README.md

@@ -4,7 +4,7 @@ BEAST is a cross-platform program for Bayesian analysis of molecular sequences u
 
 ## Download BEAST
 
-[Download BEAST v1.10.0 binaries for Mac, Windows and UNIX/Linux](https://github.com/beast-dev/beast-mcmc/releases/tag/v1.10.0)
+[Download BEAST v1.10.1 binaries for Mac, Windows and UNIX/Linux](https://github.com/beast-dev/beast-mcmc/releases/tag/v1.10.1)
 
 [The previous major release of BEAST was v1.8.4 --- binaries for Mac, Windows and UNIX/Linux](https://github.com/beast-dev/beast-mcmc/releases/tag/v1.8.4)
 

build.xml

@@ -319,10 +319,10 @@
     <!--
     <property name="version" value="1.9"/>
      -->
-    <property name="version" value="1.10.0"/>
-    <property name="jvm_version" value="1.6+"/>
+    <property name="version" value="1.10.2"/>
+    <property name="jvm_version" value="1.7+"/>
 
-    <property name="version_number" value="1.10.0"/>
+    <property name="version_number" value="1.10.2"/>
     <property name="copyright" value="Copyright 2002-2018"/>
 
     <property name="release_dir" value="release"/>
@@ -339,10 +339,12 @@
     <property name="Mac_dir" value="${release_dir}/Mac"/>
     <property name="Linux_dir" value="${release_dir}/Linux"/>
     <property name="Windows_dir" value="${release_dir}/Windows"/>
+    <property name="Windows_launchers_dir" value="${release_dir}/Windows_Launchers"/>
 
     <property name="Mac_package_dir" value="${Mac_dir}/${BEAST_name} v${version}"/>
     <property name="Linux_package_dir" value="${Linux_dir}/${BEAST_name}v${version}"/>
     <property name="Windows_package_dir" value="${Windows_dir}/${BEAST_name} v${version}"/>
+    <property name="Windows_launchers_package_dir" value="${Windows_launchers_dir}/${BEAST_name} v${version}"/>
 
     <!-- Need to either install Launch4j under {BEAST workspace}/${release}
                   or install it in the default directory and change the location of launch4j.dir -->
@@ -373,10 +375,11 @@
         </copy>
         <copy file="${dist}/beauti.jar" todir="${Windows_package_dir}/lib"/>
         <copy file="${dist}/beast.jar" todir="${Windows_package_dir}/lib"/>
-        <!-- <copy file="${dist}/beast-beagle.jar" todir="${Windows_package_dir}/lib"/> -->
+        <!--
         <copy todir="${Windows_package_dir}/lib">
             <fileset dir="${Windows_dir}/lib"/>
         </copy>
+        -->
         <copy file="${common_dir}/VERSION HISTORY.txt" todir="${Windows_package_dir}"/>
         <copy file="${common_dir}/README.txt" todir="${Windows_package_dir}"/>
 
@@ -398,6 +401,14 @@
                   productVersion="${version_number}.0"
                   txtProductVersion="${version}"/>
 
+        <!-- BEAST v?.?.?.exe -->
+        <launch4j configFile="${Windows_dir}/BEAST_launch4j.xml"
+                  outfile="${Windows_package_dir}/${BEAST_name} v${version}.exe"
+                  fileVersion="${version_number}.0"
+                  txtFileVersion="${version}"
+                  productVersion="${version_number}.0"
+                  txtProductVersion="${version}"/>
+
         <!-- TreeAnnotator v?.?.?.exe -->
         <launch4j configFile="${Windows_dir}/TreeAnnotator_launch4j.xml"
                   jar="${dist}/beast.jar"
@@ -440,6 +451,104 @@
         <echo message="Windows version release is finished."/>
     </target>
 
