diff --git a/ChangeLog.md b/ChangeLog.md
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -5,6 +5,14 @@
 ## Unreleased changes
 
 
+## Version 0.3.4
+
+-   Improve `slynx examine`; show hamming distance; show constant sites.
+-   PhyloStrict -> PhyloExplicit; and some conversion functions were changed.
+-   `tlynx coalesce` was merged into `tlynx simulate`, the syntax has changed; see
+    `tlynx simulate --help`.
+
+
 ## Version 0.3.3
 
 -   Fix test suites.
diff --git a/README.md b/README.md
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
 
 # The ELynx Suite
 
-Version: 0.3.3.
+Version: 0.3.4.
 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 0.3.3.
+    ELynx Suite version 0.3.4.
     Developed by Dominik Schrempf.
-    Compiled on August 18, 2020, at 08:07 am, UTC.
+    Compiled on August 21, 2020, at 09:40 am, UTC.
     
     Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] 
                  [-f|--force] COMMAND
@@ -136,9 +136,9 @@
 
     slynx concatenate --help
 
-    ELynx Suite version 0.3.3.
+    ELynx Suite version 0.3.4.
     Developed by Dominik Schrempf.
-    Compiled on August 18, 2020, at 08:07 am, UTC.
+    Compiled on August 21, 2020, at 09:40 am, 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 0.3.3.
+    ELynx Suite version 0.3.4.
     Developed by Dominik Schrempf.
-    Compiled on August 18, 2020, at 08:07 am, UTC.
+    Compiled on August 21, 2020, at 09:40 am, 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 0.3.3.
+    ELynx Suite version 0.3.4.
     Developed by Dominik Schrempf.
-    Compiled on August 18, 2020, at 08:07 am, UTC.
+    Compiled on August 21, 2020, at 09:40 am, 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 0.3.3.
+    ELynx Suite version 0.3.4.
     Developed by Dominik Schrempf.
-    Compiled on August 18, 2020, at 08:07 am, UTC.
+    Compiled on August 21, 2020, at 09:40 am, UTC.
     
     Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE 
                                 [--standard-chars DOUBLE]
@@ -226,9 +226,9 @@
 
     slynx simulate --help
 
-    ELynx Suite version 0.3.3.
+    ELynx Suite version 0.3.4.
     Developed by Dominik Schrempf.
-    Compiled on August 18, 2020, at 08:07 am, UTC.
+    Compiled on August 21, 2020, at 09:40 am, 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 0.3.3.
+    ELynx Suite version 0.3.4.
     Developed by Dominik Schrempf.
-    Compiled on August 18, 2020, at 08:07 am, UTC.
+    Compiled on August 21, 2020, at 09:40 am, 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 0.3.3.
+    ELynx Suite version 0.3.4.
     Developed by Dominik Schrempf.
-    Compiled on August 18, 2020, at 08:07 am, UTC.
+    Compiled on August 21, 2020, at 09:40 am, 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 0.3.3.
+    ELynx Suite version 0.3.4.
     Developed by Dominik Schrempf.
-    Compiled on August 18, 2020, at 08:07 am, UTC.
+    Compiled on August 21, 2020, at 09:40 am, UTC.
     
     Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] 
                  [-f|--force] COMMAND
@@ -379,13 +379,12 @@
                                output files.
     
     Available commands:
-      coalesce                 Simulate phylogenetic trees using the coalescent processes (see also the 'simulate' command for simulations using the birth and death process).
       compare                  Compare two phylogenetic trees (compute distances and branch-wise differences).
       connect                  Connect two phylogenetic trees in all ways (possibly honoring constraints).
       distance                 Compute distances between many phylogenetic trees.
       examine                  Compute summary statistics of phylogenetic trees.
       shuffle                  Shuffle a phylogenetic tree (keep coalescent times, but shuffle topology and leaves).
-      simulate                 Simulate phylogenetic trees using birth and death processes (see also the 'coalesce' command for simulations using the coalescent process).
+      simulate                 Simulate phylogenetic trees using a birth and death or coalescent process.
     
     
     Available tree file formats:
@@ -399,9 +398,9 @@
 
     tlynx compare --help
 
-    ELynx Suite version 0.3.3.
+    ELynx Suite version 0.3.4.
     Developed by Dominik Schrempf.
-    Compiled on August 18, 2020, at 08:07 am, UTC.
+    Compiled on August 21, 2020, at 09:40 am, UTC.
     
     Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] 
                          [-f|--newick-format FORMAT] NAMES
@@ -428,9 +427,9 @@
 
     tlynx examine --help
 
-    ELynx Suite version 0.3.3.
+    ELynx Suite version 0.3.4.
     Developed by Dominik Schrempf.
-    Compiled on August 18, 2020, at 08:07 am, UTC.
+    Compiled on August 21, 2020, at 09:40 am, UTC.
     
     Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT]
       Compute summary statistics of phylogenetic trees.
@@ -452,37 +451,35 @@
 
     tlynx simulate --help
 
-    ELynx Suite version 0.3.3.
+    ELynx Suite version 0.3.4.
     Developed by Dominik Schrempf.
-    Compiled on August 18, 2020, at 08:07 am, UTC.
+    Compiled on August 21, 2020, at 09:40 am, UTC.
     
-    Usage: tlynx simulate [-t|--nTrees INT] [-n|--nLeaves INT] [-H|--height DOUBLE] 
-                          [-M|--condition-on-mrca] [-l|--lambda DOUBLE] 
-                          [-m|--mu DOUBLE] [-r|--rho DOUBLE] [-u|--sub-sample] 
-                          [-s|--summary-statistics] [-S|--seed [INT]]
-      Simulate phylogenetic trees using birth and death processes (see also the 'coalesce' command for simulations using the coalescent process).
+    Usage: tlynx simulate (-t|--nTrees INT) (-n|--nLeaves INT) PROCESS 
+                          [-u|--sub-sample DOUBLE] [-s|--summary-statistics] 
+                          [-S|--seed [INT]]
+      Simulate phylogenetic trees using a birth and death or coalescent process.
     
