http://novita-med.pl/?komarivske=darmowe-randki-holandia&bbd=6a Shuffle sequences in DNASequenceSet.

Chulucanas lapply() or sapply() return list.
endoapply() returns the same data class, DNASequenceSet.
It is way slower, though.

shuffled.seqs <- endoapply(seqs, sample)

For faster shuffling, look at the link.
http://grokbase.com/t/r/bioconductor/133n8bw1f6/bioc-how-to-operate-on-a-dnastringset-object