diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -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. diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.5.0.2. +Version: 0.5.1.0. Reproducible evolution made easy.

@@ -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 diff --git a/slynx.cabal b/slynx.cabal --- a/slynx.cabal +++ b/slynx.cabal @@ -1,6 +1,6 @@ cabal-version: 2.2 name: slynx -version: 0.5.0.2 +version: 0.5.1.0 license: GPL-3.0-or-later license-file: LICENSE copyright: Dominik Schrempf (2020) @@ -51,18 +51,18 @@ base >=4.7 && <5, bytestring >=0.10.12.0, containers >=0.6.2.1, - elynx-markov >=0.5.0.2, - elynx-seq >=0.5.0.2, - elynx-tools >=0.5.0.2, - elynx-tree >=0.5.0.2, - hmatrix >=0.20.1, + elynx-markov >=0.5.1.0, + elynx-seq >=0.5.1.0, + elynx-tools >=0.5.1.0, + elynx-tree >=0.5.1.0, + hmatrix >=0.20.2, monad-logger >=0.3.36, mwc-random >=0.14.0.0, - optparse-applicative >=0.15.1.0, + optparse-applicative >=0.16.1.0, 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 slynx main-is: Main.hs diff --git a/src/SLynx/Simulate/Simulate.hs b/src/SLynx/Simulate/Simulate.hs --- a/src/SLynx/Simulate/Simulate.hs +++ b/src/SLynx/Simulate/Simulate.hs @@ -295,7 +295,6 @@ let alignmentLength = argsLength l $(logInfo) $ T.pack $ "Length: " <> show alignmentLength <> "." gen <- case argsSeed l of - Random -> - error "simulateCmd: seed not available; please contact maintainer." + Random -> error "simulateCmd: seed not available; please contact maintainer." Fixed s -> liftIO $ initialize s simulateAlignment phyloModel t' alignmentLength gen