diff --git a/snipit/scripts/snp_functions.py b/snipit/scripts/snp_functions.py
index 99fc5bc..bb9e6cc 100644
--- a/snipit/scripts/snp_functions.py
+++ b/snipit/scripts/snp_functions.py
@@ -261,7 +261,14 @@ def find_snps(reference_seq,input_seqs,show_indels):
 
     return snp_dict,record_snps,len(var_counter)
 
-def find_ambiguities(alignment, snp_dict):
+def find_ambiguities(alignment,snp_dict,sequence_type):
+
+
+    if sequence_type == "nt":
+        amb = NT_AMBIG
+    if sequence_type == "aa":
+        amb = AA_AMBIG
+
 
     snp_sites = collections.defaultdict(list)
     for seq in snp_dict: