Examples
This section contains small example programs that demonstrate the use of SeqAn. See here for instructions how to compile these examples.
Basics

Global Alignments | Computing an optimal global alignment between two sequences.
Local Alignments | Computing local alignments between two sequences.
Allocators | Examples for memory allocation.
Alphabets | Examples for common alphabets.
Iterator Basics | Simple iterator functions.
Rooted Iterators | Example for some functions for handling (rooted) iterators.

Index

Constraint Iterator | Example for using node predicates on a deferred suffix tree.
Index Finder | Example for using a Finder of an Index.
Index Finder StringSet | Example for using a Finder of an Index of a StringSet.
Index countChildren | Example for using a countChildren and countOccurrences for indices.
Index countOccurrencesMultiple | Example for using the functions countOccurrencesMultiple and countSequences for q-gram indices.
Index lcpAt, saAt | Example for using the functions saAt and lcpAt for esa indices.
Maximal Repeats | Example for using the MaxRepeats Iterator.
Maximal Unique Matches | Example for using the Mums Iterator.
Mummy | Simple MUMmer clone.
Suffix Array | Example for how to create a suffix array and use it as a dictionary.
Supermaximal Repeats | Example for using the SuperMaxRepeats Iterator.

Miscellaneous

Interval Tree | Construction and usage demo for the interval tree.

Modifier

ModReverse | Modifier example for reverse strings.
ModView | How to modify strings with a per-character functor.
Nested Modifiers | How to combine modifiers.

Motif Search

Motif Finder | Examples for how to start a motif search using SeqAn's Motif Finder.

Searching

Exact Searching | Exact string matching.
Approximate Searching | Approximate string matching.
Wildcard Searching | String matching using wildcards.

System

File Format I/O | Accessing sequence data in files.

SeqAn - Sequence Analysis Library - www.seqan.de

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