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Short description:
Please summarise the application in a few sentences. Avoid links here. C++ template library with many sequence analysis algorithms and datastructures.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Sequence analysis, Genomics, Phylogenetics
Principal bioinformatics method(s) (Assembly, Mapping, ...):
,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Sanger, Illumina, 454
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
Free University of Berlin
== Description == SeqAn is a C++ template library of efficient biological sequence analysis data structures and algorithms. The main aims are performance, extensibility, ease of use, and portability. It is the basis for the tools of the Reinert lab at Free University of Berlin. Illumina's latest Casava software uses SeqAn functionality. Contents include: * Various efficient string representation and alphabets. * Index datastructures (e.g. q-gram index, extended suffix arrays) and algorithms for them. * Online string search algorithms. * String filter algorithms (SWIFT, Quasar). * Graph data structures and algorithms. * Efficient implementations of alignment data structures and algorithms. * Data structure for the efficient handling of NGS data and annotations (FragmentStore). * Random number generation. == Supported Compilers == * GCC 4.x * LLVM (current trunk) * Visual Studio 2005, 2008, 2010 == Additional Links == * [https://trac.mi.fu-berlin.de/seqan/wiki/Tutorial SeqAn Tutorial (start here)] * [http://www.seqan.de/dddoc/html_devel/index.html Nightly API documentation] * [http://www.seqan.de/dddoc/html/index.html Release API documentation] * [https://trac.mi.fu-berlin.de/seqan/wiki/HowTo SeqAn How To] * [https://trac.mi.fu-berlin.de/seqan/ SeqAn Trac Wiki]
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