tlynx 0.3.4 → 0.4.0
raw patch · 10 files changed
+44/−52 lines, 10 files
Files
- ChangeLog.md +6/−0
- README.md +27/−27
- src/TLynx/Compare/Compare.hs +1/−3
- src/TLynx/Connect/Connect.hs +1/−6
- src/TLynx/Distance/Distance.hs +1/−3
- src/TLynx/Examine/Examine.hs +1/−2
- src/TLynx/Parsers.hs +1/−1
- src/TLynx/Shuffle/Shuffle.hs +2/−4
- src/TLynx/Simulate/Simulate.hs +3/−5
- tlynx.cabal +1/−1
ChangeLog.md view
@@ -5,6 +5,12 @@ ## Unreleased changes +## Version 0.4.0++- Major refactor of `elynx-tree`. All required function can now conveniently+ reexported by `ELynx.Tree`.++ ## Version 0.3.4 - Improve `slynx examine`; show hamming distance; show constant sites.
README.md view
@@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.3.4.+Version: 0.4.0. 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 0.3.4.+ ELynx Suite version 0.4.0. Developed by Dominik Schrempf.- Compiled on August 21, 2020, at 09:40 am, UTC.+ Compiled on September 4, 2020, at 13:37 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 0.3.4.+ ELynx Suite version 0.4.0. Developed by Dominik Schrempf.- Compiled on August 21, 2020, at 09:40 am, UTC.+ Compiled on September 4, 2020, at 13:37 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 0.3.4.+ ELynx Suite version 0.4.0. Developed by Dominik Schrempf.- Compiled on August 21, 2020, at 09:40 am, UTC.+ Compiled on September 4, 2020, at 13:37 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 0.3.4.+ ELynx Suite version 0.4.0. Developed by Dominik Schrempf.- Compiled on August 21, 2020, at 09:40 am, UTC.+ Compiled on September 4, 2020, at 13:37 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 0.3.4.+ ELynx Suite version 0.4.0. Developed by Dominik Schrempf.- Compiled on August 21, 2020, at 09:40 am, UTC.+ Compiled on September 4, 2020, at 13:37 pm, UTC. Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE [--standard-chars DOUBLE]@@ -226,9 +226,9 @@ slynx simulate --help - ELynx Suite version 0.3.4.+ ELynx Suite version 0.4.0. Developed by Dominik Schrempf.- Compiled on August 21, 2020, at 09:40 am, UTC.+ Compiled on September 4, 2020, at 13:37 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 0.3.4.+ ELynx Suite version 0.4.0. Developed by Dominik Schrempf.- Compiled on August 21, 2020, at 09:40 am, UTC.+ Compiled on September 4, 2020, at 13:37 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 0.3.4.+ ELynx Suite version 0.4.0. Developed by Dominik Schrempf.- Compiled on August 21, 2020, at 09:40 am, UTC.+ Compiled on September 4, 2020, at 13:37 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 0.3.4.+ ELynx Suite version 0.4.0. Developed by Dominik Schrempf.- Compiled on August 21, 2020, at 09:40 am, UTC.+ Compiled on September 4, 2020, at 13:37 pm, UTC. Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND@@ -398,9 +398,9 @@ tlynx compare --help - ELynx Suite version 0.3.4.+ ELynx Suite version 0.4.0. Developed by Dominik Schrempf.- Compiled on August 21, 2020, at 09:40 am, UTC.+ Compiled on September 4, 2020, at 13:37 pm, UTC. Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] [-f|--newick-format FORMAT] NAMES@@ -427,9 +427,9 @@ tlynx examine --help - ELynx Suite version 0.3.4.+ ELynx Suite version 0.4.0. Developed by Dominik Schrempf.- Compiled on August 21, 2020, at 09:40 am, UTC.+ Compiled on September 4, 2020, at 13:37 pm, UTC. Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT] Compute summary statistics of phylogenetic trees.