An example of motifs and a motif file
An example of a set system file
An example of aligned sequences and files
You can use the above files in order to run PhylCRM and Lever.
DEMO:
First, you should run PhylCRM_preprocess:
phylcrm_preprocess_1.1 -T HCMMRDCMC.tree -O ./runs/ -S ./wasserman_background_small/ -M 4muscle_1sd.txt -W 1000
The output of this run is here. The counts1 file shows the genomic frequency of the letters A,C,G,T.
Then, you can run PhylCRM:
phylcrm_1.1 -T HCMMRDCMC.tree -O ./runs/ -N demo -S ./wasserman_background_small/ -M 4muscle_1sd.txt -W 1000 50 -AND -BG ./runs/motif_locations.txt
Alos, you can run Lever:
lever_1.1 -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 -LP -BG ./runs/motif_locations.txt -ID set_systems.txt -statistics