forester/test_data/gsdi_test_gene_tree_sn.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                               <scientific_name>Plasmodium falciparum (maybe)</scientific_name>
  19                             </taxonomy>
  20                             <sequence>
  21                               <name>A</name>
  22                             </sequence>
  23                           </clade>
  24                           <clade>
  25                             <taxonomy>
  26                               <scientific_name>Plasmodium yoelii yoelii</scientific_name>
  27                             </taxonomy>
  28                             <sequence>
  29                               <name>A</name>
  30                             </sequence>
  31                           </clade>
  32                         </clade>
  33                         <clade>
  34                           <taxonomy>
  35                             <scientific_name>Plasmodium chabaudi strain lame</scientific_name>
  36                           </taxonomy>
  37                           <sequence>
  38                             <name>A</name>
  39                           </sequence>
  40                         </clade>
  41                       </clade>
  42                       <clade>
  43                         <taxonomy>
  44                           <scientific_name>Plasmodium yoelii yoelii</scientific_name>
  45                         </taxonomy>
  46                         <sequence>
  47                           <name>B</name>
  48                         </sequence>
  49                       </clade>
  50                     </clade>
  51                     <clade>
  52                       <name>i have no species</name>
  53                     </clade>
  54                   </clade>
  55                   <clade>
  56                     <taxonomy>
  57                       <scientific_name>Homo sapiens</scientific_name>
  58                       <common_name>Human</common_name>
  59                     </taxonomy>
  60                     <sequence>
  61                       <name>X</name>
  62                     </sequence>
  63                   </clade>
  64                 </clade>
  65                 <clade>
  66                   <taxonomy>
  67                     <scientific_name>big lizard</scientific_name>
  68                   </taxonomy>
  69                   <sequence>
  70                     <name>X</name>
  71                   </sequence>
  72                 </clade>
  73               </clade>
  74               <clade>
  75                 <taxonomy>
  76                   <id provider="ncbi">3093</id>
  77                   <scientific_name>Characium perforatum</scientific_name>
  78                 </taxonomy>
  79                 <sequence>
  80                   <name>X</name>
  81                 </sequence>
  82               </clade>
  83             </clade>
  84             <clade>
  85               <clade>
  86                 <clade>
  87                   <clade>
  88                     <taxonomy>
  89                       <code>HUMAN</code>
  90                       <scientific_name>Homo sapiens</scientific_name>
  91                       <common_name>Human</common_name>
  92                     </taxonomy>
  93                     <sequence>
  94                       <name>A</name>
  95                     </sequence>
  96                   </clade>
  97                   <clade>
  98                     <taxonomy>
  99                       <scientific_name>Mus musculus subspecies balb</scientific_name>
 100                     </taxonomy>
 101                     <sequence>
 102                       <name>A</name>
 103                     </sequence>
 104                   </clade>
 105                 </clade>
 106                 <clade>
 107                   <taxonomy>
 108                     <scientific_name>Saccharomyces cerevisiae (strain ATCC 204508 / S288c)</scientific_name>
 109                   </taxonomy>
 110                   <sequence>
 111                     <name>A</name>
 112                   </sequence>
 113                 </clade>
 114               </clade>
 115               <clade>
 116                 <clade>
 117                   <clade>
 118                     <taxonomy>
 119                       <scientific_name>Homo sapiens</scientific_name>
 120                     </taxonomy>
 121                     <sequence>
 122                       <name>E</name>
 123                     </sequence>
 124                   </clade>
 125                   <clade>
 126                     <taxonomy>
 127                       <scientific_name>Saccharomyces cerevisiae subsection strange</scientific_name>
 128                     </taxonomy>
 129                     <sequence>
 130                       <name>E</name>
 131                     </sequence>
 132                   </clade>
 133                 </clade>
 134                 <clade>
 135                   <taxonomy>
 136                     <scientific_name>Mus musculus nielsson</scientific_name>
 137                   </taxonomy>
 138                   <sequence>
 139                     <name>F</name>
 140                   </sequence>
 141                 </clade>
 142               </clade>
 143             </clade>
 144           </clade>
 145           <clade>
 146             <clade>
 147               <taxonomy>
 148                 <code>NEMVE</code>
 149                 <scientific_name>Nematostella vectensis</scientific_name>
 150                 <common_name>Starlet sea anemone</common_name>
 151               </taxonomy>
 152               <sequence>
 153                 <name>C</name>
 154               </sequence>
 155             </clade>
 156             <clade>
 157               <taxonomy>
 158                 <scientific_name>Petromyzon marinus</scientific_name>
 159                 <common_name>Sea lamprey</common_name>
 160               </taxonomy>
 161               <sequence>
 162                 <name>C</name>
 163               </sequence>
 164             </clade>
 165           </clade>
 166         </clade>
 167         <clade>
 168           <clade>
 169             <clade>
 170               <taxonomy>
 171                 <scientific_name>Mycosphaerella graminicola</scientific_name>
 172                 <synonym>Septoria tritici</synonym>
 173                 <rank>species</rank>
 174               </taxonomy>
 175               <sequence>
 176                 <name>D</name>
 177               </sequence>
 178             </clade>
 179             <clade>
 180               <taxonomy>
 181                 <scientific_name>Mycosphaerella graminicola</scientific_name>
 182               </taxonomy>
 183               <sequence>
 184                 <name>D1</name>
 185               </sequence>
 186             </clade>
 187           </clade>
 188           <clade>
 189             <taxonomy>
 190               <id provider="uniprot">64363</id>
 191               <scientific_name>Mycosphaerella pini</scientific_name>
 192             </taxonomy>
 193             <sequence>
 194               <name>D</name>
 195             </sequence>
 196           </clade>
 197         </clade>
 198       </clade>
 199       <clade>
 200         <taxonomy>
 201           <id provider="uniprot">70601</id>
 202           <scientific_name>Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)</scientific_name>
 203         </taxonomy>
 204         <sequence>
 205           <name>A</name>
 206         </sequence>
 207       </clade>
 208     </clade>
 209     <clade>
 210       <taxonomy>
 211         <code>BACTN</code>
 212         <scientific_name>Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)</scientific_name>
 213       </taxonomy>
 214       <sequence>
 215         <name>A</name>
 216       </sequence>
 217     </clade>
 218   </clade>
 219 </phylogeny>
 220 </phyloxml>