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<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.phyloxml.org" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd">
   <phylogeny rooted="true">
      <name>example from Prof. Joe Felsenstein's book "Inferring Phylogenies"</name>
      <description>phyloXML allows to use either a "branch_length" attribute or element to indicate branch lengths.</description>
      <clade>
         <clade branch_length="0.06">
            <clade branch_length="0.102">
               <name>A</name>
10              </clade>
11              <clade branch_length="0.23">
12                 <name>B</name>
13              </clade>
14           </clade>
15           <clade branch_length="0.4">
16              <name>C</name>
17           </clade>
18        </clade>
19     </phylogeny>
20 
21     <phylogeny rooted="true">
22        <name>example from Prof. Joe Felsenstein's book "Inferring Phylogenies"</name>
23        <description>phyloXML allows to use either a "branch_length" attribute or element to indicate branch lengths.</description>
24        <clade>
25           <clade>
26              <branch_length>0.06</branch_length>
27              <clade>
28                 <name>A</name>
29                 <branch_length>0.102</branch_length>
30              </clade>
31              <clade>
32                 <name>B</name>
33                 <branch_length>0.23</branch_length>
34              </clade>
35           </clade>
36           <clade>
37              <name>C</name>
38              <branch_length>0.4</branch_length>
39           </clade>
40        </clade>
41     </phylogeny>
42 
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 
62     <phylogeny rooted="true">
63        <name>same example, with species and sequence</name>
64        <clade>
65           <clade>
66              <name>AB</name>
67              <clade>
68                 <name>A</name>
69                 <taxonomy>
70                    <scientific_name>E. coli</scientific_name>
71                 </taxonomy>
72                 <sequence>
73                    <annotation>
74                       <desc>alcohol dehydrogenase</desc>
75                       <confidence type="probability">0.99</confidence>
76                    </annotation>
77                 </sequence>
78              </clade>
79              <clade>
80                 <name>B</name>
81                 <taxonomy>
82                    <scientific_name>B. subtilis</scientific_name>
83                 </taxonomy>
84                 <sequence>
85                    <annotation>
86                       <desc>alcohol dehydrogenase</desc>
87                       <confidence type="probability">0.91</confidence>
88                    </annotation>
89                 </sequence>
90              </clade>
91           </clade>
92           <clade>
93              <name>C</name>
94              <taxonomy>
95                 <scientific_name>C. elegans</scientific_name>
96              </taxonomy>
97              <sequence>
98                 <annotation>
99                    <desc>alcohol dehydrogenase</desc>
100                    <confidence type="probability">0.67</confidence>
101                 </annotation>
102              </sequence>
103           </clade>
104        </clade>
105     </phylogeny>
106 
107     <phylogeny rooted="true">
108        <name>same example, with gene duplication information and sequence relationships</name>
109        <clade>
110           <events>
111              <speciations>1</speciations>
112           </events>
113           <clade>
114              <events>
115                 <duplications>1</duplications>
116              </events>
117              <clade>
118                 <taxonomy>
119                    <scientific_name>Bacillus subtilis</scientific_name>
120                 </taxonomy>
121                 <sequence id_source="x">
122                    <symbol>adhB</symbol>
123                    <accession source="ncbi">AAB80874</accession>
124                    <name>alcohol dehydrogenase</name>
125                 </sequence>
126              </clade>
127              <clade>
128                 <taxonomy>
129                    <scientific_name>Bacillus subtilis</scientific_name>
130                 </taxonomy>
131                 <sequence id_source="y">
132                    <symbol>gbsB</symbol>
133                    <accession source="ncbi">CAB15083</accession>
134                    <name>alcohol dehydrogenase</name>
135                 </sequence>
136              </clade>
137           </clade>
138           <clade>
139              <taxonomy>
140                 <scientific_name>Caenorhabditis elegans</scientific_name>
141              </taxonomy>
142              <sequence id_source="z">
143                 <symbol>ADHX</symbol>
144                 <accession source="ncbi">Q17335</accession>
145                 <name>alcohol dehydrogenase</name>
146                 <annotation ref="InterPro:IPR002085" />
147              </sequence>
148           </clade>
149        </clade>
150        <sequence_relation id_ref_0="x" id_ref_1="y" type="paralogy" />
151        <sequence_relation id_ref_0="x" id_ref_1="z" type="orthology" />
152        <sequence_relation id_ref_0="y" id_ref_1="z" type="orthology" />
153     </phylogeny>
154 
155     <phylogeny rooted="true">
