tlynx 0.5.0.2 → 0.5.1.0
raw patch · 4 files changed
+173/−51 lines, 4 filesdep ~aesondep ~elynx-toolsdep ~elynx-treePVP ok
version bump matches the API change (PVP)
Dependency ranges changed: aeson, elynx-tools, elynx-tree, lifted-async, optparse-applicative, vector
API changes (from Hackage documentation)
Files
- ChangeLog.md +9/−0
- README.md +148/−44
- src/TLynx/Parsers.hs +9/−0
- tlynx.cabal +7/−7
ChangeLog.md view
@@ -5,6 +5,15 @@ ## Unreleased changes +## Version 0.5.1.0++- **elynx-tree:** new functions `isValidPath`, `isLeaf`, `depth`; add conversion+ topology -> tree; various internal algorithmic improvements; improved error+ messages; simplified interface to Newick parsers; parallel fold map; Nix+ flake.+- Remove unneeded dependencies.++ ## Version 0.5.0.2 - Speed up mixture model simulation.
README.md view
@@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.5.0.2.+Version: 0.5.1.0. Reproducible evolution made easy. <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>@@ -71,11 +71,11 @@ Handle evolutionary sequences. - slynx --help | head -n -16+ stack exec slynx -- --help | head -n -16 - ELynx Suite version 0.5.0.2.+ ELynx Suite version 0.5.1.0. Developed by Dominik Schrempf.- Compiled on February 19, 2021, at 13:42 pm, UTC.+ Compiled on June 12, 2021, at 14:54 pm, UTC. Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] [--no-elynx-file] COMMAND@@ -84,8 +84,8 @@ Available options: -h,--help Show this help text -V,--version Show version- -v,--verbosity VALUE Be verbose; one of: Quiet Warning Info- Debug (default: Info)+ -v,--verbosity VALUE Be verbose; one of: Quiet Warning Info Debug+ (default: Info) -o,--output-file-basename NAME Specify base name of output file -f,--force Ignore previous analysis and overwrite existing@@ -118,11 +118,11 @@ Concatenate multi sequence alignments. - slynx concatenate --help+ stack exec slynx -- concatenate --help - ELynx Suite version 0.5.0.2.+ ELynx Suite version 0.5.1.0. Developed by Dominik Schrempf.- Compiled on February 19, 2021, at 13:42 pm, UTC.+ Compiled on June 12, 2021, at 14:54 pm, UTC. Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE Concatenate sequences found in input files.@@ -139,11 +139,11 @@ Examine sequence with `slynx examine`. - slynx examine --help+ stack exec slynx -- examine --help - ELynx Suite version 0.5.0.2.+ ELynx Suite version 0.5.1.0. Developed by Dominik Schrempf.- Compiled on February 19, 2021, at 13:42 pm, UTC.+ Compiled on June 12, 2021, at 14:54 pm, UTC. Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site] Examine sequences. If data is a multi sequence alignment, additionally analyze columns.@@ -161,11 +161,11 @@ Filter sequences with `filer-rows`. - slynx filter-rows --help+ stack exec slynx -- filter-rows --help - ELynx Suite version 0.5.0.2.+ ELynx Suite version 0.5.1.0. Developed by Dominik Schrempf.- Compiled on February 19, 2021, at 13:42 pm, UTC.+ Compiled on June 12, 2021, at 14:54 pm, UTC. Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH] [--shorter-than LENGTH] [--standard-characters]@@ -184,11 +184,11 @@ Filter columns of multi sequence alignments with `filter-columns`. - slynx filter-columns --help+ stack exec slynx -- filter-columns --help - ELynx Suite version 0.5.0.2.+ ELynx Suite version 0.5.1.0. Developed by Dominik Schrempf.- Compiled on February 19, 2021, at 13:42 pm, UTC.+ Compiled on June 12, 2021, at 14:54 pm, UTC. Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE [--standard-chars DOUBLE]@@ -208,11 +208,11 @@ Simulate sequences with `slynx simulate`. - slynx simulate --help+ stack exec slynx -- simulate --help - ELynx Suite version 0.5.0.2.+ ELynx Suite version 0.5.1.0. Developed by Dominik Schrempf.- Compiled on February 19, 2021, at 13:42 pm, UTC.+ Compiled on June 12, 2021, at 14:54 pm, UTC. Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] [-m|--mixture-model MODEL] [-e|--edm-file NAME] @@ -287,11 +287,11 @@ Sub-sample columns from multi sequence alignments. - slynx sub-sample --help+ stack exec slynx -- sub-sample --help - ELynx Suite version 0.5.0.2.