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