An example of XML with randomly generated sequences and ordinal model with different number of states than in the data.

OrdinalFailSample.xml

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<beast 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" required="" version="2.6">


<data id="test" dataType="standard">
    <sequence taxon="A">0325001134145320315521441333450540150340142324031053552343434540345422555515404425225332030455334311</sequence>
    <sequence taxon="B">3303111402245533434135501501430403113451242121243211312030250523440504251354554250554133235411202323</sequence>
    <sequence taxon="C">0203545342141415331211042134245105533321245534032452154450211324241122021354024412103533542044452213</sequence>
    <sequence taxon="D">5321401114230445532511142242040052431341215151200525030545523403103545524535302424314202314031013500</sequence>
    <sequence taxon="E">0043351052054244501305531514131104414244301552044333201335431011001003353334344043123350131442222314</sequence>
    <userDataType id="StandardDataType" spec="beast.evolution.datatype.StandardData" nrOfStates="6" />
</data>


    <map name="Uniform" >beast.math.distributions.Uniform</map>

    <map name="Exponential" >beast.math.distributions.Exponential</map>

    <map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map>

    <map name="Normal" >beast.math.distributions.Normal</map>

    <map name="Beta" >beast.math.distributions.Beta</map>

    <map name="Gamma" >beast.math.distributions.Gamma</map>

    <map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map>

    <map name="prior" >beast.math.distributions.Prior</map>

    <map name="InverseGamma" >beast.math.distributions.InverseGamma</map>

    <map name="OneOnX" >beast.math.distributions.OneOnX</map>

    <run id="mcmc" spec="MCMC" chainLength="50000000">

        <state id="state" spec="State" storeEvery="5000">

            <tree id="Tree.t" spec="beast.evolution.tree.Tree" name="stateNode">


                <taxonset id="TaxonSet" spec="TaxonSet">
                    <alignment idref="test"/>

                </taxonset>

            </tree>

            <parameter id="freqParameter.s" spec="parameter.RealParameter" dimension="5" lower="0.0" name="stateNode" upper="1.0">0.20</parameter>

            <parameter id="BDBirthRate.t" spec="parameter.RealParameter" lower="0.0" name="stateNode" upper="10000.0">1.0</parameter>
                    
            <parameter id="BDDeathRate.t" spec="parameter.RealParameter" lower="0.0" name="stateNode" upper="1.0">0.5</parameter>

        </state>

        <init id="RandomTree.t" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t" taxa="@test">

            <populationModel id="ConstantPopulation0.t" spec="ConstantPopulation">

                <parameter id="randomPopSize.t" spec="parameter.RealParameter" name="popSize">1.0</parameter>

            </populationModel>

        </init>

        <distribution id="posterior" spec="util.CompoundDistribution">

            <distribution id="prior" spec="util.CompoundDistribution">

                <distribution id="BirthDeath.t" spec="beast.evolution.speciation.BirthDeathGernhard08Model" birthDiffRate="@BDBirthRate.t" relativeDeathRate="@BDDeathRate.t" tree="@Tree.t"/>

                <prior id="BirthRatePrior.t" name="distribution" x="@BDBirthRate.t">
                                    
                    <Uniform id="Uniform.2" name="distr" upper="1000.0"/>
                                
                </prior>

                <prior id="DeathRatePrior.t" name="distribution" x="@BDDeathRate.t">
                                    
                    <Uniform id="Uniform.3" name="distr"/>
                                
                </prior>

            </distribution>

            <distribution id="likelihood" spec="util.CompoundDistribution" useThreads="true">

                <distribution id="treeLikelihood" spec="ThreadedTreeLikelihood" data="@test" tree="@Tree.t" useAmbiguities="true">

                    <siteModel id="SiteModel.s" spec="SiteModel">

                        <parameter id="mutationRate.s" spec="parameter.RealParameter" estimate="false" name="mutationRate">1.0</parameter>

                        <parameter id="gammaShape.s" spec="parameter.RealParameter" estimate="false" name="shape">1.0</parameter>

                        <parameter id="proportionInvariant.s" spec="parameter.RealParameter" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
                            <substModel id="Ordinal.s" spec="Ordinal" stateNumber="5">
                            <frequencies id="estimatedFreqs.s" spec="Frequencies" frequencies="@freqParameter.s"/>
                        </substModel>
                    </siteModel>

                    <branchRateModel id="StrictClock.c" spec="beast.evolution.branchratemodel.StrictClockModel">

                        <parameter id="clockRate.c" spec="parameter.RealParameter" estimate="false" name="clock.rate">1.0</parameter>

                    </branchRateModel>

                </distribution>

            </distribution>

        </distribution>

        <operator id="FrequenciesExchanger.s" spec="DeltaExchangeOperator" delta="0.01" weight="0.1">

            <parameter idref="freqParameter.s"/>

        </operator>

        <operator id="BirthDeathTreeScaler.t" spec="ScaleOperator" scaleFactor="0.5" tree="@Tree.t" weight="3.0"/>
            
        <operator id="BirthDeathTreeRootScaler.t" spec="ScaleOperator" rootOnly="true" scaleFactor="0.5" tree="@Tree.t" weight="3.0"/>
            
        <operator id="BirthDeathUniformOperator.t" spec="Uniform" tree="@Tree.t" weight="30.0"/>
            
        <operator id="BirthDeathSubtreeSlide.t" spec="SubtreeSlide" tree="@Tree.t" weight="15.0"/>
            
        <operator id="BirthDeathNarrow.t" spec="Exchange" tree="@Tree.t" weight="15.0"/>
            
        <operator id="BirthDeathWide.t" spec="Exchange" isNarrow="false" tree="@Tree.t" weight="3.0"/>
            
        <operator id="BirthDeathWilsonBalding.t" spec="WilsonBalding" tree="@Tree.t" weight="3.0"/>
            
        <operator id="BirthRateScaler.t" spec="ScaleOperator" parameter="@BDBirthRate.t" scaleFactor="0.75" weight="3.0"/>
            
        <operator id="DeathRateScaler.t" spec="ScaleOperator" parameter="@BDDeathRate.t" scaleFactor="0.75" weight="3.0"/>

        <logger id="tracelog" spec="Logger" fileName="test.trace" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">

            <log idref="posterior"/>

            <log idref="likelihood"/>

            <log idref="prior"/>

            <log idref="treeLikelihood"/>

            <log id="TreeHeight.t" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t"/>

            <log idref="BirthDeath.t"/>
                    
            <log idref="BDBirthRate.t"/>
                    
            <log idref="BDDeathRate.t"/>

        </logger>

        <logger id="screenlog" spec="Logger" logEvery="1000">

            <log idref="posterior"/>

            <log idref="likelihood"/>

            <log idref="prior"/>

        </logger>

        <logger id="treelog.t" spec="Logger" fileName="test.trees" logEvery="1000" mode="tree">

            <log id="TreeWithMetaDataLogger.t" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t"/>

        </logger>

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

    </run>

</beast>