Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/build.xml
+++ b/build.xml
 <!-- Build BEAST 2. It is also used by Hudson BEAST_2 project. JUnit test is available for this build. -->
-<project basedir="." default="build_jar_all_BEAST" name="BUILD_BEAST_2">
+<project basedir="." default="build_jar_all_BEAST" name="BUILD_BEAST_2" 
+	xmlns:fx="javafx:com.sun.javafx.tools.ant">
    <description>
        Build BEAST 2.
        Also used by Hudson BEAST_2 project.
@@ -89,6 +90,7 @@
        <delete file="${build}/beast/app/treeannotator/TreeAnnotatorLauncher.class" />
        <delete file="${build}/beast/app/util/Utils6.class" />
        <delete file="${build}/beast/app/BEASTVersion.class" />
+        <delete file="${build}/beast/util/BEASTClassLoader.class" />
        <delete>
 	      <fileset dir="${build}/beast/core/util/" includes="Log*.class" />
    	  <fileset dir="${build}/beast/app/beastapp/" includes="BeastLauncher*.class" />
@@ -113,6 +115,7 @@
            <include name="beast/util/Package*.java" />
            <include name="beast/app/util/Arguments.java" />
            <include name="beast/core/util/Log.java" />
+	    <include name="beast/util/BEASTClassLoader.java" />
        </javac>
        <copy todir="${build}">
            <fileset dir="${src}" includes="**/*.properties" />
@@ -145,6 +148,27 @@
            <zipgroupfileset dir="${lib}" includes="commons-math3-3.1.1.jar" />
            <zipgroupfileset dir="${lib}" includes="antlr-runtime-4.7.jar"/>
        </jar>
+        
+        
+        <jar jarfile="${dist}/beauti.jar">
+            <manifest>
+                <attribute name="Built-By" value="${user.name}" />
+                <attribute name="Main-Class" value="beast.app.beauti.Beauti" />
+            </manifest>
+            <fileset dir="${build}">
+                <include name="beast/**/*.class" />
+                <include name="beast/**/*.properties" />
+                <include name="beast/**/*.png" />
+                <include name="beagle/**/*.class" />
+                <include name="org/**/*.class" />
+            </fileset>
+            <zipgroupfileset dir="${lib}" includes="jam.jar" />
+            <zipgroupfileset dir="${lib}" includes="beagle.jar" />
+            <zipgroupfileset dir="${lib}" includes="colt.jar" />
+            <zipgroupfileset dir="${lib}" includes="commons-math3-3.1.1.jar" />
+            <zipgroupfileset dir="${lib}" includes="antlr-runtime-4.7.jar"/>
+        </jar>
+        
        <jar jarfile="${dist}/launcher.jar">
            <fileset dir="${build}">
                <include name="beast/**/*Launcher*.class" />
@@ -155,10 +179,13 @@
                <include name="beast/**/Version.class" />
 		    	<include name="beast/app/util/Arguments*.class" />
                <include name="beast/util/Package*.class" />
+		<include name="beast/util/BEASTClassLoader.class" />
                <include name="beast/app/draw/icons/beauti.png"/>
                <include name="beast/core/util/Log*.class" />
           </fileset>
        </jar>
+        
+
        <jar jarfile="${dist}/beast.src.jar">
            <fileset dir="${src}">
                <include name="beast/**/*.java" />
@@ -256,10 +283,10 @@


    <!-- Release -->
-    <property name="version" value="2.5.2" />
-    <property name="version_number" value="2.5.2" />
+    <property name="version" value="2.5.3" />
+    <property name="version_number" value="2.5.3" />
    <property name="release_dir" value="release" />
-    <property name="copyright" value="Beast 2 development team 2011-2018" />
+    <property name="copyright" value="Beast 2 development team 2011-2019" />

    <property name="BEAST_name" value="BEAST" />
    <property name="beast_name" value="beast" />
@@ -1053,6 +1080,8 @@
    </target>


+	<property environment="env"/>
+	
    <!-- Create the app bundle -->
    <target name="macjre">
        <delete dir="${Mac_package_dir}" />
@@ -1300,6 +1329,214 @@



