diff --git a/build.xml b/build.xml
index 6580f30..0719e50 100644
--- a/build.xml
+++ b/build.xml
@@ -8,10 +8,11 @@
 	</description>
 
 	<!-- set global properties for this build -->
-	<property name="srcBEAST_CLASSIC" location="../beast-classic/src" />
-	<property name="buildBEAST_CLASSIC" location="../beast-classic/build" />
-	<property name="libBEAST_CLASSIC" location="../beast-classic/lib" />
-	<property name="release_dir" value="../beast-classic/release" />
+	<property name="BEAST_CLASSICdir" location="../beast-classic/" />
+	<property name="srcBEAST_CLASSIC" location="${BEAST_CLASSICdir}/src" />
+	<property name="buildBEAST_CLASSIC" location="${BEAST_CLASSICdir}/build" />
+	<property name="libBEAST_CLASSIC" location="${BEAST_CLASSICdir}/lib" />
+	<property name="release_dir" value="${BEAST_CLASSICdir}/release" />
 	<property name="distBEAST_CLASSIC" location="${buildBEAST_CLASSIC}/dist" />
 	<property name="beast2path" location="../beast2" />
 	<property name="libBeast2" location="${beast2path}/lib" />
@@ -19,8 +20,10 @@
 	<property name="beast2classpath" location="${beast2path}/build" />
 	<property name="BEASTLabspath" location="../BEASTLabs" />
 	<property name="BEASTLabsclasspath" location="${BEASTLabspath}/build" />
+    <property name="beastappdir" location="../BeastFX/" />
+    <property name="beastappclasspath" location="${beastappdir}/build" />
+    <property name="beastapplib" location="${beastappdir}/locallib" />
 	<property name="Add_on_dir" value="${release_dir}/add-on" />
-	<property name="version" value="1.5.0" />
 
     <import file="${beast2path}/build.xml" />
 
@@ -29,21 +32,31 @@
 
 	<path id="classpath">
         <pathelement path="${buildBEAST_CLASSIC}"/>
-		<fileset dir="${libBeast2}" includes="junit-4.8.2.jar"/>
-		<fileset dir="${libBeast2}" includes="commons-math3-3.1.1.jar"/>
-		<fileset dir="${libBeast2}" includes="fest.jar"/>
-		<fileset dir="${libBeast2}" includes="beagle.jar"/>
-		<fileset dir="${libBeast2}" includes="jam.jar"/>
-		<fileset dir="${libBeast2}" includes="colt.jar"/>
-		<fileset dir="${libBeast2}" includes="antlr-runtime-4.7.jar"/>
-		<fileset dir="${libBEAST_CLASSIC}" includes="mtj.jar"/>
+        <fileset dir="${libBeast2}/junit" includes="junit-platform-console-standalone-1.8.2.jar"/>
+        <fileset dir="${libBEAST_CLASSIC}" includes="mtj.jar"/>
+        <fileset dir="${libBeast2}" includes="beagle.jar"/>
+        <fileset dir="${libBeast2}" includes="antlr-runtime-4.10.1.jar"/>
+        <fileset dir="${libBeast2}" includes="beagle.jar"/> 
+        <fileset dir="${libBeast2}" includes="colt.jar"/> 
+		<fileset dir="${libBeast2}" includes="commons-math3-3.6.1.jar"/>
+		<fileset dir="${beastapplib}" includes="testfx.jar"/>
         <pathelement path="${beast2classpath}"/>
+        <pathelement path="${beastappclasspath}"/>
         <pathelement path="${BEASTLabsclasspath}"/>
 	</path>
 
 	<!-- start -->
 	<target name="initBEAST_CLASSIC">
 		<echo message="${ant.project.name}: ${ant.file}" />
+
+        <available file="${BEAST_CLASSICdir}/version.xml" property="versionAvailable"/>
+        <fail unless="versionAvailable">
+              ** Required file version.xml does not exist. **
+            </fail>
+
+        <!-- Read package name and version from xml file -->
+            <xmlproperty file="${BEAST_CLASSICdir}/version.xml" prefix="fromVersionFile" />
+        <property name="BEAST_CLASSICversion" value="${fromVersionFile.package(version)}" />
 	</target>
 
 	<target name="cleanBEAST_CLASSIC">
@@ -78,20 +91,16 @@
 		<mkdir dir="${buildBEAST_CLASSIC}" />
 
 		<!-- Compile the java code from ${srcBEAST_CLASSIC} into ${buildBEAST_CLASSIC} /bin -->
-		<javac target="1.8" srcdir="${srcBEAST_CLASSIC}" destdir="${buildBEAST_CLASSIC}" classpathref="classpath" 
+		<javac srcdir="${srcBEAST_CLASSIC}" destdir="${buildBEAST_CLASSIC}" classpathref="classpath" 
 		       fork="true"
 		       memoryinitialsize="256m"
 		       memorymaximumsize="256m"
-		 	   source="1.8"
-		       target="1.8">
-<!--
-		 	   source="1.6"
-		       target="1.6">
--->
-			<include name="beast/**/**" />
-			<include name="dr/**/**" />
+		       >
+			<include name="beastclassic/**/**" />
 			<!-- compile JUnit test classes -->
+			<!--
 			<include name="test/**" />
+			-->
 		</javac>
 		<echo message="Successfully compiled." />
 	</target>
@@ -128,8 +137,7 @@
 		</jar>
 		<jar jarfile="${distBEAST_CLASSIC}/BEAST_CLASSIC.src.jar">
 			<fileset dir="${srcBEAST_CLASSIC}">
-				<include name="beast/**/*.java" />
-				<include name="dr/**/*.java" />
+				<include name="beastclassic/**/*.java" />
 				<include name="test/**/*.java" />
 				<include name="beast/**/*.png" />
 				<include name="beast/**/*.xsl" />
@@ -140,9 +148,8 @@
 				<attribute name="Built-By" value="${user.name}" />
 			</manifest>
 			<fileset dir="${buildBEAST_CLASSIC}">
-				<include name="beast/**/*.class" />
-				<include name="dr/**/*.class" />
-				<include name="util/**/*.class" />
+				<include name="beastclassic/**/*.class" />
+				<include name="test/**/*.class" />
 				<include name="**/*.properties" />
 			</fileset>
 		</jar>
@@ -200,7 +207,7 @@
 		<mkdir dir="${Add_on_dir}/lib" />
 		<mkdir dir="${Add_on_dir}/examples" />
 		<mkdir dir="${Add_on_dir}/examples/nexus" />
-		<mkdir dir="${Add_on_dir}/templates" />
+		<mkdir dir="${Add_on_dir}/fxtemplates" />
 
 		<copy todir="${Add_on_dir}">
 			<fileset file="version.xml"/>
@@ -218,16 +225,16 @@
 		<copy todir="${Add_on_dir}">
 			<fileset dir="${distBEAST_CLASSIC}" includes="BEAST_CLASSIC.src.jar" />
 		</copy>
-		<copy todir="${Add_on_dir}/templates">
-			<fileset file="templates/discrete-trait.xml" />
-			<fileset file="templates/ClassicSubtseModels.xml" />
+		<copy todir="${Add_on_dir}/fxtemplates">
+			<fileset file="fxtemplates/discrete-trait.xml" />
+			<fileset file="fxtemplates/ClassicSubtseModels.xml" />
 		</copy>
-		<jar jarfile="${distBEAST_CLASSIC}/BEAST_CLASSIC.addon.v${version}.zip">
+		<jar jarfile="${distBEAST_CLASSIC}/BEAST_CLASSIC.addon.v${BEAST_CLASSICversion}.zip">
 			<fileset dir="${Add_on_dir}">
 				<include name="**/*" />
 			</fileset>
         </jar>
-		<echo message="Add-on version v${version} release is finished." />
+		<echo message="Add-on version v${BEAST_CLASSICversion} release is finished." />
 	</target>
 
 	<target name="tutorial">
diff --git a/examples/H5N1_HA_discrete2.xml b/examples/H5N1_HA_discrete2.xml
index 070ebd4..3d23534 100644
--- a/examples/H5N1_HA_discrete2.xml
+++ b/examples/H5N1_HA_discrete2.xml
@@ -1,5 +1,5 @@
 <beast version='2.0'
-       namespace='beast.evolution.alignment:beast.core:beast.evolution.tree:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood:beast.evolution.tree.coalescent:beast.core.parameter'>
+       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.parameter'>
 
 
 	<data dataType="nucleotide" id="alignment" name="alignment">
@@ -299,7 +299,7 @@
 		</sequence>
 	</data>
 	
-	<trait id='tipDates' spec='beast.evolution.tree.TraitSet' traitname='date' units='year' value='
+	<trait id='tipDates' spec='beast.base.evolution.tree.TraitSet' traitname='date' units='year' value='
 		A_chicken_Fujian_1042_2005 = 2005.0,
 		A_Duck_Fujian_1734_2005 = 2005.0,
 		A_duck_Fujian_897_2005 = 2005.0,
@@ -398,10 +398,10 @@
 		A_duck_Hunan_1608_2005 = 2005.0,
 		A_duck_Hunan_182_2005 = 2005.0,
 		A_blackbird_Hunan_1_2004 = 2004.0'>
-		<taxa spec='beast.evolution.alignment.TaxonSet' alignment='@alignment'/>
+		<taxa spec='beast.base.evolution.alignment.TaxonSet' alignment='@alignment'/>
 	</trait>
 
