### Download and make your own ReadyToGo_AA_GC3_labelled folder with ReadyToGo files
### Update the taxa list with the taxa files in your ReadyToGo folder
### Download the Script folder
### than run :

python3 Scripts/phylotol.py --start raw --end trees --gf_list list_ogs.txt --taxon_list taxa_list.txt --data ReadyToGo_AA_GC3_labelled --output Output --similarity_filter --sim_cutoff 0.95 --og_identifier OG6 --tree_method iqtree > log1.out