diff --git a/augur/distance.py b/augur/distance.py
index a24294407..a558dd573 100644
--- a/augur/distance.py
+++ b/augur/distance.py
@@ -245,15 +245,29 @@ def get_distance_between_nodes(node_a_sequences, node_b_sequences, distance_map)
     >>> distance_map = {"default": 0.0, "map": {"gene": {2: {('T', 'G'): 0.5}}}}
     >>> get_distance_between_nodes(node_b_sequences, node_a_sequences, distance_map)
     0.0
+
+    Ignore specific characters defined in the distance map.
+
+    >>> node_a_sequences = {"gene": "ACTGG"}
+    >>> node_b_sequences = {"gene": "A--GN"}
+    >>> distance_map = {"default": 1, "ignored_characters":["-"], "map": {}}
+    >>> get_distance_between_nodes(node_a_sequences, node_b_sequences, distance_map)
+    1
+    >>> distance_map = {"default": 1, "ignored_characters":["-", "N"], "map": {}}
+    >>> get_distance_between_nodes(node_a_sequences, node_b_sequences, distance_map)
+    0
     """
     distance_type = type(distance_map["default"])
     distance = distance_type(0)
+    ignored_characters = distance_map.get("ignored_characters",[])
 
     for gene in node_a_sequences:
         gene_length = len(node_a_sequences[gene])
 
         for site in range(gene_length):
-            if node_a_sequences[gene][site] != node_b_sequences[gene][site]:
+            if (node_a_sequences[gene][site] != node_b_sequences[gene][site]
+                and node_a_sequences[gene][site] not in ignored_characters
+                and node_b_sequences[gene][site] not in ignored_characters):
                 if gene in distance_map["map"] and site in distance_map["map"][gene]:
                     # Distances can be provided as either site- and
                     # sequence-specific dictionaries of sequence pairs to