Folded k-spectrum kernel: https://github.com/elmasee/folks
(Reference: Elmas A, Wang X, Dresch JM (2017) The folded k-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies. PLoS ONE 12(10): e0185570.)
Thermodynamic-based Model: https://github.com/arnosti-lab
(Reference: *Sayal R, *Dresch JM, Pushel I, Taylor BR, Arnosti DN (2016) Quantitative perturbation-based analysis of gene expression in early Drosophila embryo. eLife 5:e08445 (* – equal contribution))
MARZ algorithm: marzscaled
(Reference: Zellers RG, Drewell RA, Dresch JM (2015) MARZ: An algorithm to combinatorially analyze gapped n-mer models of transcription factor binding. BMC Bioinformatics. 16: 30.)
Any questions regarding software should be directed to Jacqueline Dresch at jdresch@clarku.edu.