treetime/nuc_models.py
def JC69 (mu=1.0, alphabet="nuc", **kwargs):
    """
    Jukes-Cantor 1969 model. This model assumes equal concentrations
    of the nucleotides and equal transition rates between nucleotide states.
    For more info, see: Jukes and Cantor (1969). Evolution of Protein Molecules.
                        New York: Academic Press. pp. 21–132

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

     mu : float
        substitution rate

     alphabet : str
        specify alphabet to use.
        Available alphabets are:

         'nuc' - nucleotides only, gaps ignored

         'nuc_gap' - nucleotide alphabet with gaps, gaps can be ignored optionally

    """
    num_chars = len(alphabets[alphabet])
    W, pi = np.ones((num_chars,num_chars)), np.ones(num_chars)
    gtr = GTR(alphabet=alphabet)
    gtr.assign_rates(mu=mu, pi=pi, W=W)
    return gtr
def JC69 (mu=1.0, alphabet="nuc", **kwargs):
    """
    Jukes-Cantor 1969 model. This model assumes equal concentrations
    of the nucleotides and equal transition rates between nucleotide states.
    For more info, see: Jukes and Cantor (1969). Evolution of Protein Molecules.
                        New York: Academic Press. pp. 21–132

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

     mu : float
        substitution rate

     alphabet : str
        specify alphabet to use.
        Available alphabets are:

         'nuc' - nucleotides only, gaps ignored

         'nuc_gap' - nucleotide alphabet with gaps, gaps can be ignored optionally

    """
    num_chars = len(alphabets[alphabet])
    W, pi = np.ones((num_chars,num_chars)), np.ones(num_chars)
    gtr = GTR(alphabet=alphabet)
    gtr.assign_rates(mu=mu, pi=pi, W=W)
    return gtr
Jukes-Cantor 1969 model. This model assumes equal concentrations
    of the nucleotides and equal transition rates between nucleotide states.
    For more info, see: Jukes and Cantor (1969). Evolution of Protein Molecules.
                        New York: Academic Press. pp. 21–132

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

     mu : float
        substitution rate

     alphabet : str
        specify alphabet to use.
        Available alphabets are:

         'nuc' - nucleotides only, gaps ignored

         'nuc_gap' - nucleotide alphabet with gaps, gaps can be ignored optionally