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Example 6 with DefaultBranchRateModel

use of dr.evomodel.branchratemodel.DefaultBranchRateModel in project beast-mcmc by beast-dev.

the class BeagleSeqSimTest method simulateRandomBranchAssignment.

// END: main
static void simulateRandomBranchAssignment() {
    try {
        System.out.println("Test case I dunno which: simulate random branch assignments");
        MathUtils.setSeed(666);
        int sequenceLength = 10;
        ArrayList<Partition> partitionsList = new ArrayList<Partition>();
        File treeFile = new File("/home/filip/Dropbox/BeagleSequenceSimulator/SimTree/SimTree.figtree");
        Tree tree = Utils.importTreeFromFile(treeFile);
        TreeModel treeModel = new TreeModel(tree);
        // create Frequency Model
        Parameter freqs = new Parameter.Default(Utils.UNIFORM_CODON_FREQUENCIES);
        FrequencyModel freqModel = new FrequencyModel(Codons.UNIVERSAL, freqs);
        // create base subst model
        Parameter omegaParameter = new Parameter.Default("omega", 1, 1.0);
        Parameter kappaParameter = new Parameter.Default("kappa", 1, 1.0);
        GY94CodonModel baseSubModel = new GY94CodonModel(Codons.UNIVERSAL, omegaParameter, kappaParameter, freqModel);
        RandomBranchModel substitutionModel = new RandomBranchModel(treeModel, baseSubModel, 0.25, false, -1);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // create partition
        Partition partition1 = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        0, // to
        sequenceLength - 1, // every
        1);
        //			Sequence ancestralSequence = new Sequence();
        //			ancestralSequence.appendSequenceString("TCAAGTGAGG");
        //			partition1.setRootSequence(ancestralSequence);
        partitionsList.add(partition1);
        // feed to sequence simulator and generate data
        BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
        SimpleAlignment alignment = simulator.simulate(simulateInPar, true);
        // alignment.setOutputType(SimpleAlignment.OutputType.NEXUS);
        alignment.setOutputType(SimpleAlignment.OutputType.XML);
        System.out.println(alignment.toString());
    } catch (Exception e) {
        e.printStackTrace();
    }
// END: try-catch
}
Also used : FrequencyModel(dr.evomodel.substmodel.FrequencyModel) Partition(dr.app.beagle.tools.Partition) ArrayList(java.util.ArrayList) GammaSiteRateModel(dr.evomodel.siteratemodel.GammaSiteRateModel) BeagleSequenceSimulator(dr.app.beagle.tools.BeagleSequenceSimulator) ImportException(dr.evolution.io.Importer.ImportException) IOException(java.io.IOException) DefaultBranchRateModel(dr.evomodel.branchratemodel.DefaultBranchRateModel) TreeModel(dr.evomodel.tree.TreeModel) RandomBranchModel(dr.evomodel.branchmodel.RandomBranchModel) SimpleAlignment(dr.evolution.alignment.SimpleAlignment) DefaultBranchRateModel(dr.evomodel.branchratemodel.DefaultBranchRateModel) BranchRateModel(dr.evomodel.branchratemodel.BranchRateModel) Tree(dr.evolution.tree.Tree) Parameter(dr.inference.model.Parameter) GY94CodonModel(dr.evomodel.substmodel.codon.GY94CodonModel) File(java.io.File)

Example 7 with DefaultBranchRateModel

use of dr.evomodel.branchratemodel.DefaultBranchRateModel in project beast-mcmc by beast-dev.

