https://github.com/tskit-dev/tskit

Population-scale Ancestral Recombination Graph (ARG) library
https://github.com/tskit-dev/tskit

bioinformatics genomics phylogenetics python science tree-sequences

Last synced: 3 months ago
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Population-scale Ancestral Recombination Graph (ARG) library

• Host: GitHub
• URL: https://github.com/tskit-dev/tskit
• Owner: tskit-dev
• License: mit
• Created: 2018-02-08T19:16:31.000Z (almost 8 years ago)
• Default Branch: main
• Last Pushed: 2025-10-17T12:33:55.000Z (3 months ago)
• Last Synced: 2025-10-21T20:55:54.979Z (3 months ago)
• Topics: bioinformatics, genomics, phylogenetics, python, science, tree-sequences
• Language: Python
• Homepage:
• Size: 19.4 MB
• Stars: 174
• Watchers: 12
• Forks: 78
• Open Issues: 91
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

Awesome Lists containing this project

README

          
# tskit  

[![License](https://img.shields.io/github/license/tskit-dev/tskit)](https://github.com/tskit-dev/tskit/blob/main/LICENSE)

[![Contributors](https://img.shields.io/github/contributors/tskit-dev/tskit)](https://github.com/tskit-dev/tskit/graphs/contributors)

[![Commit activity](https://img.shields.io/github/commit-activity/m/tskit-dev/tskit)](https://github.com/tskit-dev/tskit/commits/main)

[![Coverage](https://codecov.io/gh/tskit-dev/tskit/branch/main/graph/badge.svg)](https://codecov.io/gh/tskit-dev/tskit)

![OS](https://img.shields.io/badge/OS-linux%20%7C%20OSX%20%7C%20win--64-steelblue)

[Documentation (stable)](https://tskit.dev/tskit/docs/stable/) • [Documentation (latest)](https://tskit.dev/tskit/docs/latest/)

[![Docs Build](https://github.com/tskit-dev/tskit/actions/workflows/docs.yml/badge.svg)](https://github.com/tskit-dev/tskit/actions/workflows/docs.yml) [![Binary wheels](https://github.com/tskit-dev/tskit/actions/workflows/wheels.yml/badge.svg)](https://github.com/tskit-dev/tskit/actions/workflows/wheels.yml) [![Tests](https://github.com/tskit-dev/tskit/actions/workflows/tests.yml/badge.svg)](https://github.com/tskit-dev/tskit/actions/workflows/tests.yml)

Succinct tree sequences are a highly efficient way of storing a set of related DNA

sequences by encoding their ancestral history as a set of correlated trees along the

genome. The tree sequence format is output by a number of software libraries and programs

(such as [msprime](https://github.com/tskit-dev/msprime),

[SLiM](https://github.com/MesserLab/SLiM),

[fwdpp](http://molpopgen.github.io/fwdpp/), and

[tsinfer](https://tskit.dev/tsinfer/docs/stable/)) that either simulate or infer

the evolutionary history of genetic sequences. The evolutionary history of genetic

sequences is often technically referred to as an Ancestral Recombination Graph (ARG);

succinct tree sequences are fully compatible with this formulation, and tskit is a

therefore a powerful platform for processing ARGs.

The `tskit` library provides the underlying functionality used to load, examine, and

manipulate tree sequences, including efficient methods for calculating genetic

statistics. It often forms part of an installation of other software packages such as

those listed above. Please see the

[documentation](https://tskit.dev/tskit/docs/stable/) for further details, which

includes

[installation instructions](https://tskit.dev/tskit/docs/stable/installation.html).

To get started with tskit, tutorials and other content are at http://tskit.dev. For help

and support from the community you can use

[discussions](https://github.com/tskit-dev/tskit/discussions) here on github, or raise an

issue for a specific bug or feature request.

We warmly welcome contributions from the community. Raise an issue if you have an

idea you'd like to work on, or submit a PR for comments and help.

The base `tskit` library provides both a [Python](https://tskit.dev/tskit/docs/stable/python-api.html)

and [C](https://tskit.dev/tskit/docs/stable/c-api.html) API. A Rust API is provided in the

[tskit-rust](https://github.com/tskit-dev/tskit-rust) repository.

#### Python API

[![PyPI version](https://img.shields.io/pypi/v/tskit.svg)](https://pypi.org/project/tskit/)

[![Supported Python Versions](https://img.shields.io/pypi/pyversions/tskit.svg)](https://pypi.org/project/tskit/)

[![Wheel](https://img.shields.io/pypi/wheel/tskit)](https://pypi.org/project/tskit/)

[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)

Most users of `tskit` will use the python API as it provides a convenient, high-level API

to access, analyse and create tree sequences. Full documentation is

[here](https://tskit.dev/tskit/docs/stable/python-api.html).   

#### C API

[![C99](https://img.shields.io/badge/Language-C99-steelblue.svg)](https://en.wikipedia.org/wiki/C99)

The `tskit` C API provides comprehensive, low-level methods for manipulating and

processing tree-sequences. Written to the C99 standard and fully thread-safe, it can be

used with either C or C++. Full documentation is

[here](https://tskit.dev/tskit/docs/stable/c-api.html).

## Installation

```bash

python -m pip install tskit

# or

conda install -c conda-forge tskit

```