+	<target name="init-fx-tasks">
+		<echo message="java.home = ${java.home} "/>
+		<path id="fxant">
+			<filelist>
+				<file name="${java.home}/../lib/ant-javafx.jar"/>
+				<file name="${java.home}/../lib/jfxrt.jar"/> <!-- jdk9, jdk10 -->
+				<file name="${java.home}/../jre/lib/ext/jfxrt.jar"/> <!-- jdk8 -->
+			</filelist>
+		</path>
+	
+		<taskdef resource="com/sun/javafx/tools/ant/antlib.xml"      
+			uri="javafx:com.sun.javafx.tools.ant"
+			classpathref="fxant"/>
+
+	</target>
+
+    <!-- Create the app bundle -->
+    <target name="macjre3" depends="init-fx-tasks">
+    
+
+        <delete dir="${Mac_package_dir}" />
+        <!--<delete file="${Mac_dir}/pack.temp.dmg"/>-->
+        <delete file="${Mac_dir}/BEAST v${version}.dmg"/>
+        <!-- Create the release directory -->
+        <mkdir dir="${Mac_package_dir}" />
+
+        <copy todir="${Mac_package_dir}/bin">
+            <fileset dir="${Linux_dir}/jrebin" />
+        </copy>
+        <chmod dir="${Mac_package_dir}/bin" perm="755" includes="**/**" />
+
+        <copy todir="${Mac_package_dir}/examples/">
+            <fileset dir="examples/">
+                <include name="*.xml" />
+                <include name="nexus/**" />
+                <exclude name="benchmark/**" />
+            </fileset>
+        </copy>
+
+<!--    <copy file="${dist}/beauti.jar" todir="${Mac_package_dir}/lib" /> -->
+        <copy file="${dist}/launcher.jar" todir="${Mac_package_dir}/lib" />
+        <copy file="${dist}/beast.jar" todir="${Mac_package_dir}/lib" />
+        <copy file="${dist}/beast.src.jar" todir="${Mac_package_dir}/lib" />
+        <!-- <copy file="${dist}/beast-beagle.jar" todir="${Mac_package_dir}/lib"/>
+        <copy todir="${Mac_package_dir}/lib">
+            <fileset dir="${Mac_dir}/lib" />
+        </copy> -->
+
+        <copy file="${common_dir}/VERSION HISTORY.txt" todir="${Mac_package_dir}" />
+        <copy file="${common_dir}/README.txt" todir="${Mac_package_dir}" />
+        <copy file="${common_dir}/LICENSE.txt" todir="${Mac_package_dir}" />
+        
+        
+		<!--
+		<fx:signjar destdir="/tmp" alias="${AppleSigner}" verbose="true" storePass="" keyPass="">
+			<fx:fileset dir='${dist}' includes='*.jar'/>
+		</fx:signjar>
+		-->
+		
+		<fx:resources id="appRes">
+			<fx:fileset dir="${dist}" includes="launcher.jar"/>
+			<fx:fileset dir="${dist}" includes="beast.jar"/>
+			<!--
+			<fx:fileset dir="${dist}" includes="beast.src.jar"/>
+  	        <fx:fileset dir="${common_dir}" includes="VERSION HISTORY.txt"/>
+    	    <fx:fileset dir="${common_dir}" includes="README.txt"/>
+        	<fx:fileset dir="${common_dir}" includes="LICENSE.txt"/>
+            <fx:fileset dir="./examples/" includes="*.xml" />
+            <fx:fileset dir="./examples/nexus" includes="**" />
+            <fx:fileset dir="./templates" includes="**" />
+            -->
+		</fx:resources> 
+		
+		<fx:application id="fxApplication"
+			name="${BEAST_name}"
+			mainClass="beast.app.beastapp.BeastMain"
+			toolkit="fx"
+		    version="${version}"
+		>
+            <fx:argument>-window</fx:argument>
+            <fx:argument>-working</fx:argument>
+            <fx:argument>-options</fx:argument>
+		</fx:application>
+	
+		<mkdir dir="${Mac_package_dir}/build/classes/META-INF" />
+		
+				<fx:deploy
+			embedJNLP="true"
+			extension="false"
+			width="1200" height="800" 
+			includeDT="false"
+			offlineAllowed="true"
+			outdir="${Mac_package_dir}"
+			outfile="${BEAUti_name}" 
+			nativeBundles="image"
+			updatemode="background" >
+	
+	    	<fx:info title="${BEAUti_name}" vendor="${appVendor}"
+            	copyright="${BEAUti_name}, ${copyright}" description="${BEAUti_name}">
