diff --git a/PTL2/Scripts/phylotol.py b/PTL2/Scripts/phylotol.py
index bea7f50..e54a159 100644
--- a/PTL2/Scripts/phylotol.py
+++ b/PTL2/Scripts/phylotol.py
@@ -1,6 +1,5 @@
 #!/usr/bin/python3
 import os, sys, re
-import contamination
 import utils
 import preguidance
 import guidance
@@ -28,10 +27,6 @@ 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)