Charles, we have dropped the old build system in favour of CMake.You can find documentation on building for 1.3 here (note the ? version=27 for 1.3 instructions):
http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/GettingStarted?version=27Note that in the upcoming 1.4 version (hopefully released later this year), the exact instructions will differ and you will be able to find them here (no ?version, most current wiki page):
http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/GettingStarted HTH Manuel