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@@ -1,676 +0,0 @@
-
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-		       Version 3, 29 June 2007
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-IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
-  16. Limitation of Liability.
-
-  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
-THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
-GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
-USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
-  17. Interpretation of Sections 15 and 16.
-
-  If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
-		     END OF TERMS AND CONDITIONS
-
-	    How to Apply These Terms to Your New Programs
-
-  If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
-  To do so, attach the following notices to the program.  It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-    <one line to give the program's name and a brief idea of what it does.>
-    Copyright (C) <year>  <name of author>
-
-    This program is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-Also add information on how to contact you by electronic and paper mail.
-
-  If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
-    <program>  Copyright (C) <year>  <name of author>
-    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
-    This is free software, and you are welcome to redistribute it
-    under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License.  Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
-  You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-<http://www.gnu.org/licenses/>.
-
-  The GNU General Public License does not permit incorporating your program
-into proprietary programs.  If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library.  If this is what you want to do, use the GNU Lesser General
-Public License instead of this License.  But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
-
diff --git a/src/nbc/NEWS b/src/nbc/NEWS
deleted file mode 100644
index 501c1bb..0000000
--- a/src/nbc/NEWS
+++ /dev/null
@@ -1,3 +0,0 @@
-score and tabulate have been rewritten in Standard ML, to take advantage
-of certain optimizations that the MLton compiler performs, and improve
-performance. Their behavior should be unchanged, except for some speedup.
diff --git a/src/nbc/binary.sml b/src/nbc/binary.sml
deleted file mode 100644
index af5acd5..0000000
--- a/src/nbc/binary.sml
+++ /dev/null
@@ -1,26 +0,0 @@
-signature BINARY = sig
-	val fromInt32: int -> Word8Vector.vector
-	val fromInt16: int -> Word8Vector.vector
-	val fromReal: real -> Word8Vector.vector
-end
-
-structure Binary :> BINARY = struct
-	val word8VectorFromArray = Word8ArraySlice.vector o Word8ArraySlice.full
-	fun fromInt32 i =
-		let
-			val array = Word8Array.array (PackWord32Little.bytesPerElem, 0w0)
-			val word = LargeWord.fromInt i
-		in
-			PackWord32Little.update (array, 0, word)
-			; word8VectorFromArray array
-		end
-	fun fromInt16 i =
-		let
-			val array = Word8Array.array (PackWord16Little.bytesPerElem, 0w0)
-			val word = LargeWord.fromInt i
-		in
-			PackWord16Little.update (array, 0, word)
-			; word8VectorFromArray array
-		end
-	val fromReal = PackRealLittle.toBytes
-end
diff --git a/src/nbc/build.sh b/src/nbc/build.sh
deleted file mode 100644
index 3328271..0000000
--- a/src/nbc/build.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#! /bin/sh -v
-mllex substitution.lex
-mlyacc substitution.grm
-mlton -link-opt -lJudy -link-opt -lz score.mlb gzip.c
diff --git a/src/nbc/clean.sh b/src/nbc/clean.sh
deleted file mode 100644
index 58d95bf..0000000
--- a/src/nbc/clean.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#! /bin/sh -v
-rm substitution.lex.sml substitution.grm.sig substitution.grm.sml score
diff --git a/src/nbc/count.ml b/src/nbc/count.ml
deleted file mode 100644
index bd97b7b..0000000
--- a/src/nbc/count.ml
+++ /dev/null
@@ -1,60 +0,0 @@
-module ExtArray = ExtArray.Array
-let (|>) a b = b a
-
-module Options = struct
-	let parser = OptParse.OptParser.make ~version:"1.0" ()
-	let per_word =
-		let option = OptParse.StdOpt.str_option ~metavar:"file" () in
-		OptParse.OptParser.add parser ~short_name:'w' ~long_name:"per-word"
-			~help:"file to store per-word counts in" option;
-		(fun () -> match OptParse.Opt.opt option with
-			Some x -> x
-			| None ->
-				OptParse.OptParser.usage parser ();
-				exit 1
-		)
-	let total =
-		let option = OptParse.StdOpt.str_option ~metavar:"file" () in
-		OptParse.OptParser.add parser ~short_name:'t' ~long_name:"total"
-			~help:"file to store total count in" option;
-		(fun () -> match OptParse.Opt.opt option with
-			Some x -> x
-			| None ->
-				OptParse.OptParser.usage parser ();
-				exit 1
-		)
-	let order =
-		let option = OptParse.StdOpt.int_option ~default:15 () in
-		OptParse.OptParser.add parser ~short_name:'r' ~long_name:"order" option;
-		(fun () -> OptParse.Opt.get option)
-	let files = OptParse.OptParser.parse_argv parser
-	let total = total ()
-	let per_word = per_word ()
-	let order = order ()
-end
-
-let load_file order judy total name =
-	Misc.io_of_gzip name |> Fasta.enum_words order
-	|> Enum.fold (fun word total ->
-		Judy.bump judy word;
-		Judy.bump judy (Gene.reverse word);
-		total + 2
-	) total
-let load_files order names =
-	let judy = Judy.create () in
-	List.fold_left (load_file order judy) 0 names, judy
-let gzip_output_string c s = Gzip.output c s 0 (String.length s)
-let () =
-	let total_words, judy = load_files Options.order Options.files in
-	(
-		let c = open_out Options.total in
-		output_string c (string_of_int total_words ^ "\n");
-		close_out c
-	); (
-		let c = Gzip.open_out Options.per_word in
-		Judy.iter (fun word count ->
-			gzip_output_string c
-				(String.concat "" [string_of_int count; " "; word; "\n"])
-		) judy;
-		Gzip.close_out c
-	)
diff --git a/src/nbc/fail.sml b/src/nbc/fail.sml
deleted file mode 100644
index f3d324c..0000000
--- a/src/nbc/fail.sml
+++ /dev/null
@@ -1,10 +0,0 @@
-signature FAIL = sig
-	val fail: string -> 'a
-end
-
-structure Fail :> FAIL = struct
-	fun fail why = (
-		TextIO.output (TextIO.stdErr, why ^ "\n")
-		; OS.Process.exit OS.Process.failure
-	)
-end
diff --git a/src/nbc/fasta-test.mlb b/src/nbc/fasta-test.mlb
deleted file mode 100644
index 564fd11..0000000
--- a/src/nbc/fasta-test.mlb
+++ /dev/null
@@ -1,9 +0,0 @@
-local
-	local
-		fasta-all.mlb
-	in
-		functor Test
-	end
-in
-	test-generate.sml
-end
diff --git a/src/nbc/gene.mlb b/src/nbc/gene.mlb
deleted file mode 100644
index 47261ff..0000000
--- a/src/nbc/gene.mlb
+++ /dev/null
@@ -1,5 +0,0 @@
-local
-	$(SML_LIB)/basis/basis.mlb
-in
-	gene.sml
-end
diff --git a/src/nbc/gene.sml b/src/nbc/gene.sml
deleted file mode 100644
index 738e3fe..0000000
--- a/src/nbc/gene.sml
+++ /dev/null
@@ -1,49 +0,0 @@
-signature GENE = sig
-	val reverse: string -> string
-	val first: int -> string
-	val next: string -> string option
-end
-
-structure Gene :> GENE = struct
-	fun reverse s =
-		let
-			val n = size s
-			val m = n - 1
-			fun opposite c = case c of
-				#"A" => #"T"