the class ContinuousDataLikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    MultivariateDiffusionModel diffusionModel = (MultivariateDiffusionModel) xo.getChild(MultivariateDiffusionModel.class);
    BranchRateModel rateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    TreeTraitParserUtilities utilities = new TreeTraitParserUtilities();
    String traitName = TreeTraitParserUtilities.DEFAULT_TRAIT_NAME;
    TreeTraitParserUtilities.TraitsAndMissingIndices returnValue = utilities.parseTraitsFromTaxonAttributes(xo, traitName, treeModel, true);
    CompoundParameter traitParameter = returnValue.traitParameter;
    List<Integer> missingIndices = returnValue.missingIndices;
    Parameter sampleMissingParameter = returnValue.sampleMissingParameter;
    traitName = returnValue.traitName;
    final int dim = diffusionModel.getPrecisionmatrix().length;
    PrecisionType precisionType = PrecisionType.SCALAR;
    if (missingIndices.size() > 0 && !xo.getAttribute(FORCE_COMPLETELY_MISSING, false)) {
        precisionType = PrecisionType.FULL;
    }
    System.err.println("Using precisionType == " + precisionType + " for data model.");
    ContinuousTraitDataModel dataModel = new ContinuousTraitDataModel(traitName, traitParameter, missingIndices, dim, precisionType);
    ConjugateRootTraitPrior rootPrior = ConjugateRootTraitPrior.parseConjugateRootTraitPrior(xo, dim);
    boolean useTreeLength = xo.getAttribute(USE_TREE_LENGTH, false);
    boolean scaleByTime = xo.getAttribute(SCALE_BY_TIME, false);
    if (rateModel == null) {
        rateModel = new DefaultBranchRateModel();
    }
    ContinuousRateTransformation rateTransformation = new ContinuousRateTransformation.Default(treeModel, scaleByTime, useTreeLength);
    ContinuousDataLikelihoodDelegate delegate = new ContinuousDataLikelihoodDelegate(treeModel, diffusionModel, dataModel, rootPrior, rateTransformation, rateModel);
    TreeDataLikelihood treeDataLikelihood = new TreeDataLikelihood(delegate, treeModel, rateModel);
    boolean reconstructTraits = xo.getAttribute(RECONSTRUCT_TRAITS, true);
    if (reconstructTraits) {
        if (missingIndices.size() == 0) {
            ProcessSimulationDelegate simulationDelegate = new ProcessSimulationDelegate.ConditionalOnTipsRealizedDelegate(traitName, treeModel, diffusionModel, dataModel, rootPrior, rateTransformation, rateModel, delegate);
            TreeTraitProvider traitProvider = new ProcessSimulation(traitName, treeDataLikelihood, simulationDelegate);
            treeDataLikelihood.addTraits(traitProvider.getTreeTraits());
        } else {
            ProcessSimulationDelegate simulationDelegate = delegate.getPrecisionType() == PrecisionType.SCALAR ? new ProcessSimulationDelegate.ConditionalOnTipsRealizedDelegate(traitName, treeModel, diffusionModel, dataModel, rootPrior, rateTransformation, rateModel, delegate) : new ProcessSimulationDelegate.MultivariateConditionalOnTipsRealizedDelegate(traitName, treeModel, diffusionModel, dataModel, rootPrior, rateTransformation, rateModel, delegate);
