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Changes in release "0.4.0"

Contributors

  • @rmcar17 integrated new functions from IQ-TREE in Python, added multithreading support, and wrote the API refererence and quickstart.
  • @thomaskf exposed all new functions from IQ-TREE to be available from Python, and worked on multithreading support.
  • @GavinHuttley worked on setting up and writing the documentation and associated devtools, ModelFinder, and integration with cogent3 apps.
  • @YapengLang worked on bootstrapping support and extracting model parameters
  • @KatherineCaley worked on processing the ModelFinder results.

ENH

  • piqtree2 renamed piqtree to support future major releases of IQ-TREE.
  • piqtree now supports multithreading!
  • New function nj_tree constructs a rapid neighbour-joining tree from a pairwise distance matrix.
  • New function model_finder finds the best model for a given alignment.
  • New function jc_distances constructs a pairwise JC distance matrix from an alignment.
  • New function make_model allows converting an IQ-TREE string representation of a model to a Model class.
  • API for random_trees has changed - new order (num_trees, num_taxa, tree_mode, then rand_seed).
  • API for robinson_foulds has changed - now accepts a Sequence of trees.
  • Model parameters are now extracted from IQ-TREE where for now possible.
  • build_tree now supports ultrafast bootstrapping.
  • Model creation is now more robust.
  • Use piqtree.__iqtree_version__ to see what version of piqtree is being used.
  • See what can now be done in our new documentation!

DOC

Changes in release "0.3.1"

ENH

  • Add support for Lie Markov Models.
  • Base frequencies default to None (specified by model).

BUG

  • piqtree2 apps are now pickleable (they can now be run with parallel=True in the cogent3 app infrastructure)

Changes in release "0.3.0"

Contributors

  • @rmcar17 Added new classes to enhance model specification when calling build_tree and fit_tree.
  • @thomaskf fixed a bug in IQ-TREE resulting in segmentation faults on some invalid arguments.

ENH

  • build_tree and fit_tree now allow specifying base frequencies, invariable sites and rate heterogeneity options.

BUG

  • Fixed a segmentation fault on repetitive calls to IQ-TREE with particular arguments.

Changes in release "0.2.0"

Contributors

  • Richard Morris
  • Robert McArthur

ENH

  • build_tree and fit_tree now use enums for the substitution model.

BUG

  • Fixed an issue where calling build_tree or fit_tree twice, then another function with invalid input resulted in a segmentation fault.

DOC

  • Implement scriv as a tool to manage collection of changes, and automated collation into the changelog