Clover (DISABLED - will be removed on 12/22/17)

Note: Due to lack of use, this software module has been disabled and will be removed from MSI systems on 12/22/17. If you need this software, please contact


Clover is a program for identifying functional sites in DNA sequences. For a set of DNA sequences that share a common function, it will compare them to a library of sequence motifs (e.g. transcription factor binding patterns), and identify which if any of the motifs are statistically overrepresented in the sequence set.

To run this software in a Linux environment run the commands:
module load clover
Clover requires two input files: one containing DNA sequencesin FASTA format and the other sequence motifs.  Several options for sequence motifs exist.  One is JASPAR, a database of transcription factor binding site patterns.  A commercial database, TRANSFAC, is also available.  More information on using these database, including converting formats, is available on the Clover homepage.
An example of running clover is given below:
clover -t 0.05 mymotifs myseqs.fa background1.fa background2.fa
To view available options for Clover, use the following command:
clover -h
Further documentation may be found at the Clover homepage.
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