diff --git a/Bio/Alignment/AlignData.hs b/Bio/Alignment/AlignData.hs
--- a/Bio/Alignment/AlignData.hs
+++ b/Bio/Alignment/AlignData.hs
@@ -41,8 +41,6 @@
 
 -- | 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
@@ -21,10 +21,7 @@
     -- ** Other utility functions
     , defragSeq, seqmap
 
-    -- * File IO
-    -- ** Generic sequence reading
-    , readNuc, readProt
-
+    -- * File formats
     -- ** The Fasta file format ("Bio.Sequence.Fasta")
     , readFasta, hReadFasta 
     , writeFasta, hWriteFasta
@@ -70,13 +67,3 @@
 -- 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.cabal b/bio.cabal
--- a/bio.cabal
+++ b/bio.cabal
@@ -1,5 +1,5 @@
 Name:                bio
-Version:             0.4.5
+Version:             0.4.6
 License:             LGPL
 License-file:        LICENSE
 Author:              Ketil Malde