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/elynx-tools.cabal b/elynx-tools.cabal
--- a/elynx-tools.cabal
+++ b/elynx-tools.cabal
@@ -1,69 +1,68 @@
-cabal-version: 2.2
-name: elynx-tools
-version: 0.5.0
-synopsis: Tools for ELynx
-description: 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: elynx-tools
+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: Tools for ELynx
+description:
+ 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:
- ELynx.Tools
- other-modules:
- ELynx.Tools.ByteString
- ELynx.Tools.Concurrent
- ELynx.Tools.Definitions
- ELynx.Tools.Equality
- ELynx.Tools.InputOutput
- ELynx.Tools.LinearAlgebra
- ELynx.Tools.List
- ELynx.Tools.Logger
- ELynx.Tools.Misc
- ELynx.Tools.Numeric
- ELynx.Tools.Reproduction
- ELynx.Tools.Text
- Paths_elynx_tools
- autogen-modules:
- Paths_elynx_tools
- hs-source-dirs:
- src
- ghc-options: -Wall
- build-depends:
- aeson
- , attoparsec
- , base >=4.7 && <5
- , base16-bytestring
- , bytestring
- , cryptohash-sha256
- , deepseq
- , directory
- , fast-logger
- , hmatrix
- , monad-control
- , monad-logger
- , mwc-random
- , optparse-applicative
- , primitive
- , template-haskell
- , text
- , time
- , transformers
- , transformers-base
- , vector
- , zlib
- default-language: Haskell2010
+ exposed-modules: ELynx.Tools
+ hs-source-dirs: src
+ other-modules:
+ ELynx.Tools.ByteString
+ ELynx.Tools.Concurrent
+ ELynx.Tools.Definitions
+ ELynx.Tools.Equality
+ ELynx.Tools.InputOutput
+ ELynx.Tools.LinearAlgebra
+ ELynx.Tools.List
+ ELynx.Tools.Logger
+ ELynx.Tools.Misc
+ ELynx.Tools.Numeric
+ ELynx.Tools.Reproduction
+ ELynx.Tools.Text
+ Paths_elynx_tools
+
+ autogen-modules: Paths_elynx_tools
+ 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,
+ base16-bytestring >=0.1.1.7 && <0.2,
+ bytestring >=0.10.10.0 && <0.11,
+ cryptohash-sha256 >=0.11.101.0 && <0.12,
+ deepseq >=1.4.4.0 && <1.5,
+ directory >=1.3.6.0 && <1.4,
+ fast-logger >=3.0.2 && <3.1,
+ hmatrix >=0.20.0.0 && <0.21,
+ monad-control >=1.0.2.3 && <1.1,
+ monad-logger >=0.3.35 && <0.4,
+ mwc-random >=0.14.0.0 && <0.15,
+ optparse-applicative >=0.15.1.0 && <0.16,
+ primitive >=0.7.1.0 && <0.8,
+ template-haskell >=2.16.0.0 && <2.17,
+ text >=1.2.3.2 && <1.3,
+ time >=1.9.3 && <1.10,
+ transformers >=0.5.6.2 && <0.6,
+ transformers-base >=0.4.5.2 && <0.5,
+ vector >=0.12.1.2 && <0.13,
+ zlib >=0.6.2.2 && <0.7