| SeqAn - The Library for Sequence Analysis - Documentation SeqAn is the open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. SeqAn 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.
Contents 1 Getting Started 2 Contents of this Documentation 3 Concepts and Tutorials 1 Getting Started Follow the installation instructions to install SeqAn on your system. A good starting point for learning more about SeqAn is to read the tutorials, which are listed at the end of this page. This will introduce you into the basic concepts of the library and give you an overview about the content of the library. Refer to the glossary if you encounter questionable terminology. The collection of example programs demonstrate how to use the data structures and functions offered by SeqAn. Find instructions for the installation of the library and how to use the example programs here. For more information about SeqAn visit the SeqAn homepage www.seqan.de. 2 Contents of this Documentation
Overview | An introduction to the basic techniques of SeqAn and tutorials to the parts of the library. Here you can also find the glossary.
Concepts | The ontology of the generic interfaces used in SeqAn.
Classes | The data structures, most of them are class templates (some of these templates have specializations).
Specializations | Specializations of class templates using Template Subclassing.
Shortcuts | Abreviations for often used types, i.e. classes and specializations.
Functions | Global functions that work on data structures.
Metafunctions | Metafunctions that are used to determine depending types or constants depending on given types or constants at compile time.
Tags | Special types that are used as switches when passed to functions.
Adaption | Built-in types and classes of other libraries that can be accessed the same way as SeqAn datastructures.
Examples | Small programs that demonstrates the application of SeqAn functionality.
3 Concepts and Tutorials Overview
Installation | Installation of SeqAn and compiling example programs.
Sequences | Sequences in SeqAn.
Alignments | How to align sequences and managing alignments.
Files | File Input/Output.
Graphs | Graphs in SeqAn.
Indices | Substring indices in SeqAn.
Modifiers | Modifiers give a different view to other classes.
Motif Search | Finding motifs in SeqAn.
Scoring | Scoring schemes used for alignments and approximative search.
Searching | Searching in SeqAn.
Metafunctions | Metafunctions are used for getting types and constants at compile time.
Template Subclassing | Template subclassing is used in SeqAn as a generic alternative for class inheritance.
Glossary | List of terms used in SeqAn
SeqAn - Sequence Analysis Library - www.seqan.de