-				| #"T" => #"A"
-				| #"C" => #"G"
-				| #"G" => #"C"
-				| _ => c
-		in
-			CharVector.tabulate (n, fn i => opposite (String.sub (s, m - i)))
-		end
-	fun first order = CharVector.tabulate (order, fn _ => #"A")
-	fun next nmer =
-		let
-			val order = size nmer
-			fun finish (rightmostNonT, replacement) = CharVector.tabulate (
-				order
-				, fn index =>
-					case
-						Int.compare (
-							index
-							, rightmostNonT
-						)
-					of
-						LESS => String.sub (nmer, index)
-						| EQUAL => replacement
-						| GREATER => #"A"
-			)
-			fun continue index =
-				if index < 0 then NONE
-				else case String.sub (nmer, index) of
-					#"A" => SOME (finish (index, #"C"))
-					| #"C" => SOME (finish (index, #"G"))
-					| #"G" => SOME (finish (index, #"T"))
-					| #"T" => continue (index - 1)
-					| _ => raise Fail "Invalid base"
-		in
-			continue (size nmer - 1)
-		end
-end
diff --git a/src/nbc/genome.sml b/src/nbc/genome.sml
deleted file mode 100644
index 81f3183..0000000
--- a/src/nbc/genome.sml
+++ /dev/null
@@ -1,33 +0,0 @@
-signature GENOME = sig
-	exception Bad
-	type t
-	val load: string * int -> t
-	val get: t * string -> int option
-end
-
-structure Genome :> GENOME = struct
-	exception Bad
-	fun |> (x, f) = f x
-	infix |>
-
-	type t = (string, int) HashTable.hash_table
-	fun load (gname, order) =
-		let
-			val h = HashTable.mkTable
-				(HashString.hashString, op =)
-				(1024 * 1024, Fail "")
-		in
-			Options.genomeText (order, gname) |> Gzip.openIn |> Misc.sequenceLines
-			|> Sequence.map (fn s => (
-				 case Misc.split2 s of
-					SOME (count, nmer) => (
-						nmer
-						, case Int.fromString count of
-							NONE => raise Bad
-							| SOME x => x
-					) | NONE => raise Bad
-			)) |> Sequence.app (HashTable.insert h)
-			; h
-		end
-	fun get (h, nmer) = HashTable.find h nmer
-end
diff --git a/src/nbc/gzip.c b/src/nbc/gzip.c
deleted file mode 100644
index d2bf98f..0000000
--- a/src/nbc/gzip.c
+++ /dev/null
@@ -1,13 +0,0 @@
-#include <zlib.h>
-
-int
-gzreadoffset(gzFile file, voidp buf, unsigned offset, unsigned len)
-{
-	return gzread(file, buf + offset, len);
-}
-
-int
-gzwriteoffset(gzFile file, voidpc buf, unsigned offset, unsigned len)
-{
-	return gzwrite(file, buf + offset, len);
-}
diff --git a/src/nbc/gzip.sml b/src/nbc/gzip.sml
deleted file mode 100644
index fc6e5ff..0000000
--- a/src/nbc/gzip.sml
+++ /dev/null
@@ -1,164 +0,0 @@
-signature GZIP = sig
-	exception Failure
-	val openIn: string -> TextIO.instream
-	val openOut: string -> TextIO.outstream
-end
-
-structure Gzip :> GZIP = struct
-	structure Primitive :> sig
-		eqtype gzFile
-		val null: gzFile
-		val gzopen: string * string -> gzFile
-		val gzread: gzFile * CharArray.array * word * word -> int
-		val gzwritea: gzFile * CharArray.array * word * word -> int
-		val gzwritev: gzFile * CharVector.vector * word * word -> int
-		val gzclose: gzFile -> int
-	end = struct
-		type gzFile = MLton.Pointer.t
-		val null = MLton.Pointer.null
-		val gzopen = _import "gzopen": string * string -> gzFile;
-		val gzread = _import "gzreadoffset":
-			gzFile * CharArray.array * word * word -> int;
-		val gzwritea = _import "gzwriteoffset":
-			gzFile * CharArray.array * word * word -> int;
-		val gzwritev = _import "gzwriteoffset":
-			gzFile * CharVector.vector * word * word -> int;
-		val gzclose = _import "gzclose": gzFile -> int;
-	end
-
-	exception Failure
-	fun readArraySlice (g, slice) =
-		let
-			val (array, offset, length) = CharArraySlice.base slice
-			val wordoffset = Word.fromInt offset
-			val wordlength = Word.fromInt length
-		in
-			Primitive.gzread (g, array, wordoffset, wordlength)
-		end
-	fun readerFromPrimitive (name, g) =
-		let
-			val closed = ref false
-			fun error x = raise IO.Io {
-				name = name
-				, function = "readArr"
-				, cause = x
-			}
-			fun readArr slice =
-				if !closed then error IO.ClosedStream
-				else let
-					val r = readArraySlice (g, slice)
-				in
-					if r < 0 then error Failure
-					else r
-				end
-			fun close () =
-				if !closed then ()
-				else (
-					closed := true
-					; ignore (Primitive.gzclose g)
-				)
-		in
-			TextPrimIO.augmentReader (TextPrimIO.RD {
-				name = name
-				, chunkSize = 32 * 1024
-				, readVec = NONE
-				, readArr = SOME readArr
-				, readVecNB = NONE
-				, readArrNB = NONE
-				, block = NONE
-				, canInput = NONE
-				, avail = fn () => NONE
-				, getPos = NONE
-				, setPos = NONE
-				, endPos = NONE
-				, verifyPos = NONE
-				, close = close
-				, ioDesc = NONE
-			})
-		end
-	fun readerFromName name =
-		let
-			val path = name ^ "\000"
-			val g = Primitive.gzopen (path, "r\000")
-		in
-			if g = Primitive.null then NONE
-			else SOME (readerFromPrimitive (name, g))
-		end
-	fun openIn name =
-		case readerFromName name of
-			SOME x => TextIO.mkInstream (TextIO.StreamIO.mkInstream (x, ""))
-			| NONE => raise IO.Io {
-				name = name
-				, function = "openIn"
-				, cause = Failure
-			}
-	fun writeSlice (base, write) (g, slice) =
-		let
-			val (vector, offset, length) = base slice
-			val wordoffset = Word.fromInt offset
-			val wordlength = Word.fromInt length
-		in
-			write (g, vector, wordoffset, wordlength)
-		end
-	val writeVectorSlice = writeSlice (CharVectorSlice.base, Primitive.gzwritev)
-	val writeArraySlice = writeSlice (CharArraySlice.base, Primitive.gzwritea)
-	fun writerFromPrimitive (name, g) =
-		let
-			val closed = ref false
-			fun error (function, x) = raise IO.Io {
-				name = name
-				, function = function
-				, cause = x
-			}
-			fun close () =
-				if !closed then ()
-				else (
-					closed := true
-					; ignore (Primitive.gzclose g)
-				)
-			fun write (name, realWrite) slice =
-				if !closed then error (name, IO.ClosedStream)
-				else let
-					val r = realWrite (g, slice)
-				in
-					if r <= 0 then error (name, Failure)
-					else r
-				end
-			val writeVec = write ("writeVec", writeVectorSlice)
-			val writeArr = write ("writeArr", writeArraySlice)
-		in
-			TextPrimIO.augmentWriter (TextPrimIO.WR {
-				name = name
-				, chunkSize = 32 * 1024
-				, writeVec = SOME writeVec
-				, writeArr = SOME writeArr
-				, writeVecNB = NONE
-				, writeArrNB = NONE
-				, block = NONE
-				, canOutput = NONE
-				, getPos = NONE
-				, setPos = NONE
-				, endPos = NONE
-				, verifyPos = NONE
-				, close = close
-				, ioDesc = NONE
-			})
-		end
-	fun writerFromName name =
-		let
-			val path = name ^ "\000"
-			val g = Primitive.gzopen (path, "w9")
-		in
-			if g = Primitive.null then NONE
-			else SOME (writerFromPrimitive (name, g))
-		end
-	fun openOut name =
-		case writerFromName name of
-			SOME x => TextIO.mkOutstream (TextIO.StreamIO.mkOutstream (x, IO.NO_BUF))
-			| NONE => raise IO.Io {
-				name = name
-				, function = "openOut"
-				, cause = Failure
-			}
-end
-
diff --git a/src/nbc/history.mlb b/src/nbc/history.mlb
deleted file mode 100644
index e7103cc..0000000
--- a/src/nbc/history.mlb
+++ /dev/null
@@ -1,5 +0,0 @@
-local
-	$(SML_LIB)/basis/basis.mlb
-in
-	history.sml
-end
