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 Profile s. |
SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound> |
Implements a simple (naive) Aligner for a pair of Profile s. |
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. |