diff --git a/PTL2/Examplar_runs/Running_CLoop/Sisters/run_phylotol_command_line.txt b/PTL2/Examplar_runs/Running_CLoop/Sisters/run_phylotol_command_line.txt
new file mode 100644
index 0000000..457d3ac
--- /dev/null
+++ b/PTL2/Examplar_runs/Running_CLoop/Sisters/run_phylotol_command_line.txt
@@ -0,0 +1,4 @@
+### Download the Script folder
+### than run :
+
+python3 Scripts/phylotol.py --force --start trees --end trees --data Input --output Output --contamination_loop seq --sister_rules sister_rules.txt --cl_tree_method iqtree_fast > log.out