+        		<fx:icon href="${common_dir}/icons/beauti.icns"/>   
+    		</fx:info>
+			<fx:application id="BEAUtiApplication"
+				name="${BEAUti_name}"
+				mainClass="beast.app.beauti.Beauti"
+				toolkit="fx"
+			    version="${version}"
+			>
+            	<fx:argument>-capture</fx:argument>
+			</fx:application>
+			<fx:resources id="appResBEAUti">
+				<fx:fileset dir="${dist}" includes="beauti.jar"/>
+			</fx:resources> 
+			<fx:platform>
+            	<fx:jvmarg value="-Xmx4g"/>
+	            <fx:jvmarg value="-Dapple.laf.useScreenMenuBar=true"/>
+    	        <fx:jvmarg value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>
+        	    <fx:jvmarg value="-Duser.language=en"/>            
+            	<fx:jvmarg value="-Dbeast.load.jars=true"/>
+			</fx:platform>
+
+
+
+<!--
+			<fx:secondaryLauncher name="BEAUti"
+			    mainClass="beast.app.beauti.Beauti"
+			    version="${version}"
+			    title="BEAUti"
+			    description="BEAUti"
+			    copyright="${copyright}"
+			    menu="true"
+     			shortcut="false"
+     		>
+     			<fx:argument>-capture</fx:argument>
+            	<fx:jvmarg value="-Xmx4g"/>
+	            <fx:jvmarg value="-Dapple.laf.useScreenMenuBar=true"/>
+    	        <fx:jvmarg value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>
+        	    <fx:jvmarg value="-Duser.language=en"/>            
+            	<fx:jvmarg value="-Dbeast.load.jars=true"/>
+			</fx:secondaryLauncher>
+-->			
+		</fx:deploy>
+		
+		<!-- Need to use ${basedir} because somehow the ant task is calculating the directory differently -->
+		<fx:deploy
+			embedJNLP="true"
+			extension="false"
+			width="1200" height="800" 
+			includeDT="false"
+			offlineAllowed="true"
+			outdir="${Mac_package_dir}"
+			outfile="${BEAST_name}" 
+			nativeBundles="image"
+			updatemode="background" >
+	
+	    	<fx:info title="${BEAST_name}" vendor="${appVendor}"
+            	copyright="${BEAST_name}, ${copyright}" description="${BEAST_name}">
+        		<fx:icon href="${common_dir}/icons/beast.icns"/>   
+    		</fx:info>
+			<fx:application refId="fxApplication"/>
+			<fx:resources id="appResBEAUST">
+				<fx:fileset dir="${dist}" includes="beast.jar"/>
+			</fx:resources> 
+			<fx:platform>
+            	<fx:jvmarg value="-Xmx4g"/>
+	            <fx:jvmarg value="-Dapple.laf.useScreenMenuBar=true"/>
+    	        <fx:jvmarg value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>
+        	    <fx:jvmarg value="-Duser.language=en"/>            
+            	<fx:jvmarg value="-Dbeast.load.jars=true"/>
+			</fx:platform>
+
+
+
+<!--
+			<fx:secondaryLauncher name="BEAUti"
+			    mainClass="beast.app.beauti.Beauti"
+			    version="${version}"
+			    title="BEAUti"
+			    description="BEAUti"
+			    copyright="${copyright}"
+			    menu="true"
+     			shortcut="false"
+     		>
+     			<fx:argument>-capture</fx:argument>
+            	<fx:jvmarg value="-Xmx4g"/>
+	            <fx:jvmarg value="-Dapple.laf.useScreenMenuBar=true"/>
+    	        <fx:jvmarg value="-Djava.library.path=$JAVAROOT:/usr/local/lib"/>
+        	    <fx:jvmarg value="-Duser.language=en"/>            
+            	<fx:jvmarg value="-Dbeast.load.jars=true"/>
+			</fx:secondaryLauncher>
+-->			
+		</fx:deploy>
+
+
+
+        <echo message="Signing..." />
+
+        <exec executable="codesign">
+            <arg value="-s"/>
+            <arg value="${AppleSigner}"/>
+            <arg value="-v"/>
+            <arg value="${Mac_dir}/${BEAST_name}/BEAST-${version}.dmg"/>
+        </exec>
+
+        <echo message="Mac with JRE version release is finished." />
+    </target>
+
+
+

