TreeSwift

1.1.45 verified Fri May 01 auth: no python

TreeSwift is a fast tree manipulation library for Python 2 and 3, providing a simple interface for reading, writing, and analyzing phylogenetic trees. The current version is 1.1.45, with regular updates and bug fixes.

pip install treeswift

Common errors

error ModuleNotFoundError: No module named 'treeswift' ↓

cause Library not installed or installed in a different environment.

fix

Run pip install treeswift in the correct Python environment.

error TypeError: extract_tree_with() argument after * must be an iterable, not str ↓

cause Passing a string directly to `extract_tree_with` where an iterable of labels is expected.

fix

Wrap the string in a list: tree.extract_tree_with(['label']) instead of tree.extract_tree_with('label').

Warnings

gotcha `extract_tree_with` and `extract_tree_without` convert string input to a set of individual characters. If you pass a single string like 'ABC', it will be treated as {'A','B','C'} rather than preserving the string as a single label. Pass a set or list instead. ↓

fix Use `extract_tree_with(set(['ABC']))` or `extract_tree_with(['ABC'])` to keep the label intact.

deprecated `Tree.read` can read gzip files directly, but file extension handling may be simplified in future versions. ↓

fix Pass an open file handle or a path; gzip is detected internally.

gotcha `distance_between` may return incorrect values when one node is an ancestor of the other in versions prior to 1.1.39. Ensure you have the latest version. ↓

fix Upgrade to >=1.1.39: `pip install --upgrade treeswift`.

Imports

Tree

wrong

from treeswift import read_tree

correct

from treeswift import Tree

read_tree is a function; Tree is the class.

Node

wrong

from treeswift.tree import Node

correct

from treeswift import Node

Node is exported from treeswift directly.

Quickstart

Initialize a tree, read a Newick string, print the tree, and compute the distance between two leaves.

from treeswift import Tree

tree = Tree()
tree.read('((A:0.1,B:0.2):0.3,C:0.4);')
print(tree)  # Newick string

dist = tree.distance_between('A', 'C')
print(dist)  # 0.8