forester/test_data/phyloxml_test_t1.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="cc" rooted="true" rerootable="false" type="gene_tree">
   6       <name>t1</name>
   7       <clade/>
   8    </phylogeny>
   9    <phylogeny branch_length_unit="aa/m" rooted="true" type="host parasite reconciliation" rerootable="false">
  10       <name>t2</name>
  11       <clade>
  12          <name>root node</name>
  13          <clade branch_length="1">
  14             <name>node a</name>
  15             <taxonomy>
  16                <common_name>some parasite</common_name>
  17             </taxonomy>
  18             <taxonomy>
  19                <common_name>the host</common_name>
  20             </taxonomy>
  21             <sequence type="dna">
  22                <mol_seq is_aligned="false"> actgtgggggtggggaggcggaggggtgtggtacactgactactgactgactga_ctgacgatcatatgac </mol_seq>
  23             </sequence>
  24             <sequence type="dna">
  25                <mol_seq is_aligned="false">
  26                   ctgtgatgcatgcatgcatgcatgcatcgatcgccggcatgcatcgatatctacgctgactgactagctactagtcacacgtgacgcgcgcatgc***
  27                </mol_seq>
  28             </sequence>
  29          </clade>
  30          <clade>
  31             <name>node b</name>
  32             <branch_length>2</branch_length>
  33          </clade>
  34       </clade>
  35    </phylogeny>
  36    <phylogeny branch_length_unit="c" rooted="true">
  37       <name>t3</name>
  38       <id provider="treebank">1-1</id>
  39       <description>test phylogeny</description>
  40       <confidence type="ml">0.1</confidence>
  41       <clade branch_length="0.1">
  42          <name>root node</name>
  43          <confidence type="bootstrap">90</confidence>
  44          <confidence type="ml">1e-3</confidence>
  45          <confidence type="decay">2</confidence>
  46          <width>10</width>
  47          <color>
  48             <red>2</red>
  49             <green>22</green>
  50             <blue>33</blue>
  51          </color>
  52          <node_id>root id</node_id>
  53          <taxonomy>
  54             <id provider="ncbi">1</id>
  55             <code>ECDYS</code>
  56             <scientific_name>ecdysozoa</scientific_name>
  57             <common_name>molting animals</common_name>
  58             <rank>phylum</rank>
  59             <uri>http://www.ecdysozoa.org/</uri>
  60          </taxonomy>
  61          <sequence type="protein">
  62             <symbol>BCL2L14</symbol>
  63             <accession source="UniProtKB">Q9BZR8</accession>
  64             <name>Apoptosis facilitator Bcl-2-like 14 protein</name>
  65             <location>12p13-p12</location>
  66             <mol_seq is_aligned="false">MCSTSGCDLEEIPLDDDDLNTIEFKILAYY</mol_seq>
  67             <uri type="source" desc="UniProt link">http://www.pir.uniprot.org/cgi-bin/upEntry?id=B2L14_HUMAN</uri>
  68             <annotation>
  69                <desc>intracellular organelle</desc>
  70             </annotation>
  71             <annotation ref="GO:0005829"/>
  72             <annotation ref="GO:0006915" source="UniProtKB" evidence="experimental" type="function">
  73                <desc>apoptosis</desc>
  74                <confidence type="ml">1</confidence>
  75                <property datatype="xsd:double" applies_to="annotation" ref="AFFY:expression" unit="AFFY:x">0.2</property>
  76                <property datatype="xsd:string" applies_to="annotation" ref="MED:disease">lymphoma</property>
  77             </annotation>
  78          </sequence>
  79          <events>
  80             <type>mixed</type>
  81             <duplications>1</duplications>
  82             <confidence type="bs">99</confidence>
  83          </events>
  84          <distribution>
  85             <desc>irgendwo</desc>
  86             <point geodetic_datum="WGS84" alt_unit="m">
  87                <lat>35.9296730123456789</lat>
  88                <long>-78.9482370123456789</long>
  89                <alt>0</alt>
  90             </point>
  91          </distribution>
  92          <reference doi="10.1038/387489a0">
  93             <desc>
  94                Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, &amp; J. A. Lake (1997). "Evidence for a clade of nematodes, arthropods and other moulting animals". Nature 387 (6632): 489–493.