-	<userDataType spec='beast.evolution.datatype.UserDataType' id='location' 
+	<userDataType spec='beast.base.evolution.datatype.UserDataType' id='location' 
 		states='7'
 		codelength='-1'
 		codeMap='
@@ -420,8 +420,8 @@
 <!--
     <distribution spec='TraitedTreeLikelihood' id="geoTreeLikelihood" dataType='@location'>
 -->
-    <distribution spec='AncestralStateTreeLikelihood' id="geoTreeLikelihood" tag='location'>
-		<data spec='AlignmentFromTrait' userDataType='@location'>
+    <distribution spec='beastclassic.evolution.likelihood.AncestralStateTreeLikelihood' id="geoTreeLikelihood" tag='location'>
+		<data spec='beastclassic.evolution.alignment.AlignmentFromTrait' userDataType='@location'>
 		    <traitSet id='traitset' spec='TraitSet' 
 			 traitname='discrete' value="
 			 		A_chicken_Fujian_1042_2005 = Fujian,
@@ -522,12 +522,12 @@
 					A_duck_Hunan_1608_2005 = Hunan,
 					A_duck_Hunan_182_2005 = Hunan,
 					A_blackbird_Hunan_1_2004 = Hunan">
-		            <taxa spec='beast.evolution.alignment.TaxonSet' alignment='@alignment'/>
+		            <taxa spec='beast.base.evolution.alignment.TaxonSet' alignment='@alignment'/>
 			</traitSet>
 		</data>
         <tree idref="tree"/>
         <siteModel spec='SiteModel' id="geoSiteModel" gammaCategoryCount='1'>
-            <substModel spec="SVSGeneralSubstitutionModel" id="svs" eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem">        
+            <substModel spec="beastclassic.evolution.substitutionmodel.SVSGeneralSubstitutionModel" id="svs" eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem">        
                 <frequencies id='freqs' spec='Frequencies'>
                         <frequencies id='frequencies' spec='parameter.RealParameter' value='0.143 0.143 0.143 0.143 0.143 0.143 0.142'/>
                 </frequencies>
@@ -565,8 +565,8 @@
 				<input name ="frequencies" id='seq.freqs' spec='Frequencies' data="@alignment"/>
 			</substModel>
 		</siteModel>
-		<branchRateModel spec='beast.evolution.branchratemodel.UCRelaxedClockModel' id="branchRates">
-			<distr id='discreteormal' spec="beast.math.distributions.LogNormalDistributionModel" meanInRealSpace='true'>
+		<branchRateModel spec='beast.base.evolution.branchratemodel.UCRelaxedClockModel' id="branchRates">
+			<distr id='discreteormal' spec="beast.base.inference.distribution.LogNormalDistributionModel" meanInRealSpace='true'>
 				<parameter name='M' id='ucld.mean' value="0.0040" lower="0.0" upper="100.0"/>
 				<parameter name='S' id='ucld.stdev' value="0.1" lower="0.0" upper="10.0"/>
 			</distr>
@@ -576,14 +576,14 @@
     </distribution>
 
 	<!-- b/(d+s) -->
-	<RPNcalculator spec="beast.math.statistic.RPNcalculator" id="actualGeoRates" expression="relativeGeoRates rateIndicator *"> 
+	<RPNcalculator spec="beast.base.inference.util.RPNcalculator" id="actualGeoRates" expression="relativeGeoRates rateIndicator *"> 
 		<parameter idref="relativeGeoRates"/>
 		<parameter idref="rateIndicator"/>
     </RPNcalculator>
-	
-	<ParameterCumSum spec="beast.core.util.Sum" id="nonZeroRates" arg="@rateIndicator"/> 
 
-    <tree spec='beast.util.ClusterTree' id='tree' clusterType='upgma' trait="@tipDates">
+	<ParameterCumSum spec="beast.base.evolution.Sum" id="nonZeroRates" arg="@rateIndicator"/> 
+
+    <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma' trait="@tipDates">
         <input name='taxa' idref='alignment'/>
     </tree>
 
@@ -611,26 +611,26 @@
 
 		<distribution spec='CompoundDistribution' id='posterior'>
 			<distribution spec='CompoundDistribution' id='prior'>
-				<distribution  x="@constant.popSize" id="popSizePrior" spec='beast.math.distributions.Prior'>
-					<distr spec='beast.math.distributions.OneOnX' id='popSizePrior_OneOnX'/>
+				<distribution  x="@constant.popSize" id="popSizePrior" spec='beast.base.inference.distribution.Prior'>
+					<distr spec='beast.base.inference.distribution.OneOnX' id='popSizePrior_OneOnX'/>
 				</distribution>
 				<distribution id="coalescent" spec="Coalescent">
-					<treeIntervals spec='TreeIntervals' id='TreeIntervals' tree='@tree'/>
+					<treeIntervals spec="beast.base.evolution.tree.TreeIntervals" id="beast.base.evolution.tree.TreeIntervals" tree='@tree'/>
 					<populationModel spec="ConstantPopulation" id='ConstantPopulation'>
 						<parameter name="popSize" id="constant.popSize" value="90." lower="0." upper="Infinity" />
 					</populationModel>
 				</distribution>
 
 				<!-- this is a cached prior in beast1 - necessary??? --> 
-				<distribution  id='discreteTraitPrior' x="@relativeGeoRates" spec='beast.math.distributions.Prior'>
-					<distr spec='beast.math.distributions.Gamma' alpha="1." beta="1." offset="0.0"/>
+				<distribution  id='discreteTraitPrior' x="@relativeGeoRates" spec='beast.base.inference.distribution.Prior'>
+					<distr spec='beast.base.inference.distribution.Gamma' alpha="1." beta="1." offset="0.0"/>
 				</distribution>
-				<distribution  x="@geoMutationRate" id="geoMuPrior" spec='beast.math.distributions.Prior'>
-					<distr spec='beast.math.distributions.Exponential' id='geoMuPrior_Exp' mean="1." offset="0.0"/>
+				<distribution  x="@geoMutationRate" id="geoMuPrior" spec='beast.base.inference.distribution.Prior'>
+					<distr spec='beast.base.inference.distribution.Exponential' id='geoMuPrior_Exp' mean="1." offset="0.0"/>
 				</distribution>
 
-				<distribution  x="@nonZeroRates" id="nonZeroRatePrior" spec='beast.math.distributions.Prior'>
-					<distr spec='beast.math.distributions.Poisson' id='nonZeroRatePrior_Poi' lambda="0.693" offset="6.0"/>
+				<distribution  x="@nonZeroRates" id="nonZeroRatePrior" spec='beast.base.inference.distribution.Prior'>
+					<distr spec='beast.base.inference.distribution.Poisson' id='nonZeroRatePrior_Poi' lambda="0.693" offset="6.0"/>
 				</distribution>
 
 			</distribution>
@@ -667,7 +667,7 @@
         <operator id='georateScaler' spec='ScaleOperator' scaleFactor="0.75" weight="30" parameter="@relativeGeoRates" scaleAllIndependently='true'/>
 	<!-- START BSSVS discrete traits          		                               -->
 		<operator spec="BitFlipOperator" id="indicatorFlip" parameter="@rateIndicator" weight="30"/>
-		<operator spec="BitFlipBSSVSOperator" id="BSSVSoperator" indicator="@rateIndicator" mu="@geoMutationRate" weight="30"/>
+		<operator spec="beastclassic.evolution.operators.BitFlipBSSVSOperator" id="BSSVSoperator" indicator="@rateIndicator" mu="@geoMutationRate" weight="30"/>
 	<!-- END BSSVS discrete traits          		                               -->
 	<!-- END discrete traits          		                               -->
 
@@ -681,13 +681,13 @@
 			<log idref="posterior"/>
 			<log idref="prior"/>
 			<log idref="likelihood"/>
-            <log id="treeModel.rootHeight" spec='beast.evolution.tree.TreeHeightLogger' tree='@tree'/>
+            <log id="treeModel.rootHeight" spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
 			<log idref="constant.popSize"/>
 			<log idref="hky.kappa"/>
 			<log idref="gammaShape"/>
 		    <log idref="ucld.mean"/>
         	<log idref="ucld.stdev"/>
-		    <log id='rateStat' spec='beast.evolution.branchratemodel.RateStatistic' tree='@tree' branchratemodel='@branchRates'/>
+		    <log id='rateStat' spec='beast.base.evolution.RateStatistic' tree='@tree' branchratemodel='@branchRates'/>
 	<!-- START discrete traits          		                               -->
             <log idref="geoMutationRate"/>
 			<log idref="geoTreeLikelihood"/>
@@ -703,11 +703,14 @@
             <log idref="geoTreeLikelihood"/>
             <log idref="geoMutationRate"/>
             <log idref="nonZeroRates"/>
+<!--
+            <log id="geoSubstModelLogger" spec="SVSGeneralSubstitutionModelLogger" dataType="@location" model="@svs"/>
+            -->
             <log idref="actualGeoRates"/>
         </logger>
         
         <logger logEvery="10000" fileName="H5N1_discrete_geo.$(seed).trees" mode='tree'>
-			<log spec='TreeWithTraitLogger' tree='@tree'>
+			<log spec='beastclassic.evolution.tree.TreeWithTraitLogger' tree='@tree'>
 				<metadata idref="posterior"/>
 				<metadata idref="geoTreeLikelihood"/>
 				<metadata idref="branchRates"/>
@@ -724,7 +727,7 @@
             <log idref="geoTreeLikelihood"/>
             <log idref="geoMutationRate"/>
             <log idref="nonZeroRates"/>
-            <log spec='beast.evolution.tree.TreeHeightLogger' tree='@tree'/>
+            <log spec='beast.base.evolution.tree.TreeHeightLogger' tree='@tree'/>
             <log idref="constant.popSize"/>
 			<log idref="ucld.mean"/>
         	<log idref="ucld.stdev"/>
diff --git a/examples/RacRABV_LogNRRW2.xml b/examples/RacRABV_LogNRRW2.xml
index dae3897..9b1fd7c 100644
--- a/examples/RacRABV_LogNRRW2.xml
+++ b/examples/RacRABV_LogNRRW2.xml
@@ -1,4 +1,4 @@
-<?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:beast.core.parameter:beast.evolution.branchratemodel" version="2.0">
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:beast.pkgmgmt:beast.base.core:beast.base.inference.parameter:beast.base.evolution.branchratemodel" version="2.0">
 
 
     <data id="RacRABV" name="alignment">
@@ -96,7 +96,7 @@
 
 
     
-	<diffusionModel id="diffusionModel" spec='beast.continuous.MultivariateDiffusionModel'>
+	<diffusionModel id="diffusionModel" spec='beastclassic.continuous.MultivariateDiffusionModel'>
 		<precisionMatrix spec='RealParameter' id='precisionMatrix' minordimension='2'>
 <!--
 				0.05 0.002 
@@ -107,15 +107,15 @@
 		</precisionMatrix>
 	</diffusionModel>
 
