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/src/TLynx/Compare/Compare.hs b/src/TLynx/Compare/Compare.hs
--- a/src/TLynx/Compare/Compare.hs
+++ b/src/TLynx/Compare/Compare.hs
@@ -29,51 +29,48 @@
 import qualified Data.Text as T
 import qualified Data.Text.Encoding as E
 import qualified Data.Text.IO as T
-import ELynx.Tree
 import ELynx.Tools
   ( Arguments (..),
     ELynx,
     GlobalArguments (..),
     outHandle,
-    parseFileWith,
   )
+import ELynx.Tree
 import Graphics.Gnuplot.Simple
 import System.IO
 import TLynx.Compare.Options
+import TLynx.Parsers
 import Text.Printf
 
 treesOneFile ::
   FilePath ->
   ELynx
     CompareArguments
-    (Tree PhyloExplicit BS.ByteString, Tree PhyloExplicit BS.ByteString)
+    (Tree Phylo BS.ByteString, Tree Phylo BS.ByteString)
 treesOneFile tf = do
   nwF <- argsNewickFormat . local <$> ask
   $(logInfo) $ T.pack $ "Parse file '" ++ tf ++ "'."
-  ts <- liftIO $ parseFileWith (someNewick nwF) tf
+  ts <- liftIO $ parseTrees nwF tf
   let n = length ts
   case compare n 2 of
     LT -> error "Not enough trees in file."
     GT -> error "Too many trees in file."
     EQ ->
-      return
-        ( either error id $ toExplicitTree $ head ts,
-          either error id $ toExplicitTree $ head . tail $ ts
-        )
+      return (head ts, head . tail $ ts)
 
 treesTwoFiles ::
   FilePath ->
   FilePath ->
   ELynx
     CompareArguments
-    (Tree PhyloExplicit BS.ByteString, Tree PhyloExplicit BS.ByteString)
+    (Tree Phylo BS.ByteString, Tree Phylo BS.ByteString)
 treesTwoFiles tf1 tf2 = do
   nwF <- argsNewickFormat . local <$> ask
   $(logInfo) $ T.pack $ "Parse first tree file '" ++ tf1 ++ "'."
-  t1 <- liftIO $ parseFileWith (oneNewick nwF) tf1
+  t1 <- liftIO $ parseTree nwF tf1
   $(logInfo) $ T.pack $ "Parse second tree file '" ++ tf2 ++ "'."
-  t2 <- liftIO $ parseFileWith (oneNewick nwF) tf2
-  return (either error id $ toExplicitTree t1, either error id $ toExplicitTree t2)
+  t2 <- liftIO $ parseTree nwF tf2
+  return (t1, t2)
 
 -- | More detailed comparison of two trees.
 compareCmd :: ELynx CompareArguments ()
@@ -91,9 +88,9 @@
       error
         "Need two input files with one tree each or one input file with two trees."
   liftIO $ hPutStrLn outH "Tree 1:"
-  liftIO $ BL.hPutStrLn outH $ toNewick $ toPhyloTree tr1
+  liftIO $ BL.hPutStrLn outH $ toNewick tr1
   liftIO $ hPutStrLn outH "Tree 2:"
-  liftIO $ BL.hPutStrLn outH $ toNewick $ toPhyloTree tr2
+  liftIO $ BL.hPutStrLn outH $ toNewick tr2
   liftIO $ hPutStrLn outH ""
   -- Intersect trees.
   (t1, t2) <-
@@ -101,23 +98,24 @@
       then do
         let [x, y] = either error id $ intersect [tr1, tr2]
         liftIO $ hPutStrLn outH "Intersected trees are:"
-        liftIO $ BL.hPutStrLn outH $ toNewick $ toPhyloTree x
-        liftIO $ BL.hPutStrLn outH $ toNewick $ toPhyloTree y
+        liftIO $ BL.hPutStrLn outH $ toNewick x
+        liftIO $ BL.hPutStrLn outH $ toNewick y
         return (x, y)
       else return (tr1, tr2)
-  -- Check input (moved to library functions).
-  -- let lvs1  = leaves t1
-  --     lvs2  = leaves t2
-  --     lfns1 = map getName lvs1
-  --     lfns2 = map getName lvs2
-  --     s1    = S.fromList lfns1
-  --     s2    = S.fromList lfns2
-  -- if s1 == s2
-  --   then liftIO $ hPutStrLn outH "Trees have the same set of leaf names."
-  --   else error "Trees do not have the same set of leaf names."
-  -- liftIO $ hPutStrLn outH ""
 
