| Class Score A scoring scheme.
Score
EditDistance | Score ChainSoP | Score Manhattan | Score Matrix | Score Zero | Simple Score
Score<TValue, TSpec> Include Headers seqan/score.h Parameters
TValue | The value type. Default: int
TSpec | The specializing type. Default: Simple
Specializations
EditDistance | Edit distance scoring scheme.
Score ChainSoP | Scoring scheme for chaining that uses a special method for scoring the gaps between two fragments.
Score Manhattan | Scoring scheme for chaining that computes gap scores using manhattan distance.
Score Matrix | A general scoring matrix.
Score Zero | Scoring scheme for chaining that set gap scores to 0
Simple Score | Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.
Metafunctions
DefaultFindBeginPatternSpec | Type of the default findBegin pattern specialization, given a score.
Value | Type of the items in the container.
Member Functions
Score | Constructor
Functions
alignmentEvaluation | Given a multiple alignment, this function calculates all kinds of alignment statistics.
globalAlignment | Computes the best global alignment of the two sequences.
globalMsaAlignment | Computes a global multiple alignment.
localAlignment | Computes the best local alignment of two sequences.
matchRefinement | Refines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping.
multiLocalAlignment | Computes multiple local alignments of two sequences.
score | Returns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme.
score | Returns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme.
sumOfPairsScore | Given a multiple alignment, this function calculates the sum-of-pairs score.
Example Programs Local Alignments, Global Alignments SeqAn - Sequence Analysis Library - www.seqan.de

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