t/data/phyloxml_examples.xml

   1 <?xml version="1.0" encoding="UTF-8"?>\r
   2 <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\r
   3    xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd"\r
   4    xmlns="http://www.phyloxml.org">\r
   5    <phylogeny rooted="true">\r
   6       <name>example from Prof. Joe Felsenstein's book "Inferring Phylogenies"</name>\r
   7       <description>phyloXML allows to use either a "branch_length" attribute or element to indicate branch lengths.</description>\r
   8       <clade>\r
   9          <clade branch_length="0.06">\r
  10             <clade branch_length="0.102">\r
  11                <name>A</name>\r
  12             </clade>\r
  13             <clade branch_length="0.23">\r
  14                <name>B</name>\r
  15             </clade>\r
  16          </clade>\r
  17          <clade branch_length="0.4">\r
  18             <name>C</name>\r
  19          </clade>\r
  20       </clade>\r
  21    </phylogeny>\r
  22    <phylogeny rooted="true">\r
  23       <name>example from Prof. Joe Felsenstein's book "Inferring Phylogenies"</name>\r
  24       <description>phyloXML allows to use either a "branch_length" attribute or element to indicate branch lengths.</description>\r
  25       <clade>\r
  26          <clade>\r
  27             <branch_length>0.06</branch_length>\r
  28             <clade>\r
  29                <name>A</name>\r
  30                <branch_length>0.102</branch_length>\r
  31             </clade>\r
  32             <clade>\r
  33                <name>B</name>\r
  34                <branch_length>0.23</branch_length>\r
  35             </clade>\r
  36          </clade>\r
  37          <clade>\r
  38             <name>C</name>\r
  39             <branch_length>0.4</branch_length>\r
  40          </clade>\r
  41       </clade>\r
  42    </phylogeny>\r
  43    <phylogeny rooted="true">\r
  44       <name>same example, with support of type "bootstrap"</name>\r
  45       <clade>\r
  46          <clade branch_length="0.06">\r
  47             <name>AB</name>\r
  48             <confidence type="bootstrap">89</confidence>\r
  49             <clade branch_length="0.102">\r
  50                <name>A</name>\r
  51             </clade>\r
  52             <clade branch_length="0.23">\r
  53                <name>B</name>\r
  54             </clade>\r
  55          </clade>\r
  56          <clade branch_length="0.4">\r
  57             <name>C</name>\r
  58          </clade>\r
  59       </clade>\r
  60    </phylogeny>\r
  61    <phylogeny rooted="true">\r
  62       <name>same example, with species and sequence</name>\r
  63       <clade>\r
  64          <clade>\r
  65             <name>AB</name>\r
  66             <clade>\r
  67                <name>A</name>\r
  68                <taxonomy>\r
  69                   <scientific_name>E. coli</scientific_name>\r
  70                </taxonomy>\r
  71                <sequence>\r
  72                   <annotation>\r
  73                      <desc>alcohol dehydrogenase</desc>\r
  74                      <confidence type="probability">0.99</confidence>\r
  75                   </annotation>\r
  76                </sequence>\r
  77             </clade>\r
  78             <clade>\r
  79                <name>B</name>\r
  80                <taxonomy>\r
  81                   <scientific_name>B. subtilis</scientific_name>\r
  82                </taxonomy>\r
  83                <sequence>\r
  84                   <annotation>\r
  85                      <desc>alcohol dehydrogenase</desc>\r
  86                      <confidence type="probability">0.91</confidence>\r
  87                   </annotation>\r
  88                </sequence>\r
  89             </clade>\r
  90          </clade>\r
  91          <clade>\r
  92             <name>C</name>\r
  93             <taxonomy>\r
  94                <scientific_name>C. elegans</scientific_name>\r
  95             </taxonomy>\r
  96             <sequence>\r
  97                <annotation>\r
  98                   <desc>alcohol dehydrogenase</desc>\r
  99                   <confidence type="probability">0.67</confidence>\r
 100                </annotation>\r
 101             </sequence>\r
 102          </clade>\r
 103       </clade>\r
 104    </phylogeny>\r
 105    <phylogeny rooted="true">\r
 106       <name>same example, with gene duplication information and sequence relationships</name>\r
