<lamarc version="2.1">
<!-- Created by the Lamarc program -->
  <chains>
    <replicates>1</replicates>
    <bayesian-analysis>No</bayesian-analysis>
    <heating>
      <adaptive>true</adaptive>
      <temperatures> 1 1.1 1.2 1.3</temperatures>
      <swap-interval>10</swap-interval>
    </heating>
    <strategy>
      <resimulating>0.454545</resimulating>
      <tree-size>0.0909091</tree-size>
      <haplotyping>0.454545</haplotyping>
      <trait-arranger>0</trait-arranger>
    </strategy>
    <initial>
      <number>10</number>
      <samples>2000</samples>
      <discard>1000</discard>
      <interval>20</interval>
    </initial>
    <final>
      <number>2</number>
      <samples>5000</samples>
      <discard>1000</discard>
      <interval>20</interval>
    </final>
  </chains>
  <format>
    <seed>1005</seed>
    <verbosity>verbose</verbosity>
    <progress-reports>verbose</progress-reports>
    <results-file>outfile.coalrec</results-file>
    <use-in-summary>false</use-in-summary>
    <in-summary-file>insumfile.coalrec</in-summary-file>
    <use-out-summary>true</use-out-summary>
    <out-summary-file>outsumfile.coalrec</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> fixed </profiles>
      <constraints> unconstrained </constraints>
      <prior type="log">
        <paramindex> all </paramindex>
        <lower> 1e-05 </lower>
        <upper> 10 </upper>
      </prior>
    </coalescence>
    <recombination>
      <start-values> 0.1</start-values>
      <method> USER</method>
      <max-events>1000</max-events>
      <profiles> fixed </profiles>
      <constraints> unconstrained </constraints>
      <prior type="log">
        <paramindex> all </paramindex>
        <lower> 1e-05 </lower>
        <upper> 10 </upper>
      </prior>
    </recombination>
  </forces>
  <data>
    <region name="coalrec">
      <model name="F84">
        <normalize>false</normalize>
        <categories>
          <num-categories>2</num-categories>
          <rates> 0.666667 1.33333</rates>
          <probabilities> 0.5 0.5</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>1000</length>
          <locations> 2 9 18 46 51 78 82 89 90 98 104 106 114 172 197 199 222 293 326 343 391 397 417 424 426 435 438 443 464 488 499 526 546 556 575 576 595 602 614 617 621 629 642 650 653 674 690 694 699 702 711 718 719 729 770 848 851 854 856 857 915 923 940 958 974</locations>
          <offset>0</offset>
        </block>
      </spacing>
    <population name="ZMNE">
      <individual name="GG-322166855">
        <phase type="known">
        </phase>
        <sample name="00_0025   ">
          <datablock type="SNP">
            TGAAGCCCCAATTATGGTTACCACGACTTACCAGTACCTCTTAGCGACGTGGGCTCTATCTCTCA
          </datablock>
        </sample>
        <sample name="00_0032   ">
          <datablock type="SNP">
            TGAAGCCCCAATTATGGTTACCACGACTTACCAGTACCTCTTAGCGACGTGGGCTCTATCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="CA-1016758720">
        <phase type="known">
        </phase>
        <sample name="00_0022   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTACCGCTTCTTACCAGTACCTCTTAGCGACGTGGGCTCTATCTCTCA
          </datablock>
        </sample>
        <sample name="00_0003   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTACCGCTTCTTACCAGTACCTCTTAGCGACGTGGGCTCTATCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="GT-438712109">
        <phase type="known">
        </phase>
        <sample name="00_0024   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTACCGCTTCTTACCAGTACCTCTTAGCGACGTGGGCTCTATCTCTCA
          </datablock>
        </sample>
        <sample name="00_0000   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTGCCGCTTCTTATCAGTACCTCTTAGCGACGTGGGCTCTATCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="AT1063120482">
        <phase type="known">
        </phase>
        <sample name="00_0027   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTGGCGCTTCTTATCAGTACCTCTTAGCGACGTGGGCTCTATCTCTAA
          </datablock>
        </sample>
        <sample name="00_0013   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTGCCGCTTCTTATCAGTACCTCTAAGCGACGTGGGCTCTATCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="TG-108633955">
        <phase type="known">
        </phase>
        <sample name="00_0037   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTGCCGCTTCTTATCAGTACCTCTTAGCGACGTGGGCTCTATCTCTCA
          </datablock>
        </sample>
        <sample name="00_0009   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTGCCGCTTCTTCTCAGTACCACTTAGCAACGTAGACTCTAACACTCA
          </datablock>
        </sample>
      </individual>
      <individual name="GC-816174348">
        <phase type="known">
        </phase>
        <sample name="00_0034   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTACCGCTTCCTCTCAGTACCACTTAGCAACGTAGACTCTATCACTCA
          </datablock>
        </sample>
        <sample name="00_0038   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTACCGCTTCCTCTCAGTACCACTTAGCAACGTAGACTCTATCACTCA
          </datablock>
        </sample>
      </individual>
      <individual name="GG-1252698729">
        <phase type="known">
        </phase>
        <sample name="00_0023   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTACCGCTTCCTATCGGTACCACTTAGCAACGTAGACCCTATATCTCA
          </datablock>
        </sample>
        <sample name="00_0030   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATATCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="GG-173374346">
