diff --git a/ChangeLog.md b/ChangeLog.md
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -5,6 +5,20 @@
 ## Unreleased changes
 
 
+## Version 0.4.1
+
+-   Improve `TimeSpec` (Point process).
+-   Parallel evaluation strategies.
+-   Change names of some functions involving partitions. For example, `mp` was
+    renamed to `pt`.
+-   Improve documentation for (bi)partitions.
+-   Bugfix `tlynx compare`; do not throw error when branch support values are not
+    set.
+-   Add `no-elynx-file` option.
+-   Also parse Nexus files with `tlynx` commands.
+-   Bugfix `subSample`; the sub sample was reversed.
+
+
 ## Version 0.4.0
 
 -   Major refactor of `elynx-tree`. All required function can now conveniently
diff --git a/README.md b/README.md
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
 
 # The ELynx Suite
 
-Version: 0.4.0.
+Version: 0.4.1.
 Reproducible evolution made easy.
 
 <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>
@@ -90,12 +90,12 @@
 
     slynx --help | head -n -16
 
-    ELynx Suite version 0.4.0.
+    ELynx Suite version 0.4.1.
     Developed by Dominik Schrempf.
-    Compiled on September 4, 2020, at 13:37 pm, UTC.
+    Compiled on October 16, 2020, at 12:46 pm, UTC.
     
     Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] 
-                 [-f|--force] COMMAND
+                 [-f|--force] [--no-elynx-file] COMMAND
       Analyze, and simulate multi sequence alignments.
     
     Available options:
@@ -107,6 +107,7 @@
                                Specify base name of output file
       -f,--force               Ignore previous analysis and overwrite existing
                                output files.
+      --no-elynx-file          Do not write files for needed for reproducibility.
     
     Available commands:
       concatenate              Concatenate sequences found in input files.
@@ -136,9 +137,9 @@
 
     slynx concatenate --help
 
-    ELynx Suite version 0.4.0.
+    ELynx Suite version 0.4.1.
     Developed by Dominik Schrempf.
-    Compiled on September 4, 2020, at 13:37 pm, UTC.
+    Compiled on October 16, 2020, at 12:46 pm, UTC.
     
     Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE
       Concatenate sequences found in input files.
@@ -157,9 +158,9 @@
 
     slynx examine --help
 
-    ELynx Suite version 0.4.0.
+    ELynx Suite version 0.4.1.
     Developed by Dominik Schrempf.
-    Compiled on September 4, 2020, at 13:37 pm, UTC.
+    Compiled on October 16, 2020, at 12:46 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 +180,9 @@
 
     slynx filter-rows --help
 
-    ELynx Suite version 0.4.0.
+    ELynx Suite version 0.4.1.
     Developed by Dominik Schrempf.
-    Compiled on September 4, 2020, at 13:37 pm, UTC.
+    Compiled on October 16, 2020, at 12:46 pm, UTC.
     
     Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH] 
                              [--shorter-than LENGTH] [--standard-characters]
@@ -202,9 +203,9 @@
 
     slynx filter-columns --help
 
-    ELynx Suite version 0.4.0.
+    ELynx Suite version 0.4.1.
     Developed by Dominik Schrempf.
-    Compiled on September 4, 2020, at 13:37 pm, UTC.
+    Compiled on October 16, 2020, at 12:46 pm, UTC.
     
     Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE 
                                 [--standard-chars DOUBLE]
@@ -226,9 +227,9 @@
 
     slynx simulate --help
 
-    ELynx Suite version 0.4.0.
+    ELynx Suite version 0.4.1.
     Developed by Dominik Schrempf.
-    Compiled on September 4, 2020, at 13:37 pm, UTC.
+    Compiled on October 16, 2020, at 12:46 pm, UTC.
     
     Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] 
                           [-m|--mixture-model MODEL] [-e|--edm-file NAME] 
@@ -305,9 +306,9 @@
 
     slynx sub-sample --help
 
-    ELynx Suite version 0.4.0.
+    ELynx Suite version 0.4.1.
     Developed by Dominik Schrempf.
-    Compiled on September 4, 2020, at 13:37 pm, UTC.
+    Compiled on October 16, 2020, at 12:46 pm, UTC.
     
     Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE
                             (-n|--number-of-sites INT)
@@ -335,9 +336,9 @@
 
     slynx translate --help
 
-    ELynx Suite version 0.4.0.
+    ELynx Suite version 0.4.1.
     Developed by Dominik Schrempf.
-    Compiled on September 4, 2020, at 13:37 pm, UTC.
+    Compiled on October 16, 2020, at 12:46 pm, UTC.
     
     Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT)
                            (-u|--universal-code CODE)
@@ -360,12 +361,12 @@
 
     tlynx --help | head -n -16
 
-    ELynx Suite version 0.4.0.
+    ELynx Suite version 0.4.1.
     Developed by Dominik Schrempf.
-    Compiled on September 4, 2020, at 13:37 pm, UTC.
+    Compiled on October 16, 2020, at 12:46 pm, UTC.
     
     Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] 
-                 [-f|--force] COMMAND
+                 [-f|--force] [--no-elynx-file] COMMAND
       Compare, examine, and simulate phylogenetic trees.
     
     Available options:
@@ -377,6 +378,7 @@
                                Specify base name of output file
       -f,--force               Ignore previous analysis and overwrite existing
                                output files.
+      --no-elynx-file          Do not write files for needed for reproducibility.
     
