diff --git a/ChangeLog.md b/ChangeLog.md
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -2,7 +2,14 @@
 # Changelog for ELynx
 
 
-## Version 0.3.1; in development
+## Version 0.3.2; in development
+
+
+## Version 0.3.1
+
+-   Use Attoparsec.
+-   Use ByteString consistently.
+-   Remove elynx-tools dependency from libaries.
 
 
 ## Version 0.3.0
diff --git a/README.md b/README.md
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
 
 # The ELynx Suite
 
-Version: 0.3.0.
+Version: 0.3.1.
 Reproducible evolution made easy.
 
 <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>
@@ -90,9 +90,9 @@
 
     slynx --help | head -n -16
 
-    ELynx Suite version 0.3.0.
+    ELynx Suite version 0.3.1.
     Developed by Dominik Schrempf.
-    Compiled on July 30, 2020, at 12:40 pm, UTC.
+    Compiled on August 3, 2020, at 12:12 pm, UTC.
     
     Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] 
                  [-f|--force] COMMAND
@@ -136,9 +136,9 @@
 
     slynx concatenate --help
 
-    ELynx Suite version 0.3.0.
+    ELynx Suite version 0.3.1.
     Developed by Dominik Schrempf.
-    Compiled on July 30, 2020, at 12:40 pm, UTC.
+    Compiled on August 3, 2020, at 12:12 pm, UTC.
     
     Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE
       Concatenate sequences found in input files.
@@ -157,9 +157,9 @@
 
     slynx examine --help
 
-    ELynx Suite version 0.3.0.
+    ELynx Suite version 0.3.1.
     Developed by Dominik Schrempf.
-    Compiled on July 30, 2020, at 12:40 pm, UTC.
+    Compiled on August 3, 2020, at 12:12 pm, UTC.
     
     Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site]
       Examine sequences. If data is a multi sequence alignment, additionally analyze columns.
@@ -179,9 +179,9 @@
 
     slynx filter-rows --help
 
-    ELynx Suite version 0.3.0.
+    ELynx Suite version 0.3.1.
     Developed by Dominik Schrempf.
-    Compiled on July 30, 2020, at 12:40 pm, UTC.
+    Compiled on August 3, 2020, at 12:12 pm, UTC.
     
     Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH] 
                              [--shorter-than LENGTH] [--standard-characters]
@@ -202,9 +202,9 @@
 
     slynx filter-columns --help
 
-    ELynx Suite version 0.3.0.
+    ELynx Suite version 0.3.1.
     Developed by Dominik Schrempf.
-    Compiled on July 30, 2020, at 12:40 pm, UTC.
+    Compiled on August 3, 2020, at 12:12 pm, UTC.
     
     Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE 
                                 [--standard-chars DOUBLE]
@@ -226,9 +226,9 @@
 
     slynx simulate --help
 
-    ELynx Suite version 0.3.0.
+    ELynx Suite version 0.3.1.
     Developed by Dominik Schrempf.
-    Compiled on July 30, 2020, at 12:40 pm, UTC.
+    Compiled on August 3, 2020, at 12:12 pm, UTC.
     
     Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] 
                           [-m|--mixture-model MODEL] [-e|--edm-file NAME] 
@@ -305,9 +305,9 @@
 
     slynx sub-sample --help
 
-    ELynx Suite version 0.3.0.
+    ELynx Suite version 0.3.1.
     Developed by Dominik Schrempf.
-    Compiled on July 30, 2020, at 12:40 pm, UTC.
+    Compiled on August 3, 2020, at 12:12 pm, UTC.
     
     Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE
                             (-n|--number-of-sites INT)
@@ -335,9 +335,9 @@
 
     slynx translate --help
 
-    ELynx Suite version 0.3.0.
+    ELynx Suite version 0.3.1.
     Developed by Dominik Schrempf.
-    Compiled on July 30, 2020, at 12:40 pm, UTC.
+    Compiled on August 3, 2020, at 12:12 pm, UTC.
     
     Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT)
                            (-u|--universal-code CODE)
@@ -360,9 +360,9 @@
 
     tlynx --help | head -n -16
 
-    ELynx Suite version 0.3.0.
+    ELynx Suite version 0.3.1.
     Developed by Dominik Schrempf.
-    Compiled on July 30, 2020, at 12:40 pm, UTC.
+    Compiled on August 3, 2020, at 12:12 pm, UTC.
     
     Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] 
                  [-f|--force] COMMAND
@@ -399,9 +399,9 @@
 
     tlynx compare --help
 
-    ELynx Suite version 0.3.0.
+    ELynx Suite version 0.3.1.
     Developed by Dominik Schrempf.
-    Compiled on July 30, 2020, at 12:40 pm, UTC.
+    Compiled on August 3, 2020, at 12:12 pm, UTC.
     
     Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] 
                          [-f|--newick-format FORMAT] NAMES
@@ -428,9 +428,9 @@
 
     tlynx examine --help
 
-    ELynx Suite version 0.3.0.
+    ELynx Suite version 0.3.1.
     Developed by Dominik Schrempf.
-    Compiled on July 30, 2020, at 12:40 pm, UTC.
+    Compiled on August 3, 2020, at 12:12 pm, UTC.
     
     Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT]
       Compute summary statistics of phylogenetic trees.
@@ -452,9 +452,9 @@
 
     tlynx simulate --help
 
-    ELynx Suite version 0.3.0.
+    ELynx Suite version 0.3.1.
     Developed by Dominik Schrempf.
-    Compiled on July 30, 2020, at 12:40 pm, UTC.
+    Compiled on August 3, 2020, at 12:12 pm, UTC.
     
