<phyrex run.id="example" output.file="out" mcmc.chain.len="1E+7" mcmc.sample.every="1000"
        mcmc.print.every="1000" mcmc.burnin="1E+5" mutmap="no">

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

  <!-- Model of rate variation across lineages -->
  <lineagerates model="lognormal"/>

  <!-- Average (clock) rate of substitution -->
  <clockrate value="1" optimize.clock="false"/>
  
  <!-- Model of rate variation across lineages -->
  <lineagerates model="lognormal"/>
  
  <!-- Substitution model -->
  <ratematrices id="RM1">
    <instance id="M1" model="HKY85" optimise.tstv="no" tstv="4.0"/>
  </ratematrices>

  
    <!-- Freerate model of variation of rates across sites -->
  <siterates id="SR1">
    <instance id="R1" init.value="1.0"/>
    <instance id="R2" init.value="1.0"/>
    <instance id="R3" init.value="1.0"/>
    <instance id="R4" init.value="1.0"/>
    <weights  id="D1" family="gamma" optimise.freerates="no">
      <instance appliesto="R1" value="1.00"/>
    </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="yes"/>
  </branchlengths>

  <!-- Model assembly -->
  <partitionelem id="partition1" file.name="./h1n1.nxs" data.type="nt" interleaved="no">
    <mixtureelem list="T1,T1,T1,T1"/>
    <mixtureelem list="M1,M1,M1,M1"/>
    <mixtureelem list="F1,F1,F1,F1"/>
    <mixtureelem list="R1,R2,R3,R4"/>
    <mixtureelem list="L1,L1,L1,L1"/>
  </partitionelem>


  <coordinates id="coordinates" file.name="./usa_coord.txt"/>
  
  <clade id="clad1">
    <taxon value="CY130177|South_Carolina|12_13|H1N1"/>
  </clade>

  <clade id="clad2">
  <taxon value="KF647978|Idaho|12_13|H1N1"/>
  </clade>

  <clade id="clad3">
  <taxon value="KF648268|New_Mexico|12_13|H1N1"/>
  </clade>

  <clade id="clad4">
  <taxon value="KF648064|North_Carolina|12_13|H1N1"/>
  </clade>

  <clade id="clad5">
  <taxon value="KF647995|New_Hampshire|12_13|H1N1"/>
  </clade>

  <clade id="clad6">
  <taxon value="KF648000|Colorado|12_13|H1N1"/>
  </clade>

  <clade id="clad7">
    <taxon value="KF648133|Florida|12_13|H1N1"/>
  </clade>

  <clade id="clad8">
    <taxon value="KF648145|Georgia|12_13|H1N1"/>
  </clade>

  <clade id="clad9">
    <taxon value="KF648155|Vermont|12_13|H1N1"/>
  </clade>

  <clade id="clad10">
    <taxon value="KF648158|Utah|12_13|H1N1"/>
  </clade>
  
  <clade id="clad11">
  <taxon value="KF648159|Louisiana|12_13|H1N1"/>
  </clade>
  
  <clade id="clad12">
  <taxon value="KF648008|Rhode_Island|12_13|H1N1"/>
  </clade>
  
  <clade id="clad13">
  <taxon value="KF648011|New_York|12_13|H1N1"/>
  </clade>
  
  <clade id="clad14">
  <taxon value="KF647921|Maryland|12_13|H1N1"/>
  </clade>
  
  <clade id="clad15">
  <taxon value="KF647926|Missouri|12_13|H1N1"/>
  </clade>
  
  <clade id="clad16">
  <taxon value="KF647928|Texas|12_13|H1N1"/>
  </clade>
  
  <clade id="clad17">
  <taxon value="KF647936|Wyoming|12_13|H1N1"/>
  </clade>
  
  <clade id="clad18">
  <taxon value="KF648197|Indiana|12_13|H1N1"/>
  </clade>
  
  <clade id="clad19">
  <taxon value="KF648228|Mississippi|12_13|H1N1"/>
  </clade>
  
