treetime/gtr.py
def random(cls, mu=1.0, alphabet='nuc'):
        """
        Creates a random GTR model

        Parameters
        ----------

         mu : float
            Substitution rate

         alphabet : str
            Alphabet name (should be standard: 'nuc', 'nuc_gap', 'aa', 'aa_gap')


        """

        alphabet=alphabets[alphabet]
        gtr = cls(alphabet)
        n = gtr.alphabet.shape[0]
        pi = 1.0*np.random.randint(0,100,size=(n))
        W = 1.0*np.random.randint(0,100,size=(n,n)) # with gaps

        gtr.assign_rates(mu=mu, pi=pi, W=W)
        return gtr
def random(cls, mu=1.0, alphabet='nuc'):
        """
        Creates a random GTR model

        Parameters
        ----------

         mu : float
            Substitution rate

         alphabet : str
            Alphabet name (should be standard: 'nuc', 'nuc_gap', 'aa', 'aa_gap')


        """

        alphabet=alphabets[alphabet]
        gtr = cls(alphabet)
        n = gtr.alphabet.shape[0]
        pi = 1.0*np.random.randint(0,100,size=(n))
        W = 1.0*np.random.randint(0,100,size=(n,n)) # with gaps

        gtr.assign_rates(mu=mu, pi=pi, W=W)
        return gtr
def random ( cls , mu = 1.0 , alphabet = 'nuc' ) : alphabet = alphabets [ alphabet ] gtr = cls ( alphabet ) n = gtr . alphabet . shape [ 0 ] pi = 1.0 * np . random . randint ( 0 , 100 , size = ( n ) ) W = 1.0 * np . random . randint ( 0 , 100 , size = ( n , n ) ) # with gaps gtr . assign_rates ( mu = mu , pi = pi , W = W ) return gtr
Creates a random GTR model

        Parameters
        ----------

         mu : float
            Substitution rate

         alphabet : str
            Alphabet name (should be standard: 'nuc', 'nuc_gap', 'aa', 'aa_gap')
Creates a random GTR model