     Available commands:
       compare                  Compare two phylogenetic trees (compute distances and branch-wise differences).
@@ -390,6 +392,7 @@
     Available tree file formats:
       - Newick Standard: Branch support values are stored in square brackets after branch lengths.
       - Newick IqTree:   Branch support values are stored as node names after the closing bracket of forests.
+      - Newick RevBayes: Key-value pairs is provided in square brackets after node names as well as branch lengths. XXX: Key value pairs are ignored at the moment.
 
 
 ## Compare
@@ -398,9 +401,9 @@
 
     tlynx compare --help
 
-    ELynx Suite version 0.4.0.
+    ELynx Suite version 0.4.1.
     Developed by Dominik Schrempf.
-    Compiled on September 4, 2020, at 13:37 pm, UTC.
+    Compiled on October 16, 2020, at 12:46 pm, UTC.
     
     Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] 
                          [-f|--newick-format FORMAT] NAMES
@@ -427,9 +430,9 @@
 
     tlynx examine --help
 
-    ELynx Suite version 0.4.0.
+    ELynx Suite version 0.4.1.
     Developed by Dominik Schrempf.
-    Compiled on September 4, 2020, at 13:37 pm, UTC.
+    Compiled on October 16, 2020, at 12:46 pm, UTC.
     
     Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT]
       Compute summary statistics of phylogenetic trees.
@@ -451,9 +454,9 @@
 
     tlynx simulate --help
 
-    ELynx Suite version 0.4.0.
+    ELynx Suite version 0.4.1.
     Developed by Dominik Schrempf.
-    Compiled on September 4, 2020, at 13:37 pm, UTC.
+    Compiled on October 16, 2020, at 12:46 pm, UTC.
     
     Usage: tlynx simulate (-t|--nTrees INT) (-n|--nLeaves INT) PROCESS 
                           [-u|--sub-sample DOUBLE] [-s|--summary-statistics] 
@@ -488,9 +491,9 @@
 
     elynx --help | head -n -16
 
-    ELynx Suite version 0.4.0.
+    ELynx Suite version 0.4.1.
     Developed by Dominik Schrempf.
-    Compiled on September 4, 2020, at 13:37 pm, UTC.
+    Compiled on October 16, 2020, at 12:46 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
@@ -1,6 +1,6 @@
 cabal-version:  2.2
 name:           elynx-nexus
-version:        0.4.0
+version:        0.4.1
 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
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
@@ -18,10 +18,9 @@
 
 import qualified Data.ByteString.Lazy.Char8 as BL
 
--- 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.
+--
+-- At the moment writing one block only is supported.
 toNexus :: BL.ByteString -> [BL.ByteString] -> BL.ByteString
 toNexus n b = BL.unlines $ [start, begin n] <> b <> [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
@@ -13,12 +13,14 @@
 -- Creation date: Tue Apr 28 17:10:05 2020.
 module ELynx.Import.Nexus
   ( Block (..),
-    nexus,
+    nexusBlock,
   )
 where
 
+import Control.Applicative
 import Data.Attoparsec.ByteString.Char8
 import qualified Data.ByteString.Char8 as BS
+import Data.Attoparsec.Combinator
 
 -- | A Nexus block has a name (e.g., TREES), and parser for the entry.
 data Block a = Block
@@ -29,30 +31,42 @@
 -- This has to be refined. Like this, only one block can be parsed, and the
 -- block type has to be known beforehand.
 
--- | Parse a Nexus file with a given 'Block'.
-nexus :: Block a -> Parser a
-nexus b = start *> block b <* endOfInput <?> "nexus"
+-- | Parse a given 'Block' in a Nexus file.
+--
+-- The Nexus file can contain other blocks.
+nexusBlock :: Block a -> Parser a
+nexusBlock b = do
+  start
+  _ <- manyTill anyChar (lookAhead $ beginB b) <?> "nexusBlockSkipUntilBlock"
+  r <- block b <?> "nexusBlock"
+  _ <- many anyChar <?> "nexusBlockSkipUntilEnd"
+  _ <- endOfInput
+  return r
 
 start :: Parser ()
-start = (<?> "start") $ do
-  _ <- string "#NEXUS"
-  _ <- skipWhile isSpace
+start = do
+  _ <- stringCI "#nexus" <?> "nexusStart"
+  skipWhile isSpace
   return ()
 
 block :: Block a -> Parser a
-block b = beginB (name b) *> parser b <* endB <?> "block"
+block b = do
+  beginB b
+  r <- parser b <?> "blockParser"
+  endB
+  return r
 
-beginB :: BS.ByteString -> Parser ()
-beginB n = (<?> "begin") $ do
-  _ <- string "BEGIN"
-  _ <- skipWhile isSpace
-  _ <- string n
-  _ <- char ';'
-  _ <- skipWhile isSpace
+beginB :: Block a -> Parser ()
+beginB (Block n _) = do
+  _ <- stringCI "begin" <?> "blockBegin"
+  skipWhile isSpace
+  _ <- stringCI n <?> "blockName"
+  _ <- char ';' <?> "blockEnd"
+  skipWhile isSpace
   return ()
 
 endB :: Parser ()
-endB = (<?> "end") $ do
-  _ <- string "END;"
-  _ <- skipWhile isSpace
+endB = do
+  _ <- stringCI "end;" <?> "nexusEnd"
+  skipWhile isSpace
   return ()