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elynx-seq 0.3.4 → 0.4.0

raw patch · 3 files changed

+34/−28 lines, 3 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

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
elynx-seq.cabal view
@@ -1,6 +1,6 @@ cabal-version:  2.2 name:           elynx-seq-version:        0.3.4+version:        0.4.0 synopsis:       Handle molecular sequences description:    Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>. category:       Bioinformatics