def test_jc_three_tax(self): mod = JukesCantor() seq_data = ["ACGT", "ACGC", "ACGT"] leaf_data, clas, full_la = get_tree_decorators(seq_data, mod) leaf0, leaf1, leaf2 = leaf_data internal_d = clas[0] leaf0.set_brlen(0.1) leaf1.set_brlen(0.07) leaf2.set_brlen(0.05) lnL = calc_lnL(full_la, internal_d, leaves=leaf_data, internals=(), beg_subset=0, end_subset=1, beg_cat=0, end_cat=1) self.assertTrue(abs(10.12296 + lnL) < 1e-05)
def test_dna(self): jc = JukesCantor() inds = ["AC", "AG"] ldo, cla, f = get_tree_decorators(inds, jc, 1) self.assertEquals(len(ldo), 2) self.assertEquals(len(cla), 1)