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Rev: HEAD (1681) - https://secure.bioinfweb.info/Code/svn/JPhyloIO / trunk / demo / info.bioinfweb.jphyloio.demo.eventwebview / data / examples / NeXML / Simple.xml
Show File - Simple.xml  [show properties]
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<?xml version="1.0" encoding="UTF-8"?>
<nex:nexml  id="test" version="0.9" xmlns:nex="http://www.nexml.org/2009" xmlns="http://www.nexml.org/2009" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
    <otus id="taxonlist">
        <otu id="taxon1"/>
        <otu id="taxon2" label="species2"/>
        <otu id="taxon3"/>      
    </otus>
    <characters id="alignment" otus="taxonlist" xsi:type="nex:DnaSeqs">
        <format>
10              <states id="states">
11                  <state id="Adenine" symbol="A"/>
12                  <state id="Cytosine" symbol="C"/>
13                  <state id="Guanine" symbol="G"/>
14                  <state id="Thymine" symbol="T"/>
15                  <uncertain_state_set id="unspecified" symbol="N">
16                      <member state="Adenine"/>
17                      <member state="Cytosine"/>
18                      <member state="Guanine"/>
19                      <member state="Thymine"/>
20                  </uncertain_state_set>
21                  <uncertain_state_set id="gap" symbol="-"/>
22                  <uncertain_state_set id="missing" symbol="?">
23                      <member state="gap"/>
24                      <member state="Adenine"/>
25                      <member state="Cytosine"/>
26                      <member state="Guanine"/>
27                      <member state="Thymine"/>
28                  </uncertain_state_set>
29              </states>
30              <char id="char0" states="states"/>
31              <char id="char1" states="states"/>
32              <char id="char2" states="states"/>
33              <char id="char3" states="states"/>
34              <char id="char4" states="states"/>
35              <set id="charset1" char="char0 char2 char3"/>
36              <set id="charset2" char="char4 char2"/>
37          </format>
38          <matrix>
39              <row id="row1" otu="taxon1">
40                  <seq>AACTG</seq>
41              </row>
42              <row id="row2" otu="taxon2">
43                 <seq>ACGTT</seq>
44              </row>
45              <row id="row3" otu="taxon3">
46                  <seq>ACCTG</seq>
47              </row>
48          </matrix>
49      </characters>
50      <trees id="treegroup" label="trees" otus="taxonlist">
51          <tree id="tree" xsi:type="nex:FloatTree">
52              <node id="node1" otu="taxon1"/>
53              <node id="node2" otu="taxon2"/>
54              <node id="node3" otu="taxon3"/>
55              <node id="node4"/>
56              <node id="node5"/>
57              <rootedge id="rootedge" target="node4" length="0.778"/>
58              <edge id="edge1" source="node4" target="node5" length="1"/>
59              <edge id="edge2" source="node4" target="node3"/>
60              <edge id="edge3" source="node5" target="node1" length="0.98"/>
61              <edge id="edge4" source="node5" target="node2"/>
62          </tree>
63          <network id="network" xsi:type="nex:FloatNetwork">
64              <node id="node6" otu="taxon1"/>
65              <node id="node7" otu="taxon2"/>
66              <node id="node8" otu="taxon3"/>
67              <node id="node9"/>
68              <node id="node10"/>         
69              <edge id="edge5" source="node9" target="node10" length="0.44"/>
70              <edge id="edge6" source="node9" target="node8" length="0.67"/>
71              <edge id="edge7" source="node10" target="node6"/>
72              <edge id="edge8" source="node10" target="node7"/>
73              <edge id="edge9" source="node7" target="node8"/>
74          </network>
75      </trees>
76  </nex:nexml>


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