diff --git a/augur/align.py b/augur/align.py
index c9f385e1a..83de03991 100644
--- a/augur/align.py
+++ b/augur/align.py
@@ -294,7 +294,7 @@ def analyse_insertions(aln, ungapped, insertion_csv):
         for insertion_seq, strains in i_data.items():
             for strain in strains:
                 strain_data[strain][idx] = insertion_seq
-    with open(insertion_csv, 'w') as fh:
+    with open(insertion_csv, 'w', encoding='utf-8') as fh:
         print(",".join(header), file=fh)
         for strain in strain_data:
             print("{},{}".format(strain, ",".join(strain_data[strain])), file=fh)
diff --git a/augur/distance.py b/augur/distance.py
index 37c6125d6..a24294407 100644
--- a/augur/distance.py
+++ b/augur/distance.py
@@ -166,7 +166,7 @@ def read_distance_map(map_file):
     [('default', 0.0), ('map', {'SigPep': {0: {('W', 'P'): -8.3}}})]
     """
     # Load the JSON.
-    with open(map_file, "r") as fh:
+    with open(map_file, "r", encoding='utf-8') as fh:
         json_distance_map = json.load(fh)
 
     # Confirm that all required fields are present.
diff --git a/augur/export_v2.py b/augur/export_v2.py
index f3574ffed..b8358300d 100644
--- a/augur/export_v2.py
+++ b/augur/export_v2.py
@@ -783,7 +783,7 @@ def set_description(data_json, cmd_line_description_file):
     `meta.description` in *data_json* to the text provided.
     """
     try:
-        with open(cmd_line_description_file) as description_file:
+        with open(cmd_line_description_file, encoding='utf-8') as description_file:
             markdown_text = description_file.read()
             data_json['meta']['description'] = markdown_text
     except FileNotFoundError:
diff --git a/augur/filter.py b/augur/filter.py
index 0f570f356..700bdff99 100644
--- a/augur/filter.py
+++ b/augur/filter.py
@@ -16,9 +16,9 @@
 def read_vcf(filename):
     if filename.lower().endswith(".gz"):
         import gzip
-        file = gzip.open(filename, mode="rt")
+        file = gzip.open(filename, mode="rt", encoding='utf-8')
     else:
-        file = open(filename)
+        file = open(filename, encoding='utf-8')
 
     chrom_line = next(line for line in file if line.startswith("#C"))
     file.close()
@@ -55,7 +55,7 @@ def write_vcf(input_filename, output_filename, dropped_samps):
 
 def read_priority_scores(fname):
     try:
-        with open(fname) as pfile:
+        with open(fname, encoding='utf-8') as pfile:
             return defaultdict(float, {
                 elems[0]: float(elems[1])
                 for elems in (line.strip().split() for line in pfile.readlines())
@@ -169,7 +169,7 @@ def run(args):
     num_excluded_by_name = 0
     if args.exclude:
         try:
-            with open(args.exclude, 'r') as ifile:
+            with open(args.exclude, 'r', encoding='utf-8') as ifile:
                 to_exclude = set()
                 for line in ifile:
                     if line[0] != comment_char:
@@ -326,7 +326,7 @@ def run(args):
     # Note that we are also not checking for existing meta data here
     num_included_by_name = 0
     if args.include and os.path.isfile(args.include):
-        with open(args.include, 'r') as ifile:
+        with open(args.include, 'r', encoding='utf-8') as ifile:
             to_include = set(
                 [
                     line.strip()
diff --git a/augur/frequencies.py b/augur/frequencies.py
index a1dd3b572..d616e92af 100644
--- a/augur/frequencies.py
+++ b/augur/frequencies.py
@@ -82,7 +82,7 @@ def run(args):
     if args.method == "kde":
         # Load weights if they have been provided.
         if args.weights:
-            with open(args.weights, "r") as fh:
+            with open(args.weights, "r", encoding='utf-8') as fh:
                 weights = json.load(fh)
 
             weights_attribute = args.weights_attribute
diff --git a/augur/import_beast.py b/augur/import_beast.py
index 1cbfebbf7..5732c1528 100644
--- a/augur/import_beast.py
+++ b/augur/import_beast.py
@@ -231,7 +231,7 @@ def parse_nexus(tree_path, treestring_regex=r'tree [A-Za-z\_]+([0-9]+)', verbose
 
     if isinstance(tree_path,str): ## determine if path or handle was provided to function
         try:
-            handle=open(tree_path,'r')
+            handle=open(tree_path,'r', encoding='utf-8')
         except FileNotFoundError:
             print("FATAL: No such file {}".format(tree_path))
             sys.exit(2)
diff --git a/augur/lbi.py b/augur/lbi.py
index 7d5a56034..e26538b92 100644
--- a/augur/lbi.py
+++ b/augur/lbi.py
@@ -94,7 +94,7 @@ def run(args):
     tree = Bio.Phylo.read(args.tree, "newick")
 
