diff --git a/phylogenetic/defaults/clade-i/include.txt b/phylogenetic/defaults/clade-i/include.txt
index e69de29..f8ef05b 100644
--- a/phylogenetic/defaults/clade-i/include.txt
+++ b/phylogenetic/defaults/clade-i/include.txt
@@ -0,0 +1,7 @@
+# Ensure we include 2 Ia and Ib samples so we can use them to check clade assignment
+# Clade Ia
+PP601197
+KJ642618
+# Clade Ib
+PP601222
+PP601209
diff --git a/phylogenetic/rules/annotate_phylogeny.smk b/phylogenetic/rules/annotate_phylogeny.smk
index 6a15627..9d9661b 100644
--- a/phylogenetic/rules/annotate_phylogeny.smk
+++ b/phylogenetic/rules/annotate_phylogeny.smk
@@ -116,6 +116,8 @@ rule rename_clades:
         build_dir + "/{build_name}/clades_raw.json",
     output:
         node_data=build_dir + "/{build_name}/clades.json",
+    wildcard_constraints:
+        build_name="^(?!clade-i)$",
     shell:
         """
         python scripts/clades_renaming.py \
@@ -124,6 +126,19 @@ rule rename_clades:
         """
 
 
+rule clades_for_clade_I:
+    input:
+        tree=build_dir + "/clade-i/tree.nwk",
+    output:
+        node_data=build_dir + "/clade-i/clades.json",
+    shell:
+        """
+        python scripts/assign-clade-I-clades.py \
+            < {input.tree} \
+            > {output.node_data}
+        """
+
+
 rule mutation_context:
     input:
         tree=build_dir + "/{build_name}/tree.nwk",
diff --git a/phylogenetic/scripts/assign-clade-I-clades.py b/phylogenetic/scripts/assign-clade-I-clades.py
new file mode 100644
index 0000000..d6687d3
--- /dev/null
+++ b/phylogenetic/scripts/assign-clade-I-clades.py
@@ -0,0 +1,45 @@
+"""
+Labels the two child nodes of the root as clade Ia and Ib
+based on an expected tree structure. This approach is temporary and is
+necessary because the distribution of mutations at these two nodes
+(via augur ancestral) is random and thus we can't use our normal
+`augur clades` approach.
+
+This script expects certain tips to be present for each clade
+which are force-included in the analysis.
+
+Usage: provide the tree on STDIN, node-data JSON written to STDOUT
+"""
+
+import argparse
+from sys import stdin,stdout
+from Bio import Phylo
+from collections import defaultdict
+import json
+
+TIPS = {
+   "clade Ia": ["PP601197", "KJ642618"],
+   "clade Ib": ["PP601222", "PP601209"]
+}
+
+if __name__=="__main__":
+    parser = argparse.ArgumentParser(description = __doc__)
+    args = parser.parse_args()
+
+    t = Phylo.read(stdin, "newick")
+
+    node_data = { # node-data JSON
+        "nodes": defaultdict(dict),
+        "branches": defaultdict(dict),
+    }
+
+    for node in t.clade:
+        tips = set([n.name for n in node.get_terminals()])
+        for clade_name, defining_tips in TIPS.items():
+            if all([name in tips for name in defining_tips]):
+                node_data['branches'][node.name]['labels'] = {'clade': clade_name}
+                node_data['nodes'][node.name]["clade_membership"] = clade_name
+                for descendant in node.find_clades():
+                    node_data['nodes'][descendant.name]["clade_membership"] = clade_name
+
+    json.dump(node_data, stdout)