diff --git a/src/nbc/history.sml b/src/nbc/history.sml
deleted file mode 100644
index 52c1bb2..0000000
--- a/src/nbc/history.sml
+++ /dev/null
@@ -1,74 +0,0 @@
-structure History :> sig
-	type history
-	val create: int -> history
-	val clear: history -> history
-	val push: history * char -> string option * history
-end = struct
-	type history = {maximumSize: int, content: string}
-	fun create maximumSize = {maximumSize = maximumSize, content = ""}
-	fun clear {maximumSize, content = _} =
-		{maximumSize = maximumSize, content = ""}
-	fun addToString (string, newCharacter) =
-		let
-			val size = size string
-		in
-			CharVector.tabulate (
-				size + 1
-				, fn index =>
-					if index = size then newCharacter
-					else String.sub (string, index)
-			)
-		end
-	fun shiftIntoString (string, newCharacter) =
-		let
-			val size = size string
-		in
-			CharVector.tabulate (
-				size
-				, fn index =>
-					if index = size - 1 then newCharacter
-					else String.sub (string, index + 1)
-			)
-		end
-	fun push ({maximumSize, content}, newCharacter) =
-		let
-			val currentSize = size content
-		in
-			if currentSize = maximumSize then
-				let
-					val newContent = shiftIntoString (
-						content
-						, newCharacter
-					)
-				in (
-					SOME newContent
-					, {
-						maximumSize = maximumSize
-						, content = newContent
-					}
-				) end
-			else if currentSize = maximumSize - 1 then
-				let
-					val newContent = addToString (
-						content
-						, newCharacter
-					)
-				in (
-					SOME newContent
-					, {
-						maximumSize = maximumSize
-						, content = newContent
-					}
-				) end
-			else (
-				NONE
-				, {
-					maximumSize = maximumSize
-					, content = addToString (
-						content
-						, newCharacter
-					)
-				}
-			)
-		end
-end
diff --git a/src/nbc/judy.sml b/src/nbc/judy.sml
deleted file mode 100644
index 73e257b..0000000
--- a/src/nbc/judy.sml
+++ /dev/null
@@ -1,175 +0,0 @@
-signature JUDY = sig
-	exception OutOfMemory
-	type t
-	val create: unit -> t
-	val insert: t * string * int -> unit
-	val get: t * string -> int option
-	val bump: t * string -> unit
-	val first: t -> (string * int) option
-	val next: t * string -> (string * int) option
-	val sequence: t -> (string * int) Sequence.t
-	val app: (string * int -> unit) -> t -> unit
-end
-structure Judy :> JUDY = struct
-	structure Primitive :> sig
-		type judy
-		type errorDetail
-		type return
-		val judyNull: judy
-		val errorDetailNull: errorDetail
-		val get: judy * string * errorDetail -> return
-		val insert: judy ref * string * errorDetail -> return
-		val delete: judy ref * string * errorDetail -> int
-		val free: judy ref * errorDetail -> word
-		val first: judy * CharArray.array * errorDetail -> return
-		val next: judy * CharArray.array * errorDetail -> return
-		val returnIsError: return -> bool
-		val returnIsNull: return -> bool
-		val returnGet: return -> int
-		val returnSet: return * int -> unit
-	end = struct
-		type judy = MLton.Pointer.t
-		type errorDetail = MLton.Pointer.t
-		type return = MLton.Pointer.t
-		val judyNull = MLton.Pointer.null
-		val errorDetailNull = MLton.Pointer.null
-		val get = _import "JudySLGet": judy * string * errorDetail -> return;
-		val insert = _import "JudySLIns": judy ref * string * errorDetail -> return;
-		val delete = _import "JudySLDel": judy ref * string * errorDetail -> int;
-		val free = _import "JudySLFreeArray": judy ref * errorDetail -> word;
-		val first = _import "JudySLFirst": judy * CharArray.array * errorDetail -> return;
-		val next = _import "JudySLNext": judy * CharArray.array * errorDetail -> return;
-		local
-			val pjerr = MLton.Pointer.sub (MLton.Pointer.null, 0w1)
-		in
-			fun returnIsError return = return = pjerr
-		end
-		fun returnIsNull return = return = MLton.Pointer.null
-		fun returnGet return = Int32.toInt (MLton.Pointer.getInt32 (return, 0))
-		fun returnSet (return, i) = MLton.Pointer.setInt32 (return, 0, Int32.fromInt i)
-	end
-	exception OutOfMemory
-	type t = {judy: Primitive.judy ref, max: int ref}
-	fun create () = {judy = ref Primitive.judyNull, max = ref 0}
-	fun insert ({judy, max}, key, value) =
-		let
-			val return = Primitive.insert (
-				judy
-				, key ^ "\000"
-				, Primitive.errorDetailNull
-			)
-		in
-			if Primitive.returnIsError return then raise OutOfMemory
-			else let
-				val n = size key
-			in
-				if !max < n then max := n else ()
-				; Primitive.returnSet (return, value)
-			end
-		end
-	fun get ({judy, max = _}, key) =
-		let
-			val return = Primitive.get (
-				!judy
-				, key ^ "\000"
-				, Primitive.errorDetailNull
-			)
-		in
-			if Primitive.returnIsNull return then NONE
-			else SOME (Primitive.returnGet return)
-		end
-	fun bump ({judy, max}, key) =
-		let
-			val return = Primitive.insert (
-				judy
-				, key ^ "\000"
-				, Primitive.errorDetailNull
-			)
-		in
-			if Primitive.returnIsError return then raise OutOfMemory
-			else let
-				val n = size key
-			in
-				if !max < n then max := n else ()
-				; Primitive.returnSet (
-					return
-					, Primitive.returnGet return + 1
-				)
-			end
-		end
-	fun strlen array =
-		case CharArray.findi (fn (_, c) => c = #"\000") array of
-			NONE => raise Option
-			| SOME (i, _) => i
-	fun stringFromNullTerminatedArray array =
-		CharArraySlice.vector (
-			CharArraySlice.slice (array, 0, SOME (strlen array))
-		)
-	fun first {judy, max} =
-		let
-			val array = CharArray.array (!max + 1, #"\000")
-			val return = Primitive.first (
-				!judy
-				, array
-				, Primitive.errorDetailNull
-			)
-		in
-			if Primitive.returnIsNull return then NONE
-			else SOME (
-				stringFromNullTerminatedArray array
-				, Primitive.returnGet return
-			)
-		end
-	fun next ({judy, max}, key) =
-		let
-			val size = size key
-			val array = CharArray.tabulate (
-				!max + 1
-				, fn i =>
-					if i < size then String.sub (key, i)
-					else #"\000"
-			)
-			val return = Primitive.next (
-				!judy
-				, array
-				, Primitive.errorDetailNull
-			)
-		in
-			if Primitive.returnIsNull return then NONE
-			else SOME (
-				stringFromNullTerminatedArray array
-				, Primitive.returnGet return
-			)
-		end
-	fun sequence t =
-		let
-			val last = ref NONE
-			fun get () =
-				case (
-					case !last of
-						NONE => first t
-						| SOME key => next (t, key)
-				) of
-					NONE => NONE
-					| SOME (return as (key, _)) => (
-						last := SOME key
-						; SOME return
-					)
-		in
-			Sequence.from get
-		end
-	fun app f t =
-		let
-			fun apply (key, value) = (
-				f (key, value)
-				; fetch key
-			) and fetch key =
-				case next (t, key) of
-					NONE => ()
-					| SOME x => apply x
-		in
-			case first t of
-				NONE => ()
-				| SOME x => apply x
-		end
-end
diff --git a/src/nbc/kahan.sml b/src/nbc/kahan.sml
deleted file mode 100644
index 70c6b47..0000000
--- a/src/nbc/kahan.sml
+++ /dev/null
@@ -1,31 +0,0 @@
-(* Kahan summation *)
-
-signature KAHAN = sig
-	type t
-	val zero: t
-	val add: t * real -> t
-	val sum: t -> real
-	val sequence: real Sequence.t -> real
-	val list: real list -> real
-	val array: real array -> real
