diff --git a/ChangeLog.md b/ChangeLog.md
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -1,11 +1,18 @@
-# Changelog for ELynx
+# Revision history for ELynx
## Unreleased changes
+- Improve rooting functions.
+- Improve `Topology` data type (but still a lot to do).
+- Various additions to the documentation.
+- Rename `Measurable` to `HasLength`, `Supported` to `HasSupport`, and `Named`
+ to `HasLength`.
+- Cabal and stack file changes.
-## Version 0.5.0
+
+## Version 0.5.0.1
- `modLen`, `modSup`.
- Newtype wrappers for branch length, branch support, and node name. Those data
diff --git a/README.md b/README.md
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
# The ELynx Suite
-Version: 0.5.0.
+Version: 0.5.0.1.
Reproducible evolution made easy.
@@ -19,18 +19,20 @@
The library packages are:
-- **elynx-nexus:** Nexus file support.
-- **elynx-markov:** Simulate multi sequence alignments along phylogenetic trees.
-- **elynx-seq:** Handle evolutionary sequences and multi sequence alignments.
-- **elynx-tools:** Tools for the provided executables.
-- **elynx-tree:** Handle phylogenetic trees.
+- **[elynx-nexus](https://hackage.haskell.org/package/elynx-nexus):** Nexus file support.
+- **[elynx-markov](https://hackage.haskell.org/package/elynx-markov):** Simulate multi sequence alignments along phylogenetic trees.
+- **[elynx-seq](https://hackage.haskell.org/package/elynx-seq):** Handle evolutionary sequences and multi sequence alignments.
+- **[elynx-tools](https://hackage.haskell.org/package/elynx-tools):** Tools for the provided executables.
+- **[elynx-tree](https://hackage.haskell.org/package/elynx-tree):** Handle phylogenetic trees.
The executables are:
-- **slynx:** Analyze, modify, and simulate evolutionary sequences.
-- **tlynx:** Analyze, modify, and simulate phylogenetic trees.
-- **elynx:** Validate and redo past analyses.
+- **[slynx](https://hackage.haskell.org/package/slynx):** Analyze, modify, and simulate evolutionary sequences.
+- **[tlynx](https://hackage.haskell.org/package/tlynx):** Analyze, modify, and simulate phylogenetic trees.
+- **[elynx](https://hackage.haskell.org/package/elynx):** Validate and redo past analyses.
+Documentation is available on [Hackage](https://hackage.haskell.org/) (use direct links above).
+
**ELynx is actively developed. We happily receive comments, ideas, feature
requests, and pull requests!**
@@ -65,34 +67,15 @@
[PATH](https://en.wikipedia.org/wiki/PATH_(variable)) environment variable. Then, they can be used directly.
-# Documentation
-
-Documentation is available on [Hackage](https://hackage.haskell.org/).
-
-Libraries:
-
-- [elynx-nexus](https://hackage.haskell.org/package/elynx-nexus)
-- [elynx-markov](https://hackage.haskell.org/package/elynx-markov)
-- [elynx-seq](https://hackage.haskell.org/package/elynx-seq)
-- [elynx-tools](https://hackage.haskell.org/package/elynx-tools)
-- [elynx-tree](https://hackage.haskell.org/package/elynx-tree)
-
-Executables:
-
-- [elynx](https://hackage.haskell.org/package/elynx)
-- [slynx](https://hackage.haskell.org/package/slynx)
-- [tlynx](https://hackage.haskell.org/package/tlynx)
-
-
# SLynx
Handle evolutionary sequences.
slynx --help | head -n -16
- ELynx Suite version 0.5.0.
+ ELynx Suite version 0.5.0.1.
Developed by Dominik Schrempf.
- Compiled on November 10, 2020, at 14:29 pm, UTC.
+ Compiled on December 18, 2020, at 10:14 am, UTC.
Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]
[-f|--force] [--no-elynx-file] COMMAND
@@ -137,9 +120,9 @@
slynx concatenate --help
- ELynx Suite version 0.5.0.
+ ELynx Suite version 0.5.0.1.
Developed by Dominik Schrempf.
- Compiled on November 10, 2020, at 14:29 pm, UTC.
