def seperate(aln_dict, leaf_dict):
    """ Separate the query sequences from the reference sequences
    
    Parameters
    ----------
    aln_dict : Sequence dictionary with taxon label keys
    leaf_dict : Sequence dictionary with leaf label keys (queries are not in backbone tree)
    
    Returns
    -------
    separate dictionaries containing query sequences and referece sequences with taxon label keys
    
    """
    ref = dict()
    query = dict()

    for key, value in aln_dict.items():
        if key not in leaf_dict:
            query[key] = value
        else:
            ref[key] = value

    return ref, query