scikit-bio

library0.7.3pypypi✓ verified 84d ago

scikit-bio is a Python library for bioinformatics, providing data structures, algorithms, and educational resources. Version 0.7.2 (released 2025-09-15) requires Python >=3.10. Released approximately every 3-6 months, with active development on GitHub.

data ai-ml

pip install scikit-bio

github ↗package ↗homepage ↗docs ↗

INSTALL

IMPORT

SIG · SCIKIT-BIO

scikit-bio

datapythonv0.7.3

Install

16.9s avg

Import

4008ms

Disk

470MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v0.7.3 · 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

build_error

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 16.9s · import 4.008s · 459MB

470MB installed

● package 470MB

Code

Verified usage

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

DistanceMatrix

✓ from skbio import DistanceMatrix

✗ import skbio.stats.distance.DistanceMatrix

DistanceMatrix is a top-level export in skbio, not a submodule.

TreeNode

✓ from skbio import TreeNode

✗ from skbio.tree import TreeNode

TreeNode is directly available in skbio since version 0.6.0.

Create a distance matrix and parse a Newick tree.

from skbio import DistanceMatrix, TreeNode dm = DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]], ids=['a', 'b', 'c']) print(dm) tree = TreeNode.read(['((a,b),c);']) print(tree.ascii_art())

Debug

Known issues

breakingscikit-bio 0.6.0 introduced major API changes and deprecations. Code written for 0.5.x may require updates, especially in sequence I/O and tree modules.

fix

Review the migration guide in the changelog: https://github.com/scikit-bio/scikit-bio/blob/main/CHANGELOG.md

affects: >=0.6.0

deprecatedThe `skbio.math` submodule is deprecated. Use `skbio.stats` or `scipy` instead.

fix

Replace imports like `from skbio.math import ...` with `from skbio.stats import ...` or use scipy directly.

affects: >=0.6.0

gotchaDistanceMatrix in scikit-bio 0.7.x is a condensed form by default. Indexing with [i][j] may give unexpected results. Use `dm[i, j]` syntax.

fix

Always use `dm[row, col]` instead of `dm[row][col]`.

affects: >=0.7.0

Errors

Common errors & fixes

ModuleNotFoundError: No module named 'skbio.math'

The `skbio.math` submodule was deprecated in 0.6.0 and removed.

fix

Use `from skbio.stats import ...` instead, e.g., `from skbio.stats.distance import permanova`.

AttributeError: module 'skbio' has no attribute 'DNA'

The top-level `DNA`, `RNA`, `Protein` classes were removed in 0.6.0. Use `skbio.sequence.DNA` instead.

fix

Use `from skbio.sequence import DNA` or `skbio.sequence.DNA`.

Upgrade

Version history

0.7.3latest on PyPI · released Jun 1, 2026

Audit

Dependencies

No dependency data recorded yet.

Agent activity

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OpenAI (training)

Resources

githubhttps://github.com/scikit-bio/scikit-bio ↗

packagehttps://pypi.org/project/scikit-bio/ ↗

homepagehttps://scikit.bio ↗

docshttps://scikit.bio/docs/latest/ ↗