  95             </desc>
  96          </reference>
  97          <property ref="F:foo" datatype="xsd:int" applies_to="clade">bar</property>
  98          <clade>
  99             <name>node a</name>
 100             <branch_length>0.2</branch_length>
 101             <color>
 102                <red>12</red>
 103                <green>14</green>
 104                <blue>16</blue>
 105             </color>
 106             <node_id provider="nodeid">a id</node_id>
 107             <taxonomy>
 108                <id provider="ncbi">123</id>
 109                <code>CAEEL</code>
 110                <scientific_name>C elegans</scientific_name>
 111                <common_name>elegant nematode worm</common_name>
 112                <rank>species</rank>
 113                <uri>http://www.wormbase.org/</uri>
 114             </taxonomy>
 115             <sequence>
 116                <name>CAEEL_XYZ</name>
 117             </sequence>
 118          </clade>
 119          <clade>
 120             <name>node b</name>
 121             <events>
 122                <duplications>1</duplications>
 123                <confidence type="">80</confidence>
 124             </events>
 125             <binary_characters type="characters" present_count="2" lost_count="3" gained_count="1">
 126                <gained>
 127                   <bc>c</bc>
 128                </gained>
 129                <lost>
 130                   <bc>d</bc>
 131                   <bc>e</bc>
 132                   <bc>f</bc>
 133                </lost>
 134                <present>
 135                   <bc>a</bc>
 136                   <bc>b</bc>
 137                </present>
 138             </binary_characters>
 139             <clade>
 140                <name>node ba</name>
 141                <distribution>
 142                   <desc>Africa</desc>
 143                </distribution>
 144                <date unit="mya">
 145                   <desc> Silurian  </desc>
 146                   <value>435</value>
 147                   <minimum>416</minimum>
 148                   <maximum>443.7</maximum>
 149                </date>
 150             </clade>
 151             <clade>
 152                <name>node bb</name>
 153                <taxonomy>
 154                    <id provider="EOL">704294</id>
 155                    <code>NEMVE</code>
 156                    <scientific_name>Nematostella vectensis</scientific_name>
 157                    <authority>Stephenson, 1935</authority>
 158                    <common_name>starlet sea anemone</common_name>
 159                    <synonym>Nematostella vectensis Stephenson1935</synonym>
 160                    <synonym> See
 161                    Anemone
 162                    </synonym>
 163                    <synonym></synonym>
 164                    <rank>species</rank>
 165                    <uri desc="EOL" type="linkout">http://www.eol.org/pages/704294</uri>
 166                </taxonomy>
 167                <binary_characters type="domains">
 168                   <gained>
 169                      <bc>A</bc>
 170                      <bc>B</bc>
 171                      <bc>C</bc>
 172                   </gained>
 173                   <lost>
 174                      <bc>D</bc>
 175                   </lost>
 176                   <present>
 177                      <bc>X</bc>
 178                      <bc>M</bc>
 179                   </present>
 180                </binary_characters>
 181                <date>
 182                   <desc>Triassic  </desc>
 183                </date>
 184             </clade>
 185             <clade>
 186                <name>node bc</name>
 187                <sequence>
 188                   <name>bc seq</name>
 189                   <domain_architecture length="124">
 190                      <domain from="120" to="130" confidence="0.9" id=""> A </domain>
 191                      <domain from="21" to="44" confidence="2144" id="pfam"> B </domain>
 192                      <domain to="43" confidence="1.0E-89" from="34" id=""> C </domain>
 193                      <domain id="123" from="34" to="43" confidence="-1.3e-34"> D </domain>
 194                   </domain_architecture>
 195                </sequence>
 196                <date>
 197                    <value>433</value>
 198                </date>
 199             </clade>
 200          </clade>
 201       </clade>
 202    </phylogeny>
 203    <phylogeny rooted="true">
 204       <name>t4</name>
 205       <clade>
 206          <clade> </clade>
 207          <clade> </clade>
 208       </clade>
 209    </phylogeny>
 210 </phyloxml>