diff --git a/ChangeLog.md b/ChangeLog.md
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -5,6 +5,13 @@
 ## Unreleased changes
 
 
+## Version 0.6.1.0
+
+-   Split `ELynx.Tools` into separate modules because the package will be reduced.
+-   Remove the following modules from `ELynx.Tools`: `Concurrent`,
+    `LinearAlgebra`, `List`, `Misc`, and `Numeric`.
+
+
 ## Version 0.6.0.0
 
 -   **elynx-tree:** remove parallel folds with layers (`parBranchFoldMapWithLayer`
diff --git a/README.md b/README.md
--- a/README.md
+++ b/README.md
@@ -69,13 +69,13 @@
 
 # Get help
 
-For example:
-
-    slynx --help
+    cabal exec slynx -- --help
+    # OR: stack exec slynx -- --help
+    # OR: slynx --help
 
     ELynx Suite version 0.6.0.0.
     Developed by Dominik Schrempf.
-    Compiled on September 3, 2021, at 20:56 pm, UTC.
+    Compiled on September 4, 2021, at 12:58 pm, UTC.
     
     Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] 
                  [-f|--force] [--no-elynx-file] COMMAND
@@ -113,6 +113,7 @@
       - ProteinX (amino acids; including gaps)
       - ProteinS (amino acids; including gaps, and translation stops)
       - ProteinI (amino acids; including gaps, translation stops, and IUPAC codes)
+    
     ELynx
     -----
     A Haskell library and tool set for computational biology. The goal of ELynx is
@@ -126,6 +127,9 @@
     tlynx     Analyze, modify, and simulate phylogenetic trees.
     elynx     Validate and redo past analyses.
     
+    Get help for commands:
+      slynx --help
+    
     Get help for sub commands:
       slynx examine --help
 
@@ -134,11 +138,13 @@
 
 The documentation of sub commands can be accessed separately:
 
-    slynx simulate --help
+    cabal exec slynx -- simulate --help
+    # OR: stack exec slynx -- simulate --help
+    # OR: slynx simulate --help
 
     ELynx Suite version 0.6.0.0.
     Developed by Dominik Schrempf.
-    Compiled on September 3, 2021, at 20:56 pm, UTC.
+    Compiled on September 4, 2021, at 12:58 pm, UTC.
     
     Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] 
                           [-m|--mixture-model MODEL] [-e|--edm-file NAME] 
diff --git a/elynx-markov.cabal b/elynx-markov.cabal
--- a/elynx-markov.cabal
+++ b/elynx-markov.cabal
@@ -1,6 +1,6 @@
 cabal-version:  2.2
 name:           elynx-markov
-version:        0.6.0.0
+version:        0.6.1.0
 synopsis:       Simulate molecular sequences along trees
 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/test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs b/test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs
--- a/test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs
+++ b/test/ELynx/Data/MarkovProcess/AminoAcidSpec.hs
@@ -17,7 +17,7 @@
 import ELynx.Data.MarkovProcess.AminoAcid
 import qualified ELynx.Data.MarkovProcess.RateMatrix as R
 import qualified ELynx.Data.MarkovProcess.SubstitutionModel as S
-import ELynx.Tools
+import ELynx.Tools.Equality
 import Numeric.LinearAlgebra
 import Test.Hspec
 
diff --git a/test/ELynx/Data/MarkovProcess/NucleotideSpec.hs b/test/ELynx/Data/MarkovProcess/NucleotideSpec.hs
--- a/test/ELynx/Data/MarkovProcess/NucleotideSpec.hs
+++ b/test/ELynx/Data/MarkovProcess/NucleotideSpec.hs
@@ -17,7 +17,7 @@
 import ELynx.Data.MarkovProcess.Nucleotide
 import ELynx.Data.MarkovProcess.RateMatrix
 import ELynx.Data.MarkovProcess.SubstitutionModel
-import ELynx.Tools
+import ELynx.Tools.Equality
 import Test.Hspec
 
 stationaryDist :: StationaryDistribution
diff --git a/test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs b/test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs
--- a/test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs
+++ b/test/ELynx/Import/MarkovProcess/EDMModelPhylobayesSpec.hs
@@ -14,7 +14,7 @@
 where
 
 import ELynx.Import.MarkovProcess.EDMModelPhylobayes
-import ELynx.Tools
+import ELynx.Tools.InputOutput
 import Numeric.LinearAlgebra (fromList)
 import Test.Hspec
 
diff --git a/test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs b/test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs
--- a/test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs
+++ b/test/ELynx/Import/MarkovProcess/SiteprofilesPhylobayesSpec.hs
@@ -15,10 +15,9 @@
 
 import qualified Data.Vector.Storable as V
 import ELynx.Import.MarkovProcess.EDMModelPhylobayes
-  ( EDMComponent,
-  )
 import ELynx.Import.MarkovProcess.SiteprofilesPhylobayes
-import ELynx.Tools
+import ELynx.Tools.Equality
+import ELynx.Tools.InputOutput
 import Test.Hspec
 
 fn :: FilePath