# Revision history for ELynx ## Unreleased changes ## 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.