-end
-
-structure Kahan :> KAHAN = struct
-	type t = real * real
-	val zero = (0.0, 0.0)
-	fun add ((s, c), x) =
-		let
-			val y = x - c
-			val t = s + y
-		in
-			(t, t - s - y)
-		end
-	fun sum (s, c) = s
-	local
-		fun swappedAdd (a, b) = add (b, a)
-	in
-		fun sequence e = sum (Sequence.fold swappedAdd zero e)
-		fun list l = sum (foldl swappedAdd zero l)
-		fun array a = sum (Array.foldl swappedAdd zero a)
-	end
-end
diff --git a/src/nbc/main.sml b/src/nbc/main.sml
deleted file mode 100644
index 361d9ca..0000000
--- a/src/nbc/main.sml
+++ /dev/null
@@ -1,98 +0,0 @@
-structure Main = struct
-
-fun |> (x, f) = f x
-infix |>
-
-val order = Options.order
-val genomes = case Options.genomes of
-	SOME x => x |> TextIO.openIn |> Misc.sequenceLines
-	| NONE => Options.genomesDir |> Misc.sortedDirectoryNoPrefix |> Sequence.fromList
-fun input () =
-	case Fasta.sequence (Gzip.openIn Options.input) of
-		NONE => Fail.fail "input file is not FASTA format"
-		| SOME x =>
-			Sequence.map (fn (header, data) =>
-				(header, String.map Char.toUpper data)
-			) x
-fun output genome =
-	let
-		fun inner format = case format of
-			Options.Matlab {variable, file} =>
-				let
-					val matlab = Matlab.openOut file
-					val doubleArray = Matlab.beginDoubleArray (matlab, variable)
-				in {
-					write = fn (_, score) =>
-						Matlab.writeDouble (doubleArray, score)
-					, close = fn () => (
-						Matlab.concludeDoubleArray doubleArray
-						; Matlab.closeOut matlab
-					)
-				} end
-			| Options.Text filename =>
-				let
-					val gzip = Gzip.openOut filename
-				in {
-					write = fn (header, score) =>
-						TextIO.output (
-							gzip
-							, Real.fmt (StringCvt.FIX (SOME 8)) score
-						)
-					, close = fn () => TextIO.closeOut gzip
-				} end
-			| Options.Dual {text, matlab} =>
-				let
-					val text = inner (Options.Text text)
-					val matlab = inner (Options.Matlab matlab)
-				in {
-					write = fn x => (
-						#write text x
-						; #write matlab x
-					), close = fn () => (
-						#close text ()
-						; #close matlab ()
-					)
-				} end
-	in
-		inner (Options.output genome)
-	end
-fun totalWords (genome, order) =
-        let
-		val name = Options.totalWords (genome, order)
-		val input = TextIO.openIn name
-	in
-		(case Option.mapPartial Real.fromString (Misc.inputLine input) of
-			NONE => Fail.fail ("could not read number from " ^ name)
-			| SOME r => r
-		) before TextIO.closeIn input
-	end
-
-val () =
-	Sequence.app (fn gname =>
-		let
-			val {write, close} = output gname
-			val totalWords = totalWords (gname, order)
-			val genome = (
-				Stopwatch.start ("Loading genome " ^ gname)
-				; Genome.load (gname, order)
-				before Stopwatch.finish ()
-			)
-		in
-			Stopwatch.start ("Scoring fragments")
-			; input () |> Sequence.app (fn (header, fragment) =>
-				write (
-					header
-					, Score.score (
-						order
-						, Options.missConstant
-						, fn nmer => Genome.get (genome, nmer)
-						, totalWords
-						, fragment
-					)
-				)
-			); Stopwatch.finish ()
-			; close ()
-		end
-	) genomes
-
-end
diff --git a/src/nbc/matlab.sml b/src/nbc/matlab.sml
deleted file mode 100644
index 65f532d..0000000
--- a/src/nbc/matlab.sml
+++ /dev/null
@@ -1,135 +0,0 @@
-signature MATLAB = sig
-	type t
-	val openOut: string -> t
-	type doubleArray
-	val beginDoubleArray: t * string -> doubleArray
-	val writeDouble: doubleArray * real -> unit
-	val concludeDoubleArray: doubleArray -> unit
-	val writeDoubleArray: t * string * real vector -> unit
-	val closeOut: t -> unit
-end
-
-structure Matlab :> MATLAB = struct
-	fun outputReal (c, f) = BinIO.output (c, Binary.fromReal f)
-	fun outputInt32 (c, i) = BinIO.output (c, Binary.fromInt32 i)
-	fun outputInt16 (c, i) = BinIO.output (c, Binary.fromInt16 i)
-	type t = BinIO.outstream
-	type doubleArray = {
-		outstream: BinIO.outstream
-		, wholeSizePos: BinIO.StreamIO.out_pos
-		, paddedSize: int
-		, arraySizePos: BinIO.StreamIO.out_pos
-		, dataSizePos: BinIO.StreamIO.out_pos
-		, elements: int ref
-	}
-	fun pad n =
-		if n > 0 andalso n <= 4 then 4
-		else (n + 7) div 8 * 8
-	fun doubleArraySize (nameLength, arrayLength) =
-		32 + nameLength + 4 + 8 + arrayLength * 8
-	val s8Tag = 1
-	val s32Tag = 5
-	val u32Tag = 6
-	val doubleTag = 9
-	val doubleFlag = 6
-	val matrixTag = 14
-	fun lsl (x, y) = Word.toIntX (Word.<< (Word.fromInt x, Word.fromInt y))
-	fun beginDoubleArray (c, name) =
-		let
-			val nameSize = Int.min (size name, 63)
-			val name = Word8VectorSlice.vector (
-				Word8VectorSlice.slice (Byte.stringToBytes name, 0, SOME nameSize)
-			)
-			val paddedSize = pad nameSize
-			val padding = Word8Vector.tabulate (paddedSize - nameSize, fn _ => 0w0)
-			val () = outputInt32 (c, matrixTag)
-			val wholeSizePos = BinIO.getPosOut c
-			val () = (
-				outputInt32 (c, 0)
-				; outputInt32 (c, u32Tag)
-				; outputInt32 (c, 8)
-				; outputInt32 (c, doubleFlag)
-				; outputInt32 (c, 0)
-				; outputInt32 (c, s32Tag)
-				; outputInt32 (c, 8)
-				; outputInt32 (c, 1)
-			)
-			val arraySizePos = BinIO.getPosOut c
-			val () = (
-				outputInt32 (c, 0)
-				; if nameSize > 0 andalso nameSize <= 4 then
-					outputInt32 (c, lsl (nameSize, 16) + s8Tag)
-				else (
-					outputInt32 (c, s8Tag)
-					; outputInt32 (c, nameSize)
-				); BinIO.output (c, name)
-				; BinIO.output (c, padding)
-				; outputInt32 (c, doubleTag)
-			)
-			val dataSizePos = BinIO.getPosOut c
-			val () = outputInt32 (c, 0)
-		in
-			{
-				outstream = c
-				, wholeSizePos = wholeSizePos
-				, paddedSize = paddedSize
-				, arraySizePos = arraySizePos
-				, dataSizePos = dataSizePos
-				, elements = ref 0
-			}
-		end
-	fun writeDouble (da, f) = (
-		outputReal (#outstream da, f)
-		; #elements da := !(#elements da) + 1
-	)
-	fun concludeDoubleArray da =
-		let
-			val saved = BinIO.getPosOut (#outstream da)
-		in
-			BinIO.setPosOut (#outstream da, #wholeSizePos da)
-			; outputInt32 (
-				#outstream da
-				, doubleArraySize (#paddedSize da, !(#elements da))
-			); BinIO.setPosOut (#outstream da, #arraySizePos da)
-			; outputInt32 (#outstream da, !(#elements da))
-			; BinIO.setPosOut (#outstream da, #dataSizePos da)
-			; outputInt32 (#outstream da, (!(#elements da) * 8))
-			; BinIO.setPosOut (#outstream da, saved)
-		end
-	fun writeDoubleArray (c, name, array) =
-		let
-			val da = beginDoubleArray (c, name)
-		in
-			Vector.app (fn x => writeDouble (da, x)) array
-			; concludeDoubleArray da
-		end
-	fun writeHeader (c, software, version) =
-		let
-			val date = Date.fromTimeUniv (Time.now ())
-			val text = concat [
-				"MATLAB 5.0 MAT-file, written by "
-				, software, " ", version, ", "
-				, Date.fmt "%Y-%m-$d %H:%M:%S UTC" date
-			]
-			val size = size text
-			val header =
-				CharVector.tabulate (
-					124
-					, fn i =>
-						if i < size then String.sub (text, i)
-						else #" "
-				)
-		in
-			BinIO.output (c, Byte.stringToBytes header)
-			; outputInt16 (c, 0x0100)
-			; outputInt16 (c, 0x4d49)
-		end
-	fun openOut name =
-		let
-			val c = BinIO.openOut name
-		in
