forester/test_data/gsdi_test_species_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" rerootable="false">
   4   <clade>
   5     <name>cellular_organisms</name>
   6     <clade>
   7       <taxonomy>
   8         <scientific_name>Neomura</scientific_name>
   9       </taxonomy>
  10       <clade>
  11         <taxonomy>
  12           <id provider="uniprot">2759</id>
  13           <scientific_name>Eukaryota</scientific_name>
  14           <rank>superkingdom</rank>
  15         </taxonomy>
  16         <clade>
  17           <taxonomy>
  18             <id provider="uniprot">33154</id>
  19             <scientific_name>Opisthokonta</scientific_name>
  20             <common_name>Fungi/Metazoa group</common_name>
  21           </taxonomy>
  22           <clade>
  23             <name>Bilateria_Cnidaria</name>
  24             <clade>
  25               <taxonomy>
  26                 <id provider="uniprot">7742</id>
  27                 <scientific_name>Vertebrata</scientific_name>
  28               </taxonomy>
  29               <clade>
  30                 <taxonomy>
  31                   <scientific_name>Euarchontoglires</scientific_name>
  32                 </taxonomy>
  33                 <clade>
  34                   <taxonomy>
  35                     <scientific_name>Homo sapiens</scientific_name>
  36                   </taxonomy>
  37                 </clade>
  38                 <clade>
  39                   <taxonomy>
  40                     <scientific_name>Mus musculus</scientific_name>
  41                   </taxonomy>
  42                 </clade>
  43               </clade>
  44               <clade>
  45                 <taxonomy>
  46                   <scientific_name>Petromyzon marinus</scientific_name>
  47                 </taxonomy>
  48               </clade>
  49             </clade>
  50             <clade>
  51               <name>NEMVE</name>
  52               <taxonomy>
  53                 <scientific_name>Nematostella vectensis</scientific_name>
  54               </taxonomy>
  55             </clade>
  56           </clade>
  57           <clade>
  58             <name>Pezizomycotina_Saccharomycetales</name>
  59             <clade>
  60               <taxonomy>
  61                 <id provider="uniprot">41254</id>
  62                 <scientific_name>Mycosphaerella</scientific_name>
  63                 <rank>genus</rank>
  64               </taxonomy>
  65               <clade>
  66                 <name>MYCGR</name>
  67                 <taxonomy>
  68                   <scientific_name>Mycosphaerella graminicola</scientific_name>
  69                 </taxonomy>
  70               </clade>
  71               <clade>
  72                 <name>MYCPJ</name>
  73                 <taxonomy>
  74                   <scientific_name>Mycosphaerella pini</scientific_name>
  75                 </taxonomy>
  76               </clade>
  77             </clade>
  78             <clade>
  79               <clade>
  80                 <name>YEAST</name>
  81                 <taxonomy>
  82                   <scientific_name>Saccharomyces cerevisiae</scientific_name>
  83                 </taxonomy>
  84               </clade>
  85               <clade>
  86                 <taxonomy>
  87                   <code>WOAMI</code>
  88                 </taxonomy>
  89               </clade>
  90             </clade>
  91           </clade>
  92         </clade>
  93         <clade>
  94           <taxonomy>
  95             <id provider="uniprot">5820</id>
  96             <scientific_name>Plasmodium</scientific_name>
  97             <rank>genus</rank>
  98           </taxonomy>
  99           <clade>
 100             <name>PLACH</name>
 101             <taxonomy>
 102               <scientific_name>Plasmodium chabaudi</scientific_name>
 103             </taxonomy>
 104           </clade>
 105           <clade>
 106             <name>PLAFA</name>
 107             <taxonomy>
 108               <id provider="uniprot">5833</id>
 109               <code>PLAFA</code>
 110               <scientific_name>Plasmodium falciparum</scientific_name>
 111               <rank>species</rank>
 112             </taxonomy>
 113           </clade>
 114           <clade>
 115             <name>PLAYO</name>
 116             <taxonomy>
 117               <id provider="uniprot">73239</id>
 118               <code>PLAYO</code>
 119               <scientific_name>Plasmodium yoelii yoelii</scientific_name>
 120               <rank>subspecies</rank>
 121             </taxonomy>
 122           </clade>
 123         </clade>
 124       </clade>
 125       <clade>
 126         <clade>
 127           <name>PYRHO</name>
 128           <taxonomy>
 129             <id provider="uniprot">53953</id>
 130             <code>PYRHO</code>
 131             <scientific_name>Pyrococcus horikoshii</scientific_name>
 132             <rank>species</rank>
 133           </taxonomy>
 134         </clade>
 135         <clade>
 136           <name>i have no species information!</name>
 137         </clade>
 138       </clade>
 139     </clade>
 140     <clade>
 141       <name>b_193</name>
 142       <clade>
 143         <name>b_115</name>
 144         <clade>
 145           <name>KINRD</name>
 146           <taxonomy>
 147             <id provider="uniprot">266940</id>
 148             <code>KINRD</code>
 149             <scientific_name>Kineococcus radiotolerans (strain ATCC BAA-149 / DSM 14245 / SRS30216)</scientific_name>
 150           </taxonomy>
 151         </clade>
 152         <clade>
 153           <name>KOCRD</name>
 154           <taxonomy>
 155             <id provider="uniprot">378753</id>
 156             <code>KOCRD</code>
 157             <scientific_name>Kocuria rhizophila (strain ATCC 9341 / DSM 348 / NBRC 103217 / DC2201)</scientific_name>
 158           </taxonomy>
 159         </clade>
 160         <clade>
 161           <name>STRCO</name>
 162           <taxonomy>
 163             <id provider="uniprot">1902</id>
 164             <code>STRCO</code>
 165             <scientific_name>Streptomyces coelicolor</scientific_name>
 166             <rank>species</rank>
 167           </taxonomy>
 168         </clade>
 169         <clade>
 170           <name>THEFY</name>
 171           <taxonomy>
 172             <scientific_name>Thermobifida fusca (strain YX)</scientific_name>
 173           </taxonomy>
 174         </clade>
 175         <clade>
 176           <taxonomy>
 177             <scientific_name>Microlunatus phosphovorus (strain ATCC 700054 / DSM 10555 / JCM 9379 / NBRC 101784 / NCIMB 13414 / VKM Ac-1990 / NM-1)</scientific_name>
 178           </taxonomy>
 179         </clade>
 180       </clade>
 181       <clade>
 182         <name>BACTN</name>
 183         <taxonomy>
 184           <id provider="uniprot">818</id>
 185           <scientific_name>Bacteroides thetaiotaomicron</scientific_name>
 186           <rank>species</rank>
 187         </taxonomy>
 188       </clade>
 189     </clade>
 190   </clade>
 191 </phylogeny>
 192 </phyloxml>