preserving dinucleotide frequency
fasta-dinucleotide-shuffle.py -f $input -t $tag -c $n -s $seed > $output
**What it does**
This tool shuffles the sequences in the input file but preserves the dinucleotide frequency of each sequence.
The code implements the Altschul-Erikson dinucleotide shuffle algorithm, described in "Significance of nucleotide sequence alignments: A method for random sequence permutation that preserves dinucleotide and codon usage", S.F. Altschul and B.W. Erikson, Mol. Biol. Evol., 2(6):526--538, 1985.
Code adapted from http://bioinformatics.bc.edu/clotelab/RNAdinucleotideShuffle/dinucleotideShuffle.html