Code for PhyME motif scanning software. PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences S Sinha, M Blanchette, M Tompa BMC bioinformatics 5 (1), 170 https://link.springer.com/article/10.1186/1471-2105-5-170

To use the PhyME 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.