def METHOD_NAME(self):
    """Check codeml runs, generates correct output, and is the correct version."""
    ctl_file = os.path.join("PAML", "Control_files", "codeml", "codeml.ctl")
    self.cml.read_ctl_file(ctl_file)
    self.cml.alignment = os.path.join("PAML", "Alignments", "alignment.phylip")
    self.cml.tree = os.path.join("PAML", "Trees", "species.tree")
    self.cml.out_file = os.path.join("PAML", "temp.out")
    self.cml.working_dir = os.path.join("PAML", "codeml_test")
    results = self.cml.run()
    self.assertGreater(results["version"], "4.0")
    self.assertIn("NSsites", results)
    self.assertEqual(len(results["NSsites"]), 1)
    self.assertEqual(len(results["NSsites"][0]), 5)