elynx-tree 0.3.1 → 0.3.2
raw patch · 5 files changed
+47/−42 lines, 5 files
Files
- ChangeLog.md +7/−1
- README.md +27/−27
- elynx-tree.cabal +6/−12
- src/ELynx/Data/Tree/Phylogeny.hs +2/−2
- src/ELynx/Simulate/PointProcess.hs +5/−0
ChangeLog.md view
@@ -2,7 +2,13 @@ # Changelog for ELynx -## Version 0.3.2; in development+## Unreleased changes+++## Version 0.3.2++- Remove llvm dependency.+- Move away from hpack. ## Version 0.3.1
README.md view
@@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.3.1.+Version: 0.3.2. 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 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND@@ -136,9 +136,9 @@ slynx concatenate --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, 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 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, 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 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, 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 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE [--standard-chars DOUBLE]@@ -226,9 +226,9 @@ slynx simulate --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, 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 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, 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 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, 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 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND@@ -399,9 +399,9 @@ tlynx compare --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] [-f|--newick-format FORMAT] NAMES@@ -428,9 +428,9 @@ tlynx examine --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT] Compute summary statistics of phylogenetic trees.@@ -452,9 +452,9 @@ tlynx simulate --help - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: tlynx simulate [-t|--nTrees INT] [-n|--nLeaves INT] [-H|--height DOUBLE] [-M|--condition-on-mrca] [-l|--lambda DOUBLE] @@ -491,9 +491,9 @@ elynx --help | head -n -16 - ELynx Suite version 0.3.1.+ ELynx Suite version 0.3.2. Developed by Dominik Schrempf.- Compiled on August 3, 2020, at 12:12 pm, UTC.+ Compiled on August 17, 2020, at 14:19 pm, UTC. Usage: elynx COMMAND Validate and redo past ELynx analyses
elynx-tree.cabal view
@@ -1,13 +1,6 @@-cabal-version: 2.2---- This file has been generated from package.yaml by hpack version 0.34.2.------ see: https://github.com/sol/hpack------ hash: 5876c21cdef387a8327af59315c4809662b893bf5daeb4f5e60874063f34384f-+cabal-version: 2.2 name: elynx-tree-version: 0.3.1+version: 0.3.2 synopsis: Handle phylogenetic trees description: Examine, compare, and simulate phylogenetic trees in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>. category: Bioinformatics@@ -19,6 +12,7 @@ license: GPL-3.0-or-later license-file: LICENSE build-type: Simple+ extra-source-files: README.md ChangeLog.md@@ -62,7 +56,7 @@ Paths_elynx_tree hs-source-dirs: src- ghc-options: -Wall -fllvm+ ghc-options: -Wall build-depends: aeson , attoparsec@@ -97,7 +91,7 @@ Paths_elynx_tree hs-source-dirs: test- ghc-options: -Wall -fllvm+ ghc-options: -Wall build-depends: QuickCheck , attoparsec@@ -116,7 +110,7 @@ Paths_elynx_tree hs-source-dirs: bench- ghc-options: -Wall -fllvm+ ghc-options: -Wall build-depends: base >=4.7 && <5 , bytestring
src/ELynx/Data/Tree/Phylogeny.hs view
@@ -324,7 +324,7 @@ instance FromJSON Phylo -- | Branch length label.-+-- -- For conversion, see 'phyloToLengthTree' and 'lengthToPhyloTree'. newtype Length = Length {fromLength :: BranchLength} deriving (Read, Show, Eq, Ord, Generic, NFData)@@ -426,7 +426,7 @@ cleanSupport :: BranchSupport -> Tree Phylo a -> Tree Support a cleanSupport maxSup (Node (Phylo _ s) l xs) = Node (Support $ fromMaybe maxSup s) l $ map (cleanSupport maxSup) xs --- TODO: Change name. Strict is reserved for "not lazy".+-- XXX: Probably change name. Strict is reserved for "not lazy". -- | Strict branch label for phylogenetic trees. data PhyloStrict = PhyloStrict
src/ELynx/Simulate/PointProcess.hs view
@@ -48,12 +48,17 @@ ) import System.Random.MWC +-- Require near critical process if birth and death rates are closer than this value. epsNearCriticalPointProcess :: Double epsNearCriticalPointProcess = 1e-5 +-- Also the distribution of origins needs a Tailor expansion for near critical values.+--+-- TODO: Check why the two epsilons are chosen differently. epsNearCriticalTimeOfOrigin :: Double epsNearCriticalTimeOfOrigin = 1e-8 +-- Require critical process if birth and death rates are closer than this value. eps :: Double eps = 1e-12