Examples

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

Examples

See our Wiki for Basic demos. |

Basics

Computing an optimal global alignment between two sequences. | |

Computing local alignments between two sequences. | |

Examples for memory allocation. | |

Examples for common alphabets. | |

Simple iterator functions. | |

Example for some functions for handling (rooted) iterators. |

Graph

Breadth-first search through a graph. | |

Depth-first search through a graph. | |

Computing all strongly-connected-components of a graph. | |

Topological sort of a graph. | |

Computing all-pairs shortest paths. | |

Computing all-pairs shortest paths using Floyd-Warshall algorithm. | |

Hidden Markov Model code example | |

Hidden Markov Model with silent states code example | |

Ford-Fulkerson maximum flow code example | |

Kruskal's algorithm for computing a minimum spanning tree. | |

Prim's algorithm for computing a minimum spanning tree. | |

Longest increasing subsequence code example | |

Heaviest increasing subsequence code example | |

Longest common subsequence code example | |

Computing single source shortest paths using Bellman-Ford algorithm. | |

Computing single source shortest paths in a directed acyclic graph. | |

Computing single source shortest paths using Dijkstra algorithm. | |

Transitive closure code example |

Index

Example for using node predicates on a deferred suffix tree. | |

Example for using a Finder of an Index. | |

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

Example for using the MaxRepeats Iterator. | |

Example for using the Mums Iterator. | |

Simple MUMmer clone. | |

Using a Pizza & Chili Index for searching and the Pizza & Chili String for displaying. | |

Example for how to create a suffix array and use it as a dictionary. | |

Example for using the SuperMaxRepeats Iterator. |

Miscellaneous

Parsing the output of BLAST call. |

Modifier

Modifier example for reverse strings. | |

How to modify strings with a per-character functor. | |

How to combine modifiers. |

Motif Search

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

Searching

Exact string matching. | |

Approximate string matching. | |

String matching using wildcards. |

System

Accessing sequence data in files. |

SeqAn - Sequence Analysis Library - www.seqan.de