Tree: <?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> Log in or register to post comments