-	<distribution  id="precisionPrior" spec='beast.math.distributions.WishartDistribution' df='2' arg='@precisionMatrix'>
+	<distribution  id="precisionPrior" spec='beastclassic.math.distributions.WishartDistribution' df='2' arg='@precisionMatrix'>
 		<scaleMatrix spec='RealParameter' minordimension='2'>
 				1.0 0.0
 				0.0 1.0
 		</scaleMatrix>
 	</distribution>
 
-	<distribution id="rootPrior" spec='beast.math.distributions.MultivariateNormalDistribution'>
-		<arg id='rootTrait' spec='beast.evolution.tree.RootTrait' traitmap='@traitmap'/>
+	<distribution id="rootPrior" spec='beastclassic.math.distributions.MultivariateNormalDistribution'>
+		<arg id='rootTrait' spec='beastclassic.evolution.tree.RootTrait' traitmap='@traitmap'/>
 		<mean spec='RealParameter' value='0.0 0.0'/>
 		<precision spec='RealParameter' minordimension='2'>
 				0.001 0.0
@@ -125,16 +125,16 @@
 
     <branchRateModel id="branchRatesDiffusion" spec='UCRelaxedClockModel' tree='@Tree.t:RacRABV'>
         <parameter name='clock.rate' id='ucld.mean' value='1'/>
-        <distr id='lognormal' spec="beast.math.distributions.LogNormalDistributionModel"  meanInRealSpace="true">
+        <distr id='lognormal' spec="beast.base.inference.distribution.LogNormalDistributionModel"  meanInRealSpace="true">
             <M id='ucldDiffusion.mean' spec='RealParameter' value="1"/>
             <S id='ucldDiffusion.stdev' spec='RealParameter' value="0.1" lower="0" upper="5"/>
         </distr>
         <parameter spec='IntegerParameter' name='rateCategories' id='rateCategories' dimension="92" value="1"/>
     </branchRateModel>
 
-    <log id='rateStat' spec='RateStatistic' tree='@Tree.t:RacRABV' branchratemodel='@branchRatesDiffusion'/>
+    <log id='rateStat' spec='beast.base.evolution.RateStatistic' tree='@Tree.t:RacRABV' branchratemodel='@branchRatesDiffusion'/>
 
-	<traitmap id='traitmap' spec='beast.evolution.tree.TreeTraitMap' tree='@Tree.t:RacRABV' parameter='@location' traitName='location' 
+	<traitmap id='traitmap' spec='beastclassic.evolution.tree.TreeTraitMap' tree='@Tree.t:RacRABV' parameter='@location' traitName='location' 
 		randomizeupper="45 -70" randomizelower="28 -122">
 				hOH10_97.2_41.053_80.706=41.053 -80.706,
 				hWVa01_93.2_40.505_80.575=40.505 -80.575,
@@ -185,11 +185,11 @@
 				WVa22_02.7_39.635_79.995=39.635 -79.995
 	</traitmap>
 
-	<multivariateTraitLikelihood id="traitLikelihood" spec='beast.continuous.SampledMultivariateTraitLikelihood'
+	<multivariateTraitLikelihood id="traitLikelihood" spec='beastclassic.continuous.SampledMultivariateTraitLikelihood'
 		useTreeLength="true" scaleByTime="true" reportAsMultivariate="true" reciprocalRates="true" tree='@Tree.t:RacRABV'>
 		<traitParameter id='location' spec='RealParameter' value='0 0' minordimension='2'/>
-	    <data spec='AlignmentFromTraitMap' traitMap='@traitmap'>
-			<userDataType spec='beast.evolution.datatype.LocationDataType'/>
+	    <data spec='beastclassic.evolution.alignment.AlignmentFromTraitMap' traitMap='@traitmap'>
+			<userDataType spec='beastclassic.evolution.datatype.LocationDataType'/>
 		</data>
 		<siteModel spec='SiteModel' substModel='@diffusionModel'/>
 <!--
@@ -230,22 +230,22 @@
 
 
     
-<map name="Beta">beast.math.distributions.Beta</map>
-<map name="Exponential">beast.math.distributions.Exponential</map>
-<map name="InverseGamma">beast.math.distributions.InverseGamma</map>
-<map name="LogNormal">beast.math.distributions.LogNormalDistributionModel</map>
-<map name="Prior">beast.math.distributions.Prior</map>
-<map name="Gamma">beast.math.distributions.Gamma</map>
-<map name="Uniform">beast.math.distributions.Uniform</map>
-<map name="LaplaceDistribution">beast.math.distributions.LaplaceDistribution</map>
-<map name="OneOnX">beast.math.distributions.OneOnX</map>
-<map name="Normal">beast.math.distributions.Normal</map>
+<map name="Beta">beast.base.inference.distribution.Beta</map>
+<map name="Exponential">beast.base.inference.distribution.Exponential</map>
+<map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
+<map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
+<map name="Prior">beast.base.inference.distribution.Prior</map>
+<map name="Gamma">beast.base.inference.distribution.Gamma</map>
+<map name="Uniform">beast.base.inference.distribution.Uniform</map>
+<map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
+<map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
+<map name="Normal">beast.base.inference.distribution.Normal</map>
 
 
 <run chainLength="8000000" id="mcmc" spec="MCMC">
     <state id="state" storeEvery="1000">
         <tree id="Tree.t:RacRABV" name="stateNode">
-            <trait id="dateTrait.t:RacRABV" spec="beast.evolution.tree.TraitSet" traitname="date">
+            <trait id="dateTrait.t:RacRABV" spec="beast.base.evolution.tree.TraitSet" traitname="date">
 		            hOH10_97.2_41.053_80.706=1997.2,
 					hWVa01_93.2_40.505_80.575=1993.2,
 					NY01_03.4_41.057_73.794=2003.4,
@@ -310,11 +310,11 @@
 		<stateNode idref='precisionMatrix'/>
     </state>
 
-    <distribution id="posterior" spec="util.CompoundDistribution">
-        <distribution id="prior" spec="util.CompoundDistribution">
+    <distribution id="posterior" spec="beast.base.inference.CompoundDistribution">
+        <distribution id="prior" spec="beast.base.inference.CompoundDistribution">
             <distribution id="CoalescentConstant.t:RacRABV" spec="Coalescent">
                 <populationModel id="ConstantPopulation.t:RacRABV" popSize="@popSize.t:RacRABV" spec="ConstantPopulation"/>
-                <treeIntervals id="TreeIntervals.t:RacRABV" spec="TreeIntervals" tree="@Tree.t:RacRABV"/>
+                <treeIntervals id="TreeIntervals.t:RacRABV" spec="beast.base.evolution.tree.TreeIntervals" tree="@Tree.t:RacRABV"/>
             </distribution>
             <Prior id="ClockPrior.c:RacRABV" name="distribution" x="@clockRate.c:RacRABV">
                 <Uniform id="Uniform.0" name="distr"/>
@@ -331,11 +331,11 @@
 
 			<distribution idref='rootPrior'/>
 			<distribution idref='precisionPrior'/>
-            <distribution id="ucldDiffusion.stdev.prior" spec="beast.math.distributions.Prior" x="@ucldDiffusion.stdev">
-                <distr spec="beast.math.distributions.Exponential" mean='10'/>
+            <distribution id="ucldDiffusion.stdev.prior" spec="beast.base.inference.distribution.Prior" x="@ucldDiffusion.stdev">
+                <distr spec="beast.base.inference.distribution.Exponential" mean='10'/>
 			</distribution>
         </distribution>
-        <distribution id="likelihood" spec="util.CompoundDistribution">
+        <distribution id="likelihood" spec="beast.base.inference.CompoundDistribution">
             <distribution data="@RacRABV" id="treeLikelihood.RacRABV" spec="TreeLikelihood" tree="@Tree.t:RacRABV">
                 <siteModel id="SiteModel.s:RacRABV" spec="SiteModel">
                     <parameter estimate="false" id="mutationRate.s:RacRABV" name="mutationRate" value="1.0"/>
@@ -345,7 +345,7 @@
                         <frequencies id="empiricalFreqs.s:RacRABV" spec="Frequencies" data='@RacRABV'/>
                     </substModel>
                 </siteModel>
-                <branchRateModel clock.rate="@clockRate.c:RacRABV" id="StrictClock.c:RacRABV" spec="beast.evolution.branchratemodel.StrictClockModel"/>
+                <branchRateModel clock.rate="@clockRate.c:RacRABV" id="StrictClock.c:RacRABV" spec="beast.base.evolution.branchratemodel.StrictClockModel"/>
             </distribution>
 			<distribution idref='traitLikelihood'/>
         </distribution>
@@ -387,16 +387,16 @@
     <operator id="CategoriesRandomWalk" spec="IntRandomWalkOperator" windowSize='1' weight="10" parameter="@rateCategories"/>
     <operator id='CategoriesUniform' spec='UniformOperator' weight="10" parameter='@rateCategories'/>
 
-	<operator id='precisionGibbsOperator' spec='PrecisionMatrixGibbsOperator' tree='@Tree.t:RacRABV' parameter='@precisionMatrix' traitmap='@traitmap'  weight="15">
+	<operator id='precisionGibbsOperator' spec='beastclassic.evolution.operators.PrecisionMatrixGibbsOperator' tree='@Tree.t:RacRABV' parameter='@precisionMatrix' traitmap='@traitmap'  weight="15">
 		<likelihood idref='traitLikelihood'/>
 		<prior idref='precisionPrior'/>
 	</operator>
-    <operator id='traitGibbsOperator' spec='TraitGibbsOperator' tree='@Tree.t:RacRABV' precisionMatrix='@precisionMatrix' traitmap='@traitmap' weight="50">
+    <operator id='traitGibbsOperator' spec='beastclassic.evolution.operators.TraitGibbsOperator' tree='@Tree.t:RacRABV' precisionMatrix='@precisionMatrix' traitmap='@traitmap' weight="50">
 		<likelihood idref='traitLikelihood'/>
 		<!--rootprior idref="rootPrior"/-->
 	</operator>
 