            TreeTraitProvider traitProvider = new ProcessSimulation(traitName, treeDataLikelihood, simulationDelegate);
            treeDataLikelihood.addTraits(traitProvider.getTreeTraits());
            ProcessSimulationDelegate fullConditionalDelegate = new ProcessSimulationDelegate.TipRealizedValuesViaFullConditionalDelegate(traitName, treeModel, diffusionModel, dataModel, rootPrior, rateTransformation, rateModel, delegate);
            treeDataLikelihood.addTraits(new ProcessSimulation(("fc." + traitName), treeDataLikelihood, fullConditionalDelegate).getTreeTraits());
        //                String partialTraitName = getPartiallyMissingTraitName(traitName);
        //
        //                ProcessSimulationDelegate parialSimulationDelegate = new ProcessSimulationDelegate.ConditionalOnPartiallyMissingTipsDelegate(partialTraitName,
        //                        treeModel, diffusionModel, dataModel, rootPrior, rateTransformation, rateModel, delegate);
        //
        //                TreeTraitProvider partialTraitProvider = new ProcessSimulation(partialTraitName,
        //                        treeDataLikelihood, parialSimulationDelegate);
        //
        //                treeDataLikelihood.addTraits(partialTraitProvider.getTreeTraits());
        }
    }
    return treeDataLikelihood;
}
Also used : PrecisionType(dr.evomodel.treedatalikelihood.continuous.cdi.PrecisionType) DefaultBranchRateModel(dr.evomodel.branchratemodel.DefaultBranchRateModel) CompoundParameter(dr.inference.model.CompoundParameter) TreeModel(dr.evomodel.tree.TreeModel) MultivariateDiffusionModel(dr.evomodel.continuous.MultivariateDiffusionModel) ConjugateRootTraitPrior(dr.evomodel.treedatalikelihood.continuous.ConjugateRootTraitPrior) ContinuousTraitDataModel(dr.evomodel.treedatalikelihood.continuous.ContinuousTraitDataModel) TreeTraitProvider(dr.evolution.tree.TreeTraitProvider) ContinuousRateTransformation(dr.evomodel.treedatalikelihood.continuous.ContinuousRateTransformation) TreeDataLikelihood(dr.evomodel.treedatalikelihood.TreeDataLikelihood) BranchRateModel(dr.evomodel.branchratemodel.BranchRateModel) DefaultBranchRateModel(dr.evomodel.branchratemodel.DefaultBranchRateModel) ProcessSimulation(dr.evomodel.treedatalikelihood.ProcessSimulation) TreeTraitParserUtilities(dr.evomodelxml.treelikelihood.TreeTraitParserUtilities) CompoundParameter(dr.inference.model.CompoundParameter) Parameter(dr.inference.model.Parameter) ContinuousDataLikelihoodDelegate(dr.evomodel.treedatalikelihood.continuous.ContinuousDataLikelihoodDelegate) ProcessSimulationDelegate(dr.evomodel.treedatalikelihood.ProcessSimulationDelegate)