+    <target name="windows_launchers" depends="dist"
+            description="release Windows (launchers) version of BEAST, BEAUTI, TreeAnnotator, LogCombiner">
+
+        <delete dir="${Windows_launchers_package_dir}"/>
+        <!-- Create the release directory -->
+        <mkdir dir="${Windows_launchers_package_dir}"/>
+
+        <property name="launch4j.dir" location="${Windows_launchers_dir}/launch4j"/>
+        <taskdef name="launch4j" classname="net.sf.launch4j.ant.Launch4jTask"
+                 classpath="${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar"/>
+
+        <copy todir="${Windows_launchers_package_dir}/doc">
+            <fileset dir="${common_dir}/doc"/>
+        </copy>
+        <copy todir="${Windows_launchers_package_dir}/examples">
+            <fileset dir="examples"/>
+        </copy>
+        <copy todir="${Windows_launchers_package_dir}/native">
+            <fileset dir="native">
+                <exclude name="deprecated/**"/>
+            </fileset>
+        </copy>
+        <copy todir="${Windows_launchers_package_dir}/bin">
+            <fileset dir="${Windows_dir}/scripts"/>
+        </copy>
+        <copy file="${dist}/beauti.jar" todir="${Windows_launchers_package_dir}/lib"/>
+        <copy file="${dist}/beast.jar" todir="${Windows_launchers_package_dir}/lib"/>
+        <!--
+        <copy todir="${Windows_package_dir}/lib">
+            <fileset dir="${Windows_dir}/lib"/>
+        </copy>
+        -->
+        <copy file="${common_dir}/VERSION HISTORY.txt" todir="${Windows_launchers_package_dir}"/>
+        <copy file="${common_dir}/README.txt" todir="${Windows_launchers_package_dir}"/>
+
+        <!-- BEAUTi v?.?.?.exe -->
+        <launch4j configFile="${Windows_launchers_dir}/BEAUti_launch4j.xml"
+                  outfile="${Windows_launchers_package_dir}/${BEAUti_name} v${version}.exe"
+                  fileVersion="${version_number}.0"
+                  txtFileVersion="${version}"
+                  productVersion="${version_number}.0"
+                  txtProductVersion="${version}"/>
+
+        <!-- BEAST v?.?.?.exe -->
+        <launch4j configFile="${Windows_launchers_dir}/BEAST_launch4j.xml"
+                  outfile="${Windows_launchers_package_dir}/${BEAST_name} v${version}.exe"
+                  fileVersion="${version_number}.0"
+                  txtFileVersion="${version}"
+                  productVersion="${version_number}.0"
+                  txtProductVersion="${version}"/>
+
+        <!-- BEAST v?.?.?.exe -->
+        <launch4j configFile="${Windows_launchers_dir}/BEAST_launch4j.xml"
+                  outfile="${Windows_launchers_package_dir}/${BEAST_name} v${version}.exe"
+                  fileVersion="${version_number}.0"
+                  txtFileVersion="${version}"
+                  productVersion="${version_number}.0"
+                  txtProductVersion="${version}"/>
+
+        <!-- TreeAnnotator v?.?.?.exe -->
+        <launch4j configFile="${Windows_launchers_dir}/TreeAnnotator_launch4j.xml"
+                  outfile="${Windows_launchers_package_dir}/${TreeAnnotator_name} v${version}.exe"
+                  fileVersion="${version_number}.0"
+                  txtFileVersion="${version}"
+                  productVersion="${version_number}.0"
+                  txtProductVersion="${version}"/>
+
+        <!-- LogCombiner v?.?.?.exe -->
+        <launch4j configFile="${Windows_launchers_dir}/LogCombiner_launch4j.xml"
+                  outfile="${Windows_launchers_package_dir}/${LogCombiner_name} v${version}.exe"
+                  fileVersion="${version_number}.0"
+                  txtFileVersion="${version}"
+                  productVersion="${version_number}.0"
+                  txtProductVersion="${version}"/>
+
+        <launch4j configFile="${Windows_launchers_dir}/TreeStat_launch4j.xml"
+                  outfile="${Windows_launchers_package_dir}/${TreeStat_name} v${version}.exe"
+                  fileVersion="${version_number}.0"
+                  txtFileVersion="${version}"
+                  productVersion="${version_number}.0"
+                  txtProductVersion="${version}"/>
+
+        <!-- LogAnalyser v?.?.?.exe
+          <launch4j configFile="${Windows_dir}/LogAnalyser_launch4j.xml"
+                    jar="${dist}/beast.jar"
+                    outfile="${Windows_package_dir}/${LogAnalyser_name}v${version}.exe"
+                    fileVersion="${version}.0"
+                    txtFileVersion="${version}"
+                    productVersion="${version}.0"
+                    txtProductVersion="${version}"/>	-->
+
+        <zip destfile="${release_dir}/${BEAST_name} v${version}_launchers.zip">
+            <zipfileset dir="${Windows_launchers_package_dir}" prefix="${BEAST_name} v${version}"/>
+        </zip>
+
+        <echo message="Windows launchers version release is finished."/>
+    </target>
+
     <target name="linux" depends="dist"
             description="release Linux/Unix version of BEAST, BEAUTI, TreeAnnotator, LogCombiner">
         <delete dir="${Linux_package_dir}"/>
@@ -469,9 +578,6 @@
         <copy file="${dist}/beauti.jar" todir="${Linux_package_dir}/lib"/>
         <copy file="${dist}/beast.jar" todir="${Linux_package_dir}/lib"/>
         <!-- <copy file="${dist}/beast-beagle.jar" todir="${Linux_package_dir}/lib"/> -->
-        <copy todir="${Linux_package_dir}/lib">
-            <fileset dir="${Linux_dir}/lib"/>
-        </copy>
         <copy file="${common_dir}/VERSION HISTORY.txt" todir="${Linux_package_dir}"/>
         <copy file="${common_dir}/README.txt" todir="${Linux_package_dir}"/>
 
