diff --git a/SelectSequencesFromMSA.cabal b/SelectSequencesFromMSA.cabal
--- a/SelectSequencesFromMSA.cabal
+++ b/SelectSequencesFromMSA.cabal
@@ -1,5 +1,5 @@
 name:                SelectSequencesFromMSA
-version:             1.0.2
+version:             1.0.3
 synopsis:            SelectSequences is a tool for selection of a represenative subset of sequences from a multiple sequence alignment in clustal format.
 description:         SelectSequences is a tool for selection of a represenative subset of sequences from a multiple sequence alignment in clustal format.
                      .
@@ -25,8 +25,8 @@
 
 source-repository this
   type:     git
-  location: https://github.com/eggzilla/SelectSequencesFromMSA/tree/1.0.2
-  tag:      1.0.2
+  location: https://github.com/eggzilla/SelectSequencesFromMSA/tree/1.0.3
+  tag:      1.0.3
                      
 executable SelectSequencesFromMSA
   Hs-Source-Dirs:      ./src/Bio/
diff --git a/src/Bio/SelectSequences.hs b/src/Bio/SelectSequences.hs
--- a/src/Bio/SelectSequences.hs
+++ b/src/Bio/SelectSequences.hs
@@ -18,7 +18,8 @@
     optimalIdentity :: Double,
     maximalIdenity :: Double,
     referenceSequence :: Bool,
-    distanceMatrixPath :: String
+    distanceMatrixPath :: String,
+    reformatIdOption :: String
   } deriving (Show,Data,Typeable)
 
 options :: Options
@@ -30,7 +31,8 @@
     optimalIdentity = (80 :: Double) &= name "i" &= help "Optimize for this percentage of mean pairwise identity (Default: 80)",
     maximalIdenity = (95 :: Double) &= name "m" &= help "Sequences with a higher percentage of pairwise Identity will be removed. (Default: 95)",
     referenceSequence = True &= name "x" &= help "The first sequence (=reference sequence) is always present in the output alignment per default. Default: True",
-    distanceMatrixPath = "" &= name "d" &= help "Path to distance matrix output file, only internal for interal sequence selection, e.g. /home/user/distmat (Default: )"
+    distanceMatrixPath = "" &= name "d" &= help "Path to distance matrix output file, only internal for interal sequence selection, e.g. /home/user/distmat (Default: )",
+    reformatIdOption = "RNAcode" &= name "r" &= help "Defines how sequence id is reformated, e.g. fitting for RNAcode or not (Default: RNAcode)"
   } &= summary "SelectSequences" &= help "Florian Eggenhofer 2016" &= verbosity
 
 main :: IO ()
@@ -48,7 +50,7 @@
           Control.Monad.unless (null distanceMatrixPath) (writeFile distanceMatrixPath idMatrix)
         else print ("A problem occured selecting sequences: " ++ fromLeft resultStatus)
     else do
-      resultStatus <- preprocessClustalForRNAz inputClustalPath (selectedOutputPath ++ "/") seqenceNumber optimalIdentity maximalIdenity referenceSequence
+      resultStatus <- preprocessClustalForRNAz inputClustalPath (selectedOutputPath ++ "/") seqenceNumber optimalIdentity maximalIdenity referenceSequence reformatIdOption
       if isRight resultStatus
         then do
           let (_,resultAln) = fromRight resultStatus
diff --git a/src/Bio/SelectSequencesLibrary.hs b/src/Bio/SelectSequencesLibrary.hs
--- a/src/Bio/SelectSequencesLibrary.hs
+++ b/src/Bio/SelectSequencesLibrary.hs
@@ -70,8 +70,8 @@
   selectedClustalText <- readFile selectedClustalpath
   return (Right ([],selectedClustalText))
 
