The following implementation of Weeder 2.0 is available for download, under the GNU GENERAL PUBLIC LICENSE (GPL) Version 3.

Unix/Linux/MacOSX Code (version 2.0)
Weeder 2.0 can process very large sequence sets. (i.e. coming from genome-wide ChIP experiments)

The packge includes a README.txt file with installation and usage instructions. It includes also oligo frequency files for Homo sapiens, Mus musculus, Drosophila melanogaster, Arabidopsis thaliana and Saccharomyces cerevisiae.

Notice that the oligo frequency files used by previous versions of Weeder are no longer compatible with Weeder 2.0. If oligo frequencies for your organism of interest are not included in the package you can download the Weeder 2.0 frequency maker and compute them on your local machine.

To convert matrices output by Weeder 2.0 to the format used by Pscan and Pscan-ChIP use the Matrix Converter tool.

Notice also that Weeder 2.0 does not need and is not compatible with accessory scripts from previous Weeder versions like weederlauncher.out and locator.out.

NEW! Weeder 2.0 is now available also via the Galaxy Tool Shed!
We wish to kindly thank Ian Donaldson and Peter Briggs from the Bioinformatics Core Facility at University of Manchester for providing the Galaxy community with the Weeder 2.0 Galaxy repository.