GitHub - tskit-dev/tskit: Population-scale Ancestral Recombination Graph (ARG) library (original) (raw)

Documentation (stable) • Documentation (latest)

The succinct tree sequence (tskit) format is an efficient way of representing the genetic history - sometimes known as anAncestral Recombination Graph or ARG - of a set of related DNA sequences. Tskit is used by a number of software libraries and programs (such asmsprime,SLiM,fwdpp, andtsinfer) 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 thedocumentation for further details, which includesinstallation instructions.

To get started with tskit, tutorials and other content are at http://tskit.dev. For help and support from the community you can usediscussions 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 Pythonand C API. A Rust API is provided in thetskit-rust repository.

Python API

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 ishere.

C API

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 ishere.

Installation

python -m pip install tskit

or

conda install -c conda-forge tskit