SeqAn3 API Documentation

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.

Getting Started

1. Install SeqAn

It’s as easy as following the installation instructions.

2. Learn SeqAn

The SeqAn Tutorials in the SeqAn Manual will introduce you into SeqAn’s basic concepts and show you how to use its data structures and functions.

3. Think SeqAn

(Since our library uses advanced C++ template programming techniques, we recommend you to read our glossary of language entity types for a quick introduction.)

4. Use SeqAn

(Search the library for classes, functions, etc. using the search bar to the left. Need some orientation? Check the typical tasks below.)

Typical Tasks

If you know what you want to do but not how to achieve this with SeqAn, this sections gives you a nice overview of the components that might help you.

Alternatively you might want to check the SeqAn Tutorials.

File I/O

SeqAn has support for most common file formats in Bioinformatics. The following lists the most convenient access methods.

Sequence Alignment

Sequence alignment and multiple sequence alignment are classic problems in Bioinformatics.

Graph

Often, graphs come in handy to model subproblems in sequence analysis. SeqAn provides basic support for graphs and graph algorithms.