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/elynx-nexus.cabal b/elynx-nexus.cabal
--- a/elynx-nexus.cabal
+++ b/elynx-nexus.cabal
@@ -4,10 +4,10 @@
 --
 -- see: https://github.com/sol/hpack
 --
--- hash: 9c674ee4c190e6ed28b942de7dd8ded7fdc03eb4fb5b0fbcdbc6560f57bcba4a
+-- hash: b78b847dab23ec4452d24d3ccc5a20019353a0324d5fd7c51781f4033fda34d0
 
 name:           elynx-nexus
-version:        0.3.0
+version:        0.3.1
 synopsis:       Import and export Nexus files
 description:    Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>.
 category:       Bioinformatics
@@ -39,9 +39,9 @@
       src
   ghc-options: -Wall -fllvm
   build-depends:
-      base >=4.7 && <5
+      attoparsec
+    , base >=4.7 && <5
     , bytestring
-    , megaparsec
   default-language: Haskell2010
 
 test-suite seq-test
diff --git a/src/ELynx/Export/Nexus.hs b/src/ELynx/Export/Nexus.hs
--- a/src/ELynx/Export/Nexus.hs
+++ b/src/ELynx/Export/Nexus.hs
@@ -16,21 +16,20 @@
   )
 where
 
-import Data.ByteString.Lazy.Char8 (ByteString)
-import qualified Data.ByteString.Lazy.Char8 as L
+import qualified Data.ByteString.Lazy.Char8 as BL
 
--- This has to be refined. Like this, only one block can be parsed, and the
+-- XXX: This has to be refined. Like this, only one block can be parsed, and the
 -- block type has to be known beforehand.
 
 -- | Create nexus file with block name and block body.
-toNexus :: ByteString -> [ByteString] -> ByteString
-toNexus n b = L.unlines $ [start, begin n] <> b <> [end]
+toNexus :: BL.ByteString -> [BL.ByteString] -> BL.ByteString
+toNexus n b = BL.unlines $ [start, begin n] <> b <> [end]
 
-start :: ByteString
+start :: BL.ByteString
 start = "#NEXUS"
 
-begin :: ByteString -> ByteString
+begin :: BL.ByteString -> BL.ByteString
 begin n = "BEGIN " <> n <> ";"
 
-end :: ByteString
+end :: BL.ByteString
 end = "END;"
diff --git a/src/ELynx/Import/Nexus.hs b/src/ELynx/Import/Nexus.hs
--- a/src/ELynx/Import/Nexus.hs
+++ b/src/ELynx/Import/Nexus.hs
@@ -12,25 +12,17 @@
 --
 -- Creation date: Tue Apr 28 17:10:05 2020.
 module ELynx.Import.Nexus
-  ( Parser,
-    Block (..),
+  ( Block (..),
     nexus,
   )
 where
 
-import Control.Monad (void)
-import Data.ByteString.Internal (c2w)
-import Data.ByteString.Lazy.Char8 (ByteString)
-import Data.Void (Void)
-import Text.Megaparsec
-import Text.Megaparsec.Byte
-
--- | Megaparsec shortcut.
-type Parser = Parsec Void ByteString
+import Data.Attoparsec.ByteString.Char8
+import qualified Data.ByteString.Char8 as BS
 
 -- | A Nexus block has a name (e.g., TREES), and parser for the entry.
 data Block a = Block
-  { name :: ByteString,
+  { name :: BS.ByteString,
     parser :: Parser a
   }
 
@@ -39,24 +31,28 @@
 
 -- | Parse a Nexus file with a given 'Block'.
 nexus :: Block a -> Parser a
-nexus b = start *> block b
+nexus b = start *> block b <* endOfInput <?> "nexus"
 
 start :: Parser ()
-start = void $ string "#NEXUS" <* space
+start = (<?> "start") $ do
+  _ <- string "#NEXUS"
+  _ <- skipWhile isSpace
+  return ()
 
 block :: Block a -> Parser a
-block b = between (begin $ name b) end (parser b)
+block b = beginB (name b) *> parser b <* endB <?> "block"
 
-begin :: ByteString -> Parser ()
-begin n = do
+beginB :: BS.ByteString -> Parser ()
+beginB n = (<?> "begin") $ do
   _ <- string "BEGIN"
-  _ <- space
+  _ <- skipWhile isSpace
   _ <- string n
-  _ <- char (c2w ';')
-  _ <-
-    space
-      <?> "block-begin"
+  _ <- char ';'
+  _ <- skipWhile isSpace
   return ()
 
-end :: Parser ()
-end = void $ string "END;" <* space
+endB :: Parser ()
+endB = (<?> "end") $ do
+  _ <- string "END;"
+  _ <- skipWhile isSpace
+  return ()