Example 8 with DefaultBranchRateModel

use of dr.evomodel.branchratemodel.DefaultBranchRateModel in project beast-mcmc by beast-dev.

the class MultiPartitionDataLikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    boolean useAmbiguities = xo.getAttribute(USE_AMBIGUITIES, false);
    int instanceCount = xo.getAttribute(INSTANCE_COUNT, 1);
    if (instanceCount < 1) {
        instanceCount = 1;
    }
    String ic = System.getProperty(BEAGLE_INSTANCE_COUNT);
    if (ic != null && ic.length() > 0) {
        instanceCount = Integer.parseInt(ic);
    }
    if (DEBUG) {
        System.out.println("instanceCount: " + instanceCount);
    }
    List<PatternList> patternLists = xo.getAllChildren(PatternList.class);
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    List<SiteRateModel> siteRateModels = xo.getAllChildren(SiteRateModel.class);
    FrequencyModel rootFreqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
    List<BranchModel> branchModels = xo.getAllChildren(BranchModel.class);
    if (branchModels == null) {
        if (DEBUG) {
            System.out.println("branchModels == null");
        }
        branchModels = new ArrayList<BranchModel>();
        List<SubstitutionModel> substitutionModels = xo.getAllChildren(SubstitutionModel.class);
        if (substitutionModels == null) {
            if (DEBUG) {
                System.out.println("substitutionModels == null");
            }
            for (SiteRateModel siteRateModel : siteRateModels) {
                SubstitutionModel substitutionModel = ((GammaSiteRateModel) siteRateModel).getSubstitutionModel();
                if (substitutionModel == null) {
                    throw new XMLParseException("No substitution model available for TreeDataLikelihood: " + xo.getId());
                }
                branchModels.add(new HomogeneousBranchModel(substitutionModel, rootFreqModel));
            }
        }
        if (DEBUG) {
            System.out.println("branchModels size: " + branchModels.size());
        }
        for (BranchModel branchModel : branchModels) {
            System.out.println("  " + branchModel.getId() + "  " + branchModel.getModelName());
        }
    }
    BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    if (branchRateModel == null) {
        branchRateModel = new DefaultBranchRateModel();
    }
    if (DEBUG) {
        System.out.println("BranchRateModel: " + branchRateModel.getId());
    }
    TipStatesModel tipStatesModel = (TipStatesModel) xo.getChild(TipStatesModel.class);
    PartialsRescalingScheme scalingScheme = PartialsRescalingScheme.DEFAULT;
    boolean delayScaling = true;
    if (xo.hasAttribute(SCALING_SCHEME)) {
        scalingScheme = PartialsRescalingScheme.parseFromString(xo.getStringAttribute(SCALING_SCHEME));
        if (scalingScheme == null)
            throw new XMLParseException("Unknown scaling scheme '" + xo.getStringAttribute(SCALING_SCHEME) + "' in " + "OldBeagleTreeLikelihood object '" + xo.getId());
    }
    if (xo.hasAttribute(DELAY_SCALING)) {
        delayScaling = xo.getBooleanAttribute(DELAY_SCALING);
    }
    if (instanceCount == 1) {
        if (DEBUG) {
            System.out.println("instanceCount == 1");
        }
        return createTreeDataLikelihood(patternLists, treeModel, branchModels, siteRateModels, branchRateModel, tipStatesModel, useAmbiguities, scalingScheme, delayScaling, xo);
    }
    if (tipStatesModel != null) {
        throw new XMLParseException("BEAGLE_INSTANCES option cannot be used with a TipStateModel (i.e., a sequence error model).");
    }
    List<PatternList> patternInstanceLists = new ArrayList<PatternList>();
    for (int j = 0; j < patternLists.size(); j++) {
        for (int i = 0; i < instanceCount; i++) {
            patternInstanceLists.add(new Patterns(patternLists.get(j), i, instanceCount));
        }
    }
    return createTreeDataLikelihood(patternLists, treeModel, branchModels, siteRateModels, branchRateModel, null, useAmbiguities, scalingScheme, delayScaling, xo);
}
Also used : FrequencyModel(dr.evomodel.substmodel.FrequencyModel) PatternList(dr.evolution.alignment.PatternList) ArrayList(java.util.ArrayList) HomogeneousBranchModel(dr.evomodel.branchmodel.HomogeneousBranchModel) GammaSiteRateModel(dr.evomodel.siteratemodel.GammaSiteRateModel) PartialsRescalingScheme(dr.evomodel.treelikelihood.PartialsRescalingScheme) BranchModel(dr.evomodel.branchmodel.BranchModel) HomogeneousBranchModel(dr.evomodel.branchmodel.HomogeneousBranchModel) SubstitutionModel(dr.evomodel.substmodel.SubstitutionModel) GammaSiteRateModel(dr.evomodel.siteratemodel.GammaSiteRateModel) SiteRateModel(dr.evomodel.siteratemodel.SiteRateModel) DefaultBranchRateModel(dr.evomodel.branchratemodel.DefaultBranchRateModel) TipStatesModel(dr.evomodel.tipstatesmodel.TipStatesModel) TreeModel(dr.evomodel.tree.TreeModel) BranchRateModel(dr.evomodel.branchratemodel.BranchRateModel) DefaultBranchRateModel(dr.evomodel.branchratemodel.DefaultBranchRateModel) Patterns(dr.evolution.alignment.Patterns)

Example 9 with DefaultBranchRateModel

use of dr.evomodel.branchratemodel.DefaultBranchRateModel in project beast-mcmc by beast-dev.

