Here you can find the programs related to motif finding in INCLUSive as stand-alone executables.

If you have any questions or remarks, please do not hesitate to contact me.

If you like to be informed on updates and new versions of our programs, you should join our INCLUSive mailing list.

If you publish results which you obtained with our software, you can show your appreciation by citing one of our papers:

• Thijs G., Lescot M., Marchal K., Rombauts S., De Moor B., Rouzé P., Moreau Y., 2001. A higher order background model improves the detection of regulatory elements by Gibbs Sampling, Bioinformatics, 17(12),1113-1122.
• Thijs G., Marchal K., Lescot M., Rombauts S., De Moor B., Rouzé P., Moreau Y., 2002. A Gibbs Sampling method to detect over-represented motifs in upstream regions of coexpressed genes, Journal of Computational Biology (special issue Recomb'2001), 9(2), 447-464.
• Thijs G., Moreau Y., De Smet F., Mathys J., Lescot M., Rombauts S., Rouzé P., De Moor B., Marchal K., 2002. INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling, Bioinformatics, 18(2), 331-332.

Linux executables version 3.2 are statically linked against libstdc++6. Normally, they should run on any linux distribution. There are also optimise3d 64bit executables available.
To install the executables you should save them on your local disk, best in a directory that is in your path, and you probably also need to set the mode to executable (eg. chmod 755 MotifSampler).
Windows executables are compiled from C++ code with MingW compiler tools and should be run in a command prompt.
MACOSX executables are compiled for power pc under version 10.4.4 of the os.
Warning! You can savely neglect the 'free invalid pointer' messages. They are inserted by the improved compiler and just tell me to fix these memory leaks.

Program	Description	Version
MotifSampler	Program to find over-represented motifs in sets of sequences	3.2 Linux	help
		3.2 Linux x86-64
		3.2 macosx ppc
		3.1.1 Windows
MotifScanner	Screen sequences with known motif using probabilistic sequence model.	3.2 Linux	help
		3.2 Linux x86-64
		3.2 macosx ppc
		3.1.1 Windows
MotifLocator	Screen sequences with known motif based on classical position-weight matrix scoring scheme	3.2 Linux	help
		3.2 Linux x86-64
		3.2 macosx ppc
		3.1.1 Windows
CreateBackgroundModel	Tool to create higher-order background model from input sequences	3.2 Linux	help
		3.2 Linux x86-64
		3.2 macosx ppc
		3.1.1 Windows
BackgroundScore	Tool to score sequence with the background model.	3.2 Linux	help
		3.2 Linux x86-64
		3.2 macosx ppc
		3.1.1 Windows
MotifComparison	Tool to compare motifs based on Kullback-Leiber distance.	3.2 Linux	help
		3.2 Linux x86-64
		3.2 macosx ppc
		3.1.1 Windows
MotifRanking	Tool to rank the motifs found with MotifSampler according to their score.	3.2 Linux	help
		3.2 Linux x86-64
		3.2 macosx ppc
		3.1.1 Windows

• Background models.