| Class Score A scoring scheme.
Score
Pam | Score ChainSoP | Score Manhattan | Score Matrix | Score Zero | Simple Score
Score<TValue, TSpec> Parameters
TValue | The value type. Default: int
TSpec | The specializing type. Default: Simple Score
Specializations
Pam | Pam scoring matrices.
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.
Member Functions
Score | Constructor
~Score | Destructor
Functions
alignmentEvaluation | Given a multiple alignment, this function calculates all kinds of alignment statistics.
globalAlignment | Computes the best global alignment of the two sequences.
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 | The score for aligning two values according to a scoring scheme.
smithWaterman | Computes the best local alignment of the (two) sequences given in align.
smithWatermanGetNext | Computes next best local alignment.
sumOfPairsScore | Given a multiple alignment, this function calculates the sum-of-pairs score.
Example Programs Global Alignments, Local Alignments SeqAn - Sequence Analysis Library - www.seqan.de