From 0d2c7c948457247fcfbcd3d3678ebf40aa7b4062 Mon Sep 17 00:00:00 2001
From: "Fabio K. Mendes" <binhologia@gmail.com>
Date: Wed, 24 Oct 2018 22:54:15 +1300
Subject: [PATCH] Renamed example files.

---
 examples/CLaSSE_fixed_tree_example.xml | 130 -------------
 examples/CLaSSE_gene_tree_example.xml  | 246 -------------------------
 2 files changed, 376 deletions(-)
 delete mode 100644 examples/CLaSSE_fixed_tree_example.xml
 delete mode 100644 examples/CLaSSE_gene_tree_example.xml

diff --git a/examples/CLaSSE_fixed_tree_example.xml b/examples/CLaSSE_fixed_tree_example.xml
deleted file mode 100644
index 92a20fc..0000000
--- a/examples/CLaSSE_fixed_tree_example.xml
+++ /dev/null
@@ -1,130 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" required="BEAST v2.5.0" version="2.5">
-
-<run id="mcmc" spec="MCMC" chainLength="1000000">
-    <state id="state" storeEvery="10000">
-        <stateNode idref="SympatricRate"/>
-        <stateNode idref="SubsympatricRate"/>
-        <stateNode idref="VicariantRate"/>
-        <stateNode idref="JumpRate"/>
-        <stateNode idref="Mu"/>
-        <stateNode idref="FlatQMatrix"/>
-    </state>
-
-    <distribution id="posterior" spec="util.CompoundDistribution">   
-
-        <distribution id="prior" spec="util.CompoundDistribution">        
-
-            <distribution id="SympatricRatePrior" spec="beast.math.distributions.Prior" x="@SympatricRate"> 
-            	<distr id="LogNormal.SympatricRate" spec="beast.math.distributions.LogNormalDistributionModel" offset="0.0" meanInRealSpace="false">
-            		<parameter name="M" value="-1.465125" estimate="false"/>
-            		<parameter name="S" value="1.0" estimate="false"/>
-            	</distr>
-            </distribution>
-                       
-            <distribution id="SubsympatricRatePrior" spec="beast.math.distributions.Prior" x="@SubsympatricRate"> 
-            	<distr id="LogNormal.SubSympatricRate" spec="beast.math.distributions.LogNormalDistributionModel" offset="0.0" meanInRealSpace="false">
-            		<parameter name="M" value="-1.465125" estimate="false"/>
-            		<parameter name="S" value="1.0" estimate="false"/>
-            	</distr>
-            </distribution>
-                       
-            <distribution id="VicariantRatePrior" spec="beast.math.distributions.Prior" x="@VicariantRate"> 
-            	<distr id="LogNormal.VicariantRate" spec="beast.math.distributions.LogNormalDistributionModel" offset="0.0" meanInRealSpace="false">
-            		<parameter name="M" value="-1.465125" estimate="false"/>
-            		<parameter name="S" value="1.0" estimate="false"/>
-            	</distr>
-            </distribution>
-            
-            <distribution id="JumpRatePrior" spec="beast.math.distributions.Prior" x="@JumpRate"> 
-            	<distr id="LogNormal.JumpRate" spec="beast.math.distributions.LogNormalDistributionModel" offset="0.0" meanInRealSpace="false">
-            		<parameter name="M" value="-1.465125" estimate="false"/>
-            		<parameter name="S" value="1.0" estimate="false"/>
-            	</distr>
-            </distribution>
-            
-            <distribution id="MuPrior" spec="beast.math.distributions.Prior" x="@Mu"> 
-            	<distr id="LogNormal.Mu" spec="beast.math.distributions.LogNormalDistributionModel" offset="0.0" meanInRealSpace="false">
-            		<parameter name="M" value="-1.465125" estimate="false"/>
-            		<parameter name="S" value="1.0" estimate="false"/>
-            	</distr>