+ Compiled on December 18, 2020, at 10:14 am, UTC.
Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE
Concatenate sequences found in input files.
@@ -158,9 +141,9 @@
slynx examine --help
- ELynx Suite version 0.5.0.
+ ELynx Suite version 0.5.0.1.
Developed by Dominik Schrempf.
- Compiled on November 10, 2020, at 14:29 pm, UTC.
+ Compiled on December 18, 2020, at 10:14 am, UTC.
Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site]
Examine sequences. If data is a multi sequence alignment, additionally analyze columns.
@@ -180,9 +163,9 @@
slynx filter-rows --help
- ELynx Suite version 0.5.0.
+ ELynx Suite version 0.5.0.1.
Developed by Dominik Schrempf.
- Compiled on November 10, 2020, at 14:29 pm, UTC.
+ Compiled on December 18, 2020, at 10:14 am, UTC.
Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH]
[--shorter-than LENGTH] [--standard-characters]
@@ -203,9 +186,9 @@
slynx filter-columns --help
- ELynx Suite version 0.5.0.
+ ELynx Suite version 0.5.0.1.
Developed by Dominik Schrempf.
- Compiled on November 10, 2020, at 14:29 pm, UTC.
+ Compiled on December 18, 2020, at 10:14 am, UTC.
Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE
[--standard-chars DOUBLE]
@@ -227,9 +210,9 @@
slynx simulate --help
- ELynx Suite version 0.5.0.
+ ELynx Suite version 0.5.0.1.
Developed by Dominik Schrempf.
- Compiled on November 10, 2020, at 14:29 pm, UTC.
+ Compiled on December 18, 2020, at 10:14 am, UTC.
Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]
[-m|--mixture-model MODEL] [-e|--edm-file NAME]
@@ -306,9 +289,9 @@
slynx sub-sample --help
- ELynx Suite version 0.5.0.
+ ELynx Suite version 0.5.0.1.
Developed by Dominik Schrempf.
- Compiled on November 10, 2020, at 14:29 pm, UTC.
+ Compiled on December 18, 2020, at 10:14 am, UTC.
Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE
(-n|--number-of-sites INT)
@@ -336,9 +319,9 @@
slynx translate --help
- ELynx Suite version 0.5.0.
+ ELynx Suite version 0.5.0.1.
Developed by Dominik Schrempf.
- Compiled on November 10, 2020, at 14:29 pm, UTC.
+ Compiled on December 18, 2020, at 10:14 am, UTC.
Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT)
(-u|--universal-code CODE)
@@ -361,9 +344,9 @@
tlynx --help | head -n -16
- ELynx Suite version 0.5.0.
+ ELynx Suite version 0.5.0.1.
Developed by Dominik Schrempf.
- Compiled on November 10, 2020, at 14:29 pm, UTC.
+ Compiled on December 18, 2020, at 10:14 am, UTC.
Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]
[-f|--force] [--no-elynx-file] COMMAND
@@ -401,9 +384,9 @@
tlynx compare --help
- ELynx Suite version 0.5.0.
+ ELynx Suite version 0.5.0.1.
Developed by Dominik Schrempf.
- Compiled on November 10, 2020, at 14:29 pm, UTC.
+ Compiled on December 18, 2020, at 10:14 am, UTC.
Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect]
[-f|--newick-format FORMAT] NAMES
@@ -430,9 +413,9 @@
tlynx examine --help
- ELynx Suite version 0.5.0.
+ ELynx Suite version 0.5.0.1.
Developed by Dominik Schrempf.
- Compiled on November 10, 2020, at 14:29 pm, UTC.
+ Compiled on December 18, 2020, at 10:14 am, UTC.
Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT]
Compute summary statistics of phylogenetic trees.
@@ -454,9 +437,9 @@
tlynx simulate --help
- ELynx Suite version 0.5.0.
+ ELynx Suite version 0.5.0.1.
Developed by Dominik Schrempf.
- Compiled on November 10, 2020, at 14:29 pm, UTC.
+ Compiled on December 18, 2020, at 10:14 am, UTC.
