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

Example 1 with HKY

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

the class UnorderedAlignmentsTest method getSiteModel.

public static SiteModel getSiteModel() throws Exception {
    Frequencies frequencies = new Frequencies();
    frequencies.initByName("frequencies", new RealParameter("0.25 0.25 0.25 0.25"));
    HKY hky = new HKY();
    hky.initByName("kappa", new RealParameter("1.0"), "frequencies", frequencies);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", new RealParameter("0.005"), "substModel", hky);
    return siteModel;
}

Example 2 with HKY

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

the class TreeLikelihoodTest method testHKY85ILikelihood.

@Test
public void testHKY85ILikelihood() throws Exception {
    // Set up HKY85+I model: estimated freqs, kappa = 38.564672, 0 gamma categories, prop invariant = 0.701211
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    Frequencies freqs = new Frequencies();
    freqs.initByName("data", data);
    HKY hky = new HKY();
    hky.initByName("kappa", "38.564672", "frequencies", freqs);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "shape", "0.137064", "proportionInvariant", "0.701211", "substModel", hky);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1789.912401996943, BEASTTestCase.PRECISION);
    likelihood.initByName("useAmbiguities", true, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1789.912401996943, BEASTTestCase.PRECISION);
}

Example 3 with HKY

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

the class TreeLikelihoodTest method testHKY85GLikelihood.

@Test
public void testHKY85GLikelihood() throws Exception {
    // Set up HKY85+G model: estimated freqs, kappa = 38.82974, 4 gamma categories, shape = 0.137064
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    Frequencies freqs = new Frequencies();
    freqs.initByName("data", data);
    HKY hky = new HKY();
    hky.initByName("kappa", "38.82974", "frequencies", freqs);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 4, "shape", "0.137064", "proportionInvariant", "0.0", "substModel", hky);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    System.err.println(logP - -1789.7593576610134);
    assertEquals(logP, -1789.7593576610134, BEASTTestCase.PRECISION);
    likelihood.initByName("useAmbiguities", true, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1789.7593576610134, BEASTTestCase.PRECISION);
}

Example 4 with HKY

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

the class TreeLikelihoodTest method testAscertainedJC69Likelihood.

@Test
public void testAscertainedJC69Likelihood() throws Exception {
    // as testJC69Likelihood but with ascertained alignment
    Alignment data = BEASTTestCase.getAscertainedAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    Frequencies freqs = new Frequencies();
    freqs.initByName("data", data, "estimate", false);
    HKY hky = new HKY();
    hky.initByName("kappa", "1.0", "frequencies", freqs);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", hky);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    // the following number comes from Beast 1.6
    assertEquals(logP, -737.7140695360017, BEASTTestCase.PRECISION);
}

Example 5 with HKY

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

the class TreeLikelihoodTest method testK80Likelihood.

@Test
public void testK80Likelihood() throws Exception {
    // Set up K80 model: uniform freqs, kappa = 27.402591, 0 gamma categories
    Alignment data = BEASTTestCase.getAlignment();
    Tree tree = BEASTTestCase.getTree(data);
    Frequencies freqs = new Frequencies();
    freqs.initByName("data", data, "estimate", false);
    HKY hky = new HKY();
    hky.initByName("kappa", "27.40259", "frequencies", freqs);
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", "1.0", "gammaCategoryCount", 1, "substModel", hky);
    TreeLikelihood likelihood = newTreeLikelihood();
    likelihood.initByName("data", data, "tree", tree, "siteModel", siteModel);
    double logP = 0;
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1856.303048876734, BEASTTestCase.PRECISION);
    likelihood.initByName("useAmbiguities", true, "data", data, "tree", tree, "siteModel", siteModel);
    logP = likelihood.calculateLogP();
    assertEquals(logP, -1856.303048876734, BEASTTestCase.PRECISION);
}