diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -4,6 +4,10 @@ ## Unreleased changes + +## Version 0.5.0.2 + +- Speed up mixture model simulation. - Improve rooting functions. - Improve `Topology` data type (but still a lot to do). - Various additions to the documentation. diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.5.0.1. +Version: 0.5.0.2. Reproducible evolution made easy.

@@ -73,9 +73,9 @@ slynx --help | head -n -16 - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] [--no-elynx-file] COMMAND @@ -90,7 +90,7 @@ 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. + --no-elynx-file Do not write data required to reproduce an analysis. Available commands: concatenate Concatenate sequences found in input files. @@ -120,9 +120,9 @@ slynx concatenate --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE Concatenate sequences found in input files. @@ -141,9 +141,9 @@ slynx examine --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site] Examine sequences. If data is a multi sequence alignment, additionally analyze columns. @@ -163,9 +163,9 @@ slynx filter-rows --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH] [--shorter-than LENGTH] [--standard-characters] @@ -186,9 +186,9 @@ slynx filter-columns --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE [--standard-chars DOUBLE] @@ -210,9 +210,9 @@ slynx simulate --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] [-m|--mixture-model MODEL] [-e|--edm-file NAME] @@ -289,9 +289,9 @@ slynx sub-sample --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE (-n|--number-of-sites INT) @@ -319,9 +319,9 @@ slynx translate --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT) (-u|--universal-code CODE) @@ -344,9 +344,9 @@ tlynx --help | head -n -16 - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] [--no-elynx-file] COMMAND @@ -361,7 +361,7 @@ 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. + --no-elynx-file Do not write data required to reproduce an analysis. Available commands: compare Compare two phylogenetic trees (compute distances and branch-wise differences). @@ -384,9 +384,9 @@ tlynx compare --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] [-f|--newick-format FORMAT] NAMES @@ -413,9 +413,9 @@ tlynx examine --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT] Compute summary statistics of phylogenetic trees. @@ -437,9 +437,9 @@ tlynx simulate --help - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: tlynx simulate (-t|--nTrees INT) (-n|--nLeaves INT) PROCESS [-u|--sub-sample DOUBLE] [-s|--summary-statistics] @@ -474,9 +474,9 @@ elynx --help | head -n -16 - ELynx Suite version 0.5.0.1. + ELynx Suite version 0.5.0.2. Developed by Dominik Schrempf. - Compiled on December 18, 2020, at 10:14 am, UTC. + Compiled on February 19, 2021, at 13:42 pm, UTC. Usage: elynx COMMAND Validate and redo past ELynx analyses diff --git a/elynx-tree.cabal b/elynx-tree.cabal --- a/elynx-tree.cabal +++ b/elynx-tree.cabal @@ -1,6 +1,6 @@ cabal-version: 2.2 name: elynx-tree -version: 0.5.0.1 +version: 0.5.0.2 license: GPL-3.0-or-later license-file: LICENSE copyright: Dominik Schrempf (2020) @@ -76,20 +76,20 @@ 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 >=4.14.1.0 && <4.15, - bytestring >=0.10.10.0 && <0.11, - comonad >=5.0.6 && <5.1, - containers >=0.6.2.1 && <0.7, - deepseq >=1.4.4.0 && <1.5, - double-conversion >=2.0.2.0 && <2.1, - elynx-nexus >=0.5.0.1 && <0.6, - math-functions >=0.3.4.1 && <0.4, - mwc-random >=0.14.0.0 && <0.15, - parallel >=3.2.2.0 && <3.3, - primitive >=0.7.1.0 && <0.8, - statistics >=0.15.2.0 && <0.16 + aeson >=1.5.5.1, + attoparsec >=0.13.2.5, + base >=4.14.1.0, + bytestring >=0.10.12.0, + comonad >=5.0.8, + containers >=0.6.2.1, + deepseq >=1.4.4.0, + double-conversion >=2.0.2.0, + elynx-nexus >=0.5.0.2, + math-functions >=0.3.4.1, + mwc-random >=0.14.0.0, + parallel >=3.2.2.0, + primitive >=0.7.1.0, + statistics >=0.15.2.0 test-suite tree-test type: exitcode-stdio-1.0 @@ -113,14 +113,14 @@ default-language: Haskell2010 ghc-options: -Wall -Wunused-packages build-depends: - QuickCheck >=2.13.2 && <2.14, - attoparsec >=0.13.2.4 && <0.14, - base >=4.14.1.0 && <4.15, - bytestring >=0.10.10.0 && <0.11, - containers >=0.6.2.1 && <0.7, - elynx-tools >=0.5.0.1 && <0.6, + QuickCheck >=2.14.2, + attoparsec >=0.13.2.5, + base >=4.14.1.0, + bytestring >=0.10.12.0, + containers >=0.6.2.1, + elynx-tools >=0.5.0.2, elynx-tree -any, - hspec >=2.7.4 && <2.8 + hspec >=2.7.8 benchmark tree-bench type: exitcode-stdio-1.0 @@ -137,9 +137,9 @@ build-depends: base >=4.7 && <5, - criterion >=1.5.7.0 && <1.6, - elynx-tools >=0.5.0.1 && <0.6, + criterion >=1.5.9.0, + elynx-tools >=0.5.0.2, elynx-tree -any, - microlens >=0.4.11.2 && <0.5, - mwc-random >=0.14.0.0 && <0.15, - parallel >=3.2.2.0 && <3.3 + microlens >=0.4.11.2, + mwc-random >=0.14.0.0, + parallel >=3.2.2.0