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          <taxonomy>
  53             <id provider="ncbi">1</id>
  54             <code>ECDYS</code>
  55             <scientific_name>ecdysozoa</scientific_name>
  56             <common_name>molting animals</common_name>
  57             <rank>phylum</rank>
  58             <uri>http://www.ecdysozoa.org/</uri>
  59          </taxonomy>
  60          <sequence type="protein">
  61             <symbol>BCL2L14</symbol>
  62             <accession source="UniProtKB">Q9BZR8</accession>
  63             <name>Apoptosis facilitator Bcl-2-like 14 protein</name>
  64             <location>12p13-p12</location>
  65             <mol_seq is_aligned="false">MCSTSGCDLEEIPLDDDDLNTIEFKILAYY</mol_seq>
  66             <uri type="source" desc="UniProt link">http://www.pir.uniprot.org/cgi-bin/upEntry?id=B2L14_HUMAN</uri>
  67             <annotation>
  68                <desc>intracellular organelle</desc>
  69             </annotation>
  70             <annotation ref="GO:0005829"/>
  71             <annotation ref="GO:0006915" source="UniProtKB" evidence="experimental" type="function">
  72                <desc>apoptosis</desc>
  73                <confidence type="ml">1</confidence>
  74                <property datatype="xsd:double" applies_to="annotation" ref="AFFY:expression" unit="AFFY:x">0.2</property>
  75                <property datatype="xsd:string" applies_to="annotation" ref="MED:disease">lymphoma</property>
  76             </annotation>
  77             <cross_references>
  78                <accession source="UNIPROTKB">383</accession>
  79                <accession source="PDB">1G5M</accession>
  80                <accession source="KEGG">hsa:596</accession>
  81                <accession source="PDB">2G5M</accession>
  82             </cross_references>
  83          </sequence>
  84          <events>
  85             <type>mixed</type>
  86             <duplications>1</duplications>
  87             <confidence type="bs">99</confidence>
  88          </events>
  89          <distribution>
  90             <desc>irgendwo</desc>
  91             <point geodetic_datum="WGS84" alt_unit="m">
  92                <lat>35.9296730123456789</lat>
  93                <long>-78.9482370123456789</long>
  94                <alt>0</alt>
  95             </point>
  96          </distribution>
  97          <reference doi="10.1038/387489a0">
  98             <desc>
  99                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.
 100             </desc>
 101          </reference>
 102          <property ref="F:foo" datatype="xsd:int" applies_to="clade">bar</property>
 103          <clade>
 104             <name>node a</name>
 105             <branch_length>0.2</branch_length>
 106             <color>
 107                <red>12</red>
 108                <green>14</green>
 109                <blue>16</blue>
 110             </color>
 111             <taxonomy>
 112                <id provider="ncbi">123</id>
 113                <code>CAEEL</code>
 114                <scientific_name>C elegans</scientific_name>
 115                <common_name>elegant nematode worm</common_name>
 116                <rank>species</rank>
 117                <uri>http://www.wormbase.org/</uri>
 118             </taxonomy>
 119             <sequence>
 120                <name>CAEEL_XYZ</name>
 121             </sequence>
 122             <events>
 123                 <duplications>1</duplications>
 124             </events>
 125          </clade>
 126          <clade>
 127             <name>node b</name>
 128             <events>
 129                <duplications>1</duplications>
 130                <confidence type="">80</confidence>
 131             </events>
 132             <binary_characters type="characters" present_count="2" lost_count="3" gained_count="1">
 133                <gained>
 134                   <bc>c</bc>
 135                </gained>
 136                <lost>
 137                   <bc>d</bc>
 138                   <bc>e</bc>
 139                   <bc>f</bc>
 140                </lost>
 141                <present>
 142                   <bc>a</bc>
 143                   <bc>b</bc>
 144                </present>
 145             </binary_characters>
 146             <clade>
 147                <name>node ba</name>
 148                <distribution>
 149                   <desc>Africa</desc>
 150                </distribution>
 151                <date unit="mya">
 152                   <desc> Silurian  </desc>
 153                   <value>435</value>
 154                   <minimum>416</minimum>
 155                   <maximum>443.7</maximum>
 156                </date>
 157             </clade>
 158             <clade>
 159                <name>node bb</name>
 160                <taxonomy>
 161                    <id provider="EOL">704294</id>
 162                    <code>NEMVE</code>
 163                    <scientific_name>Nematostella vectensis</scientific_name>
 164                    <authority>Stephenson, 1935</authority>
 165                    <common_name>starlet sea anemone</common_name>
 166                    <synonym>Nematostella vectensis Stephenson1935</synonym>
 167                    <synonym> See
 168                    Anemone
 169                    </synonym>
 170                    <synonym></synonym>
 171                    <rank>species</rank>
 172                    <uri desc="EOL" type="linkout">http://www.eol.org/pages/704294</uri>
 173                </taxonomy>
 174                <binary_characters type="domains">
 175                   <gained>
 176                      <bc>A</bc>
 177                      <bc>B</bc>
 178                      <bc>C</bc>
 179                   </gained>
 180                   <lost>
 181                      <bc>D</bc>
 182                   </lost>
 183                   <present>
 184                      <bc>X</bc>
 185                      <bc>M</bc>
 186                   </present>
 187                </binary_characters>
 188                <date>
 189                   <desc>Triassic  </desc>
 190                </date>
 191             </clade>
 192             <clade>
 193                <name>node bc</name>
 194                <sequence>
 195                   <name>bc seq</name>
 196                   <domain_architecture length="124">
 197                      <domain from="120" to="130" confidence="0.9" id=""> A </domain>
 198                      <domain from="21" to="44" confidence="0" id="pfam"> B </domain>
 199                      <domain to="43" confidence="1.0E-89" from="34" id=""> C </domain>
 200                      <domain id="123" from="34" to="43" confidence="1.3e-34"> D </domain>
 201                   </domain_architecture>
 202                </sequence>
 203                <events>
 204                    <speciations>1</speciations>
 205                </events>
 206                <date>
 207                    <value>433</value>
 208                </date>
 209             </clade>
 210          </clade>
 211       </clade>
 212    </phylogeny>
 213    <phylogeny rooted="true">
 214       <name>t4</name>
 215       <clade>
 216          <clade> </clade>
 217          <clade> </clade>
 218       </clade>
 219    </phylogeny>
 220 </phyloxml>