<phyml run.id="lg4x" output.file="lg4x.tests" branch.test="no">

  <!-- Tree topology: start with BioNJ and then SPRs -->
  <topology> 
    <instance id="T1" init.tree="bionj" optimise.tree="no"/> 
  </topology>
  

  <!-- Four rate matrices, read from files -->
  <ratematrices id="RM1"> 
    <instance id="M1" model="customaa" ratematrix.file="../examples/lg4x/X1.mat"/> 
    <instance id="M2" model="customaa" ratematrix.file="../examples/lg4x/X2.mat"/> 
    <instance id="M3" model="customaa" ratematrix.file="../examples/lg4x/X3.mat"/> 
    <instance id="M4" model="customaa" ratematrix.file="../examples/lg4x/X4.mat"/> 
  </ratematrices>
  
  <!-- Freerate model of variation of rates across sites -->
  <siterates id="SR1">
    <instance id="R1" init.value="0.197063"/>
    <instance id="R2" init.value="0.750275"/>
    <instance id="R3" init.value="1.951569"/>
    <instance id="R4" init.value="5.161586"/>
    <weights  id="D1" family="freerates" optimise.freerates="yes">
      <instance appliesto="R1" value="0.422481"/>
      <instance appliesto="R2" value="0.336848"/>
      <instance appliesto="R3" value="0.180132"/>
      <instance appliesto="R4" value="0.060539"/>
    </weights>
  </siterates>
  
  <!-- Amino-acid equilibrium frequencies are given by the models -->
  <equfreqs id="EF1">
    <instance id="F1" aa.freqs="model"/>
    <instance id="F2" aa.freqs="model"/>
    <instance id="F3" aa.freqs="model"/>
    <instance id="F4" aa.freqs="model"/>
  </equfreqs>


  <!-- One vector of branch lengths -->
  <branchlengths id="BL1" >
    <instance id="L1" optimise.lens="yes"/>
  </branchlengths>


  <!-- Mixture model assemblage -->
  <partitionelem id="partition1" file.name="../examples/proteic" data.type="aa" interleaved="yes">
    <mixtureelem list="T1, T1, T1, T1"/>
    <mixtureelem list="M1, M2, M3, M4"/>
    <mixtureelem list="F1, F2, F3, F4"/>
    <mixtureelem list="R1, R2, R3, R4"/>
    <mixtureelem list="L1, L1, L1, L1"/>
  </partitionelem>

  
</phyml>


