treetime/gtr_site_specific.py
def custom(cls, mu=1.0, pi=None, W=None, **kwargs):
        """
        Create a GTR model by specifying the matrix explicitly

        Parameters
        ----------

         mu : float
            Substitution rate

         W : nxn matrix
            Substitution matrix

         pi : n vector
            Equilibrium frequencies

         **kwargs:
            Key word arguments to be passed

        Keyword Args
        ------------

         alphabet : str
            Specify alphabet when applicable. If the alphabet specification is
            required, but no alphabet is specified, the nucleotide alphabet will be used as
            default.

        """
        gtr = cls(**kwargs)
        gtr.assign_rates(mu=mu, pi=pi, W=W)
        return gtr
def custom(cls, mu=1.0, pi=None, W=None, **kwargs):
        gtr = cls(**kwargs)
        gtr.assign_rates(mu=mu, pi=pi, W=W)
        return gtr
def custom ( cls , mu = 1.0 , pi = None , W = None , * * kwargs ) : gtr = cls ( * * kwargs ) gtr . assign_rates ( mu = mu , pi = pi , W = W ) return gtr
Create a GTR model by specifying the matrix explicitly

        Parameters
        ----------

         mu : float
            Substitution rate

         W : nxn matrix
            Substitution matrix

         pi : n vector
            Equilibrium frequencies

         **kwargs:
            Key word arguments to be passed

        Keyword Args
        ------------

         alphabet : str
            Specify alphabet when applicable. If the alphabet specification is
            required, but no alphabet is specified, the nucleotide alphabet will be used as
            default.
Create a GTR model by specifying the matrix explicitly