ShuffleFastaSeq

ShuffleFastaSeq is a Windows form application, written in C#, to shuffle FASTA-formatted sequences. The random permutation is obtained using a simple variation of the Fisher-Yates alghorithm implemented by Durstenfeld (https://en.wikipedia.org/wiki/Fisher%E2%80%93Yates_shuffle) ( Knuth DE. The art of computer programming: seminumerical algorithms. 3rd ed. Boston: Addison-Wesley; 1997). The input file contains one or more 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