-	<operator spec='RootTraitRandowWalkOperator' windowSize="10.0" weight="5" parameter='@location' traitmap='@traitmap' />
+	<operator spec='beastclassic.evolution.operators.RootTraitRandowWalkOperator' windowSize="10.0" weight="5" parameter='@location' traitmap='@traitmap' />
 
 
     <logger fileName="RacRABV.lnRRW.$(seed).log" id="tracelog" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
@@ -412,7 +412,7 @@
 		<log idref='rootPrior'/>
 		<log idref='precisionPrior'/>
 
-        <log id="TreeHeight.t:RacRABV.7taxa" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:RacRABV"/>
+        <log id="TreeHeight.t:RacRABV.7taxa" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:RacRABV"/>
         <parameter idref="clockRate.c:RacRABV" name="log"/>
         <parameter idref="kappa.s:RacRABV" name="log"/>
         <parameter idref="popSize.t:RacRABV" name="log"/>
@@ -434,7 +434,7 @@
     </logger>
 
     <logger fileName="$(tree)R.$(seed).trees" id="treelog.t:RacRABV1.lnRRW" logEvery="1000" mode="tree">
-        <log id="TreeWithMetaDataLogger.t:RacRABV" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:RacRABV">
+        <log id="TreeWithMetaDataLogger.t:RacRABV" spec="beast.base.evolution.TreeWithMetaDataLogger" tree="@Tree.t:RacRABV">
 			<metadata idref='location'/>
 			<branchratemodel idref='branchRatesDiffusion'/>
 		</log>
@@ -442,13 +442,13 @@
 
 
 <!--
-    <init spec='beast.util.TreeParser' id='tree1' initial="@Tree.t:RacRABV" taxa="@RacRABV">
+    <init spec='beast.base.evolution.tree.TreeParser' id='tree1' initial="@Tree.t:RacRABV" taxa="@RacRABV">
 		<input name='newick'>
 (((NY03_03.4_42.934_76.565:8.273346380513605,NY01_03.4_41.057_73.794:8.273346380513605):8.778378960669347,hOH10_97.2_41.053_80.706:10.851725341182906):0.9308011547075559,hWVa01_93.2_40.505_80.575:7.782526495890462)
 		</input>
 	</init>
 -->
-    <init estimate="false" id="RandomTree.t:RacRABV" initial="@Tree.t:RacRABV" spec="beast.evolution.tree.RandomTree" taxa="@RacRABV">
+    <init estimate="false" id="RandomTree.t:RacRABV" initial="@Tree.t:RacRABV" spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@RacRABV">
         <populationModel id="ConstantPopulation0.t:RacRABV" spec="ConstantPopulation">
             <parameter id="randomPopSize.t:RacRABV" name="popSize" value="1"/>
         </populationModel>
diff --git a/examples/beast1/testBinaryDollo2.xml b/examples/beast1/testBinaryDollo2.xml
index f15a9ad..56244c9 100644
--- a/examples/beast1/testBinaryDollo2.xml
+++ b/examples/beast1/testBinaryDollo2.xml
@@ -1,5 +1,5 @@
 <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'>
+    namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
 
     <data id="alignment" spec='AscertainedAlignment'>
 		<userDataType spec='beast.evolution.datatype.MutationDeathType' deathChar='0' extantCode='1'/>
@@ -33,9 +33,9 @@
 	<state>
 		<parameter name='stateNode' id='deathRate' lower="0.0" value="1.0"/>
 
-<!--		<stateNode id='tree' spec='beast.util.TreeParser' newick='(Ar:1.2587335224961815,((Dr:0.48328238018013014,An:0.48328238018013014):0.7573037533374662,(Ho:1.0658133023983523,Ca:1.0658133023983523):0.17477283111924424):0.018147388978585033)'>
+<!--		<stateNode id='tree' spec='beast.base.evolution.tree.TreeParser' newick='(Ar:1.2587335224961815,((Dr:0.48328238018013014,An:0.48328238018013014):0.7573037533374662,(Ho:1.0658133023983523,Ca:1.0658133023983523):0.17477283111924424):0.018147388978585033)'>
 (Ar:0.8884959699821183,((Dr:0.13514331794790563,An:0.13514331794790563):0.621722055422071,(Ho:0.7495724084782432,Ca:0.7495724084782432):0.007292964891733478):0.1316305966121416);'>-->
-		<stateNode id='tree' spec='beast.util.TreeParser' newick='(Ar:3,((Dr:1,An:1):1,(Ho:1,Ca:1):1):1);'>
+		<stateNode id='tree' spec='beast.base.evolution.tree.TreeParser' newick='(Ar:3,((Dr:1,An:1):1,(Ho:1,Ca:1):1):1);'>
 			<taxonset id='taxa' spec='TaxonSet' alignment='@alignment'/>
 		</stateNode>
 	</state>
@@ -74,7 +74,7 @@
             <log idref="posterior"/>
             <log idref="prior"/>
             <log idref="likelihood"/>
-            <log spec='beast.evolution.tree.TreeHeightLogger' tree='@tree'/>
+            <log spec='beast.base.evolution.tree.TreeHeightLogger' tree='@tree'/>
         </logger>
 
         <logger logEvery="10000" fileName="binaryDollo2.trees">
diff --git a/examples/testDiscreteSmall.xml b/examples/testDiscreteSmall.xml
index dee9b69..74b4030 100644
--- a/examples/testDiscreteSmall.xml
+++ b/examples/testDiscreteSmall.xml
@@ -1,5 +1,5 @@
 <beast version='2.0'
-       namespace='beast.evolution.alignment:beast.core:beast.evolution.tree:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood:beast.evolution.tree.coalescent:beast.core.parameter'>
+       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.parameter'>
 
 	<data dataType="nucleotide" id="alignment" name="alignment">
 		<sequence id="1976.609_CY005917_A/Mall/ALB/31/1976_5.NA" taxon="NA">
@@ -18,16 +18,16 @@
 			ATGGAGAGAATAGTGCTTCTTCTTGCAATAATCGGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAGAAGACACACAACGGGAAGCTCTGCAACCCAGATGGAGTGAAGCCTCTAATTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTTATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGGCCTCTGTTACCCAGGGGATTTCAATGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCGATCATGGAGCCTCATCAGGGGTGAGCTCAGCATGTTCCTATCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAATAATACATACCCACCAATAAAGGTGAGCTACAACAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCCAATGATGAGGCAGAGCAGATAAAGATCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCTATCAATTTCGATAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCGATTATGAAAAGTGAATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAATTCTAGTATGCCATTCCACAACATACACCCTCTCACCGTCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTCGCGACTGGACTCAGAAATGCCCCTCAAAGAGAGGGAGGAAGAAAAAAGAGAGGACTATTTGGAGCCATAGCAGGGTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAACGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCATTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
 		</sequence>
 	</data>
-	<trait spec='beast.evolution.tree.TraitSet' traitname='date' units='year' id='tipDates' value='
+	<trait spec='beast.base.evolution.tree.TraitSet' traitname='date' units='year' id='tipDates' value='
 		NA = 1976.0,
 		A_chicken_Fujian_1042_2005 = 2005.0,
 		A_duck_HongKong_821_2002 = 2002.0,
 		A_chicken_Guangdong_174_2004 = 2004.0,
 		A_chicken_Hebei_326_2005 = 2005.0'>
-		<taxa spec='beast.evolution.alignment.TaxonSet' alignment='@alignment'/>
+		<taxa spec='beast.base.evolution.alignment.TaxonSet' alignment='@alignment'/>
 	</trait>
 	
-	<userDataType spec='beast.evolution.datatype.UserDataType' id='location' 
+	<userDataType spec='beast.base.evolution.datatype.UserDataType' id='location' 
 		states='3'
 		codelength='-1'
 		codeMap='
@@ -40,9 +40,9 @@
 	    <distribution spec='AncestralStateTreeLikelihood' useJava="false" id="NP.traitedtreeLikelihood" data='@NP.locations' tree="@NP.tree" siteModel="@geoSiteModel" tag="location"/>
 -->
 
-    <distribution spec='AncestralStateTreeLikelihood' useJava="false" id="traitedtreeLikelihood" tag="location" useAmbiguities='false'> 
-		<leaftrait parameter='@trait(A_chicken_Fujian_1042_2005)' taxon='A_chicken_Fujian_1042_2005' spec='LeafTrait'/>
-    	<data spec="AlignmentFromTrait" userDataType="@location">
+    <distribution spec='beastclassic.evolution.likelihood.AncestralStateTreeLikelihood' useJava="false" id="traitedtreeLikelihood" tag="location" useAmbiguities='false'> 
+		<leaftrait parameter='@trait(A_chicken_Fujian_1042_2005)' taxon='A_chicken_Fujian_1042_2005' spec='beastclassic.evolution.likelihood.LeafTrait'/>
+    	<data spec="beastclassic.evolution.alignment.AlignmentFromTrait" userDataType="@location">
 			<traitSet id='traitset' spec='TraitSet'  
 			 traitname='discrete' value="
 						NA = Hebei,
@@ -50,12 +50,12 @@
 						A_duck_HongKong_821_2002 = HongKong,
 						A_chicken_Guangdong_174_2004 = Guangdong,
 						A_chicken_Hebei_326_2005 = Hebei">
-				<taxa spec='beast.evolution.alignment.TaxonSet' alignment='@alignment'/>
+				<taxa spec='beast.base.evolution.alignment.TaxonSet' alignment='@alignment'/>
 			</traitSet>
 		</data>
         <tree idref="tree"/>
         <siteModel spec='SiteModel' id="geoSiteModel" gammaCategoryCount='1'>
-            <substModel spec="SVSGeneralSubstitutionModel" id="svs" rateIndicator='@rateIndicator'>        
+            <substModel spec="beastclassic.evolution.substitutionmodel.SVSGeneralSubstitutionModel" id="svs" rateIndicator='@rateIndicator'>        
             <!--substModel spec="GeneralSubstitutionModel"-->        
                 <frequencies id='freqs' spec='Frequencies'>
                         <frequencies id='frequencies' spec='parameter.RealParameter' value='.33 .33 .34'/>
@@ -64,7 +64,7 @@
             </substModel>
             <!--mutationRate idref="geoMutationRate"/-->
         </siteModel>
-		<branchRateModel id="StrictClockModel" spec="beast.evolution.branchratemodel.StrictClockModel">
+		<branchRateModel id="StrictClockModel" spec="beast.base.evolution.branchratemodel.StrictClockModel">
 			<parameter id="geoclock.rate" name="clock.rate" value="1.0"/>
 		</branchRateModel>
     </distribution>
@@ -81,8 +81,8 @@
 				<input name ="frequencies" id='seq.freqs' spec='Frequencies' data="@alignment"/>
 			</substModel>
 		</siteModel>
-		<branchRateModel spec='beast.evolution.branchratemodel.UCRelaxedClockModel' id="branchRates">
-			<distr id='lognormal' spec="beast.math.distributions.LogNormalDistributionModel" meanInRealSpace="true">
+		<branchRateModel spec='beast.base.evolution.branchratemodel.UCRelaxedClockModel' id="branchRates">
+			<distr id='lognormal' spec="beast.base.inference.distribution.LogNormalDistributionModel" meanInRealSpace="true">
 				<parameter name='M' id='ucld.mean' value="1." lower="0.0" upper="Infinity"/>
 				<parameter name='S' id='ucld.stdev' value="0.33333" lower="0.0" upper="Infinity"/>
 			</distr>
@@ -93,7 +93,7 @@
    
