new tk/Multinomial module

lib/tk/multinomial.ml

+open Core_kernel
+open Phylogenetics
+
+let site_loop tree alignment f =
+  let leaves =
+    Convergence_tree.leaves tree
+    |> List.map ~f:(fun (n, cond) ->
+        match Alignment.find_sequence alignment n with
+        | None -> failwithf "Could not find %s in alignment" n ()
+        | Some seq -> seq, cond
+      )
+  in
+  let seqs0, seqs1 = List.partition_map leaves ~f:Either.(function
+      | (aa, `Ancestral) -> First aa
+      | (aa, `Convergent) -> Second aa
+    )
+  in
+  let counts seqs i =
+    Amino_acid.Table.init (fun aa ->
+        let aa = Amino_acid.to_char aa in
+        List.count seqs ~f:(fun s -> Char.equal s.[i] aa)
+      )
+  in
+  let site i =
+    let c0 = (counts seqs0 i :> int array) in
+    let c1 = (counts seqs1 i :> int array) in
+    f c0 c1
+  in
+  let n = Alignment.ncols alignment in
+  List.init n ~f:site