ShuffleFastaSeq
This application can be used to shuffle sequences in FASTA format.
...The number of shufflings (n) for each sequence can be set; by default n is 100. The output file contains n shuffled copies in FASTA format for each input sequence.
For example (n=3):
Input file:
>a
ACGGT
>b
GCCCATTC
Output file:
>a
TCGAG
>a
CGAGT
>a
TGCGA
>b
CACTCCGT
>b
CCCGTATC
>b
CCTTCAGC