|
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. |