Class
Align
An alignment of sequences.
Include Headers
seqan/align.h
Parameters
Type of the ungapped sequences. Metafunctions: Source | |
The specializing type. Metafunctions: Spec |
Remarks
The default implementation of Align stores the alignment in a set of TSpec> objects.
Hence, the default implementation is row-based, so it will be faster to access the alignment row-wise than column-wise.
Metafunctions
| Type of a column in an alignment. | |
| Type of column container of an alignment. | |
| Type of column container of an alignment. | |
| Type for reading values. | |
| Reference type. | |
| Type of a row in an alignment. | |
| Type of row container of an alignment. | |
| Type of row container of an alignment. | |
| The underlying sequence for alignments or gaps data structures. | |
| Type of the items in the container. |
Functions
| Calculates a banded alignment around a Seed. | |
| Calculates a banded alignment around a chain of seeds. | |
| A column in an alignment. | |
| The container of columns in an alignment. | |
| Makes an object independent from other objects. | |
| Turns a HSP from a Blast search into an Alignment object. | |
| Constructs a alignment from a ChainedSeed. | |
| Computes the best global alignment of the two sequences. | |
| Integrates an alignment into another by copying the gaps. | |
| Integrates an alignment into another by copying the gaps. | |
| 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. | |
| A row in an alignment. | |
| The container of rows in an alignment. | |
| Loads the sequences of a stringset into an alignment. | |
| Gets the string set of an alignment graph. |
Example Programs
See Also
SeqAn - Sequence Analysis Library - www.seqan.de