Skip to content
Commits on Source (3)
Expand all Hide whitespace changes
Inline Side-by-side
README.md
View file @ f3152232
......@@ -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
View file @ f3152232
......@@ -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
View file @ f3152232
......@@ -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
View file @ f3152232
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
View file @ f3152232
......@@ -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
View file @ f3152232
<?xml version="1.0" standalone="yes"?>
 
<!-- Generated by BEAUTi v1.6.0pre -->
<!-- Generated by BEAUTi v1.6.0pre -->
<!-- by Alexei J. Drummond and Andrew Rambaut -->
<!-- Department of Computer Science, University of Auckland and -->
<!-- Institute of Evolutionary Biology, University of Edinburgh -->
......@@ -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>
<parameter idref="constant.popSize"/>
</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"/>
</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
View file @ f3152232
<?xml version="1.0" standalone="yes"?>
 
<!-- Generated by BEAUTi v1.6.0pre -->
<!-- Generated by BEAUTi v1.6.0pre -->
<!-- by Alexei J. Drummond and Andrew Rambaut -->
<!-- Department of Computer Science, University of Auckland and -->
<!-- Institute of Evolutionary Biology, University of Edinburgh -->
......@@ -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/Microsatellite/microsatellite.xml deleted 100644 → 0
View file @ f6fcfdf8
This diff is collapsed.
examples/StarBEAST/YuleMultiLoci.xml deleted 100644 → 0
View file @ f6fcfdf8
This diff is collapsed.
examples/StarBEAST/YuleSingleLocus.xml deleted 100644 → 0
View file @ f6fcfdf8
This diff is collapsed.
examples/StarBEAST/birthDeathMultiLoci.xml deleted 100644 → 0
View file @ f6fcfdf8
This diff is collapsed.
examples/StarBEAST/brithDeathSingleLocus.xml deleted 100644 → 0
View file @ f6fcfdf8
This diff is collapsed.
examples/TestXML/testMC3.xml
View file @ f3152232
......@@ -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
View file @ f3152232
......@@ -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
View file @ f3152232
......@@ -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 0 → 100644
View file @ f3152232
<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 0 → 100644
View file @ f3152232
<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 0 → 100644
View file @ f3152232
<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 0 → 100644
View file @ f3152232
<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 0 → 100644
View file @ f3152232
<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>