<beast version='2.0'
       namespace='beast.evolution.alignment:beast.core:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood'>


    <data id="alignment" dataType="nucleotide">
        <sequence taxon="human">?</sequence>
        <sequence taxon="chimp">?</sequence>
        <sequence taxon="bonobo">?</sequence>
        <sequence taxon="gorilla">?</sequence>
        <sequence taxon="orangutan">?</sequence>
        <sequence taxon="siamang">?</sequence>
    </data>



    <tree id='tree' spec='beast.util.TreeParser' IsLabelledNewick='true' newick='((((human:0.02096625515232275,(chimp:0.014857143159686462,bonobo:0.014857143159686462):0.0061091119926362895):0.012862878672687175,gorilla:0.033829133825009926):0.029471223948245952,orangutan:0.06330035777325588):0.0031773962188650223,siamang:0.0664777539921209)' taxa='@alignment'/>


    <run spec="beast.app.seqgen.SequenceSimulator" id="seqgen" data='@alignment' tree='@tree' sequencelength='3000'>
	    <siteModel spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
<!--
			<substModel spec='JukesCantor' id='JC69'/>
-->
			<substModel spec='HKY' id='hky'>
			    <parameter name='kappa' id="hky.kappa" value="5.0" lower="0.0"/>
				<frequencies id='freqs' spec='Frequencies'>
				    <data idref='alignment'/>
				</frequencies>
			</substModel>

<!--
            <substModel id="GTR" spec="GTR">
				<parameter dimension="1" id="rateAC.alignment" lower="0.0" minordimension="1" name="rateAC" value="0.01"/>
				<parameter dimension="1" id="rateAG.alignment" lower="0.0" minordimension="1" name="rateAG" value="5.0"/>
				<parameter dimension="1" id="rateAT.alignment" lower="0.0" minordimension="1" name="rateAT" value="0.2"/>
				<parameter dimension="1" id="rateCG.alignment" lower="0.0" minordimension="1" name="rateCG" value="0.03"/>
				<parameter dimension="1" id="rateCT.alignment" lower="0.0" minordimension="1" name="rateCT" value="1.0"/>
				<parameter dimension="1" id="rateGT.alignment" lower="0.0" minordimension="1" name="rateGT" value="0.1"/>
                <frequencies id="freqs" spec="Frequencies">
					<parameter name='frequencies' value='0.25 0.25 0.25 0.25'/>
				</frequencies>
            </substModel>
-->
<!--
            <substModel id="TN93" spec="GTR">
				<parameter dimension="1" id="rateAC.alignment" lower="0.0" minordimension="1" name="rateAC" value="0.5"/>
				<parameter dimension="1" id="rateAG.alignment" lower="0.0" minordimension="1" name="rateAG" value="5.0"/>
				<parameter dimension="1" id="rateAT.alignment" lower="0.0" minordimension="1" name="rateAT" value="0.5"/>
				<parameter dimension="1" id="rateCG.alignment" lower="0.0" minordimension="1" name="rateCG" value="0.5"/>
				<parameter dimension="1" id="rateCT.alignment" lower="0.0" minordimension="1" name="rateCT" value="1.0"/>
				<parameter dimension="1" id="rateGT.alignment" lower="0.0" minordimension="1" name="rateGT" value="0.5"/>
                <frequencies id="freqs" spec="Frequencies">
					<parameter name='frequencies' value='0.25 0.25 0.25 0.25'/>
				</frequencies>
            </substModel>
-->
<!--
            <substModel id="TIM" spec="GTR">
				<parameter dimension="1" id="rateAC.alignment" lower="0.0" minordimension="1" name="rateAC" value="0.2"/>
				<parameter dimension="1" id="rateAG.alignment" lower="0.0" minordimension="1" name="rateAG" value="5.0"/>
				<parameter dimension="1" id="rateAT.alignment" lower="0.0" minordimension="1" name="rateAT" value="0.5"/>
				<parameter dimension="1" id="rateCG.alignment" lower="0.0" minordimension="1" name="rateCG" value="0.5"/>
				<parameter dimension="1" id="rateCT.alignment" lower="0.0" minordimension="1" name="rateCT" value="1.0"/>
				<parameter dimension="1" id="rateGT.alignment" lower="0.0" minordimension="1" name="rateGT" value="0.2"/>
                <frequencies id="freqs" spec="Frequencies">
					<parameter name='frequencies' value='0.25 0.25 0.25 0.25'/>
				</frequencies>
            </substModel>
-->
<!--
            <substModel id="new" spec="GTR">
				<parameter dimension="1" id="rateAC.alignment" lower="0.0" minordimension="1" name="rateAC" value="0.2"/>
				<parameter dimension="1" id="rateAG.alignment" lower="0.0" minordimension="1" name="rateAG" value="5.0"/>
				<parameter dimension="1" id="rateAT.alignment" lower="0.0" minordimension="1" name="rateAT" value="0.5"/>
				<parameter dimension="1" id="rateCG.alignment" lower="0.0" minordimension="1" name="rateCG" value="0.1"/>
				<parameter dimension="1" id="rateCT.alignment" lower="0.0" minordimension="1" name="rateCT" value="1.0"/>
				<parameter dimension="1" id="rateGT.alignment" lower="0.0" minordimension="1" name="rateGT" value="0.2"/>
                <frequencies id="freqs" spec="Frequencies">
					<parameter name='frequencies' value='0.25 0.25 0.25 0.25'/>
				</frequencies>
            </substModel>
-->
	    </siteModel>

        <branchRateModel id="StrictClock" spec="beast.evolution.branchratemodel.StrictClockModel">
            <parameter dimension="1" estimate="false" id="clockRate" minordimension="1" name="clock.rate" value="1.0"/>
        </branchRateModel>
	</run>
</beast>