     Available options:
       -h,--help                Show this help text
       -V,--version             Show version
-      -t,--nTrees INT          Number of trees (default: 10)
-      -n,--nLeaves INT         Number of leaves per tree (default: 5)
-      -H,--height DOUBLE       Fix tree height (no default)
-      -M,--condition-on-mrca   Do not condition on height of origin but on height of
-                               MRCA
-      -l,--lambda DOUBLE       Birth rate lambda (default: 1.0)
-      -m,--mu DOUBLE           Death rate mu (default: 0.9)
-      -r,--rho DOUBLE          Sampling probability rho (default: 1.0)
-      -u,--sub-sample          Perform sub-sampling; see below.
-      -s,--summary-statistics  Only output number of children for each branch
+      -t,--nTrees INT          Number of trees
+      -n,--nLeaves INT         Number of leaves per tree
+      -u,--sub-sample DOUBLE   Perform sub-sampling; see below.
+      -s,--summary-statistics  For each branch, print length and number of children
       -S,--seed [INT]          Seed for random number generator; list of 32 bit
                                integers with up to 256 elements (default: random)
       -h,--help                Show this help text
     
-    Height of Trees: if no tree height is given, the heights will be randomly drawn from the expected distribution given the number of leaves, the birth and the death rate.
-    Summary statistics only: only print (NumberOfExtantChildren BranchLength) pairs for each branch of each tree. The trees are separated by a newline character.
-    Sub-sampling: simulate one big tree with n'=round(n/rho), n'>=n, leaves, and randomly sample sub-trees with n leaves. Hence, with rho=1.0, the same tree is reported over and over again.
-    Gernhard, T. (2008). The conditioned reconstructed process. Journal of Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005
+    Available processes:
+      birthdeath               Birth and death process
+      coalescent               Coalescent process
+    
+    See, for example, 'tlynx simulate birthdeath --help'.
+    Sub-sample with probability p:
+      1. Simulate one big tree with n'=round(n/p), n'>=n, leaves;
+      2. Randomly sample sub-trees with n leaves.
+      (With p=1.0, the same tree is reported over and over again.)
 
 
 # ELynx
@@ -491,9 +488,9 @@
 
     elynx --help | head -n -16
 
-    ELynx Suite version 0.3.3.
+    ELynx Suite version 0.3.4.
     Developed by Dominik Schrempf.
-    Compiled on August 18, 2020, at 08:07 am, UTC.
+    Compiled on August 21, 2020, at 09:40 am, UTC.
     
