diff --git a/SelectSequencesFromMSA.cabal b/SelectSequencesFromMSA.cabal
--- a/SelectSequencesFromMSA.cabal
+++ b/SelectSequencesFromMSA.cabal
@@ -1,5 +1,5 @@
 name:                SelectSequencesFromMSA
-version:             1.0.4
+version:             1.0.5
 synopsis:            Selects a representative subset of sequences from multiple sequence alignment.
 description:         SelectSequences is a tool for selection of a representative subset of sequences from a multiple sequence alignment in clustal format.
                      .
@@ -26,8 +26,8 @@
 
 source-repository this
   type:     git
-  location: https://github.com/eggzilla/SelectSequencesFromMSA/tree/1.0.4
-  tag:      1.0.4
+  location: https://github.com/eggzilla/SelectSequencesFromMSA/tree/1.0.5
+  tag:      1.0.5
                      
 executable SelectSequencesFromMSA
   Hs-Source-Dirs:      ./src/Bio/
@@ -38,5 +38,5 @@
 Library
   Hs-Source-Dirs:      ./src/
   ghc-options:         -Wall -fno-warn-unused-do-bind
-  build-depends:       base >=4.5 && <5, cmdargs, ViennaRNAParser>=1.3.2, process, directory, biofasta, parsec, biocore, bytestring, either-unwrap, containers, ClustalParser>=1.2.2, vector, matrix, filepath, text, transformers, text-metrics
+  build-depends:       base >=4.5 && <5, cmdargs, ViennaRNAParser>=1.3.2, process, directory, biofasta, parsec, biocore, bytestring, either-unwrap, containers, ClustalParser>=1.2.3, vector, matrix, filepath, text, transformers, text-metrics
   Exposed-Modules:     Bio.SelectSequencesLibrary
diff --git a/src/Bio/SelectSequences.hs b/src/Bio/SelectSequences.hs
--- a/src/Bio/SelectSequences.hs
+++ b/src/Bio/SelectSequences.hs
@@ -13,6 +13,7 @@
 data Options = Options
   { inputClustalPath :: String,
     outputPath :: String,
+    outputFileName :: String,
     toogleExternalSelectSequences :: Bool,
     seqenceNumber :: Int,
     optimalIdentity :: Double,
@@ -26,6 +27,7 @@
 options = Options
   { inputClustalPath = def &= name "c" &= help "Path to input clustal file",
     outputPath = def &= name "o" &= help "Path to output directory. Default: current working directory",
+    outputFileName = "results.selected" &= name "f" &= help "Output filename. Default: results.selected",
     toogleExternalSelectSequences = False &= name "e" &= help "Use only replacement of alignment characters and external 'selectSequence.pl'. Default: False",
     seqenceNumber = (6 :: Int) &= name "n" &= help "Number of sequences in the output alignment. (Default: 6)",
     optimalIdentity = (80 :: Double) &= name "i" &= help "Optimize for this percentage of mean pairwise identity (Default: 80)",
@@ -42,7 +44,7 @@
   let selectedOutputPath = if null outputPath then currentWorkDirectory else outputPath
   if toogleExternalSelectSequences
     then do
-      resultStatus <- preprocessClustalForRNAzExternal inputClustalPath (selectedOutputPath ++ "/") seqenceNumber (truncate optimalIdentity) (truncate maximalIdenity) referenceSequence
+      resultStatus <- preprocessClustalForRNAzExternal inputClustalPath (selectedOutputPath ++ "/") outputFileName seqenceNumber (truncate optimalIdentity) (truncate maximalIdenity) referenceSequence
       if isRight resultStatus
         then do
           let (idMatrix,_) = fromRight resultStatus
@@ -50,7 +52,7 @@
           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 reformatIdOption
+      resultStatus <- preprocessClustalForRNAz inputClustalPath (selectedOutputPath ++ "/") outputFileName seqenceNumber optimalIdentity maximalIdenity referenceSequence reformatIdOption
       if isRight resultStatus
         then do
           return ()
diff --git a/src/Bio/SelectSequencesLibrary.hs b/src/Bio/SelectSequencesLibrary.hs
--- a/src/Bio/SelectSequencesLibrary.hs
+++ b/src/Bio/SelectSequencesLibrary.hs
@@ -28,8 +28,8 @@
          identityPercent = 1 - (fromIntegral distanceDouble/fromIntegral maximumDistance)
 
