docs: def _calculate_Phi_x(self):
          """Calculate `Phi_x` (stationary state) from `phi`."""
          self.Phi_x = scipy.ones(N_CODON, dtype='float')
          for codon in range(N_CODON):
              for pos in range(3):
                  self.Phi_x[codon] *= self.phi[pos][CODON_NT_INDEX[pos][codon]]
          self.Phi_x /= self.Phi_x.sum()