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.
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
2 Contents of this Documentation
OverviewAn introduction to the basic techniques of SeqAn and tutorials to the parts of the library. Here you can also find the glossary.
ConceptsThe ontology of the generic interfaces used in SeqAn.
ClassesThe data structures, most of them are class templates (some of these templates have specializations).
SpecializationsSpecializations of class templates using Template Subclassing.
ShortcutsAbreviations for often used types, i.e. classes and specializations.
FunctionsGlobal functions that work on data structures.
MetafunctionsMetafunctions that are used to determine depending types or constants depending on given types or constants at compile time.
TagsSpecial types that are used as switches when passed to functions.
AdaptionBuilt-in types and classes of other libraries that can be accessed the same way as SeqAn datastructures.
ExamplesSmall programs that demonstrates the application of SeqAn functionality.
3 Concepts and Tutorials
InstallationInstallation of SeqAn and compiling example programs.
SequencesSequences in SeqAn.
AlignmentsHow to align sequences and how to manage alignments.
FilesFile Input/Output.
GraphsGraphs in SeqAn.
IndicesSubstring indices in SeqAn.
ModifiersModifiers give a different view to other classes.
Motif SearchFinding motifs in SeqAn.
ScoringScoring schemes used for alignments and approximative search.
SearchingSearching in SeqAn.
MetafunctionsMetafunctions are used for getting types and constants at compile time.
Template SubclassingTemplate subclassing is used in SeqAn as a generic alternative for class inheritance.
GlossaryList of terms used in SeqAn
SeqAn - Sequence Analysis Library -