diff --git a/ClustalParser.cabal b/ClustalParser.cabal
--- a/ClustalParser.cabal
+++ b/ClustalParser.cabal
@@ -5,7 +5,7 @@
 -- PVP summary:      +-+------- breaking API changes
 --                   | | +----- non-breaking API additions
 --                   | | | +--- code changes with no API change
-version:             1.1.2
+version:             1.1.3
 synopsis:            Libary for parsing Clustal tools output
 description:         Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna, cmalign
                      .
@@ -36,8 +36,8 @@
 
 source-repository this
   type:     git
-  location: https://github.com/eggzilla/ClustalParser/tree/1.1.2
-  tag:      1.1.2
+  location: https://github.com/eggzilla/ClustalParser/tree/1.1.3
+  tag:      1.1.3
 
 library
   -- Modules exported by the library.
diff --git a/ClustalParserTest.hs b/ClustalParserTest.hs
--- a/ClustalParserTest.hs
+++ b/ClustalParserTest.hs
@@ -9,7 +9,7 @@
   args <- getArgs
   let input_file = (head args)                                     
   -- read Clustal outputfile
-  parsedinput <- readStructuralClustalAlignment input_file
+  parsedinput <- readClustalAlignment input_file
   --parsedinput <- readStructuralClustalAlignment input_file
   --print (entrySequenceIdentifier (head (structuralAlignmentEntries(fromRight parsedinput))))
   print (fromRight parsedinput)
diff --git a/changelog b/changelog
--- a/changelog
+++ b/changelog
@@ -1,4 +1,7 @@
 -*-change-log-*-
+1.1.3 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 4. July 2015
+        * Nucleotide sequences are now parsed by a unified function in line
+	with IUPAC nucleotide code
 1.1.2 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 3. July 2015
         * Included parsing of optional field in mlocarna clustal output
 1.1.1 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 2. July 2015
diff --git a/src/Bio/ClustalParser.hs b/src/Bio/ClustalParser.hs
--- a/src/Bio/ClustalParser.hs
+++ b/src/Bio/ClustalParser.hs
@@ -150,7 +150,7 @@
 genParserClustalEntrySlice = do
   sliceIdentifier <- many1 (noneOf " ")
   spacer <- many1 (char ' ')
-  sliceSequence <- many1 (oneOf ".SNYRUAGCT-uagct")
+  sliceSequence <- parseNucleotideAlignmentEntry
   newline
   return $ ClustalAlignmentEntrySlice sliceIdentifier sliceSequence (length spacer)
 
@@ -225,7 +225,7 @@
 genParserStructuralClustalEntrySlice = do
   sliceIdentifier <- many1 (noneOf " ")
   many1 (char ' ')
-  sliceSequence <- many1 (oneOf ".SNYRUAGCT-uagtc")
+  sliceSequence <- parseNucleotideAlignmentEntry
   newline
   return $ StructuralClustalAlignmentEntrySlice (filter (/='\n') sliceIdentifier) sliceSequence
 
@@ -254,3 +254,27 @@
 -- | Parse Clustal summary (printed to STDOUT) from file
 readClustalSummary :: String -> IO (Either ParseError ClustalSummary)       
 readClustalSummary = parseFromFile genParserClustalSummary
+
+-- | Parse nucleotide sequence. Allowed letters according to IUPAC
+parseNucleotideSequence :: GenParser Char st String
+parseNucleotideSequence = do
+  nucleotideSequence <- many1 (oneOf "RYSWKMBDHVNATUGCryswkmbdhvnatugc") 
+  return $ nucleotideSequence
+
+-- | Parse nucleotide alignment entry. Allowed letters according to IUPAC and commonly used gap characters
+parseNucleotideAlignmentEntry :: GenParser Char st String
+parseNucleotideAlignmentEntry = do
+  entry <- many1 (oneOf "~_-.RYSWKMBDHVNATUGCryswkmbdhvnatugc") 
+  return $ entry
+
+-- | Parse protein amino acid code sequence. Allowed letters according to IUPAC
+parseProteinSequence :: GenParser Char st String
+parseProteinSequence = do
+  proteinSequence <- many1 (oneOf "ABCDEFGHIKLMNPQRSTVWXYZabcdefghiklmnpqrstvwxyz") 
+  return $ proteinSequence
+
+-- | Parse protein amino acid code alignment entry. Allowed letters according to IUPAC and commonly used gap characters
+parseProteinAlignmentEntry :: GenParser Char st String
+parseProteinAlignmentEntry = do
+  entry <- many1 (oneOf "~_-.ABCDEFGHIKLMNPQRSTVWXYZabcdefghiklmnpqrstvwxyz") 
+  return $ entry