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-seq.cabal b/elynx-seq.cabal
--- a/elynx-seq.cabal
+++ b/elynx-seq.cabal
@@ -1,6 +1,6 @@
 cabal-version:  2.2
 name:           elynx-seq
-version:        0.4.0
+version:        0.4.1
 synopsis:       Handle molecular sequences
 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/Data/Alphabet/Alphabet.hs b/src/ELynx/Data/Alphabet/Alphabet.hs
--- a/src/ELynx/Data/Alphabet/Alphabet.hs
+++ b/src/ELynx/Data/Alphabet/Alphabet.hs
@@ -20,7 +20,7 @@
 -- 2. Sets of 'Character's form 'Alphabet's; each 'Alphabet' has a specification
 -- 'AlphabetSpec'.
 --
--- New alphabets have to be added manually in this module.
+-- New alphabets have to be added manually to this module.
 --
 -- This way of handling characters and alphabets IS NOT TYPE SAFE, but much, much
 -- faster. A second layer of modules such as 'ELynx.Data.Character.Nucleotide'
diff --git a/src/ELynx/Data/Sequence/Alignment.hs b/src/ELynx/Data/Sequence/Alignment.hs
--- a/src/ELynx/Data/Sequence/Alignment.hs
+++ b/src/ELynx/Data/Sequence/Alignment.hs
@@ -308,7 +308,7 @@
 -- Sample the given sites from a matrix.
 subSampleMatrix :: V.Unbox a => [Int] -> M.Matrix a -> M.Matrix a
 subSampleMatrix is m =
-  M.fromColumns $ foldl' (\a i -> M.takeColumn m i : a) [] is
+  M.fromColumns $ foldl' (\a i -> M.takeColumn m i : a) [] (reverse is)
 
 -- | Sample the given sites from a multi sequence alignment.
 subSample :: [Int] -> Alignment -> Alignment
diff --git a/test/ELynx/Data/Sequence/AlignmentSpec.hs b/test/ELynx/Data/Sequence/AlignmentSpec.hs
--- a/test/ELynx/Data/Sequence/AlignmentSpec.hs
+++ b/test/ELynx/Data/Sequence/AlignmentSpec.hs
@@ -26,7 +26,7 @@
 fastaNucleotideIUPACFN = "data/NucleotideIUPAC.fasta"
 
 ssData :: M.Matrix Character
-ssData = M.fromLists $ map (reverse . map fromChar) ["AAA", "GAA", "TAA"]
+ssData = M.fromLists $ map (map fromChar) ["AAA", "GAA", "TAA"]
 
 ssA :: Alignment
 ssA =