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>
9 <clade branch_length="0.06">
10 <clade branch_length="0.102">
13 <clade branch_length="0.23">
17 <clade branch_length="0.4">
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>
27 <branch_length>0.06</branch_length>
30 <branch_length>0.102</branch_length>
34 <branch_length>0.23</branch_length>
39 <branch_length>0.4</branch_length>
43 <phylogeny rooted="true">
44 <name>same example, with support of type "bootstrap"</name>
46 <clade branch_length="0.06">
48 <confidence type="bootstrap">89</confidence>
49 <clade branch_length="0.102">
52 <clade branch_length="0.23">
56 <clade branch_length="0.4">
61 <phylogeny rooted="true">
62 <name>same example, with species and sequence</name>
69 <scientific_name>E. coli</scientific_name>
73 <desc>alcohol dehydrogenase</desc>
74 <confidence type="probability">0.99</confidence>
81 <scientific_name>B. subtilis</scientific_name>
85 <desc>alcohol dehydrogenase</desc>
86 <confidence type="probability">0.91</confidence>
94 <scientific_name>C. elegans</scientific_name>
98 <desc>alcohol dehydrogenase</desc>
99 <confidence type="probability">0.67</confidence>
105 <phylogeny rooted="true">
106 <name>same example, with gene duplication information and sequence relationships</name>
109 <speciations>1</speciations>
113 <duplications>1</duplications>
117 <scientific_name>Bacillus subtilis</scientific_name>
119 <sequence id_source="x">
120 <symbol>adhB</symbol>
121 <accession source="ncbi">AAB80874</accession>
122 <name>alcohol dehydrogenase</name>
127 <scientific_name>Bacillus subtilis</scientific_name>
129 <sequence id_source="y">
130 <symbol>gbsB</symbol>
131 <accession source="ncbi">CAB15083</accession>
132 <name>alcohol dehydrogenase</name>
138 <scientific_name>Caenorhabditis elegans</scientific_name>
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"/>
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"/>
152 <phylogeny rooted="true">
153 <name>similar example, with more detailed sequence data</name>
158 <id provider="NCBI">6645</id>
160 <scientific_name>Octopus vulgaris</scientific_name>
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"/>
173 <id provider="NCBI">44689</id>
175 <scientific_name>Dictyostelium discoideum</scientific_name>
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"/>
189 <id provider="NCBI">1488</id>
191 <scientific_name>Clostridium acetobutylicum</scientific_name>
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"/>
204 <phylogeny rooted="false">
205 <name>network, node B is connected to TWO nodes: AB and C</name>
207 <clade id_source="ab" branch_length="0.06">
209 <clade id_source="a" branch_length="0.102">
212 <clade id_source="b" branch_length="0.23">
216 <clade id_source="c" branch_length="0.4">
220 <clade_relation id_ref_0="b" id_ref_1="c" type="network_connection"/>
222 <phylogeny rooted="true">
223 <name>same example, using property elements to indicate a "depth" value for marine organisms</name>
229 <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 1200 </property>
233 <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 2300 </property>
238 <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 200 </property>
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>
248 <clade id_source="id_a">
251 <clade id_source="id_b">
255 <clade id_source="id_c">
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>
263 <phylogeny rooted="true">
264 <name>monitor lizards</name>
265 <description>a pylogeny of some monitor lizards</description>
268 <id provider="NCBI">8556</id>
269 <scientific_name>Varanus</scientific_name>
271 <uri desc="EMBL REPTILE DATABASE">http://www.embl-heidelberg.de/~uetz/families/Varanidae.html</uri>
275 <id provider="NCBI">62046</id>
276 <scientific_name>Varanus niloticus</scientific_name>
277 <common_name>Nile monitor</common_name>
286 <scientific_name>Odatria</scientific_name>
287 <rank>subgenus</rank>
291 <id provider="NCBI">169855</id>
292 <scientific_name>Varanus storri</scientific_name>
293 <common_name>Storr's monitor</common_name>
297 <desc>Australia</desc>
302 <id provider="NCBI">62053</id>
303 <scientific_name>Varanus timorensis</scientific_name>
304 <common_name>Timor monitor</common_name>
314 <phylogeny rooted="true">
315 <name>A tree with phylogeographic information</name>
321 <desc>Hirschweg, Winterthur, Switzerland</desc>
322 <point geodetic_datum="WGS84">
324 <long>8.769303</long>
332 <desc>Nagoya, Aichi, Japan</desc>
333 <point geodetic_datum="WGS84">
335 <long>136.915863</long>
343 <desc>ETH Zürich</desc>
344 <point geodetic_datum="WGS84">
346 <long>8.548108</long>
355 <desc>San Diego</desc>
356 <point geodetic_datum="WGS84">
358 <long>-117.217543</long>
365 <phylogeny rooted="true">
366 <name>A tree with date information</name>
372 <desc>Silurian</desc>
379 <desc>Devonian</desc>
387 <desc>Ediacaran</desc>
393 <phylogeny rooted="true">
394 <name>Using another XML language to store an alignment</name>
409 <align:alignment xmlns:align="http://example.org/align">
410 <seq name="A">acgtcgcggcccgtggaagtcctctcct</seq>
411 <seq name="B">aggtcgcggcctgtggaagtcctctcct</seq>
412 <seq name="C">taaatcgc--cccgtgg-agtccc-cct</seq>