   -- Distances.
+  analyzeDistance outH t1 t2
+
+  -- Bipartitions.
+  when (argsBipartitions l) $ analyzeBipartitions outH t1 t2
+  liftIO $ hClose outH
+
+analyzeDistance ::
+  Handle ->
+  Tree Phylo BS.ByteString ->
+  Tree Phylo BS.ByteString ->
+  ELynx CompareArguments ()
+analyzeDistance outH t1 t2 = do
   let formatD str val = T.justifyLeft 25 ' ' str <> "  " <> val
   liftIO $ hPutStrLn outH "Distances."
   liftIO $
@@ -125,114 +123,127 @@
       formatD
         "Symmetric"
         (T.pack $ show $ symmetric t1 t2)
-  liftIO $
-    T.hPutStrLn outH $
-      formatD
-        "Branch score"
-        (T.pack $ show $ branchScore t1 t2)
-  let t1' = normalizeBranchSupport t1
-      t2' = normalizeBranchSupport t2
-  $(logDebug) "Trees with normalized branch support values:"
-  $(logDebug) $ E.decodeUtf8 $ BL.toStrict $ toNewick $ toPhyloTree t1'
-  $(logDebug) $ E.decodeUtf8 $ BL.toStrict $ toNewick $ toPhyloTree t2'
-  liftIO $
-    T.hPutStrLn outH $
-      formatD
-        "Incompatible split"
-        (T.pack $ show $ incompatibleSplits t1' t2')
-  liftIO $
-    T.hPutStrLn outH $
-      formatD
-        "Incompatible split (0.10)"
-        (T.pack $ show $ incompatibleSplits (collapse 0.1 t1') (collapse 0.1 t2'))
-  liftIO $
-    T.hPutStrLn outH $
-      formatD
-        "Incompatible split (0.50)"
-        (T.pack $ show $ incompatibleSplits (collapse 0.5 t1') (collapse 0.5 t2'))
-  -- liftIO $ T.hPutStrLn outH $ formatD "Incompatible split (0.60)"
-  --   (T.pack $ show $ incompatibleSplits (collapse 0.6 t1') (collapse 0.6 t2'))
-  -- liftIO $ T.hPutStrLn outH $ formatD "Incompatible split (0.70)"
-  --   (T.pack $ show $ incompatibleSplits (collapse 0.7 t1') (collapse 0.7 t2'))
-  liftIO $
-    T.hPutStrLn outH $
-      formatD
-        "Incompatible split (0.80)"
-        (T.pack $ show $ incompatibleSplits (collapse 0.8 t1') (collapse 0.8 t2'))
-  liftIO $
-    T.hPutStrLn outH $
-      formatD
-        "Incompatible split (0.90)"
-        (T.pack $ show $ incompatibleSplits (collapse 0.9 t1') (collapse 0.9 t2'))
-  -- liftIO $ T.hPutStrLn outH $ formatD "Incompatible split (1.01)"
-  --   (T.pack $ show $ incompatibleSplits (collapse 1.01 t1') (collapse 1.01 t2'))
-  -- liftIO $ BL.hPutStrLn outH $ toNewick (collapse 1.01 t1')
+  case (phyloToLengthTree t1, phyloToLengthTree t2) of
+    (Right t1', Right t2') -> do
+      liftIO $
+        T.hPutStrLn outH $
+          formatD
+            "Branch score"
+            (T.pack $ show $ branchScore t1' t2')
+    _ -> do
+      $(logInfo) "Some branches do not have length values."
+      $(logInfo) "Distances involving length cannot be calculated."
+  case (toExplicitTree t1, toExplicitTree t2) of
+    (Right t1', Right t2') -> do
+      let t1n = normalizeBranchSupport t1'
+          t2n = normalizeBranchSupport t2'
+      $(logDebug) "Trees with normalized branch support values:"
+      $(logDebug) $ E.decodeUtf8 $ BL.toStrict $ toNewick $ toPhyloTree t1n
+      $(logDebug) $ E.decodeUtf8 $ BL.toStrict $ toNewick $ toPhyloTree t2n
+      liftIO $
+        T.hPutStrLn outH $
+          formatD
+            "Incompatible split"
+            (T.pack $ show $ incompatibleSplits t1n t2n)
+      liftIO $
+        T.hPutStrLn outH $
+          formatD
+            "Incompatible split (0.10)"
+            (T.pack $ show $ incompatibleSplits (collapse 0.1 t1n) (collapse 0.1 t2n))
+      liftIO $
+        T.hPutStrLn outH $
+          formatD
+            "Incompatible split (0.50)"
+            (T.pack $ show $ incompatibleSplits (collapse 0.5 t1n) (collapse 0.5 t2n))
+      -- liftIO $ T.hPutStrLn outH $ formatD "Incompatible split (0.60)"
+      --   (T.pack $ show $ incompatibleSplits (collapse 0.6 t1n) (collapse 0.6 t2n))
+      -- liftIO $ T.hPutStrLn outH $ formatD "Incompatible split (0.70)"
+      --   (T.pack $ show $ incompatibleSplits (collapse 0.7 t1n) (collapse 0.7 t2n))
+      liftIO $
+        T.hPutStrLn outH $
+          formatD
+            "Incompatible split (0.80)"
+            (T.pack $ show $ incompatibleSplits (collapse 0.8 t1n) (collapse 0.8 t2n))
+      liftIO $
+        T.hPutStrLn outH $
+          formatD
+            "Incompatible split (0.90)"
+            (T.pack $ show $ incompatibleSplits (collapse 0.9 t1n) (collapse 0.9 t2n))
+    -- liftIO $ T.hPutStrLn outH $ formatD "Incompatible split (1.01)"
+    --   (T.pack $ show $ incompatibleSplits (collapse 1.01 t1n) (collapse 1.01 t2n))
+    -- liftIO $ BL.hPutStrLn outH $ toNewick (collapse 1.01 t1n)
+    _ -> do
+      $(logInfo) "Some branches do not have support values."
+      $(logInfo) "Distances involving branch support cannot be calculated."
 