+ ELynx Suite version 0.5.1.0. Developed by Dominik Schrempf.- Compiled on February 19, 2021, at 13:42 pm, UTC.+ Compiled on June 12, 2021, at 14:54 pm, UTC. Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE (-n|--number-of-sites INT)@@ -317,11 +317,11 @@ Translate sequences. - slynx translate --help+ stack exec slynx -- translate --help - ELynx Suite version 0.5.0.2.+ ELynx Suite version 0.5.1.0. Developed by Dominik Schrempf.- Compiled on February 19, 2021, at 13:42 pm, UTC.+ Compiled on June 12, 2021, at 14:54 pm, UTC. Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT) (-u|--universal-code CODE)@@ -342,11 +342,11 @@ Handle phylogenetic trees in Newick format. - tlynx --help | head -n -16+ stack exec tlynx -- --help | head -n -16 - ELynx Suite version 0.5.0.2.+ ELynx Suite version 0.5.1.0. Developed by Dominik Schrempf.- Compiled on February 19, 2021, at 13:42 pm, UTC.+ Compiled on June 12, 2021, at 14:54 pm, UTC. Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] [--no-elynx-file] COMMAND@@ -355,8 +355,8 @@ Available options: -h,--help Show this help text -V,--version Show version- -v,--verbosity VALUE Be verbose; one of: Quiet Warning Info- Debug (default: Info)+ -v,--verbosity VALUE Be verbose; one of: Quiet Warning Info Debug+ (default: Info) -o,--output-file-basename NAME Specify base name of output file -f,--force Ignore previous analysis and overwrite existing@@ -382,11 +382,11 @@ Compute distances between phylogenetic trees. - tlynx compare --help+ stack exec tlynx -- compare --help - ELynx Suite version 0.5.0.2.+ ELynx Suite version 0.5.1.0. Developed by Dominik Schrempf.- Compiled on February 19, 2021, at 13:42 pm, UTC.+ Compiled on June 12, 2021, at 14:54 pm, UTC. Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] [-f|--newick-format FORMAT] NAMES@@ -407,15 +407,90 @@ -h,--help Show this help text +## Connect++Connect two phylogenetic tree in all ways (possibly honoring constraints).++ stack exec tlynx -- connect --help++ ELynx Suite version 0.5.1.0.+ Developed by Dominik Schrempf.+ Compiled on June 12, 2021, at 14:54 pm, UTC.+ + Usage: tlynx connect [-f|--newick-format FORMAT] [-c|--contraints CONSTRAINTS]+ TREE-FILE-A TREE-FILE-B+ Connect two phylogenetic trees in all ways (possibly honoring constraints).+ + Available options:+ -h,--help Show this help text+ -V,--version Show version+ -f,--newick-format FORMAT+ Newick tree format: Standard, IqTree, or RevBayes;+ default: Standard; for detailed help, see 'tlynx+ --help'+ -c,--contraints CONSTRAINTS+ File containing one or more Newick trees to be used+ as constraints+ TREE-FILE-A File containing the first Newick tree+ TREE-FILE-B File containing the second Newick tree+ -h,--help Show this help text+++## Distancce++Compute distances between many phylogenetic trees.++ stack exec tlynx -- distance --help++ ELynx Suite version 0.5.1.0.+ Developed by Dominik Schrempf.+ Compiled on June 12, 2021, at 14:54 pm, UTC.+ + Usage: tlynx distance (-d|--distance MEASURE) [-n|--normalize] [-t|--intersect] + [-s|--summary-statistics] + [-m|--master-tree-file MASTER-TREE-File] + [-f|--newick-format FORMAT] [INPUT-FILES]+ Compute distances between many phylogenetic trees.+ + Available options:+ -h,--help Show this help text+ -V,--version Show version+ -d,--distance MEASURE Type of distance to calculate (available distance+ measures are listed below)+ -n,--normalize Normalize trees before distance calculation; only+ affect distances depending on branch lengths+ -t,--intersect Compare intersections; i.e., before comparison, drop+ leaves that are not present in the other tree+ -s,--summary-statistics Report summary statistics only+ -m,--master-tree-file MASTER-TREE-File+ Compare all trees to the tree in the master tree+ file.+ -f,--newick-format FORMAT+ Newick tree format: Standard, IqTree, or RevBayes;+ default: Standard; for detailed help, see 'tlynx+ --help'+ INPUT-FILES Read tree(s) from INPUT-FILES; if more files are+ given, one tree is expected per file+ -h,--help Show this help text+ + Distance measures:+ symmetric Symmetric distance (Robinson-Foulds distance).