     Usage: elynx COMMAND
       Validate and redo past ELynx analyses
diff --git a/src/TLynx/Coalesce/Coalesce.hs b/src/TLynx/Coalesce/Coalesce.hs
deleted file mode 100644
--- a/src/TLynx/Coalesce/Coalesce.hs
+++ /dev/null
@@ -1,145 +0,0 @@
-{-# LANGUAGE OverloadedStrings #-}
-{-# LANGUAGE TemplateHaskell #-}
-{-# LANGUAGE TupleSections #-}
-
--- TODO: MERGE WITH SIMULATE.
-
--- |
---   Description :  Simulate reconstructed trees using the coalescent process
---   Copyright   :  (c) Dominik Schrempf 2020
---   License     :  GPL-3.0-or-later
---
---   Maintainer  :  dominik.schrempf@gmail.com
---   Stability   :  unstable
---   Portability :  portable
---
--- Creation date: Tue Feb 3 17:00:00 2020.
-module TLynx.Coalesce.Coalesce
-  ( coalesce,
-  )
-where
-
-import Control.Concurrent (getNumCapabilities)
-import Control.Concurrent.Async.Lifted.Safe
-  ( mapConcurrently,
-  )
-import Control.Monad
-import Control.Monad.IO.Class
-import Control.Monad.Logger
-import Control.Monad.Trans.Reader (ask)
-import Control.Parallel.Strategies
-import qualified Data.ByteString.Builder as BB
-import qualified Data.ByteString.Lazy.Char8 as BL
-import Data.Maybe
-import qualified Data.Sequence as Seq
-import qualified Data.Text as T
-import qualified Data.Text.Lazy as LT
-import qualified Data.Text.Lazy.Encoding as LT
-import ELynx.Data.Tree
-import ELynx.Export.Tree.Newick (toNewick)
-import ELynx.Simulate.Coalescent (simulate)
-import ELynx.Tools
-import System.Random.MWC (initialize)
-import TLynx.Coalesce.Options
-import TLynx.Simulate.Simulate (nSubSamples)
-
--- | Simulate phylogenetic trees.
-coalesce :: ELynx CoalesceArguments ()
-coalesce = do
-  l <- local <$> ask
-  let s = argsSumStat l
-  logNewSection "Arguments"
-  $(logInfo) $ T.pack $ reportCoalesceArguments l
-  logNewSection "Simulation"
-  c <- liftIO getNumCapabilities
-  $(logInfo) $ T.pack $ "Number of used cores: " <> show c
-  trs <- case argsRho l of
-    Nothing -> simulateNTreesConcurrently
-    Just _ -> simulateAndSubSampleNTreesConcurrently
-  let ls =
-        if s
-          then parMap rpar (formatNChildSumStat . toNChildSumStat) trs
-          else parMap rpar toNewick (map lengthToPhyloTree trs)
-  let res = BL.unlines ls
-  out "simulated trees" res ".tree"
-
-simulateNTreesConcurrently :: ELynx CoalesceArguments (Forest Length Int)
-simulateNTreesConcurrently = do
-  (CoalesceArguments nT nL _ _ (Fixed s)) <- local <$> ask
-  c <- liftIO getNumCapabilities
-  gs <- liftIO $ initialize s >>= \g -> splitGen c g
-  let chunks = getChunks c nT
-  trss <-
-    liftIO $
-      mapConcurrently
-        (\(n, g) -> replicateM n $ simulate nL g)
-        (zip chunks gs)
-  return $ concat trss
-
-simulateAndSubSampleNTreesConcurrently ::
-  ELynx CoalesceArguments (Forest Length Int)
-simulateAndSubSampleNTreesConcurrently = do
-  (CoalesceArguments nT nL mR _ (Fixed s)) <- local <$> ask
-  c <- liftIO getNumCapabilities
-  let r =
-        fromMaybe
-          ( error
-              "cimulateAndSubSampleNTreesConcurrently: no sampling probability given."
-          )
-          mR
-  let nLeavesBigTree = (round $ fromIntegral nL / r) :: Int
-  gs <- liftIO $ initialize s >>= \g -> splitGen c g
-  let chunks = getChunks c nT
-  tr <- liftIO $ simulate nLeavesBigTree (head gs)
-  logNewSection $
-    T.pack $
-      "Simulate one big tree with "
-        <> show nLeavesBigTree
-        <> " leaves."
-  -- Log the base tree.
-  $(logInfo) $ LT.toStrict $ LT.decodeUtf8 $ toNewick $ lengthToPhyloTree tr
-  logNewSection $
-    T.pack $
-      "Sub sample "
-        <> show nT
-        <> " trees with "
-        <> show nL
-        <> " leaves."
-  let lvs = Seq.fromList $ leaves tr
-  trss <-
-    liftIO $
-      mapConcurrently
-        (\(nSamples, g) -> nSubSamples nSamples lvs nL tr g)
-        (zip chunks gs)
-  let trs = catMaybes $ concat trss
-  return $ map prune trs
-
--- | Pair of branch length with number of extant children.
-type BrLnNChildren = (BranchLength, Int)
-
--- | Possible summary statistic of phylogenetic trees. A list of tuples
--- (BranchLength, NumberOfExtantChildrenBelowThisBranch).
-type NChildSumStat = [BrLnNChildren]
-
--- | Format the summary statistics in the following form:
--- @
---    nLeaves1 branchLength1
---    nLeaves2 branchLength2
---    ....
-formatNChildSumStat :: NChildSumStat -> BL.ByteString
-formatNChildSumStat s =
-  BB.toLazyByteString . mconcat $ map formatNChildSumStatLine s
-
-formatNChildSumStatLine :: BrLnNChildren -> BB.Builder
-formatNChildSumStatLine (l, n) =
-  BB.intDec n <> BB.char8 ' ' <> BB.doubleDec l <> BB.char8 '\n'
-
--- | Compute NChilSumStat for a phylogenetic tree.
-toNChildSumStat :: Measurable e => Tree e a -> NChildSumStat
-toNChildSumStat (Node br _ []) = [(getLen br, 1)]
-toNChildSumStat (Node br _ ts) = (getLen br, sumCh) : concat nChSS
-  where
-    nChSS = map toNChildSumStat ts
-    sumCh = sum $ map (snd . head) nChSS
-
--- TODO: MERGE WITH SIMULATE.
diff --git a/src/TLynx/Coalesce/Options.hs b/src/TLynx/Coalesce/Options.hs
deleted file mode 100644
--- a/src/TLynx/Coalesce/Options.hs
+++ /dev/null
@@ -1,125 +0,0 @@
-{-# LANGUAGE DeriveGeneric #-}
-
--- |
--- Module      :  TLynx.Coalesce.Options
--- Description :  Argument parser for @slynx coalesce@
--- Copyright   :  (c) Dominik Schrempf 2020
--- License     :  GPL-3.0-or-later
---
--- Maintainer  :  dominik.schrempf@gmail.com
--- Stability   :  unstable
--- Portability :  portable
---
--- Creation date: Fri May  3 11:51:07 2019.
-module TLynx.Coalesce.Options
-  ( CoalesceArguments (..),
-    coalesceArguments,
-    reportCoalesceArguments,
-    coalesceFooter,
-  )
-where
-
-import Data.List
-import ELynx.Tools
-import Options.Applicative
-
--- | Arguments need to simulate phylogenetic trees using the coalescent process.
-data CoalesceArguments = CoalesceArguments
-  { -- | Number of simulated trees.
-    argsNTrees :: Int,
-    -- | Number of leaves per tree.
-    argsNLeaves :: Int,
-    -- | Perform random sub-sampling with given sampling rate.
-    argsRho :: Maybe Double,
-    -- | Only print summary statistics?
-    argsSumStat :: Bool,
-    -- | Seed of NRG, random if 'Nothing'.
-    argsSeed :: Seed
-  }
-  deriving (Eq, Show, Generic)
-
-instance Reproducible CoalesceArguments where
-  inFiles _ = []
-  outSuffixes _ = [".tree"]
-  getSeed = Just . argsSeed
-  setSeed a s = a {argsSeed = Fixed s}
-  parser = coalesceArguments
-  cmdName = "coalesce"
-  cmdDsc =
-    [ "Simulate phylogenetic trees using the coalescent processes (see also the 'simulate' command for simulations using the birth and death process)."
-    ]
-  cmdFtr = coalesceFooter
-
-instance FromJSON CoalesceArguments
-
-instance ToJSON CoalesceArguments
-
--- | Print useful information about the provided arguments.
-reportCoalesceArguments :: CoalesceArguments -> String
-reportCoalesceArguments a =
-  intercalate
-    "\n"
-    [ "Number of simulated trees: " ++ show (argsNTrees a),
-      "Number of leaves per tree: " ++ show (argsNLeaves a),
-      "Sub-sampling: " ++ ssStr,
-      "Summary statistics only: " ++ show (argsSumStat a)
-    ]
-  where
-    ssStr = case argsRho a of
-      Nothing -> "No"
-      Just r -> "Yes, with probability " <> show r
-
--- | Command line parser.
-coalesceArguments :: Parser CoalesceArguments
-coalesceArguments =
-  CoalesceArguments
-    <$> nTreeOpt
-    <*> nLeavesOpt
-    <*> rhoOpt
-    <*> sumStatOpt
-    <*> seedOpt
-
-nTreeOpt :: Parser Int
-nTreeOpt =
-  option auto $
-    long "nTrees"
-      <> short 't'
-      <> metavar "INT"
-      <> value 10
-      <> showDefault
-      <> help "Number of trees"
-
-nLeavesOpt :: Parser Int
-nLeavesOpt =
-  option auto $
-    long "nLeaves"
-      <> short 'n'
-      <> metavar "INT"
-      <> value 5
-      <> showDefault
-      <> help "Number of leaves per tree"
-
-rhoOpt :: Parser (Maybe Double)
-rhoOpt =
-  optional $
-    option auto $
-      long "sub-sample"
-        <> short 'r'
-        <> metavar "DOUBLE"
-        <> showDefault
-        <> help
-          "Perform random sub-sampling with sampling probability rho (see below)"
-
-sumStatOpt :: Parser Bool
-sumStatOpt =
-  switch $
-    long "summary-statistics" <> short 's' <> showDefault
-      <> help
-        "Only output number of children for each branch"
-
--- | And a footer.
-coalesceFooter :: [String]
-coalesceFooter =
-  [ "Sub-sampling: simulate one big tree with n'=round(n/rho), n'>=n, leaves, and randomly sample sub-trees with n leaves. Hence, with rho=1.0, the same tree is reported over and over again.",
-    "Summary statistics: only print (NumberOfExtantChildren BranchLength) pairs for each branch of each tree. The trees are separated by a newline character."
-  ]
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
@@ -48,7 +48,7 @@
   FilePath ->
   ELynx
     CompareArguments
-    (Tree PhyloStrict BS.ByteString, Tree PhyloStrict BS.ByteString)
+    (Tree PhyloExplicit BS.ByteString, Tree PhyloExplicit BS.ByteString)
 treesOneFile tf = do
   nwF <- argsNewickFormat . local <$> ask
   $(logInfo) $ T.pack $ "Parse file '" ++ tf ++ "'."
@@ -59,8 +59,8 @@
     GT -> error "Too many trees in file."
     EQ ->
       return
-        ( either error id $ toStrictTree $ head ts,
-          either error id $ toStrictTree $ head . tail $ ts
+        ( either error id $ toExplicitTree $ head ts,
+          either error id $ toExplicitTree $ head . tail $ ts
         )
 
