The following implementations of Weeder are available for download, under the GNU GENERAL PUBLIC LICENSE (GPL) Version 3.

Unix/Linux/Cygwin Source Code (NEW: version 1.4.2)
Weeder 1.4.2 can process very large sequence sets (i.e. coming from genome-wide ChIP experiments)
In version 1.4.2 we fixed a bug that caused inconsistent output in case of motifs with a large number (more than 64K) of occurrences.
Manual and installation instructions (also included in the package)

Windows Executable Files (still version 1.3, can process up to 5000 sequences)
Important: the Windows version has to be run from a MS/DOS prompt (Run->Cmd)
Important (2): to run the Windows executables, keep the cygwin dll file in the same directory of the executables.