update wrt phylogenetics

lib/orthomam.ml

@@ -68,22 +68,13 @@ let tag_tree t tagged_leaves =
   Fitch.fitch ~n:2 ~category t
   |> transfer_tag_to_branches
 
-let with_inner_newick_tree tree ~f =
-  let open Phylogenetics in
-  match (tree : Newick.t) with
-  | Tree t -> Newick.Tree (f t)
-  | Branch (Branch { tip ; data }) ->
-    Newick.Branch (
-      Tree.branch data (f tip)
-    )
-
 let%pworkflow clip_tree_on_alignment tree ali =
   let open Phylogenetics in
   let tree = Newick.from_file [%path tree] in
   let ali = Phylip.read_exn ~strict:false [%path ali] in
   let ali_species = List.map ali.items ~f:(fun it -> it.name) in
   let clipped_tree =
-    with_inner_newick_tree tree ~f:(fun tree ->
+    Newick.map_inner_tree tree ~f:(fun tree ->
         match
           Tree.leafset_generated_subtree tree
             (fun bi -> bi.Newick.name) ali_species
@@ -105,7 +96,7 @@ let tree_of_convergent_species tree species =
 
     let ensembl_tree = Newick.from_file omm_tree in
     let tagged_tree =
-      with_inner_newick_tree ensembl_tree ~f:(fun t ->
+      Newick.map_inner_tree ensembl_tree ~f:(fun t ->
           tag_tree t (String.Set.of_list species)
         )
     in