@@ -451,9 +451,9 @@ tlynx simulate --help - ELynx Suite version 0.3.4.+ ELynx Suite version 0.4.0. Developed by Dominik Schrempf.- Compiled on August 21, 2020, at 09:40 am, UTC.+ Compiled on September 4, 2020, at 13:37 pm, UTC. Usage: tlynx simulate (-t|--nTrees INT) (-n|--nLeaves INT) PROCESS [-u|--sub-sample DOUBLE] [-s|--summary-statistics] @@ -488,9 +488,9 @@ elynx --help | head -n -16 - ELynx Suite version 0.3.4.+ ELynx Suite version 0.4.0. Developed by Dominik Schrempf.- Compiled on August 21, 2020, at 09:40 am, UTC.+ Compiled on September 4, 2020, at 13:37 pm, UTC. Usage: elynx COMMAND Validate and redo past ELynx analyses
src/TLynx/Compare/Compare.hs view
@@ -29,9 +29,7 @@ import qualified Data.Text as T import qualified Data.Text.Encoding as E import qualified Data.Text.IO as T-import ELynx.Data.Tree-import ELynx.Export.Tree.Newick (toNewick)-import ELynx.Import.Tree.Newick+import ELynx.Tree import ELynx.Tools ( Arguments (..), ELynx,
src/TLynx/Connect/Connect.hs view
@@ -23,12 +23,7 @@ import qualified Data.ByteString.Char8 as BS import qualified Data.ByteString.Lazy.Char8 as BL import qualified Data.Set as S-import ELynx.Data.Tree-import ELynx.Export.Tree.Newick (toNewick)-import ELynx.Import.Tree.Newick- ( oneNewick,- someNewick,- )+import ELynx.Tree import ELynx.Tools ( Arguments (..), ELynx,
src/TLynx/Distance/Distance.hs view
@@ -40,9 +40,7 @@ import qualified Data.Text.Lazy as LT import qualified Data.Text.Lazy.Encoding as LT import qualified Data.Vector.Unboxed as V-import ELynx.Data.Tree-import ELynx.Export.Tree.Newick-import ELynx.Import.Tree.Newick+import ELynx.Tree import ELynx.Tools import Statistics.Sample import System.IO
src/TLynx/Examine/Examine.hs view
@@ -25,8 +25,7 @@ import Data.Containers.ListUtils (nubOrd) import Data.List ((\\)) import qualified Data.Text as T-import ELynx.Data.Tree-import ELynx.Import.Tree.Newick+import ELynx.Tree import ELynx.Tools import System.IO ( Handle,
src/TLynx/Parsers.hs view
@@ -17,7 +17,7 @@ where import Data.List (intercalate)-import ELynx.Import.Tree.Newick+import ELynx.Tree ( NewickFormat (..), description, )
src/TLynx/Shuffle/Shuffle.hs view
@@ -26,10 +26,8 @@ import Control.Monad.Logger (logDebug, logInfo) import Control.Monad.Trans.Reader (ask) import qualified Data.ByteString.Lazy.Char8 as BL-import ELynx.Data.Tree-import ELynx.Export.Tree.Newick (toNewick)-import ELynx.Import.Tree.Newick (oneNewick)-import ELynx.Simulate.PointProcess+import ELynx.Tree+import ELynx.Tree.Simulate.PointProcess ( PointProcess (PointProcess), toReconstructedTree, )
src/TLynx/Simulate/Simulate.hs view
@@ -22,7 +22,6 @@ -- Elsevier BV, 2009, 261, 58-66 module TLynx.Simulate.Simulate ( simulate,- nSubSamples, ) where @@ -44,10 +43,9 @@ import qualified Data.Text as T import qualified Data.Text.Lazy as LT import qualified Data.Text.Lazy.Encoding as LT-import ELynx.Data.Tree-import ELynx.Export.Tree.Newick-import qualified ELynx.Simulate.Coalescent as CS-import qualified ELynx.Simulate.PointProcess as PP+import ELynx.Tree+import qualified ELynx.Tree.Simulate.Coalescent as CS+import qualified ELynx.Tree.Simulate.PointProcess as PP import ELynx.Tools import System.Random.MWC import TLynx.Simulate.Options
tlynx.cabal view
@@ -1,6 +1,6 @@ cabal-version: 2.2 name: tlynx-version: 0.3.4+version: 0.4.0 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