Introduction

This is the documentation for tskit, the tree sequence toolkit. 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 external software libraries and programs (such as msprime, SLiM, fwdpp, and tsinfer) that either simulate or infer the evolutionary history of genetic sequences. This library provides the underlying functionality that such software uses to load, examine, and manipulate tree sequences, including efficient methods for calculating genetic statistics.

Note

This documentation is under active development and may be incomplete in some areas. If you would like to help improve it, please open an issue or pull request at GitHub.