This section contains small example programs that demonstrate the use of SeqAn. See here for instructions how to compile these examples.
Global AlignmentsComputing an optimal global alignment between two sequences.
Local AlignmentsComputing local alignments between two sequences.
AllocatorsExamples for memory allocation.
AlphabetsExamples for common alphabets.
Iterator BasicsSimple iterator functions.
Rooted IteratorsExample for some functions for handling (rooted) iterators.
String BasicsBasic string class handling.
Breadth-First SearchBreadth-first search through a graph.
Depth-First Search Depth-first search through a graph.
Strongly Connected ComponentsComputing all strongly-connected-components of a graph.
Topological SortTopological sort of a graph.
Needleman-Wunsch AlgorithmNeedleman-Wunsch alignment code example
Gotohs AlgorithmGotoh alignment code example
Hirschbergs AlgorithmHirschberg with Gotoh alignment code example
Smith-Waterman AlgorithmSmith-Waterman local alignment code example.
All Pairs Shortest PathComputing all-pairs shortest paths.
Floyd-Warshall AlgorithmComputing all-pairs shortest paths using Floyd-Warshall algorithm.
Maximum FlowFord-Fulkerson maximum flow code example
Kruskals AlgorithmKruskal's algorithm for computing a minimum spanning tree.
Prims AlgorithmPrim's algorithm for computing a minimum spanning tree.
T-CoffeeT-Coffee code example
Longest Increasing SubsequenceLongest increasing subsequence code example
Heaviest Increasing SubsequenceHeaviest increasing subsequence code example
Longest Common SubsequenceLongest common subsequence code example
Bellman-Ford AlgorithmComputing single source shortest paths using Bellman-Ford algorithm.
Shortest Path in DAGsComputing single source shortest paths in a directed acyclic graph.
Dijkstras AlgorithmComputing single source shortest paths using Dijkstra algorithm.
Transitive ClosureTransitive closure code example
Constraint IteratorExample for using node predicates on a deferred suffix tree.
Index FinderExample for using a Finder of an Index.
Index Finder StringSetExample for using a Finder of an Index of a StringSet.
Maximal RepeatsExample for using the MaxRepeats Iterator.
Maximal Unique MatchesExample for using the MUMs Iterator.
MummySimple MUMmer clone.
Pizza & Chili IndexUsing a Pizza & Chili Index for searching and the Pizza & Chili String for displaying.
Suffix ArrayExample for how to create a suffix array and use it as a dictionary.
Supermaximal RepeatsExample for using the SuperMaxRepeats Iterator.
Blast ReportsParsing the output of BLAST call.
ModReverseModifier example for reverse strings.
ModViewHow to modify strings with a per-character functor.
Nested ModifiersHow to combine modifiers.
Motif Search
Motif FinderExamples for how to start a motif search using SeqAn's Motif Finder.
Exact SearchingExact string matching.
Approximate SearchingApproximate string matching.
Wildcard SearchingString matching using wildcards.
File Format I/OAccessing sequence data in files.
SeqAn - Sequence Analysis Library - www.seqan.de