| Class Specialization Simple Score Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.
Score
Simple Score
Specialization of Score 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 MultiSeed.
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. (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)
Example Programs Global Alignments, Local Alignments SeqAn - Sequence Analysis Library - www.seqan.de