| 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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