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