        <phase type="known">
        </phase>
        <sample name="00_0031   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATATCTCA
          </datablock>
        </sample>
        <sample name="00_0002   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATATCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="CA-1985314239">
        <phase type="known">
        </phase>
        <sample name="00_0018   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATATCTCA
          </datablock>
        </sample>
        <sample name="00_0014   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="GC-780785816">
        <phase type="known">
        </phase>
        <sample name="00_0005   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
          </datablock>
        </sample>
        <sample name="00_0036   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="GG1351601435">
        <phase type="known">
        </phase>
        <sample name="00_0010   ">
          <datablock type="SNP">
            CCACATCGTAGACGTTCGTACCGCTTCTTATCGGTACCACTTAGCAACGTAGACCCTATCTCCCA
          </datablock>
        </sample>
        <sample name="00_0001   ">
          <datablock type="SNP">
            CCACATCGTTGACATTCGCACTGGTTTTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="CA-402572214">
        <phase type="known">
        </phase>
        <sample name="00_0011   ">
          <datablock type="SNP">
            CCACATCGTTGACATTCGCACTGGTTTTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
          </datablock>
        </sample>
        <sample name="00_0004   ">
          <datablock type="SNP">
            CCACATCGTTGACATTCGCACTGGTTTTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="AC1355139237">
        <phase type="known">
        </phase>
        <sample name="00_0033   ">
          <datablock type="SNP">
            CCACATCGTTGACATTCGCACTGGTTTTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
          </datablock>
        </sample>
        <sample name="00_0029   ">
          <datablock type="SNP">
            CCACATCGTTGACATTCGCACTGGTTTTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="GA865732508">
        <phase type="known">
        </phase>
        <sample name="00_0006   ">
          <datablock type="SNP">
            CCACATCGTTGACATTCGCACTGGTTTTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
          </datablock>
        </sample>
        <sample name="00_0015   ">
          <datablock type="SNP">
            CCACATCGTTGACATTCGCACTGGTTTTTATCGGTACCACTTAGCAACGTAGACCCTATCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="GA1359434591">
        <phase type="known">
        </phase>
        <sample name="00_0028   ">
          <datablock type="SNP">
            CCACATCGTTGACATTCGCACTGGTTTTCATTATTACCACATAGTGTCTCAGGTTCATTCTCTCA
          </datablock>
        </sample>
        <sample name="00_0035   ">
          <datablock type="SNP">
            CCACATCGTTGACATTCGCACTGGTTTTCATTATTACCACATAGTGTCTCAGGTTCATTCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="AT-1640691234">
        <phase type="known">
        </phase>
        <sample name="00_0007   ">
          <datablock type="SNP">
            CCGCATCGTTGACATTCGCACTGGTTTTCATTAGCGCCATATAGTGTATCAAGTTCATTCTCTCA
          </datablock>
        </sample>
        <sample name="00_0026   ">
          <datablock type="SNP">
            CCACATCGTTGACACTCGCACTGGTTCTCATTAGCGCCATATAGTGTATCAAGTTCATTCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="AG774387657">
        <phase type="known">
        </phase>
        <sample name="00_0019   ">
          <datablock type="SNP">
            CCACATCGTTGACACTCGCACTGGTTCTCATTAGCGCCATATAGTGTATCAAGTTCATTCTCTCA
          </datablock>
        </sample>
        <sample name="00_0020   ">
          <datablock type="SNP">
            CCACATCGTTGACACTCGCACTGGTTCTCATTAGCGCCATATAGTGTATCAAGTTCATTCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="TA864034704">
        <phase type="known">
        </phase>
        <sample name="00_0021   ">
          <datablock type="SNP">
            CCACATCGTTGACACTCGCACTGGTTCTCATTAGCGCCATATAGTGTATCAAGTTCATTCTCTCA
          </datablock>
        </sample>
        <sample name="00_0016   ">
          <datablock type="SNP">
            CCACATCGTTGACACTCGCACTGGTTCTCATTAGCGCCATATGGTGTATCAAGTTCATTCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="GT-545862557">
        <phase type="known">
        </phase>
        <sample name="00_0017   ">
          <datablock type="SNP">
            CCACATCGTTGACATTCGCACTGGTTCTCATTAGCGGCATATGGTGTATCAAGTTCATTCTCTCA
          </datablock>
        </sample>
        <sample name="00_0039   ">
          <datablock type="SNP">
            CCACATTGTTGACATTCGCACTGGTTCTCATTAGCGCCATATAATGTATCAAGTTTATTCTCTCA
          </datablock>
        </sample>
      </individual>
      <individual name="GT502571314">
        <phase type="known">
        </phase>
        <sample name="00_0008   ">
          <datablock type="SNP">
            CCACATCGTTGACATTCGCACTGGTTCTCATTAGCGCCATATAGTGTATCAAGTTCATTCTTTCG
          </datablock>
        </sample>
        <sample name="00_0012   ">
          <datablock type="SNP">
            CCACATCGTTGACATTCGCACTGGTTCTCATTAGCGCTATATAGTGTATCAAGTTCATTCTCTCG
          </datablock>
        </sample>
      </individual>
    </population>
    </region>
  </data>
</lamarc>