-            </distribution>
-            
-            <distribution id="FlatQMatrixPrior" spec="beast.math.distributions.Prior" x="@FlatQMatrix"> 
-            	<distr id="LogNormal.FlatQMatrix" spec="beast.math.distributions.Exponential" offset="0.0" mean="0.01"/>
-            </distribution>
-        </distribution> <!-- END prior -->
-        
-        <distribution id="likelihood" spec="util.CompoundDistribution" useThreads="true">
-			<distribution id="StateDependentSpeciationExtinctionProcess" spec="SSE.StateDependentSpeciationExtinctionProcess" incorporateCladogenesis="true">
-			    <tree id="FixedTree" spec="beast.util.TreeParser" IsLabelledNewick="true" adjustTipHeights="false" newick="(((Human:1.0,Chimp:1.0):1.0,Gorilla:2.0):1.0,Orang:3.0);" offset="0" singlechild="false">
-			        <taxonset id="TaxonSet" spec="TaxonSet">
-			            <taxon id="Human" spec="Taxon"/>
-			            <taxon id="Chimp" spec="Taxon"/>
-			            <taxon id="Gorilla" spec="Taxon"/>
-			            <taxon id="Orang" spec="Taxon"/>
-			        </taxonset>
-			    </tree>
-			
-			    <traitStash id="TraitStash" spec="SSE.TraitStash" value="Human=2,Chimp=2,Gorilla=2,Orang=3" numberOfStates="4">
-			        <taxa idref="TaxonSet"/>
-			    </traitStash>
-
-			    <instantaneousRateMatrix id="InstantaneousRateMatrix" spec="SSE.InstantaneousRateMatrix" numberOfStates="4">
-			        <parameter id="FlatQMatrix" dimension="12" lower="0.0" name="flatQMatrix">0.0 0.0 0.0 0.01 0.0 0.01 0.01 0.0 0.01 0.0 0.01 0.01</parameter>
-			    </instantaneousRateMatrix>
-			
-			    <cladogeneticStash id="CladogeneticSpeciationRateStash" spec="SSE.CladogeneticSpeciationRateStash">
-			        <cladoTriplets id="CladoTriplet" spec="SSE.CladoTriplet" leftChildState="1" parentState="1" rightChildState="1" speciationType="SYMPATRY"/>
-			        <cladoTriplets id="CladoTriplet1" spec="SSE.CladoTriplet" leftChildState="2" parentState="2" rightChildState="2" speciationType="SYMPATRY"/>
-			        <cladoTriplets id="CladoTriplet2" spec="SSE.CladoTriplet" leftChildState="3" parentState="3" rightChildState="3" speciationType="SYMPATRY"/>
-			        <cladoTriplets id="CladoTriplet3" spec="SSE.CladoTriplet" leftChildState="2" parentState="2" rightChildState="3" speciationType="JUMPDISPERSAL"/>
-			        <cladoTriplets id="CladoTriplet4" spec="SSE.CladoTriplet" leftChildState="2" parentState="3" rightChildState="3" speciationType="JUMPDISPERSAL"/>
-			        <cladoTriplets id="CladoTriplet5" spec="SSE.CladoTriplet" leftChildState="2" parentState="4" rightChildState="3" speciationType="VICARIANCE"/>
-			        <cladoTriplets id="CladoTriplet6" spec="SSE.CladoTriplet" leftChildState="2" parentState="4" rightChildState="4" speciationType="SUBSYMPATRY"/>
-			        <cladoTriplets id="CladoTriplet7" spec="SSE.CladoTriplet" leftChildState="3" parentState="4" rightChildState="4" speciationType="SUBSYMPATRY"/>
-			        <sympatricRate id="SympatricRate" spec="parameter.RealParameter">0.32222224</sympatricRate>
-			        <subsympatricRate id="SubsympatricRate" spec="parameter.RealParameter">0.05370370666666666</subsympatricRate>
-			        <vicariantRate id="VicariantRate" spec="parameter.RealParameter">0.05370370666666666</vicariantRate>
-			        <jumpRate id="JumpRate" spec="parameter.RealParameter">0.01</jumpRate>
-			    </cladogeneticStash>
-			
-			    <mu id="Mu" dimension="4" spec="parameter.RealParameter">0.1 0.1 0.1 0.1</mu>
-			