-  -- Bipartitions.
-  when
-    (argsBipartitions l)
-    ( do
-        let bp1 = either error id $ bipartitions t1
-            bp2 = either error id $ bipartitions t2
-            bp1Only = bp1 S.\\ bp2
-            bp2Only = bp2 S.\\ bp1
-        unless
-          (S.null bp1Only)
-          ( do
-              liftIO $ hPutStrLn outH ""
-              liftIO $
-                hPutStrLn outH "Bipartitions in Tree 1 that are not in Tree 2."
-              -- let bp1Strs = map (bphuman BL.unpack . bpmap getName) (S.toList bp1Only)
-              forM_ bp1Only (liftIO . hPutStrLn outH . bpHuman)
-          )
-        -- let bp1Strs = map (bphuman BL.unpack) (S.toList bp1Only)
-        -- liftIO $ hPutStrLn outH $ intercalate "\n" bp1Strs)
-        unless
-          (S.null bp2Only)
-          ( do
-              liftIO $ hPutStrLn outH ""
-              liftIO $
-                hPutStrLn outH "Bipartitions in Tree 2 that are not in Tree 1."
-              forM_ bp2Only (liftIO . hPutStrLn outH . bpHuman)
-          )
-        -- Common bipartitions and their respective differences in branch lengths.
-        liftIO $ hPutStrLn outH ""
-        let bpCommon = bp1 `S.intersection` bp2
-        if S.null bpCommon
-          then do
-            liftIO $ hPutStrLn outH "There are no common bipartitions."
-            liftIO $ hPutStrLn outH "No plots have been generated."
-          else do
-            let bpToBrLen1 = M.map getLen $ either error id $ bipartitionToBranch t1
-                bpToBrLen2 = M.map getLen $ either error id $ bipartitionToBranch t2
+analyzeBipartitions ::
+  Handle ->
+  Tree Phylo BS.ByteString ->
+  Tree Phylo BS.ByteString ->
+  ELynx CompareArguments ()
+analyzeBipartitions outH t1 t2 =
+  case (phyloToLengthTree t1, phyloToLengthTree t2) of
+    (Right t1l, Right t2l) -> do
+      let bp1 = either error id $ bipartitions t1l
+          bp2 = either error id $ bipartitions t2l
+          bp1Only = bp1 S.\\ bp2
+          bp2Only = bp2 S.\\ bp1
+      unless
+        (S.null bp1Only)
+        ( do
+            liftIO $ hPutStrLn outH ""
             liftIO $
-              hPutStrLn
-                outH
-                "Common bipartitions and their respective differences in branch lengths."
-            -- Header.
-            liftIO $ hPutStrLn outH header
-            forM_
-              bpCommon
-              ( liftIO
-                  . hPutStrLn outH
-                  . getCommonBpStr bpToBrLen1 bpToBrLen2
-              )
-            -- XXX: This circumvents the extension checking, and hash creation for
-            -- elynx files.
-            bn <- outFileBaseName . global <$> ask
-            case bn of
-              Nothing ->
-                $(logInfo) "No output file name provided. Do not generate plots."
-              Just fn -> do
-                let compareCommonBps =
-                      [ (bpToBrLen1 M.! b, bpToBrLen2 M.! b)
-                        | b <- S.toList bpCommon
-                      ]
-                liftIO $ epspdfPlot fn (plotBps compareCommonBps)
-                $(logInfo)
-                  "Comparison of branch lengths plot generated (EPS and PDF)"
-    )
-  liftIO $ hClose outH
+              hPutStrLn outH "Bipartitions in Tree 1 that are not in Tree 2."
+            -- let bp1Strs = map (bphuman BL.unpack . bpmap getName) (S.toList bp1Only)
+            forM_ bp1Only (liftIO . hPutStrLn outH . bpHuman)
+        )
+      -- let bp1Strs = map (bphuman BL.unpack) (S.toList bp1Only)
+      -- liftIO $ hPutStrLn outH $ intercalate "\n" bp1Strs)
+      unless
+        (S.null bp2Only)
+        ( do
+            liftIO $ hPutStrLn outH ""
+            liftIO $
+              hPutStrLn outH "Bipartitions in Tree 2 that are not in Tree 1."
+            forM_ bp2Only (liftIO . hPutStrLn outH . bpHuman)
+        )
+      -- Common bipartitions and their respective differences in branch lengths.
+      liftIO $ hPutStrLn outH ""
+      let bpCommon = bp1 `S.intersection` bp2
+      if S.null bpCommon
+        then do
+          liftIO $ hPutStrLn outH "There are no common bipartitions."
+          liftIO $ hPutStrLn outH "No plots have been generated."
+        else do
+          let bpToBrLen1 = M.map getLen $ either error id $ bipartitionToBranch t1l
+              bpToBrLen2 = M.map getLen $ either error id $ bipartitionToBranch t2l
+          liftIO $
+            hPutStrLn
+              outH
+              "Common bipartitions and their respective differences in branch lengths."
+          -- Header.
+          liftIO $ hPutStrLn outH header
+          forM_
+            bpCommon
+            ( liftIO
+                . hPutStrLn outH
+                . getCommonBpStr bpToBrLen1 bpToBrLen2
+            )
+          -- XXX: This circumvents the extension checking, and hash creation for
+          -- elynx files.
+          bn <- outFileBaseName . global <$> ask
+          case bn of
+            Nothing ->
+              $(logInfo) "No output file name provided. Do not generate plots."
+            Just fn -> do
+              let compareCommonBps =
+                    [ (bpToBrLen1 M.! b, bpToBrLen2 M.! b)
+                      | b <- S.toList bpCommon
+                    ]
+              liftIO $ epspdfPlot fn (plotBps compareCommonBps)
+              $(logInfo)
+                "Comparison of branch lengths plot generated (EPS and PDF)"
+    _ -> $(logWarn) "Not all branches have a length! Can not analyze bipartitions."
 
