diff --git a/PTL2/Scripts/phylotol.py b/PTL2/Scripts/phylotol.py
index e54a159..bea7f50 100644
--- a/PTL2/Scripts/phylotol.py
+++ b/PTL2/Scripts/phylotol.py
@@ -1,5 +1,6 @@
 #!/usr/bin/python3
 import os, sys, re
+import contamination
 import utils
 import preguidance
 import guidance
@@ -27,6 +28,10 @@ if __name__ == '__main__':
 		print('\nBuilding trees\n')
 		trees.run(params)
 
+	if params.contamination_loop != None:
+		print('\nRunning contamination loop\n')
+		contamination.run(params)
+
 	if params.concatenate:
 		print('\nChoosing orthologs and concatenating alignments...\n')
 		concatenate.run(params)