Randomly shuffled sequences are routinely used in sequence analysis to evaluate the statistical significance of a biological sequence. In many cases, biologists need sophisticated shuffling tools that preserve not only the counts of distinct letters but also higher-order statistics such as doublet counts, triplet counts, and, in general, k-let counts.
Jiang, M., Anderson, J., Gillespie, J., & Mayne, M. (2008). uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts. BMC Bioinformatics, 9. https://doi.org/10.1186/1471-2105-9-192