diff --git a/augur/ancestral.py b/augur/ancestral.py
index 64b25d6fe..af88335a0 100644
--- a/augur/ancestral.py
+++ b/augur/ancestral.py
@@ -268,7 +268,7 @@ def run(args):
         if args.root_sequence:
             for fmt in ['fasta', 'genbank']:
                 try:
-                    ref = str(SeqIO.read(args.root_sequence, fmt).seq)
+                    ref = str(SeqIO.read(args.root_sequence, fmt).seq).upper()
                     break
                 except:
                     pass