@@ -534,7 +640,7 @@
 					useJavaXKey="true"
                     icon="${common_dir}/icons/beast.icns"
                     jvmversion="${jvm_version}"
-                    vmoptions="-d64 -Xmx2048M"
+                    vmoptions="-Xmx2048M"
                     arguments="-window -working -options"
                     highresolutioncapable="true"
                     version="${version}"
@@ -563,11 +669,11 @@
         <jarbundler dir="${Mac_package_dir}"
                     name="${BEAUti_name} v${version}"
                     mainclass="dr.app.beauti.BeautiApp"
-                    stubfile="${packaging_tools}/mac/universalJavaApplicationStub   "
+                    stubfile="${packaging_tools}/mac/universalJavaApplicationStub_BEAST"
 					useJavaXKey="true"
                     icon="${common_dir}/icons/beauti.icns"
                     jvmversion="${jvm_version}"
-                    vmoptions="-d64 -Xmx2048M"
+                    vmoptions="-Xmx2048M"
                     arguments=""
                     version="${version}"
                     highresolutioncapable="true"
@@ -606,7 +712,7 @@
 					useJavaXKey="true"
                     icon="${common_dir}/icons/utility.icns"
                     jvmversion="${jvm_version}"
-                    vmoptions="-d64 -Xmx2048M"
+                    vmoptions="-Xmx2048M"
                     highresolutioncapable="true"
                     arguments=""
                     version="${version}"
@@ -635,7 +741,7 @@
 					useJavaXKey="true"
                     icon="${common_dir}/icons/utility.icns"
                     jvmversion="${jvm_version}"
-                    vmoptions="-d64 -Xmx4096M"
+                    vmoptions="-Xmx4096M"
                     highresolutioncapable="true"
                     arguments=""
                     version="${version}"
@@ -664,7 +770,7 @@
 					useJavaXKey="true"
                     icon="${common_dir}/icons/TreeStat.icns"
                     jvmversion="${jvm_version}"
-                    vmoptions="-d64 -Xmx1024M"
+                    vmoptions="-Xmx1024M"
                     highresolutioncapable="true"
                     arguments=""
                     version="${version}"

build_tempest.xml

@@ -95,7 +95,7 @@
         </jar>
     </target>
 
-    <property name="version" value="1.5.1" />
+    <property name="version" value="1.5.2" />
     <property name="packaging_tools" value="packaging_tools" />
     <property name="release_dir" value="release_tempest" />
     <property name="name" value="TempEst" />
@@ -198,7 +198,8 @@
                         arguments=""
                         vmoptions="-Xmx1024M"
                         version="${version}"
-                        copyright="${name} v${version}, Copyright 2006-2017, Andrew Rambaut"
+                        highresolutioncapable="true"
+                        copyright="${name} v${version}, Copyright 2006-2018, Andrew Rambaut"
                         bundleid="tempest" >
             <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
             <jarfileset dir="${dist}">

debian/changelog

-beast-mcmc (1.10.0+dfsg-1) UNRELEASED; urgency=medium
+beast-mcmc (1.10.2+dfsg-1) UNRELEASED; urgency=medium
 
   [ Andreas Tille ]
   * New upstream version
   * Exclude Latex doc creation
   * New Build-Depends: libejml-java
   * New versioned Build-Depends: libhmsbeagle-java (>= 3.0.2)
+  * New upstream version
+  * Standards-Version: 4.2.1
 
   [ Jelmer Vernooij ]
   * Use secure copyright file specification URI.
   * Trim trailing whitespace.
 
