diff --git a/inst/scripts/ape.R b/inst/scripts/ape.R
new file mode 100644
index 0000000..4931489
--- /dev/null
+++ b/inst/scripts/ape.R
@@ -0,0 +1,23 @@
+library(ape)
+## For some reason, this ML option is really fast (maybe I should use this one instead)
+## I would need to map taxonomic levels for internal nodes
+ace_result <- ape::ace(
+    x = x, phy = phy, type = "discrete",
+    method = "ML", model = "ER", CI = TRUE,
+    marginal = TRUE, kappa = 0
+)
+
+pruned_tree <- keep.tip(phy = mpa_tree, tip = rownames(m1))
+ace_result <- ape::ace(
+    x = states, phy = pruned_tree, type = "discrete",
+    method = "ML", model = "ER", CI = TRUE,
+    marginal = TRUE, kappa = 0
+)
+
+
+states <- vector('character', nrow(m1))
+for (i in seq_along(states)) {
+    states[i] <- paste0(sort(names(which(m1[i,] > 0))), collapse = ":")
+}
+names(states) <- rownames(m1)
+states[which(grepl(':', states))] <- NA