 header :: String
 header = intercalate "  " $ cols ++ ["Bipartition"]
@@ -274,6 +285,9 @@
              YLabel "Branch lengths, tree 2"
            ]
     ps1 = PlotStyle Points (DefaultStyle 1)
-    m = maximum $ map fst xs ++ map snd xs
+    -- m = minimum $ map fst xs ++ map snd xs
+    mx = maximum $ map fst xs
+    my = maximum $ map snd xs
+    m = min mx my
     line = [(0, 0), (m, m)]
     ps2 = PlotStyle Lines (DefaultStyle 1)
diff --git a/src/TLynx/Connect/Connect.hs b/src/TLynx/Connect/Connect.hs
--- a/src/TLynx/Connect/Connect.hs
+++ b/src/TLynx/Connect/Connect.hs
@@ -23,17 +23,17 @@
 import qualified Data.ByteString.Char8 as BS
 import qualified Data.ByteString.Lazy.Char8 as BL
 import qualified Data.Set as S
-import ELynx.Tree
 import ELynx.Tools
   ( Arguments (..),
     ELynx,
     fromBs,
     outHandle,
-    parseFileWith,
     tShow,
   )
+import ELynx.Tree
 import System.IO
 import TLynx.Connect.Options
+import TLynx.Parsers
 
 -- Connect two trees with a branch in all possible ways.
 --
@@ -85,27 +85,29 @@
 
 compatibleAll :: (Show a, Ord a) => Tree e a -> [Constraint a] -> Bool
 compatibleAll t@(Node _ _ [l, r]) cs =
-  all (compatible (either error id $ partition l)) (map getP cs)
-    && all (compatible (either error id $ partition r)) (map getP cs)
+  all (compatible partitionLeft . getP) cs
+    && all (compatible partitionRight . getP) cs
   where
     lvs = S.fromList $ leaves t
-    getP x = either error id $ mp [x, lvs S.\\ x]
+    getP x = either error id $ pt [x, lvs S.\\ x]
+    partitionLeft = either error id $ partition l
+    partitionRight = either error id $ partition r
 compatibleAll _ _ = error "Tree is not bifurcating."
 
 compatibleWith ::
   (Show b, Ord b) => (a -> b) -> [Constraint a] -> Tree e a -> Bool
 compatibleWith f cs t = compatibleAll (fmap f t) (map (S.map f) cs)
 
