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Class Summary |
| Alignments |
Static utility to easily run alignment routines. |
| FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound> |
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment
Profile. |
| FractionalIdentityScorer<S extends Sequence<C>,C extends Compound> |
Implements an algorithm which computes a score for a sequence alignment pair. |
| FractionalSimilarityInProfileScorer<S extends Sequence<C>,C extends Compound> |
Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment
Profile. |
| FractionalSimilarityScorer<S extends Sequence<C>,C extends Compound> |
Implements an algorithm which computes a score for a sequence alignment pair. |
| GuideTree<S extends Sequence<C>,C extends Compound> |
Implements a data structure for a guide tree used during progressive multiple sequence alignment. |
| NeedlemanWunsch<S extends Sequence<C>,C extends Compound> |
Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last
Compound of each Sequence). |
| SimpleAlignedSequence<S extends Sequence<C>,C extends Compound> |
Implements a data structure for a Sequence within an alignment. |
| SimpleGapPenalty |
Implements a data structure for the gap penalties used during a sequence alignment routine. |
| SimpleProfile<S extends Sequence<C>,C extends Compound> |
Implements a data structure for the results of sequence alignment. |
| SimpleProfilePair<S extends Sequence<C>,C extends Compound> |
Implements a data structure for the results of the alignment of a pair of Profiles. |
| SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound> |
Implements a simple (naive) Aligner for a pair of Profiles. |
| SimpleSequencePair<S extends Sequence<C>,C extends Compound> |
Implements a data structure for the results of pairwise sequence alignment. |
| SimpleSubstitutionMatrix<C extends Compound> |
Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one
Compound in a sequence for another. |
| SmithWaterman<S extends Sequence<C>,C extends Compound> |
Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each
Sequence). |
| StandardRescoreRefiner<S extends Sequence<C>,C extends Compound> |
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| SubstitutionMatrixHelper |
Static utility to access substitution matrices that come bundled with BioJava. |