     Usage: tlynx simulate [-t|--nTrees INT] [-n|--nLeaves INT] [-H|--height DOUBLE] 
                           [-M|--condition-on-mrca] [-l|--lambda DOUBLE] 
@@ -491,9 +491,9 @@
 
     elynx --help | head -n -16
 
-    ELynx Suite version 0.3.0.
+    ELynx Suite version 0.3.1.
     Developed by Dominik Schrempf.
-    Compiled on July 30, 2020, at 12:40 pm, UTC.
+    Compiled on August 3, 2020, at 12:12 pm, UTC.
     
     Usage: elynx COMMAND
       Validate and redo past ELynx analyses
diff --git a/app/Main.hs b/app/Main.hs
--- a/app/Main.hs
+++ b/app/Main.hs
@@ -21,20 +21,18 @@
 import Control.Monad
 import Data.Aeson
 import qualified Data.Aeson.Types as J
-import qualified Data.ByteString.Char8 as B
+import qualified Data.ByteString.Char8 as BS
 import Data.Maybe
-import Data.Version (Version)
+import Data.Version
 import ELynx.Tools
 import Options
 import Options.Applicative
 import qualified SLynx.Options as S
-import SLynx.SLynx (slynx)
+import SLynx.SLynx
 import System.Environment
-  ( withArgs,
-    withProgName,
-  )
 import qualified TLynx.Options as T
-import TLynx.TLynx (tlynx)
+import TLynx.TLynx
+import Paths_elynx
 
 parseProgName :: Value -> J.Parser String
 parseProgName = withObject "progName" $ \o -> o .: "progName"
@@ -82,7 +80,7 @@
       else Right ()
 
 -- Does the file match the base 16 checksum?
-checkFile :: FilePath -> B.ByteString -> IO (Either String ())
+checkFile :: FilePath -> BS.ByteString -> IO (Either String ())
 checkFile fp h = do
   h' <- hashFile fp
   return $
@@ -92,8 +90,8 @@
         Left $
           unlines
             [ "SHA256 sum does not match for a file:",
-              fp ++ " has check sum " ++ B.unpack h',
-              "Stored check sum is " ++ B.unpack h
+              fp ++ " has check sum " ++ BS.unpack h',
+              "Stored check sum is " ++ BS.unpack h
             ]
 
 checkVersion :: Version -> Either String ()
@@ -130,7 +128,7 @@
   chA <- checkArgs s
   let chV = checkVersion (rVersion s)
       chH = checkHash s
-  chFs <- zipWithM checkFile (files s) (map B.pack $ checkSums s)
+  chFs <- zipWithM checkFile (files s) (map BS.pack $ checkSums s)
   return $ sequence_ (chA : chV : chH : chFs)
 
 validateAllReproductions :: AllReproductions -> IO (Either String ())
@@ -182,7 +180,7 @@
     putStrLn "Use the --force (-f) option to skip this test."
     runValidate (ValidateArguments fp)
   repr <- getAllR fp
-  let as = getArgs repr
+  let as = getELynxArgs repr
   as' <-
     if "-f" `notElem` as && "--force" `notElem` as
       then do
@@ -190,7 +188,7 @@
           "Force option required to redo analysis. Add -f (force) to arguments."
         return $ "-f" : as
       else return as
-  withProgName (getProgName repr) $ withArgs as' $ redo repr
+  withProgName (getELynxProgName repr) $ withArgs as' $ redo repr
 
 setForce :: Arguments a -> Arguments a
 setForce (Arguments g l) = Arguments g {forceReanalysis = Force True} l
diff --git a/app/Options.hs b/app/Options.hs
--- a/app/Options.hs
+++ b/app/Options.hs
@@ -13,8 +13,8 @@
 -- Creation date: Thu Apr 23 19:17:17 2020.
 module Options
   ( AllReproductions (..),
-    getProgName,
-    getArgs,
+    getELynxProgName,
+    getELynxArgs,
     ValidateArguments (..),
     RedoArguments (..),
     CommandArguments (..),
@@ -33,14 +33,14 @@
   | T (Reproduction (Arguments T.CommandArguments))
 
 -- | Get program name irrespective of which program has been run.
-getProgName :: AllReproductions -> String
-getProgName (S x) = progName x
-getProgName (T x) = progName x
+getELynxProgName :: AllReproductions -> String
+getELynxProgName (S x) = progName x
+getELynxProgName (T x) = progName x
 
 -- | Get arguments irrespective of which program has been run.
-getArgs :: AllReproductions -> [String]
-getArgs (S x) = argsStr x
-getArgs (T x) = argsStr x
+getELynxArgs :: AllReproductions -> [String]
+getELynxArgs (S x) = argsStr x
+getELynxArgs (T x) = argsStr x
 
 newtype ValidateArguments = ValidateArguments
   {vElynxFile :: FilePath}
diff --git a/elynx.cabal b/elynx.cabal
--- a/elynx.cabal
+++ b/elynx.cabal
@@ -4,10 +4,10 @@
 --
 -- see: https://github.com/sol/hpack
 --
--- hash: 50f818ff6abb7f056acee6c87a8f19f18892a8752f0f49c3ca76452a38458d8f
+-- hash: e81e8aa22d417db9cf1d89217af0751026e9dd347ebb4d5abe8545db3ea1d80e
 
 name:           elynx
-version:        0.3.0
+version:        0.3.1
 synopsis:       Validate and (optionally) redo ELynx analyses
 description:    Please see the README on GitHub at <https://github.com/dschrempf/elynx>.
 category:       Bioinformatics