-			    <pi id="Pi" dimension="8" spec="parameter.RealParameter">0.0 0.0 0.0 0.0 0.25 0.25 0.25 0.25</pi>
-			</distribution> <!-- END SSE -->
-        </distribution> <!-- END Likelihood -->
-    </distribution> <!-- END Posterior -->
-
-    <operator id="SympatricRateScaler" spec="ScaleOperator" parameter="@SympatricRate" scaleFactor="0.75" weight="3.0"/>
-    <operator id="SubsympatricRateScaler" spec="ScaleOperator" parameter="@SubsympatricRate" scaleFactor="0.75" weight="3.0"/>
-    <operator id="VicariantRateScaler" spec="ScaleOperator" parameter="@VicariantRate" scaleFactor="0.75" weight="3.0"/>
-    <operator id="JumpRateScaler" spec="ScaleOperator" parameter="@JumpRate" scaleFactor="0.75" weight="3.0"/>
-    <operator id="MuScaler" spec="ScaleOperator" parameter="@Mu" scaleFactor="0.75" weight="3.0"/>
-    <operator id="FlatQMatrixScaler" spec="ScaleOperator" parameter="@FlatQMatrix" scaleFactor="0.75" weight="3.0"/>
-
-    <logger id="tracelog" fileName="CLaSSE_fixed_tree.log" logEvery="10000" model="@posterior" sanitiseHeaders="true" sort="smart">
-        <log idref="posterior"/>
-        <log idref="likelihood"/>
-        <log idref="prior"/>
-        <log idref="SympatricRate"/>
-        <log idref="SubsympatricRate"/>
-        <log idref="VicariantRate"/>
-        <log idref="JumpRate"/>
-        <log idref="Mu"/>
-        <log idref="FlatQMatrix"/>
-    </logger>
-
-    <logger id="screenlog" logEvery="10000">
-        <log idref="posterior"/>
-        <log id="ESS.0" spec="util.ESS" arg="@posterior"/>
-        <log idref="likelihood"/>
-        <log idref="prior"/>
-    </logger>
-
-    <logger id="treelog.t:firsthalf" fileName="CLaSSE_fixed_tree.trees" logEvery="1000000" mode="tree">
-        <log id="TreeWithMetaDataLogger" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@FixedTree"/>
-    </logger>
-
-</run>
-</beast>
\ No newline at end of file
diff --git a/examples/CLaSSE_gene_tree_example.xml b/examples/CLaSSE_gene_tree_example.xml
deleted file mode 100644
index f13f2bd..0000000
--- a/examples/CLaSSE_gene_tree_example.xml
+++ /dev/null
@@ -1,246 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast beautitemplate='Standard' beautistatus='' namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" required="BEAST v2.5.0" version="2.5">
-        
-    <data id="seq0" name="alignment">
-        <sequence id="seq_sp10" taxon="sp10" totalcount="4" value="CAATCTGCAATTCGAGATGCGTGATTTGAGGCCTCACGTT"/>
-        <sequence id="seq_sp11" taxon="sp11" totalcount="4" value="CAATCTGCAATTCGAGATGCATGATTTGAGGCCTCACGTT"/>
-        <sequence id="seq_sp12" taxon="sp12" totalcount="4" value="GAATCTGCAATCCGAGATGCATGATTTGAACCCTCACGTT"/>
-        <sequence id="seq_sp13" taxon="sp13" totalcount="4" value="CAATCTGCAATTCGAGATGCATGATTTGAGTCCTCACGTT"/>
-        <sequence id="seq_sp14" taxon="sp14" totalcount="4" value="CGATCTGCAAATCGAAATGCAGGATTTTGAGCCTCACGTT"/>
-        <sequence id="seq_sp15" taxon="sp15" totalcount="4" value="CGATCTGCAAATCGAAATGCATGATTTTGAGCCTCACGTT"/>
-        <sequence id="seq_sp16" taxon="sp16" totalcount="4" value="CAATCCGCAATTCGAGATGCATGATTTGAGGCCTCAAGTT"/>
-        <sequence id="seq_sp17" taxon="sp17" totalcount="4" value="CAATCTGCAATTCGAGATGCATGATTTGAGGCCTCACGTT"/>
-        <sequence id="seq_sp18" taxon="sp18" totalcount="4" value="CAATCTGCAATTCGAGATGGATGATTTGAGGCCTCAAGTT"/>
-        <sequence id="seq_sp19" taxon="sp19" totalcount="4" value="CAATCTGCAATTCGAGACGCATAATTTGAGGCCTCACGTT"/>
-        <sequence id="seq_sp20" taxon="sp20" totalcount="4" value="CAATTTGTAGTGAGACATACATGATTTGAGGCCTCACGTT"/>
