ChIPMunk
Kulakovskiy et al. Deep and wide digging for binding motifs in ChIP-Seq data . Bioinformatics, 26(20):2622-3, 2010.

MEME
T.L. Bailey and C. Elkan. Fitting a mixture model by expectation maximization to discover motifs in biopolymers . Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp.28-36, AAAI Press, Menlo Park, California, 1994.

Weeder
Pavesi et al. An algorithm for finding signals of unknown length in DNA sequences . Bioinformatics, 17:S207–S214, 2001.

XXMotif
Luehr et al. The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences . Nucleic Acids Research, 40(Web Server issue):W104-W109, 2012.

MOTIFSIM v.2.1
N.T.L. Tran and C.-H. Huang. MOTIFSIM 2.1: An Enhanced Software Platform for Detecting Similarity in Multiple DNA Motif Data Sets . Journal of Computational Biology, 24(9):895-905, 2017.

MOTIFSIM v.1.0
N.T.L. Tran and C.-H. Huang. MOTIFSIM: A Web Tool for Detecting Similarity in Multiple DNA Motif Datasets. BioTechniques, 59(1):26-33, 2015.