Example #1
0
 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)