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">
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>
24 <taxonomy id_source="qwerty1">
25 <id provider="ncbi">1</id>
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>
33 <uri type="img">http://www.molting.org/m.jpg</uri>
34 <uri type="source" desc="original source">http://www.ecdysozoa.org/</uri>
37 <id provider="ncbi">123</id>
38 <synonym>Æ Ä ä, ö and ü>– —</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>
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accession source="UniProtKB" comment="outdated"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>
55 <desc>intracellular organelle</desc>
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
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>
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>
74 <sequence type="protein">
79 <duplications>1</duplications>
80 <confidence type="bs">99</confidence>
84 <point geodetic_datum="WGS84" alt_unit="m">
85 <lat>35.9296730123456789</lat>
86 <long>-78.9482370123456789</long>
89 <point geodetic_datum="WGS84" alt_unit="m">
90 <lat>129.549495485834893</lat>
91 <long>-78.00000000000000</long>
101 <reference doi="10.1038/387489a0">
103 Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, &
104 J. A. Lake (1997). "Evidence for a clade of nematodes, arthropods and other moulting animals".
105 Nature 387 (6632): 489–493.
108 <reference doi="10.1036/59494">
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>
114 <branch_length>0.2</branch_length>
121 <id provider="ncbi">123</id>
123 <scientific_name>C elegans</scientific_name>
124 <common_name>elegant nematode worm</common_name>
126 <uri>http://www.wormbase.org/</uri>
128 <sequence id_source="xyz">
129 <name>CAEEL_XYZ</name>
131 <sequence id_source="abc">
132 <name>CAEEL_ABC</name>
136 <duplications>58</duplications>
137 <speciations>59403</speciations>
138 <losses>58485</losses>
139 <confidence type="p">0.9901</confidence>
145 <duplications>1</duplications>
146 <confidence type="">80</confidence>
148 <binary_characters type="characters" present_count="2" lost_count="3" gained_count="1">
168 <desc>Silurian</desc>
170 <minimum>416</minimum>
171 <maximum>443.7</maximum>
174 <clade collapse="false">
177 <id provider="EOL">704294</id>
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>
188 <uri desc="EOL" type="linkout">http://www.eol.org/pages/704294</uri>
190 <binary_characters type="domains">
205 <desc>Triassic</desc>
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>
220 <speciations>1</speciations>
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>
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>
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>
237 <phylogeny rooted="true" rerootable="true">
238 <name>phylogeny2</name>
248 <phylogeny rooted="true" rerootable="true">
249 <name>phylogeny3</name>
251 <clade id_source="i0">
254 <clade id_source="i1">
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>
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>