- -- Andreas Tille <tille@debian.org>  Thu, 21 Jun 2018 17:50:40 +0200
+ -- Andreas Tille <tille@debian.org>  Tue, 16 Oct 2018 20:54:48 +0200
 
 beast-mcmc (1.8.4+dfsg.1-3) unstable; urgency=medium
 

debian/control

@@ -24,7 +24,7 @@ Build-Depends: debhelper (>= 11~),
                libitext1-java,
                libejml-java,
                libjlapack-java
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/beast-mcmc
 Vcs-Git: https://salsa.debian.org/med-team/beast-mcmc.git
 Homepage: http://beast.bio.ed.ac.uk/

examples/Benchmarks/benchmark1.xml

@@ -10114,7 +10114,7 @@
 	<!-- throughout the time spanned by the genealogy.                           -->
 	<constantSize id="constant" units="years">
 		<populationSize>
-			<parameter id="constant.popSize" value="52.0" lower="0.0" upper="Infinity"/>
+			<parameter id="constant.popSize" value="52.0" lower="0.0"/>
 		</populationSize>
 	</constantSize>
@@ -10153,7 +10153,7 @@
 	<!-- The strict clock (Uniform rates across branches)                        -->
 	<strictClockBranchRates id="branchRates">
 		<rate>
-			<parameter id="clock.rate" value="3.6E-4" lower="0.0" upper="Infinity"/>
+			<parameter id="clock.rate" value="3.6E-4" lower="0.0"/>
 		</rate>
 	</strictClockBranchRates>
@@ -10167,7 +10167,7 @@
 			</frequencyModel>
 		</frequencies>
 		<kappa>
-			<parameter id="kappa" value="2.0" lower="0.0" upper="Infinity"/>
+			<parameter id="kappa" value="2.0" lower="0.0"/>
 		</kappa>
 	</HKYModel>
@@ -10233,9 +10233,18 @@
 				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
 					<parameter idref="kappa"/>
 				</logNormalPrior>
-				<oneOnXPrior>
+                <dirichletPrior alpha="1.0" sumsTo="1.0">
+                    <parameter idref="frequencies"/>
+                </dirichletPrior>
+                <ctmcScalePrior>
+                    <ctmcScale>
+                        <parameter idref="clock.rate"/>
+                    </ctmcScale>
+                    <treeModel idref="treeModel"/>
+                </ctmcScalePrior>
+                <logNormalPrior mean="1.0" stdev="1.5" offset="0.0" meanInRealSpace="false">
                     <parameter idref="constant.popSize"/>
-				</oneOnXPrior>
+                </logNormalPrior>
 				<coalescentLikelihood idref="coalescent"/>
 			</prior>
 			<likelihood id="likelihood">
@@ -10264,7 +10273,7 @@
 		</log>
 		<!-- write log to file                                                       -->
-		<!--
+
 		<log id="fileLog" logEvery="1000" fileName="benchmark1.log" overwrite="true">
 			<posterior idref="posterior"/>
 			<prior idref="prior"/>
@@ -10283,7 +10292,7 @@
 			<strictClockBranchRates idref="branchRates"/>
 			<posterior idref="posterior"/>
 		</logTree>
-		-->
+
 	</mcmc>
 	<report>
 		<property name="timer">

examples/Benchmarks/benchmark2.xml

@@ -647,7 +647,7 @@
 	<!-- a Yule speciation process (a pure birth process).                       -->
 	<yuleModel id="yule" units="substitutions">
 		<birthRate>
-			<parameter id="yule.birthRate" value="1.0" lower="0.0" upper="Infinity"/>
+			<parameter id="yule.birthRate" value="1.0" lower="0.0"/>
 		</birthRate>
 	</yuleModel>
@@ -708,19 +708,19 @@
 			</frequencyModel>
 		</frequencies>
 		<rateAC>
-			<parameter id="ac" value="1.0" lower="0.0" upper="Infinity"/>
+			<parameter id="ac" value="1.0" lower="0.0"/>
 		</rateAC>
 		<rateAG>
-			<parameter id="ag" value="1.0" lower="0.0" upper="Infinity"/>
+			<parameter id="ag" value="1.0" lower="0.0"/>
 		</rateAG>
 		<rateAT>
-			<parameter id="at" value="1.0" lower="0.0" upper="Infinity"/>
+			<parameter id="at" value="1.0" lower="0.0"/>
 		</rateAT>
 		<rateCG>
-			<parameter id="cg" value="1.0" lower="0.0" upper="Infinity"/>
+			<parameter id="cg" value="1.0" lower="0.0"/>
 		</rateCG>
 		<rateGT>
-			<parameter id="gt" value="1.0" lower="0.0" upper="Infinity"/>
+			<parameter id="gt" value="1.0" lower="0.0"/>
 		</rateGT>
 	</gtrModel>
@@ -730,7 +730,7 @@
 			<gtrModel idref="gtr"/>
 		</substitutionModel>
 		<gammaShape gammaCategories="4">
-			<parameter id="alpha" value="0.5" lower="0.0" upper="1000.0"/>
+			<parameter id="alpha" value="0.5" lower="0.0"/>
 		</gammaShape>
 	</siteModel>
 	<treeLikelihood id="treeLikelihood" useAmbiguities="false">
@@ -812,6 +812,15 @@
 				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
 					<parameter idref="gt"/>
 				</gammaPrior>
+				<exponentialPrior mean="0.5" offset="0.0">
+					<parameter idref="alpha"/>
+				</exponentialPrior>
+				<dirichletPrior alpha="1.0" sumsTo="1.0">
+					<parameter idref="frequencies"/>
+				</dirichletPrior>
+				<logNormalPrior mean="1.0" stdev="1.5" offset="0.0" meanInRealSpace="false">
+					<parameter idref="yule.birthRate"/>
+				</logNormalPrior>
 				<speciationLikelihood idref="speciation"/>
 			</prior>
 			<likelihood id="likelihood">
@@ -837,6 +846,9 @@
 			<column label="clock.rate" sf="6" width="12">
 				<parameter idref="clock.rate"/>
 			</column>
+			<column label="alpha" sf="6" width="12">
+				<parameter idref="alpha"/>
+			</column>
 		</log>
 		<!-- write log to file                                                       -->

