def test_likelihood_calculation(self):
# get a tree
tree = Newick.parse(sample_tree_string, Newick.NewickTree)
# get a model
input_xml_string = get_sample_xml_string()
model = deserialize_mixture_model(input_xml_string)
# get an alignment
alignment = Fasta.CodonAlignment(
StringIO(long_sample_codon_alignment_string))
# get the likelihood
log_likelihood = PhyLikelihood.get_log_likelihood(
tree, alignment, model)
