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CHAPTER 13. GENERAL SEQUENCE ANALYSES
or right-click a sequence | Toolbox | General Sequence Analyses (
Sequence ( )
200
) | Shuffle
This opens the dialog displayed in figure 13.1:
Figure 13.1: Choosing sequence for shuffling.
If a sequence was selected before choosing the Toolbox action, this sequence is now listed in
the Selected Elements window of the dialog. Use the arrows to add or remove sequences or
sequence lists from the selected elements.
Click Next to determine how the shuffling should be performed.
In this step, shown in figure 13.2:
For nucleotides, the following parameters can be set:
Figure 13.2: Parameters for shuffling.
• Mononucleotide shuffling. Shuffle method generating a sequence of the exact same
mononucleotide frequency
• Dinucleotide shuffling. Shuffle method generating a sequence of the exact same dinucleotide frequency
• Mononucleotide sampling from zero order Markov chain. Resampling method generating
a sequence of the same expected mononucleotide frequency.