diff --git a/augur/align.py b/augur/align.py
index 4c7d5d99c..6f15228ed 100644
--- a/augur/align.py
+++ b/augur/align.py
@@ -196,7 +196,7 @@ def read_sequences(*fnames):
     seqs = {}
     try:
         for fname in fnames:
-            for record in SeqIO.parse(fname, 'fasta'):
+            for record in SeqIO.parse(fname, 'fasta-pearson'):
                 if record.name in seqs and record.seq != seqs[record.name].seq:
                     raise AlignmentError("Detected duplicate input strains \"%s\" but the sequences are different." % record.name)
                     # if the same sequence then we can proceed (and we only take one)
@@ -240,7 +240,7 @@ def read_reference(ref_fname):
         raise AlignmentError("ERROR: Cannot read reference sequence."
                              "\n\tmake sure the file \"%s\" exists"%ref_fname)
     try:
-        ref_seq = SeqIO.read(ref_fname, 'genbank' if ref_fname.split('.')[-1] in ['gb', 'genbank'] else 'fasta')
+        ref_seq = SeqIO.read(ref_fname, 'genbank' if ref_fname.split('.')[-1] in ['gb', 'genbank'] else 'fasta-pearson')
     except:
         raise AlignmentError("ERROR: Cannot read reference sequence."
                 "\n\tmake sure the file %s contains one sequence in genbank or fasta format"%ref_fname)
diff --git a/augur/ancestral.py b/augur/ancestral.py
index aa4f805f4..0cb3e9929 100644
--- a/augur/ancestral.py
+++ b/augur/ancestral.py
@@ -398,7 +398,7 @@ def run(args):
         aln = args.alignment
         ref = None
         if args.root_sequence:
-            for fmt in ['fasta', 'genbank']:
+            for fmt in ['fasta-pearson', 'genbank']:
                 try:
                     ref = str(SeqIO.read(args.root_sequence, fmt).seq).upper()
                     break
diff --git a/augur/reconstruct_sequences.py b/augur/reconstruct_sequences.py
index 478801855..acc11e348 100644
--- a/augur/reconstruct_sequences.py
+++ b/augur/reconstruct_sequences.py
@@ -73,7 +73,7 @@ def run(args):
     if(is_vcf):
         node_data["nodes"][root_node]['aa_sequences'] = {}
         with open_file(args.vcf_aa_reference) as handle:
-            for record in SeqIO.parse(handle, "fasta"):
+            for record in SeqIO.parse(handle, "fasta-pearson"):
                 if record.id==args.gene:
                     #'root' may not be same as 'reference', so apply any mutations at root here!
                     node_data["nodes"][root_node]['aa_sequences'][record.id] = get_sequence(str(record.seq), node_data["nodes"][root_node]["aa_muts"][record.id])
diff --git a/augur/sequence_traits.py b/augur/sequence_traits.py
index 1d09ac6b2..1fa2ef5e1 100644
--- a/augur/sequence_traits.py
+++ b/augur/sequence_traits.py
@@ -91,7 +91,7 @@ def mutation_struct():
                 samps = header[sampLoc:]
                 nsamp = len(samps)
 
-    for refSeq in SeqIO.parse(ref_file, format='fasta'):
+    for refSeq in SeqIO.parse(ref_file, format='fasta-pearson'):
         prots[refSeq.name]['reference'] = str(refSeq.seq)
         posN = np.unique(prots[refSeq.name]['positions'])
         prots[refSeq.name]['positions'] = list(posN)