 treesTwoFiles ::
@@ -68,14 +68,14 @@
   FilePath ->
   ELynx
     CompareArguments
-    (Tree PhyloStrict BS.ByteString, Tree PhyloStrict BS.ByteString)
+    (Tree PhyloExplicit BS.ByteString, Tree PhyloExplicit BS.ByteString)
 treesTwoFiles tf1 tf2 = do
   nwF <- argsNewickFormat . local <$> ask
   $(logInfo) $ T.pack $ "Parse first tree file '" ++ tf1 ++ "'."
   t1 <- liftIO $ parseFileWith (oneNewick nwF) tf1
   $(logInfo) $ T.pack $ "Parse second tree file '" ++ tf2 ++ "'."
   t2 <- liftIO $ parseFileWith (oneNewick nwF) tf2
-  return (either error id $ toStrictTree t1, either error id $ toStrictTree t2)
+  return (either error id $ toExplicitTree t1, either error id $ toExplicitTree t2)
 
 -- | More detailed comparison of two trees.
 compareCmd :: ELynx CompareArguments ()
@@ -93,9 +93,9 @@
       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 $ fromStrictTree tr1
+  liftIO $ BL.hPutStrLn outH $ toNewick $ toPhyloTree tr1
   liftIO $ hPutStrLn outH "Tree 2:"
-  liftIO $ BL.hPutStrLn outH $ toNewick $ fromStrictTree tr2
+  liftIO $ BL.hPutStrLn outH $ toNewick $ toPhyloTree tr2
   liftIO $ hPutStrLn outH ""
   -- Intersect trees.
   (t1, t2) <-
@@ -103,8 +103,8 @@
       then do
         let [x, y] = either error id $ intersect [tr1, tr2]
         liftIO $ hPutStrLn outH "Intersected trees are:"
-        liftIO $ BL.hPutStrLn outH $ toNewick $ fromStrictTree x
-        liftIO $ BL.hPutStrLn outH $ toNewick $ fromStrictTree y
+        liftIO $ BL.hPutStrLn outH $ toNewick $ toPhyloTree x
+        liftIO $ BL.hPutStrLn outH $ toNewick $ toPhyloTree y
         return (x, y)
       else return (tr1, tr2)
   -- Check input (moved to library functions).
@@ -135,8 +135,8 @@
   let t1' = normalizeBranchSupport t1
       t2' = normalizeBranchSupport t2
   $(logDebug) "Trees with normalized branch support values:"
-  $(logDebug) $ E.decodeUtf8 $ BL.toStrict $ toNewick $ fromStrictTree t1'
-  $(logDebug) $ E.decodeUtf8 $ BL.toStrict $ toNewick $ fromStrictTree t2'
+  $(logDebug) $ E.decodeUtf8 $ BL.toStrict $ toNewick $ toPhyloTree t1'
+  $(logDebug) $ E.decodeUtf8 $ BL.toStrict $ toNewick $ toPhyloTree t2'
   liftIO $
     T.hPutStrLn outH $
       formatD
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
@@ -122,7 +122,7 @@
   (tl, tr) <- parseTrees l r
   let ts = connectTrees tl tr
   $(logInfo) $ "Connected trees: " <> tShow (length ts)
-  liftIO $ BL.hPutStr h $ BL.unlines $ map (toNewick . lengthToPhyloTree) ts
+  liftIO $ BL.hPutStr h $ BL.unlines $ map (toNewick . measurableToPhyloTree) ts
 
