PRANK is a probabilistic multiple alignment program for DNA,
codon and amino-acid sequences. It’s based on a novel algorithm
that treats insertions correctly and avoids over-estimation
of the number of deletion events. In addition, PRANK borrows
ideas from maximum likelihood methods used in phylogenetics
and correctly takes into account the evolutionary distances
between sequences. Lastly, PRANK allows for defining a
potential structure for sequences to be aligned and then,
simultaneously with the alignment, predicts the locations
of structural units in the sequences.