  
 	<!-- b/(d+s) -->
-	<RPNcalculator spec="beast.math.statistic.RPNcalculator" id="actualGeoRates" expression="relativeGeoRates rateIndicator *"> 
+	<RPNcalculator spec="beast.base.inference.util.RPNcalculator" id="actualGeoRates" expression="relativeGeoRates rateIndicator *"> 
 		<parameter idref="relativeGeoRates"/>
 		<parameter idref="rateIndicator"/>
     </RPNcalculator>
@@ -101,7 +101,7 @@
 <!--
 	<ParameterCumSum spec="beast.core.util.ParameterCumSum" id="nonZeroRates" arg="@rateIndicator"/> 
 -->
-    <tree spec='beast.util.ClusterTree' id='tree' clusterType='upgma' trait="@tipDates">
+    <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma' trait="@tipDates">
         <input name='taxa' idref='alignment'/>
     </tree>
 		
@@ -134,31 +134,31 @@
 			<distribution spec='CompoundDistribution' id='prior'>
 <!--
 				<distribution id="transitionMatrixWellConnected" spec="beast.math.distributions.TransitionMatrixPrior" substitutionModel="@svs" rateIndicator="@rateIndicator"/>
-				<distribution  x="@nonZeroRates" id="nonZeroRatePrior" spec='beast.math.distributions.Prior'>
-					<distr spec='beast.math.distributions.Poisson' id='nonZeroRatePrior_Poi' mean="0.693" offset="3.0"/>
+				<distribution  x="@nonZeroRates" id="nonZeroRatePrior" spec='beast.base.inference.distribution.Prior'>
+					<distr spec='beast.base.inference.distribution.Poisson' id='nonZeroRatePrior_Poi' mean="0.693" offset="3.0"/>
 				</distribution>
 -->
-				<distribution  x="@popSize" id="popSizePrior" spec='beast.math.distributions.Prior'>
-					<distr spec='beast.math.distributions.OneOnX' id='popSizePrior_OneOnX'/>
+				<distribution  x="@popSize" id="popSizePrior" spec='beast.base.inference.distribution.Prior'>
+					<distr spec='beast.base.inference.distribution.OneOnX' id='popSizePrior_OneOnX'/>
 				</distribution>
-				<distribution  x="@ucld.mean" id="ucld.meanPrior" spec='beast.math.distributions.Prior'>
-					<distr spec='beast.math.distributions.Exponential' id='ucld.meanPrior_Exp' mean="1." offset="0.0"/>
+				<distribution  x="@ucld.mean" id="ucld.meanPrior" spec='beast.base.inference.distribution.Prior'>
+					<distr spec='beast.base.inference.distribution.Exponential' id='ucld.meanPrior_Exp' mean="1." offset="0.0"/>
 				</distribution>
-				<distribution  x="@ucld.stdev" id="ucld.stdevPrior" spec='beast.math.distributions.Prior'>
-					<distr spec='beast.math.distributions.Exponential' id='ucld.stdevPrior_Exp' mean="0.333333333333" offset="0.0"/>
+				<distribution  x="@ucld.stdev" id="ucld.stdevPrior" spec='beast.base.inference.distribution.Prior'>
+					<distr spec='beast.base.inference.distribution.Exponential' id='ucld.stdevPrior_Exp' mean="0.333333333333" offset="0.0"/>
 				</distribution>
-				<distribution  id='kappaPrior' x="@hky.kappa" spec='beast.math.distributions.Prior'>
-					<distr spec='beast.math.distributions.LogNormalDistributionModel' M="1." S="1.25" offset="0.0" meanInRealSpace="false"/>
+				<distribution  id='kappaPrior' x="@hky.kappa" spec='beast.base.inference.distribution.Prior'>
+					<distr spec='beast.base.inference.distribution.LogNormalDistributionModel' M="1." S="1.25" offset="0.0" meanInRealSpace="false"/>
 				</distribution>
-				<distribution  id='geoclockPrior' x="@geoclock.rate" spec='beast.math.distributions.Prior'>
-					<distr spec='beast.math.distributions.Gamma' alpha="0.001" beta="1000." offset="0.0"/>
+				<distribution  id='geoclockPrior' x="@geoclock.rate" spec='beast.base.inference.distribution.Prior'>
+					<distr spec='beast.base.inference.distribution.Gamma' alpha="0.001" beta="1000." offset="0.0"/>
 				</distribution>
-				<distribution  id='discreteTraitPrior' x="@relativeGeoRates" spec='beast.math.distributions.Prior'>
-					<distr spec='beast.math.distributions.Gamma' alpha="1." beta="1." offset="0.0"/>
+				<distribution  id='discreteTraitPrior' x="@relativeGeoRates" spec='beast.base.inference.distribution.Prior'>
+					<distr spec='beast.base.inference.distribution.Gamma' alpha="1." beta="1." offset="0.0"/>
 				</distribution>
 				<distribution spec='CompoundDistribution' id='coalescentLikelihood'>
 					<distribution id="coalescent" spec="Coalescent">
-						<treeIntervals spec='TreeIntervals' id='TreeIntervals'>
+						<treeIntervals spec="beast.base.evolution.tree.TreeIntervals" id="beast.base.evolution.tree.TreeIntervals">
 							 <tree idref="tree"/>
 						</treeIntervals>
 						<populationModel spec="ConstantPopulation" id='ConstantPopulation' popSize='@popSize'/>
@@ -172,7 +172,7 @@
 <!--
 	    <operator id="UniformOperator.chicken_trait" spec="UniformOperator" parameter="@trait(A_chicken_Fujian_1042_2005)" weight="30.0"/>
 -->
-	    <operator id="IntegerOperator.blackbird_Hunan" spec="GeneralIntegerOperator" parameter="@trait(A_chicken_Fujian_1042_2005)" weight="30.0">
+	    <operator id="IntegerOperator.blackbird_Hunan" spec="beastclassic.evolution.operators.GeneralIntegerOperator" parameter="@trait(A_chicken_Fujian_1042_2005)" weight="30.0">
 			<index id='chicken_indices' spec='parameter.IntegerParameter' value='0 2'/>
 		</operator>
 
@@ -186,7 +186,7 @@
 		<operator id='ucldStdevScaler' spec='ScaleOperator' parameter="@ucld.stdev" scaleFactor="0.75" weight="3"/>		
 
 	 	<operator id='geoMuScaler' spec='ScaleOperator' scaleFactor="0.9" weight="3" parameter="@geoclock.rate"/>  
-		<operator spec="BitFlipBSSVSOperator" id="BSSVSoperator" indicator="@rateIndicator" mu="@geoclock.rate" weight="30"/>
+		<operator spec="beastclassic.evolution.operators.BitFlipBSSVSOperator" id="BSSVSoperator" indicator="@rateIndicator" mu="@geoclock.rate" weight="30"/>
 	
         <operator spec='Uniform' weight="20" tree="@tree"/>
         <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="1.0" rootOnly='true' tree="@tree"/>
@@ -209,7 +209,7 @@
             <log idref="prior"/>
             <log idref="coalescentLikelihood"/>
             <log idref="traitedtreeLikelihood"/>
-            <log spec='beast.evolution.tree.TreeHeightLogger' tree='@tree'/>
+            <log spec='beast.base.evolution.tree.TreeHeightLogger' tree='@tree'/>
             <log idref="popSize"/>
             <log idref="hky.kappa"/>							
 			<log idref="ucld.mean"/>
@@ -231,7 +231,7 @@
         </logger>
         
 		<logger logEvery="10000" fileName="testPhylogeo_H5N1_4taxa_$(seed).trees" mode="tree">
-			<log spec='TreeWithTraitLogger' tree='@tree'>
+			<log spec='beastclassic.evolution.tree.TreeWithTraitLogger' tree='@tree'>
 				<metadata idref="posterior"/>
 				<metadata idref="traitedtreeLikelihood"/>
 				<metadata idref="branchRates"/>
@@ -249,7 +249,7 @@
             <log idref="traitedtreeLikelihood"/>
             <log idref="geoclock.rate"/>
 <!--            <log idref="nonZeroRates"/>-->
-            <log spec='beast.evolution.tree.TreeHeightLogger' tree='@tree'/>
+            <log spec='beast.base.evolution.tree.TreeHeightLogger' tree='@tree'/>
 							
             <log idref="hky.kappa"/>
 			<log idref="ucld.mean"/>
diff --git a/examples/testSkyRide.xml b/examples/testSkyRide.xml
index ae9f264..2ef6f58 100644
--- a/examples/testSkyRide.xml
+++ b/examples/testSkyRide.xml
@@ -1,4 +1,4 @@
-<?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" version="2.0">
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast beautitemplate='Standard' beautistatus='' namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood" version="2.0">
 