 107       <clade>\r
 108          <events>\r
 109             <speciations>1</speciations>\r
 110          </events>\r
 111          <clade>\r
 112             <events>\r
 113                <duplications>1</duplications>\r
 114             </events>\r
 115             <clade>\r
 116                <taxonomy>\r
 117                   <scientific_name>Bacillus subtilis</scientific_name>\r
 118                </taxonomy>\r
 119                <sequence id_source="x">\r
 120                   <symbol>adhB</symbol>\r
 121                   <accession source="ncbi">AAB80874</accession>\r
 122                   <name>alcohol dehydrogenase</name>\r
 123                </sequence>\r
 124             </clade>\r
 125             <clade>\r
 126                <taxonomy>\r
 127                   <scientific_name>Bacillus subtilis</scientific_name>\r
 128                </taxonomy>\r
 129                <sequence id_source="y">\r
 130                   <symbol>gbsB</symbol>\r
 131                   <accession source="ncbi">CAB15083</accession>\r
 132                   <name>alcohol dehydrogenase</name>\r
 133                </sequence>\r
 134             </clade>\r
 135          </clade>\r
 136          <clade>\r
 137             <taxonomy>\r
 138                <scientific_name>Caenorhabditis elegans</scientific_name>\r
 139             </taxonomy>\r
 140             <sequence id_source="z">\r
 141                <symbol>ADHX</symbol>\r
 142                <accession source="ncbi">Q17335</accession>\r
 143                <name>alcohol dehydrogenase</name>\r
 144                <annotation ref="InterPro:IPR002085"/>\r
 145             </sequence>\r
 146          </clade>\r
 147       </clade>\r
 148       <sequence_relation id_ref_0="x" id_ref_1="y" type="paralogy"/>\r
 149       <sequence_relation id_ref_0="x" id_ref_1="z" type="orthology"/>\r
 150       <sequence_relation id_ref_0="y" id_ref_1="z" type="orthology"/>\r
 151    </phylogeny>\r
 152    <phylogeny rooted="true">\r
 153       <name>similar example, with more detailed sequence data</name>\r
 154       <clade>\r
 155          <clade>\r
 156             <clade>\r
 157                <taxonomy>\r
 158                   <id provider="NCBI">6645</id>\r
 159                   <code>OCTVU</code>\r
 160                   <scientific_name>Octopus vulgaris</scientific_name>\r
 161                </taxonomy>\r
 162                <sequence>\r
 163                   <symbol>ADHX</symbol>\r
 164                   <accession source="UniProtKB">P81431</accession>\r
 165                   <name>Alcohol dehydrogenase class-3</name>\r
 166                   <mol_seq>TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD</mol_seq>\r
 167                   <annotation ref="EC:1.1.1.1"/>\r
 168                   <annotation ref="GO:0004022"/>\r
 169                </sequence>\r
 170             </clade>\r
 171             <clade>\r
 172                <taxonomy>\r
 173                   <id provider="NCBI">44689</id>\r
 174                   <code>DICDI</code>\r
 175                   <scientific_name>Dictyostelium discoideum</scientific_name>\r
 176                </taxonomy>\r
 177                <sequence>\r
 178                   <symbol>RT4I1</symbol>\r
 179                   <accession source="UniProtKB">Q54II4</accession>\r
 180                   <name>Reticulon-4-interacting protein 1 homolog, mitochondrial precursor</name>\r
 181                   <mol_seq>MKGILLNGYGESLDLLEYKTDLPVPKPIKSQVLIKIHSTSINPLDNVMRK</mol_seq>\r
 182                   <annotation ref="GO:0008270"/>\r
 183                   <annotation ref="GO:0016491"/>\r
 184                </sequence>\r
 185             </clade>\r
 186          </clade>\r
 187          <clade>\r
 188             <taxonomy>\r
 189                <id provider="NCBI">1488</id>\r
 190                <code>CLOAB</code>\r
 191                <scientific_name>Clostridium acetobutylicum</scientific_name>\r
 192             </taxonomy>\r
 193             <sequence>\r
 194                <symbol>ADHB</symbol>\r
 195                <accession source="UniProtKB">Q04945</accession>\r
 196                <name>NADH-dependent butanol dehydrogenase B</name>\r
 197                <mol_seq>MVDFEYSIPTRIFFGKDKINVLGRELKKYGSKVLIVYGGGSIKRNGIYDK</mol_seq>\r
 198                <annotation ref="GO:0046872"/>\r
 199                <annotation ref="KEGG:Tetrachloroethene degradation"/>\r
