Set parameters of likelihood model - inst -
        using values in dictionary - partition_parameters -,
        and - tree -

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)