    <target name="doc" description="Create Developer Docs for Beast 2" depends='javadoc'>
        <copy file="doc/tutorial.slides.part1.pdf" tofile="release/common/doc/develop/" />

--- a/debian/changelog
+++ b/debian/changelog
-beast2-mcmc (2.5.2+dfsg-1) UNRELEASED; urgency=medium
+beast2-mcmc (2.6.0+dfsg-1) unstable; urgency=medium

-  * New upstream release 
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0

- -- Olivier Sallou <osallou@debian.org>  Sun, 10 Mar 2019 16:23:06 +0000
+ -- Andreas Tille <tille@debian.org>  Wed, 31 Jul 2019 14:37:15 +0200

 beast2-mcmc (2.5.1+dfsg-2) unstable; urgency=medium


--- a/debian/compat
+++ b/debian/compat
-12
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille@debian.org>,
           Olivier Sallou <osallou@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
               javahelper,
               ant,
               ant-optional,
@@ -17,7 +17,7 @@ Build-Depends: debhelper (>= 12~),
               junit4,
               texlive-latex-base,
               texlive-latex-extra
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/beast2-mcmc
 Vcs-Git: https://salsa.debian.org/med-team/beast2-mcmc.git
 Homepage: http://www.beast2.org
@@ -26,7 +26,7 @@ Package: beast2-mcmc
 Architecture: all
 Depends: ${shlibs:Depends},
         ${misc:Depends},
-         libhmsbeagle-java (>= 1.1r1092),
+         libhmsbeagle-java,
         ${java:Depends},
         default-jre | java9-runtime
 Suggests: beast2-mcmc-doc

--- a/debian/patches/remove_mac_only_code.patch
+++ b/debian/patches/remove_mac_only_code.patch
@@ -6,15 +6,15 @@ Last-Update: Sat, 26 Jan 2019 08:08:17 +0100

 --- a/src/beast/app/beauti/Beauti.java
 +++ b/src/beast/app/beauti/Beauti.java
-@@ -1235,6 +1235,7 @@
+@@ -1286,6 +1286,7 @@ public class Beauti extends JTabbedPane
             if (Utils.isMac() && Utils6.isMajorAtLeast(Utils6.JAVA_1_8)) {
                 // set up application about-menu for Mac
                 // Mac-only stuff
 +/*
                 try {
-                     URL url = ClassLoader.getSystemResource(ModelBuilder.ICONPATH + "beauti.png");
+                     URL url = BEASTClassLoader.classLoader.getResource(ModelBuilder.ICONPATH + "beauti.png");
                     Icon icon = null;
-@@ -1272,10 +1273,7 @@
+@@ -1323,10 +1324,7 @@ public class Beauti extends JTabbedPane
                     };
 
                     // https://github.com/CompEvol/beast2/issues/805
@@ -22,10 +22,10 @@ Last-Update: Sat, 26 Jan 2019 08:08:17 +0100
                         beast.app.util.Utils.macOSXRegistration(application);
 -                    else // <= Java 8
 -                        jam.mac.Utils.macOSXRegistration(application);
-                 } catch (Exception e) {
+                 } catch (Throwable e) {
                     // ignore
                 }
-@@ -1288,6 +1286,7 @@
+@@ -1339,6 +1337,7 @@ public class Beauti extends JTabbedPane
                         // ignore
                     }
                 }

--- a/examples/testHKY.json
+++ b/examples/testHKY.json
-{version: "2.3",
+{version: "2.5",
 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",

 // this is a comment, which is non-standard JSON
@@ -10,40 +10,32 @@ map: [
 ],

 beast: [
-	{id: "alignment.org",
+	{id: "alignment",
 	 spec: "Alignment",
-	 bonobo    :"AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA",
-	 chimp     :"AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA",
-	 gorilla   :"AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA",
-	 human     :"AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA",
-	 orangutan :"AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA--CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA",
-	 siamang   :"AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA"
+	 sequence: [
+		 {spec: "Sequence", totalcount: 4, taxon: "human", value: "\n AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA\n " },
+		 {spec: "Sequence", totalcount: 4, taxon: "chimp", value: "\n AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA\n " },
+		 {spec: "Sequence", totalcount: 4, taxon: "bonobo", value: "\n AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA\n " },
+		 {spec: "Sequence", totalcount: 4, taxon: "gorilla", value: "\n AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA\n " },
+		 {spec: "Sequence", totalcount: 4, taxon: "orangutan", value: "\n AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA--CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA\n " },
+		 {spec: "Sequence", totalcount: 4, taxon: "siamang", value: "\n AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA\n " }
+	  ]
 	},

 	{id: "mcmc",
-	 spec: "MCMC", chainLength: 10000000,
-	 state: { storeEvery: 100000,
-		 stateNode: [
-			 {id: "hky.kappa", lower: 0.0, value: [ 1.0 ] },
-			 {id: "tree", spec: "beast.evolution.tree.Tree" }
-		  ]
-		},
+	 spec: "MCMC", chainLength: "5000000", preBurnin: 50000,
 	 init: [
 		{id: "coalescentSimulator",
-		 spec: "beast.evolution.tree.RandomTree", initial: "@tree",
-		 taxa: {id: "alignment",
-			 spec: "FilteredAlignment", filter: "::", data: "@alignment.org",
-				 constantSiteWeights: { lower: 0, upper: 0, dimension: 4, value: [ 100, 200, 300, 400 ] }
-			},
-		 populationModel: {spec: "ConstantPopulation",
-				 popSize: { value: [ 1.0 ] }
-			}
+		 spec: "beast.evolution.tree.RandomTree", taxa: "@alignment",
+			 populationModel: {spec: "ConstantPopulation", popSize: "1.0" },
+			 initial: {id: "tree", spec: "beast.evolution.tree.Tree" }
 		}
 	  ],
 	 distribution: {id: "posterior",
 		 spec: "util.CompoundDistribution",
 		 distribution: [
-			{spec: "beast.math.distributions.Prior", x: "@hky.kappa",
+			{spec: "beast.math.distributions.Prior",
+				 x: {id: "hky.kappa", spec: "parameter.RealParameter", lower: 0.0, value: [ 1.0 ] },
 				 distr: {spec: "beast.math.distributions.OneOnX" }
 			},
 			{id: "treeLikelihood",
@@ -52,7 +44,7 @@ beast: [
 				 spec: "SiteModel", gammaCategoryCount: 1,
 				 substModel: {id: "hky",
 					 spec: "HKY", kappa: "@hky.kappa",
-						 frequencies: {id: "freqs", data: "@alignment" }
+						 frequencies: {id: "freqs", spec: "Frequencies", data: "@alignment" }
 					}
 				}
 			}
@@ -61,27 +53,26 @@ beast: [
 	 operator: [
 		 {id: "kappaScaler", spec: "ScaleOperator", parameter: "@hky.kappa", scaleFactor: 0.5, weight: 1.0 },
 		 {id: "treeScaler", spec: "ScaleOperator", tree: "@tree", scaleFactor: 0.5, weight: 1.0 },
-		 {id: "subtreeSlide1", spec: "SubtreeSlide", tree: "@tree", weight: 5.0 },
+		 {id: "subtreeSlide", spec: "SubtreeSlide", tree: "@tree", weight: 5.0 },
 		 {id: "uniform", spec: "Uniform", tree: "@tree", weight: 10.0 },
-		 {id: "subtreeSlide2", spec: "SubtreeSlide", optimise: false, tree: "@tree", weight: 5.0 },
 		 {id: "narrow", spec: "Exchange", tree: "@tree", weight: 1.0 },
 		 {id: "wide", spec: "Exchange", isNarrow: false, tree: "@tree", weight: 1.0 },
 		 {id: "wilsonBalding", spec: "WilsonBalding", tree: "@tree", weight: 1.0 }
 	  ],
 	 logger: [
-		{ fileName: "test.$(seed).log", logEvery: 10000, model: "@treeLikelihood",
+		{spec: "Logger", fileName: "test.$(seed).log", logEvery: 10000, model: "@treeLikelihood",
 		 log: [
 			 {idref: "treeLikelihood" },
 			 {idref: "hky.kappa" },
 			 {spec: "beast.evolution.tree.TreeHeightLogger", tree: "@tree" }
 		  ]
 		},
-		{ fileName: "test.$(seed).trees", logEvery: 10000,
+		{spec: "Logger", fileName: "test.$(seed).trees", logEvery: 10000,
 		 log: [
 			 {idref: "tree" }
 		  ]
 		},
-		{ logEvery: 10000, model: "@treeLikelihood",
+		{spec: "Logger", logEvery: 10000, model: "@treeLikelihood",
 		 log: [
 			 {idref: "treeLikelihood" },
 			 {spec: "util.ESS", arg: "@treeLikelihood" },