 200             </sequence>\r
 201          </clade>\r
 202       </clade>\r
 203    </phylogeny>\r
 204    <phylogeny rooted="false">\r
 205       <name>network, node B is connected to TWO nodes: AB and C</name>\r
 206       <clade>\r
 207          <clade id_source="ab" branch_length="0.06">\r
 208             <name>AB</name>\r
 209             <clade id_source="a" branch_length="0.102">\r
 210                <name>A</name>\r
 211             </clade>\r
 212             <clade id_source="b" branch_length="0.23">\r
 213                <name>B</name>\r
 214             </clade>\r
 215          </clade>\r
 216          <clade id_source="c" branch_length="0.4">\r
 217             <name>C</name>\r
 218          </clade>\r
 219       </clade>\r
 220       <clade_relation id_ref_0="b" id_ref_1="c" type="network_connection"/>\r
 221    </phylogeny>\r
 222    <phylogeny rooted="true">\r
 223       <name>same example, using property elements to indicate a "depth" value for marine organisms</name>\r
 224       <clade>\r
 225          <clade>\r
 226             <name>AB</name>\r
 227             <clade>\r
 228                <name>A</name>\r
 229                <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 1200 </property>\r
 230             </clade>\r
 231             <clade>\r
 232                <name>B</name>\r
 233                <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 2300 </property>\r
 234             </clade>\r
 235          </clade>\r
 236          <clade>\r
 237             <name>C</name>\r
 238             <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 200 </property>\r
 239          </clade>\r
 240       </clade>\r
 241    </phylogeny>\r
 242    <phylogeny rooted="true">\r
 243       <name>same example, using property elements to indicate a "depth" value for marine organisms by using id refs in\r
 244          order to have property elements outside of the tree topology</name>\r
 245       <clade>\r
 246          <clade>\r
 247             <name>AB</name>\r
 248             <clade id_source="id_a">\r
 249                <name>A</name>\r
 250             </clade>\r
 251             <clade id_source="id_b">\r
 252                <name>B</name>\r
 253             </clade>\r
 254          </clade>\r
 255          <clade id_source="id_c">\r
 256             <name>C</name>\r
 257          </clade>\r
 258       </clade>\r
 259       <property id_ref="id_a" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 1200 </property>\r
 260       <property id_ref="id_b" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 2300 </property>\r
 261       <property id_ref="id_c" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 200 </property>\r
 262    </phylogeny>\r
 263    <phylogeny rooted="true">\r
 264       <name>monitor lizards</name>\r
 265       <description>a pylogeny of some monitor lizards</description>\r
 266       <clade>\r
 267          <taxonomy>\r
 268             <id provider="NCBI">8556</id>\r
 269             <scientific_name>Varanus</scientific_name>\r
 270             <rank>genus</rank>\r
 271             <uri desc="EMBL REPTILE DATABASE">http://www.embl-heidelberg.de/~uetz/families/Varanidae.html</uri>\r
 272          </taxonomy>\r
 273          <clade>\r
 274             <taxonomy>\r
 275                <id provider="NCBI">62046</id>\r
 276                <scientific_name>Varanus niloticus</scientific_name>\r
 277                <common_name>Nile monitor</common_name>\r
 278                <rank>species</rank>\r
 279             </taxonomy>\r
 280             <distribution>\r
 281                <desc>Africa</desc>\r
 282             </distribution>\r
 283          </clade>\r
 284          <clade>\r
 285             <taxonomy>\r
 286                <scientific_name>Odatria</scientific_name>\r
 287                <rank>subgenus</rank>\r
 288             </taxonomy>\r
 289             <clade>\r
 290                <taxonomy>\r
 291                   <id provider="NCBI">169855</id>\r
 292                   <scientific_name>Varanus storri</scientific_name>\r
 293                   <common_name>Storr's monitor</common_name>\r
 294                   <rank>species</rank>\r
 295                </taxonomy>\r
 296                <distribution>\r
 297                   <desc>Australia</desc>\r
 298                </distribution>\r
 299             </clade>\r
