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Contents

Part I Background
1 Sequence Analysis .......................................................... 3
2 The SeqAn Library (Versions 1 and 2) ................................... 7
3 Modern C++ ................................................................. 33
Part II SeqAn3
4 The Design of SeqAn3...................................................... 89
5 Library Structure and Small Modules ................................... 125
6 The Alphabet Module ...................................................... 145
7 The Range Module ......................................................... 187
8 The Input/Output Module ................................................. 219
9 The Search Module ......................................................... 243
10 The Alignment Module .................................................... 271
Part III Lambda
11 Lambda: An Application Built with SeqAn ............................. 299
Part IV Conclusion and Appendix
12 Conclusion................................................................... 321
Appendix A ....................................................................... 325
References......................................................................... 339

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