-        <sequence id="seq_sp21" taxon="sp21" totalcount="4" value="CAGTCTGTAATGAGACATACATGATTTGAGGCCTCACGTT"/>
-        <sequence id="seq_sp22" taxon="sp22" totalcount="4" value="CAATCTGCCATTTGAGATGCATGATTTGAGGCCTCAAGTT"/>
-        <sequence id="seq_sp23" taxon="sp23" totalcount="4" value="CAATCTGCAATTCGAGATGCATGATTTGAGGCCTCAAGTT"/>
-        <sequence id="seq_sp24" taxon="sp24" totalcount="4" value="CAGTCTGCAATTCGAGACGCATAATTTGAGGCCTCACGTT"/>
-        <sequence id="seq_sp25" taxon="sp25" totalcount="4" value="CAATCTGCAATTCGAGACGCATAATTTGAGGCCTCACGTT"/>
-        <sequence id="seq_sp26" taxon="sp26" totalcount="4" value="CAATCTGCAATTCGAGATGCATGATTTGGGGCCTCACGTT"/>
-        <sequence id="seq_sp27" taxon="sp27" totalcount="4" value="CAATCTGCAATTCGAGACGCATAATTTGAGGCCTCACATT"/>
-        <sequence id="seq_sp28" taxon="sp28" totalcount="4" value="CAATCTGCAATTCGAGACGCATAATTTGAGGCCTCACATT"/>
-        <sequence id="seq_sp29" taxon="sp29" totalcount="4" value="CAATCTGCAATTCGAGACGCATAATTTGAGGCCTCACATT"/>
-        <sequence id="seq_sp3" taxon="sp3" totalcount="4" value="CAATGTGCAATTCGAGATGCACGATTTAAGGCCTCACGTT"/>
-        <sequence id="seq_sp30" taxon="sp30" totalcount="4" value="CAATCTGCAATTCTAGATGCATGATTTGGGGCCTCACGTT"/>
-        <sequence id="seq_sp31" taxon="sp31" totalcount="4" value="CAATCTGCAATTCTAGATGCATGATTTGGGGCCTCACGTT"/>
-        <sequence id="seq_sp32" taxon="sp32" totalcount="4" value="CAACCTGCAATTCGAGACGCATAATTTGAGGCCTCACATT"/>
-        <sequence id="seq_sp33" taxon="sp33" totalcount="4" value="CAACCTGCAATTCGAGACGCATAATTTGAGGCCTCACATT"/>
-        <sequence id="seq_sp5" taxon="sp5" totalcount="4" value="CGATCTGCAATTCGAGATGCACGATTTGAGGCCTTGCATC"/>
-        <sequence id="seq_sp6" taxon="sp6" totalcount="4" value="CGATCTGCAATTCGAGAAGCATGCTTTGAGACCTCATATT"/>
-        <sequence id="seq_sp7" taxon="sp7" totalcount="4" value="CGACTTGCAATTCGAGAAGCATGATTTGAGGCCTCACACT"/>
-        <sequence id="seq_sp8" taxon="sp8" totalcount="4" value="CGATCTGCAGTTCGAGATCCATGATTTGAGGCCTCACATT"/>
-        <sequence id="seq_sp9" taxon="sp9" totalcount="4" value="CAATCTGCAATTGGAGATGCATGATTTGGGGCCTCACGTT"/>
-      
-      	<taxonset id="TaxonSet" spec="TaxonSet">
-			<taxon id="sp3" spec="Taxon"/>
-		 	<taxon id="sp5" spec="Taxon"/>
-		 	<taxon id="sp6" spec="Taxon"/>
-		 	<taxon id="sp7" spec="Taxon"/>
-		 	<taxon id="sp8" spec="Taxon"/>
-		 	<taxon id="sp9" spec="Taxon"/>
-		 	<taxon id="sp10" spec="Taxon"/>
-		 	<taxon id="sp11" spec="Taxon"/>
-		 	<taxon id="sp12" spec="Taxon"/>
-		 	<taxon id="sp13" spec="Taxon"/>
-		 	<taxon id="sp14" spec="Taxon"/>
-		 	<taxon id="sp15" spec="Taxon"/>
-		 	<taxon id="sp16" spec="Taxon"/>
-		 	<taxon id="sp17" spec="Taxon"/>
-		 	<taxon id="sp18" spec="Taxon"/>
-		 	<taxon id="sp19" spec="Taxon"/>
-		 	<taxon id="sp20" spec="Taxon"/>
-		 	<taxon id="sp21" spec="Taxon"/>
-		 	<taxon id="sp22" spec="Taxon"/>
-		 	<taxon id="sp23" spec="Taxon"/>
-		 	<taxon id="sp24" spec="Taxon"/>
-		 	<taxon id="sp25" spec="Taxon"/>
-		 	<taxon id="sp26" spec="Taxon"/>
-		 	<taxon id="sp27" spec="Taxon"/>
-		 	<taxon id="sp28" spec="Taxon"/>
-		 	<taxon id="sp29" spec="Taxon"/>
-		 	<taxon id="sp30" spec="Taxon"/>
-		 	<taxon id="sp31" spec="Taxon"/>
-		 	<taxon id="sp32" spec="Taxon"/>
-		 	<taxon id="sp33" spec="Taxon"/>
-      	</taxonset>
-    </data>
-      
-    <map name="Uniform" >beast.math.distributions.Uniform</map>    
-    <map name="Exponential" >beast.math.distributions.Exponential</map>    
-    <map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map>
