Commit 0a04b4e5 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.5.0+dfsg

parent 4a8dd9ec

.classpath

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<?xml version="1.0" encoding="UTF-8"?>

<classpath>

	<classpathentry kind="src" path="src"/>

	<classpathentry kind="lib" path="lib/beagle.jar"/>

	<classpathentry kind="lib" path="lib/colt.jar"/>

	<classpathentry kind="lib" path="lib/debug-1.0.jar"/>

	<classpathentry kind="lib" path="lib/fest.jar"/>

	<classpathentry kind="lib" path="lib/jam.jar"/>

	<classpathentry kind="lib" path="lib/junit-4.8.2.jar"/>

	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>

	<classpathentry kind="lib" path="lib/antlr-runtime-4.7.jar"/>

	<classpathentry kind="lib" path="lib/commons-math3-3.6.1.jar" sourcepath="lib/commons-math3-3.6.1-sources.jar"/>

	<classpathentry kind="output" path="build"/>

</classpath>

build.xml

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File changed.

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examples/testOpSubSchedule.xml

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<beast version='2.0'

       namespace='beast.evolution.alignment:beast.core:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood'>





    <!-- The sequence alignment                                                  -->

    <!-- ntax=6 nchar=768                                                        -->

    <!-- npatterns=69                                                            -->

    <data id="alignment" dataType="nucleotide">

        <sequence taxon="human">

            AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA

        </sequence>

        <sequence taxon="chimp">

            AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA

        </sequence>

        <sequence taxon="bonobo">

            AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA

        </sequence>

        <sequence taxon="gorilla">

            AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA

        </sequence>

        <sequence taxon="orangutan">

            AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA--CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA

        </sequence>

        <sequence taxon="siamang">

            AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA

        </sequence>

    </data>



    <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->

    <input spec='HKY' id='hky'>

        <kappa idref='hky.kappa'/>

        <frequencies id='freqs' spec='Frequencies'>

            <data idref='alignment'/>

        </frequencies>

    </input>



    <!-- site model                                                              -->

    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>

        <!--

            <parameter name='shape' id='shape' value='0.5'/>

            <parameter name='proportionInvariant' id='propInvar' value='0.2'/>

        -->

        <substModel idref='hky'/>

    </input>



    <input spec='TreeLikelihood' id="treeLikelihood">

        <data idref="alignment"/>

        <tree idref="tree"/>

        <siteModel idref="siteModel"/>

    </input>



    <parameter id="hky.kappa" value="1.0" lower="0.0"/>



    <tree id='tree'/>



    <tree spec='beast.util.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>

        <taxa idref='alignment'/>

    </tree>

    <tree spec='beast.evolution.tree.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>

        <populationModel spec='ConstantPopulation'>

            <popSize spec='parameter.RealParameter' value='1'/>

        </populationModel>

    </tree>





    <run spec="MCMC" id="mcmc" chainLength="1000000" preBurnin="50000">



        <init idref='coalescentSimulator'/>

        <distribution spec='CompoundDistribution' id='posterior'>

            <distribution spec='beast.math.distributions.Prior' x='@hky.kappa'>

                <distr spec='beast.math.distributions.OneOnX'/>

            </distribution>

            <distribution id='likelihood' idref="treeLikelihood"/>

        </distribution>



         <operatorschedule id="operatorSchedule" spec="OperatorSchedule">

            <!-- assign 50% of total weight to operators that apply to the tree operations  -->

            <subschedule id="operatorTrees" spec="OperatorSchedule" weight="50" weightIsPercentage="true" operatorPattern="^.*tree.*"/>

         </operatorschedule>



        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" parameter="@hky.kappa"/>

        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>



        <operator id='subtreeSlide' spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>



        <operator id='uniform' spec='Uniform' weight="10" tree="@tree"/>

        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>

        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>

        <operator id='wilsonBalding' spec='WilsonBalding' weight="1" tree="@tree"/>



        <logger logEvery="10000" fileName="test.$(seed).log">

            <model idref='likelihood'/>

            <log idref="likelihood"/>

            <log idref='hky.kappa'/>

            <log spec='beast.evolution.tree.TreeHeightLogger' tree='@tree'/>

        </logger>

        <logger logEvery="10000" fileName="test.$(seed).trees">

            <log idref="tree"/>

        </logger>

        <logger logEvery="10000">

            <model idref='likelihood'/>

            <log idref="likelihood"/>

            <ESS spec='ESS' name='log' arg="@likelihood"/>

            <log idref='hky.kappa'/>

            <ESS spec='ESS' name='log' arg="@hky.kappa"/>

        </logger>

    </run>



</beast>

examples/testUCLNclock.json

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{version: "2.4",

{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",



beast: [

release/Linux/bin/applauncher

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#!/bin/sh



if [ -z "$BEAST" ]; then

	## resolve links - $0 may be a link to application

	PRG="$0"



	# need this for relative symlinks

	while [ -h "$PRG" ] ; do

	    ls=`ls -ld "$PRG"`

	    link=`expr "$ls" : '.*-> \(.*\)$'`

	    if expr "$link" : '/.*' > /dev/null; then

		PRG="$link"

	    else

		PRG="`dirname "$PRG"`/$link"

	    fi

	done



	# make it fully qualified

	saveddir=`pwd`

	BEAST0=`dirname "$PRG"`/..

	BEAST=`cd "$BEAST0" && pwd`

	cd "$saveddir"

fi



BEAST_LIB="$BEAST/lib"



if [ -z "$JAVA_HOME" ]; then

  JAVA=java

else

  JAVA=$JAVA_HOME/bin/java

fi

$JAVA -Dlauncher.wait.for.exit=true -Xms256m -Xmx1024m -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.tools.AppLauncherLauncher $*