treetime/nuc_models.py
def T92(mu=1.0, pi_GC=0.5, kappa=0.1, **kwargs):
    """
    Tamura 1992 model. Extending Kimura  (1980) model for the case where a
    G+C-content bias exists. Link:
    Tamura K (1992),  Mol.  Biol. Evol. 9 (4): 678–687.  DOI: 10.1093/oxfordjournals.molbev.a040752

    Current implementation of the model does not account for the gaps

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

     mu : float
        substitution rate

     pi_GC : float
        relative GC content

     kappa : float
        relative transversion/transition rate

    """

    W = _create_transversion_transition_W(kappa)
    # A C G T
    if pi_CG >=1.:
        raise ValueError("The relative CG content specified is larger than 1.0!")
    pi = np.array([(1.-pi_CG)*0.5, pi_CG*0.5, pi_CG*0.5, (1-pi_CG)*0.5])
    gtr = GTR(alphabet=alphabets['nuc_nogap'])
    gtr.assign_rates(mu=mu, pi=pi, W=W)
    return gtr
def T92(mu=1.0, pi_GC=0.5, kappa=0.1, **kwargs):
    """
    Tamura 1992 model. Extending Kimura  (1980) model for the case where a
    G+C-content bias exists. Link:
    Tamura K (1992),  Mol.  Biol. Evol. 9 (4): 678–687.  DOI: 10.1093/oxfordjournals.molbev.a040752

    Current implementation of the model does not account for the gaps

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

     mu : float
        substitution rate

     pi_GC : float
        relative GC content

     kappa : float
        relative transversion/transition rate

    """

    W = _create_transversion_transition_W(kappa)
    # A C G T
    if pi_CG >=1.:
        raise ValueError("The relative CG content specified is larger than 1.0!")
    pi = np.array([(1.-pi_CG)*0.5, pi_CG*0.5, pi_CG*0.5, (1-pi_CG)*0.5])
    gtr = GTR(alphabet=alphabets['nuc_nogap'])
    gtr.assign_rates(mu=mu, pi=pi, W=W)
    return gtr
def T92 ( mu = 1.0 , pi_GC = 0.5 , kappa = 0.1 , * * kwargs ) : W = _create_transversion_transition_W ( kappa ) # A C G T if pi_CG >= 1. : raise ValueError ( "The relative CG content specified is larger than 1.0!" ) pi = np . array ( [ ( 1. - pi_CG ) * 0.5 , pi_CG * 0.5 , pi_CG * 0.5 , ( 1 - pi_CG ) * 0.5 ] ) gtr = GTR ( alphabet = alphabets [ 'nuc_nogap' ] ) gtr . assign_rates ( mu = mu , pi = pi , W = W ) return gtr
Tamura 1992 model. Extending Kimura  (1980) model for the case where a
    G+C-content bias exists. Link:
    Tamura K (1992),  Mol.  Biol. Evol. 9 (4): 678–687.  DOI: 10.1093/oxfordjournals.molbev.a040752

    Current implementation of the model does not account for the gaps

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

     mu : float
        substitution rate

     pi_GC : float
        relative GC content

     kappa : float
        relative transversion/transition rate
Tamura 1992 model . Extending Kimura ( 1980 ) model for the case where a G + C - content bias exists . Link : Tamura K ( 1992 ) Mol . Biol . Evol . 9 ( 4 ) : 678–687 . DOI : 10 . 1093 / oxfordjournals . molbev . a040752