//final File temp_seqs_file = new File( _options.getTempDir() + ForesterUtil.FILE_SEPARATOR + "s.fasta" );
final BufferedWriter writer = new BufferedWriter( new FileWriter( temp_seqs_file ) );
SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 );
writer.close();
final List<String> opts = processMafftOptions();
//final File temp_seqs_file = new File( _options.getTempDir() + ForesterUtil.FILE_SEPARATOR + "s.fasta" );
final BufferedWriter writer = new BufferedWriter( new FileWriter( temp_seqs_file ) );
SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 );
writer.close();
final List<String> opts = processMafftOptions();