-preprocessClustalForRNAz :: String -> String -> Int -> Double -> Double -> Bool -> IO (Either String (String,String))
-preprocessClustalForRNAz clustalFilepath outputPath seqenceNumber optimalIdentity maximalIdenity referenceSequence = do
+preprocessClustalForRNAz :: String -> String -> Int -> Double -> Double -> Bool -> String -> IO (Either String (String,String))
+preprocessClustalForRNAz clustalFilepath outputPath seqenceNumber optimalIdentity maximalIdenity referenceSequence reformatOption = do
   clustalText <- TI.readFile clustalFilepath
   let clustalTextLines = T.lines clustalText
   parsedClustalInput <- readClustalAlignment clustalFilepath
@@ -80,7 +80,7 @@
     then
       if isRight parsedClustalInput
         then do
-          let (idMatrix,filteredClustalInput) = rnaCodeSelectSeqs2 (fromRight parsedClustalInput) seqenceNumber optimalIdentity maximalIdenity referenceSequence
+          let (idMatrix,filteredClustalInput) = rnaCodeSelectSeqs2 (fromRight parsedClustalInput) seqenceNumber optimalIdentity maximalIdenity referenceSequence reformatOption
           writeFile selectedClustalpath (show filteredClustalInput)
           let formatedIdMatrix = show (fmap formatIdMatrix idMatrix)
           return (Right (formatedIdMatrix,selectedClustalpath))
@@ -99,8 +99,8 @@
 
 
 -- | Sequence preselection for RNAz and RNAcode                   
-rnaCodeSelectSeqs2 :: ClustalAlignment -> Int -> Double -> Double -> Bool -> (Matrix (Maybe (Int,Int,Double)),ClustalAlignment)
-rnaCodeSelectSeqs2 currentClustalAlignment targetSeqNumber optimalIdentity maximalIdentity referenceSequence = (identityMatrix,newClustalAlignment)
+rnaCodeSelectSeqs2 :: ClustalAlignment -> Int -> Double -> Double -> Bool -> String -> (Matrix (Maybe (Int,Int,Double)),ClustalAlignment)
+rnaCodeSelectSeqs2 currentClustalAlignment targetSeqNumber optimalIdentity maximalIdentity referenceSequence reformatOption = (identityMatrix,newClustalAlignment)
   where entryVector = V.fromList (alignmentEntries currentClustalAlignment)
         entrySequences = V.map entryAlignedSequence entryVector
         entryReformatedSequences = V.map (T.map reformatRNACodeAln) entrySequences
@@ -120,7 +120,9 @@
         selectedEntryIndices = selectEntryIndices referenceSequence targetSeqNumber sortedIndices
         selectedEntries = map (\ind -> entryVector V.! (ind-1)) selectedEntryIndices
         selectedEntryHeader = map entrySequenceIdentifier selectedEntries
-        reformatedSelectedEntryHeader =  map (T.map reformatRNACodeId) selectedEntryHeader
+        selectedReformatFunction = selectReformatFunction reformatOption
+        reformatedSelectedEntryHeader =  map (T.map selectedReformatFunction) selectedEntryHeader
+        --reformatedSelectedEntryHeader =  map (T.map reformatRNACodeId) selectedEntryHeader
         selectedEntrySequences = map (\ind -> entryReformatedSequences V.! (ind-1)) selectedEntryIndices
         --gapfreeEntrySequences = T.transpose (T.filter (\a -> not (T.all isGap a)) (T.transpose selectedEntrySequences))
         gapfreeEntrySequences = T.transpose (filter (not . T.all isGap) (T.transpose selectedEntrySequences))
@@ -128,13 +130,19 @@
         emptyConservationTrack = setEmptyConservationTrack gapfreeEntries (conservationTrack currentClustalAlignment)
         newClustalAlignment = currentClustalAlignment {alignmentEntries = gapfreeEntries, conservationTrack = emptyConservationTrack}
 
+selectReformatFunction :: String -> (Char -> Char)
+selectReformatFunction reformatOption
+  | reformatOption == "RNAcode" = reformatRNACodeId
+  | otherwise = id
+
 selectEntryIndices :: Bool -> Int -> [Int] -> [Int]
 selectEntryIndices referenceSequence targetSeqNumber sortedIndices
-  | referenceSequence = if (1 :: Int) `elem` firstX then firstX else 1:firstXm1
+  | referenceSequence = if (1 :: Int) `elem` firstX then firstRefX else 1:firstXm1
   | otherwise = firstX
     where firstXm1 = take (targetSeqNumber - 1)  sortedIndices
           firstX = take targetSeqNumber sortedIndices
-
+          firstRefX =(1 :: Int):(filter (\i -> i /= (1 :: Int)) firstX)
+ 
 setEmptyConservationTrack :: [ClustalAlignmentEntry] -> T.Text -> T.Text
 setEmptyConservationTrack alnentries currentConservationTrack
   | null alnentries = currentConservationTrack
@@ -242,3 +250,4 @@
   | c == 'c' = 'C'
   | c == 'a' = 'A'
   | otherwise = c
+