Commit ce781477 authored by Philippe Veber's avatar Philippe Veber
Browse files

orthomam: fixed echolocating species list + inference of ancestral state

parent ad585854
......@@ -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" ;
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment