forester/aptx/aptx_example_files/phyloxml_seq_annotation.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   <name>same example, with species and sequence</name>
   5   <clade>
   6     <clade>
   7       <name>AB</name>
   8       <clade>
   9         <name>A</name>
  10         <taxonomy>
  11           <scientific_name>E. coli</scientific_name>
  12         </taxonomy>
  13         <sequence>
  14           <annotation>
  15             <desc>a_function</desc>
  16             <confidence type="probability">0.99</confidence>
  17           </annotation>
  18         </sequence>
  19       </clade>
  20       <clade>
  21         <name>B</name>
  22         <taxonomy>
  23           <scientific_name>B. subtilis</scientific_name>
  24         </taxonomy>
  25         <sequence>
  26           <annotation>
  27             <desc>b_function</desc>
  28             <confidence type="probability">0.91</confidence>
  29           </annotation>
  30         </sequence>
  31       </clade>
  32     </clade>
  33     <clade>
  34       <name>C</name>
  35       <taxonomy>
  36         <scientific_name>C. elegans</scientific_name>
  37       </taxonomy>
  38       <sequence>
  39         <annotation>
  40           <desc>c_function</desc>
  41           <confidence type="probability">0.67</confidence>
  42         </annotation>
  43       </sequence>
  44     </clade>
  45   </clade>
  46 </phylogeny>
  47 </phyloxml>