Example Program
Local Alignments
Computing local alignments between two sequences.
File "alignment_local.cpp"
1#include <iostream>
2#include <seqan/align.h>
3#include <seqan/graph.h>
4
5using namespace std;
6using namespace seqan;
7
8int main()
9{
This program computes the best local alignment between two given sequences.
10    Align< String<char> > ali;
11    appendValue(rows(ali), "aphilologicaltheorem");
12    appendValue(rows(ali), "bizarreamphibology");
13    cout << "Score = " << localAlignment(ali, Score<int>(3,-3,-2), SmithWaterman()) << endl;
14    cout << ali;
15
16    return 0;
17}
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