     # Load branch lengths.
-    with open(args.branch_lengths, "r") as json_fh:
+    with open(args.branch_lengths, "r", encoding='utf-8') as json_fh:
         branch_lengths = json.load(json_fh)
 
     # Annotate branch lengths and dates onto tree nodes.
diff --git a/augur/parse.py b/augur/parse.py
index 23b627ae0..6fc6bb2c3 100644
--- a/augur/parse.py
+++ b/augur/parse.py
@@ -92,7 +92,7 @@ def run(args):
         strain_key = args.fields[0]
 
     # loop over sequences, parse fasta header of each sequence
-    with open(args.output_sequences, 'w') as output:
+    with open(args.output_sequences, 'w', encoding='utf-8') as output:
         for seq in seqs:
             fields = map(str.strip, seq.description.split(args.separator))
             tmp_meta = dict(zip(args.fields, fields))
diff --git a/augur/reconstruct_sequences.py b/augur/reconstruct_sequences.py
index b5acb407e..981f835b8 100644
--- a/augur/reconstruct_sequences.py
+++ b/augur/reconstruct_sequences.py
@@ -73,7 +73,7 @@ def run(args):
     #if VCF, read in the reference seq for each gene, put on root
     if(is_vcf):
         node_data["nodes"][root_node]['aa_sequences'] = {}
-        with open(args.vcf_aa_reference) as handle:
+        with open(args.vcf_aa_reference, encoding='utf-8') as handle:
             for record in SeqIO.parse(handle, "fasta"):
                 if record.id==args.gene:
                     #'root' may not be same as 'reference', so apply any mutations at root here!
diff --git a/augur/traits.py b/augur/traits.py
index 185f26851..701303e58 100644
--- a/augur/traits.py
+++ b/augur/traits.py
@@ -145,7 +145,7 @@ def run(args):
     if args.weights:
         weight_dict = {c:{} for c in args.columns}
         sep = ',' if args.weights.endswith('csv') else '\t'
-        with open(args.weights, 'r') as fh:
+        with open(args.weights, 'r', encoding='utf-8') as fh:
             for line in fh:
                 if line[0]=='#':
                     continue
@@ -187,7 +187,7 @@ def run(args):
             models[column]['transition_matrix'] = [list(x) for x in gtr.W]
 
         if gtr:
-            with open(out_prefix+'%s.mugration_model.txt'%column, 'w') as ofile:
+            with open(out_prefix+'%s.mugration_model.txt'%column, 'w', encoding='utf-8') as ofile:
                 ofile.write('Map from character to field name\n')
                 for k,v in alphabet.items():
                     ofile.write(k+':\t'+str(v)+'\n')
diff --git a/augur/translate.py b/augur/translate.py
index 5348429eb..244b86c12 100644
--- a/augur/translate.py
+++ b/augur/translate.py
@@ -285,7 +285,7 @@ def assign_aa_fasta(tree, translations):
 def get_genes_from_file(fname):
     genes = []
     if os.path.isfile(fname):
-        with open(fname) as ifile:
+        with open(fname, encoding='utf-8') as ifile:
             for line in ifile:
                 fields = line.strip().split('#')
                 if fields[0].strip():
diff --git a/augur/tree.py b/augur/tree.py
index a83336640..5c878a22d 100644
--- a/augur/tree.py
+++ b/augur/tree.py
@@ -136,13 +136,13 @@ def build_iqtree(aln_file, out_file, substitution_model="GTR", clean_up=True, nt
         aln_file    file name of input aligment
         out_file    file name to write tree to
     '''
-    with open(aln_file) as ifile:
+    with open(aln_file, encoding='utf-8') as ifile:
         tmp_seqs = ifile.readlines()
 
     # IQ-tree messes with taxon names. Hence remove offending characters, reinstaniate later
     tmp_aln_file = aln_file.replace(".fasta", "-delim.fasta")
     log_file = tmp_aln_file.replace(".fasta", ".iqtree.log")
-    with open(tmp_aln_file, 'w') as ofile:
+    with open(tmp_aln_file, 'w', encoding='utf-8') as ofile:
         for line in tmp_seqs:
             ofile.write(line.replace('/', '_X_X_').replace('|','_Y_Y_').replace("(","_X_Y_").replace(")","_Y_X_"))
 
@@ -256,7 +256,7 @@ def write_out_informative_fasta(compress_seq, alignment, stripFile=None):
 
