def hmmalign_sequences(self, hmm, sequences, output_file):
cmd = '<STR_LIT>' % (hmm, sequences)<EOL>output = extern.run(cmd)<EOL>with open(output_file, '<STR_LIT:w>') as f:<EOL><INDENT>SeqIO.write(SeqIO.parse(StringIO(output), '<STR_LIT>'), f, '<STR_LIT>')<EOL><DEDENT>
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