No bases or residues are changed, only their order. The number of shuffled sequences output can be set by the '-shuffle' qualifier. Here is a sample session with shuffleseq making two randomised copies of the input sequence. The USA of one or more sequences. Each run will produce a different sequence.
Data files None.
This program may be useful for producing sets of sequences which can be used to check the statistics of sequence similarity finding software. Diagnostic Error Messages None. It always exits with status 0. Known bugs None. This program is intended to be used by everyone and everything, from naive users to embedded scripts.