     #If want a position map, print:
     if printPositionMap:
-        with open(fasta_file+".positions.txt", 'w') as the_file:
+        with open(fasta_file+".positions.txt", 'w', encoding='utf-8') as the_file:
             the_file.write("\n".join(pos))
 
     return fasta_file
@@ -294,7 +294,7 @@ def mask_sites_in_multiple_sequence_alignment(alignment_file, excluded_sites_fil
     # Write the masked alignment to disk one record at a time.
     alignment_file_path = Path(alignment_file)
     masked_alignment_file = str(alignment_file_path.parent / ("masked_%s" % alignment_file_path.name))
-    with open(masked_alignment_file, "w") as oh:
+    with open(masked_alignment_file, "w", encoding='utf-8') as oh:
         for record in alignment:
             # Convert to a mutable sequence to enable masking with Ns.
             sequence = record.seq.tomutable()
diff --git a/augur/utils.py b/augur/utils.py
index b20e768c0..8aa917d5a 100644
--- a/augur/utils.py
+++ b/augur/utils.py
@@ -26,10 +26,10 @@ def open_file(fname, mode):
         if "t" not in mode:
             # For interoperability, gzip needs to open files in "text" mode
             mode = mode + "t"
-        with gzip.open(fname, mode) as fh:
+        with gzip.open(fname, mode, encoding='utf-8') as fh:
             yield fh
     else:
-        with open(fname, mode) as fh:
+        with open(fname, mode, encoding='utf-8') as fh:
             yield fh
 
 def is_vcf(fname):
@@ -47,9 +47,9 @@ def is_vcf(fname):
 def myopen(fname, mode):
     if fname.endswith('.gz'):
         import gzip
-        return gzip.open(fname, mode)
+        return gzip.open(fname, mode, encoding='utf-8')
     else:
-        return open(fname, mode)
+        return open(fname, mode, encoding='utf-8')
 
 def get_json_name(args, default=None):
     if args.output_node_data:
@@ -231,7 +231,7 @@ def read_node_data(fnames, tree=None):
     node_data = {"nodes": {}}
     for fname in fnames:
         if os.path.isfile(fname):
-            with open(fname) as jfile:
+            with open(fname, encoding='utf-8') as jfile:
                 tmp_data = json.load(jfile)
             if tmp_data.get("annotations"):
                 try:
@@ -327,7 +327,7 @@ def write_json(data, file_name, indent=(None if os.environ.get("AUGUR_MINIFY_JSO
     if include_version:
         data["generated_by"] = {"program": "augur", "version": get_augur_version()}
 
-    with open(file_name, 'w') as handle:
+    with open(file_name, 'w', encoding='utf-8') as handle:
         json.dump(data, handle, indent=indent, sort_keys=True)
 
 
@@ -348,7 +348,7 @@ def load_features(reference, feature_names=None):
             return None
         limit_info = dict( gff_type = ['gene'] )
 
-        with open(reference) as in_handle:
+        with open(reference, encoding='utf-8') as in_handle:
             for rec in GFF.parse(in_handle, limit_info=limit_info):
                 for feat in rec.features:
                     if feature_names is not None: #check both tags; user may have used either
@@ -468,7 +468,7 @@ def add_line(line):
 
     if overrides:
         if os.path.isfile(overrides):
-            with open(overrides) as fh:
+            with open(overrides, encoding='utf-8') as fh:
                 for line in fh:
                     add_line(line)
         else:
@@ -497,7 +497,7 @@ def write_VCF_translation(prot_dict, vcf_file_name, ref_file_name):
 
     #prepare the header of the VCF & write out
     header=["#CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]+seqNames
-    with open(vcf_file_name, 'w') as the_file:
+    with open(vcf_file_name, 'w', encoding='utf-8') as the_file:
         the_file.write( "##fileformat=VCFv4.2\n"+
                         "##source=NextStrain_Protein_Translation\n"+
                         "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n")
@@ -552,10 +552,10 @@ def write_VCF_translation(prot_dict, vcf_file_name, ref_file_name):
             vcfWrite.append("\t".join(output))
 
     #write it all out
-    with open(ref_file_name, 'w') as the_file:
+    with open(ref_file_name, 'w', encoding='utf-8') as the_file:
         the_file.write("\n".join(refWrite))
 
-    with open(vcf_file_name, 'a') as the_file:
+    with open(vcf_file_name, 'a', encoding='utf-8') as the_file:
         the_file.write("\n".join(vcfWrite))
 
     if vcf_file_name.lower().endswith('.gz'):
@@ -869,7 +869,7 @@ def read_mask_file(mask_file):
         Sorted list of unique zero-indexed sites
     """
     mask_sites = []
-    with open(mask_file) as mf:
+    with open(mask_file, encoding='utf-8') as mf:
         for idx, line in enumerate(l.strip() for l in mf.readlines()):
             if "\t" in line:
                 line = line.split("\t")[1]