t/data/01_basic.xml

   1 <nex:nexml generator="Bio::Phylo::Project v.0.17_RC9_841" version="0.8" xmlns="http://www.nexml.org/1.0" xmlns:nex="http://www.nexml.org/1.0" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.nexml.org/1.0 http://www.nexml.org/1.0/nexml.xsd">
   2 <!-- this is a simple test file generated from a NEXUS file -->
   3 <otus id="otus1">
   4     <otu id="otu2" label="otuA"/>
   5     <otu id="otu3" label="otuB"/>
   6     <otu id="otu4" label="otuC"/>
   7     <otu id="otu5" label="otuD"/>
   8     <otu id="otu6" label="otuE"/>
   9     <otu id="otu7" label="otuF"/>
  10   </otus>
  11   <trees id="trees16" otus="otus1">
  12     <tree id="tree18" label="'the tree'" xsi:type="nex:IntTree">
  13       <node id="node19" root="true"/>
  14       <node id="node20" label="otuA" otu="otu2"/>
  15       <node id="node21"/>
  16       <node id="node22"/>
  17       <node id="node27"/>
  18       <node id="node23"/>
  19       <node id="node26" label="otuD" otu="otu5"/>
  20       <node id="node28" label="otuE" otu="otu6"/>
  21       <node id="node29" label="otuF" otu="otu7"/>
  22       <node id="node24" label="otuB" otu="otu3"/>
  23       <node id="node25" label="otuC" otu="otu4"/>
  24       <edge id="edge20" length="4" source="node19" target="node20"/>
  25       <edge id="edge21" length="1" source="node19" target="node21"/>
  26       <edge id="edge22" length="1" source="node21" target="node22"/>
  27       <edge id="edge27" length="2" source="node21" target="node27"/>
  28       <edge id="edge23" length="1" source="node22" target="node23"/>
  29       <edge id="edge26" length="2" source="node22" target="node26"/>
  30       <edge id="edge28" length="1" source="node27" target="node28"/>
  31       <edge id="edge29" length="1" source="node27" target="node29"/>
  32       <edge id="edge24" length="1" source="node23" target="node24"/>
  33       <edge id="edge25" length="1" source="node23" target="node25"/>
  34     </tree>
  35   </trees>
  36   <characters id="characters8" otus="otus1" xsi:type="nex:StandardCells">
  37     <format>
  38       <states id="states10">
  39         <state id="s1" symbol="0"/>
  40         <state id="s2" symbol="1"/>
  41         <state id="s3" symbol="2"/>
  42         <state id="s4" symbol="3"/>
  43         <state id="s5" symbol="4"/>
  44         <state id="s6" symbol="5"/>
  45         <state id="s7" symbol="6"/>
  46         <state id="s8" symbol="7"/>
  47         <state id="s9" symbol="8"/>
  48         <state id="s10" symbol="9"/>
  49         <uncertain_state_set id="s11" symbol="-"></uncertain_state_set>
  50         <uncertain_state_set id="s12" symbol="?">
  51           <member state="s1"/>
  52           <member state="s2"/>
  53           <member state="s3"/>
  54           <member state="s4"/>
  55           <member state="s5"/>
  56           <member state="s6"/>
  57           <member state="s7"/>
  58           <member state="s8"/>
  59           <member state="s9"/>
  60           <member state="s10"/>
  61           <member state="s11"/>
  62         </uncertain_state_set>
  63       </states>
  64       <char id="c1" states="states10"/>
  65     </format>
  66     <matrix>
  67       <row id="row9" label="otuA" otu="otu2">
  68         <cell char="c1" state="s1"/>
  69       </row>
  70       <row id="row11" label="otuB" otu="otu3">
  71         <cell char="c1" state="s3"/>
  72       </row>
  73       <row id="row12" label="otuC" otu="otu4">
  74         <cell char="c1" state="s3"/>
  75       </row>
  76       <row id="row13" label="otuD" otu="otu5">
  77         <cell char="c1" state="s1"/>
  78       </row>
  79       <row id="row14" label="otuE" otu="otu6">
  80         <cell char="c1" state="s2"/>
  81       </row>
  82       <row id="row15" label="otuF" otu="otu7">
  83         <cell char="c1" state="s1"/>
  84       </row>
  85     </matrix>
  86   </characters>
  87 </nex:nexml>