Usage: tlynx simulate (-t|--nTrees INT) (-n|--nLeaves INT) PROCESS
[-u|--sub-sample DOUBLE] [-s|--summary-statistics]
@@ -491,9 +474,9 @@
elynx --help | head -n -16
- ELynx Suite version 0.5.0.
+ ELynx Suite version 0.5.0.1.
Developed by Dominik Schrempf.
- Compiled on November 10, 2020, at 14:29 pm, UTC.
+ Compiled on December 18, 2020, at 10:14 am, UTC.
Usage: elynx COMMAND
Validate and redo past ELynx analyses
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
@@ -44,7 +44,7 @@
v = BL.pack val
-- | Examine branches of a tree.
-summarizeLengths :: Measurable e => Tree e a -> BL.ByteString
+summarizeLengths :: HasLength e => Tree e a -> BL.ByteString
summarizeLengths t =
BL.intercalate
"\n"
@@ -64,7 +64,7 @@
nf <- argsNewickFormat . local <$> ask
liftIO $ parseTrees nf fp
-examineTree :: Named a => Handle -> Tree Phylo a -> IO ()
+examineTree :: HasName a => Handle -> Tree Phylo a -> IO ()
examineTree h t = do
hPutStrLn h $ "Number of leaves: " ++ show (length lvs)
let l = phyloToLengthTree t
diff --git a/src/TLynx/Parsers.hs b/src/TLynx/Parsers.hs
--- a/src/TLynx/Parsers.hs
+++ b/src/TLynx/Parsers.hs
@@ -10,8 +10,7 @@
--
-- Creation date: Wed Apr 22 13:34:35 2020.
module TLynx.Parsers
- (
- parseTree,
+ ( parseTree,
parseTrees,
NewickFormat,
newickFormat,
@@ -69,13 +68,21 @@
<> short 'f'
<> metavar "FORMAT"
<> value Standard
- <> help ("Newick tree format: " ++ nwlist ++ "; default: Standard; for detailed help, see 'tlynx --help'")
+ <> help
+ ( "Newick tree format: "
+ ++ nwlist
+ ++ "; default: Standard; for detailed help, see 'tlynx --help'"
+ )
where
nwfs = map show (allValues :: [NewickFormat])
nwlist = intercalate ", " (init nwfs) <> ", or " <> last nwfs
-- | Help for different 'NewickFormat's.
newickHelp :: [String]
-newickHelp = map (toListItem . description) (allValues :: [NewickFormat]) ++ ["- Nexus file including Newick trees"]
+newickHelp =
+ map
+ (toListItem . describeNewickFormat)
+ (allValues :: [NewickFormat])
+ ++ ["- Nexus file including Newick trees"]
where
toListItem = ("- Newick " ++)
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
@@ -231,7 +231,7 @@
BB.intDec n <> BB.char8 ' ' <> BB.doubleDec (fromLength l) <> BB.char8 '\n'
-- Compute NChilSumStat for a phylogenetic tree.
-toNChildSumStat :: Measurable e => Tree e a -> NChildSumStat
+toNChildSumStat :: HasLength e => Tree e a -> NChildSumStat
toNChildSumStat (Node br _ []) = [(getLen br, 1)]
toNChildSumStat (Node br _ ts) = (getLen br, sumCh) : concat nChSS
where
diff --git a/tlynx.cabal b/tlynx.cabal
--- a/tlynx.cabal
+++ b/tlynx.cabal
@@ -1,79 +1,78 @@
-cabal-version: 2.2
-name: tlynx
-version: 0.5.0
-synopsis: Handle phylogenetic trees
-description: Examine, compare, and simulate phylogenetic trees in a reproducible way. Please see the README on GitHub at .
-category: Bioinformatics
-homepage: https://github.com/dschrempf/elynx#readme
-bug-reports: https://github.com/dschrempf/elynx/issues
-author: Dominik Schrempf
-maintainer: dominik.schrempf@gmail.com
-copyright: Dominik Schrempf (2020)
-license: GPL-3.0-or-later
-license-file: LICENSE
-build-type: Simple
+cabal-version: 2.2
+name: tlynx
+version: 0.5.0.1
+license: GPL-3.0-or-later
+license-file: LICENSE
+copyright: Dominik Schrempf (2020)
+maintainer: dominik.schrempf@gmail.com
+author: Dominik Schrempf
+homepage: https://github.com/dschrempf/elynx#readme
+bug-reports: https://github.com/dschrempf/elynx/issues
+synopsis: Handle phylogenetic trees
+description:
+ Examine, compare, and simulate phylogenetic trees in a reproducible way. Please see the README on GitHub at .
