Interface Summary
FitnessFunction This interface defines the invocation of a fitness function.

Class Summary
DarwinsCrucible This is a framework for running simulations of successive mutation and natural selection.
DynamicDuo This is the framework for doing pairwise alignments.
IdentityComparator This trivial comparison function returns "1" if the elements are completely identical, and "0" if they are not.
MonomerComparator This is the base implementation for comparing two monomers.
Needleman This implements the Needleman/Wunsch algorithm, with gap penalties, including end gap penalties.
PSSMFitnessFunction This class implements a fitness function based on a PSSM.
SequenceAligner This interface describes any algorithm for doing pair-wise alignment of sequences.
SequenceFetcher Give this class the name of a sequence, and it will fetch it via the web.
SimilarityMatrixComparator This is a simple implementation of a similarity matrix for comparing monomers.