def _align_sequences_to_hmm(self, hmm_file, sequences_file, output_alignment_file):
ss = SequenceSearcher(hmm_file)<EOL>with tempfile.NamedTemporaryFile(prefix='<STR_LIT>', suffix='<STR_LIT>') as tempalign:<EOL><INDENT>ss.hmmalign_sequences(hmm_file, sequences_file, tempalign.name)<EOL>ss.alignment_correcter([tempalign.name], output_alignment_file)<EOL><DEDENT>
Align sequences to an HMM, and write an alignment of
        these proteins after cleanup so that they can be used for tree-making

        Parameters
        ----------
        sequences_file: str
            path to file of unaligned protein sequences
        hmm_file: str
            path to hmm file
        output_alignment_file: str
            write alignment to this file

        Returns
        -------
        nothing