No Yes -maxnamelen Margin size for the sequence name. Normal collision check. So if any other residue matches the identical score then a collision has occurred. If another residue has a greater than or equal to matching score and these do not match then a collision has occurred. If any of these give a top score for matching or identical scores then a collision has occured.
Data files Prettyplot uses a comparison matrix file to calculate similarity to the consensus.
Users can provide their own data files in their own directories. It exits with status 0 unless an error is reported. Gert Vriend added the star marking. This program is intended to be used by everyone and everything, from naive users to embedded scripts.