From 833677b335ba2b8010d6b87e771df472f0ba93af Mon Sep 17 00:00:00 2001
From: rbouckaert <higgs.ml@gmail.com>
Date: Mon, 25 May 2015 08:17:02 +1200
Subject: [PATCH] add example

---
 build.xml             |   8 +--
 examples/cladeage.xml | 128 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 132 insertions(+), 4 deletions(-)
 create mode 100644 examples/cladeage.xml

diff --git a/build.xml b/build.xml
index c6eef7b..d8211a9 100644
--- a/build.xml
+++ b/build.xml
@@ -15,7 +15,7 @@
 	<property name="libCA" location="lib" />
 	<property name="release_dir" value="release" />
 	<property name="distCA" location="${buildCA}/dist" />
-	<property name="beast2path" location="../beast2.1.3"/>
+	<property name="beast2path" location="../beast2"/>
 	<property name="libBeast2" location="${beast2path}/lib" />
 	<property name="srcBeast2" location="${beast2path}/src" />
 	<property name="beast2classpath" location="${beast2path}/build" />
@@ -74,8 +74,8 @@
 		       fork="true"
 		       memoryinitialsize="256m"
 		       memorymaximumsize="256m"
-			   source="1.6"
-		       target="1.6">
+			   source="1.8"
+		       target="1.8">
 			<include name="beast/**/**" />
 			<!-- compile JUnit test classes -->
 			<include name="test/beast/**" />
@@ -324,7 +324,7 @@
 		            name="${CladeAge_name}"
 		            mainclass="${main_class_CladeAge}"
 		            icon="${common_dirCA}/icons/cladeage.icns"
-		            jvmversion="1.6+"
+		            jvmversion="1.8+"
 		            vmoptions="-Xmx1024M"
 		            arguments="-window -working -options"
 		            version="${versionCA}"
diff --git a/examples/cladeage.xml b/examples/cladeage.xml
new file mode 100644
index 0000000..c81b59e
--- /dev/null
+++ b/examples/cladeage.xml
@@ -0,0 +1,128 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast beautitemplate='Standard' beautistatus='' namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" version="2.0">
+
+
+    <data id="6primates" name="alignment">
+                    <sequence id="seq_human" taxon="human" totalcount="4" value="AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA"/>
+                    <sequence id="seq_chimp" taxon="chimp" totalcount="4" value="AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA"/>
+                    <sequence id="seq_bonobo" taxon="bonobo" totalcount="4" value="AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA"/>
+                    <sequence id="seq_gorilla" taxon="gorilla" totalcount="4" value="AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA"/>
+                    <sequence id="seq_orangutan" taxon="orangutan" totalcount="4" value="AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA--CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA"/>
+                    <sequence id="seq_siamang" taxon="siamang" totalcount="4" value="AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA"/>
+                </data>
+
+
+    
+
+
+    
+
+
+    
+<map name="Beta">beast.math.distributions.Beta</map>
+<map name="Exponential">beast.math.distributions.Exponential</map>
+<map name="InverseGamma">beast.math.distributions.InverseGamma</map>
+<map name="LogNormal">beast.math.distributions.LogNormalDistributionModel</map>
+<map name="Gamma">beast.math.distributions.Gamma</map>
+<map name="Uniform">beast.math.distributions.Uniform</map>
+<map name="prior">beast.math.distributions.Prior</map>
+<map name="LaplaceDistribution">beast.math.distributions.LaplaceDistribution</map>
+<map name="OneOnX">beast.math.distributions.OneOnX</map>
+<map name="Normal">beast.math.distributions.Normal</map>
+
+
+<run chainLength="10000000" id="mcmc" spec="MCMC">
+    <state id="state" storeEvery="5000">
+        <tree id="Tree.t:6primates" name="stateNode">
+            <taxonset id="TaxonSet.6primates" spec="TaxonSet">
+                <data idref="6primates" name="alignment"/>
+            </taxonset>
+        </tree>
+        <parameter id="birthRate.t:6primates" name="stateNode" value="1.0"/>
+    </state>
+
+    <distribution id="posterior" spec="util.CompoundDistribution">
+        <distribution id="prior" spec="util.CompoundDistribution">
+            <distribution birthDiffRate="@birthRate.t:6primates" id="YuleModel.t:6primates" spec="beast.evolution.speciation.YuleModel" tree="@Tree.t:6primates"/>
+            <prior id="YuleBirthRatePrior.t:6primates" name="distribution" x="@birthRate.t:6primates">
