Class
Score
A scoring scheme.
Parameters
The value type. Default: int | |
The specializing type. Default: Simple Score |
Specializations
| Edit distance scoring scheme. | |
| Pam scoring matrices. | |
| Scoring scheme for chaining that uses a special method for scoring the gaps between two fragments. | |
| Scoring scheme for chaining that computes gap scores using manhattan distance. | |
| A general scoring matrix. | |
| Scoring scheme for chaining that set gap scores to 0 | |
| Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps. |
Functions
| Given a multiple alignment, this function calculates all kinds of alignment statistics. | |
| Computes the best global alignment of the two sequences. | |
| Computes the best local alignment of two sequences. | |
| 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. | |
| Computes multiple local alignments of two sequences. | |
| The score for aligning two values according to a scoring scheme. | |
| Computes the best local alignment of the (two) sequences given in align. | |
| Computes next best local alignment. | |
| Given a multiple alignment, this function calculates the sum-of-pairs score. |
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de