-    <map name="Normal" >beast.math.distributions.Normal</map>    
-    <map name="Beta" >beast.math.distributions.Beta</map>    
-    <map name="Gamma" >beast.math.distributions.Gamma</map>    
-    <map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map>    
-    <map name="prior" >beast.math.distributions.Prior</map>    
-    <map name="InverseGamma" >beast.math.distributions.InverseGamma</map>    
-    <map name="OneOnX" >beast.math.distributions.OneOnX</map>
-    
-    <run id="mcmc" spec="MCMC" chainLength="10000000">            
-
-      <state id="state" storeEvery="1000">              
-		<tree id="Tree.t:seq0" name="stateNode">
-	  		<taxonset idref="TaxonSet"/>
-		</tree>
-
-        <stateNode idref="SympatricRate"/>
-        <stateNode idref="SubsympatricRate"/>
-        <stateNode idref="VicariantRate"/>
-        <stateNode idref="Mu"/>
-        <stateNode idref="FlatQMatrix"/>
-                    
-        <parameter id="kappa.s:seq0" lower="0.0" name="stateNode">2.0</parameter>
-
-	<parameter id="freqParameter.s:seq0" dimension="4" lower="0.0" name="stateNode" upper="1.0">0.25</parameter>
-      </state>
-            
-      <init id="RandomTree.t:seq0" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:seq0" taxa="@seq0">
-        <populationModel id="ConstantPopulation0.t:seq0" spec="ConstantPopulation">
-          <parameter id="randomPopSize.t:seq0" name="popSize">1.0</parameter>
-        </populationModel>
-      </init>
-        
-      <distribution id="posterior" spec="util.CompoundDistribution">
-        <distribution id="prior" spec="util.CompoundDistribution">
-	  <distribution id="StateDependentSpeciationExtinctionProcess" spec="SSE.StateDependentSpeciationExtinctionProcess" incorporateCladogenesis="true">
-
-	    <tree idref="Tree.t:seq0"/>
-
-	    <traitStash id="TraitStash" spec="SSE.TraitStash" value="sp3=2,sp5=2,sp6=1,sp7=1,sp8=1,sp9=2,sp10=3,sp11=1,sp12=2,sp13=1,sp14=1,sp15=1,sp16=2,sp17=1,sp18=1,sp19=2,sp20=1,sp21=3,sp22=1,sp23=3,sp24=2,sp25=3,sp26=2,sp27=3,sp28=1,sp29=2,sp30=1,sp31=1,sp32=1,sp33=3" numberOfStates="3">
-	      <taxa idref="TaxonSet"/>
-	    </traitStash>
-
-	    <instantaneousRateMatrix id="InstantaneousRateMatrix" spec="SSE.InstantaneousRateMatrix" numberOfStates="3">
-	      <parameter id="FlatQMatrix" dimension="6" lower="0.0" name="flatQMatrix">0.0904668366494489 0.0202843843027949 0.00972537517081946 0.0681905102895057 0.151011495283785 0.00458054289802842 </parameter>
-	    </instantaneousRateMatrix>
-
-	    <cladogeneticStash id="CladogeneticSpeciationRateStash" spec="SSE.CladogeneticSpeciationRateStash">
-	      <cladoTriplets id="CladoTriplet1" spec="SSE.CladoTriplet" leftChildState="1" parentState="3" rightChildState="3" speciationType="SUBSYMPATRY"/>
-	      <cladoTriplets id="CladoTriplet2" spec="SSE.CladoTriplet" leftChildState="2" parentState="3" rightChildState="3" speciationType="SUBSYMPATRY"/>
-	      <cladoTriplets id="CladoTriplet3" spec="SSE.CladoTriplet" leftChildState="1" parentState="1" rightChildState="1" speciationType="SYMPATRY"/>
-	      <cladoTriplets id="CladoTriplet4" spec="SSE.CladoTriplet" leftChildState="2" parentState="2" rightChildState="2" speciationType="SYMPATRY"/>
-	      <cladoTriplets id="CladoTriplet5" spec="SSE.CladoTriplet" leftChildState="3" parentState="3" rightChildState="3" speciationType="SYMPATRY"/>
-	      <cladoTriplets id="CladoTriplet6" spec="SSE.CladoTriplet" leftChildState="1" parentState="3" rightChildState="2" speciationType="VICARIANCE"/>
