Thanks to those who replied.
I compared shuffleseq with make_randon_dna (the latter with flags: -n
-order 1).
The test was a piece of software that recognises certain complex
patterns within genomes. As controls for that pattern recognition
process, the genomes were iteratively shuffled 100 times with both
the shuffling applications (by iteratively I mean shuffle once then
pipe the output back in to re-shuffle and so on).
There seemed to be no difference in the background scores for
shuffling once, 10 times etc up to 100 times. I therefore infer that
the slight background rate that was troubling me is not an artefact
of poor shuffing.
Therefore, the answer to the original question, I reckon, is:
shuffleseq is just as good if you choose to shuffle once as to
shuffle 100 times. The same is true for make_randon_dna. There is
nothing to separate the two programs in performance.
D.
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