def _align_sequences_to_hmm(self, hmm_file, sequences_file, output_alignment_file):
        '''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
        '''

        ss = SequenceSearcher(hmm_file)
        with tempfile.NamedTemporaryFile(prefix='graftm', suffix='.aln.fasta') as tempalign:
            ss.hmmalign_sequences(hmm_file, sequences_file, tempalign.name)
            ss.alignment_correcter([tempalign.name], output_alignment_file)
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