 connectAndFilter ::
   Handle -> FilePath -> FilePath -> FilePath -> ELynx ConnectArguments ()
@@ -138,4 +138,4 @@
       ts' = filter (compatibleWith getName cs) ts
   $(logInfo) $ "Connected  trees: " <> tShow (length ts)
   $(logInfo) $ "Compatible trees: " <> tShow (length ts')
-  liftIO $ BL.hPutStr h $ BL.unlines $ map (toNewick . lengthToPhyloTree) ts'
+  liftIO $ BL.hPutStr h $ BL.unlines $ map (toNewick . measurableToPhyloTree) ts'
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
@@ -35,7 +35,6 @@
 import qualified Data.ByteString.Lazy.Char8 as BL
 import Data.List hiding (intersect)
 import Data.Maybe
--- TODO: Remove text dependency.
 import qualified Data.Text as T
 import qualified Data.Text.IO as T
 import qualified Data.Text.Lazy as LT
@@ -179,14 +178,14 @@
         IncompatibleSplit val -> collapse val . normalizeBranchSupport
         _ -> id
   -- The trees can be prepared now.
-  let trees' :: Forest PhyloStrict BS.ByteString
-      trees' = map (collapseF . normalizeF . either error id . toStrictTree) trees
+  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 . fromStrictTree) trees'
+  $(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 . toStrictTree) pt
+          let t = (either error id . toExplicitTree) pt
            in [(0, i, distanceMeasure t t') | (i, t') <- zip [1 ..] trees']
       ds = map (\(_, _, x) -> x) dsTriplets
       dsVec = V.fromList ds
diff --git a/src/TLynx/Options.hs b/src/TLynx/Options.hs
--- a/src/TLynx/Options.hs
+++ b/src/TLynx/Options.hs
@@ -20,7 +20,6 @@
 
 import ELynx.Tools
 import Options.Applicative
-import TLynx.Coalesce.Options
 import TLynx.Compare.Options
 import TLynx.Connect.Options
 import TLynx.Distance.Options
@@ -31,8 +30,7 @@
 
 -- | The different TLynx commands and their arguments.
 data CommandArguments
-  = Coalesce CoalesceArguments
-  | Compare CompareArguments
+  = Compare CompareArguments
   | Connect ConnectArguments
   | Distance DistanceArguments
   | Examine ExamineArguments
@@ -41,7 +39,6 @@
   deriving (Eq, Show, Generic)
 
 instance Reproducible CommandArguments where
-  inFiles (Coalesce a) = inFiles a
   inFiles (Compare a) = inFiles a
   inFiles (Connect a) = inFiles a
   inFiles (Distance a) = inFiles a
@@ -49,7 +46,6 @@
   inFiles (Shuffle a) = inFiles a
   inFiles (Simulate a) = inFiles a
 
-  outSuffixes (Coalesce a) = outSuffixes a
   outSuffixes (Compare a) = outSuffixes a
   outSuffixes (Connect a) = outSuffixes a
   outSuffixes (Distance a) = outSuffixes a
@@ -57,7 +53,6 @@
   outSuffixes (Shuffle a) = outSuffixes a
   outSuffixes (Simulate a) = outSuffixes a
 
-  getSeed (Coalesce a) = getSeed a
   getSeed (Compare a) = getSeed a
   getSeed (Connect a) = getSeed a
   getSeed (Distance a) = getSeed a
@@ -65,7 +60,6 @@
   getSeed (Shuffle a) = getSeed a
   getSeed (Simulate a) = getSeed a
 
-  setSeed (Coalesce a) = Coalesce . setSeed a
   setSeed (Compare a) = Compare . setSeed a
   setSeed (Connect a) = Connect . setSeed a
   setSeed (Distance a) = Distance . setSeed a
@@ -87,9 +81,6 @@
 
 instance ToJSON CommandArguments
 
-coalesceCommand :: Mod CommandFields CommandArguments
-coalesceCommand = createCommandReproducible Coalesce
-
 compareCommand :: Mod CommandFields CommandArguments
 compareCommand = createCommandReproducible Compare
 
@@ -111,8 +102,7 @@
 commandArguments :: Parser CommandArguments
 commandArguments =
   hsubparser $
-    coalesceCommand
-      <> compareCommand
+    compareCommand
       <> connectCommand
       <> distanceCommand
       <> examineCommand
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
@@ -69,7 +69,7 @@
     Random -> error "Seed not available; please contact maintainer."
     Fixed s -> liftIO $ initialize s
   ts <- liftIO $ shuffleT (nReplicates l) (height t) cs ls gen
-  liftIO $ BL.hPutStr h $ BL.unlines $ map (toNewick . lengthToPhyloTree) ts
+  liftIO $ BL.hPutStr h $ BL.unlines $ map (toNewick . measurableToPhyloTree) ts
   liftIO $ hClose h
 
 shuffleT ::
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
@@ -1,4 +1,5 @@
 {-# LANGUAGE DeriveGeneric #-}
+{-# LANGUAGE OverloadedStrings #-}
 
 -- |
 -- Module      :  TLynx.Simulate.Options
@@ -12,10 +13,11 @@
 --
 -- Creation date: Fri May  3 11:51:07 2019.
 module TLynx.Simulate.Options
-  ( SimulateArguments (..),
+  ( Height (..),
+    Process (..),
+    SimulateArguments (..),
     simulateArguments,
     reportSimulateArguments,
-    simulateFooter,
   )
 where
 
@@ -23,25 +25,59 @@
 import ELynx.Tools
 import Options.Applicative
 
+-- | Condition on tree height (origin or most recent common ancestor).
+data Height = Origin Double | Mrca Double
+  deriving (Eq, Generic)
+
+instance Show Height where
+  show (Origin o) = "Condition on height of origin: " ++ show o
+  show (Mrca m) = "Condition on height of MRCA: " ++ show m
+
+instance FromJSON Height
+
+instance ToJSON Height
+
+-- | Process to be used for simulation.
+data Process
+  = BirthDeath
+      { -- | Birth rate.
+        bdLambda :: Double,
+        -- | Death rate.
+        bdMu :: Double,
+        -- | Sampling rate.
+        bdRho :: Maybe Double,
+        -- | Condition on height?
+        bdHeight :: Maybe Height
+      }
+  | Coalescent
+  deriving (Eq, Show, Generic)
+
+instance FromJSON Process
+
+instance ToJSON Process
+
+reportProcess :: Process -> String
+reportProcess (BirthDeath l m mr mh) =
+  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
+    ]
+reportProcess Coalescent = "Model: Coalescent process"
+
 -- | Arguments need to simulate phylogenetic trees using birth and death processes.
 data SimulateArguments = SimulateArguments
   { -- | Simulated trees.
     argsNTrees :: Int,
     -- | Number of leaves.
     argsNLeaves :: Int,
-    -- | Tree height (time to origin or MRCA).
-    argsHeight :: Maybe Double,
-    -- | False: condition on origin; True:
-    -- condition on MRCA.
-    argsConditionMRCA :: Bool,
-    -- | Birth rate.
-    argsLambda :: Double,
-    -- | Death rate.
-    argsMu :: Double,
-    -- | Smapling rate.
-    argsRho :: Double,
-    -- | Perform actual sub-sampling.
-    argsSubSample :: Bool,
+    -- | Process.
+    argsProcess :: Process,
+    -- | Perform sub-sampling with given probability.
+    argsSubSample :: Maybe Double,
     -- | Only print summary statistics?
     argsSumStat :: Bool,
     -- | Seed of NRG, random if 'Nothing'.
@@ -56,9 +92,7 @@
   setSeed a s = a {argsSeed = Fixed s}
   parser = simulateArguments
   cmdName = "simulate"
-  cmdDsc =
-    [ "Simulate phylogenetic trees using birth and death processes (see also the 'coalesce' command for simulations using the coalescent process)."
-    ]
+  cmdDsc = ["Simulate phylogenetic trees using a birth and death or coalescent process."]
   cmdFtr = simulateFooter
 
