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SeqAn - The Library for Sequence Analysis

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SeqAn3 is out and hosted in a different repository
We recommend using SeqAn3 for new applications.

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 permissive 3-clause BSD License. The licenses for the applications themselves can be found in the LICENSE files.


Older compiler versions might work but are neither supported nor tested.

Linux, macOS, FreeBSD

  • GCC ≥ 11
  • Clang/LLVM ≥ 15
  • Intel oneAPI C++ Compiler 2024.0.2 (IntelLLVM)


  • Visual C++ ≥ 17.0 / Visual Studio ≥ 2022

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.

Build system

  • To build tests, demos, and official SeqAn applications you also need CMake ≥ 3.12.

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

Documentation Resources