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.
String Basics	Basic string class handling.

Graph

Breadth-First Search	Breadth-first search through a graph.
Depth-First Search	Depth-first search through a graph.
Strongly Connected Components	Computing all strongly-connected-components of a graph.
Topological Sort	Topological sort of a graph.
Needleman-Wunsch Algorithm	Needleman-Wunsch alignment code example
Gotohs Algorithm	Gotoh alignment code example
Hirschbergs Algorithm	Hirschberg with Gotoh alignment code example
Smith-Waterman Algorithm	Smith-Waterman local alignment code example.
All Pairs Shortest Path	Computing all-pairs shortest paths.
Floyd-Warshall Algorithm	Computing all-pairs shortest paths using Floyd-Warshall algorithm.
Heuristic Matching	Path-growing code example
Maximum Flow	Ford-Fulkerson maximum flow code example
Kruskals Algorithm	Kruskal's algorithm for computing a minimum spanning tree.
Prims Algorithm	Prim's algorithm for computing a minimum spanning tree.
MSA with Neighbor-Joining	Progressive multiple sequence alignment using neighbor joining for building the guide tree.
MSA with UPGMA	Progressive multiple sequence alignment using UPGMA for building the guide tree
T-Coffee	T-Coffee code example
Longest Increasing Subsequence	Longest increasing subsequence code example
Heaviest Increasing Subsequence	Heaviest increasing subsequence code example
Longest Common Subsequence	Longest common subsequence code example
Bellman-Ford Algorithm	Computing single source shortest paths using Bellman-Ford algorithm.
Shortest Path in DAGs	Computing single source shortest paths in a directed acyclic graph.
Dijkstras Algorithm	Computing single source shortest paths using Dijkstra algorithm.
Transitive Closure	Transitive closure code example

Index

Index Finder	Example for using a Finder of an Index.
Index Finder StringSet	Example for using a Finder of an Index of a StringSet.
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.

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.

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