156        <name>similar example, with more detailed sequence data</name>
157        <clade>
158           <clade>
159              <clade>
160                 <taxonomy>
161                    <id provider="NCBI">6645</id>
162                    <code>OCTVU</code>
163                    <scientific_name>Octopus vulgaris</scientific_name>
164                 </taxonomy>
165                 <sequence>
166                    <symbol>ADHX</symbol>
167                    <accession source="UniProtKB">P81431</accession>
168                    <name>Alcohol dehydrogenase class-3</name>
169                    <mol_seq>TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD</mol_seq>
170                    <annotation ref="EC:1.1.1.1" />
171                    <annotation ref="GO:0004022" />
172                 </sequence>
173              </clade>
174              <clade>
175                 <taxonomy>
176                    <id provider="NCBI">44689</id>
177                    <code>DICDI</code>
178                    <scientific_name>Dictyostelium discoideum</scientific_name>
179                 </taxonomy>
180                 <sequence>
181                    <symbol>RT4I1</symbol>
182                    <accession source="UniProtKB">Q54II4</accession>
183                    <name>Reticulon-4-interacting protein 1 homolog, mitochondrial precursor</name>
184                    <mol_seq>MKGILLNGYGESLDLLEYKTDLPVPKPIKSQVLIKIHSTSINPLDNVMRK</mol_seq>
185                    <annotation ref="GO:0008270" />
186                    <annotation ref="GO:0016491" />
187                 </sequence>
188              </clade>
189           </clade>
190           <clade>
191              <taxonomy>
192                 <id provider="NCBI">1488</id>
193                 <code>CLOAB</code>
194                 <scientific_name>Clostridium acetobutylicum</scientific_name>
195              </taxonomy>
196              <sequence>
197                 <symbol>ADHB</symbol>
198                 <accession source="UniProtKB">Q04945</accession>
199                 <name>NADH-dependent butanol dehydrogenase B</name>
200                 <mol_seq>MVDFEYSIPTRIFFGKDKINVLGRELKKYGSKVLIVYGGGSIKRNGIYDK</mol_seq>
201                 <annotation ref="GO:0046872" />
202                 <annotation ref="KEGG:Tetrachloroethene degradation" />
203              </sequence>
204           </clade>
205        </clade>
206     </phylogeny>
207 
208     <phylogeny rooted="false">
209        <name>network, node B is connected to TWO nodes: AB and C</name>
210        <clade>
211           <clade id_source="ab" branch_length="0.06">
212              <name>AB</name>
213              <clade id_source="a" branch_length="0.102">
214                 <name>A</name>
215              </clade>
216              <clade id_source="b" branch_length="0.23">
217                 <name>B</name>
218              </clade>
219           </clade>
220           <clade id_source="c" branch_length="0.4">
221              <name>C</name>
222           </clade>
223        </clade>
224        <clade_relation id_ref_0="b" id_ref_1="c" type="network_connection" />
225     </phylogeny>
226 
227     <phylogeny rooted="true">
228        <name>same example, using property elements to indicate a "depth" value for marine organisms</name>
229        <clade>
230           <clade>
231              <name>AB</name>
232              <clade>
233                 <name>A</name>
234                 <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 1200 </property>
235              </clade>
236              <clade>
237                 <name>B</name>
238                 <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 2300 </property>
239              </clade>
240           </clade>
241           <clade>
242              <name>C</name>
243              <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 200 </property>
244           </clade>
245        </clade>
246     </phylogeny>
247 
248     <phylogeny rooted="true">
249        <name>same example, using property elements to indicate a "depth" value for marine organisms by using id refs in
250           order to have property elements outside of the tree topology</name>
251        <clade>
252           <clade>
253              <name>AB</name>
254              <clade id_source="id_a">
255                 <name>A</name>
256              </clade>
257              <clade id_source="id_b">
258                 <name>B</name>
259              </clade>
260           </clade>
261           <clade id_source="id_c">
262              <name>C</name>
263           </clade>
264        </clade>
265        <property id_ref="id_a" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 1200 </property>
266        <property id_ref="id_b" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 2300 </property>
267        <property id_ref="id_c" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 200 </property>
268     </phylogeny>
269 
270     <phylogeny rooted="true">
271        <name>monitor lizards</name>
272        <description>a pylogeny of some monitor lizards</description>
273        <clade>
274           <taxonomy>
275              <id provider="NCBI">8556</id>
276              <scientific_name>Varanus</scientific_name>
277              <rank>genus</rank>
278              <uri desc="EMBL REPTILE DATABASE">http://www.embl-heidelberg.de/~uetz/families/Varanidae.html</uri>