  <clade id="clad20">
  <taxon value="KF648239|Tennessee|12_13|H1N1"/>
  </clade>
  
  <clade id="clad21">
  <taxon value="KF648034|Arizona|12_13|H1N1"/>
  </clade>
  
  <clade id="clad22">
  <taxon value="KF648037|Kentucky|12_13|H1N1"/>
  </clade>
  
  <clade id="clad23">
  <taxon value="KF648038|Kansas|12_13|H1N1"/>
  </clade>
  
  <clade id="clad24">
  <taxon value="KF647919|Alabama|12_13|H1N1"/>
  </clade>
  
  <clade id="clad25">
  <taxon value="KF647931|Wisconsin|12_13|H1N1"/>
  </clade>
  
  <clade id="clad26">
  <taxon value="KF647932|Pennsylvania|12_13|H1N1"/>
  </clade>
  
  <clade id="clad27">
  <taxon value="KF647958|Nebraska|12_13|H1N1"/>
  </clade>
  
  <clade id="clad28">
  <taxon value="KF647971|Oklahoma|12_13|H1N1"/>
  </clade>
  
  <clade id="clad29">
  <taxon value="KF647902|Iowa|12_13|H1N1"/>
  </clade>
  
  <clade id="clad30">
  <taxon value="KF648002|Minnesota|12_13|H1N1"/>
  </clade>
  
  <clade id="clad31">
  <taxon value="KF648040|New_Jersey|12_13|H1N1"/>
  </clade>
  
  <clade id="clad32">
  <taxon value="KF648101|Ohio|12_13|H1N1"/>
  </clade>
  
  <clade id="clad33">
  <taxon value="KF648260|Washington|12_13|H1N1"/>
  </clade>
  
  <clade id="clad34">
  <taxon value="CY170697|California|12_13|H1N1"/>
  </clade>
  
  <clade id="clad35">
  <taxon value="CY168881|Massachusetts|12_13|H1N1"/>
  </clade>

  <clade id="clad36">  
  <taxon value="CY171161|Illinois|12_13|H1N1"/>
  </clade>

  
  <calibration id="cal1">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad1"/>
  </calibration>
  
  <calibration id="cal2">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad2"/>
  </calibration>
  
  <calibration id="cal3">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad3"/>
  </calibration>
  
  <calibration id="cal4">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad4"/>
  </calibration>
  
  <calibration id="cal5">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad5"/>
  </calibration>
  
  <calibration id="cal6">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad6"/>
  </calibration>

  <calibration id="cal7">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad7"/>
  </calibration>

  <calibration id="cal8">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad8"/>
  </calibration>

  <calibration id="cal9">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad9"/>
  </calibration>
  <calibration id="cal10">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad10"/>
  </calibration>
  <calibration id="cal11">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad11"/>
  </calibration>
  <calibration id="cal12">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad12"/>
  </calibration>
  <calibration id="cal13">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad13"/>
  </calibration>
  <calibration id="cal14">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad14"/>
  </calibration>

  <calibration id="cal15">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad15"/>
  </calibration>
  <calibration id="cal16">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad16"/>
  </calibration>
  <calibration id="cal17">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad17"/>
  </calibration>
  <calibration id="cal18">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad18"/>
  </calibration>
  <calibration id="cal19">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad19"/>
  </calibration>
  <calibration id="cal20">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad20"/>
  </calibration>
  <calibration id="cal21">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad21"/>
  </calibration>
  <calibration id="cal22">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad22"/>
  </calibration>
  <calibration id="cal23">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad23"/>
  </calibration>
  <calibration id="cal24">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad24"/>
  </calibration>
  <calibration id="cal25">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad25"/>
  </calibration>
  <calibration id="cal26">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad26"/>
  </calibration>
  <calibration id="cal27">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad27"/>
  </calibration>
  <calibration id="cal28">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad28"/>
  </calibration>
  <calibration id="cal29">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad29"/>
  </calibration>
  <calibration id="cal30">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad30"/>
  </calibration>
  <calibration id="cal31">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad31"/>
  </calibration>
  <calibration id="cal32">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad32"/>
  </calibration>
  <calibration id="cal33">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad33"/>
  </calibration>
  <calibration id="cal34">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad34"/>
  </calibration>
  <calibration id="cal35">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad35"/>
  </calibration>
  <calibration id="cal36">
    <lower>0</lower>
    <upper>0</upper>
    <appliesto clade.id="clad36"/>
  </calibration>

</phyrex>


