Examples with JukesCantor beast.evolution.substitutionmodel.JukesCantor used on opensource projects

Example 11 with JukesCantor

use of beast.evolution.substitutionmodel.JukesCantor in project beast2 by CompEvol.

the class TreeLikelihoodTest method testJC69Likelihood.

public double[] testJC69Likelihood(Alignment data, Tree tree) throws Exception {
    // Set up JC69 model: uniform freqs, kappa = 1, 0 gamma categories
    JukesCantor JC = new JukesCantor();
    JC.initAndValidate();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "0.6", "substModel", JC);
    // NB The rate in the JC model used here is actually alpha * 3 in the usual sense, because
    // it's divided by 3 before multiplying in the exponent (not sure why)
    System.out.println("Without tip likelihoods:");
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel, "scaling", TreeLikelihood.Scaling.none);
    double[] logP = new double[2];
    logP[0] = likelihood.calculateLogP();
    System.out.println(logP[0]);
    System.out.println("With tip likelihoods:");
    likelihood.initByName("useTipLikelihoods", true, "data", data, "tree", tree, "siteModel", siteModel, "scaling", TreeLikelihood.Scaling.none);
    logP[1] = likelihood.calculateLogP();
    System.out.println(logP[1]);
    return logP;
}