279           </taxonomy>
280           <clade>
281              <taxonomy>
282                 <id provider="NCBI">62046</id>
283                 <scientific_name>Varanus niloticus</scientific_name>
284                 <common_name>Nile monitor</common_name>
285                 <rank>species</rank>
286              </taxonomy>
287              <distribution>
288                 <desc>Africa</desc>
289              </distribution>
290           </clade>
291           <clade>
292              <taxonomy>
293                 <scientific_name>Odatria</scientific_name>
294                 <rank>subgenus</rank>
295              </taxonomy>
296              <clade>
297                 <taxonomy>
298                    <id provider="NCBI">169855</id>
299                    <scientific_name>Varanus storri</scientific_name>
300                    <common_name>Storr's monitor</common_name>
301                    <rank>species</rank>
302                 </taxonomy>
303                 <distribution>
304                    <desc>Australia</desc>
305                 </distribution>
306              </clade>
307              <clade>
308                 <taxonomy>
309                    <id provider="NCBI">62053</id>
310                    <scientific_name>Varanus timorensis</scientific_name>
311                    <common_name>Timor monitor</common_name>
312                    <rank>species</rank>
313                 </taxonomy>
314                 <distribution>
315                    <desc>Asia</desc>
316                 </distribution>
317              </clade>
318           </clade>
319        </clade>
320     </phylogeny>
321 
322     <phylogeny rooted="true">
323        <name>A tree with phylogeographic information</name>
324        <clade>
325           <clade>
326              <clade>
327                 <name>A</name>
328                 <distribution>
329                    <desc>Hirschweg, Winterthur, Switzerland</desc>
330                    <point geodetic_datum="WGS84" alt_unit="m">
331                       <lat>47.481277</lat>
332                       <long>8.769303</long>
333                       <alt>472</alt>
334                    </point>
335                 </distribution>
336              </clade>
337              <clade>
338                 <name>B</name>
339                 <distribution>
340                    <desc>Nagoya, Aichi, Japan</desc>
341                    <point geodetic_datum="WGS84" alt_unit="m">
342                       <lat>35.155904</lat>
343                       <long>136.915863</long>
344                       <alt>10</alt>
345                    </point>
346                 </distribution>
347              </clade>
348              <clade>
349                 <name>C</name>
350                 <distribution>
351                    <desc>ETH Zürich</desc>
352                    <point geodetic_datum="WGS84" alt_unit="m">
353                       <lat>47.376334</lat>
354                       <long>8.548108</long>
355                       <alt>452</alt>
356                    </point>
357                 </distribution>
358              </clade>
359           </clade>
360           <clade>
361              <name>D</name>
362              <distribution>
363                 <desc>San Diego</desc>
364                 <point geodetic_datum="WGS84" alt_unit="m">
365                    <lat>32.880933</lat>
366                    <long>-117.217543</long>
367                    <alt>104</alt>
368                 </point>
369              </distribution>
370           </clade>
371        </clade>
372     </phylogeny>
373 
374     <phylogeny rooted="true">
375        <name>A tree with date information</name>
376        <clade>
377           <clade>
378              <clade>
379                 <name>A</name>
380                 <date unit="mya">
381                    <desc>Silurian</desc>
382                    <value>425</value>
383                    <minimum>416.0</minimum>
384                    <maximum>443.7</maximum>
385                 </date>
386              </clade>
387              <clade>
388                 <name>B</name>
389                 <date unit="mya">
390                    <desc>Devonian</desc>
391                    <value>320</value>
392                 </date>
393              </clade>
394           </clade>
395           <clade>
396              <name>C</name>
397              <date unit="mya">
398                 <desc>Ediacaran</desc>
399                 <value>600</value>
400              </date>
401           </clade>
402        </clade>
403     </phylogeny>
404 
405     <phylogeny rooted="true">
406        <name>Using another XML language to store an alignment</name>
407        <clade>
408           <clade>
409              <clade>
410                 <name>A</name>
411              </clade>
412              <clade>
413                 <name>B</name>
414              </clade>
415           </clade>
416           <clade>
417              <name>C</name>
418           </clade>
419        </clade>
420     </phylogeny>
421 
422     <align:alignment xmlns:align="http://example.org/align">
423        <seq name="A">acgtcgcggcccgtggaagtcctctcct</seq>
424        <seq name="B">aggtcgcggcctgtggaagtcctctcct</seq>
425        <seq name="C">taaatcgc--cccgtgg-agtccc-cct</seq>
426     </align:alignment>
427 
428  </phyloxml>


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