From f9c3e198d0f6d474a7f701941268b29d3996555e Mon Sep 17 00:00:00 2001
From: Richard Neher <richard.neher@unibas.ch>
Date: Tue, 26 Sep 2023 17:05:35 +0200
Subject: [PATCH] fix: upper case root sequence for ancestral reconstruction

---
 augur/ancestral.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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