--- a/examples/testUCLNclock.json
+++ b/examples/testUCLNclock.json
@@ -17,12 +17,13 @@ beast: [
 	},

 	{id: "mcmc",
-	 spec: "MCMC", chainLength: 10000000,
-	 state: {id: "state", storeEvery: 5000,
+	 spec: "MCMC", chainLength: "10000000",
+	 state: {id: "state",
+		 spec: "State", storeEvery: 5000,
 		 stateNode: [
 			{id: "Tree.t:dna",
 			 spec: "beast.evolution.tree.Tree",
-				 taxonset: {id: "TaxonSet.dna", alignment: "@dna" }
+				 taxonset: {id: "TaxonSet.dna", spec: "TaxonSet", alignment: "@dna" }
 			},
 			 {id: "birthRate.t:dna", spec: "parameter.RealParameter", value: [ 1.0 ] },
 			 {id: "kappa.s:dna", spec: "parameter.RealParameter", lower: 0.0, value: [ 2.0 ] },
@@ -67,7 +68,7 @@ beast: [
 					 spec: "SiteModel", mutationRate: "1.0", shape: "1.0", proportionInvariant: "0.0",
 					 substModel: {id: "hky.s:dna",
 						 spec: "HKY", kappa: "@kappa.s:dna",
-							 frequencies: {id: "estimatedFreqs.s:dna", frequencies: "@freqParameter.s:dna" }
+							 frequencies: {id: "estimatedFreqs.s:dna", spec: "Frequencies", frequencies: "@freqParameter.s:dna" }
 						}
 					},
 				 branchRateModel: {id: "RelaxedClock.c:dna",
@@ -101,7 +102,8 @@ beast: [
 		}
 	  ],
 	 logger: [
-		{id: "tracelog", fileName: "dna.log", logEvery: 1000, model: "@posterior", sort: "smart", sanitiseHeaders: true,
+		{id: "tracelog",
+		 spec: "Logger", fileName: "dna.log", logEvery: 1000, model: "@posterior", sort: "smart", sanitiseHeaders: true,
 		 log: [
 			 {idref: "posterior" },
 			 {idref: "likelihood" },
@@ -116,7 +118,8 @@ beast: [
 			 {idref: "freqParameter.s:dna" }
 		  ]
 		},
-		{id: "screenlog", logEvery: 1000,
+		{id: "screenlog",
+		 spec: "Logger", logEvery: 1000,
 		 log: [
 			 {idref: "posterior" },
 			 {id: "ESS.0", spec: "util.ESS", arg: "@posterior" },
@@ -124,7 +127,8 @@ beast: [
 			 {idref: "prior" }
 		  ]
 		},
-		{id: "treelog.t:dna", fileName: "$(tree).trees", logEvery: 1000, mode: "tree",
+		{id: "treelog.t:dna",
+		 spec: "Logger", fileName: "$(tree).trees", logEvery: 1000, mode: "tree",
 		 log: [
 			 {id: "TreeWithMetaDataLogger.t:dna", spec: "beast.evolution.tree.TreeWithMetaDataLogger", tree: "@Tree.t:dna", branchratemodel: "@RelaxedClock.c:dna" }
 		  ]

--- a/release/Windows/AppLauncher_launch4j.xml
+++ b/release/Windows/AppLauncher_launch4j.xml
@@ -14,7 +14,7 @@
  </jre>    
  <versionInfo>
    <fileDescription>AppLauncher</fileDescription>
-    <copyright>Beast 2 development team 2002-2018</copyright>
+    <copyright>Beast 2 development team 2002-2019</copyright>
    <productName>AppLauncher</productName>
    <internalName>AppLauncher</internalName>
    <originalFilename>AppLauncher.exe</originalFilename>