-			writeHeader (c, Program.name, Program.version)
-			; c
-		end
-	val closeOut = BinIO.closeOut
-end
diff --git a/src/nbc/misc.sml b/src/nbc/misc.sml
deleted file mode 100644
index 4790bbc..0000000
--- a/src/nbc/misc.sml
+++ /dev/null
@@ -1,125 +0,0 @@
-signature MISC = sig
-	val inputLine: TextIO.instream -> string option
-	val sequenceFromRead: (TextIO.instream -> 'a option) -> TextIO.instream -> 'a Sequence.t
-	val sequenceLines: TextIO.instream -> string Sequence.t
-	val sortedDirectoryNoPrefix: string -> string list
-	val sortedDirectory: string -> string list
-	val substitute: (string * string) list -> string -> string option
-	val basenameWithoutExtension: string -> string
-	val split2: string -> (string * string) option
-	val longestCommonSubstring: string list -> string
-end
-
-structure Misc :> MISC = struct
-	fun |> (x, f) = f x
-	infix |>
-	fun \ f x y = f (x, y)
-	fun sequenceFromRead f ioc = Sequence.from (fn () => f ioc)
-	fun inputLine instream = case TextIO.inputLine instream of
-		NONE => NONE
-		| SOME x => SOME (String.substring (x, 0, size x - 1))
-	val sequenceLines = sequenceFromRead inputLine
-	fun sortedDirectoryNoPrefix d =
-		let
-			val h = OS.FileSys.openDir d
-			fun loop l =
-				case OS.FileSys.readDir h of
-					NONE => (
-						OS.FileSys.closeDir h
-						; ListMergeSort.sort (op >) l
-					) | SOME n => loop (
-						if String.sub (n, 0) = #"." then l
-						else n :: l
-					)
-		in
-			loop nil
-		end
-	fun sortedDirectory d =
-		map (\OS.Path.concat d) (sortedDirectoryNoPrefix d)
-	fun assoc list key =
-		case
-			List.find (fn (possibility, _) => possibility = key) list
-		of
-			NONE => NONE
-			| SOME (_, answer) => SOME answer
-	local
-		exception NotFound
-	in
-		fun substitute v s =
-			Substitution.substitute
-				(fn s => (case assoc v s of
-					NONE => raise NotFound
-					| SOME x => x
-				)) s
-			handle NotFound => NONE
-	end
-	fun basenameWithoutExtension s = OS.Path.base (OS.Path.file s)
-	local
-		fun index f (string, offset) =
-			let
-				val last = size string
-				fun loop i =
-					if i = last then ~1
-					else if f (String.sub (string, i)) then i
-					else loop (i + 1)
-			in
-				loop offset
-			end
-	in
-		val indexWhitespace = index Char.isSpace
-		val indexNonWhitespace = index (not o Char.isSpace)
-	end
-	fun split2 s =
-		let
-			val f1b = indexNonWhitespace (s, 0)
-		in
-			if f1b = ~1 then NONE
-			else let
-				val f1e = indexWhitespace (s, f1b + 1)
-			in
-				if f1e = ~1 then NONE
-				else let
-					val f2b = indexNonWhitespace (s, f1e + 1)
-				in
-					if f2b = ~1 then NONE
-					else let
-						val f2e = indexWhitespace (s, f2b + 1)
-					in
-						if f2e = ~1 then SOME (
-							substring (s, f1b, f1e - f1b)
-							, substring (s, f2b, size s - f2b)
-						) else if indexNonWhitespace (s, f2e + 1) = ~1 then
-							SOME (
-								substring (s, f1b, f1e - f1b)
-								, substring (s, f2b, f2e - f2b)
-							)
-						else NONE
-					end
-				end
-			end
-		end
-	fun longestCommonSubstring strings =
-		case
-			foldl (fn (a, b) => (case b of
-				NONE => SOME a
-				| SOME b => if size a < size b then SOME a else SOME b
-			)) NONE strings
-		of
-			NONE => ""
-			| SOME shortest => let
-				val minimumSize = size shortest
-				fun loop (size, offset) =
-					let
-						fun next () =
-							if size + offset = minimumSize then
-								loop (size - 1, 0)
-							else loop (size, offset + 1)
-						val sub = substring (shortest, offset, size)
-					in
-						if List.all (String.isSubstring sub) strings then sub
-						else next ()
-					end
-			in
-				loop (minimumSize, 0)
-			end
-end
diff --git a/src/nbc/nmer-test.mlb b/src/nbc/nmer-test.mlb
deleted file mode 100644
index c363f4a..0000000
--- a/src/nbc/nmer-test.mlb
+++ /dev/null
@@ -1,9 +0,0 @@
-local
-	local
-		nmer-all.mlb
-	in
-		functor Test
-	end
-in
-	test-generate.sml
-end
diff --git a/src/nbc/options.sml b/src/nbc/options.sml
deleted file mode 100644
index 907c95a..0000000
--- a/src/nbc/options.sml
+++ /dev/null
@@ -1,202 +0,0 @@
-signature OPTIONS = sig
-	val order: int
-	val input: string
-	val genomesDir: string
-	val genomes: string option
-	val genomeText: int * string -> string
-	val totalWords: string * int -> string
-	val missConstant: real
-	datatype output =
-		Matlab of {variable: string, file: string}
-		| Text of string
-		| Dual of {text: string, matlab: {variable: string, file: string}}
-	val output: string -> output
-	val arguments: string list
-end
-
-structure Options :> OPTIONS = struct
-	fun |> (x, f) = f x
-	infix |>
-	datatype outformat = Otext | Omatlab | Odual
-	local
-		val order = ref 15
-		val fasta = ref NONE
-		val genomesDir = ref "/var/lib/genomes"
-		val genomes = ref NONE
-		val genomeText = ref "$genomes_dir/$genome/${order}perword.gz"
-		val totalWords = ref "$genomes_dir/$genome/${order}total"
-		val missConstant = ref (1.0 / 26067530.0 / 1000000.0)
-		val outFormat = ref Otext
-		val variable = ref "ps_g"
-		val outFile = ref "$input-$order-$genome.$extension"
-		fun withDefault (description, default) = concat (
-			description
-			:: " ("
-			:: (case default of
-				NONE => ["no default)"]
-				| SOME x => ["default: ", x, ")"])
-		)
-		val options = [
-			{
-				short = "r", long = ["order"]
-				, help = withDefault
-					("Set the length of words used in matches", NONE)
-				, desc = GetOpt.ReqArg (
-					fn x => case Int.fromString x of
-						NONE => Fail.fail
-							"given order is not a valid integer"
-						| SOME y => order := y
-					, "integer"
-				)
-			}, {
-				short = "a", long = ["fasta-input"]
-				, help = "FASTA input file"
-				, desc = GetOpt.ReqArg (fn x => fasta := SOME x, "filename")
-			}, {
-				short = "j", long = ["genomes-dir"]
-				, help = withDefault (
-					"Set the directory where genomes are stored"
-					, SOME (!genomesDir)
-				), desc = GetOpt.ReqArg (fn x => genomesDir := x, "directory")
-			}, {
-				short = "g", long = ["genome-list"]
-				, help = withDefault (
-					"Read genomes from this file, one per line"
-					, !genomes
-				), desc = GetOpt.ReqArg (fn x => genomes := SOME x, "filename")
-			}, {
-				short = "w", long = ["genome-text"]
-				, help = withDefault (
-					"Filename to read per-word counts from"
-					, SOME (!genomeText)
-				), desc = GetOpt.ReqArg (fn x => genomeText := x, "filename")
-			}, {
-				short = "t", long = ["total-words"]
-				, help = withDefault (
-					"Filename to read total word counts from"
-					, SOME (!totalWords)
-				), desc = GetOpt.ReqArg (fn x => totalWords := x, "filename")
-			}, {
-				short = "k", long = ["miss-constant"]
-				, help = withDefault (
-					"Set the constant used for scoring missing words"
-					, SOME (Real.toString (!missConstant))
-				), desc = GetOpt.ReqArg (
-					fn x => (case Real.fromString x of 
-						SOME y => missConstant := y
-						| NONE => Fail.fail
-							"given miss constant is not a valid number"
-					), "number"
-				)
-			}, {
-				short = "x", long = ["text"]
-				, help = "Select gzipped text output (default)"
-				, desc = GetOpt.NoArg (fn () => outFormat := Otext)
