diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -2,7 +2,7 @@ # Changelog for ELynx -## Version 0.2.1 +## Version 0.2.2 - Validation and repetition of previous analyses is finally possible with the new `elynx` binary. diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.2.1. +Version: 0.2.2. Reproducible evolution made easy. A Haskell library and tool set for computational biology. The goal of ELynx is @@ -70,7 +70,7 @@ ELynx Suite version 0.2.1. Developed by Dominik Schrempf. - Compiled on April 27, 2020, at 06:31 am, UTC. + Compiled on April 27, 2020, at 12:08 pm, UTC. Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND @@ -132,7 +132,7 @@ ELynx Suite version 0.2.1. Developed by Dominik Schrempf. - Compiled on April 27, 2020, at 06:31 am, UTC. + Compiled on April 27, 2020, at 12:08 pm, UTC. Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE Concatenate sequences found in input files. @@ -170,7 +170,7 @@ ELynx Suite version 0.2.1. Developed by Dominik Schrempf. - Compiled on April 27, 2020, at 06:31 am, UTC. + Compiled on April 27, 2020, at 12:08 pm, UTC. Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site] Examine sequences. If data is a multi sequence alignment, additionally analyze columns. @@ -209,7 +209,7 @@ ELynx Suite version 0.2.1. Developed by Dominik Schrempf. - Compiled on April 27, 2020, at 06:31 am, UTC. + Compiled on April 27, 2020, at 12:08 pm, UTC. Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH] [--shorter-than LENGTH] [--standard-characters] @@ -249,7 +249,7 @@ ELynx Suite version 0.2.1. Developed by Dominik Schrempf. - Compiled on April 27, 2020, at 06:31 am, UTC. + Compiled on April 27, 2020, at 12:08 pm, UTC. Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE [--standard-chars DOUBLE] @@ -290,7 +290,7 @@ ELynx Suite version 0.2.1. Developed by Dominik Schrempf. - Compiled on April 27, 2020, at 06:31 am, UTC. + Compiled on April 27, 2020, at 12:08 pm, UTC. Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] [-m|--mixture-model MODEL] [-e|--edm-file NAME] @@ -383,7 +383,7 @@ ELynx Suite version 0.2.1. Developed by Dominik Schrempf. - Compiled on April 27, 2020, at 06:31 am, UTC. + Compiled on April 27, 2020, at 12:08 pm, UTC. Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE (-n|--number-of-sites INT) @@ -429,7 +429,7 @@ ELynx Suite version 0.2.1. Developed by Dominik Schrempf. - Compiled on April 27, 2020, at 06:31 am, UTC. + Compiled on April 27, 2020, at 12:08 pm, UTC. Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT) (-u|--universal-code CODE) @@ -471,7 +471,7 @@ ELynx Suite version 0.2.1. Developed by Dominik Schrempf. - Compiled on April 27, 2020, at 06:31 am, UTC. + Compiled on April 27, 2020, at 12:08 pm, UTC. Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND @@ -526,7 +526,7 @@ ELynx Suite version 0.2.1. Developed by Dominik Schrempf. - Compiled on April 27, 2020, at 06:31 am, UTC. + Compiled on April 27, 2020, at 12:08 pm, UTC. Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] [-f|--newick-format FORMAT] NAME @@ -571,7 +571,7 @@ ELynx Suite version 0.2.1. Developed by Dominik Schrempf. - Compiled on April 27, 2020, at 06:31 am, UTC. + Compiled on April 27, 2020, at 12:08 pm, UTC. Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT] Compute summary statistics of phylogenetic trees. @@ -611,7 +611,7 @@ ELynx Suite version 0.2.1. Developed by Dominik Schrempf. - Compiled on April 27, 2020, at 06:31 am, UTC. + Compiled on April 27, 2020, at 12:08 pm, UTC. Usage: tlynx simulate [-t|--nTrees INT] [-n|--nLeaves INT] [-H|--height DOUBLE] [-M|--condition-on-mrca] [-l|--lambda DOUBLE] @@ -666,7 +666,7 @@ ELynx Suite version 0.2.1. Developed by Dominik Schrempf. - Compiled on April 27, 2020, at 06:31 am, UTC. + Compiled on April 27, 2020, at 12:08 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: 1.12 name: elynx-tree -version: 0.2.1 +version: 0.2.2 license: GPL-3 license-file: LICENSE copyright: Dominik Schrempf (2020) @@ -55,7 +55,7 @@ base >=4.13.0.0 && <4.14, bytestring >=0.10.10.0 && <0.11, containers >=0.6.2.1 && <0.7, - elynx-tools >=0.2.1 && <0.3, + elynx-tools >=0.2.2 && <0.3, math-functions >=0.3.3.0 && <0.4, megaparsec >=8.0.0 && <8.1, mwc-random >=0.14.0.0 && <0.15, @@ -82,7 +82,7 @@ base >=4.13.0.0 && <4.14, bytestring >=0.10.10.0 && <0.11, containers >=0.6.2.1 && <0.7, - elynx-tools >=0.2.1 && <0.3, + elynx-tools >=0.2.2 && <0.3, elynx-tree -any, hspec >=2.7.1 && <2.8, hspec-megaparsec >=2.1.0 && <2.2, @@ -106,7 +106,7 @@ bytestring >=0.10.10.0 && <0.11, containers >=0.6.2.1 && <0.7, criterion >=1.5.6.2 && <1.6, - elynx-tools >=0.2.1 && <0.3, + elynx-tools >=0.2.2 && <0.3, elynx-tree -any, math-functions >=0.3.3.0 && <0.4, megaparsec >=8.0.0 && <8.1, diff --git a/src/ELynx/Simulate/PointProcess.hs b/src/ELynx/Simulate/PointProcess.hs --- a/src/ELynx/Simulate/PointProcess.hs +++ b/src/ELynx/Simulate/PointProcess.hs @@ -233,26 +233,6 @@ toReconstructedTree' is vs l trs hs = toReconstructedTree' is' vs' l trs'' hs' -- For the algorithm, see 'ELynx.Coalescent.simulate', but index starts -- at zero. - - - - - - - - - - - - - - - - - - - - where !i = head is !is' = tail is