def Cov(self):
<EOL>M = np.zeros((self.N, self.N))<EOL>for n in self.tree.find_clades():<EOL><INDENT>if n == self.tree.root:<EOL><INDENT>continue<EOL><DEDENT>M[np.meshgrid(n._ii, n._ii)] += self.branch_variance(n)<EOL><DEDENT>return M<EOL>
calculate the covariance matrix of the tips assuming variance
has accumulated along branches of the tree accoriding to the
the provided
Returns
-------

 M : (np.array)
    covariance matrix with tips arranged standard transersal order.