docs: def _update_likelihood_model(self, inst, partition_parameters, tree):
          """ 
          Set parameters of likelihood model - inst -
          using values in dictionary - partition_parameters -,
          and - tree -
          """
          # Build transition matrix from dict
          model = partition_parameters['model']
          freqs = partition_parameters.get('frequencies')
          if model == 'LG':
              subs_model = phylo_utils.models.LG(freqs)
          elif model == 'WAG':
              subs_model = phylo_utils.models.WAG(freqs)
          elif model == 'GTR':
              rates = partition_parameters.get('rates')
              subs_model = phylo_utils.models.GTR(rates, freqs, True)
          else:
              raise ValueError("Can't handle this model: {}".format(model))
          tm = phylo_utils.markov.TransitionMatrix(subs_model)
          
          # Read alpha value
          alpha = partition_parameters['alpha']
          inst.set_tree(tree)
          inst.update_alpha(alpha)
          inst.update_transition_matrix(tm)