v0.1.2

v0.1.2 - 2023-09-20

Added

• Basic Python bindings to this crate usign PyO3. Behind python feature. Used for the phylotree python package.
• Adding Yule process to tree simulation
• Adding drawing method to visualize trees as svgs. Only radial layout for now.
• Added part of the ETE3 test suite
• Added possibility to search for nodes with a user specified closure.
• Possibility to output newick with different formats (with/without comments, no lengths, only leaf names, ...) with tree::Tree::to_formatted_newick
• Random resolution of polytomies
• Added ladderisation function
• Added commands to CLI:
  • Collapse: set branches under a given threshold to 0
  • Resolve: randomly resolve multifurcations
  • Remove: remove tips from the tree
  • Deduplicate: given a sequence alignment, remove tips corresponding to duplicated sequences
  • Draw: draw a tree to a svg file

Changed

• More efficient method to compute pairwise distances. Inspired by the PhyloDM crate.
• Added new simulation methods to generate command of CLI.

0.1.1

Initial release of phylotree

• Basic tree creation + manipulation
• Distance matrix computation
• Basic CLI for manipulating trees from the command line
• Rustoc documentation for the library