def prettify_alignment(aln):
    """
    Converts all bases to uppercase and removes auto reverse-complement prefix (_R_).
    This modifies the alignment in place.

    Parameters
    ----------
    aln : MultipleSeqAlign
        Biopython Alignment
    """
    for seq in aln:
        seq.seq = seq.seq.upper()
        if seq.id.startswith('_R_'):
            seq.id = seq.id[3:]
            print(
                'Sequence "{}" was reverse-complemented by the alignment program.'
                .format(seq.id))
        if seq.name.startswith('_R_'):
            seq.name = seq.name[3:]
        if seq.description.startswith('_R_'):
            seq.description = seq.description[3:]
