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.
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.
All Pairs Shortest PathComputing all-pairs shortest paths.
Floyd-Warshall AlgorithmComputing all-pairs shortest paths using Floyd-Warshall algorithm.
HMMHidden Markov Model code example
HMM Silent StatesHidden Markov Model with silent states code example
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.
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.
Index countChildrenExample for using a countChildren and countOccurrences for indices.
Index countOccurrencesMultipleExample for using the functions countOccurrencesMultiple and countSequences for q-gram indices.
Index lcpAt, saAtExample for using the functions saAt and lcpAt for esa indices.
Maximal RepeatsExample for using the MaxRepeats Iterator.
Maximal Unique MatchesExample for using the Mums Iterator.
MummySimple MUMmer clone.
Suffix ArrayExample for how to create a suffix array and use it as a dictionary.
Supermaximal RepeatsExample for using the SuperMaxRepeats Iterator.
Interval TreeConstruction and usage demo for the interval tree.
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

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