Examples
This section contains small example programs that demonstrate the use of SeqAn.
See here for instructions how to compile these examples.
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. |
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 a countChildren and countOccurrences for indices. | |
Example for using the functions countOccurrencesMultiple and countSequences for q-gram indices. | |
Example for using the functions saAt and lcpAt for esa indices. | |
Example for using the MaxRepeats Iterator. | |
Example for using the Mums Iterator. | |
Simple MUMmer clone. | |
Example for how to create a suffix array and use it as a dictionary. | |
Example for using the SuperMaxRepeats Iterator. |
Miscellaneous
Construction and usage demo for the interval tree. |
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