--- a/release/Windows/AppLauncher_launch4j_jre.xml
+++ b/release/Windows/AppLauncher_launch4j_jre.xml
@@ -15,7 +15,7 @@
  </jre>    
  <versionInfo>
    <fileDescription>AppLauncher</fileDescription>
-    <copyright>Beast 2 development team 2002-2018</copyright>
+    <copyright>Beast 2 development team 2002-2019</copyright>
    <productName>AppLauncher</productName>
    <internalName>AppLauncher</internalName>
    <originalFilename>AppLauncher.exe</originalFilename>

--- a/release/Windows/BEAST_launch4j.xml
+++ b/release/Windows/BEAST_launch4j.xml
@@ -14,7 +14,7 @@
  </jre>    
  <versionInfo>
    <fileDescription>BEAST2</fileDescription>    
-    <copyright>Beast 2 development team 2002-2018</copyright>
+    <copyright>Beast 2 development team 2002-2019</copyright>
    <productName>BEAST2</productName>
    <internalName>BEAST2</internalName>
    <originalFilename>BEAST2.exe</originalFilename>    

--- a/release/Windows/BEAST_launch4j_jre.xml
+++ b/release/Windows/BEAST_launch4j_jre.xml
@@ -15,7 +15,7 @@
  </jre>    
  <versionInfo>
    <fileDescription>BEAST2</fileDescription>    
-    <copyright>Beast 2 development team 2002-2018</copyright>
+    <copyright>Beast 2 development team 2002-2019</copyright>
    <productName>BEAST2</productName>
    <internalName>BEAST2</internalName>
    <originalFilename>BEAST2.exe</originalFilename>    

--- a/release/Windows/BEAUti_launch4j.xml
+++ b/release/Windows/BEAUti_launch4j.xml
@@ -14,7 +14,7 @@
  </jre>    
  <versionInfo>
    <fileDescription>BEAUti2</fileDescription>
-    <copyright>Beast 2 development team 2002-2018</copyright>
+    <copyright>Beast 2 development team 2002-2019</copyright>
    <productName>BEAUti2</productName>
    <internalName>BEAUti2</internalName>
    <originalFilename>BEAUti2.exe</originalFilename>    

--- a/release/Windows/BEAUti_launch4j_jre.xml
+++ b/release/Windows/BEAUti_launch4j_jre.xml
@@ -15,7 +15,7 @@
  </jre>    
  <versionInfo>
    <fileDescription>BEAUti2</fileDescription>
-    <copyright>Beast 2 development team 2002-2018</copyright>
+    <copyright>Beast 2 development team 2002-2019</copyright>
    <productName>BEAUti2</productName>
    <internalName>BEAUti2</internalName>
    <originalFilename>BEAUti2.exe</originalFilename>    

--- a/release/Windows/LogCombiner_launch4j.xml
+++ b/release/Windows/LogCombiner_launch4j.xml
@@ -14,7 +14,7 @@
  </jre>    
  <versionInfo>
    <fileDescription>LogCombiner</fileDescription>    
-    <copyright>Beast 2 development team 2002-2018</copyright>
+    <copyright>Beast 2 development team 2002-2019</copyright>
    <productName>LogCombiner</productName>
    <internalName>LogCombiner</internalName>
    <originalFilename>LogCombiner.exe</originalFilename>    

--- a/release/Windows/LogCombiner_launch4j_jre.xml
+++ b/release/Windows/LogCombiner_launch4j_jre.xml
@@ -14,7 +14,7 @@
  </jre>    
  <versionInfo>
    <fileDescription>LogCombiner</fileDescription>    
-    <copyright>Beast 2 development team 2002-2018</copyright>
+    <copyright>Beast 2 development team 2002-2019</copyright>
    <productName>LogCombiner</productName>
    <internalName>LogCombiner</internalName>
    <originalFilename>LogCombiner.exe</originalFilename>    

--- a/release/Windows/TreeAnnotator_launch4j.xml
+++ b/release/Windows/TreeAnnotator_launch4j.xml
@@ -13,7 +13,7 @@
  </jre>    
  <versionInfo>
    <fileDescription>TreeAnnotator</fileDescription>    
-    <copyright>Beast 2 development team 2002-2018</copyright>
+    <copyright>Beast 2 development team 2002-2019</copyright>
    <productName>TreeAnnotator</productName>
    <internalName>TreeAnnotator</internalName>
    <originalFilename>TreeAnnotator.exe</originalFilename>    

