treezy 0.0.2

Simple library for manipulating phylogenetic trees

treezy

treezy is a simple Python library for manipulating phylogenetic trees, including reading from and writing to files.

Features

• Parse and manipulate phylogenetic trees
• Read and write trees with branch annotations and comments
• Lightweight and easy to integrate into existing Python projects

Installation

pip install treezy

To build treezy from source you can run

git clone https://github.com/4ment/treezy
pip install treezy/

Usage

from treezy.tree import Tree

newick = '((A:[&rate=0.1,cat=0]1,B:[&rate=0.1,cat=0]2):[&rate=0.2,cat=1]3,C:[&rate=0.2,cat=1]4);'
tree = Tree.from_newick(newick)
tree.parse_branch_comment({'rate': lambda rate: float(rate)})
for node in tree:
    if not node.is_root:
        node.distance *= node.branch_annotations['rate']
print(tree)
# ((A:0.1,B:0.2):0.6,C:0.8);

Contributing

Contributions are welcome! Please open issues or submit pull requests.

License

This project is licensed under the MIT License. See LICENSE for details.