examples/TestXML/testMC3.xml

@@ -145,7 +145,7 @@
 	<!-- throughout the time spanned by the genealogy.                           -->
 	<constantSize id="constant" units="years">
 		<populationSize>
-			<parameter id="constant.popSize" value="380.0" lower="0.0" upper="38000.0"/>
+			<parameter id="constant.popSize" value="380.0" lower="0.0"/>
 		</populationSize>
 	</constantSize>
 
@@ -180,7 +180,7 @@
 	<!-- The strict clock (Uniform rates across branches)                        -->
 	<strictClockBranchRates id="branchRates">
 		<rate>
-			<parameter id="clock.rate" value="2.3E-5" lower="0.0" upper="100.0"/>
+			<parameter id="clock.rate" value="2.3E-5" lower="0.0"/>
 		</rate>
 	</strictClockBranchRates>
 
@@ -195,7 +195,7 @@
 			</frequencyModel>
 		</frequencies>
 		<kappa>
-			<parameter id="hky.kappa" value="1.0" lower="0.0" upper="100.0"/>
+			<parameter id="hky.kappa" value="1.0" lower="0.0"/>
 		</kappa>
 	</hkyModel>
 
@@ -205,7 +205,7 @@
 			<hkyModel idref="hky"/>
 		</substitutionModel>
 		<gammaShape gammaCategories="4">
-			<parameter id="siteModel.alpha" value="0.5" lower="0.0" upper="100.0"/>
+			<parameter id="siteModel.alpha" value="0.5" lower="0.0"/>
 		</gammaShape>
 	</siteModel>
 
@@ -260,6 +260,26 @@
 	<mcmc id="mcmc" chainLength="10000000" autoOptimize="true" preBurnin="0">
 		<posterior id="posterior">
 			<prior id="prior">
+
+				<exponentialPrior mean="0.5" offset="0.0">
+					<parameter idref="siteModel.alpha"/>
+				</exponentialPrior>
+
+				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
+					<parameter idref="hky.kappa"/>
+				</logNormalPrior>
+
+				<logNormalPrior mean="1.0" stdev="1.5" offset="0.0" meanInRealSpace="false">
+					<parameter idref="constant.popSize"/>
+				</logNormalPrior>
+
+				<ctmcScalePrior>
+					<ctmcScale>
+						<parameter idref="clock.rate"/>
+					</ctmcScale>
+					<treeModel idref="treeModel"/>
+				</ctmcScalePrior>
+
 				<coalescentLikelihood idref="coalescent"/>
 			</prior>
 			<likelihood id="likelihood">

examples/TestXML/testMultiThreading.xml

@@ -155,7 +155,7 @@
 	<!-- throughout the time spanned by the genealogy.                           -->
 	<constantSize id="constant" units="years">
 		<populationSize>
-			<parameter id="constant.popSize" value="380.0" lower="0.0" upper="380000.0"/>
+			<parameter id="constant.popSize" value="380.0" lower="0.0"/>
 		</populationSize>
 	</constantSize>
 
@@ -190,7 +190,7 @@
 	<!-- The strict clock (Uniform rates across branches)                        -->
 	<strictClockBranchRates id="branchRates">
 		<rate>
-			<parameter id="clock.rate" value="2.3E-5" lower="0.0" upper="100.0"/>
+			<parameter id="clock.rate" value="2.3E-5" lower="0.0"/>
 		</rate>
 	</strictClockBranchRates>
 
