shuffleseq takes a sequence as input and outputs one or more sequences whose order has been randomly shuffled. No bases or residues are changed, only their order.

Here is a sample session with shuffleseq making two randomised copies of the input sequence:

% shuffleseq -shuffle 2
Shuffles a set of sequences maintaining composition
Input sequence(s): embl:mmam
Output sequence [mmam.fasta]:

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

[-outseq] (seqoutall)

Output sequence(s) USA.

Advanced qualifiers:

-shuffle (integer)

Number of shuffles.