Class Specialization
Simple Score
Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.
 Score
Simple Score
Score<TValue, Simple>
Parameters
 TValue The value type.Default: int
Specialization of
Functions
 alignmentEvaluation Given a multiple alignment, this function calculates all kinds of alignment statistics. (Score) bandedAlignment Calculates a banded alignment around a Seed. bandedChainAlignment Calculates a banded alignment around a chain of seeds. extendSeed Extends a seed. extendSeeds Extenstion of seeds. getAlignment Constructs a alignment from a ChainedSeed. globalAlignment Computes the best global alignment of the two sequences. (Score) localAlignment Computes the best local alignment of two sequences. (Score) 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. 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. (Score) multiLocalAlignment Computes multiple local alignments of two sequences. (Score) score The score for aligning two values according to a scoring scheme. (Score) scoreGap Score for gaps. scoreGapExtend Score for extending gaps. scoreGapOpen Score for opening a gap. scoreMatch Match score. scoreMismatch Mismatch score. scoreSeed Calculates the score of a seed. smithWaterman Computes the best local alignment of the (two) sequences given in align. (Score) smithWatermanGetNext Computes next best local alignment. (Score) sumOfPairsScore Given a multiple alignment, this function calculates the sum-of-pairs score. (Score)
Shortcuts
 SimpleScore Simple scoring scheme.
Example Programs