+category: Bioinformatics
+build-type: Simple
extra-source-files:
README.md
ChangeLog.md
source-repository head
- type: git
- location: https://github.com/dschrempf/elynx
+ type: git
+ location: https://github.com/dschrempf/elynx
library
- exposed-modules:
- TLynx.Compare.Compare
- TLynx.Compare.Options
- TLynx.Connect.Connect
- TLynx.Connect.Options
- TLynx.Distance.Distance
- TLynx.Distance.Options
- TLynx.Examine.Examine
- TLynx.Examine.Options
- TLynx.Options
- TLynx.Parsers
- TLynx.Shuffle.Options
- TLynx.Shuffle.Shuffle
- TLynx.Simulate.Options
- TLynx.Simulate.Simulate
- TLynx.TLynx
- other-modules:
- Paths_tlynx
- autogen-modules:
- Paths_tlynx
- hs-source-dirs:
- src
- ghc-options: -Wall
- build-depends:
- aeson
- , attoparsec
- , base >=4.7 && <5
- , bytestring
- , comonad
- , containers
- , elynx-tools
- , elynx-tree
- , gnuplot
- , lifted-async
- , monad-logger
- , mwc-random
- , optparse-applicative
- , parallel
- , statistics
- , text
- , transformers
- , vector
- default-language: Haskell2010
+ exposed-modules:
+ TLynx.Compare.Compare
+ TLynx.Compare.Options
+ TLynx.Connect.Connect
+ TLynx.Connect.Options
+ TLynx.Distance.Distance
+ TLynx.Distance.Options
+ TLynx.Examine.Examine
+ TLynx.Examine.Options
+ TLynx.Options
+ TLynx.Parsers
+ TLynx.Shuffle.Options
+ TLynx.Shuffle.Shuffle
+ TLynx.Simulate.Options
+ TLynx.Simulate.Simulate
+ TLynx.TLynx
+ hs-source-dirs: src
+ other-modules: Paths_tlynx
+ autogen-modules: Paths_tlynx
+ default-language: Haskell2010
+ ghc-options: -Wall -Wunused-packages
+ build-depends:
+ aeson >=1.5.4.1 && <1.6,
+ attoparsec >=0.13.2.4 && <0.14,
+ base >=4.7 && <5,
+ bytestring >=0.10.10.0 && <0.11,
+ comonad >=5.0.6 && <5.1,
+ containers >=0.6.2.1 && <0.7,
+ elynx-tools >=0.5.0.1 && <0.6,
+ elynx-tree >=0.5.0.1 && <0.6,
+ gnuplot >=0.5.6.1 && <0.6,
+ lifted-async >=0.10.1.2 && <0.11,
+ monad-logger >=0.3.35 && <0.4,
+ mwc-random >=0.14.0.0 && <0.15,
+ optparse-applicative >=0.15.1.0 && <0.16,
+ parallel >=3.2.2.0 && <3.3,
+ statistics >=0.15.2.0 && <0.16,
+ text >=1.2.3.2 && <1.3,
+ transformers >=0.5.6.2 && <0.6,
+ vector >=0.12.1.2 && <0.13
+
executable tlynx
- main-is: Main.hs
- other-modules:
- Paths_tlynx
- hs-source-dirs:
- app
- ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
- build-depends:
- base >=4.7 && <5
- , tlynx
- default-language: Haskell2010
+ main-is: Main.hs
+ hs-source-dirs: app
+ other-modules: Paths_tlynx
+ default-language: Haskell2010
+ ghc-options:
+ -Wall -Wunused-packages -threaded -rtsopts -with-rtsopts=-N
+
+ build-depends:
+ base >=4.7 && <5,
+ tlynx -any