diff --git a/PhyloToL-Part-2.md b/PhyloToL-Part-2.md
index ea476bb..34b4429 100644
--- a/PhyloToL-Part-2.md
+++ b/PhyloToL-Part-2.md
@@ -26,6 +26,13 @@ You will also need to create a 'rules' file. The format here varies between the
 
 ## Running
 
+To run the CL, use a similar command structure as described for running PhyloToL part 2 above, and add the `--contamination_loop` parameter to activate the contamination loop and specify a mode and the path to a rules file. Available parameters are:
+
+| Parameter  | required | Options | Description | default |
+| ------------- | ------------- | ------------- | ------------- | ------------- |
+| --contamination_loop  | yes | seq, clade | The mode in which to run the loop | none |
+| --nloops  | no | _int_ | Number of iterations | 5 |
+