diff --git a/phylogenetic/defaults/clade-i/auspice_config.json b/phylogenetic/defaults/clade-i/auspice_config.json
index a924efc..52d78f7 100644
--- a/phylogenetic/defaults/clade-i/auspice_config.json
+++ b/phylogenetic/defaults/clade-i/auspice_config.json
@@ -55,8 +55,12 @@
   "geo_resolutions": [
     "country"
   ],
+  "metadata_columns": [
+    "strain"
+  ],
   "display_defaults": {
     "color_by": "country",
+    "tip_label": "strain",
     "map_triplicate": true,
     "distance_measure": "num_date",
     "transmission_lines": false
diff --git a/phylogenetic/defaults/hmpxv1/auspice_config.json b/phylogenetic/defaults/hmpxv1/auspice_config.json
index 89e32dc..a6adee5 100644
--- a/phylogenetic/defaults/hmpxv1/auspice_config.json
+++ b/phylogenetic/defaults/hmpxv1/auspice_config.json
@@ -60,8 +60,12 @@
   "geo_resolutions": [
     "country"
   ],
+  "metadata_columns": [
+    "strain"
+  ],
   "display_defaults": {
     "color_by": "lineage",
+    "tip_label": "strain",
     "map_triplicate": true,
     "distance_measure": "num_date",
     "transmission_lines": false
diff --git a/phylogenetic/defaults/hmpxv1_big/auspice_config.json b/phylogenetic/defaults/hmpxv1_big/auspice_config.json
index 034350c..797892f 100644
--- a/phylogenetic/defaults/hmpxv1_big/auspice_config.json
+++ b/phylogenetic/defaults/hmpxv1_big/auspice_config.json
@@ -65,8 +65,12 @@
   "geo_resolutions": [
     "country"
   ],
+  "metadata_columns": [
+    "strain"
+  ],
   "display_defaults": {
     "color_by": "lineage",
+    "tip_label": "strain",
     "map_triplicate": true,
     "distance_measure": "num_date",
     "transmission_lines": false
diff --git a/phylogenetic/defaults/mpxv/auspice_config.json b/phylogenetic/defaults/mpxv/auspice_config.json
index 046ac83..790a535 100644
--- a/phylogenetic/defaults/mpxv/auspice_config.json
+++ b/phylogenetic/defaults/mpxv/auspice_config.json
@@ -70,8 +70,12 @@
   "geo_resolutions": [
     "country"
   ],
+  "metadata_columns": [
+    "strain"
+  ],
   "display_defaults": {
     "color_by": "clade_membership",
+    "tip_label": "strain",
     "map_triplicate": true,
     "distance_measure": "div",
     "transmission_lines": false
diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
index 1501eb2..0ee20d4 100644
--- a/phylogenetic/rules/export.smk
+++ b/phylogenetic/rules/export.smk
@@ -89,8 +89,8 @@ rule export:
         description=config["description"],
         auspice_config=config["auspice_config"],
     output:
-        auspice_json=build_dir + "/{build_name}/raw_tree.json",
-        root_sequence=build_dir + "/{build_name}/raw_tree_root-sequence.json",
+        auspice_json=build_dir + "/{build_name}/tree.json",
+        root_sequence=build_dir + "/{build_name}/tree_root-sequence.json",
     params:
         strain_id=config["strain_id_field"],
     shell:
@@ -107,25 +107,3 @@ rule export:
             --include-root-sequence \
             --output {output.auspice_json}
         """
-
-
-rule final_strain_name:
-    input:
-        auspice_json=build_dir + "/{build_name}/raw_tree.json",
-        metadata=build_dir + "/{build_name}/metadata.tsv",
-        root_sequence=build_dir + "/{build_name}/raw_tree_root-sequence.json",
-    output:
-        auspice_json=build_dir + "/{build_name}/tree.json",
-        root_sequence=build_dir + "/{build_name}/tree_root-sequence.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}
-        cp {input.root_sequence} {output.root_sequence}
-        """
diff --git a/phylogenetic/scripts/set_final_strain_name.py b/phylogenetic/scripts/set_final_strain_name.py
deleted file mode 100644
index 08ca935..0000000
--- 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)