@@ -205,7 +205,7 @@
 			</frequencyModel>
 		</frequencies>
 		<kappa>
-			<parameter id="hky1.kappa" value="1.0" lower="0.0" upper="Infinity"/>
+			<parameter id="hky1.kappa" value="1.0" lower="0.0"/>
 		</kappa>
 	</hkyModel>
 	<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
@@ -219,7 +219,7 @@
 			</frequencyModel>
 		</frequencies>
 		<kappa>
-			<parameter id="hky2.kappa" value="1.0" lower="0.0" upper="Infinity"/>
+			<parameter id="hky2.kappa" value="1.0" lower="0.0"/>
 		</kappa>
 	</hkyModel>
 	<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
@@ -233,7 +233,7 @@
 			</frequencyModel>
 		</frequencies>
 		<kappa>
-			<parameter id="hky3.kappa" value="1.0" lower="0.0" upper="Infinity"/>
+			<parameter id="hky3.kappa" value="1.0" lower="0.0"/>
 		</kappa>
 	</hkyModel>
 
@@ -243,10 +243,10 @@
 			<hkyModel idref="hky1"/>
 		</substitutionModel>
 		<relativeRate>
-			<parameter id="siteModel1.mu" value="1.0" lower="0.0" upper="Infinity"/>
+			<parameter id="siteModel1.mu" value="1.0" lower="0.0"/>
 		</relativeRate>
 		<gammaShape gammaCategories="4">
-			<parameter id="siteModel1.alpha" value="0.5" lower="0.0" upper="Infinity"/>
+			<parameter id="siteModel1.alpha" value="0.5" lower="0.0"/>
 		</gammaShape>
 	</siteModel>
 	<!-- site model                                                              -->
@@ -255,10 +255,10 @@
 			<hkyModel idref="hky2"/>
 		</substitutionModel>
 		<relativeRate>
-			<parameter id="siteModel2.mu" value="1.0" lower="0.0" upper="Infinity"/>
+			<parameter id="siteModel2.mu" value="1.0" lower="0.0"/>
 		</relativeRate>
 		<gammaShape gammaCategories="4">
-			<parameter id="siteModel2.alpha" value="0.5" lower="0.0" upper="Infinity"/>
+			<parameter id="siteModel2.alpha" value="0.5" lower="0.0"/>
 		</gammaShape>
 	</siteModel>
 	<!-- site model                                                              -->
@@ -267,10 +267,10 @@
 			<hkyModel idref="hky3"/>
 		</substitutionModel>
 		<relativeRate>
-			<parameter id="siteModel3.mu" value="1.0" lower="0.0" upper="Infinity"/>
+			<parameter id="siteModel3.mu" value="1.0" lower="0.0"/>
 		</relativeRate>
 		<gammaShape gammaCategories="4">
-			<parameter id="siteModel3.alpha" value="0.5" lower="0.0" upper="Infinity"/>
+			<parameter id="siteModel3.alpha" value="0.5" lower="0.0"/>
 		</gammaShape>
 	</siteModel>
 
@@ -361,6 +361,36 @@
 	<mcmc id="mcmc" chainLength="100000" autoOptimize="true">
 		<posterior id="posterior">
 			<prior id="prior">
+				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
+					<parameter idref="hky1.kappa"/>
+				</logNormalPrior>
+				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
+					<parameter idref="hky2.kappa"/>
+				</logNormalPrior>
+				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
+					<parameter idref="hky3.kappa"/>
+				</logNormalPrior>
+				<exponentialPrior mean="0.5" offset="0.0">
+					<parameter idref="siteModel1.alpha"/>
+				</exponentialPrior>
+				<exponentialPrior mean="0.5" offset="0.0">
+					<parameter idref="siteModel2.alpha"/>
+				</exponentialPrior>
+				<exponentialPrior mean="0.5" offset="0.0">
+					<parameter idref="siteModel3.alpha"/>
+				</exponentialPrior>
+				<dirichletPrior alpha="1.0" sumsTo="3.0">
+					<parameter idref="allMus"/>
+				</dirichletPrior>
+				<ctmcScalePrior>
+					<ctmcScale>
+						<parameter idref="clock.rate"/>
+					</ctmcScale>
+					<treeModel idref="treeModel"/>
+				</ctmcScalePrior>
+				<logNormalPrior mean="1.0" stdev="1.5" offset="0.0" meanInRealSpace="false">
+					<parameter idref="constant.popSize"/>
+				</logNormalPrior>
 				<coalescentLikelihood idref="coalescent"/>
 			</prior>
 			<likelihood id="likelihood" threads="3">
@@ -370,6 +400,7 @@
 			</likelihood>
 		</posterior>
 		<operators idref="operators"/>
+
 		<log id="screenLog" logEvery="10000">
 			<column label="Posterior" dp="4" width="12">
 				<posterior idref="posterior"/>
@@ -387,6 +418,7 @@
 				<parameter idref="clock.rate"/>
 			</column>
 		</log>
+
 		<log id="fileLog" logEvery="10000" fileName="testMultiThreading.log">
 			<posterior idref="posterior"/>
 			<prior idref="prior"/>
@@ -408,6 +440,7 @@
 			<treeLikelihood idref="treeLikelihood3"/>
 			<coalescentLikelihood idref="coalescent"/>
 		</log>
+
 		<logTree id="treeFileLog" logEvery="10000" nexusFormat="true" fileName="testMultiThreading.trees">
 			<treeModel idref="treeModel"/>
 			<posterior idref="posterior"/>