-			}, {
-				short = "m", long = ["matlab"]
-				, help = "Select Matlab binary output"
-				, desc = GetOpt.NoArg (fn () => outFormat := Omatlab)
-			}, {
-				short = "u", long = ["dual"]
-				, help = "Select both gzipped text and Matlab binary output"
-				, desc = GetOpt.NoArg (fn () => outFormat := Odual)
-			}, {
-				short = "v", long = ["variable"]
-				, help = withDefault (
-					"Set Matlab output variable"
-					, SOME (!variable)
-				), desc = GetOpt.ReqArg (fn x => variable := x, "name")
-			}, {
-				short = "o", long = ["output-file"]
-				, help = withDefault (
-					"Set output filename(s)"
-					, SOME (!outFile)
-				), desc = GetOpt.ReqArg (fn x => outFile := x, "filename")
-			}
-		]
-		val optionsWithHelp = {
-			short = "h", long = ["help"]
-			, help = "Display help"
-			, desc = GetOpt.NoArg (fn () => (
-				print (
-					GetOpt.usageInfo {
-						header = "score <options>"
-						, options = options
-					} ^ "\n"
-				); OS.Process.exit OS.Process.success
-			))
-		} :: options
-	in
-		val (_, arguments) = GetOpt.getOpt {
-			argOrder = GetOpt.Permute
-			, options = optionsWithHelp
-			, errFn = print
-		} (CommandLine.arguments ())
-		val order = !order
-		val input = case !fasta of 
-			NONE => Fail.fail "No input file given"
-			| SOME x => x
-		val genomesDir = !genomesDir
-		val genomes = !genomes
-		val genomeText = fn (order, genome) => (
-			case
-				Misc.substitute [
-					("genomes_dir", genomesDir)
-					, ("genome", genome)
-					, ("order", Int.toString order)
-				] (!genomeText)
-			of
-				NONE => Fail.fail "bad per-word count filename syntax"
-				| SOME x => x
-		)
-		val totalWords = fn (genome, order) => (
-			case
-				Misc.substitute [
-					("genomes_dir", genomesDir)
-					, ("genome", genome)
-					, ("order", Int.toString order)
-				] (!totalWords)
-			of
-				NONE => Fail.fail "bad total word count filename syntax"
-				| SOME x => x
-		)
-		val missConstant = !missConstant
-		datatype output =
-			Matlab of {variable: string, file: string}
-			| Text of string
-			| Dual of {text: string, matlab: {variable: string, file: string}}
-		fun output genome =
-			let
-				val common = [
-					("input", Misc.basenameWithoutExtension input)
-					, ("order", Int.toString order)
-					, ("genome", genome)
-				]
-				fun textName () =
-					case Misc.substitute
-						(("extension", "txt.gz") :: common) (!outFile)
-					of
-						NONE => Fail.fail "bad text output filename syntax"
-						| SOME x => x
-				fun matlabName () =
-					case Misc.substitute
-						(("extension", "mat") :: common) (!outFile)
-					of
-						NONE => Fail.fail "bad Matlab output filename syntax"
-						| SOME x => x
-			in
-				case !outFormat of
-					Otext => Text (textName ())
-					| Omatlab => Matlab {
-						variable = !variable
-						, file = matlabName ()
-					} | Odual => Dual {
-						text = textName ()
-						, matlab = {
-							variable = !variable
-							, file = matlabName ()
-						}
-					}
-			end
-	end
-end
diff --git a/src/nbc/program.sml b/src/nbc/program.sml
deleted file mode 100644
index df787ad..0000000
--- a/src/nbc/program.sml
+++ /dev/null
@@ -1,9 +0,0 @@
-signature PROGRAM = sig
-	val version: string
-	val name: string
-end
-
-structure Program :> PROGRAM = struct
-	val version = "2.0"
-	val name = "Naive Bayes Classifier - Score"
-end
diff --git a/src/nbc/score.mlb b/src/nbc/score.mlb
deleted file mode 100644
index 662bb83..0000000
--- a/src/nbc/score.mlb
+++ /dev/null
@@ -1,27 +0,0 @@
-$(SML_LIB)/basis/basis.mlb
-$(SML_LIB)/basis/mlton.mlb
-$(SML_LIB)/smlnj-lib/Util/smlnj-lib.mlb
-$(SML_LIB)/mlyacc-lib/mlyacc-lib.mlb
-fail.sml
-sequence.sml
-ann "allowFFI true" in
-	judy.sml
-	gzip.sml
-end
-substitution.grm.sig
-substitution.grm.sml
-substitution.lex.sml
-substitution.sml
-misc.sml
-options.sml
-storejudy.sml
-genome.sml
-nmer.sml
-kahan.sml
-score.sml
-binary.sml
-program.sml
-matlab.sml
-stopwatch.sml
-fasta.sml
-main.sml
diff --git a/src/nbc/score.sml b/src/nbc/score.sml
deleted file mode 100644
index 90d569a..0000000
--- a/src/nbc/score.sml
+++ /dev/null
@@ -1,30 +0,0 @@
-signature SCORE = sig
-	val score: int * real * (string -> int option) * real * string -> real
-end
-
-structure Score :> SCORE = struct
-	fun |> (x, f) = f x
-	infix |>
-
-	fun addCount (hitsum, fcount, gcount, totalWords) =
-		Kahan.add (hitsum, Real.fromInt fcount * Math.ln (Real.fromInt gcount / totalWords))
-	fun addNmer (totalWords, getGenomeCount) (nmer, ref fcount, (misses, anyhits, hitsum)) =
-		case getGenomeCount nmer of
-			NONE => (misses + 1, anyhits, hitsum)
-			| SOME gcount => (
-				misses, true
-				, addCount (hitsum, fcount, gcount, totalWords)
-			)
-	fun score (order, missConstant, getGenomeCount, totalWords, fragment) =
-		let
-			val add = addNmer (totalWords, getGenomeCount)
-			val seed = (0, false, Kahan.zero)
-			val (misses, anyhits, hitsum) =
-				Nmer.count (order, fragment) |> HashTable.foldi add seed
-		in
-			if anyhits then
-				Kahan.add (hitsum, Math.ln missConstant * Real.fromInt misses)
-				|> Kahan.sum
-			else Real.negInf
-		end
-end
diff --git a/src/nbc/sequence.sml b/src/nbc/sequence.sml
deleted file mode 100644
index 73a3fbf..0000000
--- a/src/nbc/sequence.sml
+++ /dev/null
@@ -1,74 +0,0 @@
-signature SEQUENCE = sig
-	type 'a t
-	val fold: ('a * 'b -> 'b) -> 'b -> 'a t -> 'b
-	val from: (unit -> 'a option) -> 'a t
-	val map: ('a -> 'b) -> 'a t -> 'b t
-	val app: ('a -> unit) -> 'a t -> unit
-	val fromArray: 'a array -> 'a t
-	val fromList: 'a list -> 'a t
-	val toList: 'a t -> 'a list
-	val toArray: 'a t -> 'a array
-end
-
-structure Sequence :> SEQUENCE = struct
-	type 'a t = unit -> 'a option
-	fun fold f seed t =
-		let
-			fun loop x =
-				case t () of
-					NONE => x
-					| SOME y => loop (f (y, x))
-		in
-			loop seed
-		end
-	fun from t = t
-	fun map f t =
-		fn () => (
-			case t () of
-				NONE => NONE
-				| SOME x => SOME (f x)
-		)
-	fun app f t =
-		let
-			fun loop () =
-				case t () of
-					NONE => ()
-					| SOME x => (
-						f x
-						; loop ()
-					)
-		in
-			loop ()
-		end
-	fun fromArray a =
-		let
-			val i = ref 0
-			fun f () =
-				if !i >= Array.length a then NONE
-				else
-					SOME (Array.sub (a, !i))
-					before i := !i + 1
-		in
-			from f
-		end
-	fun fromList l =
-		let
-			val c = ref l
-			fun f () =
-				case !c of
-					x :: y => (c := y; SOME x)
-					| nil => NONE
-		in
-			from f
-		end
-	fun toList t =
-		let
-			fun loop l =
-				case t () of
-					NONE => rev l
-					| SOME x => loop (x :: l)
-		in
-			loop nil
-		end
-	fun toArray t = Array.fromList (toList t)
-end
diff --git a/src/nbc/stopwatch.sml b/src/nbc/stopwatch.sml
deleted file mode 100644
index 43547ed..0000000
--- a/src/nbc/stopwatch.sml
+++ /dev/null
@@ -1,24 +0,0 @@
-signature STOPWATCH = sig
-	exception FinishWithoutStart
-	val start: string -> unit
-	val finish: unit -> unit
-end
-structure Stopwatch :> STOPWATCH = struct
-	exception FinishWithoutStart
-	local
-		val time = ref NONE
-	in
-		fun start doing = (
-			print (concat [doing, "..."])
