scikit-bio

0.7.2 verified Fri May 01 auth: no python

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.

pip install scikit-bio

Common errors

error ModuleNotFoundError: No module named 'skbio.math' ↓

cause 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.

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

cause 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.

Warnings

breaking scikit-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

deprecated The `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.

gotcha DistanceMatrix 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]`.

Imports

DistanceMatrix
wrong
```
import skbio.stats.distance.DistanceMatrix
```
correct
```
from skbio import DistanceMatrix
```
DistanceMatrix is a top-level export in skbio, not a submodule.
TreeNode
wrong
```
from skbio.tree import TreeNode
```
correct
```
from skbio import TreeNode
```
TreeNode is directly available in skbio since version 0.6.0.

Quickstart

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())