def hmmalign_sequences(self, hmm, sequences, output_file):
        '''Run hmmalign and convert output to aligned fasta format

        Parameters
        ----------
        hmm: str
            path to hmm file
        sequences: str
            path to file of sequences to be aligned
        output_file: str
            write sequences to this file

        Returns
        -------
        nothing
        '''

        cmd = 'hmmalign --trim %s %s' % (hmm, sequences)
        output = extern.run(cmd)
        with open(output_file, 'w') as f:
            SeqIO.write(SeqIO.parse(StringIO(output), 'stockholm'), f, 'fasta')
Run hmmalign and convert output to aligned fasta format

        Parameters
        ----------
        hmm: str
            path to hmm file
        sequences: str
            path to file of sequences to be aligned
        output_file: str
            write sequences to this file

        Returns
        -------
        nothing