diff --git a/phylogenetic/rules/annotate_phylogeny.smk b/phylogenetic/rules/annotate_phylogeny.smk
index 61e94b8..ea8f4e1 100644
--- a/phylogenetic/rules/annotate_phylogeny.smk
+++ b/phylogenetic/rules/annotate_phylogeny.smk
@@ -28,7 +28,7 @@ rule translate:
     input:
         tree = "results/{gene}/tree.nwk",
         node_data = "results/{gene}/nt_muts.json",
-        reference = lambda wildcard: "defaults/measles_reference.gb" if wildcard.gene in ["genome"] else "defaults/measles_reference_{gene}.gb"
+        reference = lambda wildcard: config["files"]["reference" if wildcard.gene == "genome" else f"reference_{wildcard.gene}"]
     output:
         node_data = "results/{gene}/aa_muts.json"
     shell:
diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
index effbf01..53ca492 100644
--- a/phylogenetic/rules/export.smk
+++ b/phylogenetic/rules/export.smk
@@ -14,7 +14,7 @@ rule export:
         nt_muts = "results/{gene}/nt_muts.json",
         aa_muts = "results/{gene}/aa_muts.json",
         colors = config["files"]["colors"],
-        auspice_config = lambda wildcard: "defaults/auspice_config.json" if wildcard.gene in ["genome"] else "defaults/auspice_config_N450.json",
+        auspice_config = lambda wildcard: config["files"]["auspice_config" if wildcard.gene == "genome" else f"auspice_config_{wildcard.gene}"],
         description=config["files"]["description"]
     output:
         auspice_json = "auspice/measles_{gene}.json"