Revision history for ELynx

Unreleased changes

Version 0.7.2.0

• slynx: Allow global normalization of mixture models.

Version 0.7.1.0

• Be less strict with quoted identifiers/names in phylogenetic trees.
• Be less strict with FASTA identifiers.
• Update tooling (GHC 9.2.4).

Version 0.7.0.1

• Random 1.2: Parallel functions now require an `IOGenM` random number generator.
• Fix splitting of the random number generator.

Version 0.6.1.1

• Remove plotting functionality (gnuplot incompatible with ghc922).
• Read files strictly.
• Refactor; flatten model hierarchy.

Version 0.6.1.0

• Split ELynx.Tools into separate modules because the package will be reduced.
• Remove the following modules from ELynx.Tools: Concurrent, LinearAlgebra, List, Misc, and Numeric.

Version 0.6.0.0

• elynx-tree: remove parallel folds with layers (parBranchFoldMapWithLayer too special and slow).
• elynx-tree: fix various tree instances; add zip trees with appropriate instances.
• Remove monad-logger dependency and implement lighter alternative.
• Significant changes to the tool chain.

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.
• Improve rooting functions.
• Improve Topology data type (but still a lot to do).
• Various additions to the documentation.
• Rename Measurable to HasLength, Supported to HasSupport, and Named to HasLength.
• Cabal and stack file changes.

Version 0.5.0.1

• 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).
• Parallel evaluation strategies.
• Change names of some functions involving partitions. For example, mp was renamed to pt.
• Improve documentation for (bi)partitions.
• Bugfix tlynx compare; do not throw error when branch support values are not set.
• Add no-elynx-file option.
• Also parse Nexus files with tlynx commands.
• Bugfix subSample; the sub sample was reversed.

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.
• PhyloStrict -> PhyloExplicit; and some conversion functions were changed.
• tlynx coalesce was merged into tlynx simulate, the syntax has changed; see tlynx simulate --help.

Version 0.3.3

• Fix test suites.

Version 0.3.2

• Remove llvm dependency.
• Move away from hpack.

Version 0.3.1

• Use Attoparsec.
• Use ByteString consistently.
• Remove elynx-tools dependency from libaries.

Version 0.3.0

• elynx-nexus: library to import and export Nexus files.
• elynx-tree: major refactor and big cleanup; use rose trees with branch labels.
• elynx-tree: provide zippers.

Version 0.2.2

• Validation and repetition of previous analyses is finally possible with the new elynx binary.
• A library elynx-markov for running Markov processes along phylogenetic trees has been split off elynx-seq. This library performs the computations when executing slynx simulate ....
• Many other small improvements.