test-main

    public static void main(String... args) throws IOException, Importer.ImportException {
        final TreeModel tree = new TreeModel(new NewickImporter("(a:1,b:1);").importNextTree());
        final SimpleAlignment alignment = new SimpleAlignment();
        alignment.setDataType(Nucleotides.INSTANCE);
        alignment.addSequence(new Sequence(new Taxon("a"), "A"));
        alignment.addSequence(new Sequence(new Taxon("b"), "C"));
        final PatternList patterns = new SitePatterns(alignment);
        final SiteModel siteModel = new GammaSiteModel(new GTR(new Variable.D(1, 1), new Variable.D(1, 1), new Variable.D(1, 1), new Variable.D(1, 1), new Variable.D(1, 1), new Variable.D(1, 1), new FrequencyModel(Nucleotides.INSTANCE, new double[]{0.25, 0.25, 0.25, 0.25})));
        final TreeLikelihood likelihood = new TreeLikelihood(patterns, tree, siteModel, new DefaultBranchRateModel(), null, true, false, true, true, false);
        final Variable<Double> var = tree.createNodeHeightsParameter(true, true, false);
        final int index = 0;
        var.setValue(index, 0.0);
        System.out.println(Differentiable.differentiate(likelihood::getLogLikelihood, var, index));
        System.out.println(likelihood.differentiate(var, index));
//        for (double t = 0; t <= 4.0; t += 1.0 / 32) {
//            var.setValue(index, t);
//            System.out.println(t + "," + likelihood.getLogLikelihood());
//        }
    }