<?xml version="1.0" standalone="yes"?>
<!-- Test calibration implementation: 5 taxa - prior on 2-taxon clade, uniform prior  -->
<beast version='2.0'
       namespace='beast.evolution.alignment:beast.evolution.speciation:beast.core:beast.evolution.tree.coalescent:beast.util:beast.core.util:beast.evolution.likelihood:beast.math.distributions:beast.evolution.operators'>

  <taxonset spec='TaxonSet' id='taxa'>
	<taxon spec='Taxon' id='a'/> 
	<taxon spec='Taxon' id='b'/>
	<taxon spec='Taxon' id='c'/> 
	<taxon spec='Taxon' id='d'/>
	<taxon spec='Taxon' id='e'/>
   </taxonset>

  <input spec='CalibratedYuleModel' type="full" id="cyule">
    <birthRate spec='parameter.RealParameter' value="2.0"/>
    <tree idref='tree'/>

    <calibrations spec='CalibrationPoint' id='cal'>
      <taxonset spec='TaxonSet'>
	<taxon idref='a'/> 
	<taxon idref='b'/>
      </taxonset>
      <distr id="Uniform" lower="4.0" upper="7.0" spec="Uniform"/>
    </calibrations>
  </input>

  <run spec="MCMC" id="mcmc" chainLength="10000">
    <init spec='CalibratedYuleInitialTree' id='startTree' initial='@tree'
	  taxonset='@taxa' calibrations='@cal'>
    </init>

    <state>
      <stateNode spec='beast.evolution.tree.Tree' id='tree'/>
    </state>

    <distribution spec='CompoundDistribution' id='posterior'>
      <distribution id="cyule.prior" idref='cyule'/>
    </distribution>

    <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.5" tree="@tree"/>

    <logger logEvery="100" fileName="test_5t_2c_i.$(seed).log">
      <model idref='posterior'/>
      <log idref="posterior"/>
      <log idref="cyule"/>
    </logger>
    <logger logEvery="100" fileName="test_5t_2c_i.$(seed).trees">
        <log idref="tree"/>
    </logger>
    <logger logEvery="1000">
      <model idref='posterior'/>
      <log idref="cyule"/>
    </logger>
  </run>
</beast>
