newick

library1.11.0pypypi✓ verified 90d ago

A Python module to read and write the Newick format, commonly used for phylogenetic trees. Current version: 1.11.0. Release cadence is irregular; maintained on GitHub.

data serialization

pip install newick

package ↗homepage ↗

INSTALL

IMPORT

SIG · NEWICK

newick

datapythonv1.11.0

Install

1.5s avg

Import

51ms

Disk

16MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.11.0 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

installs and imports cleanly · install 0.0s · import 0.056s · 17.9MB

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 1.5s · import 0.046s · 18MB

16MB installed

● package 16MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

loads

✓ from newick import loads

Standard import for parsing Newick strings.

dumps

✓ from newick import dumps

Standard import for writing Newick strings.

load

✓ from newick import load

Load Newick from a file.

dump

✓ from newick import dump

Write Newick to a file.

Parses a Newick string into a tree of Node objects and serializes back.

from newick import loads, dumps # Load a Newick string tree = loads('(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);') # tree is a list of Node objects (rooted at index 0) node = tree[0] print(node.name) # None (internal node) print(node.descendants) # list of Nodes print(node.length) # None (for root) # Modify the tree and dump back to string node.name = 'root' newick_str = dumps(node) print(newick_str)

Debug

Known issues

gotchaloads() returns a list of Node objects, not a single Node. For a tree with one root, access index 0.

fix

tree = loads(newick_str)[0]

affects: all

gotchaNode names can include special characters like ':' or ',' but must be quoted. The library may fail to parse if names contain unescaped special characters.

fix

Ensure node names are properly escaped or quoted in the Newick string.

affects: all

deprecatedThe 'read' and 'write' functions (from newick import read, write) are deprecated as of v1.9.0. Use load/dump instead.

fix

Use load() for reading files and dump() for writing.

affects: >=1.9.0

breakingIn v1.9.0, the internal Node class changed: removed 'ancestor' attribute and added 'parent'. Code relying on 'node.ancestor' will break.

fix

Use 'node.parent' instead of 'node.ancestor'.

affects: >=1.9.0

Errors

Common errors & fixes

AttributeError: module 'newick' has no attribute 'loads'

Installed old version (<1.0) that lacked loads/dumps; or named conflict with other module.

fix

Upgrade to latest: pip install --upgrade newick. Check import: from newick import loads

IndexError: list index out of range when accessing tree[0]

The Newick string is empty or malformed (e.g., missing semicolon). loads() returns empty list.

fix

Ensure the Newick string is valid and ends with ';'. Check: tree = loads(newick_str); assert tree

TypeError: expects a string or file-like object

Passed a Node object to load() instead of a file path or string.

fix

Use dumps(node) to serialize, not load(). load() is for reading from file.

ValueError: Node name contains illegal characters

Node name includes unescaped newick special characters like '(', ')', ':', ',', ';'.

fix

Quote the name using single quotes in the Newick string, e.g., "'My:Node'".

Upgrade

Version history

1.11.0latest on PyPI · released Jan 14, 2026

Audit

Dependencies

No dependency data recorded yet.

Agent activity

15 hits · last 30 days

node

Anthropic

Resources

packagehttps://pypi.org/project/newick/ ↗

homepagehttps://gitlab.mpcdf.mpg.de/dlce-eva/python-newick ↗