diff --git a/phylogenetic/build-configs/ci/config.yaml b/phylogenetic/build-configs/ci/config.yaml
index f58e32f..1bfdef7 100644
--- a/phylogenetic/build-configs/ci/config.yaml
+++ b/phylogenetic/build-configs/ci/config.yaml
@@ -2,6 +2,7 @@ custom_rules:
   - build-configs/ci/copy_example_data.smk
 
 reference: "defaults/reference.fasta"
+ancestral_root_seq: "defaults/reference.fasta"
 genome_annotation: "defaults/genome_annotation.gff3"
 genbank_reference: "defaults/reference.gb"
 include: "defaults/hmpxv1/include.txt"
diff --git a/phylogenetic/rules/annotate_phylogeny.smk b/phylogenetic/rules/annotate_phylogeny.smk
index 9dea6a3..ccb2414 100644
--- a/phylogenetic/rules/annotate_phylogeny.smk
+++ b/phylogenetic/rules/annotate_phylogeny.smk
@@ -31,13 +31,19 @@ rule ancestral:
         node_data=build_dir + "/{build_name}/nt_muts.json",
     params:
         inference="joint",
+        root_sequence=lambda w: (
+            f"--root-sequence {config['ancestral_root_seq']!r}"
+            if config.get("ancestral_root_seq")
+            else ""
+        ),
     shell:
         """
         augur ancestral \
             --tree {input.tree} \
             --alignment {input.alignment} \
             --output-node-data {output.node_data} \
-            --inference {params.inference}
+            --inference {params.inference} \
+            {params.root_sequence}
         """