
 251         </sequence>
 252       </clade>
 253     </clade>
 254     <clade>
 255       <taxonomy>
 256         <id provider="uniprot">226186</id>
 257         <code>BACTN</code>
 258         <scientific_name>Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)</scientific_name>
 259       </taxonomy>
 260       <sequence>
 261         <name>A</name>
 262       </sequence>
 263     </clade>
 264   </clade>
 265 </phylogeny>
 266 </phyloxml>