 300             <clade>\r
 301                <taxonomy>\r
 302                   <id provider="NCBI">62053</id>\r
 303                   <scientific_name>Varanus timorensis</scientific_name>\r
 304                   <common_name>Timor monitor</common_name>\r
 305                   <rank>species</rank>\r
 306                </taxonomy>\r
 307                <distribution>\r
 308                   <desc>Asia</desc>\r
 309                </distribution>\r
 310             </clade>\r
 311          </clade>\r
 312       </clade>\r
 313    </phylogeny>\r
 314    <phylogeny rooted="true">\r
 315       <name>A tree with phylogeographic information</name>\r
 316       <clade>\r
 317          <clade>\r
 318             <clade>\r
 319                <name>A</name>\r
 320                <distribution>\r
 321                   <desc>Hirschweg, Winterthur, Switzerland</desc>\r
 322                   <point geodetic_datum="WGS84">\r
 323                      <lat>47.481277</lat>\r
 324                      <long>8.769303</long>\r
 325                      <alt>472</alt>\r
 326                   </point>\r
 327                </distribution>\r
 328             </clade>\r
 329             <clade>\r
 330                <name>B</name>\r
 331                <distribution>\r
 332                   <desc>Nagoya, Aichi, Japan</desc>\r
 333                   <point geodetic_datum="WGS84">\r
 334                      <lat>35.155904</lat>\r
 335                      <long>136.915863</long>\r
 336                      <alt>10</alt>\r
 337                   </point>\r
 338                </distribution>\r
 339             </clade>\r
 340             <clade>\r
 341                <name>C</name>\r
 342                <distribution>\r
 343                   <desc>ETH Zürich</desc>\r
 344                   <point geodetic_datum="WGS84">\r
 345                      <lat>47.376334</lat>\r
 346                      <long>8.548108</long>\r
 347                      <alt>452</alt>\r
 348                   </point>\r
 349                </distribution>\r
 350             </clade>\r
 351          </clade>\r
 352          <clade>\r
 353             <name>D</name>\r
 354             <distribution>\r
 355                <desc>San Diego</desc>\r
 356                <point geodetic_datum="WGS84">\r
 357                   <lat>32.880933</lat>\r
 358                   <long>-117.217543</long>\r
 359                   <alt>104</alt>\r
 360                </point>\r
 361             </distribution>\r
 362          </clade>\r
 363       </clade>\r
 364    </phylogeny>\r
 365    <phylogeny rooted="true">\r
 366       <name>A tree with date information</name>\r
 367       <clade>\r
 368          <clade>\r
 369             <clade>\r
 370                <name>A</name>\r
 371                <date unit="mya">\r
 372                   <desc>Silurian</desc>\r
 373                   <value>425</value>\r
 374                   <minimum>416.0</minimum>\r
 375                   <maximum>443.7</maximum>\r
 376                </date>\r
 377             </clade>\r
 378             <clade>\r
 379                <name>B</name>\r
 380                <date unit="mya">\r
 381                   <desc>Devonian</desc>\r
 382                   <value>320</value>\r
 383                </date>\r
 384             </clade>\r
 385          </clade>\r
 386          <clade>\r
 387             <name>C</name>\r
 388             <date unit="mya">\r
 389                <desc>Ediacaran</desc>\r
 390                <value>600</value>\r
 391             </date>\r
 392          </clade>\r
 393       </clade>\r
 394    </phylogeny>\r
 395    <phylogeny rooted="true">\r
 396       <name>Using another XML language to store an alignment</name>\r
 397       <clade>\r
 398          <clade>\r
 399             <clade>\r
 400                <name>A</name>\r
 401             </clade>\r
 402             <clade>\r
 403                <name>B</name>\r
 404             </clade>\r
 405          </clade>\r
 406          <clade>\r
 407             <name>C</name>\r
 408          </clade>\r
 409       </clade>\r
 410    </phylogeny>\r
 411    <align:alignment xmlns:align="http://example.org/align">\r
 412       <seq name="A">acgtcgcggcccgtggaagtcctctcct</seq>\r
 413       <seq name="B">aggtcgcggcctgtggaagtcctctcct</seq>\r
 414       <seq name="C">taaatcgc--cccgtgg-agtccc-cct</seq>\r
 415    </align:alignment>\r
 416 </phyloxml>\r