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).

SimpleGapPenalty

Implements a data structure for the gap penalties used during a sequence alignment routine.

SimpleProfileProfileAligner<S extends Sequence<C>,​C extends Compound>

Implements a simple (naive) Aligner for a pair of Profiles.

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>   SubstitutionMatrixScorer<S extends Sequence<C>,​C extends Compound>

Scores using a substitution matrix.