-parseTrees ::
+parseTreeTuple ::
   FilePath ->
   FilePath ->
   ELynx
     ConnectArguments
     (Tree Length BS.ByteString, Tree Length BS.ByteString)
-parseTrees l r = do
+parseTreeTuple l r = do
   nwF <- nwFormat . local <$> ask
-  tl <- liftIO $ parseFileWith (oneNewick nwF) l
-  tr <- liftIO $ parseFileWith (oneNewick nwF) r
+  tl <- liftIO $ parseTree nwF l
+  tr <- liftIO $ parseTree nwF r
   $(logInfo) "Tree 1:"
   $(logInfo) $ fromBs $ toNewick tl
   $(logInfo) "Tree 2:"
@@ -114,7 +116,7 @@
 
 connectOnly :: Handle -> FilePath -> FilePath -> ELynx ConnectArguments ()
 connectOnly h l r = do
-  (tl, tr) <- parseTrees l r
+  (tl, tr) <- parseTreeTuple l r
   let ts = connectTrees tl tr
   $(logInfo) $ "Connected trees: " <> tShow (length ts)
   liftIO $ BL.hPutStr h $ BL.unlines $ map (toNewick . measurableToPhyloTree) ts
@@ -123,10 +125,10 @@
   Handle -> FilePath -> FilePath -> FilePath -> ELynx ConnectArguments ()
 connectAndFilter h c l r = do
   nwF <- nwFormat . local <$> ask
-  cts <- liftIO $ parseFileWith (someNewick nwF) c
+  cts <- liftIO $ parseTrees nwF c
   $(logInfo) "Constraints:"
   $(logInfo) $ fromBs $ BL.intercalate "\n" $ map toNewick cts
-  (tl, tr) <- parseTrees l r
+  (tl, tr) <- parseTreeTuple l r
   let ts = connectTrees tl tr
       cs = map S.fromList $ concatMap multifurcatingGroups cts :: [Constraint BS.ByteString]
       -- Only collect trees that are compatible with the constraints.
diff --git a/src/TLynx/Distance/Distance.hs b/src/TLynx/Distance/Distance.hs
--- a/src/TLynx/Distance/Distance.hs
+++ b/src/TLynx/Distance/Distance.hs
@@ -40,11 +40,12 @@
 import qualified Data.Text.Lazy as LT
 import qualified Data.Text.Lazy.Encoding as LT
 import qualified Data.Vector.Unboxed as V
-import ELynx.Tree
 import ELynx.Tools
+import ELynx.Tree
 import Statistics.Sample
 import System.IO
 import TLynx.Distance.Options
+import TLynx.Parsers
 import Text.Printf
 
 median :: Ord a => [a] -> a
@@ -84,16 +85,6 @@
       (j, y) <- zip is xs
   ]
 
