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ATTENTION: SeqAn3 is out and hosted in a different repository:
All new applications should be based on SeqAn3 and all existing applications that receive updates should be ported.

SeqAn - The Library for Sequence Analysis

What Is SeqAn?

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.


The SeqAn library itself, the tests and demos are licensed under the very permissing 3-clause BSD License. The licenses for the applications themselves can be found in the LICENSE files.


Linux, MacOS, FreeBSD:
  • GCC ≥ 5 [limited GCC-4.9 support on Linux]
  • Clang/LLVM ≥ 3.6 [limited Clang-3.5 support on Linux]
  • Intel Compiler ≥ 17.0.0 on Linux
  • Visual C++ ≥ 14.0 / Visual Studio ≥ 2015
  • Intel Compiler ≥ 17.0.0 / Visual Studio ≥ 2015u2
  • Clang/C2 ≥ 3.8.0 / Visual Studio ≥ 2015u3 [experimental, requires CMake ≥ 3.6]
Architecture support:
  • Intel/AMD platforms, including optimisations for modern instruction sets (POPCNT, SSE4, AVX2, AVX512)
  • All Debian release architectures supported, including most ARM and all PowerPC platforms.
To build tests, demos, and official SeqAn applications you also need:
  • CMake ≥ 3.0 [CMake ≥ 3.4 recommended]

Some of the official applications might have additional requirements or work only on a subset of platforms.

Documentation Resources