+ incompatible-split[VAL] Incompatible split distance. Collapse branches with (normalized)+ support less than 0.0<=VAL<=1.0 before distance calculation;+ if, let's say, VAL>0.7, only well supported differences contribute+ to the total distance.+ branch-score Branch score distance.++ ## Examine Compute summary statistics of phylogenetic trees. - tlynx examine --help+ stack exec tlynx -- examine --help - ELynx Suite version 0.5.0.2.+ ELynx Suite version 0.5.1.0. Developed by Dominik Schrempf.- Compiled on February 19, 2021, at 13:42 pm, UTC.+ Compiled on June 12, 2021, at 14:54 pm, UTC. Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT] Compute summary statistics of phylogenetic trees.@@ -431,15 +506,44 @@ -h,--help Show this help text +## Shuffle++Shuffle a phylogenetic tree (keep coalescent times, but shuffle topology and+leaves).++ stack exec tlynx -- shuffle --help++ ELynx Suite version 0.5.1.0.+ Developed by Dominik Schrempf.+ Compiled on June 12, 2021, at 14:54 pm, UTC.+ + Usage: tlynx shuffle [-f|--newick-format FORMAT] [-n|--replicates N] TREE-FILE + [-S|--seed [INT]]+ Shuffle a phylogenetic tree (keep coalescent times, but shuffle topology and leaves).+ + Available options:+ -h,--help Show this help text+ -V,--version Show version+ -f,--newick-format FORMAT+ Newick tree format: Standard, IqTree, or RevBayes;+ default: Standard; for detailed help, see 'tlynx+ --help'+ -n,--replicates N Number of trees to generate+ TREE-FILE File containing a Newick tree+ -S,--seed [INT] Seed for random number generator; list of 32 bit+ integers with up to 256 elements (default: random)+ -h,--help Show this help text++ ## Simulate Simulate phylogenetic trees using birth and death processes. - tlynx simulate --help+ stack exec tlynx -- simulate --help - ELynx Suite version 0.5.0.2.+ ELynx Suite version 0.5.1.0. Developed by Dominik Schrempf.- Compiled on February 19, 2021, at 13:42 pm, UTC.+ Compiled on June 12, 2021, at 14:54 pm, UTC. Usage: tlynx simulate (-t|--nTrees INT) (-n|--nLeaves INT) PROCESS [-u|--sub-sample DOUBLE] [-s|--summary-statistics] @@ -472,11 +576,11 @@ Validate and (optionally) redo past ELynx analyses. - elynx --help | head -n -16+ stack exec elynx -- --help | head -n -16 - ELynx Suite version 0.5.0.2.+ ELynx Suite version 0.5.1.0. Developed by Dominik Schrempf.- Compiled on February 19, 2021, at 13:42 pm, UTC.+ Compiled on June 12, 2021, at 14:54 pm, UTC. Usage: elynx COMMAND Validate and redo past ELynx analyses
src/TLynx/Parsers.hs view
@@ -86,3 +86,12 @@ ++ ["- Nexus file including Newick trees"] where toListItem = ("- Newick " ++)++-- Short description of the supported Newick formats.+describeNewickFormat :: NewickFormat -> String+describeNewickFormat Standard =+ "Standard: Branch support values are stored in square brackets after branch lengths."+describeNewickFormat IqTree =+ "IqTree: Branch support values are stored as node names after the closing bracket of forests."+describeNewickFormat RevBayes =+ "RevBayes: Key-value pairs is provided in square brackets after node names as well as branch lengths. XXX: Key value pairs are ignored at the moment."
tlynx.cabal view
@@ -1,6 +1,6 @@ cabal-version: 2.2 name: tlynx-version: 0.5.0.2+version: 0.5.1.0 license: GPL-3.0-or-later license-file: LICENSE copyright: Dominik Schrempf (2020)@@ -46,24 +46,24 @@ default-language: Haskell2010 ghc-options: -Wall -Wunused-packages build-depends:- aeson >=1.5.5.1,+ aeson >=1.5.6.0, attoparsec >=0.13.2.5, base >=4.7 && <5, bytestring >=0.10.12.0, comonad >=5.0.8, containers >=0.6.2.1,- elynx-tools >=0.5.0.2,- elynx-tree >=0.5.0.2,+ elynx-tools >=0.5.1.0,+ elynx-tree >=0.5.1.0, gnuplot >=0.5.6.1,- lifted-async >=0.10.1.2,+ lifted-async >=0.10.2, monad-logger >=0.3.36, mwc-random >=0.14.0.0,- optparse-applicative >=0.15.1.0,+ optparse-applicative >=0.16.1.0, parallel >=3.2.2.0, statistics >=0.15.2.0, text >=1.2.4.1, transformers >=0.5.6.2,- vector >=0.12.2.0+ vector >=0.12.3.0 executable tlynx main-is: Main.hs