Documentation (stable) • Documentation (latest)
The succinct tree sequence (tskit) format is an efficient way of representing the genetic history - sometimes known as an Ancestral Recombination Graph or ARG - of a set of related DNA sequences. Tskit` is used
by a number of software libraries and programs (such as
msprime,
SLiM,
fwdpp, and
tsinfer) 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 for further details, which
includes
installation instructions.
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 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
and C API. A Rust API is provided in the
tskit-rust repository.
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.
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.
python -m pip install tskit
# or
conda install -c conda-forge tskit