An alignment of sequences.
Align<TSource, TSpec>
Type of the ungapped sequences.
Metafunctions: Source
The specializing type.
Metafunctions: Spec
ColType of a column in an alignment.
ColsType of column container of an alignment.
GetValueType for reading values.
ReferenceReference type.
RowType of a row in an alignment.
RowsType of row container of an alignment.
SourceThe underlying sequence for alignments or gaps data structures.
ValueType of the items in the container.
bandedAlignmentCalculates a banded alignment around a Seed.
bandedChainAlignment Calculates a banded alignment around a chain of seeds.
colA column in an alignment.
colsThe container of columns in an alignment.
detachMakes an object independent from other objects.
getAlignment Constructs a alignment from a ChainedSeed.
globalAlignmentComputes the best global alignment of the two sequences.
rowA row in an alignment.
rowsThe container of rows in an alignment.
setStringsLoads the sequences of a stringset into an alignment.
smithWatermanComputes the best local alignment of the (two) sequences given in align.
smithWatermanGetNextComputes next best local alignment.
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.
See Also
SeqAn - Sequence Analysis Library -