forester/test_data/phyloxml_test_1.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/1.20/phyloxml.xsd"
   4           xmlns="http://www.phyloxml.org">
   5     <phylogeny branch_length_unit="c" rooted="true" rerootable="true" type="gene_tree">
   6         <name>tree 0</name>
   7         <id provider="treebank">1-1</id>
   8         <description>test phylogeny</description>
   9         <date>2002-05-30T09:00:00</date>
  10         <confidence type="ml">0.999</confidence>
  11         <confidence type="pp">0.955</confidence>
  12         <clade branch_length="0.1" id_source="id111" collapse="true">
  13             <name>root node</name>
  14             <confidence type="bootstrap">90</confidence>
  15             <confidence type="ml" stddev="1.1E-10">1e-3</confidence>
  16             <confidence type="decay">2</confidence>
  17             <width>10.5</width>
  18             <color>
  19                 <red>2</red>
  20                 <green>22</green>
  21                 <blue>33</blue>
  22                 <alpha>123</alpha>
  23             </color>
  24             <taxonomy id_source="qwerty1">
  25                 <id provider="ncbi">1</id>
  26                 <code>ECDYS</code>
  27                 <scientific_name>ecdysozoa</scientific_name>
  28                 <authority>authority, 1999</authority>
  29                 <common_name>molting animals</common_name>
  30                 <synonym>Ecdy</synonym>
  31                 <synonym>The Ecdysozoa</synonym>
  32                 <rank>phylum</rank>
  33                 <uri type="img">http://www.molting.org/m.jpg</uri>
  34                 <uri type="source" desc="original source">http://www.ecdysozoa.org/</uri>
  35             </taxonomy>
  36             <taxonomy>
  37                 <id provider="ncbi">123</id>
  38                 <synonym>Æ Ä ä, ö and ü>– —</synonym>
  39                 <synonym>한글</synonym>
  40                 <synonym>日本語ひらがなカタカナ</synonym>
  41                 <synonym>русский алфавит</synonym>
  42                 <synonym>繁體字</synonym>
  43                 <synonym>ภาษาไทย</synonym>
  44                 <synonym>Tiếng Việt</synonym>
  45             </taxonomy>
  46             <sequence type="protein" id_source="idsource">
  47                 <symbol>BCL2L14</symbol>
  48                 <accession source="UniProtKB" comment="outdated">Q9BZR8</accession>
  49                 <name>Apoptosis facilitator Bcl-2-like 14 protein</name>
  50                 <gene_name>bcl2l14</gene_name>
  51                 <location>12p13-p12</location>
  52                 <mol_seq is_aligned="true">MCSTSGCDLEEIPLDDDDLNTIEFKILAYY</mol_seq>
  53                 <uri type="source" desc="UniProt link">http://www.pir.uniprot.org/cgi-bin/upEntry?id=B2L14_HUMAN</uri>
  54                 <annotation>
  55                     <desc>intracellular organelle</desc>
  56                 </annotation>
  57                 <annotation ref="GO:0005829"/>
  58                 <annotation ref="GO:0006915" source="UniProtKB" evidence="experimental" type="function">
  59                     <desc>apoptosis</desc>
  60                     <confidence type="ml" stddev="0.3">1</confidence>
  61                     <property datatype="xsd:double" applies_to="annotation" ref="AFFY:expression" unit="AFFY:x">0.2
  62                     </property>
  63                     <property datatype="xsd:string" applies_to="annotation" ref="MED:disease">lymphoma</property>
  64                     <uri type="source" desc="google">http://www.google.com</uri>
  65                     <uri type="source2" desc="bing">http://www.bing.com</uri>
  66                 </annotation>
  67                 <cross_references>
  68                     <accession source="UNIPROTKB">383</accession>
  69                     <accession source="PDB">1G5M</accession>
  70                     <accession source="KEGG">hsa:596</accession>
  71                     <accession source="PDB" comment="?">2G5M</accession>
  72                 </cross_references>
  73             </sequence>
  74             <sequence type="protein">
  75                 <symbol>BCL2</symbol>
  76             </sequence>
  77             <events>
  78                 <type>mixed</type>
  79                 <duplications>1</duplications>
  80                 <confidence type="bs">99</confidence>
  81             </events>
  82             <distribution>
  83                 <desc>irgendwo</desc>
  84                 <point geodetic_datum="WGS84" alt_unit="m">
  85                     <lat>35.9296730123456789</lat>
  86                     <long>-78.9482370123456789</long>
  87                     <alt>1303</alt>
  88                 </point>
  89                 <point geodetic_datum="WGS84" alt_unit="m">
  90                     <lat>129.549495485834893</lat>
  91                     <long>-78.00000000000000</long>
  92                     <alt>1400</alt>
  93                 </point>
  94             </distribution>
  95             <distribution>
  96                 <desc>anderswo</desc>
  97             </distribution>
  98             <date unit="MYA">
  99                 <desc>Silurian</desc>
 100             </date>
 101             <reference doi="10.1038/387489a0">
 102                 <desc>
 103                     Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, &amp;
