Stubb program for scanning DNA sequences with position weight matrix motifs. A probabilistic method to detect regulatory modules S Sinha, E Van Nimwegen, ED Siggia Bioinformatics 19 (suppl 1), i292 https://academic.oup.com/bioinformatics/article/19/suppl_1/i292/228197?login=true
To use the Stubb software, you will also need to install the LAGAN alignment toolkit: http://lagan.stanford.edu/ A copy of the LAGAN software is included in the phyme distribution. However, LAGAN comes with a separate license that must be read and agreed upon.