Provides classes for representing, manipulating, and comparing motifs.

Each Motif contains a reference to an Alphabet, which defines what bases can be used. Three different Alphabets are defined: Alphabet.PRIMARY, Alphabet.FULL, and Alphabet.ACGTRY. Currently Alphabet.FULL is used so that Motifs can represent consensus sequences. New Alphabets can be added if needed. See {@link edu.dartmouth.bglab.motif.Alphabet Alphabet} for details.

MotifLists allow sets of related Motifs to be grouped together so that they can be evaluated as a set or combined into a single motif.

MotifUtils adds peripheral functionality to the Motif and MotifList classes. The distinction between what functionality is contained in Motif and MotifUtils is fuzzy, so check both classes before implementing new methods.

The remaining classes are Comparators for comparing motifs.

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