--- -- Compute distances between adjacent pairs of a list of input trees. Use given
--- -- distance measure.
--- adjacent ::
---   -- | Distance function.
---   (a -> a -> b) ->
---   -- | Input values.
---   [a] ->
---   [b]
--- adjacent dist trs = [dist x y | (x, y) <- zip trs (tail trs)]
-
 -- | Compute distance functions between phylogenetic trees.
 distance :: ELynx DistanceArguments ()
 distance = do
@@ -107,7 +98,7 @@
     Nothing -> return Nothing
     Just f -> do
       $(logInfo) $ T.pack $ "Read master tree from file: " <> f <> "."
-      t <- liftIO $ parseFileWith (oneNewick nwFormat) f
+      t <- liftIO $ parseTree nwFormat f
       $(logInfo) "Compute distances between all trees and master tree."
       return $ Just t
   let tfps = argsInFiles l
@@ -115,13 +106,13 @@
     [] -> error "No tree input files given."
     [tf] -> do
       $(logInfo) "Read trees from single file."
-      ts <- liftIO $ parseFileWith (someNewick nwFormat) tf
+      ts <- liftIO $ parseTrees nwFormat tf
       $(logInfo) $ tShow (length ts) <> " trees found in file."
       $(logInfo) "Trees are indexed with integers."
       return (ts, map show [0 .. length ts - 1])
     _ -> do
       $(logInfo) "Read trees from files."
-      ts <- liftIO $ mapM (parseFileWith (oneNewick nwFormat)) tfps
+      ts <- liftIO $ mapM (parseTree nwFormat) tfps
       $(logInfo) "Trees are named according to their file names."
       return (ts, tfps)
   when (null trees) (error "Not enough trees found in files.")
@@ -145,14 +136,17 @@
             ++ "."
     BranchScore -> $(logInfo) "Use branch score distance."
   let distanceMeasure' ::
-        (Measurable e1, Measurable e2) =>
-        Tree e1 BS.ByteString ->
-        Tree e2 BS.ByteString ->
+        Tree Phylo BS.ByteString ->
+        Tree Phylo BS.ByteString ->
         Double
       distanceMeasure' t1 t2 = either error id $ case dist of
         Symmetric -> second fromIntegral $ symmetric t1 t2
-        IncompatibleSplit _ -> second fromIntegral $ incompatibleSplits t1 t2
-        BranchScore -> branchScore t1 t2
+        IncompatibleSplit val -> second fromIntegral $ incompatibleSplits
+                                 (collapse val $ normalizeBranchSupport $ either error id $ phyloToSupportTree t1)
+                                 (collapse val $ normalizeBranchSupport $ either error id $ phyloToSupportTree t2)
+        BranchScore ->
+          branchScore (normalizeF $ either error id $ phyloToLengthTree t1) (normalizeF $ either error id $ phyloToLengthTree t2)
+        where normalizeF = if argsNormalize l then normalizeBranchLengths else id
   -- Possibly intersect trees before distance calculation.
   when (argsIntersect l) $
     $(logInfo) "Intersect trees before calculation of distances."
@@ -167,24 +161,9 @@
   -- Possibly normalize trees.
   when (argsNormalize l) $
     $(logInfo) "Normalize trees before calculation of distances."
-  let normalizeF = if argsNormalize l then normalizeBranchLengths else id
-  -- Possibly collapse unsupported nodes.
-  let collapseF = case dist of
-        -- For the incompatible split distance we have to collapse branches with
-        -- support lower than the given value. Before doing so, we normalize the
-        -- branch support values.
-        IncompatibleSplit val -> collapse val . normalizeBranchSupport
-        _ -> id
-  -- The trees can be prepared now.
-  let trees' :: Forest PhyloExplicit BS.ByteString
-      trees' = map (collapseF . normalizeF . either error id . toExplicitTree) trees
-  $(logDebug) "The prepared trees are:"
-  $(logDebug) $ LT.toStrict $ LT.decodeUtf8 $ BL.unlines $ map (toNewick . toPhyloTree) trees'
   let dsTriplets = case mtree of
-        Nothing -> pairwise distanceMeasure trees'
-        Just pt ->
-          let t = (either error id . toExplicitTree) pt
-           in [(0, i, distanceMeasure t t') | (i, t') <- zip [1 ..] trees']
+        Nothing -> pairwise distanceMeasure trees
+        Just masterTree -> [(0, i, distanceMeasure masterTree t') | (i, t') <- zip [1 ..] trees]
       ds = map (\(_, _, x) -> x) dsTriplets
       dsVec = V.fromList ds
   liftIO $
diff --git a/src/TLynx/Examine/Examine.hs b/src/TLynx/Examine/Examine.hs
--- a/src/TLynx/Examine/Examine.hs
+++ b/src/TLynx/Examine/Examine.hs
@@ -25,13 +25,14 @@
 import Data.Containers.ListUtils (nubOrd)
 import Data.List ((\\))
 import qualified Data.Text as T
-import ELynx.Tree
 import ELynx.Tools
+import ELynx.Tree
 import System.IO
   ( Handle,
     hPutStrLn,
   )
 import TLynx.Examine.Options
+import TLynx.Parsers
 import Text.Printf
 
 pretty :: BranchLength -> String
@@ -62,7 +63,7 @@
 readTrees fp = do
   $(logInfo) $ T.pack $ "Read tree(s) from file " <> fp <> "."
   nf <- argsNewickFormat . local <$> ask
-  liftIO $ parseFileWith (someNewick nf) fp
+  liftIO $ parseTrees nf fp
 
 examineTree :: Named a => Handle -> Tree Phylo a -> IO ()
 examineTree h t = do
diff --git a/src/TLynx/Parsers.hs b/src/TLynx/Parsers.hs
--- a/src/TLynx/Parsers.hs
+++ b/src/TLynx/Parsers.hs
@@ -1,6 +1,6 @@
 -- |
 -- Module      :  TLynx.Parsers
--- Description :  Common parsers
+-- Description :  Parse Newick/Nexus tree files
 -- Copyright   :  (c) Dominik Schrempf 2020
 -- License     :  GPL-3.0-or-later
 --
@@ -10,20 +10,58 @@
 --
 -- Creation date: Wed Apr 22 13:34:35 2020.
 module TLynx.Parsers
-  ( NewickFormat,
+  (
+    parseTree,
+    parseTrees,
+    NewickFormat,
     newickFormat,
     newickHelp,
   )
 where
 
-import Data.List (intercalate)
+import qualified Data.ByteString.Char8 as BS
+import Data.List
+import ELynx.Tools
 import ELynx.Tree
-  ( NewickFormat (..),
-    description,
-  )
-import ELynx.Tools (allValues)
 import Options.Applicative
 