 instance FromJSON SimulateArguments
@@ -72,21 +106,14 @@
     "\n"
     [ "Number of simulated trees: " ++ show (argsNTrees a),
       "Number of leaves per tree: " ++ show (argsNLeaves a),
-      "Height of trees: " ++ hStr,
-      "Birth rate: " ++ show (argsLambda a),
-      "Death rate: " ++ show (argsMu a),
-      "Sampling probability: " ++ show (argsRho a),
-      "Perform sub-sampling: " ++ show (argsSubSample a),
+      reportProcess (argsProcess a),
+      "Perform sub-sampling: " ++ ssStr,
       "Summary statistics only: " ++ show (argsSumStat a)
     ]
   where
-    hStr = case argsHeight a of
-      Nothing -> "Random height of origin"
-      Just h ->
-        show h ++ ", conditioned on "
-          ++ if argsConditionMRCA a
-            then "MRCA"
-            else "origin"
+    ssStr = case argsSubSample a of
+      Nothing -> "No"
+      Just p -> "Yes, with probability " ++ show p
 
 -- | Command line parser.
 simulateArguments :: Parser SimulateArguments
@@ -94,11 +121,7 @@
   SimulateArguments
     <$> nTreeOpt
     <*> nLeavesOpt
-    <*> treeHeightOpt
-    <*> conditionMRCAOpt
-    <*> lambdaOpt
-    <*> muOpt
-    <*> rhoOpt
+    <*> process
     <*> subSampleOpt
     <*> sumStatOpt
     <*> seedOpt
@@ -109,8 +132,6 @@
     long "nTrees"
       <> short 't'
       <> metavar "INT"
-      <> value 10
-      <> showDefault
       <> help "Number of trees"
 
 nLeavesOpt :: Parser Int
@@ -119,34 +140,14 @@
     long "nLeaves"
       <> short 'n'
       <> metavar "INT"
-      <> value 5
-      <> showDefault
       <> help "Number of leaves per tree"
 
-treeHeightOpt :: Parser (Maybe Double)
-treeHeightOpt =
-  optional $
-    option auto $
-      long "height"
-        <> short 'H'
-        <> metavar "DOUBLE"
-        <> help "Fix tree height (no default)"
-
-conditionMRCAOpt :: Parser Bool
-conditionMRCAOpt =
-  switch $
-    long "condition-on-mrca" <> short 'M' <> showDefault
-      <> help
-        "Do not condition on height of origin but on height of MRCA"
-
 lambdaOpt :: Parser Double
 lambdaOpt =
   option auto $
     long "lambda"
       <> short 'l'
       <> metavar "DOUBLE"
-      <> value 1.0
-      <> showDefault
       <> help "Birth rate lambda"
 
 muOpt :: Parser Double
@@ -155,40 +156,85 @@
     long "mu"
       <> short 'm'
       <> metavar "DOUBLE"
-      <> value 0.9
-      <> showDefault
       <> help "Death rate mu"
 
 rhoOpt :: Parser Double
 rhoOpt =
   option auto $
-    long "rho" <> short 'r' <> metavar "DOUBLE" <> value 1.0
-      <> help
-        "Sampling probability rho (default: 1.0)"
+    long "rho"
+      <> short 'r'
+      <> metavar "DOUBLE"
+      <> help "Sampling probability rho"
 
-subSampleOpt :: Parser Bool
+mrca :: Parser Height
+mrca =
+  Mrca
+    <$> option
+      auto
+      ( long "mrca"
+          <> metavar "DOUBLE"
+          <> help "Condition on height of most recent common ancestor"
+      )
+
+origin :: Parser Height
+origin =
+  Origin
+    <$> option
+      auto
+      ( long "origin"
+          <> metavar "DOUBLE"
+          <> help "Condition on height of origin"
+      )
+
+birthDeath :: Parser Process
+birthDeath = BirthDeath <$> lambdaOpt <*> muOpt <*> optional rhoOpt <*> optional (mrca <|> origin)
+
+coalescent :: Parser Process
+coalescent = pure Coalescent
+
+process :: Parser Process
+process =
+  hsubparser $
+    ( command
+        "birthdeath"
+        ( info
+            birthDeath
+            ( progDesc "Birth and death process"
+                <> footer "Height: If no tree height is given, the heights will be randomly drawn from the expected distribution given the number of leaves, the birth and the death rate assuming a uniform prior."
+            )
+        )
+        <> command
+          "coalescent"
+          (info coalescent (progDesc "Coalescent process"))
+    )
+      <> metavar "PROCESS"
+      <> commandGroup "Available processes:"
+
+subSampleOpt :: Parser (Maybe Double)
 subSampleOpt =
-  switch $
-    long "sub-sample" <> short 'u' <> showDefault
-      <> help
-        "Perform sub-sampling; see below."
+  optional $
+    option auto $
+      long
+        "sub-sample"
+        <> short 'u'
+        <> metavar "DOUBLE"
+        <> showDefault
+        <> help "Perform sub-sampling; see below."
 