the class TreeDataLikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    boolean useAmbiguities = xo.getAttribute(USE_AMBIGUITIES, false);
    // TreeDataLikelihood doesn't currently support Instances defined from the command line
    //        int instanceCount = xo.getAttribute(INSTANCE_COUNT, 1);
    //        if (instanceCount < 1) {
    //            instanceCount = 1;
    //        }
    //
    //        String ic = System.getProperty(BEAGLE_INSTANCE_COUNT);
    //        if (ic != null && ic.length() > 0) {
    //            instanceCount = Integer.parseInt(ic);
    //        }
    List<PatternList> patternLists = new ArrayList<PatternList>();
    List<SiteRateModel> siteRateModels = new ArrayList<SiteRateModel>();
    List<BranchModel> branchModels = new ArrayList<BranchModel>();
    boolean hasSinglePartition = false;
    PatternList patternList = (PatternList) xo.getChild(PatternList.class);
    if (patternList != null) {
        hasSinglePartition = true;
        patternLists.add(patternList);
        GammaSiteRateModel siteRateModel = (GammaSiteRateModel) xo.getChild(GammaSiteRateModel.class);
        siteRateModels.add(siteRateModel);
        FrequencyModel rootFreqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
        BranchModel branchModel = (BranchModel) xo.getChild(BranchModel.class);
        if (branchModel == null) {
            SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
            if (substitutionModel == null) {
                substitutionModel = siteRateModel.getSubstitutionModel();
            }
            if (substitutionModel == null) {
                throw new XMLParseException("No substitution model available for partition in DataTreeLikelihood: " + xo.getId());
            }
            branchModel = new HomogeneousBranchModel(substitutionModel, rootFreqModel);
        }
        branchModels.add(branchModel);
    }
    int k = 0;
    for (int i = 0; i < xo.getChildCount(); i++) {
        if (xo.getChildName(i).equals(PARTITION)) {
            if (hasSinglePartition) {
                throw new XMLParseException("Either a single set of patterns should be given or multiple 'partitions' elements within DataTreeLikelihood: " + xo.getId());
            }
            k += 1;
            XMLObject cxo = (XMLObject) xo.getChild(i);
            patternList = (PatternList) cxo.getChild(PatternList.class);
            patternLists.add(patternList);
            GammaSiteRateModel siteRateModel = (GammaSiteRateModel) cxo.getChild(GammaSiteRateModel.class);
            siteRateModels.add(siteRateModel);
            FrequencyModel rootFreqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
            BranchModel branchModel = (BranchModel) cxo.getChild(BranchModel.class);
            if (branchModel == null) {
                SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
                if (substitutionModel == null) {
                    substitutionModel = siteRateModel.getSubstitutionModel();
                }
                if (substitutionModel == null) {
                    throw new XMLParseException("No substitution model available for partition " + k + " in DataTreeLikelihood: " + xo.getId());
                }
                branchModel = new HomogeneousBranchModel(substitutionModel, rootFreqModel);
            }
            branchModels.add(branchModel);
        }
    }
    if (patternLists.size() == 0) {
        throw new XMLParseException("Either a single set of patterns should be given or multiple 'partitions' elements within DataTreeLikelihood: " + xo.getId());
    }
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    if (branchRateModel == null) {
        branchRateModel = new DefaultBranchRateModel();
    }
    TipStatesModel tipStatesModel = (TipStatesModel) xo.getChild(TipStatesModel.class);
    PartialsRescalingScheme scalingScheme = PartialsRescalingScheme.DEFAULT;
    boolean delayScaling = true;
    if (xo.hasAttribute(SCALING_SCHEME)) {
        scalingScheme = PartialsRescalingScheme.parseFromString(xo.getStringAttribute(SCALING_SCHEME));
        if (scalingScheme == null)
            throw new XMLParseException("Unknown scaling scheme '" + xo.getStringAttribute(SCALING_SCHEME) + "' in " + "BeagleDataLikelihood object '" + xo.getId());
    }
    if (xo.hasAttribute(DELAY_SCALING)) {
        delayScaling = xo.getBooleanAttribute(DELAY_SCALING);
    }
    if (tipStatesModel != null) {
        throw new XMLParseException("BEAGLE_INSTANCES option cannot be used with a TipStateModel (i.e., a sequence error model).");
    }
    return createTreeDataLikelihood(patternLists, branchModels, siteRateModels, treeModel, branchRateModel, null, useAmbiguities, scalingScheme, delayScaling);
}
Also used : FrequencyModel(dr.evomodel.substmodel.FrequencyModel) ArrayList(java.util.ArrayList) PatternList(dr.evolution.alignment.PatternList) HomogeneousBranchModel(dr.evomodel.branchmodel.HomogeneousBranchModel) GammaSiteRateModel(dr.evomodel.siteratemodel.GammaSiteRateModel) PartialsRescalingScheme(dr.evomodel.treelikelihood.PartialsRescalingScheme) BranchModel(dr.evomodel.branchmodel.BranchModel) HomogeneousBranchModel(dr.evomodel.branchmodel.HomogeneousBranchModel) SubstitutionModel(dr.evomodel.substmodel.SubstitutionModel) GammaSiteRateModel(dr.evomodel.siteratemodel.GammaSiteRateModel) SiteRateModel(dr.evomodel.siteratemodel.SiteRateModel) DefaultBranchRateModel(dr.evomodel.branchratemodel.DefaultBranchRateModel) TipStatesModel(dr.evomodel.tipstatesmodel.TipStatesModel) TreeModel(dr.evomodel.tree.TreeModel) BranchRateModel(dr.evomodel.branchratemodel.BranchRateModel) DefaultBranchRateModel(dr.evomodel.branchratemodel.DefaultBranchRateModel)