 
     <data id="x" name="alignment">
@@ -45,22 +45,22 @@
 
 
     
-<map name="Beta">beast.math.distributions.Beta</map>
-<map name="Exponential">beast.math.distributions.Exponential</map>
-<map name="InverseGamma">beast.math.distributions.InverseGamma</map>
-<map name="LogNormal">beast.math.distributions.LogNormalDistributionModel</map>
-<map name="Gamma">beast.math.distributions.Gamma</map>
-<map name="Uniform">beast.math.distributions.Uniform</map>
-<map name="prior">beast.math.distributions.Prior</map>
-<map name="LaplaceDistribution">beast.math.distributions.LaplaceDistribution</map>
-<map name="OneOnX">beast.math.distributions.OneOnX</map>
-<map name="Normal">beast.math.distributions.Normal</map>
+<map name="Beta">beast.base.inference.distribution.Beta</map>
+<map name="Exponential">beast.base.inference.distribution.Exponential</map>
+<map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
+<map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
+<map name="Gamma">beast.base.inference.distribution.Gamma</map>
+<map name="Uniform">beast.base.inference.distribution.Uniform</map>
+<map name="prior">beast.base.inference.distribution.Prior</map>
+<map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
+<map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
+<map name="Normal">beast.base.inference.distribution.Normal</map>
 
 
 <run chainLength="10000000" id="mcmc" spec="MCMC">
     <state id="state" storeEvery="5000">
         <tree id="Tree.t:x" name="stateNode">
-            <trait id="dateTrait.t:x" spec="beast.evolution.tree.TraitSet" traitname="date-forward">
+            <trait id="dateTrait.t:x" spec="beast.base.evolution.tree.TraitSet" traitname="date-forward">
 W2P1D0=0.0, <!-- oldest sample -->
 W2P12D0=0.0,
 W2P4D5=5.0,
@@ -109,8 +109,8 @@ W2P7D54=54.0 <!-- newest sample -->
 		<stateNode idref="skyridePrecision"/>
     </state>
 
-    <distribution id="posterior" spec="util.CompoundDistribution">
-        <distribution id="prior" spec="util.CompoundDistribution">
+    <distribution id="posterior" spec="beast.base.inference.CompoundDistribution">
+        <distribution id="prior" spec="beast.base.inference.CompoundDistribution">
             <prior id="ClockPrior.c:x" name="distribution" x="@clockRate.c:x">
                 <Uniform id="Uniform.01" name="distr"/>
             </prior>
@@ -129,7 +129,7 @@ W2P7D54=54.0 <!-- newest sample -->
 			</prior>
 
 			<!-- Generate a gmrfSkyrideLikelihood for GMRF Bayesian Skyride process      -->
-			<distribution id="skyride" timeAwareSmoothing="true" spec='beast.evolution.tree.coalescent.GMRFSkyrideLikelihood'> <!-- randomizeTree="false" -->
+			<distribution id="skyride" timeAwareSmoothing="true" spec='beastclassic.evolution.tree.coalescent.GMRFSkyrideLikelihood'> <!-- randomizeTree="false" -->
 				<!-- skyride.logPopSize is in log units unlike other popSize                 -->
 				<populationSizes id="skyrideLogPopSize" dimension="32" value="6.29156913955832"  spec='parameter.RealParameter'/>
 				<groupSizes id="skyrideGroupSize" dimension="32" spec='parameter.RealParameter' value='1'/>
@@ -138,7 +138,7 @@ W2P7D54=54.0 <!-- newest sample -->
 			</distribution>
 
         </distribution>
-        <distribution id="likelihood" spec="util.CompoundDistribution">
+        <distribution id="likelihood" spec="beast.base.inference.CompoundDistribution">
             <distribution data="@x" id="treeLikelihood.x" spec="TreeLikelihood" tree="@Tree.t:x">
                 <siteModel id="SiteModel.s:x" spec="SiteModel">
                     <parameter estimate="false" id="mutationRate.s:x" name="mutationRate" value="1.0"/>
@@ -148,13 +148,13 @@ W2P7D54=54.0 <!-- newest sample -->
                         <frequencies frequencies="@freqParameter.s:x" id="estimatedFreqs.s:x" spec="Frequencies"/>
                     </substModel>
                 </siteModel>
-                <branchRateModel clock.rate="@clockRate.c:x" id="StrictClock.c:x" spec="beast.evolution.branchratemodel.StrictClockModel"/>
+                <branchRateModel clock.rate="@clockRate.c:x" id="StrictClock.c:x" spec="beast.base.evolution.branchratemodel.StrictClockModel"/>
             </distribution>
         </distribution>
     </distribution>
 
 
-    <operator spec='GMRFSkyrideBlockUpdateOperator' weight="10" scaleFactor="8.6" maxIterations="200" 
+    <operator spec='beastclassic.evolution.operators.GMRFSkyrideBlockUpdateOperator' weight="10" scaleFactor="8.6" maxIterations="200" 
                                  stopValue="0.01" likelihood='@skyride'/> <!-- autoOptimize="true" -->
 
     <operator id="treeScaler.t:x" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:x" weight="3.0"/>
@@ -189,7 +189,7 @@ W2P7D54=54.0 <!-- newest sample -->
         <log idref="likelihood"/>
         <log idref="prior"/>
         <log idref="treeLikelihood.x"/>
-        <log id="TreeHeight.t:x" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:x"/>
+        <log id="TreeHeight.t:x" spec="beast.base.evolution.tree.TreeHeightLogger" tree="@Tree.t:x"/>
         <log idref="skyride"/>
         <parameter idref="clockRate.c:x" name="log"/>
         <parameter idref="kappa.s:x" name="log"/>
@@ -208,14 +208,14 @@ W2P7D54=54.0 <!-- newest sample -->
     </logger>
 
     <logger fileName="$(tree).trees" id="treelog.t:x" logEvery="1000" mode="tree">
-        <log id="TreeWithMetaDataLogger.t:x" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:x"/>
+        <log id="TreeWithMetaDataLogger.t:x" spec="beast.base.evolution.TreeWithMetaDataLogger" tree="@Tree.t:x"/>
     </logger>
 
-	<init spec='beast.util.TreeParser' taxa='@x' initial="@Tree.t:x" 
+	<init spec='beast.base.evolution.tree.TreeParser' taxa='@x' initial="@Tree.t:x" 
 	newick='(((W2P9D5:12.983825646947054,W2P1D12:19.983825646947054):1.4300293642999122,(W2P4D5:9.646627021951318,W2P12D0:4.646627021951318):4.767227989295648):2.83185397871398,((((W2P15D12:9.25378069647568,W2P2D12:9.25378069647568):5.922840926698534,W2P8D5:8.176621623174213):2.3648365710890573,((W2P14D34:15.50233134492035,(((((((W2P1D41:2.943850833708977,W2P7D54:15.943850833708977):6.8498083253444,(W2P9D41:6.564234686676009,W2P5D41:6.564234686676009):3.2294244723773673):0.2867007415795406,((W2P7D41:8.669841624381775,W2P1D34:1.6698416243817746):0.6754795479372646,(W2P1D54:16.848540346534538,W2P1D48:10.848540346534538):5.4967808257845014):0.735038728313878):2.9595902436285435,W2P6D30:2.0399501442614607):1.1480961231673916,((W2P3D30:0.03984799282374141,W2P2D41:11.039847992823741):0.4012903086709265,(W2P2D34:4.318186805880355,(W2P5D34:3.057643645446614,W2P1D36:5.057643645446614):1.2605431604337411):0.12295149561431273):2.7469079659341844):1.8665474390668777,(W2P12D36:10.222552036590518,W2P7D30:4.222552036590518):0.8320416699052124):1.6043505950953403,(W2P4D30:4.658228892638782,W2P5D30:4.658228892638782):2.0007154089522885):4.84338704332928):11.996957431429294,((W2P2D30:13.104495226550377,W2P1D30:13.104495226550377):3.7104294789770904,(((W2P1D18:1.3110203951392165,W2P2D18:1.3110203951392165):1.1266782721563402,W2P4D18:2.4376986672955567):0.35489927639714125,W2P3D18:2.792597943692698):2.022326761834769):6.684364070822177):12.042169417913627):5.272942023996379,W2P1D0:10.81440021825965):1.4313087717012962);'>
 	</init>
 <!--
-    <init estimate="false" id="RandomTree.t:x" initial="@Tree.t:x" spec="beast.evolution.tree.RandomTree" taxa="@x">
+    <init estimate="false" id="RandomTree.t:x" initial="@Tree.t:x" spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@x">
         <populationModel id="ConstantPopulation0.t:x" spec="ConstantPopulation">
             <parameter id="randomPopSize.t:x" name="popSize" value="10000"/>
         </populationModel>
diff --git a/fxtemplates/ClassicSubtseModels.xml b/fxtemplates/ClassicSubtseModels.xml
new file mode 100644
index 0000000..d401707
--- /dev/null
+++ b/fxtemplates/ClassicSubtseModels.xml
@@ -0,0 +1,22 @@
+<beast version='2.0'
+       namespace='beast.app.beauti:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.branchratemodel:beast.base.evolution.speciation:beast.base.evolution.tree.coalescent:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:beast.evolution:beast.base.inference.distribution'>
+
+    <mergewith point='substModelTemplates'>
+        <!-- empirical amino acid substitution models -->
+        <subtemplate id='LG' class='beastclassic.evolution.substitutionmodel.LG'
+                     suppressInputs='beastclassic.evolution.substitutionmodel.LG.beastclassic,
+                     	beastclassic.evolution.substitutionmodel.LG.rates,
+                     	beastclassic.evolution.substitutionmodel.LG.frequencies'
+                     mainid='LG.s:$(n)'>
+            <![CDATA[<plugin spec='LG' id='LG.s:$(n)'/>]]></subtemplate>
+        <subtemplate id="FLU" class='beastclassic.evolution.substitutionmodel.FLU'
+                     suppressInputs='beastclassic.evolution.substitutionmodel.FLU.eigenSystem,
+                     	beastclassic.evolution.substitutionmodel.FLU.rates,
+                     	beastclassic.evolution.substitutionmodel.FLU.frequencies'
+                     mainid='FLU.s:$(n)'>
+            <![CDATA[<plugin spec='FLU' id='FLU.s:$(n)'/>]]></subtemplate>
+    </mergewith>
+    
+    
+</beast>
+
diff --git a/templates/discrete-trait.xml b/fxtemplates/discrete-trait.xml
similarity index 73%
rename from templates/discrete-trait.xml
rename to fxtemplates/discrete-trait.xml
index dc46bf4..2634add 100644
--- a/templates/discrete-trait.xml
+++ b/fxtemplates/discrete-trait.xml
@@ -1,10 +1,10 @@
 <beast version='2.0'
-       namespace='beast.app.beauti:beast.core:beast.evolution.branchratemodel:beast.evolution.speciation:beast.evolution.Tree.t:coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood:beast.evolution:beast.math.distributions'>
+       namespace='beast.app.beauti:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.branchratemodel:beast.base.evolution.speciation:beast.evolution.Tree.t:coalescent:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:beast.evolution:beast.base.inference.distribution'>
 
