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Shuffle randomizes the order of the symbols in a sequence without changing the composition.
Shuffle uses a random number generator to scramble the positions of the symbols in a sequence. The generator is initialized with the current time, so repeated shuffles should yield different results.
Here is a session using Shuffle to randomize the bases of gamma.seq:
% shuffle
SHUFFLE of what sequence ? gamma.seq
Begin (* 1 *) ?
End (* 11375 *) ?
Reverse (* No *) ?
What should I call the output file (* gamma.shuffle *) ?
%
The file gamma.shuffle now contains the shuffled contents of gamma.seq.
Shuffle accepts a single sequence as input. The function of Shuffle depends on whether your input sequence(s) are protein or nucleotide. Programs determine the type of a sequence by the presence of either Type: N or Type: P on the last line of the text heading just above the sequence. If your sequence(s) are not the correct type, turn to Appendix VI for information on how to change or set the type of a sequence.
Sample extracts sequence fragments randomly from sequence(s). You can set a sampling rate to determine how many fragments Sample extracts. Corrupt randomly introduces small numbers of substitutions, insertions, and deletions into nucleotide sequence(s).
Shuffle scrambles the dinucleotide (neighbor) frequencies.
All parameters for this program may be put on the command line. Use the parameter -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
Minimal Syntax: % shuffle [-INfile=]gamma.seq -Default Prompted Parameters: -BEGin=1 first symbol to shuffle -END=11375 last symbol to shuffle -REVerse shuffle the back strand [-OUTfile=]gamma.shuffle output file name Local Data Files: None Optional Parameters: -NONUMbering suppresses the numbering in the output file
None.
The parameters listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
suppresses the numbering in the output file.
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