--- a/release/Windows/TreeAnnotator_launch4j_jre.xml
+++ b/release/Windows/TreeAnnotator_launch4j_jre.xml
@@ -14,7 +14,7 @@
  </jre>    
  <versionInfo>
    <fileDescription>TreeAnnotator</fileDescription>    
-    <copyright>Beast 2 development team 2002-2018</copyright>
+    <copyright>Beast 2 development team 2002-2019</copyright>
    <productName>TreeAnnotator</productName>
    <internalName>TreeAnnotator</internalName>
    <originalFilename>TreeAnnotator.exe</originalFilename>    

--- a/release/common/README.txt
+++ b/release/common/README.txt
-                    BEAST v2.5.1 2018
-                 Beast 2 development team 2011-2018
+                    BEAST v2.5.2 2019
+                 Beast 2 development team 2011-2019

-Last updated: September 2018
+Last updated: January 2019

 Contents:
 1) INTRODUCTION
@@ -187,7 +187,7 @@ ___________________________________________________________________________
 BEAST is an extremely complex program and as such will inevitably have
 bugs. Please email us to discuss any problems:

-<remco@cs.auckland.ac.nz>
+<r.bouckaert@auckland.ac.nz>
 <alexei@cs.auckland.ac.nz>
 <a.rambaut@ed.ac.uk>
 <msuchard@ucla.edu>

--- a/release/common/VERSION HISTORY.txt
+++ b/release/common/VERSION HISTORY.txt
-                    BEAST v2.5.1 2018
-                 Beast 2 development team 2011-2018
+                    BEAST v2.5.2 2019
+                 Beast 2 development team 2011-2019
 Version History
-Last updated: September 2018
+Last updated: September 2019

 All issues can be viewed at https://github.com/CompEvol/beast2/issues
 ================================================================================
+Version 2.5.2
+	More robust release for Windows that includes JRE
+	Fix AppLauncher for OS X
+	Robustify start scripts for OS X, Linux
+	Implement rate parameterisation for uncorrelated relaxed clock model
+	Improved error messages	
+	Relaxed API giving more access to package developers
+	Node.getMetaData() now returns null on key not found
+	Pass -Xss arguments through launchers to set stack size
+	DOIs point to preferred resolver
+	Fix multi-threading issue with parameteric distributions
+	Remove posterior ESS from screen log
+
 Version 2.5.1
 	Add -X flag to all applications, so more memory can be allocated
 	Fix some OS X with Java 9+ anomalies

--- a/src/beast/app/BEASTVersion.java
+++ b/src/beast/app/BEASTVersion.java
@@ -19,7 +19,7 @@ public class BEASTVersion extends Version {
    /**
     * Version string: assumed to be in format x.x.x
     */
-    private static final String VERSION = "2.5.2";
+    private static final String VERSION = "2.5.3";

    private static final String DATE_STRING = "2002-2019";

@@ -50,9 +50,9 @@ public class BEASTVersion extends Version {
                "Designed and developed by",
                "Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard",
                "",
-                "Department of Computer Science",
+                "Centre for Computational Evolution",
                "University of Auckland",
-                "remco@cs.auckland.ac.nz",
+                "r.bouckaert@auckland.ac.nz",
                "alexei@cs.auckland.ac.nz",
                "",
                "Institute of Evolutionary Biology",
@@ -85,8 +85,8 @@ public class BEASTVersion extends Version {
        return
                "<p>Designed and developed by<br>" +
                        "Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard</p>" +
-                        "<p>Department of Computer Science, University of Auckland<br>" +
-                        "<a href=\"mailto:remco@cs.auckland.ac.nz\">remco@cs.auckland.ac.nz</a><br>" +
+                        "<p>Centre for Computational Evolution, University of Auckland<br>" +
+                        "<a href=\"mailto:r.bouckaert@auckland.ac.nz\">r.bouckaert@auckland.ac.nz</a><br>" +
                        "<a href=\"mailto:alexei@cs.auckland.ac.nz\">alexei@cs.auckland.ac.nz</a></p>" +
                        "<p>Institute of Evolutionary Biology, University of Edinburgh<br>" +
                        "<a href=\"mailto:a.rambaut@ed.ac.uk\">a.rambaut@ed.ac.uk</a></p>" +