open Core_kernel
open Phylogenetics

type condition = [`Ancestral | `Convergent]

type branch_info = {
  condition : condition ;
  length : float ;
}

type t = (unit, string, branch_info) Tree.t

val of_newick_tree : Newick.tree -> (t, [> `Msg of string]) result

val to_newick_tree : t -> Newick.tree

val from_file : string -> (t, [> `Msg of string]) result

val leaves : t -> (string * condition) list

val infer_binary_condition_on_branches :
  ?gain_relative_cost:float ->
  Newick.tree ->
  convergent_leaves:String.Set.t ->
  Newick.tree

val reset_transitions : Newick.tree -> Newick.tree

val remove_nodes_with_single_child : Newick.tree -> Newick.tree

val alignment_counts_map :
  t ->
  Alignment.t ->
  (int Amino_acid.table -> int Amino_acid.table -> 'a) ->
  'a list