 
 <mergewith point='aux-partitions-panels'>
-		<alignmentProvider id="Add Continuous Geography" spec='beast.app.beauti.BeautiLocationTraitProvider' template='@LocationTrait'/>
-		<alignmentProvider id="Add Discrete Trait" spec='beast.app.beauti.BeautiDiscreteTraitProvider' template='@DiscreteTrait'/>
+		<alignmentProvider id="Add Continuous Geography" spec='beastclassic.app.beauti.BeautiLocationTraitProvider' template='@LocationTrait'/>
+		<alignmentProvider id="Add Discrete Trait" spec='beastclassic.app.beauti.BeautiDiscreteTraitProvider' template='@DiscreteTrait'/>
 <!--
 		<panel spec='BeautiPanelConfig' panelname="Discrete Trait" tiptext="Discrete Trait details"
             path='distribution/distribution[id="prior"]/distribution[id="discrete-trait"]/distribution'
@@ -16,22 +16,22 @@
 
 <mergewith point='aux-partitiontemplate'>
 -->
-        <subtemplate id='DiscreteTrait' class='beast.evolution.alignment.AlignmentFromTrait' mainid='$(n)'
+        <subtemplate id='DiscreteTrait' class='beastclassic.evolution.alignment.AlignmentFromTrait' mainid='$(n)'
 suppressInputs='beast.evolution.substitutionmodel.SVSGeneralSubstitutionModel.rates,
 				beast.evolution.substitutionmodel.SVSGeneralSubstitutionModel.rateIndicator,
 				beast.evolution.substitutionmodel.SVSGeneralSubstitutionModel.eigenSystem,
 				beast.evolution.substitutionmodel.SVSGeneralSubstitutionModel.frequencies'>
 <![CDATA[
         <!--distribution spec="CompoundDistribution" id="discrete-trait.$(n)" ignore="true"-->
-			<distribution id="traitedtreeLikelihood.$(n)" spec='AncestralStateTreeLikelihood' useJava="true" tag="location" tree='@Tree.t:$(n)'> 
-				<data spec="beast.evolution.alignment.AlignmentFromTrait" id='$(n)'>
-					<userDataType spec='beast.evolution.datatype.UserDataType' id='traitDataType.$(n)' 
+			<distribution id="traitedtreeLikelihood.$(n)" spec='beastclassic.evolution.likelihood.AncestralStateTreeLikelihood' useJava="true" tag="location" tree='@Tree.t:$(n)'> 
+				<data spec="beast.base.evolution.alignment.AlignmentFromTrait" id='$(n)'>
+					<userDataType spec='beast.base.evolution.datatype.UserDataType' id='traitDataType.$(n)' 
 						states='4'
 						codelength='-1'
 						codeMap='A = 0, B = 1, C = 2, D = 3, ? = 0 1 2 3, - = 0 1 2 3'/>
 <!--
-					<traitSet id='traitset.$(n)' spec='beast.evolution.tree.TraitSet' traitname='discrete' value="">
-						<taxa spec='beast.evolution.alignment.TaxonSet' alignment='@$(n)'/>
+					<traitSet id='traitset.$(n)' spec='beast.base.evolution.tree.TraitSet' traitname='discrete' value="">
+						<taxa spec='beast.base.evolution.alignment.TaxonSet' alignment='@$(n)'/>
 
 					</traitSet>
 -->
@@ -40,7 +40,7 @@ suppressInputs='beast.evolution.substitutionmodel.SVSGeneralSubstitutionModel.ra
 				        <proportionInvariant spec='parameter.RealParameter' id='proportionInvariant.s:$(n)' value='0.0' lower='0' upper='1' estimate='false'/>
 				        <mutationRate        spec='parameter.RealParameter' id='mutationRate.s:$(n)' value='1.0'        estimate='false'/>
 				        <shape               spec='parameter.RealParameter' id='gammaShape.s:$(n)' value='1.0'         estimate='false'/>
-					<substModel spec="SVSGeneralSubstitutionModel" id="svs.s:$(n)">
+					<substModel spec="beastclassic.evolution.substitutionmodel.SVSGeneralSubstitutionModel" id="svs.s:$(n)">
 						<rateIndicator id='rateIndicator.s:$(n)' spec='parameter.BooleanParameter' value='true' dimension='6'/>
 					    <frequencies id='traitfreqs.s:$(n)' spec='Frequencies'>
 					            <frequencies id='traitfrequencies.s:$(n)' spec='parameter.RealParameter' value='.25 .25 .25 .25'/>
@@ -48,36 +48,36 @@ suppressInputs='beast.evolution.substitutionmodel.SVSGeneralSubstitutionModel.ra
 					    <rates id='relativeGeoRates.s:$(n)' spec='parameter.RealParameter' value='1.' dimension='6'/>
 					</substModel>
 				</siteModel>
-				<branchRateModel id="StrictClockModel.c:$(n)" spec="beast.evolution.branchratemodel.StrictClockModel">
+				<branchRateModel id="StrictClockModel.c:$(n)" spec="beast.base.evolution.branchratemodel.StrictClockModel">
 					<parameter id="traitClockRate.c:$(n)" name="clock.rate" value="1.0"/>
 				</branchRateModel>
 			</distribution>
         <!--/distribution-->
 
 		<logger id='treeWithTraitLogger.$(n)' logEvery="10000" fileName="$(n)_tree_with_trait.trees" mode="tree">
-			<log id="treeWithTraitLoggerItem.t:$(n)" spec='beast.evolution.tree.TreeWithTraitLogger' tree='@Tree.t:$(n)'>
+			<log id="treeWithTraitLoggerItem.t:$(n)" spec='beast.base.evolution.tree.TreeWithTraitLogger' tree='@Tree.t:$(n)'>
 				<metadata idref="posterior"/>
 				<metadata idref="traitedtreeLikelihood.$(n)"/>
 			</log>
 		</logger>
 
-		<ParameterCumSum spec="beast.core.util.Sum" id="nonZeroRates.s:$(n)" arg="@rateIndicator.s:$(n)"/> 
+		<ParameterCumSum spec="beast.base.evolution.Sum" id="nonZeroRates.s:$(n)" arg="@rateIndicator.s:$(n)"/> 
 
 
-		<distribution  id='geoclockPrior.c:$(n)' x="@traitClockRate.c:$(n)" spec='beast.math.distributions.Prior'>
-			<distr spec='beast.math.distributions.Gamma' offset="0.0">
+		<distribution  id='geoclockPrior.c:$(n)' x="@traitClockRate.c:$(n)" spec='beast.base.inference.distribution.Prior'>
+			<distr spec='beast.base.inference.distribution.Gamma' offset="0.0">
 				<alpha spec='parameter.RealParameter' estimate='false' value='0.001'/>
 				<beta spec='parameter.RealParameter' estimate='false' value='1000.0'/>
 			</distr>
 		</distribution>
-		<distribution  id='relativeGeoRatesPrior.s:$(n)' x="@relativeGeoRates.s:$(n)" spec='beast.math.distributions.Prior'>
-			<distr spec='beast.math.distributions.Gamma' offset="0.0">
+		<distribution  id='relativeGeoRatesPrior.s:$(n)' x="@relativeGeoRates.s:$(n)" spec='beast.base.inference.distribution.Prior'>
+			<distr spec='beast.base.inference.distribution.Gamma' offset="0.0">
 				<alpha spec='parameter.RealParameter' estimate='false' value='1.0'/>
 				<beta spec='parameter.RealParameter' estimate='false' value='1.0'/>
 			</distr>
 		</distribution>
-		<distribution  id="nonZeroRatePrior.s:$(n)" x="@nonZeroRates.s:$(n)"  spec='beast.math.distributions.Prior'>
-			<distr spec='beast.math.distributions.Poisson' offset="6.0">
+		<distribution  id="nonZeroRatePrior.s:$(n)" x="@nonZeroRates.s:$(n)"  spec='beast.base.inference.distribution.Prior'>
+			<distr spec='beast.base.inference.distribution.Poisson' offset="6.0">
 				<lambda spec='parameter.RealParameter' estimate='false' value='0.693'/>
 			</distr>
 		</distribution>
@@ -87,9 +87,9 @@ suppressInputs='beast.evolution.substitutionmodel.SVSGeneralSubstitutionModel.ra
 		<operator id="indicatorFlip.s:$(n)" spec="BitFlipOperator" parameter="@rateIndicator.s:$(n)" weight="30"/>
 
 	 	<operator id='geoMuScaler.c:$(n)' spec='ScaleOperator' scaleFactor="0.9" weight="3" parameter="@traitClockRate.c:$(n)"/>  
-		<operator id="BSSVSoperator.c:$(n)" spec="BitFlipBSSVSOperator" indicator="@rateIndicator.s:$(n)" mu="@traitClockRate.c:$(n)" weight="30"/>
+		<operator id="BSSVSoperator.c:$(n)" spec="beastclassic.evolution.operators.BitFlipBSSVSOperator" indicator="@rateIndicator.s:$(n)" mu="@traitClockRate.c:$(n)" weight="30"/>
 
-		<log id='geoSubstModelLogger.s:$(n)' spec='SVSGeneralSubstitutionModelLogger' model="@svs.s:$(n)" dataType="@traitDataType.$(n)" useLocationNames="true"/>
+		<log id='geoSubstModelLogger.s:$(n)' spec='beastclassic.evolution.substitutionmodel.SVSGeneralSubstitutionModelLogger' model="@svs.s:$(n)" dataType="@traitDataType.$(n)" useLocationNames="true"/>
 ]]>
 
          <connect srcID='traitedtreeLikelihood.$(n)'              targetID='likelihood' inputName='distribution' if="isInitializing"/>
@@ -124,41 +124,41 @@ suppressInputs='beast.evolution.substitutionmodel.SVSGeneralSubstitutionModel.ra
 	</subtemplate>
 
 
-        <subtemplate id='LocationTrait' class='beast.evolution.alignment.AlignmentFromTraitMap' mainid='$(n)'
+        <subtemplate id='LocationTrait' class='beastclassic.evolution.alignment.AlignmentFromTraitMap' mainid='$(n)'
 suppressInputs='beast.evolution.substitutionmodel.LocationSubstitutionModel.frequencies,
 				beast.math.distributions.MultivariateNormalDistribution.arg'>
 <![CDATA[
-	<multivariateTraitLikelihood id="locationtreeLikelihood.$(n)" spec='beast.continuous.SampledMultivariateTraitLikelihood'
+	<multivariateTraitLikelihood id="locationtreeLikelihood.$(n)" spec='beastclassic.continuous.SampledMultivariateTraitLikelihood'
 		useTreeLength="true" scaleByTime="true" reportAsMultivariate="true" reciprocalRates="true" tree='@Tree.t:$(n)'>
 		<traitParameter id='location.$(n)' spec='parameter.RealParameter' value='0 0' minordimension='2'/>
-	    <data spec='beast.evolution.alignment.AlignmentFromTraitMap' id='$(n)'>
+	    <data spec='beastclasssic.evolution.alignment.AlignmentFromTraitMap' id='$(n)'>
 			<userDataType spec='beast.evolution.datatype.LocationDataType'/>
-			<traitMap id='traitmap.s:$(n)' spec='beast.evolution.tree.TreeTraitMap' tree='@Tree.t:$(n)' parameter='@location.$(n)' traitName='location' 
+			<traitMap id='traitmap.s:$(n)' spec='beastclassic.evolution.tree.TreeTraitMap' tree='@Tree.t:$(n)' parameter='@location.$(n)' traitName='location' 
 				randomizeupper="90 180" randomizelower="-90 -180">
 			</traitMap>
 		</data>
 		<siteModel spec='SiteModel' id="geoContSiteModel.s:$(n)">
-			<substModel id="diffusionModel.s:$(n)" spec='beast.continuous.MultivariateDiffusionModel'>
+			<substModel id="diffusionModel.s:$(n)" spec='beastclassic.continuous.MultivariateDiffusionModel'>
 				<precisionMatrix spec='parameter.RealParameter' id='precisionMatrix.s:$(n)' minordimension='2' estimate='true'>
 0.365 -1.78E-4
 -1.78E-4 5.16E-2
 				</precisionMatrix>
 			</substModel>
 		</siteModel>
-        <branchRateModel spec='beast.evolution.branchratemodel.StrictClockModel' id='StrictClock.c:$(n)'>
+        <branchRateModel spec='beast.base.evolution.branchratemodel.StrictClockModel' id='StrictClock.c:$(n)'>
             <clock.rate id='clockRate.c:$(n)' spec='parameter.RealParameter' value='1.0' estimate='false'/>
         </branchRateModel>
     </multivariateTraitLikelihood>
 
-	<distribution  id="precisionPrior.$(n)" spec='beast.math.distributions.WishartDistribution' df='2' arg='@precisionMatrix.s:$(n)'>
+	<distribution  id="precisionPrior.$(n)" spec='beastclassic.math.distributions.WishartDistribution' df='2' arg='@precisionMatrix.s:$(n)'>
 		<scaleMatrix spec='parameter.RealParameter' minordimension='2'>
 				1.0 0.0
 				0.0 1.0
 		</scaleMatrix>
 	</distribution>
 
-	<distribution id="rootPrior.$(n)" spec='beast.math.distributions.MultivariateNormalDistribution'>
-		<arg id='rootTrait.$(n)' spec='beast.evolution.tree.RootTrait' traitmap='@traitmap.s:$(n)'/>
+	<distribution id="rootPrior.$(n)" spec='beastclassic.math.distributions.MultivariateNormalDistribution'>
+		<arg id='rootTrait.$(n)' spec='beastclassic.evolution.tree.RootTrait' traitmap='@traitmap.s:$(n)'/>
 		<mean spec='parameter.RealParameter' value='0.0 0.0'/>
 		<precision spec='parameter.RealParameter' minordimension='2'>
 				0.001 0.0
@@ -166,27 +166,27 @@ suppressInputs='beast.evolution.substitutionmodel.LocationSubstitutionModel.freq
 		</precision>
 	</distribution>
 
-    <log id='rateStat.$(n)' spec='beast.evolution.branchratemodel.RateStatistic' tree='@Tree.t:$(n)' treeLikelihood='@locationtreeLikelihood.$(n)'/>
+    <log id='rateStat.$(n)' spec='beast.base.evolution.RateStatistic' tree='@Tree.t:$(n)' treeLikelihood='@locationtreeLikelihood.$(n)'/>
 
 
 
 
-    <plugin id='ClockPrior.c:$(n)' spec='beast.math.distributions.Prior' x='@clockRate.c:$(n)'>
-        <distr spec="beast.math.distributions.Uniform" upper='Infinity'/>
+    <plugin id='ClockPrior.c:$(n)' spec='beast.base.inference.distribution.Prior' x='@clockRate.c:$(n)'>
+        <distr spec="beast.base.inference.distribution.Uniform" upper='Infinity'/>
     </plugin>
 
     <operator id='StrictClockRateScaler.c:$(n)' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter='@clockRate.c:$(n)'/>
 
-    <operator id='precisionGibbsOperator.s:$(n)' spec='PrecisionMatrixGibbsOperator' tree='@Tree.t:$(n)' parameter='@precisionMatrix.s:$(n)' traitmap='@traitmap.s:$(n)'  weight="15"
+    <operator id='precisionGibbsOperator.s:$(n)' spec='beastclassic.evolution.operators.PrecisionMatrixGibbsOperator' tree='@Tree.t:$(n)' parameter='@precisionMatrix.s:$(n)' traitmap='@traitmap.s:$(n)'  weight="15"
 		prior='@precisionPrior.$(n)'>
 	    <likelihood idref='locationtreeLikelihood.$(n)'/>
     </operator>
 
-    <operator id='traitGibbsOperator.$(n)' spec='TraitGibbsOperator' tree='@Tree.t:$(n)' precisionMatrix='@precisionMatrix.s:$(n)' traitmap='@traitmap.s:$(n)' weight="50">
+    <operator id='traitGibbsOperator.$(n)' spec='beastclassic.evolution.operators.TraitGibbsOperator' tree='@Tree.t:$(n)' precisionMatrix='@precisionMatrix.s:$(n)' traitmap='@traitmap.s:$(n)' weight="50">
 		<likelihood idref='locationtreeLikelihood.$(n)'/>
     </operator>
 
-    <operator id='RootTraitRandowWalkOperator.$(n)' spec='RootTraitRandowWalkOperator' windowSize="10.0" weight="5" parameter='@location.$(n)' traitmap='@traitmap.s:$(n)' />
+    <operator id='RootTraitRandowWalkOperator.$(n)' spec='beastclassic.evolution.operators.RootTraitRandowWalkOperator' windowSize="10.0" weight="5" parameter='@location.$(n)' traitmap='@traitmap.s:$(n)' />
 
 
 ]]>
diff --git a/templates/ClassicSubtseModels.xml b/templates/ClassicSubtseModels.xml
deleted file mode 100644
index d981e39..0000000
--- a/templates/ClassicSubtseModels.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<beast version='2.0'
-       namespace='beast.app.beauti:beast.core:beast.evolution.branchratemodel:beast.evolution.speciation:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood:beast.evolution:beast.math.distributions'>
-
-    <mergewith point='substModelTemplates'>
-        <!-- empirical amino acid substitution models -->
-        <subtemplate id='LG' class='beast.evolution.substitutionmodel.LG'
-                     suppressInputs='beast.evolution.substitutionmodel.LG.eigenSystem,beast.evolution.substitutionmodel.LG.rates,beast.evolution.substitutionmodel.LG.frequencies'
-                     mainid='LG.s:$(n)'>
-            <![CDATA[<plugin spec='LG' id='LG.s:$(n)'/>]]></subtemplate>
-        <subtemplate id="FLU" class='beast.evolution.substitutionmodel.FLU'
-                     suppressInputs='beast.evolution.substitutionmodel.FLU.eigenSystem,beast.evolution.substitutionmodel.FLU.rates,beast.evolution.substitutionmodel.FLU.frequencies'
-                     mainid='FLU.s:$(n)'>
-            <![CDATA[<plugin spec='FLU' id='FLU.s:$(n)'/>]]></subtemplate>
-    </mergewith>
-    
-    
-</beast>
-
diff --git a/version.xml b/version.xml
index bfb607f..4005b78 100644
--- a/version.xml
+++ b/version.xml
@@ -1,4 +1,6 @@
-<package name='BEAST_CLASSIC' version='1.5.0'>
-	<depends on='beast2' atleast='2.6.0'/>
-	<depends on='BEASTLabs' atleast='1.9.0'/>
+<package name='BEAST_CLASSIC' version='1.6.0'>
+        <depends on='BEAST.base' atleast='2.7.0'/>
+        <depends on='BEAST.app' atleast='2.7.0'/>
+        <depends on='BEASTLabs' atleast='2.0.0'/>
+
 </package>