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<?xml version="1.0" encoding="ISO-8859-1"?>
<!--
For an explanation of the structure of the root element
and the taxa element refer to the file taxa.xml.
-->
<nex:nexml
version="0.9"
xml:base="http://example.org/"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xsi:schemaLocation="http://www.nexml.org/2009 ../xsd/nexml.xsd"
xmlns:nex="http://www.nexml.org/2009"
xmlns:cdao="http://www.evolutionaryontology.org/cdao/1.0/cdao.owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns="http://www.nexml.org/2009">
<otus id="tax1" label="RootTaxaBlock">
<otu id="t1"/>
<otu id="t2"/>
<otu id="t3"/>
<otu id="t4"/>
<otu id="t5"/>
</otus>
<!--
The trees block is structured as follows:
* the root element takes the same attributes as
characters elements do: an id, a reference
to a taxa element, and various optional
attributes.
* the trees element contains one or more tree/network
elements, which are the same structure as
GraphML documents (http://graphml.graphdrawing.org/),
with the following extentions:
- there are two subclasses (xsi:type="nex:Tree" and
xsi:type="nex:Network"), which only differ in the
constrained in-degree of node elements (one for
trees, one or more for networks)
- node elements can have an additional taxon attribute
to refer to a taxon element defined earlier
- edge elements can have a 'length' attribute
to specify edge length/weight, which is a
IEEE 754-1985 compliant floating point number on
trees of type FloatTree.
-->
<trees otus="tax1" id="Trees" label="TreesBlockFromXML">
<!--
A tree with float edges.
-->
<tree id="tree1" xsi:type="nex:FloatTree" label="tree1">
<node id="n1" label="n1" root="true"/>
<node id="n2" label="n2" otu="t1"/>
<node id="n3" label="n3"/>
<node id="n4" label="n4" about="#n4">
<meta
id="dict1"
property="cdao:has_tag"
content="true"
xsi:type="nex:LiteralMeta"
datatype="xsd:boolean"/>
</node>
<node id="n5" label="n5" otu="t3"/>
<node id="n6" label="n6" otu="t2"/>
<node id="n7" label="n7"/>
<node id="n8" label="n8" otu="t5"/>
<node id="n9" label="n9" otu="t4"/>
<edge source="n1" target="n3" id="e1" length="0.34534"/>
<edge source="n1" target="n2" id="e2" length="0.4353"/>
<edge source="n3" target="n4" id="e3" length="0.324"/>
<edge source="n3" target="n7" id="e4" length="0.3247"/>
<edge source="n4" target="n5" id="e5" length="0.234"/>
<edge source="n4" target="n6" id="e6" length="0.3243"/>
<edge source="n7" target="n8" id="e7" length="0.32443"/>
<edge source="n7" target="n9" id="e8" length="0.2342"/>
</tree>
<!--
A tree with int edges.
-->
<tree id="tree2" xsi:type="nex:IntTree" label="tree2">
<node id="tree2n1" label="n1"/>
<node id="tree2n2" label="n2" otu="t1"/>
<node id="tree2n3" label="n3"/>
<node id="tree2n4" about="#tree2n4" label="n4">
<meta
id="tree2dict1"
property="cdao:has_tag"
content="true"
xsi:type="nex:LiteralMeta"
datatype="xsd:boolean"/>
</node>
<node id="tree2n5" label="n5" otu="t3"/>
<node id="tree2n6" label="n6" otu="t2"/>
<node id="tree2n7" label="n7"/>
<node id="tree2n8" label="n8" otu="t5"/>
<node id="tree2n9" label="n9" otu="t4"/>
<edge source="tree2n1" target="tree2n3" id="tree2e1" length="1"/>
<edge source="tree2n1" target="tree2n2" id="tree2e2" length="2"/>
<edge source="tree2n3" target="tree2n4" id="tree2e3" length="3"/>
<edge source="tree2n3" target="tree2n7" id="tree2e4" length="1"/>
<edge source="tree2n4" target="tree2n5" id="tree2e5" length="2"/>
<edge source="tree2n4" target="tree2n6" id="tree2e6" length="1"/>
<edge source="tree2n7" target="tree2n8" id="tree2e7" length="1"/>
<edge source="tree2n7" target="tree2n9" id="tree2e8" length="1"/>
</tree>
<!--
A network with int edges.
-->
<network id="tree3" xsi:type="nex:IntNetwork" label="tree2">
<node id="tree3n1" label="tree3n1"/>
<node id="tree3n2" label="tree3n2" otu="t1"/>
<node id="tree3n3" label="tree3n3"/>
<node id="tree3n4" label="tree3n4"/>
<node id="tree3n5" label="tree3n5" otu="t3"/>
<node id="tree3n6" label="tree3n6" otu="t2"/>
<node id="tree3n7" label="tree3n7"/>
<node id="tree3n8" label="tree3n8" otu="t5"/>
<node id="tree3n9" label="tree3n9" otu="t4"/>
<edge source="tree3n1" target="tree3n3" id="tree3e1" length="1"/>
<edge source="tree3n1" target="tree3n2" id="tree3e2" length="2"/>
<edge source="tree3n3" target="tree3n4" id="tree3e3" length="3"/>
<edge source="tree3n3" target="tree3n7" id="tree3e4" length="1"/>
<edge source="tree3n4" target="tree3n5" id="tree3e5" length="2"/>
<edge source="tree3n4" target="tree3n6" id="tree3e6" length="1"/>
<edge source="tree3n7" target="tree3n6" id="tree3e7" length="1"/> <!-- extra edge -->
<edge source="tree3n7" target="tree3n8" id="tree3e9" length="1"/>
<edge source="tree3n7" target="tree3n9" id="tree3e8" length="1"/>
</network>
</trees>
</nex:nexml>
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