 sumStatOpt :: Parser Bool
 sumStatOpt =
   switch $
     long "summary-statistics" <> short 's' <> showDefault
       <> help
-        "Only output number of children for each branch"
+        "For each branch, print length and number of children"
 
-citation :: String
-citation =
-  "Gernhard, T. (2008). The conditioned reconstructed process. Journal of Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005"
+-- citation :: String
+-- citation =
+--   "Gernhard, T. (2008). The conditioned reconstructed process. Journal of Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005"
 
 -- | And a footer.
 simulateFooter :: [String]
 simulateFooter =
-  [ "Height of Trees: if no tree height is given, the heights will be randomly drawn from the expected distribution given the number of leaves, the birth and the death rate.",
-    "Summary statistics only: only print (NumberOfExtantChildren BranchLength) pairs for each branch of each tree. The trees are separated by a newline character.",
-    "Sub-sampling: simulate one big tree with n'=round(n/rho), n'>=n, leaves, and randomly sample sub-trees with n leaves. Hence, with rho=1.0, the same tree is reported over and over again.",
-    citation
+  [ "See, for example, 'tlynx simulate birthdeath --help'.",
+    "Sub-sample with probability p:\n  1. Simulate one big tree with n'=round(n/p), n'>=n, leaves;\n  2. Randomly sample sub-trees with n leaves.\n  (With p=1.0, the same tree is reported over and over again.)"
   ]
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
@@ -33,11 +33,11 @@
 import Control.Monad
 import Control.Monad.IO.Class
 import Control.Monad.Logger
-import Control.Monad.Trans.Reader (ask)
+import Control.Monad.Trans.Reader hiding (local)
 import Control.Parallel.Strategies
 import qualified Data.ByteString.Builder as BB
 import qualified Data.ByteString.Lazy.Char8 as BL
-import Data.Foldable (toList)
+import Data.Foldable
 import Data.Maybe
 import qualified Data.Sequence as Seq
 import qualified Data.Set as Set
@@ -45,28 +45,17 @@
 import qualified Data.Text.Lazy as LT
 import qualified Data.Text.Lazy.Encoding as LT
 import ELynx.Data.Tree
-import ELynx.Export.Tree.Newick (toNewick)
-import ELynx.Simulate.PointProcess
-  ( TimeSpec,
-    simulateNReconstructedTrees,
-    simulateReconstructedTree,
-  )
+import ELynx.Export.Tree.Newick
+import qualified ELynx.Simulate.Coalescent as CS
+import qualified ELynx.Simulate.PointProcess as PP
 import ELynx.Tools
 import System.Random.MWC
-  ( GenIO,
-    initialize,
-  )
 import TLynx.Simulate.Options
 
--- | Simulate phylogenetic trees.
+-- | Simulate phylogenetic trees using birth and death process.
 simulate :: ELynx SimulateArguments ()
 simulate = do
-  l <- local <$> ask
-  let SimulateArguments nTrees nLeaves tHeight mrca lambda mu rho subS sumS (Fixed s) =
-        l
-  -- error "simulate: seed not available; please contact maintainer."
-  when (isNothing tHeight && mrca) $
-    error "Cannot condition on MRCA (-M) when height is not given (-H)."
+  l@(SimulateArguments nTrees nLeaves pr subS sumS (Fixed s)) <- local <$> ask
   c <- liftIO getNumCapabilities
   logNewSection "Arguments"
   $(logInfo) $ T.pack $ reportSimulateArguments l
@@ -74,64 +63,88 @@
   $(logInfo) $ T.pack $ "Number of used cores: " <> show c
   gs <- liftIO $ initialize s >>= \gen -> splitGen c gen
   let chunks = getChunks c nTrees
-      timeSpec = fmap (,mrca) tHeight
-  trs <-
-    if subS
-      then
-        simulateAndSubSampleNTreesConcurrently
-          nLeaves
-          lambda
-          mu
-          rho
-          timeSpec
-          chunks
-          gs
-      else simulateNTreesConcurrently nLeaves lambda mu rho timeSpec chunks gs
+  trs <- case pr of
+    (BirthDeath lambda mu mRho mHeight) -> 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 ->
+          bdSimulateAndSubSampleNTreesConcurrently
+            nLeaves
+            lambda
+            mu
+            rho
+            p
+            timeSpec
+            chunks
+            gs
+    Coalescent -> case subS of
+      Nothing -> liftIO $ coalSimulateNTreesConcurrently nLeaves chunks gs
+      Just p -> coalSimulateAndSubSampleNTreesConcurrently nLeaves p chunks gs
   let ls =
         if sumS
           then parMap rpar (formatNChildSumStat . toNChildSumStat) trs
-          else parMap rpar toNewick $ map lengthToPhyloTree trs
+          else parMap rpar toNewick $ map measurableToPhyloTree trs
   let res = BL.unlines ls
   out "simulated trees" res ".tree"
 
-simulateNTreesConcurrently ::
+bdSimulateNTreesConcurrently ::
   Int ->
   Double ->
   Double ->
   Double ->
-  TimeSpec ->
+  PP.TimeSpec ->
   [Int] ->
   [GenIO] ->
-  ELynx SimulateArguments (Forest Length Int)
-simulateNTreesConcurrently nLeaves l m r timeSpec chunks gs = do
+  IO (Forest Length Int)
+bdSimulateNTreesConcurrently nLeaves l m r timeSpec chunks gs = do
   let l' = l * r
       m' = m - l * (1.0 - r)
   trss <-
-    liftIO $
+    mapConcurrently
+      (\(n, g) -> PP.simulateNReconstructedTrees n nLeaves timeSpec l' m' g)
+      (zip chunks gs)
+  return $ concat trss
+
+coalSimulateNTreesConcurrently ::
+  Int ->
+  [Int] ->
+  [GenIO] ->
+  IO (Forest Length Int)
+coalSimulateNTreesConcurrently nL chunks gs = do
+  trss <-
       mapConcurrently
-        (\(n, g) -> simulateNReconstructedTrees n nLeaves timeSpec l' m' g)
+        (\(n, g) -> replicateM n $ CS.simulate nL g)
         (zip chunks gs)
   return $ concat trss
 
