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ShuffleFastaSeq 2016-04-11
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This is a Windows portable application to shuffle sequences in FASTA format.
Run ShuffleFastaSeq.exe, click on "open file" button and choose the input fasta file, set number of simulations (default is 100), and click on "save file" button to produce shuffled fasta sequences. 
Source: readme.txt, updated 2016-04-10