diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
index c344b50a..32bdb8dd 100644
--- a/phylogenetic/rules/export.smk
+++ b/phylogenetic/rules/export.smk
@@ -95,7 +95,8 @@ rule prepare_auspice_config:
             ],
             "display_defaults": {
               "map_triplicate": True,
-              "color_by": params.replace_clade_key
+              "color_by": params.replace_clade_key,
+              "tip_label": "strain"
             },
             "filters": [
               "country",
@@ -110,6 +111,7 @@ rule prepare_auspice_config:
             ],
             "metadata_columns": [
               "accession",
+              "strain",
               "url"
             ]
           }
@@ -150,7 +152,7 @@ rule export:
         auspice_config = "results/defaults/{gene}/auspice_config_{serotype}.json",
         colors = "results/colors_{serotype}.tsv",
     output:
-        auspice_json = "results/{gene}/raw_dengue_{serotype}.json"
+        auspice_json = "results/{gene}/dengue_{serotype}.json"
     params:
         strain_id = config.get("strain_id_field", "strain"),
     shell:
@@ -167,25 +169,6 @@ rule export:
             --output {output.auspice_json}
         """
 
-rule final_strain_name:
-    input:
-        auspice_json="results/{gene}/raw_dengue_{serotype}.json",
-        metadata="data/metadata_{serotype}.tsv",
-    output:
-        auspice_json="auspice/dengue_{serotype}_{gene}.json"
-    params:
-        strain_id=config.get("strain_id_field", "strain"),
-        display_strain_field=config.get("display_strain_field", "strain"),
-    shell:
-        """
-        python3 scripts/set_final_strain_name.py \
-            --metadata {input.metadata} \
-            --metadata-id-columns {params.strain_id} \
-            --input-auspice-json {input.auspice_json} \
-            --display-strain-name {params.display_strain_field} \
-            --output {output.auspice_json}
-        """
-
 rule tip_frequencies:
     """
     Estimating KDE frequencies for tips
@@ -196,7 +179,7 @@ rule tip_frequencies:
     output:
         tip_freq = "auspice/dengue_{serotype}_{gene}_tip-frequencies.json"
     params:
-        strain_id = config["display_strain_field"],
+        strain_id = config["strain_id_field"],
         min_date = config["tip_frequencies"]["min_date"],
         max_date = config["tip_frequencies"]["max_date"],
         narrow_bandwidth = config["tip_frequencies"]["narrow_bandwidth"],
diff --git a/phylogenetic/scripts/set_final_strain_name.py b/phylogenetic/scripts/set_final_strain_name.py
deleted file mode 100755
index 08ca9359..00000000
--- a/phylogenetic/scripts/set_final_strain_name.py
+++ /dev/null
@@ -1,38 +0,0 @@
-import pandas as pd
-import json, argparse
-from augur.io import read_metadata
-
-def replace_name_recursive(node, lookup):
-    if node["name"] in lookup:
-        node["name"] = lookup[node["name"]]
-
-    if "children" in node:
-        for child in node["children"]:
-            replace_name_recursive(child, lookup)
-
-if __name__=="__main__":
-    parser = argparse.ArgumentParser(
-        description="Swaps out the strain names in the Auspice JSON with the final strain name",
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter
-    )
-
-    parser.add_argument('--input-auspice-json', type=str, required=True, help="input auspice_json")
-    parser.add_argument('--metadata', type=str, required=True, help="input data")
-    parser.add_argument('--metadata-id-columns', nargs="+", help="names of possible metadata columns containing identifier information, ordered by priority. Only one ID column will be inferred.")
-    parser.add_argument('--display-strain-name', type=str, required=True, help="field to use as strain name in auspice")
-    parser.add_argument('--output', type=str, metavar="JSON", required=True, help="output Auspice JSON")
-    args = parser.parse_args()
-
-    metadata = read_metadata(args.metadata, id_columns=args.metadata_id_columns)
-    name_lookup = {}
-    for ri, row in metadata.iterrows():
-        strain_id = row.name
-        name_lookup[strain_id] = args.display_strain_name if pd.isna(row[args.display_strain_name]) else row[args.display_strain_name]
-
-    with open(args.input_auspice_json, 'r') as fh:
-        data = json.load(fh)
-
-    replace_name_recursive(data['tree'], name_lookup)
-
-    with open(args.output, 'w') as fh:
-        json.dump(data, fh)