localAlignment

| Function localAlignment Computes the best local alignment of two sequences. localAlignment(align, score, tag) localAlignment(align, score) localAlignment(align, sw_finder, score, cutoff, tag) localAlignment(align, sw_finder, score, cutoff, diagLow, diagHigh, tag) localAlignment(strSet, score, tag) localAlignment(graph, score, tag) localAlignment(file, strSet, score, tag) Include Headers seqan/graph_align.h Parameters
align | Alignment object to use. Types: Align
cutoff | Alignments with scores < cutoff will be discarded.
diagLow | The lowest diagonal of the alignment matrix that will be computed for banded alignment.
diagHigh | The highest diagonal of the alignment matrix that will be computed for banded alignment.
tag | A tag indicating the alignment algorithm to use Types: BandedWatermanEggert, SmithWaterman, WatermanEggert Remarks: SmithWaterman
strSet | A string set with 2 sequences. Types: StringSet Remarks: If an alignment graph is used that graph must contain a string set with two sequences
graph | The alignment graph having 2 sequences. Types: Alignment Graph
file | A file stream or std::cout to write a textual alignment
score | The score values to be used for computing the alignment. Types: Score
Return Values The maximum score of the best local alignment. Example Programs Local Alignments See Also LocalAlignmentFinder, Local Alignment Algorithms SeqAn - Sequence Analysis Library - www.seqan.de

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