 -- | Call for external preprocessClustalForRNAz
-preprocessClustalForRNAzExternal :: String -> String -> Int -> Int -> Int -> Bool -> IO (Either String (String,String))
-preprocessClustalForRNAzExternal clustalFilepath outputPath seqenceNumber optimalIdentity maximalIdenity referenceSequence = do
+preprocessClustalForRNAzExternal :: String -> String -> String -> Int -> Int -> Int -> Bool -> IO (Either String (String,String))
+preprocessClustalForRNAzExternal clustalFilepath outputPath outputFileName seqenceNumber optimalIdentity maximalIdenity referenceSequence = do
   clustalText <- TI.readFile clustalFilepath
   let reformatedClustalPath = outputPath ++ "result.reformated"
   --change clustal format for rnazSelectSeqs.pl
@@ -48,8 +48,8 @@
   return (Right ([],selectedClustalText))
 
 -- | Call for external preprocessClustalForRNAcode - RNAcode additionally to RNAz requirements does not accept pipe,underscore, doublepoint symbols
-preprocessClustalForRNAcodeExternal :: String -> String -> Int -> Int -> Int -> Bool -> IO (Either String (String,String))
-preprocessClustalForRNAcodeExternal clustalFilepath outputPath seqenceNumber optimalIdentity maximalIdenity referenceSequence = do
+preprocessClustalForRNAcodeExternal :: String -> String -> String -> Int -> Int -> Int -> Bool -> IO (Either String (String,String))
+preprocessClustalForRNAcodeExternal clustalFilepath outputPath outputFileName seqenceNumber optimalIdentity maximalIdenity referenceSequence = do
   clustalText <- TI.readFile clustalFilepath
   let reformatedClustalPath = outputPath ++ "result.reformated"
   --change clustal format for rnazSelectSeqs.pl
@@ -59,7 +59,7 @@
   let reformatedClustalText = T.map reformatRNACodeAln headerlessClustalTextLines
   TI.writeFile reformatedClustalPath (headerClustalTextLines `T.append` T.singleton '\n' `T.append` reformatedClustalText)
   --select representative entries from result.Clustal with select_sequences
-  let selectedClustalpath = outputPath ++ "result.selected"
+  let selectedClustalpath = outputPath ++ outputFileName
   let sequenceNumberOption = " -n "  ++ show seqenceNumber  ++ " "
   let optimalIdentityOption = " -i "  ++ show optimalIdentity  ++ " "
   let maximalIdentityOption = " --max-id="  ++ show maximalIdenity  ++ " "
@@ -70,13 +70,12 @@
   selectedClustalText <- readFile selectedClustalpath
   return (Right ([],selectedClustalText))
 
-preprocessClustalForRNAz :: String -> String -> Int -> Double -> Double -> Bool -> String -> IO (Either String (String,String))
-preprocessClustalForRNAz clustalFilepath outputPath seqenceNumber optimalIdentity maximalIdenity referenceSequence reformatOption = do
+preprocessClustalForRNAz :: String -> String -> String -> Int -> Double -> Double -> Bool -> String -> IO (Either String (String,String))
+preprocessClustalForRNAz clustalFilepath outputPath outputFileName seqenceNumber optimalIdentity maximalIdenity referenceSequence reformatOption = do
   clustalText <- TI.readFile clustalFilepath
   let clustalTextLines = T.lines clustalText
   parsedClustalInput <- readClustalAlignment clustalFilepath
-  print parsedClustalInput
-  let selectedClustalpath = outputPath ++ "result.selected"
+  let selectedClustalpath = outputPath ++ outputFileName
   if length clustalTextLines > 5
     then
       if isRight parsedClustalInput