orthomam: fixed echolocating species list + inference of ancestral state

lib/orthomam.ml

@@ -77,7 +77,15 @@ let tag_tree t tagged_leaves =
         if String.Set.mem tagged_leaves l then 1 else 0
       )
   in
-  Fitch.fitch ~n:2 ~category t
+  let cost x y =
+    match x, y with
+    | 0, 1 -> 2.
+    | 1, 0 -> 1.
+    | 0, 0
+    | 1, 1 -> 0.
+    | _ -> assert false
+  in
+  Fitch.fitch ~cost ~n:2 ~category t
   |> transfer_tag_to_branches
 
 let%pworkflow clip_tree_on_alignment tree ali =
@@ -431,6 +439,7 @@ let species_with_echolocation = [
   "Miniopterus_natalensis" ;
   (* "Pteropus_vampyrus" ; unsure, i'd say no *)
   (* "Pteropus alecto" ; unsure, i'd say no *)
+  "Rhinolophus_sinicus" ;
   "Lipotes_vexillifer" ;
   "Hipposideros_armiger" ;
   "Physeter_catodon" ;