-simulateAndSubSampleNTreesConcurrently ::
+bdSimulateAndSubSampleNTreesConcurrently ::
   Int ->
   Double ->
   Double ->
   Double ->
-  TimeSpec ->
+  Double ->
+  PP.TimeSpec ->
   [Int] ->
   [GenIO] ->
   ELynx SimulateArguments (Forest Length Int)
-simulateAndSubSampleNTreesConcurrently nLeaves l m r timeSpec chunks gs = do
-  let nLeavesBigTree = (round $ fromIntegral nLeaves / r) :: Int
+bdSimulateAndSubSampleNTreesConcurrently nLeaves l m r p timeSpec chunks gs = do
+  let nLeavesBigTree = (round $ fromIntegral nLeaves / p) :: Int
+      l' = l * r
+      m' = m - l * (1.0 - r)
   logNewSection $
     T.pack $
       "Simulate one big tree with "
         <> show nLeavesBigTree
         <> " leaves."
-  tr <- liftIO $ simulateReconstructedTree nLeavesBigTree timeSpec l m (head gs)
+  tr <- liftIO $ PP.simulateReconstructedTree nLeavesBigTree timeSpec l' m' (head gs)
   -- Log the base tree.
-  $(logInfo) $ LT.toStrict $ LT.decodeUtf8 $ toNewick $ lengthToPhyloTree tr
+  $(logInfo) $ LT.toStrict $ LT.decodeUtf8 $ toNewick $ measurableToPhyloTree tr
   logNewSection $
     T.pack $
       "Sub sample "
@@ -148,7 +161,39 @@
   let trs = catMaybes $ concat trss
   return $ map prune trs
 
--- | Extract a random subtree with @N@ leaves of a tree with @M@ leaves, where
+coalSimulateAndSubSampleNTreesConcurrently ::
+  Int ->
+  Double ->
+  [Int] ->
+  [GenIO] ->
+  ELynx SimulateArguments (Forest Length Int)
+coalSimulateAndSubSampleNTreesConcurrently nL p chunks gs = do
+  let nLeavesBigTree = (round $ fromIntegral nL / p) :: Int
+  logNewSection $
+    T.pack $
+      "Simulate one big tree with "
+        <> show nLeavesBigTree
+        <> " leaves."
+  tr <- liftIO $ CS.simulate nLeavesBigTree (head gs)
+  -- Log the base tree.
+  $(logInfo) $ LT.toStrict $ LT.decodeUtf8 $ toNewick $ measurableToPhyloTree tr
+  logNewSection $
+    T.pack $
+      "Sub sample "
+        <> show (sum chunks)
+        <> " trees with "
+        <> show nL
+        <> " leaves."
+  let lvs = Seq.fromList $ leaves tr
+  trss <-
+    liftIO $
+      mapConcurrently
+        (\(nSamples, g) -> nSubSamples nSamples lvs nL tr g)
+        (zip chunks gs)
+  let trs = catMaybes $ concat trss
+  return $ map prune trs
+
+-- Extract a random subtree with @N@ leaves of a tree with @M@ leaves, where
 -- @M>N@ (otherwise error). The complete list of leaves (names are assumed to be
 -- unique) has to be provided as a 'Seq.Seq', and a 'Seq.Set', so that fast
 -- sub-sampling as well as lookup are fast and so that these data structures do
@@ -170,18 +215,20 @@
     let lsSets = map Set.fromList lss
     return [dropLeavesWith (`Set.notMember` ls) tree | ls <- lsSets]
 
--- | Pair of branch length with number of extant children.
+-- Pair of branch length with number of extant children.
 type BrLnNChildren = (BranchLength, Int)
 
--- | Possible summary statistic of phylogenetic trees. A list of tuples
+-- Possible summary statistic of phylogenetic trees. A list of tuples
 -- (BranchLength, NumberOfExtantChildrenBelowThisBranch).
 type NChildSumStat = [BrLnNChildren]
 
--- | Format the summary statistics in the following form:
+-- Format the summary statistics in the following form:
+--
 -- @
---    nLeaves1 branchLength1
---    nLeaves2 branchLength2
---    ....
+--   nLeaves1 branchLength1
+--   nLeaves2 branchLength2
+--   ....
+-- @
 formatNChildSumStat :: NChildSumStat -> BL.ByteString
 formatNChildSumStat s =
   BB.toLazyByteString . mconcat $ map formatNChildSumStatLine s
@@ -190,7 +237,7 @@
 formatNChildSumStatLine (l, n) =
   BB.intDec n <> BB.char8 ' ' <> BB.doubleDec l <> BB.char8 '\n'
 
--- | Compute NChilSumStat for a phylogenetic tree.
+-- Compute NChilSumStat for a phylogenetic tree.
 toNChildSumStat :: Measurable e => Tree e a -> NChildSumStat
 toNChildSumStat (Node br _ []) = [(getLen br, 1)]
 toNChildSumStat (Node br _ ts) = (getLen br, sumCh) : concat nChSS
diff --git a/src/TLynx/TLynx.hs b/src/TLynx/TLynx.hs
--- a/src/TLynx/TLynx.hs
+++ b/src/TLynx/TLynx.hs
@@ -16,7 +16,6 @@
 where
 
 import ELynx.Tools
-import TLynx.Coalesce.Coalesce
 import TLynx.Compare.Compare
 import TLynx.Connect.Connect
 import TLynx.Distance.Distance
@@ -30,8 +29,6 @@
 -- | Run TLynx with given arguments.
 tlynx :: Arguments CommandArguments -> IO ()
 tlynx c = case local c of
-  Coalesce _ ->
-    eLynxWrapper c (\(Arguments g (Coalesce l)) -> Arguments g l) coalesce
   Compare _ ->
     eLynxWrapper c (\(Arguments g (Compare l)) -> Arguments g l) compareCmd
   Connect _ ->
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:        0.3.3
+version:        0.3.4
 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
@@ -23,8 +23,6 @@
 
 library
   exposed-modules:
-      TLynx.Coalesce.Coalesce
-      TLynx.Coalesce.Options
       TLynx.Compare.Compare
       TLynx.Compare.Options
       TLynx.Connect.Connect