+printError :: String -> String -> String -> IO a
+printError fn new nex = do
+  putStrLn $ "Error of Newick parser: " <> new <> "."
+  putStrLn $ "Error of Nexus  parser: " <> nex <> "."
+  error $ "Could not read tree file: " <> fn <> "."
+
+-- | Parse a Newick tree file or a Nexus file with Newick trees.
+--
+-- Error if no or more than one trees are found.
+-- Error if both file formats fail to parse.
+parseTree :: NewickFormat -> FilePath -> IO (Tree Phylo BS.ByteString)
+parseTree fmt fn = do
+  parseResultNewick <- runParserOnFile (oneNewick fmt) fn
+  case parseResultNewick of
+    Right r -> return r
+    Left eNewick -> do
+      parseResultNexus <- runParserOnFile (nexusTrees fmt) fn
+      case parseResultNexus of
+        Right [] -> error $ "No tree found in Nexus file " <> fn <> "."
+        Right [(_, t)] -> return t
+        Right _ -> error $ "More than one tree found in Nexus file " <> fn <> "."
+        Left eNexus -> printError fn eNewick eNexus
+
+-- | Parse a Newick tree file or a Nexus file with Newick trees.
+--
+-- Error if both file formats fail to parse.
+parseTrees :: NewickFormat -> FilePath -> IO (Forest Phylo BS.ByteString)
+parseTrees fmt fn = do
+  parseResultNewick <- runParserOnFile (someNewick fmt) fn
+  case parseResultNewick of
+    Right r -> return r
+    Left eNewick -> do
+      parseResultNexus <- runParserOnFile (nexusTrees fmt) fn
+      case parseResultNexus of
+        Right r -> return $ map snd r
+        Left eNexus -> printError fn eNewick eNexus
+
 -- | Parse 'NewickFormat'.
 newickFormat :: Parser NewickFormat
 newickFormat =
@@ -39,6 +77,6 @@
 
 -- | Help for different 'NewickFormat's.
 newickHelp :: [String]
-newickHelp = map (toListItem . description) (allValues :: [NewickFormat])
+newickHelp = map (toListItem . description) (allValues :: [NewickFormat]) ++ ["- Nexus file including Newick trees"]
   where
     toListItem = ("- Newick " ++)
diff --git a/src/TLynx/Shuffle/Shuffle.hs b/src/TLynx/Shuffle/Shuffle.hs
--- a/src/TLynx/Shuffle/Shuffle.hs
+++ b/src/TLynx/Shuffle/Shuffle.hs
@@ -26,15 +26,16 @@
 import Control.Monad.Logger (logDebug, logInfo)
 import Control.Monad.Trans.Reader (ask)
 import qualified Data.ByteString.Lazy.Char8 as BL
+import ELynx.Tools
 import ELynx.Tree
 import ELynx.Tree.Simulate.PointProcess
   ( PointProcess (PointProcess),
     toReconstructedTree,
   )
-import ELynx.Tools
 import System.IO (hClose)
 import System.Random.MWC (GenIO, initialize)
 import TLynx.Shuffle.Options
+import TLynx.Parsers
 
 -- | Shuffle a tree. Get all coalescent times, shuffle them. Get all leaves,
 -- shuffle them. Connect the shuffled leaves with the shuffled coalescent times.
@@ -45,7 +46,7 @@
   l <- local <$> ask
   h <- outHandle "results" ".tree"
   let nwF = nwFormat l
-  tPhylo <- liftIO $ parseFileWith (oneNewick nwF) (inFile l)
+  tPhylo <- liftIO $ parseTree nwF (inFile l)
   $(logInfo) "Input tree:"
   $(logInfo) $ fromBs $ toNewick tPhylo
   let t = either error id $ phyloToLengthTree tPhylo
diff --git a/src/TLynx/Simulate/Options.hs b/src/TLynx/Simulate/Options.hs
--- a/src/TLynx/Simulate/Options.hs
+++ b/src/TLynx/Simulate/Options.hs
@@ -1,5 +1,7 @@
 {-# LANGUAGE DeriveGeneric #-}
 {-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE StandaloneDeriving #-}
+{-# OPTIONS_GHC -Wno-orphans #-}
 
 -- |
 -- Module      :  TLynx.Simulate.Options
@@ -13,8 +15,7 @@
 --
 -- Creation date: Fri May  3 11:51:07 2019.
 module TLynx.Simulate.Options
-  ( Height (..),
-    Process (..),
+  ( Process (..),
     SimulateArguments (..),
     simulateArguments,
     reportSimulateArguments,
@@ -22,20 +23,23 @@
 where
 
 import Data.List
-import ELynx.Tools
+import Data.Maybe
+import ELynx.Tools hiding (Random)
+import ELynx.Tree.Simulate.PointProcess (TimeSpec (..))
 import Options.Applicative
 
--- | Condition on tree height (origin or most recent common ancestor).
-data Height = Origin Double | Mrca Double
-  deriving (Eq, Generic)
+deriving instance Eq TimeSpec
 
