def HKY85(mu=<NUM_LIT:1.0>, pi=None, kappa=<NUM_LIT:0.1>, **kwargs):
if pi is None:<EOL><INDENT>pi=<NUM_LIT>*np.ones(<NUM_LIT:4>, dtype=float)<EOL><DEDENT>num_chars = len(alphabets['<STR_LIT>'])<EOL>if num_chars != pi.shape[<NUM_LIT:0>] :<EOL><INDENT>pi = np.ones((num_chars, ), dtype=float)<EOL>print ("<STR_LIT>"<EOL>"<STR_LIT>")<EOL><DEDENT>W = _create_transversion_transition_W(kappa)<EOL>pi /= pi.sum()<EOL>gtr = GTR(alphabet=alphabets['<STR_LIT>'])<EOL>gtr.assign_rates(mu=mu, pi=pi, W=W)<EOL>return gtr<EOL>
Hasegawa, Kishino and Yano 1985 model. Allows different concentrations of the
nucleotides (as in F81) + distinguishes between transition/transversionsubstitutions
(similar to K80). Link:
Hasegawa, Kishino, Yano (1985), J. Mol. Evol. 22 (2): 160–174. doi:10.1007/BF02101694

Current implementation of the model does not account for the gaps

Parameters
-----------


 mu : float
    Substitution rate

 pi : numpy.array
    Nucleotide concentrations

 kappa : float
    Ratio of transversion/transition substitution rates