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[jalview.git] / forester / test_data / phyloxml_test_atv.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 branch_length_unit="c" rooted="true">
6         <name>t3</name>
7         <id provider="treebank">1-1</id>
8         <description>test phylogeny</description>
9         <confidence type="ml">0.1</confidence>
10         <clade branch_length="0.1">
11             <name>root node</name>
12             <confidence type="bootstrap">90</confidence>
13             <confidence type="ml">1e-3</confidence>
14             <confidence type="decay">2</confidence>
15             <width>10</width>
16             <color>
17                 <red>2</red>
18                 <green>22</green>
19                 <blue>33</blue>
20             </color>
21             <node_id>root id</node_id>
22             <taxonomy>
23                 <id provider="ncbi">1</id>
24                 <code>ECDYS</code>
25                 <scientific_name>ecdysozoa</scientific_name>
26                 <common_name>molting animals</common_name>
27                 <rank>phylum</rank>
28                 <uri>http://www.ecdysozoa.org/</uri>
29             </taxonomy>
30             <sequence type="protein">
31                 <symbol>BCL2L14</symbol>
32                 <accession source="UniProtKB">Q9BZR8</accession>
33                 <name>Apoptosis facilitator Bcl-2-like 14 protein</name>
34                 <location>12p13-p12</location>
35                 <mol_seq>MCSTSGCDLEEIPLDDDDLNTIEFKILAYY</mol_seq>
36                 <uri type="source" desc="UniProt link">http://www.pir.uniprot.org/cgi-bin/upEntry?id=B2L14_HUMAN</uri>
37                 <annotation ref="GO:0006915" source="UniProtKB" evidence="experimental" type="function">
38                     <desc>apoptosis</desc>
39                     <confidence type="ml">1</confidence>
40                     <property datatype="xsd:double" applies_to="annotation" ref="AFFY:expression" unit="AFFY:x">0.2</property>
41                     <property datatype="xsd:string" applies_to="annotation" ref="MED:disease">lymphoma</property>
42                 </annotation>
43                 <annotation ref="GO:0005829"/>
44                 <annotation>
45                     <desc>intracellular organelle</desc>
46                 </annotation>
47             </sequence>
48             <events>
49                 <type>mixed</type>
50                 <duplications>1</duplications>
51                 <confidence type="bs">99</confidence>
52             </events>
53             <distribution>
54                 <desc>irgendwo</desc>
55                 <point geodetic_datum="WGS84">
56                     <lat>35.9296730123456789</lat>
57                     <long>-78.9482370123456789</long>
58                     <alt>0</alt>
59                 </point>
60             </distribution>
61             <reference doi="10.1074/jbc.M005889200"/>
62             <property ref="F:foo" datatype="xsd:int" applies_to="clade">bar</property>
63             <clade>
64                 <name>node a</name>
65                 <branch_length>0.2</branch_length>
66                 <color>
67                     <red>12</red>
68                     <green>14</green>
69                     <blue>16</blue>
70                 </color>
71                 <node_id provider="nodeid">a id</node_id>
72                 <taxonomy>
73                     <id provider="ncbi">123</id>
74                     <code>CAEEL</code>
75                     <scientific_name>C elegans</scientific_name>
76                     <common_name>elegant nematode worm</common_name>
77                     <rank>species</rank>
78                     <uri>http://www.wormbase.org/</uri>
79                 </taxonomy>
80                 <sequence>
81                     <name>CAEEL_XYZ</name>
82                 </sequence>
83             </clade>
84             <clade>
85                 <name>node b</name>
86                 <events>
87                     <duplications>1</duplications>
88                     <confidence type="">80</confidence>
89                 </events>
90                 <binary_characters type="characters" present_count="2" lost_count="3" gained_count="1">
91                     <gained>
92                         <bc>c</bc>
93                     </gained>
94                     <lost>
95                         <bc>d</bc>
96                         <bc>e</bc>
97                         <bc>f</bc>
98                     </lost>
99                     <present>
100                         <bc>a</bc>
101                         <bc>b</bc>
102                     </present>
103                 </binary_characters>
104                 <clade>
105                     <name>node ba</name>
106                     <distribution>
107                         <desc>Africa</desc>
108                     </distribution>
109                 </clade>
110                 <clade>
111                     <name>node bb</name>
112                     <binary_characters type="domains">
113                         <gained>
114                             <bc>A</bc>
115                             <bc>B</bc>
116                             <bc>C</bc>
117                         </gained>
118                         <lost>
119                             <bc>D</bc>
120                         </lost>
121                         <present>
122                             <bc>X</bc>
123                             <bc>M</bc>
124                         </present>
125                     </binary_characters>
126                 </clade>
127                 <clade>
128                     <name>node bc</name>
129                     <sequence>
130                         <name>bc seq</name>
131                         <domain_architecture length="124">
132                             <domain from="120" to="130" confidence="0.9" id=""> A </domain>
133                             <domain from="21" to="44" confidence="2144" id="pfam"> B </domain>
134                             <domain to="43" confidence="1.0E-89" from="34" id=""> C </domain>
135                             <domain id="123" from="34" to="43" confidence="-1.3e-34"> D </domain>
136                         </domain_architecture>
137                     </sequence>
138                 </clade>
139             </clade>
140         </clade>
141     </phylogeny>
142 </phyloxml>