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="cc" rooted="true" rerootable="false" type="gene_tree">
9 <phylogeny branch_length_unit="aa/m" rooted="true" type="host parasite reconciliation" rerootable="false">
12 <name>root node</name>
13 <clade branch_length="1">
16 <common_name>some parasite</common_name>
19 <common_name>the host</common_name>
22 <mol_seq is_aligned="false"> actgtgggggtggggaggcggaggggtgtggtacactgactactgactgactga_ctgacgatcatatgac </mol_seq>
25 <mol_seq is_aligned="false">
26 ctgtgatgcatgcatgcatgcatgcatcgatcgccggcatgcatcgatatctacgctgactgactagctactagtcacacgtgacgcgcgcatgc***
32 <branch_length>2</branch_length>
36 <phylogeny branch_length_unit="c" rooted="true">
38 <id provider="treebank">1-1</id>
39 <description>test phylogeny</description>
40 <confidence type="ml">0.1</confidence>
41 <clade branch_length="0.1">
42 <name>root node</name>
43 <confidence type="bootstrap">90</confidence>
44 <confidence type="ml">1e-3</confidence>
45 <confidence type="decay">2</confidence>
53 <id provider="ncbi">1</id>
55 <scientific_name>ecdysozoa</scientific_name>
56 <common_name>molting animals</common_name>
58 <uri>http://www.ecdysozoa.org/</uri>
60 <sequence type="protein">
61 <symbol>BCL2L14</symbol>
62 <accession source="UniProtKB">Q9BZR8</accession>
63 <name>Apoptosis facilitator Bcl-2-like 14 protein</name>
64 <location>12p13-p12</location>
65 <mol_seq is_aligned="false">MCSTSGCDLEEIPLDDDDLNTIEFKILAYY</mol_seq>
66 <uri type="source" desc="UniProt link">http://www.pir.uniprot.org/cgi-bin/upEntry?id=B2L14_HUMAN</uri>
68 <desc>intracellular organelle</desc>
70 <annotation ref="GO:0005829"/>
71 <annotation ref="GO:0006915" source="UniProtKB" evidence="experimental" type="function">
72 <desc>apoptosis</desc>
73 <confidence type="ml">1</confidence>
74 <property datatype="xsd:double" applies_to="annotation" ref="AFFY:expression" unit="AFFY:x">0.2</property>
75 <property datatype="xsd:string" applies_to="annotation" ref="MED:disease">lymphoma</property>
78 <accession source="UNIPROTKB">383</accession>
79 <accession source="PDB">1G5M</accession>
80 <accession source="KEGG">hsa:596</accession>
81 <accession source="PDB">2G5M</accession>
86 <duplications>1</duplications>
87 <confidence type="bs">99</confidence>
91 <point geodetic_datum="WGS84" alt_unit="m">
92 <lat>35.9296730123456789</lat>
93 <long>-78.9482370123456789</long>
97 <reference doi="10.1038/387489a0">
99 Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). "Evidence for a clade of nematodes, arthropods and other moulting animals". Nature 387 (6632): 489–493.
102 <property ref="F:foo" datatype="xsd:int" applies_to="clade">bar</property>
105 <branch_length>0.2</branch_length>
112 <id provider="ncbi">123</id>
114 <scientific_name>C elegans</scientific_name>
115 <common_name>elegant nematode worm</common_name>
117 <uri>http://www.wormbase.org/</uri>
120 <name>CAEEL_XYZ</name>
126 <duplications>1</duplications>
127 <confidence type="">80</confidence>
129 <binary_characters type="characters" present_count="2" lost_count="3" gained_count="1">
149 <desc> Silurian </desc>
151 <minimum>416</minimum>
152 <maximum>443.7</maximum>
158 <id provider="EOL">704294</id>
160 <scientific_name>Nematostella vectensis</scientific_name>
161 <authority>Stephenson, 1935</authority>
162 <common_name>starlet sea anemone</common_name>
163 <synonym>Nematostella vectensis Stephenson1935</synonym>
169 <uri desc="EOL" type="linkout">http://www.eol.org/pages/704294</uri>
171 <binary_characters type="domains">
186 <desc>Triassic </desc>
193 <domain_architecture length="124">
194 <domain from="120" to="130" confidence="0.9" id=""> A </domain>
195 <domain from="21" to="44" confidence="2144" id="pfam"> B </domain>
196 <domain to="43" confidence="1.0E-89" from="34" id=""> C </domain>
197 <domain id="123" from="34" to="43" confidence="-1.3e-34"> D </domain>
198 </domain_architecture>
207 <phylogeny rooted="true">