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//![main]
#include <iostream>
#include <seqan/align.h>
using namespace seqan;
int main()
{
typedef String<char> TSequence; // sequence type
typedef StringSet<TSequence> TStringSet; // container for strings
typedef StringSet<TSequence, Dependent<> > TDepStringSet; // dependent string set
typedef Graph<Alignment<TDepStringSet> > TAlignGraph; // alignment graph
//![main]
//![init]
TSequence seq1 = "blablubalu";
TSequence seq2 = "abba";
TStringSet sequences;
appendValue(sequences, seq1);
appendValue(sequences, seq2);
TAlignGraph alignG(sequences);
//![init]
//![alignment]
int score = globalAlignment(alignG, Score<int, Simple>(1, -1, -1), AlignConfig<true, true, true, true>(), LinearGaps());
std::cout << "Score: " << score << std::endl;
std::cout << alignG << std::endl;
return 0;
}
//![alignment]
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