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 (about 8 years ago)
• Default Branch: main
• Last Pushed: 2025-10-17T12:33:55.000Z (6 months ago)
• Last Synced: 2025-10-21T20:55:54.979Z (6 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)

The succinct tree sequence (`tskit`) format is an efficient way of representing

the genetic history - sometimes known as an

[Ancestral Recombination Graph or ARG](https://doi.org/10.1093/genetics/iyae100) -

of a set of related DNA sequences. `Tskit` is used

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 ancestry of genetic sequences.

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

manipulate ARGs in the tree sequence format, including efficient access to the

sequence of correlated trees along a genome and general methods to calculate

genetic statistics. `Tskit` 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

```