diff --git a/Bio/Alignment/AlignData.hs b/Bio/Alignment/AlignData.hs
--- a/Bio/Alignment/AlignData.hs
+++ b/Bio/Alignment/AlignData.hs
@@ -41,6 +41,8 @@
 
 -- | Gaps are coded as '*'s, this function removes them, and returns
 --   the sequence along with the list of gap positions.
+--   note that gaps are positioned relative to the *gapped* sequence 
+--   (contrast to stmassembler/Cluster.hs)
 extractGaps :: SeqData -> (SeqData,Gaps)
 extractGaps str = (BC.filter (/='*') str,BC.elemIndices '*' str)
 
diff --git a/Bio/Sequence.hs b/Bio/Sequence.hs
--- a/Bio/Sequence.hs
+++ b/Bio/Sequence.hs
@@ -21,7 +21,10 @@
     -- ** Other utility functions
     , defragSeq, seqmap
 
-    -- * File formats
+    -- * File IO
+    -- ** Generic sequence reading
+    , readNuc, readProt
+
     -- ** The Fasta file format ("Bio.Sequence.Fasta")
     , readFasta, hReadFasta 
     , writeFasta, hWriteFasta
@@ -67,3 +70,13 @@
 -- sequence-oriented stuff
 import Bio.Sequence.Entropy
 import Bio.Sequence.HashWord
+
+-- | Read nucleotide sequences in any format - Fasta, SFF, FastQ, 2bit, PHD...
+readNuc :: FilePath -> IO [Sequence Nuc]
+readNuc = undefined
+          -- check file contents
+          -- magic number
+
+-- | Read protein sequences in any supported format (i.e. Fasta)
+readProt :: FilePath -> IO [Sequence Amino]
+readProt xs = map castSeq `fmap` readFasta xs
diff --git a/Bio/Util/TestBase.hs b/Bio/Util/TestBase.hs
deleted file mode 100644
--- a/Bio/Util/TestBase.hs
+++ /dev/null
@@ -1,123 +0,0 @@
-{-# OPTIONS -fglasgow-exts #-}
-
-module Bio.Util.TestBase where
-
-import Control.Monad (liftM)
-import System.CPUTime
-import System.Time
-import Test.QuickCheck
-import System.Random
--- import Data.Char (ord)
-import Data.Word
-import Data.ByteString.Lazy (pack)
-
-import Bio.Sequence.SeqData
-
-data Test = forall t . Testable t => T String t
-
-newtype Nucleotide = N Char deriving Show
-newtype Quality    = Q Word8 deriving Show
-
-fromN :: Nucleotide -> Char
-fromN (N c) = c
-
-fromQ :: Quality -> Word8
-fromQ (Q c) = c
-
--- | For testing, variable lengths
-newtype EST = E (Sequence Nuc) deriving Show
-newtype ESTq = Eq (Sequence Nuc) deriving Show
-newtype Protein = P (Sequence Amino) deriving Show
-
--- | For benchmarking, fixed lengths
-newtype EST_short = ES (Sequence Nuc) deriving Show
-newtype EST_long  = EL (Sequence Nuc) deriving Show
-newtype EST_set  = ESet [Sequence Nuc] deriving Show
-
--- | Take time (CPU and wall clock) and report it
-time :: String -> IO () -> IO ()
-time msg action = do
-    d1 <- getClockTime
-    t1 <- getCPUTime
-    action
-    t2 <- getCPUTime
-    d2 <- getClockTime
-    putStrLn $ "\n"++msg++", CPU time: " ++ showT (t2-t1) ++ ", wall clock: "
-                 ++ timeDiffToString (diffClockTimes d2 d1)
-
--- | Print a CPUTime difference
-showT :: Integral a => a -> String
-showT t = show (fromIntegral t/1e12::Double)++"s"
-
--- | Shamelessly stolen from FPS
-integralRandomR :: (Integral a, RandomGen g) => (a,a) -> g -> (a,g)
-integralRandomR  (a,b) g = case randomR (fromIntegral a :: Integer,
-                                         fromIntegral b :: Integer) g of
-                            (x,g') -> (fromIntegral x, g')
-
--- | Constrained position generators
-
-genOffset :: Gen Offset
-genOffset = do isneg <- arbitrary
-               nnoff <- genNonNegOffset
-               return $ (if isneg then negate else id) nnoff
-
-genNonNegOffset :: Gen Offset
-genNonNegOffset = liftM (subtract 1) genPositiveOffset
-
-genPositiveOffset :: Gen Offset
-genPositiveOffset = do scale <- chooseInteger (1, 13)
-                       liftM fromIntegral $ chooseInteger (1, 2^scale)
-    where chooseInteger :: (Integer, Integer) -> Gen Integer
-          chooseInteger = choose
-
-
-instance Random Word8 where
-    randomR = integralRandomR
-    random = randomR (minBound,maxBound)
-
-instance Arbitrary Word8 where
-    arbitrary = choose (0,255)
-
-instance Arbitrary Nucleotide where
-    arbitrary = elements (map N "aaacccgggtttn")
-
-instance Arbitrary Quality where
-    arbitrary = do c <- choose (0,60)
-                   return (Q c)
-
-instance Arbitrary ESTq where
-    arbitrary = do n <- choose (1,100)
-                   s <- vector n
-                   q <- vector n
-                   return $ Eq $ Seq (fromStr "qctest")
-                              (fromStr $ map fromN s) (Just $ pack $ map fromQ q)
-
-instance Arbitrary EST where
-    arbitrary = do n <- choose (1,100)
-                   s <- vector n
-                   return $ E $ Seq (fromStr "qctest")
-                              (fromStr $ map fromN s) Nothing
-
--- instance Arbitrary Char where
---    arbitrary = elements (['A'..'Z']++['a'..'z']++" \t\n\r")
-
-instance Arbitrary EST_short where
-    arbitrary = do let n = 200
-                   s <- vector n
-                   q <- vector n
-                   return $ ES $ Seq (fromStr "qctest")
-                              (fromStr $ map fromN s) (Just $ pack $ map fromQ q)
-
-instance Arbitrary EST_long where
-    arbitrary = do let n = 1000
-                   s <- vector n
-                   q <- vector n
-                   return $ EL $ Seq (fromStr "qctest")
-                              (fromStr $ map fromN s) (Just $ pack $ map fromQ q)
-
--- 1000 ESTs of length 1000
-instance Arbitrary EST_set where
-    arbitrary = do let n = 1000
-                   s <- vector n
-                   return (ESet $ map (\(EL x) -> x) s)
diff --git a/bio.cabal b/bio.cabal
--- a/bio.cabal
+++ b/bio.cabal
@@ -1,5 +1,5 @@
 Name:                bio
-Version:             0.4.6
+Version:             0.4.7
 License:             LGPL
 License-file:        LICENSE
 Author:              Ketil Malde
@@ -50,7 +50,7 @@
                      Bio.Alignment.Soap,
 		     Bio.Alignment.BED, Bio.Alignment.PSL
                      Bio.Clustering,
-                     Bio.Util, Bio.Util.Parsex, Bio.Util.TestBase
+                     Bio.Util, Bio.Util.Parsex
 		 Bio.Location.Strand, Bio.Location.Position,
 		 Bio.Location.ContigLocation, Bio.Location.Location, Bio.Location.LocMap,
 		 Bio.Location.OnSeq, Bio.Location.SeqLocation, Bio.Location.SeqLocMap,