examples/TestXML/testPMD.xml

@@ -1366,7 +1366,7 @@
 	<!-- throughout the time spanned by the genealogy.                           -->
 	<constantSize id="constant" units="years">
 		<populationSize>
-			<parameter id="constant.popSize" value="496432.69917113904" lower="0.0" upper="Infinity"/>
+			<parameter id="constant.popSize" value="496432.69917113904" lower="0.0"/>
 		</populationSize>
 	</constantSize>
 	
@@ -1401,7 +1401,7 @@
 	<!-- The strict clock (Uniform rates across branches)                        -->
 	<strictClockBranchRates id="branchRates">
 		<rate>
-			<parameter id="clock.rate" value="4.0E-7" lower="0.0" upper="100.0"/>
+			<parameter id="clock.rate" value="4.0E-7" lower="0.0"/>
 		</rate>
 	</strictClockBranchRates>
 	
@@ -1415,7 +1415,7 @@
 			</frequencyModel>
 		</frequencies>
 		<kappa>
-			<parameter id="kappa" value="1.0" lower="1.0E-8" upper="Infinity"/>
+			<parameter id="kappa" value="1.0" lower="0.0"/>
 		</kappa>
 	</HKYModel>
 	
@@ -1428,7 +1428,7 @@
 	
 	<sequenceErrorModel id="errorModel" type="transitions">
 		<ageRelatedErrorRate>
-			<parameter id="errorModel.ageRate" value="4.0E-7" lower="0.0" upper="100.0"/>
+			<parameter id="errorModel.ageRate" value="4.0E-7" lower="0.0"/>
 		</ageRelatedErrorRate>
 	</sequenceErrorModel>
 	
@@ -1487,12 +1487,24 @@
 	<mcmc id="mcmc" chainLength="10000000" autoOptimize="true">
 		<posterior id="posterior">
 			<prior id="prior">
-				<jeffreysPrior>
+				<logNormalPrior mean="1.0" stdev="1.5" offset="0.0" meanInRealSpace="false">
 					<parameter idref="constant.popSize"/>
-				</jeffreysPrior>
-				<jeffreysPrior>
+				</logNormalPrior>
+				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
 					<parameter idref="kappa"/>
-				</jeffreysPrior>
+				</logNormalPrior>
+				<dirichletPrior alpha="1.0" sumsTo="1.0">
+					<parameter idref="frequencies"/>
+				</dirichletPrior>
+				<ctmcScalePrior>
+					<ctmcScale>
+						<parameter idref="clock.rate"/>
+					</ctmcScale>
+					<treeModel idref="treeModel"/>
+				</ctmcScalePrior>
+				<exponentialPrior mean="0.5" offset="0.0">
+					<parameter idref="errorModel.ageRate"/>
+				</exponentialPrior>
 				<coalescentLikelihood idref="coalescent"/>
 			</prior>
 			<likelihood id="likelihood">
@@ -1500,6 +1512,7 @@
 			</likelihood>
 		</posterior>
 		<operators idref="operators"/>
+
 		<log id="screenLog" logEvery="1000">
 			<column label="Posterior" dp="4" width="12">
 				<posterior idref="posterior"/>
@@ -1517,6 +1530,7 @@
 				<parameter idref="clock.rate"/>
 			</column>
 		</log>
+
 		<log id="fileLog" logEvery="1000" fileName="testPMD.log">
 			<posterior idref="posterior"/>
 			<prior idref="prior"/>
@@ -1529,6 +1543,7 @@
 			<treeLikelihood idref="treeLikelihood"/>
 			<coalescentLikelihood idref="coalescent"/>
 		</log>
+
 		<logTree id="treeFileLog" logEvery="1000" nexusFormat="true" fileName="testPMD.trees" sortTranslationTable="true">
 			<treeModel idref="treeModel"/>
 			<posterior idref="posterior"/>

