forester/test_data/phyloxml_test_atv.xml

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
   3     xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd"
   4     xmlns="http://www.phyloxml.org">
   5     <phylogeny branch_length_unit="c" rooted="true">
   6         <name>t3</name>
   7         <id provider="treebank">1-1</id>
   8         <description>test phylogeny</description>
   9         <confidence type="ml">0.1</confidence>
  10         <clade branch_length="0.1">
  11             <name>root node</name>
  12             <confidence type="bootstrap">90</confidence>
  13             <confidence type="ml">1e-3</confidence>
  14             <confidence type="decay">2</confidence>
  15             <width>10</width>
  16             <color>
  17                 <red>2</red>
  18                 <green>22</green>
  19                 <blue>33</blue>
  20             </color>
  21             <node_id>root id</node_id>
  22             <taxonomy>
  23                 <id provider="ncbi">1</id>
  24                 <code>ECDYS</code>
  25                 <scientific_name>ecdysozoa</scientific_name>
  26                 <common_name>molting animals</common_name>
  27                 <rank>phylum</rank>
  28                 <uri>http://www.ecdysozoa.org/</uri>
  29             </taxonomy>
  30             <sequence type="protein">
  31                 <symbol>BCL2L14</symbol>
  32                 <accession source="UniProtKB">Q9BZR8</accession>
  33                 <name>Apoptosis facilitator Bcl-2-like 14 protein</name>
  34                 <location>12p13-p12</location>
  35                 <mol_seq>MCSTSGCDLEEIPLDDDDLNTIEFKILAYY</mol_seq>
  36                 <uri type="source" desc="UniProt link">http://www.pir.uniprot.org/cgi-bin/upEntry?id=B2L14_HUMAN</uri>
  37                 <annotation ref="GO:0006915" source="UniProtKB" evidence="experimental" type="function">
  38                     <desc>apoptosis</desc>
  39                     <confidence type="ml">1</confidence>
  40                     <property datatype="xsd:double" applies_to="annotation" ref="AFFY:expression" unit="AFFY:x">0.2</property>
  41                     <property datatype="xsd:string" applies_to="annotation" ref="MED:disease">lymphoma</property>
  42                 </annotation>
  43                 <annotation ref="GO:0005829"/>
  44                 <annotation>
  45                     <desc>intracellular organelle</desc>
  46                 </annotation>
  47             </sequence>
  48             <events>
  49                 <type>mixed</type>
  50                 <duplications>1</duplications>
  51                 <confidence type="bs">99</confidence>
  52             </events>
  53             <distribution>
  54                 <desc>irgendwo</desc>
  55                 <point geodetic_datum="WGS84">
  56                     <lat>35.9296730123456789</lat>
  57                     <long>-78.9482370123456789</long>
  58                     <alt>0</alt>
  59                 </point>
  60             </distribution>
  61             <reference doi="10.1074/jbc.M005889200"/>
  62             <property ref="F:foo" datatype="xsd:int" applies_to="clade">bar</property>
  63             <clade>
  64                 <name>node a</name>
  65                 <branch_length>0.2</branch_length>
  66                 <color>
  67                     <red>12</red>
  68                     <green>14</green>
  69                     <blue>16</blue>
  70                 </color>
  71                 <node_id provider="nodeid">a id</node_id>
  72                 <taxonomy>
  73                     <id provider="ncbi">123</id>
  74                     <code>CAEEL</code>
  75                     <scientific_name>C elegans</scientific_name>
  76                     <common_name>elegant nematode worm</common_name>
  77                     <rank>species</rank>
  78                     <uri>http://www.wormbase.org/</uri>
  79                 </taxonomy>
  80                 <sequence>
  81                     <name>CAEEL_XYZ</name>
  82                 </sequence>
  83             </clade>
  84             <clade>
  85                 <name>node b</name>
  86                 <events>
  87                     <duplications>1</duplications>
  88                     <confidence type="">80</confidence>
  89                 </events>
  90                 <binary_characters type="characters" present_count="2" lost_count="3" gained_count="1">
  91                     <gained>
  92                         <bc>c</bc>
  93                     </gained>
  94                     <lost>
  95                         <bc>d</bc>
  96                         <bc>e</bc>
  97                         <bc>f</bc>
  98                     </lost>
  99                     <present>
 100                         <bc>a</bc>
 101                         <bc>b</bc>
 102                     </present>
 103                 </binary_characters>
 104                 <clade>
 105                     <name>node ba</name>
 106                     <distribution>
 107                         <desc>Africa</desc>
 108                     </distribution>
 109                 </clade>
 110                 <clade>
 111                     <name>node bb</name>
 112                     <binary_characters type="domains">
 113                         <gained>
 114                             <bc>A</bc>
 115                             <bc>B</bc>
 116                             <bc>C</bc>
 117                         </gained>
 118                         <lost>
 119                             <bc>D</bc>
 120                         </lost>
 121                         <present>
 122                             <bc>X</bc>
 123                             <bc>M</bc>
 124                         </present>
 125                     </binary_characters>
 126                 </clade>
 127                 <clade>
 128                     <name>node bc</name>
 129                     <sequence>
 130                         <name>bc seq</name>
 131                         <domain_architecture length="124">
 132                             <domain from="120" to="130" confidence="0.9" id=""> A </domain>
 133                             <domain from="21" to="44" confidence="2144" id="pfam"> B </domain>
 134                             <domain to="43" confidence="1.0E-89" from="34" id=""> C </domain>
 135                             <domain id="123" from="34" to="43" confidence="-1.3e-34"> D </domain>
 136                         </domain_architecture>
 137                     </sequence>
 138                 </clade>
 139             </clade>
 140         </clade>
 141     </phylogeny>
 142 </phyloxml>