-	      <vicariantRate id="VicariantRate" spec="parameter.RealParameter">0.0038387571442539</vicariantRate> <!-- e.g., 0.05 -->
-	      <sympatricRate id="SympatricRate" spec="parameter.RealParameter">0.00631326954961372</sympatricRate> <!-- e.g., 0.05 -->
-	      <subsympatricRate id="SubsympatricRate" spec="parameter.RealParameter">0.0240574244176969</subsympatricRate> <!-- e.g., 0.05 -->
-	    </cladogeneticStash>
-
-	    <mu id="Mu" dimension="3" spec="parameter.RealParameter">0.00838562664575875 0.0170486086508596 0.00692971966345795 </mu>
-
-	    <pi id="Pi" dimension="6" spec="parameter.RealParameter">0 0 0 0.333333333333 0.333333333333 0.333333333333</pi>
-	  </distribution>
-	  
-	  <distribution id="SympatricRatePrior" spec="beast.math.distributions.Prior" x="@SympatricRate">
-	    <distr id="Exponential.SympatricRate" spec="beast.math.distributions.Exponential" offset="0.0" mean="0.05"/>
-          </distribution>
-                       
-          <distribution id="SubsympatricRatePrior" spec="beast.math.distributions.Prior" x="@SubsympatricRate">
-	    <distr id="Exponential.SubsympatricRate" spec="beast.math.distributions.Exponential" offset="0.0" mean="0.05"/>
-	  </distribution>
-                       
-          <distribution id="VicariantRatePrior" spec="beast.math.distributions.Prior" x="@VicariantRate">
-	    <distr id="Exponential.VicariantRate" spec="beast.math.distributions.Exponential" offset="0.0" mean="0.05"/>
-          </distribution>
-                        
-          <distribution id="MuPrior" spec="beast.math.distributions.Prior" x="@Mu"> 
-	    <distr id="Exponential.Mu" spec="beast.math.distributions.Exponential" offset="0.0" mean="0.0125"/>
-	  </distribution>
-            
-          <distribution id="FlatQMatrixPrior" spec="beast.math.distributions.Prior" x="@FlatQMatrix"> 
-	    <distr id="Exponential.FlatQMatrix" spec="beast.math.distributions.Exponential" offset="0.0" mean="0.05"/>
-	  </distribution>
-
-	  <distribution id="root.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="true" tree="@Tree.t:seq0">
-	    <taxonset idref="TaxonSet"/>
-	    <LogNormal id="LogNormalDistributionModel.1" name="distr">
-              <parameter id="RealParameter.3" estimate="false" name="M">3.4</parameter>
-              <parameter id="RealParameter.4" estimate="false" lower="0.0" name="S" upper="5.0">1.0E-6</parameter>
-	    </LogNormal>
-	  </distribution>
-	    
-          <prior id="KappaPrior.s:seq0" name="distribution" x="@kappa.s:seq0">
-            <LogNormal id="LogNormalDistributionModel.0" name="distr">
-              <parameter id="RealParameter.1" estimate="false" name="M">1.0</parameter>
-              <parameter id="RealParameter.2" estimate="false" name="S">1.25</parameter>
-            </LogNormal>
-          </prior>
-        </distribution>
-                    
-      <distribution id="likelihood" spec="util.CompoundDistribution" useThreads="true">
-          <distribution id="treeLikelihood.seq0" spec="ThreadedTreeLikelihood" data="@seq0" tree="@Tree.t:seq0">
-            <siteModel id="SiteModel.s:seq0" spec="SiteModel">
-              <parameter id="mutationRate.s:seq0" estimate="false" name="mutationRate">1.0</parameter>
-              <parameter id="gammaShape.s:seq0" estimate="false" name="shape">1.0</parameter>
-              <parameter id="proportionInvariant.s:seq0" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
-
-	      <substModel id="hky.s:seq0" spec="HKY" kappa="@kappa.s:seq0">
