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/Setup.hs b/Setup.hs
--- a/Setup.hs
+++ b/Setup.hs
@@ -1,2 +1,3 @@
 import Distribution.Simple
+
 main = defaultMain
diff --git a/slynx.cabal b/slynx.cabal
--- a/slynx.cabal
+++ b/slynx.cabal
@@ -1,6 +1,6 @@
 cabal-version:  2.2
 name:           slynx
-version:        0.3.3
+version:        0.3.4
 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
@@ -60,6 +60,7 @@
     , monad-logger
     , mwc-random
     , optparse-applicative
+    , statistics
     , text
     , transformers
     , vector
diff --git a/src/SLynx/Examine/Examine.hs b/src/SLynx/Examine/Examine.hs
--- a/src/SLynx/Examine/Examine.hs
+++ b/src/SLynx/Examine/Examine.hs
@@ -22,13 +22,16 @@
 import Control.Monad.Trans.Reader (ask)
 import qualified Data.ByteString.Lazy.Char8 as BL
 import qualified Data.Set as S
+import qualified Data.Vector.Unboxed as V
 import qualified ELynx.Data.Alphabet.Alphabet as A
 import qualified ELynx.Data.Alphabet.Character as C
 import qualified ELynx.Data.Sequence.Alignment as M
+import qualified ELynx.Data.Sequence.Distance as D
 import qualified ELynx.Data.Sequence.Sequence as Seq
 import ELynx.Tools
 import SLynx.Examine.Options
 import SLynx.Tools
+import qualified Statistics.Sample as Sm
 import Text.Printf
 
 pRow :: String -> String -> BL.ByteString
@@ -42,9 +45,12 @@
   BL.unlines
     [ BL.pack
         "Sequences have equal length (multi sequence alignment, or single sequence).",
-      pRow "Total number of columns in alignment:" $ show (M.length a),
-      pRow "Number of columns without gaps:" $ show (M.length aNoGaps),
-      pRow "Number of columns with standard characters only:" $
+      BL.pack "Number of columns in alignment:",
+      pRow "  Total:" $ show aL,
+      pRow "  Constant:" $ show nConstant,
+      pRow "  Constant (including gaps or unknowns):" $ show nConstantSoft,
+      pRow "  Without gaps:" $ show (M.length aNoGaps),
+      pRow "  With standard characters only:" $
         show (M.length aOnlyStd),
       BL.empty,
       pRow "Total number of characters:" $ show nTot,
@@ -71,6 +77,12 @@
                 M.alphabet a,
       BL.pack $ unwords $ map (printf "%.3f") charFreqs,
       BL.empty,
+      BL.pack "Pairwise hamming distances (per site):",
+      pRow "  Mean:" $ printf "%.3f" hMean,
+      pRow "  Standard deviation:" $ printf "%.3f" $ sqrt hVar,
+      pRow "  Minimum:" $ printf "%.3f" hMin,
+      pRow "  Maximum:" $ printf "%.3f" hMax,
+      BL.empty,
       BL.pack "Mean effective number of states (measured using entropy):",
       pRow "Across whole alignment:" $ printf "%.3f" kEffMean,
       pRow "Across columns without gaps:" $ printf "%.3f" kEffMeanNoGaps,
@@ -85,6 +97,9 @@
     ]
     <> perSiteBS
   where
+    aL = M.length a
+    nConstant = M.length $ M.filterColsConstant a
+    nConstantSoft = M.length $ M.filterColsConstantSoft a
     nTot = M.length a * M.nSequences a
     nIUPAC = M.countIUPACChars a
     nGaps = M.countGaps a
@@ -93,18 +108,32 @@
     percentGaps = 100 * fromIntegral nGaps / fromIntegral nTot :: Double
     percentUnknowns = 100 * fromIntegral nUnknowns / fromIntegral nTot :: Double
     aNoGaps = M.filterColsNoGaps a
+    aNoGapsFreq = M.toFrequencyData aNoGaps
     aOnlyStd = M.filterColsOnlyStd aNoGaps
+    aOnlyStdFreq = M.toFrequencyData aOnlyStd
     charFreqsPerSite = M.toFrequencyData a
     charFreqs = M.distribution charFreqsPerSite
+    seqs = M.toSequences a
+    normlz x = fromIntegral x / fromIntegral aL
+    pairwiseHamming =
+      V.fromList
+        [ either error normlz $ D.hamming x y
+          | x <- seqs,
+            y <- seqs,
+            x /= y
+        ]
+    (hMean, hVar) = Sm.meanVariance pairwiseHamming
+    hMin = V.minimum pairwiseHamming
+    hMax = V.maximum pairwiseHamming
     kEffs = M.kEffEntropy charFreqsPerSite
-    kEffsNoGaps = M.kEffEntropy . M.toFrequencyData $ aNoGaps
-    kEffsOnlyStd = M.kEffEntropy . M.toFrequencyData $ aOnlyStd
+    kEffsNoGaps = M.kEffEntropy aNoGapsFreq
+    kEffsOnlyStd = M.kEffEntropy aOnlyStdFreq
     kEffMean = sum kEffs / fromIntegral (length kEffs)
     kEffMeanNoGaps = sum kEffsNoGaps / fromIntegral (length kEffsNoGaps)
     kEffMeanOnlyStd = sum kEffsOnlyStd / fromIntegral (length kEffsOnlyStd)
     kEffsHomo = M.kEffHomoplasy charFreqsPerSite
-    kEffsNoGapsHomo = M.kEffHomoplasy . M.toFrequencyData $ aNoGaps
-    kEffsOnlyStdHomo = M.kEffHomoplasy . M.toFrequencyData $ aOnlyStd
+    kEffsNoGapsHomo = M.kEffHomoplasy aNoGapsFreq
+    kEffsOnlyStdHomo = M.kEffHomoplasy aOnlyStdFreq
     kEffMeanHomo = sum kEffsHomo / fromIntegral (length kEffsHomo)
     kEffMeanNoGapsHomo =
       sum kEffsNoGapsHomo / fromIntegral (length kEffsNoGapsHomo)
diff --git a/src/SLynx/SLynx.hs b/src/SLynx/SLynx.hs
--- a/src/SLynx/SLynx.hs
+++ b/src/SLynx/SLynx.hs
@@ -24,8 +24,6 @@
 import SLynx.SubSample.SubSample
 import SLynx.Translate.Translate
 
--- TODO: Use a class here (e.g., elynx-wrappable) which defines the extractor function.
-
 -- | Run SLynx with given arguments.
 slynx :: Arguments CommandArguments -> IO ()
 slynx c = case local c of