dendropy

library5.0.8pypypi✓ verified 86d ago

A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. Current version 5.0.8 (requires Python >=3.7). The library has undergone major API changes from v4 to v5 (e.g., removal of deprecated modules, new tree structure classes). Release cadence is irregular, with v5.0.0 released in late 2023 and subsequent bugfix releases.

data ai-ml

pip install dendropy

github ↗package ↗homepage ↗docs ↗

INSTALL

IMPORT

SIG · DENDROPY

dendropy

datapythonv5.0.8

Install

2.0s avg

Import

261ms

Disk

24MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v5.0.8 · 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 0.266s · 21.8MB

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 2.0s · import 0.256s · 22MB

24MB installed

● package 24MB

Code

Verified usage

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

Tree

✓ from dendropy import Tree

✗ from dendropy.tree import Tree

Tree class is now directly available under dendropy (since v4). Using dendropy.tree is deprecated and may be removed.

TaxonNamespace

✓ from dendropy import TaxonNamespace

✗ from dendropy.datamodel import taxonmodel

TaxonNamespace is now directly under dendropy; the old path was restructured in v5.

Load a tree from a Newick file and print it.

import dendropy tree = dendropy.Tree() # Read from a file (Newick example) tree = dendropy.Tree.get(path='example.tre', schema='newick') print(tree.as_string(schema='newick'))

Debug

Known issues

breakingDendroPy v5 introduced breaking changes: removal of deprecated modules (e.g., 'dendropy.utility', 'dendropy.dataio') and renaming of some classes. Code written for v4 may not work directly.

fix

Update imports to use the new 'dendropy' top-level namespace. Refer to migration guide on GitHub.

affects: <5.0.0

gotchaWhen reading trees, ensure the schema argument matches the file format exactly (e.g., 'newick', 'nexus', 'nexml'). Incorrect schema often leads to 'No tree found' or parsing errors.

fix

Double-check the file format and use the correct schema string. For example, use schema='nexus' for NEXUS files.

affects: all

Errors

Common errors & fixes

dendropy.exception.DendroPyError: No trees found in file.

Incorrect schema argument or file contains no trees (e.g., only taxon definitions).

fix

Specify the correct schema, e.g., Tree.get(..., schema='nexus') for NEXUS files. Ensure file contains tree data.

AttributeError: module 'dendropy' has no attribute 'tree'

Old code trying to access 'dendropy.tree' directly (v4 pattern). 'tree' is no longer a submodule; use 'dendropy.Tree'.

fix

Replace 'dendropy.tree' with 'dendropy.Tree'.

Upgrade

Version history

5.0.8latest on PyPI · released Jun 4, 2025

Audit

Dependencies

No dependency data recorded yet.

Agent activity

16 hits · last 30 days

node

OpenAI (training)

Resources

githubhttp://github.com/jeetsukumaran/DendroPy ↗

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

homepagehttps://dendropy.org ↗

docshttps://jeetsukumaran.github.io/DendroPy/ ↗