<lamarc version="2.1">
<!-- Created by the Lamarc program -->
  <chains>
    <replicates>1</replicates>
    <bayesian-analysis>Yes</bayesian-analysis>
    <heating>
      <adaptive>false</adaptive>
      <temperatures> 1</temperatures>
      <swap-interval>1</swap-interval>
    </heating>
    <strategy>
      <resimulating>0.454545</resimulating>
      <tree-size>0.0909091</tree-size>
      <haplotyping>0</haplotyping>
      <trait-arranger>0</trait-arranger>
      <bayesian>0.454545</bayesian>
    </strategy>
    <initial>
      <number>3</number>
      <samples>200</samples>
      <discard>1000</discard>
      <interval>20</interval>
    </initial>
    <final>
      <number>1</number>
      <samples>500</samples>
      <discard>1000</discard>
      <interval>20</interval>
    </final>
  </chains>
  <format>
    <seed>1005</seed>
    <verbosity>verbose</verbosity>
    <progress-reports>verbose</progress-reports>
    <results-file>outfile.bayes</results-file>
    <use-in-summary>false</use-in-summary>
    <in-summary-file>insumfile.bayes</in-summary-file>
    <use-out-summary>false</use-out-summary>
    <out-summary-file>outsumfile.bayes</out-summary-file>
    <use-curvefiles>true</use-curvefiles>
    <curvefile-prefix>curvefile</curvefile-prefix>
    <use-tracefile>true</use-tracefile>
    <tracefile-prefix>tracefile</tracefile-prefix>
    <use-newicktreefile>false</use-newicktreefile>
    <newicktreefile-prefix>newick</newicktreefile-prefix>
    <out-xml-file>menuinfile</out-xml-file>
  </format>
  <forces>
    <coalescence>
      <start-values> 0.01</start-values>
      <method> USER</method>
      <max-events>1000</max-events>
      <profiles> percentile </profiles>
      <constraints> unconstrained </constraints>
      <prior type="log">
        <paramindex> all </paramindex>
        <lower> 1e-05 </lower>
        <upper> 10 </upper>
      </prior>
    </coalescence>
  </forces>
  <data>
    <region name="region 1">
      <model name="F84">
        <normalize>false</normalize>
        <categories>
          <num-categories>1</num-categories>
          <rates> 1</rates>
          <probabilities> 1</probabilities>
          <autocorrelation>1</autocorrelation>
        </categories>
        <relative-murate>1</relative-murate>
        <base-freqs> calculated </base-freqs>
        <ttratio>2</ttratio>
      </model>
      <effective-popsize>1</effective-popsize>
      <spacing>
        <block>
          <map-position>0</map-position>
          <length>68</length>
          <offset>0</offset>
        </block>
      </spacing>
    <population name="Population JYRM">
      <individual name="germ_10   ">
        <sample name="germ_10   ">
          <datablock type="DNA">
            TCATTTCCGGTGCAAACCGAATCTCAGCTTGATTAATCTGGATCACCCAGAAGAGCTCTTAAAACGCA
          </datablock>
        </sample>
      </individual>
      <individual name="germ_11   ">
        <sample name="germ_11   ">
          <datablock type="DNA">
            AGATTTGGGGTGCAATGGGAATCTCTCGTTGATTATAGTGGATCAGGGAGAAGAGGACTTAAAACCGT
          </datablock>
        </sample>
      </individual>
      <individual name="germ_20   ">
        <sample name="germ_20   ">
          <datablock type="DNA">
            ACTTTTGCCGTGCATAGCCAATCTGACCATGATTTAACAGGATCTCGCTGAAGACCAGATAAAAGGGA
          </datablock>
        </sample>
      </individual>
      <individual name="germ_21   ">
        <sample name="germ_21   ">
          <datablock type="DNA">
            ACAATTGCGCTGCTAAGCGTATCACACCTAGATAAAACTCGATGACGCACAAGTGCAGTAAAATCGGA
          </datablock>
        </sample>
      </individual>
      <individual name="germ_30   ">
        <sample name="germ_30   ">
          <datablock type="DNA">
            ACATATGCGGAGGAAAGCGATTGTCACCTTCAATAAACTGCAACACGCAGTACAGCAGTTTATACGGA
          </datablock>
        </sample>
      </individual>
      <individual name="germ_31   ">
        <sample name="germ_31   ">
          <datablock type="DNA">
            ACATTAGCGGTCCAAAGCGAAACTCACCTTGTTTAAACTGGTTCACGCAGATGAGCAGTTATAACGGA
          </datablock>
        </sample>
      </individual>
    </population>
    </region>
  </data>
</lamarc>