 104                     J. A. Lake (1997). "Evidence for a clade of nematodes, arthropods and other moulting animals".
 105                     Nature 387 (6632): 489–493.
 106                 </desc>
 107             </reference>
 108             <reference doi="10.1036/59494">
 109             </reference>
 110             <property ref="F:foo" datatype="xsd:int" applies_to="clade">2</property>
 111             <property ref="F:bar" datatype="xsd:int" applies_to="clade">33</property>
 112             <clade>
 113                 <name>node a</name>
 114                 <branch_length>0.2</branch_length>
 115                 <color>
 116                     <red>12</red>
 117                     <green>14</green>
 118                     <blue>16</blue>
 119                 </color>
 120                 <taxonomy>
 121                     <id provider="ncbi">123</id>
 122                     <code>CAEEL</code>
 123                     <scientific_name>C elegans</scientific_name>
 124                     <common_name>elegant nematode worm</common_name>
 125                     <rank>species</rank>
 126                     <uri>http://www.wormbase.org/</uri>
 127                 </taxonomy>
 128                 <sequence id_source="xyz">
 129                     <name>CAEEL_XYZ</name>
 130                 </sequence>
 131                 <sequence id_source="abc">
 132                     <name>CAEEL_ABC</name>
 133                 </sequence>
 134                 <events>
 135                     <type>other</type>
 136                     <duplications>58</duplications>
 137                     <speciations>59403</speciations>
 138                     <losses>58485</losses>
 139                     <confidence type="p">0.9901</confidence>
 140                 </events>
 141             </clade>
 142             <clade>
 143                 <name>node b</name>
 144                 <events>
 145                     <duplications>1</duplications>
 146                     <confidence type="">80</confidence>
 147                 </events>
 148                 <binary_characters type="characters" present_count="2" lost_count="3" gained_count="1">
 149                     <gained>
 150                         <bc>c</bc>
 151                     </gained>
 152                     <lost>
 153                         <bc>d</bc>
 154                         <bc>e</bc>
 155                         <bc>f</bc>
 156                     </lost>
 157                     <present>
 158                         <bc>a</bc>
 159                         <bc>b</bc>
 160                     </present>
 161                 </binary_characters>
 162                 <clade>
 163                     <name>node ba</name>
 164                     <distribution>
 165                         <desc>Africa</desc>
 166                     </distribution>
 167                     <date unit="mya">
 168                         <desc>Silurian</desc>
 169                         <value>435</value>
 170                         <minimum>416</minimum>
 171                         <maximum>443.7</maximum>
 172                     </date>
 173                 </clade>
 174                 <clade collapse="false">
 175                     <name>node bb</name>
 176                     <taxonomy>
 177                         <id provider="EOL">704294</id>
 178                         <code>NEMVE</code>
 179                         <scientific_name>Nematostella vectensis</scientific_name>
 180                         <authority>Stephenson, 1935</authority>
 181                         <common_name>starlet sea anemone</common_name>
 182                         <synonym>Nematostella vectensis Stephenson1935</synonym>
 183                         <synonym>See
 184                             Anemone
 185                         </synonym>
 186                         <synonym></synonym>
 187                         <rank>species</rank>
 188                         <uri desc="EOL" type="linkout">http://www.eol.org/pages/704294</uri>
 189                     </taxonomy>
 190                     <binary_characters type="domains">
 191                         <gained>
 192                             <bc>A</bc>
 193                             <bc>B</bc>
 194                             <bc>C</bc>
 195                         </gained>
 196                         <lost>
 197                             <bc>D</bc>
 198                         </lost>
 199                         <present>
 200                             <bc>X</bc>
 201                             <bc>M</bc>
 202                         </present>
 203                     </binary_characters>
 204                     <date>
 205                         <desc>Triassic</desc>
 206                     </date>
 207                 </clade>
 208                 <clade>
 209                     <name>node bc</name>
 210                     <sequence>
 211                         <name>bc seq</name>
 212                         <domain_architecture length="124">
 213                             <domain from="120" to="130" confidence="0.9">A</domain>
 214                             <domain from="21" to="44" confidence="0" id="pfam">B</domain>
 215                             <domain to="43" confidence="1.0E-89" from="34" id="">C</domain>
 216                             <domain id="123" from="34" to="43" confidence="1.3e-34">D</domain>
 217                         </domain_architecture>
 218                     </sequence>
 219                     <events>
 220                         <speciations>1</speciations>
 221                     </events>
 222                     <date>
 223                         <value>433</value>
 224                     </date>
 225                 </clade>
 226             </clade>
 227         </clade>
 228         <sequence_relation id_ref_0="abc" id_ref_1="xyz" distance="0.34" type="ultra_paralogy">
 229             <confidence type="pp" stddev="1.1E-10">1e-3</confidence>
 230         </sequence_relation>
 231         <sequence_relation id_ref_0="xyz" id_ref_1="abc" distance="2" type="unknown">
 232             <confidence type="pp" stddev="1.245836">99.0000001</confidence>
 233         </sequence_relation>
 234         <property datatype="xsd:double" applies_to="phylogeny" ref="TIME:time" unit="TIME:MYA">2</property>
 235         <property datatype="xsd:string" applies_to="phylogeny" ref="GO:function">cell death</property>
 236     </phylogeny>
 237     <phylogeny rooted="true" rerootable="true">
 238         <name>phylogeny2</name>
 239         <clade>
 240             <clade>
 241                 <name>A</name>
 242             </clade>
 243             <clade>
 244                 <name>B</name>
 245             </clade>
 246         </clade>
 247     </phylogeny>
 248     <phylogeny rooted="true" rerootable="true">
 249         <name>phylogeny3</name>
 250         <clade>
 251             <clade id_source="i0">
 252                 <name>C</name>
 253             </clade>
 254             <clade id_source="i1">
 255                 <name>D</name>
 256             </clade>
 257         </clade>
 258         <clade_relation id_ref_0="i0" id_ref_1="i1" distance="0.34" type="parent">
 259             <confidence type="pp" stddev="1.1E-10">1e-3</confidence>
 260         </clade_relation>
 261         <clade_relation id_ref_0="i1" id_ref_1="i0" distance="2" type="child">
 262             <confidence type="pp" stddev="1.1E-20">1e-4</confidence>
 263         </clade_relation>
 264     </phylogeny>
 265 </phyloxml>