+                <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
+            </prior>
+        </distribution>
+        <distribution id="likelihood" spec="util.CompoundDistribution">
+            <distribution data="@6primates" id="treeLikelihood.6primates" spec="TreeLikelihood" tree="@Tree.t:6primates">
+                <siteModel id="SiteModel.s:6primates" spec="SiteModel">
+                    <parameter estimate="false" id="mutationRate.s:6primates" name="mutationRate" value="1.0"/>
+                    <parameter estimate="false" id="gammaShape.s:6primates" name="shape" value="1.0"/>
+                    <parameter estimate="false" id="proportionInvariant.s:6primates" lower="0.0" name="proportionInvariant" upper="1.0" value="0.0"/>
+                    <substModel id="JC69.s:6primates" spec="JukesCantor"/>
+                </siteModel>
+                <branchRateModel id="StrictClock.c:6primates" spec="beast.evolution.branchratemodel.StrictClockModel">
+                    <parameter estimate="false" id="clockRate.c:6primates" name="clock.rate" value="1.0"/>
+                </branchRateModel>
+            </distribution>
+        </distribution>
+        <distribution id="fossilCalibrations" spec="util.CompoundDistribution">
+            <distribution id="Human-Chimp.fossilprior" spec="beast.math.distributions.FossilPrior" tree="@Tree.t:6primates">
+                <fossilDistr id="FossilCallibration.0" maxDivRate="0.012" maxOccuranceAge="7.0" maxSamplingGap="0.02" maxSamplingRate="0.012" maxTurnoverRate="0.12" minDivRate="0.011" minOccuranceAge="6.0" minSamplingGap="0.01" minSamplingRate="0.011" minTurnoverRate="0.11" spec="beast.math.distributions.FossilCalibration"/>
+                <taxonset id="Human-Chimp" spec="TaxonSet">
+                    <taxon id="bonobo" spec="Taxon"/>
+                    <taxon id="chimp" spec="Taxon"/>
+                </taxonset>
+            </distribution>
+        </distribution>
+    </distribution>
+
+    <operator id="YuleBirthRateScaler.t:6primates" parameter="@birthRate.t:6primates" scaleFactor="0.75" spec="ScaleOperator" weight="3.0"/>
+
+    <operator id="treeScaler.t:6primates" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:6primates" weight="3.0"/>
+
+    <operator id="treeRootScaler.t:6primates" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:6primates" weight="3.0"/>
+
+    <operator id="UniformOperator.t:6primates" spec="Uniform" tree="@Tree.t:6primates" weight="30.0"/>
+
+    <operator id="SubtreeSlide.t:6primates" spec="SubtreeSlide" tree="@Tree.t:6primates" weight="15.0"/>
+
+    <operator id="narrow.t:6primates" spec="Exchange" tree="@Tree.t:6primates" weight="15.0"/>
+
+    <operator id="wide.t:6primates" isNarrow="false" spec="Exchange" tree="@Tree.t:6primates" weight="3.0"/>
+
+    <operator id="WilsonBalding.t:6primates" spec="WilsonBalding" tree="@Tree.t:6primates" weight="3.0"/>
+
+    <logger fileName="6primates.log" id="tracelog" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
+        <log idref="posterior"/>
+        <log idref="likelihood"/>
+        <log idref="prior"/>
+        <log idref="treeLikelihood.6primates"/>
+        <log id="TreeHeight.t:6primates" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:6primates"/>
+        <log idref="YuleModel.t:6primates"/>
+        <parameter idref="birthRate.t:6primates" name="log"/>
+        <log idref="Human-Chimp.fossilprior"/>
+    </logger>
+
+    <logger id="screenlog" logEvery="1000">
+        <log idref="posterior"/>
+        <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+        <log idref="likelihood"/>
+        <log idref="prior"/>
+    </logger>
+
+    <logger fileName="$(tree).trees" id="treelog.t:6primates" logEvery="1000" mode="tree">
+        <log id="TreeWithMetaDataLogger.t:6primates" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:6primates"/>
+    </logger>
+
+    <init estimate="false" id="RandomTree.t:6primates" initial="@Tree.t:6primates" spec="beast.evolution.tree.RandomTree" taxa="@6primates">
+        <populationModel id="ConstantPopulation0.t:6primates" spec="ConstantPopulation">
+            <parameter id="randomPopSize.t:6primates" name="popSize" value="1"/>
+        </populationModel>
+    </init>
+
+</run>
+
+
+
+<!-- DO NOT EDIT the following machine generated text, they are used in Beauti 
+
+
+
+-->
+
+</beast>