-                <frequencies id="equalFreqs.s:seq0" spec="Frequencies" data="@seq0" estimate="false"/>
-              </substModel>
-            </siteModel>
-                                    
-            <branchRateModel id="StrictClock.c:seq0" spec="beast.evolution.branchratemodel.StrictClockModel">
-              <parameter id="clockRate.c:seq0" estimate="false" name="clock.rate">0.006568651</parameter>
-            </branchRateModel>
-                                
-          </distribution>
-      </distribution>
-    </distribution>
-
-      <operator id="TreeScaler.t:seq0" spec="ScaleOperator" scaleFactor="0.5" tree="@Tree.t:seq0" weight="3.0"/>
-            
-      <operator id="TreeRootScaler.t:seq0" spec="ScaleOperator" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:seq0" weight="3.0"/>
-            
-      <operator id="UniformOperator.t:seq0" spec="Uniform" tree="@Tree.t:seq0" weight="30.0"/>
-            
-      <operator id="SubtreeSlide.t:seq0" spec="SubtreeSlide" tree="@Tree.t:seq0" weight="15.0"/>
-            
-      <operator id="Narrow.t:seq0" spec="Exchange" tree="@Tree.t:seq0" weight="15.0"/>
-            
-      <operator id="Wide.t:seq0" spec="Exchange" isNarrow="false" tree="@Tree.t:seq0" weight="3.0"/>
-            
-      <operator id="WilsonBalding.t:seq0" spec="WilsonBalding" tree="@Tree.t:seq0" weight="3.0"/>
-
-      <operator id="KappaScaler.s:seq0" spec="ScaleOperator" parameter="@kappa.s:seq0" scaleFactor="0.5" weight="0.1"/>
-	
-      <operator id="FrequenciesExchanger.s:seq0" spec="DeltaExchangeOperator" delta="0.01" weight="0.1">
-        <parameter idref="freqParameter.s:seq0"/>
-      </operator>
-      
-      <operator id="SympatricRateScaler" spec="ScaleOperator" parameter="@SympatricRate" scaleFactor="0.75" weight="3.0"/>
-      
-      <operator id="SubsympatricRateScaler" spec="ScaleOperator" parameter="@SubsympatricRate" scaleFactor="0.75" weight="3.0"/>
-      
-      <operator id="VicariantRateScaler" spec="ScaleOperator" parameter="@VicariantRate" scaleFactor="0.75" weight="3.0"/>
-      
-      <operator id="MuScaler" spec="ScaleOperator" parameter="@Mu" scaleFactor="0.75" weight="3.0"/>
-      
-      <operator id="FlatQMatrixScaler" spec="ScaleOperator" parameter="@FlatQMatrix" scaleFactor="0.75" weight="3.0"/>
-
-      <logger id="tracelog" fileName="seq0.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">                    
-        <log idref="posterior"/>                    
-        <log idref="likelihood"/>                    
-        <log idref="prior"/>                    
-        <log idref="treeLikelihood.seq0"/>                    
-		<log idref="SympatricRate"/>
-        <log idref="SubsympatricRate"/>
-        <log idref="VicariantRate"/>
-        <log idref="Mu"/>
-        <log idref="FlatQMatrix"/>
-        <log id="TreeHeight.t:seq0" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:seq0"/>         <log idref="kappa.s:seq0"/>
-      </logger>
-            
-      <logger id="screenlog" logEvery="5000">                    
-        <log idref="posterior"/>                    
-        <log id="ESS.0" spec="util.ESS" arg="@posterior"/>                    
-        <log idref="likelihood"/>                    
-        <log idref="prior"/>                
-      </logger>
-            
-      <logger id="treelog.t:seq0" fileName="$(tree).trees" logEvery="1000" mode="tree">
-        <log id="TreeWithMetaDataLogger.t:seq0" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:seq0"/>
-      </logger>
-        
-    </run>
-</beast>