-			; time := SOME (Time.now ())
-		)
-		fun finish () = case !time of
-			SOME t => (
-				print (concat [
-					" done in "
-					, Time.toString (Time.- (Time.now (), t))
-					, " seconds.\n"
-				]); time := NONE
-			) | NONE => raise FinishWithoutStart
-	end
-end
diff --git a/src/nbc/storejudy.sml b/src/nbc/storejudy.sml
deleted file mode 100644
index c6385be..0000000
--- a/src/nbc/storejudy.sml
+++ /dev/null
@@ -1,17 +0,0 @@
-signature STORE_JUDY = sig
-	type t
-	val load: (int * string) Sequence.t -> t
-	val get: t * string -> int option
-end
-
-structure StoreJudy :> STORE_JUDY = struct
-	type t = Judy.t
-	fun load e =
-		let
-			val j = Judy.create ()
-		in
-			Sequence.app (fn (count, nmer) => Judy.insert (j, nmer, count)) e
-			; j
-		end
-	val get = Judy.get
-end
diff --git a/src/nbc/substitution.grm b/src/nbc/substitution.grm
deleted file mode 100644
index 58505b5..0000000
--- a/src/nbc/substitution.grm
+++ /dev/null
@@ -1,50 +0,0 @@
-%%
-%name SubstitutionGrm
-%pos int
-%arg (lookup): string -> string
-%term
-	DOLLAR
-	| TEXT of string
-	| LEFT_PARENTHESIS
-	| LEFT_BRACE
-	| RIGHT_PARENTHESIS
-	| RIGHT_BRACE
-	| EOF
-%nonterm
-	STRING of string
-	| LIST of string list
-	| PORTION of string
-	| VARIABLE of string
-	| PARENTHESIZED of string list
-	| INSIDE_PARENTHESES of string list
-	| BRACED of string list
-	| INSIDE_BRACES of string list
-%eop EOF
-%noshift EOF
-%start STRING
-%%
-STRING: LIST (concat LIST)
-LIST:
-	(nil)
-	| PORTION LIST (PORTION :: LIST)
-PORTION:
-	TEXT (TEXT)
-	| VARIABLE (lookup VARIABLE)
-VARIABLE:
-	DOLLAR TEXT (TEXT)
-	| PARENTHESIZED (concat PARENTHESIZED)
-	| BRACED (concat BRACED)
-PARENTHESIZED:
-	LEFT_PARENTHESIS INSIDE_PARENTHESES RIGHT_PARENTHESIS (INSIDE_PARENTHESES)
-INSIDE_PARENTHESES:
-	(nil)
-	| TEXT INSIDE_PARENTHESES (TEXT :: INSIDE_PARENTHESES)
-	| LEFT_PARENTHESIS INSIDE_PARENTHESES RIGHT_PARENTHESIS INSIDE_PARENTHESES
-		("(" :: INSIDE_PARENTHESES1 @ ")" :: INSIDE_PARENTHESES2)
-BRACED:
-	LEFT_BRACE INSIDE_BRACES RIGHT_BRACE (INSIDE_BRACES)
-INSIDE_BRACES:
-	(nil)
-	| TEXT INSIDE_BRACES (TEXT :: INSIDE_BRACES)
-	| LEFT_BRACE INSIDE_BRACES RIGHT_BRACE INSIDE_BRACES
-		("{" :: INSIDE_BRACES1 @ "}" :: INSIDE_BRACES2)
diff --git a/src/nbc/substitution.lex b/src/nbc/substitution.lex
deleted file mode 100644
index e460121..0000000
--- a/src/nbc/substitution.lex
+++ /dev/null
@@ -1,54 +0,0 @@
-type svalue = Tokens.svalue
-type ('a, 'b) token = ('a, 'b) Tokens.token
-type pos = int
-type lexresult = (svalue, pos) token
-type arg = int ref
-fun eof _ = Tokens.EOF (~1, ~1)
-%%
-%full
-%header (functor SubstitutionLexFun (structure Tokens: SubstitutionGrm_TOKENS));
-%arg (nesting);
-%s VARIABLE PARENTHESIZED BRACED;
-text = ([^$] | "\\$")+;
-dollar = "$";
-leftparenthesis = "(";
-rightparenthesis = ")";
-notparenthesis = [^()]+;
-leftbrace = "{";
-rightbrace = "}";
-notbrace = [^{}]+;
-other = [A-Za-z0-9_]+;
-%%
-<INITIAL>{text} => (Tokens.TEXT (yytext, yypos, yypos + size yytext));
-<INITIAL>{dollar} => (YYBEGIN VARIABLE; Tokens.DOLLAR (yypos, yypos + 1));
-<INITIAL>{dollar}{leftparenthesis} => (
-	YYBEGIN PARENTHESIZED
-	; nesting := !nesting + 1
-	; Tokens.LEFT_PARENTHESIS (yypos, yypos + 1)
-);
-<INITIAL>{dollar}{leftbrace} => (
-	YYBEGIN BRACED
-	; nesting := !nesting + 1
-	; Tokens.LEFT_BRACE (yypos, yypos + 1)
-);
-<VARIABLE>{other} => (YYBEGIN INITIAL; Tokens.TEXT (yytext, yypos, yypos + size yytext));
-<PARENTHESIZED>{notparenthesis} => (Tokens.TEXT (yytext, yypos, yypos + size yytext));
-<PARENTHESIZED>{leftparenthesis} => (
-	nesting := !nesting + 1
-	; Tokens.LEFT_PARENTHESIS (yypos, yypos + 1)
-);
-<PARENTHESIZED>{rightparenthesis} => (
-	nesting := !nesting - 1
-	; if !nesting = 0 then YYBEGIN INITIAL else ()
-	; Tokens.RIGHT_PARENTHESIS (yypos, yypos + 1)
-);
-<BRACED>{notbrace} => (Tokens.TEXT (yytext, yypos, yypos + size yytext));
-<BRACED>{leftbrace} => (
-	nesting := !nesting + 1
-	; Tokens.LEFT_BRACE (yypos, yypos + 1)
-);
-<BRACED>{rightbrace} => (
-	nesting := !nesting - 1
-	; if !nesting = 0 then YYBEGIN INITIAL else ()
-	; Tokens.RIGHT_BRACE (yypos, yypos + 1)
-);
diff --git a/src/nbc/substitution.sml b/src/nbc/substitution.sml
deleted file mode 100644
index 57d55cf..0000000
--- a/src/nbc/substitution.sml
+++ /dev/null
@@ -1,26 +0,0 @@
-signature SUBSTITUTION = sig
-	val substitute: (string -> string) -> string -> string option
-end
-
-structure Substitution :> SUBSTITUTION = struct
-	structure LrVals = SubstitutionGrmLrValsFun (structure Token = LrParser.Token)
-	structure Lex = SubstitutionLexFun (structure Tokens = LrVals.Tokens)
-	structure Parser = JoinWithArg (
-		structure ParserData = LrVals.ParserData
-		structure Lex = Lex
-		structure LrParser = LrParser
-	)
-	fun substitute lookup source =
-		let
-			val position = ref 0
-			val instream = TextIO.openString source
-			fun read n = TextIO.inputN (instream, n)
-			val lexer = Parser.makeLexer read (ref 0)
-			fun error (_, _, _) = ()
-			val (result, _) = Parser.parse (0, lexer, error, lookup)
-			val () = TextIO.closeIn instream
-		in
-			SOME result
-		end
-		handle Parser.ParseError => NONE
-end
diff --git a/src/nbc/tabulate.ml b/src/nbc/tabulate.ml
deleted file mode 100644
index dbfbe43..0000000
--- a/src/nbc/tabulate.ml
+++ /dev/null
@@ -1,190 +0,0 @@
-let (|>) a b = b a
-let car, cdr = fst, snd
-let odd n = n land 1 = 1
-let even n = not (odd n)
-module ExtArray = ExtArray.Array
