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TwitterWelcome to SeqAn
What is SeqAn?
SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.
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| Programming Language: | ISO C++ |
| Supported Platforms: | Windows: Visual C++ 8 (.net 2005), Visual C++ 9 (.net 2008), Visual C++ 10 (2010, SP1 recommended), MinGW Linux, Mac OS X: G++ 4.x, LLVM |
| License: | BSD (3-clause) |
| For details about SeqAn you can refer to the SeqAn book from CRC Press which is for example available from Amazon. Please use our mailing list and Trac for questions or bug reports. |  |
News
05.12.2011
SeqAn Trac Moved
The SeqAn Trac instance has moved to http://trac.seqan.de. Please update your bookmarks!
SeqAn Workshop 2011
This year's SeqAn workshop will take place in the Week from September 12-16, 2011. There will be overview talks about recent and future developments, tutorials for new and advanced users, presentations on the integration of SeqAn into workflow engines such as KNIME, and plans about parallelization of SeqAn, with a presentation of Convey Computers.
Also, there will be discussions on user's wishes for future development, user talks on case studies. Furthermore, there will be breakout sessions for ongoing projects, most notably the DFG SPP 1307 "Algorithm Engineering" and (most likely) the BMBF VIP project "BioStore".
Up-to-date information can be found on the Workshop Website.
Please drop a short line to 
Sabrina Krakau about how many people of your group might come. This is for planning purposes and does not imply any commitment from your side.
15.04.2011
Seqan Subversion Repository Restructured
We cleaned up the repository structure: It is now easier to understand, and more in line with traditional C/C++ project structures. Furthermore, the new structure separates core components, extra components, and personal/group work areas ("sandboxes").
Detailed information can be found in the Trac Wiki.
08.02.2011
SeqAn Version 1.3 RC1 is replaced by 1.3
The SeqAn team finished the last changes in the 1.3 RC1 version of SeqAn.
The downloadable file has been replaced by version 1.3.
21.12.2010
New version 1.3 RC1 released
We just released a new version 1.3 RC1 of SeqAn. You can download it here. What's new in this release:
- Functionality
- Development support
- New test system. Templates for applications and tests are available.
- Harmonized naming conventions.
- Documentation and Distribution
- Added a new WIKI based tutorial.
- The documentation can now be built in less than one minute.
- Nightly builds and Hourly documentation builds are available.
- Changed license to 3-clause BSD license.
Have a look at the ChangeLog for a comprehensive list of new features.
20.12.2010
Illumina's Casava pipeline uses SeqAn
The SeqAn team has intensified the collaboration with Illumina and is happy to announce that Illumina's latest Casava software uses SeqAn functionality.
26.08.2010
SeqAn retreat 2010
The 2nd SeqAn retreat will take place in Berlin from October 4th to October 10th 2010.
Get an introduction to SeqAn or discuss and try ideas hands-on in the field of genomic sequence analysis.
For more information please download the program or see the retreat wiki.
19.11.2009
The SeqAn book has appeared
For more information please visit the CRC Press website.
15.09.2009
New Version 1.2 released
We just released a new version 1.2 of SeqAn. You can download it here. What's new in this release:
- 5 more applications, i.e. DFI, MicroRazerS, PairAlign, SeqCons, TreeRecon
- stable release of RazerS supporting paired-end read mapping and configurable sensitivity
- new alignment algorithms, e.g. banded, configurable alignments (overlap, semi-global, ...)
- realignment algorithm
- NGS data structures and formats, e.g. SAM, Amos, ...
- new alphabets, e.g. Dna with base call qualities, profile characters
- auxiliary data structures and algorithms, e.g. double ended queue, command line parser
- positional scores
- CMake support
11.06.2009
Trac and SVN moved
Due to restrictions of our Webserver we were enforced to move Trac and SVN to a seperate server. The new URLs are:
| Trac | |
| SVN |
If you work with a repository that you have checked out before the move, you can switch to the new server with:
svn switch --relocate https://www.seqan.de/svn https://svn.mi.fu-berlin.de/seqan
or if you don't have an account at the Free University Berlin:
svn switch --relocate www.seqan.de/svn svn.mi.fu-berlin.de/seqan
11.06.2009
SeqAn mailing list
We created a mailing list seqan-dev for SeqAn specific or users-help-users discussions. Send e-mail to seqan-dev
lists.fu-berlin.de.
08.06.2008
New Version 1.1 released
We just released a new version 1.1 of SeqAn. You can download it here.
15.02.2008
SeqAn Trac online
We now offer a bug tracking system. Following the Development link, you can
- Watch the list of changes of SeqAn under "Timeline".
- Watch our future plans and milestones under "Roadmap".
- Browse the current SeqAn source as well as the source of former snapshots and releases under "Browse Source".
- Report a bug and track it until the bug is fixed under "View Tickets" and "New Ticket"
Enjoy!
09.01.2008
SeqAn paper published
The official SeqAn paper was published in the BMC Bioinformatics journal:
A. Döring, D. Weese, T. Rausch, and K. Reinert, SeqAn - An efficient, generic C++ library for sequence analysis, BMC Bioinformatics 2008, 9:11
In this paper we describe the design and content of SeqAn and demonstrate its use by giving two examples.
21.12.2007
SeqAn released
We released the version 1.0 of our sequence library. See this tutorial page for installation instructions.