release/Windows_Launchers/BEAST_launch4j.xml

+<launch4jConfig>
+  <headerType>gui</headerType>
+  <icon>../common/icons/beast.ico</icon>
+  <jar>./lib/beast.jar</jar>
+  <dontWrapJar>true</dontWrapJar>
+  <cmdLine>-window -working -options</cmdLine>
+  <jre>
+    <minVersion>1.6.0</minVersion>
+    <initialHeapSize>256</initialHeapSize>
+    <maxHeapSize>2048</maxHeapSize>
+  </jre>    
+  <versionInfo>
+    <fileDescription>BEAST</fileDescription>    
+        <copyright>2002-2018</copyright>
+    <productName>BEAST</productName>
+    <internalName>BEAST</internalName>
+    <originalFilename>BEAST.exe</originalFilename>    
+  </versionInfo>
+</launch4jConfig>

release/Windows_Launchers/BEAUti_launch4j.xml

+<launch4jConfig>
+  <headerType>gui</headerType>
+  <icon>../common/icons/beauti.ico</icon>
+  <jar>./lib/beauti.jar</jar>
+  <dontWrapJar>true</dontWrapJar>
+  <jre>
+    <minVersion>1.6.0</minVersion>
+    <initialHeapSize>256</initialHeapSize>
+    <maxHeapSize>1024</maxHeapSize>
+  </jre>    
+  <versionInfo>
+    <fileDescription>BEAUti</fileDescription>
+        <copyright>2002-2018</copyright>
+    <productName>BEAUti</productName>
+    <internalName>BEAUti</internalName>
+    <originalFilename>BEAUti.exe</originalFilename>    
+  </versionInfo>
+</launch4jConfig>

release/Windows_Launchers/LogAnalyser_launch4j.xml

+<launch4jConfig>
+  <headerType>console</headerType>
+  <icon>../common/icons/utility.ico</icon>
+  <classPath>
+  	<mainClass>dr.app.tools.LogAnalyser</mainClass>
+  	<cp>./lib/beast.jar</cp>
+  </classPath>
+  <jre>
+    <minVersion>1.6.0</minVersion>
+    <initialHeapSize>256</initialHeapSize>
+    <maxHeapSize>2048</maxHeapSize>
+  </jre>    
+  <versionInfo>
+    <fileDescription>LogAnalyser</fileDescription>    
+        <copyright>2002-2018</copyright>
+    <productName>LogAnalyser</productName>
+    <internalName>LogAnalyser</internalName>
+    <originalFilename>LogAnalyser.exe</originalFilename>    
+  </versionInfo>
+</launch4jConfig>

release/Windows_Launchers/LogCombiner_launch4j.xml

+<launch4jConfig>
+  <headerType>gui</headerType>
+  <icon>../common/icons/utility.ico</icon>
+  <classPath>
+  	<mainClass>dr.app.tools.LogCombiner</mainClass>
+  	<cp>./lib/beast.jar</cp>
+  </classPath>
+  <dontWrapJar>true</dontWrapJar>
+  <jre>
+    <minVersion>1.6.0</minVersion>
+    <initialHeapSize>256</initialHeapSize>
+    <maxHeapSize>2048</maxHeapSize>
+  </jre>    
+  <versionInfo>
+    <fileDescription>LogCombiner</fileDescription>    
+        <copyright>2002-2018</copyright>
+    <productName>LogCombiner</productName>
+    <internalName>LogCombiner</internalName>
+    <originalFilename>LogCombiner.exe</originalFilename>    
+  </versionInfo>
+</launch4jConfig>

release/Windows_Launchers/TreeAnnotator_launch4j.xml

+<launch4jConfig>
+  <headerType>gui</headerType>
+  <icon>../common/icons/utility.ico</icon>
+  <classPath>
+  	<mainClass>dr.app.tools.TreeAnnotator</mainClass>
+  	<cp>./lib/beast.jar</cp>
+  </classPath>
+  <dontWrapJar>true</dontWrapJar>
+  <jre>
+    <minVersion>1.6.0</minVersion>
+    <initialHeapSize>256</initialHeapSize>
+    <maxHeapSize>4096</maxHeapSize>
+  </jre>    
+  <versionInfo>
+    <fileDescription>TreeAnnotator</fileDescription>    
+        <copyright>2002-2018</copyright>
+    <productName>TreeAnnotator</productName>
+    <internalName>TreeAnnotator</internalName>
+    <originalFilename>TreeAnnotator.exe</originalFilename>    
+  </versionInfo>
+</launch4jConfig>