diff --git a/phylogenetic/rules/annotate_phylogeny.smk b/phylogenetic/rules/annotate_phylogeny.smk
index 2eb89284..4e3338e4 100644
--- a/phylogenetic/rules/annotate_phylogeny.smk
+++ b/phylogenetic/rules/annotate_phylogeny.smk
@@ -26,7 +26,6 @@ rule ancestral:
     input:
         tree = "results/{gene}/tree_{serotype}.nwk",
         alignment = "results/{gene}/aligned_{serotype}.fasta",
-        root_sequence = lambda wildcard: "config/reference_{serotype}_genome.gb" if wildcard.gene in ['genome'] else "results/config/reference_{serotype}_{gene}.gb",
     output:
         node_data = "results/{gene}/nt-muts_{serotype}.json"
     params:
@@ -37,7 +36,6 @@ rule ancestral:
             --tree {input.tree} \
             --alignment {input.alignment} \
             --output-node-data {output.node_data} \
-            --root-sequence {input.root_sequence} \
             --inference {params.inference}
         """