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) gamma.set_tree(t) print gamma.get_likelihood() print gamma.get_sitewise_likelihoods() print gamma.get_sitewise_likelihoods().sum(0) gamma.update_alpha(1.0) print gamma.get_likelihood() print gamma.get_sitewise_likelihoods() print gamma.get_sitewise_likelihoods().sum(0) gamma.update_transition_matrix(TransitionMatrix(K80(3))) print gamma.get_likelihood() print gamma.get_sitewise_likelihoods() print gamma.get_sitewise_likelihoods().sum(0)