I am using a Perl script to randomly shuffle DNA. This script uses the Perl module http://search.cpan.org/~salva/Array-Shuffle-0.03/lib/Array/Shuffle.pm that appears to work OK for my purposes.

The problem is that I am not sure whether the theory behind what I am doing (to randomly shuffle DNA sequence) is statistically valid and biological valid for the purposes of my research.

I've explained my entire problem at http://math.stackexchange.com/questions/1279699/how-to-best-randomly-shuffle-dna-sequence, because I thought it is more math / stats related, than Perl coding related, but I've received no useful feedback there.

I've always received useful advice here, so I am trying my luck. Thank you!

In reply to Window size for shuffling DNA? by onlyIDleft

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