-instance Show Height where
+deriving instance Generic TimeSpec
+
+instance Show TimeSpec where
+  show Random = "Random"
   show (Origin o) = "Condition on height of origin: " ++ show o
   show (Mrca m) = "Condition on height of MRCA: " ++ show m
 
-instance FromJSON Height
+instance FromJSON TimeSpec
 
-instance ToJSON Height
+instance ToJSON TimeSpec
 
 -- | Process to be used for simulation.
 data Process
@@ -47,7 +51,7 @@
         -- | Sampling rate.
         bdRho :: Maybe Double,
         -- | Condition on height?
-        bdHeight :: Maybe Height
+        bdHeight :: TimeSpec
       }
   | Coalescent
   deriving (Eq, Show, Generic)
@@ -57,14 +61,14 @@
 instance ToJSON Process
 
 reportProcess :: Process -> String
-reportProcess (BirthDeath l m mr mh) =
+reportProcess (BirthDeath l m mr ts) =
   intercalate
     "\n"
     [ "Model: Birth and death process",
       "  Birth rate: " ++ show l,
       "  Death rate: " ++ show m,
       "  Sampling probability: " ++ maybe "1.0" show mr,
-      "  Height specification: " ++ maybe "Random" show mh
+      "  Height specification: " ++ show ts
     ]
 reportProcess Coalescent = "Model: Coalescent process"
 
@@ -166,7 +170,7 @@
       <> metavar "DOUBLE"
       <> help "Sampling probability rho"
 
-mrca :: Parser Height
+mrca :: Parser TimeSpec
 mrca =
   Mrca
     <$> option
@@ -176,7 +180,7 @@
           <> help "Condition on height of most recent common ancestor"
       )
 
-origin :: Parser Height
+origin :: Parser TimeSpec
 origin =
   Origin
     <$> option
@@ -186,8 +190,11 @@
           <> help "Condition on height of origin"
       )
 
+timeSpec :: Parser TimeSpec
+timeSpec = fromMaybe Random <$> optional (mrca <|> origin)
+
 birthDeath :: Parser Process
-birthDeath = BirthDeath <$> lambdaOpt <*> muOpt <*> optional rhoOpt <*> optional (mrca <|> origin)
+birthDeath = BirthDeath <$> lambdaOpt <*> muOpt <*> optional rhoOpt <*> timeSpec
 
 coalescent :: Parser Process
 coalescent = pure Coalescent
diff --git a/src/TLynx/Simulate/Simulate.hs b/src/TLynx/Simulate/Simulate.hs
--- a/src/TLynx/Simulate/Simulate.hs
+++ b/src/TLynx/Simulate/Simulate.hs
@@ -43,10 +43,10 @@
 import qualified Data.Text as T
 import qualified Data.Text.Lazy as LT
 import qualified Data.Text.Lazy.Encoding as LT
+import ELynx.Tools
 import ELynx.Tree
 import qualified ELynx.Tree.Simulate.Coalescent as CS
 import qualified ELynx.Tree.Simulate.PointProcess as PP
-import ELynx.Tools
 import System.Random.MWC
 import TLynx.Simulate.Options
 
@@ -62,13 +62,8 @@
   gs <- liftIO $ initialize s >>= \gen -> splitGen c gen
   let chunks = getChunks c nTrees
   trs <- case pr of
-    (BirthDeath lambda mu mRho mHeight) -> do
+    (BirthDeath lambda mu mRho timeSpec) -> do
       let rho = fromMaybe 1.0 mRho
-          -- This is bad code, but I don't want to change the definition of 'TimeSpec'.
-          timeSpec = case mHeight of
-            Nothing -> Nothing
-            Just (Mrca h) -> Just (h, True)
-            Just (Origin h) -> Just (h, False)
       case subS of
         Nothing -> liftIO $ bdSimulateNTreesConcurrently nLeaves lambda mu rho timeSpec chunks gs
         Just p ->
@@ -116,9 +111,9 @@
   IO (Forest Length Int)
 coalSimulateNTreesConcurrently nL chunks gs = do
   trss <-
-      mapConcurrently
-        (\(n, g) -> replicateM n $ CS.simulate nL g)
-        (zip chunks gs)
+    mapConcurrently
+      (\(n, g) -> replicateM n $ CS.simulate nL g)
+      (zip chunks gs)
   return $ concat trss
 
 bdSimulateAndSubSampleNTreesConcurrently ::
diff --git a/tlynx.cabal b/tlynx.cabal
--- a/tlynx.cabal
+++ b/tlynx.cabal
@@ -1,6 +1,6 @@
 cabal-version:  2.2
 name:           tlynx
-version:        0.4.0
+version:        0.4.1
 synopsis:       Handle phylogenetic trees
 description:    Examine, compare, and simulate phylogenetic trees in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>.
 category:       Bioinformatics