tskit

library1.0.3pypypi✓ verified 85d ago

tskit is the tree sequence toolkit for storing, manipulating, and analyzing genealogical trees and genetic variation. Current version is 1.0.2. Originally developed in the TSKIT project, it has a slow release cadence with maintenance releases as needed. Requires Python >=3.11 since version 1.0.2.

data

pip install tskit

github ↗package ↗homepage ↗docs ↗changelog ↗

INSTALL

IMPORT

SIG · TSKIT

tskit

datapythonv1.0.3

Install

4.7s avg

Import

699ms

Disk

97MB

Pass rate

8/ 10

Env Coverage8 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.0.1 · 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

glibc

py 3.10

✕ build_error

✓ 5.1s

py 3.11

✓ —

✓ 4.6s

py 3.12

✓ —

✓ 4.3s

py 3.13

✓ —

✓ 4.2s

py 3.9

✕ build_error

✓ 5.5s

97MB installed

● package 97MB

Code

Verified usage

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

tskit

✓ import tskit

tskit is a single module; there is no subpackage import.

Simulate a small tree sequence with msprime and compute basic statistics.

import tskit import msprime # Simulate a tree sequence using msprime ts = msprime.simulate(10, length=1e4, recombination_rate=1e-8, random_seed=1) print(ts.num_trees) print(ts.num_samples) # Load a tree sequence from a file (if available) # ts = tskit.load('example.trees') # Basic statistics print(ts.diversity())

Debug

Known issues

breakingTreeSequence.tables now returns a zero-copy immutable view (since 1.0.0b3). To modify tables, use TreeSequence.dump_tables() first.

fix

Replace ts.tables with ts.dump_tables() if you need to mutate.

affects: >=1.0.0b3

deprecatedts.samples(population=...) now raises ValueError if the population ID is a string (e.g. population name) instead of silently returning no samples (since 1.0.1).

fix

Use population IDs (integers) or map names to IDs first.

affects: >=1.0.1

gotchaMutation parents must be consistent with tree topology. Invalid mutation parent relationships cause LibraryError when constructing TreeSequence from tables.

fix

Ensure mutation.parent column is valid (parent mutation must occur at an earlier position or same position and be an ancestor in the tree).

affects: >=1.0.0b1

gotchaWhen writing VCF with individuals, default node filtering changed: non-sample nodes from individuals are now excluded by default (since 0.6.4). Use include_non_sample_nodes=True to include them.

fix

If you need non-sample nodes, pass include_non_sample_nodes=True to write_vcf().

affects: >=0.6.4

Errors

Common errors & fixes

AttributeError: module 'tskit' has no attribute 'load'

You typed tskit.load instead of tskit.load. The correct function is tskit.load (lowercase L).

fix

Use tskit.load('file.trees')

_tskit.LibraryError: Bad mutation parent

Mutation parent inconsistencies: parent mutation is not ancestral to child mutation at the same site or has a different position.

fix

Check and correct mutation.parent column in tables. Ensure parent mutation appears earlier in the mutation table or is a valid ancestor.

ValueError: The population ID must be an integer, not a string

Passing a population name string to ts.samples(population='pop_name')

fix

Use integer IDs: population_id = ts.population('pop_name').id or set population=0.

ValueError: The number of nodes does not match

Attempting to load a tree sequence from tables with missing or extra nodes (e.g., node table not sorted correctly).

fix

Ensure node table has the correct number of nodes and that edges reference existing nodes.

Upgrade

Version history

1.0.3latest on PyPI · released May 14, 2026

Audit

Dependencies

No dependency data recorded yet.

Agent activity

42 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/tskit-dev/tskit ↗

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

homepagehttps://tskit.dev/tskit ↗

docshttps://tskit.dev/tskit/docs/stable ↗

changeloghttps://tskit.dev/tskit/docs/stable/changelogs.html ↗