<phytime run.id="example" output.file="out" mcmc.chain.len="1E+7" mcmc.sample.every="100"
         mcmc.print.every="50" mcmc.burnin="10000" mutmap="no" r.seed="1567773784">

  <!-- Tree topology -->
  <topology> 
    <instance id="T1" init.tree="bionj" optimise.tree="yes"/>
  </topology>
  

  <!-- Model of rate variation across lineages -->
  <lineagerates model="lognormal"/>
  
  <!-- Substitution model -->
  <ratematrices id="RM1">
    <instance id="M1" model="HKY85" optimise.tstv="yes" tstv="4.0"/>
  </ratematrices>

  
  <!-- Freerate model of variation of rates across sites -->
  <siterates id="SR1">
    <instance id="R3" init.value="0.5"/>
    <instance id="R2" init.value="1.0"/>
    <instance id="R1" init.value="2.0"/>
    <weights  id="D1" family="freerates" optimise.freerates="yes">
      <instance appliesto="R3" value="0.33"/>
      <instance appliesto="R2" value="0.33"/>
      <instance appliesto="R1" value="0.33"/>
    </weights>
  </siterates>

  
  <!-- Nucleotide frequencies -->
  <equfreqs id="EF1">
    <instance id="F1" optimise.freqs="no"/>
  </equfreqs>


  <!-- Vector of edge lengths -->
  <branchlengths id="BL1" >
    <instance id="L1" optimise.lens="no"/>
  </branchlengths>

  <!-- Model assembly -->
  <partitionelem id="partition1" file.name="./seq.txt" data.type="nt" interleaved="no">
    <mixtureelem list="T1,T1,T1"/>
    <mixtureelem list="M1,M1,M1"/>
    <mixtureelem list="F1,F1,F1"/>
    <mixtureelem list="R1,R2,R3"/>
    <mixtureelem list="L1,L1,L1"/>
  </partitionelem>

  <clade id="Gymno1">
    <taxon value="Gymno_Araucaria"/>
    <taxon value="Gymno_Ginkgo"/>
    <taxon value="Gymno_Juniperus"/>
    <taxon value="Gymno_Sciadopitys"/>
  </clade>

  <clade id="Gymno2">
    <taxon value="Gymno_Araucaria"/>
    <taxon value="Gymno_Juniperus"/>
    <taxon value="Gymno_Sciadopitys"/>
  </clade>
  
  <calibration id="cal1">
    <lower>40</lower>
    <upper>60</upper>
    <!-- <appliesto clade.id="Gymno2"/> -->
    <appliesto clade.id="Gymno1" probability="0.8"/>
    <appliesto clade.id="Gymno2" probability="0.2"/>
  </calibration>

  <calibration id="cal2">
    <lower>50</lower>
    <upper>200</upper>
    <appliesto clade.id="Gymno1">
    </appliesto>
  </calibration>

</phytime>


