def _align_sequences(self, input_sequences_path, output_alignment_path,<EOL>threads):
logging.debug("<STR_LIT>")<EOL>cmd = "<STR_LIT>" % (<EOL>threads,<EOL>output_alignment_path)<EOL>inputs = []<EOL>with open(input_sequences_path) as f:<EOL><INDENT>for name,seq,_ in SequenceIO().each(f):<EOL><INDENT>inputs.append('<STR_LIT>' % name)<EOL>inputs.append(seq.replace('<STR_LIT:*>','<STR_LIT>'))<EOL><DEDENT><DEDENT>extern.run(cmd, stdin="<STR_LIT:\n>".join(inputs))<EOL>
Align sequences into alignment_file

        Parameters
        ----------
        input_sequences_path: str
            path to input sequences in fasta format
        output_alignment_path: str
            path to output alignment path
        threads: str
            number of threads to use
        Returns
        -------
        Nothing