-module ExtList = ExtList.List
-module ExtString = ExtString.String
-module Program = struct
-	let name = "Naive Bayes Classifier - Tabulate"
-	let version = "1.0"
-end
-let chop_extra s = ExtString.strip ~chars:"_- " s
-let any_alphanumeric s =
-	let e = String.length s in
-	let rec loop i =
-		if i = e then false
-		else match s.[i] with
-			'a'..'z' | 'A'..'Z' | '0'..'9' -> true
-			| _ -> loop (i + 1)
-	in loop 0
-let guess_prefix filenames =
-	let s =
-		List.map Misc.basename_without_extension filenames
-			|> Misc.longest_common_substring |> chop_extra
-	in
-	if any_alphanumeric s then s
-	else ""
-module Options = struct
-	let parser = OptParse.OptParser.make ~version:Program.version ()
-	let genomes =
-		let option = OptParse.StdOpt.str_option ~metavar:"file" () in
-		OptParse.OptParser.add parser ~short_name:'g' ~long_name:"genome-list" option;
-		(fun () -> match OptParse.Opt.opt option with
-			Some x -> x
-			| None ->
-				OptParse.OptParser.usage parser ();
-				exit 1
-		)
-	let columns =
-		let option = OptParse.StdOpt.int_option ~default:200 () in
-		OptParse.OptParser.add parser ~short_name:'c' ~long_name:"columns" option;
-		(fun () -> OptParse.Opt.get option)
-	let template =
-		let option = OptParse.StdOpt.str_option ~metavar:"template"
-			~default:"$prefix-$n.csv.gz" () in
-		OptParse.OptParser.add parser ~short_name:'t' ~long_name:"output-template" option;
-		(fun () -> OptParse.Opt.get option)
-	let given_prefix =
-		let x = ref None in
-		OptParse.StdOpt.str_callback ~metavar:"prefix" (fun s -> x := Some s)
-			|> OptParse.OptParser.add parser ~short_name:'p'
-				~long_name:"output-prefix";
-		(fun () -> !x)
-	let files = OptParse.OptParser.parse_argv parser
-	let prefix = match given_prefix () with
-		None -> (
-			match guess_prefix files with
-				"" -> "table"
-				| s -> s
-		) | Some x -> x
-	let string_of_int n = Printf.sprintf "%08u" n
-	let output n = template () |> Misc.substitute ["prefix", prefix; "n", string_of_int n]
-end
-
-exception Collide of string * string * string
-let match_files_to_genomes genomes files =
-	let g = Array.of_list genomes in
-	let gl = Array.length g in
-	let gi = Array.init gl (fun i -> i) in
-	Array.sort (fun ai bi -> compare (String.length g.(bi)) (String.length g.(ai))) gi;
-	let gf = Array.make gl None in
-	List.iter (fun file ->
-		try (
-			let i = ExtArray.find (fun i -> ExtString.exists file g.(i)) gi in
-			match gf.(i) with
-				None -> gf.(i) <- Some file
-				| Some other_file -> raise (Collide (g.(i), other_file, file))
-		) with Not_found -> () (* file does not match any genomes *)
-	) files;
-	let r = ref [] in
-	for i = gl - 1 downto 0 do
-		match gf.(i) with
-			None -> () (* no file matches a given genome *)
-			| Some file -> r := (g.(i), file) :: !r
-	done;
-	!r
-
-let columns = Options.columns ()
-let genomes, files =
-	let genomes = Misc.io_of_file (Options.genomes ()) |> Misc.enum_of_lines
-		|> ExtList.of_enum in
-	let g, f = match_files_to_genomes genomes Options.files |> List.split in
-	Array.of_list g,
-	f |> List.map (fun x -> x, x |> open_in |> IO.input_channel) |> Array.of_list
-
-let newfile, newline, cell, finish = 
-	let i = ref 0 in
-	let open_file () =
-		i := !i + 1;
-		let filename = Options.output !i in
-		Gzip.open_out filename
-	in
-	let c = ref None in
-	let force_out () =
-		match !c with
-			None ->
-				let d = open_file () in
-				c := Some d;
-				d
-			| Some d -> d
-	in
-	let start_of_line = ref true in
-	(* newfile *) (fun () ->
-		(match !c with
-			Some c -> Gzip.close_out c
-			| None -> ());
-		i := !i + 1;
-		c := None
-	),
-	(* newline *) (fun () ->
-		let c = force_out () in
-		Gzip.output_char c '\n';
-		start_of_line := true
-	),
-	(* cell *) (fun s ->
-		let c = force_out () in
-		if not !start_of_line then Gzip.output_char c ',';
-		Gzip.output c s 0 (String.length s);
-		start_of_line := false
-	),
-	(* finish *) (fun () ->
-		match !c with
-			Some c -> Gzip.close_out c
-			| None -> ()
-	)
-
-let read_two_fields (filename, c) =
-		let line = IO.read_line c in
-		match Misc.split2 line with
-			Some x -> x
-			| None ->
-				Printf.eprintf "\
-					There is something wrong with the file %s. \
-					The offending line is:\n%s\n" filename line;
-				exit 1
-
-let output_file () =
-	newfile ();
-	let yes_we_have_input =
-		let x = ref false in
-		(fun () ->
-			if !x then ()
-			else (
-				cell "names";
-				x := true
-			)
-		)
-	in
-	let a = Array.make columns "" in
-	let rec loop i =
-		if i < columns then (
-			try (
-				let name, datum = read_two_fields files.(0) in
-				yes_we_have_input ();
-				cell name;
-				a.(i) <- datum;
-				loop (i + 1)
-			) with IO.No_more_input ->
-				if i > 0 then Array.sub a 0 i
-				else raise End_of_file
-		) else a
-	in
-	let a = loop 0 in
-	let these_columns = Array.length a in
-	newline ();
-	cell genomes.(0);
-	for i = 0 to these_columns - 1 do cell a.(i) done;
-	newline ();
-	for i = 1 to Array.length genomes - 1 do
-		cell genomes.(i);
-		for j = 0 to these_columns - 1 do
-			let _, datum = read_two_fields files.(i) in
-			cell datum
-		done;
-		newline ()
-	done
-
-let () =
-	try while true do output_file () done
-	with End_of_file -> finish ()
diff --git a/src/nbc/test-generate.sml b/src/nbc/test-generate.sml
deleted file mode 100644
index 77cafd3..0000000
--- a/src/nbc/test-generate.sml
+++ /dev/null
@@ -1 +0,0 @@
-structure Test = Test ()