Example 10 with DefaultBranchRateModel

use of dr.evomodel.branchratemodel.DefaultBranchRateModel in project beast-mcmc by beast-dev.

the class CompleteHistorySimulatorTest method testHKYSimulation.

public void testHKYSimulation() {
    Parameter kappa = new Parameter.Default(1, 2.0);
    double[] pi = { 0.45, 0.05, 0.25, 0.25 };
    Parameter freqs = new Parameter.Default(pi);
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    HKY hky = new HKY(kappa, f);
    int stateCount = hky.getDataType().getStateCount();
    Parameter mu = new Parameter.Default(1, 0.5);
    Parameter alpha = new Parameter.Default(1, 0.5);
    GammaSiteRateModel siteModel = new GammaSiteRateModel("gammaModel", mu, alpha, 4, null);
    siteModel.setSubstitutionModel(hky);
    BranchRateModel branchRateModel = new DefaultBranchRateModel();
    double analyticResult = TreeUtils.getTreeLength(tree, tree.getRoot()) * mu.getParameterValue(0);
    int nSites = 200;
    double[] register1 = new double[stateCount * stateCount];
    double[] register2 = new double[stateCount * stateCount];
    // Count all jumps
    MarkovJumpsCore.fillRegistrationMatrix(register1, stateCount);
    // Move some jumps from 1 to 2
    register1[1 * stateCount + 2] = 0;
    register2[1 * stateCount + 2] = 1;
    register1[1 * stateCount + 3] = 0;
    register2[1 * stateCount + 3] = 1;
    register1[2 * stateCount + 3] = 0;
    register2[2 * stateCount + 3] = 1;
    runSimulation(tree, siteModel, branchRateModel, nSites, new double[][] { register1, register2 }, analyticResult);
}
Also used : FrequencyModel(dr.evomodel.substmodel.FrequencyModel) BranchRateModel(dr.evomodel.branchratemodel.BranchRateModel) DefaultBranchRateModel(dr.evomodel.branchratemodel.DefaultBranchRateModel) HKY(dr.evomodel.substmodel.nucleotide.HKY) Parameter(dr.inference.model.Parameter) GammaSiteRateModel(dr.evomodel.siteratemodel.GammaSiteRateModel) DefaultBranchRateModel(dr.evomodel.branchratemodel.DefaultBranchRateModel)

Aggregations

BranchRateModel (dr.evomodel.branchratemodel.BranchRateModel)20 DefaultBranchRateModel (dr.evomodel.branchratemodel.DefaultBranchRateModel)20 GammaSiteRateModel (dr.evomodel.siteratemodel.GammaSiteRateModel)17 FrequencyModel (dr.evomodel.substmodel.FrequencyModel)16 Parameter (dr.inference.model.Parameter)15 TreeModel (dr.evomodel.tree.TreeModel)14 HomogeneousBranchModel (dr.evomodel.branchmodel.HomogeneousBranchModel)12 ArrayList (java.util.ArrayList)11 Tree (dr.evolution.tree.Tree)10 Partition (dr.app.beagle.tools.Partition)9 BeagleSequenceSimulator (dr.app.beagle.tools.BeagleSequenceSimulator)8 NewickImporter (dr.evolution.io.NewickImporter)8 HKY (dr.evomodel.substmodel.nucleotide.HKY)8 ImportException (dr.evolution.io.Importer.ImportException)7 IOException (java.io.IOException)7 SimpleAlignment (dr.evolution.alignment.SimpleAlignment)5 BranchModel (dr.evomodel.branchmodel.BranchModel)5 PatternList (dr.evolution.alignment.PatternList)4 Sequence (dr.evolution.sequence.Sequence)4 SiteRateModel (dr.evomodel.siteratemodel.SiteRateModel)4