Dear all, we have completed the restructuring and there should be no major glitches left. We moved the files, updated the source code, tutorial and documentation. Please report any problems with the update to the mailing list or in a ticket. If you have any further questions we would be more than happy to answer them! In order to circumvent problems, we recommend you to perform a clean checkout of SeqAn: svn co http://svn.mi.fu-berlin.de/seqan/trunk/seqan seqan-trunk The following should work then (assuming you are using Makefiles on Linux/Os X): $ mkdir build/Debug $ cd build/Debug $ cmake ../.. $ make test_basic $ ./core/tests/test_basic/test_basic ... the basic test will run ... We are sorry for any caused inconvenience. Kind Regards, The SeqAn Development Team