You can use the following files to run PhylCRM_preprocess (to generate the motif statistics) followed by Lever_2.0:
An example of motifs and a motif file
An example of a set system file
An example of aligned sequences and files
An example of a file containing foreground (FG) gene sets
DEMO:
1) First, run PhylCRM_preprocess (to generate the motif statistics):
phylcrm_preprocess_1.1 -T HCMMRDCMC.tree -O ./runs/ -S ./wasserman_background_small/ -M 4muscle_1sd.txt -F FG_sets.txt -W 1000
The output of this run is here. The counts1 file shows the genomic frequency of the letters A,C,G,T.
2) Then, run Lever_2.0:
a) With LOESS-fit length correction (note the "-LC"):
lever_2.0 -T HCMMRDCMC.tree -O ./runs/ -N demo_lever -S ./wasserman_background_small/ -M 4muscle_1sd.txt -W 1000 50 -AND 1 -OR 0 -CO 3 -BG ./runs/motif_locations.txt -ID set_systems.txt -statistics -LC
OR
b) Without LOESS-fit length correction (without the "-LC"):
lever_2.0 -T HCMMRDCMC.tree -O ./runs/ -N demo_lever -S ./wasserman_background_small/ -M 4muscle_1sd.txt -W 1000 50 -AND 1 -OR 0 -CO 3 -BG ./runs/motif_locations.txt -ID set_systems.txt -statistics