diff --git a/ChangeLog.md b/ChangeLog.md
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -5,6 +5,16 @@
## Unreleased changes
+## Version 0.5.0
+
+- `modLen`, `modSup`.
+- Newtype wrappers for branch length, branch support, and node name. Those data
+ types and some functions were also renamed.
+- Add `Path`, and `getSubTreeUnsafe` to tree zipper.
+- Rename `unsafe` functions so that `unsafe` is at the end.
+- Many small changes.
+
+
## Version 0.4.1
- Improve `TimeSpec` (Point process).
diff --git a/README.md b/README.md
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
# The ELynx Suite
-Version: 0.4.1.
+Version: 0.5.0.
Reproducible evolution made easy.
@@ -90,9 +90,9 @@
slynx --help | head -n -16
- ELynx Suite version 0.4.1.
+ ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
- Compiled on October 16, 2020, at 12:46 pm, UTC.
+ Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]
[-f|--force] [--no-elynx-file] COMMAND
@@ -137,9 +137,9 @@
slynx concatenate --help
- ELynx Suite version 0.4.1.
+ ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
- Compiled on October 16, 2020, at 12:46 pm, UTC.
+ Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE
Concatenate sequences found in input files.
@@ -158,9 +158,9 @@
slynx examine --help
- ELynx Suite version 0.4.1.
+ ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
- Compiled on October 16, 2020, at 12:46 pm, UTC.
+ Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site]
Examine sequences. If data is a multi sequence alignment, additionally analyze columns.
@@ -180,9 +180,9 @@
slynx filter-rows --help
- ELynx Suite version 0.4.1.
+ ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
- Compiled on October 16, 2020, at 12:46 pm, UTC.
+ Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH]
[--shorter-than LENGTH] [--standard-characters]
@@ -203,9 +203,9 @@
slynx filter-columns --help
- ELynx Suite version 0.4.1.
+ ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
- Compiled on October 16, 2020, at 12:46 pm, UTC.
+ Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE
[--standard-chars DOUBLE]
@@ -227,9 +227,9 @@
slynx simulate --help
- ELynx Suite version 0.4.1.
+ ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
- Compiled on October 16, 2020, at 12:46 pm, UTC.
+ Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]
[-m|--mixture-model MODEL] [-e|--edm-file NAME]
@@ -306,9 +306,9 @@
slynx sub-sample --help
- ELynx Suite version 0.4.1.
+ ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
- Compiled on October 16, 2020, at 12:46 pm, UTC.
+ Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE
(-n|--number-of-sites INT)
@@ -336,9 +336,9 @@
slynx translate --help
- ELynx Suite version 0.4.1.
+ ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
- Compiled on October 16, 2020, at 12:46 pm, UTC.
+ Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT)
(-u|--universal-code CODE)
@@ -361,9 +361,9 @@
tlynx --help | head -n -16
- ELynx Suite version 0.4.1.
+ ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
- Compiled on October 16, 2020, at 12:46 pm, UTC.
+ Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]
[-f|--force] [--no-elynx-file] COMMAND
@@ -401,9 +401,9 @@
tlynx compare --help
- ELynx Suite version 0.4.1.
+ ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
- Compiled on October 16, 2020, at 12:46 pm, UTC.
+ Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect]
[-f|--newick-format FORMAT] NAMES
@@ -430,9 +430,9 @@
tlynx examine --help
- ELynx Suite version 0.4.1.
+ ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
- Compiled on October 16, 2020, at 12:46 pm, UTC.
+ Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT]
Compute summary statistics of phylogenetic trees.
@@ -454,9 +454,9 @@
tlynx simulate --help
- ELynx Suite version 0.4.1.
+ ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
- Compiled on October 16, 2020, at 12:46 pm, UTC.
+ Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: tlynx simulate (-t|--nTrees INT) (-n|--nLeaves INT) PROCESS
[-u|--sub-sample DOUBLE] [-s|--summary-statistics]
@@ -491,9 +491,9 @@
elynx --help | head -n -16
- ELynx Suite version 0.4.1.
+ ELynx Suite version 0.5.0.
Developed by Dominik Schrempf.
- Compiled on October 16, 2020, at 12:46 pm, UTC.
+ Compiled on November 10, 2020, at 14:29 pm, UTC.
Usage: elynx COMMAND
Validate and redo past ELynx analyses
diff --git a/elynx-nexus.cabal b/elynx-nexus.cabal
--- a/elynx-nexus.cabal
+++ b/elynx-nexus.cabal
@@ -1,6 +1,6 @@
cabal-version: 2.2
name: elynx-nexus
-version: 0.4.1
+version: 0.5.0
synopsis: Import and export Nexus files
description: Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at .
category: Bioinformatics