diff --git a/phylogenetic/defaults/auspice_config.json b/phylogenetic/defaults/auspice_config.json
index 58656fc..973bf12 100644
--- a/phylogenetic/defaults/auspice_config.json
+++ b/phylogenetic/defaults/auspice_config.json
@@ -46,8 +46,12 @@
     "region"
   ],
   "display_defaults": {
-    "map_triplicate": true
+    "map_triplicate": true,
+    "tip_label": "strain"
   },
+  "metadata_columns": [
+    "strain"
+  ],
   "filters": [
     "country",
     "region",
diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
index 9b9ada0..77d020f 100644
--- a/phylogenetic/rules/export.smk
+++ b/phylogenetic/rules/export.smk
@@ -38,7 +38,7 @@ rule export:
         auspice_config = "defaults/auspice_config.json",
         description = "defaults/description.md"
     output:
-        auspice_json = "results/raw_zika.json"
+        auspice_json = "auspice/zika.json"
     params:
         strain_id = config.get("strain_id_field", "strain"),
     shell:
@@ -54,22 +54,3 @@ rule export:
             --include-root-sequence-inline \
             --output {output.auspice_json}
         """
-
-rule final_strain_name:
-    input:
-        auspice_json="results/raw_zika.json",
-        metadata="data/metadata_all.tsv"
-    output:
-        auspice_json="auspice/zika.json"
-    params:
-        strain_id=config["strain_id_field"],
-        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}
-        """
diff --git a/phylogenetic/scripts/set_final_strain_name.py b/phylogenetic/scripts/set_final_strain_name.py
deleted file mode 100644
index d104ca1..0000000
--- a/phylogenetic/scripts/set_final_strain_name.py
+++ /dev/null
@@ -1,51 +0,0 @@
-import pandas as pd
-import json, argparse
-from augur.io import read_metadata
-
-def replace_name_recursive(node, lookup, saveoldcolumn):
-    if node["name"] in lookup:
-        if saveoldcolumn == "accession":
-            node["node_attrs"][saveoldcolumn] = node["name"]
-        elif saveoldcolumn == "genbank_accession":
-            node["node_attrs"][saveoldcolumn] = {}
-            node["node_attrs"][saveoldcolumn]["value"] = node["name"]
-        else:
-            node["node_attrs"][saveoldcolumn] = node["name"]
-
-        node["name"] = lookup[node["name"]]
-
-    if "children" in node:
-        for child in node["children"]:
-            replace_name_recursive(child, lookup, saveoldcolumn)
-
-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)
-
-    if args.display_strain_name in metadata.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, args.metadata_id_columns[0])
-    else:
-        with open(args.input_auspice_json, 'r') as fh:
-            data = json.load(fh)
-
-    with open(args.output, 'w') as fh:
-        json.dump(data, fh, allow_nan=False, indent=None, separators=",:")