partials_dict = {"1": partials_1, "2": partials_2, "3": partials_3, "4": partials_4, "5": partials_5} t = "(((1:0.2,2:0.2)7:0.1,3:0.2)6:0.1,(4:0.2,5:0.2)8:0.1)0;" t = "((1:0.2,2:0.2):0.1,3:0.2,(4:0.2,5:0.2):0.2);" runner = LnlModel(tm, partials_dict) runner.set_tree(t) print runner.run(True) print runner.get_sitewise_likelihoods() gamma = GammaMixture(400, 4) gamma.init_models(tm, partials_dict, scale_freq=3) gamma.set_tree(t) print gamma.get_likelihood() print gamma.get_sitewise_likelihoods() kappa = 2 k80 = K80(kappa) tm = TransitionMatrix(k80) partials_dict = { "1": seq_to_partials("ACCCT"), "2": seq_to_partials("TCCCT"), "3": seq_to_partials("TCGGT"), "4": seq_to_partials("ACCCA"), "5": seq_to_partials("CCCCC"), } gamma = GammaMixture(0.03, 4) gamma.init_models(tm, partials_dict, scale_freq=200)