Welcome to tsinfer’s documentation!#
This is the documentation for tsinfer, a method for inferring correlated genealogies (a.k.a. tree sequence or ARGs) from genetic variation data.
Besides this manual, there are a number of other resources available for learning about tskit and tsinfer:
The tskit tutorials site contains in-depth tutorials on analysis of the tskit tree sequences produced by tsinfer.
Our Discussions board is a great place to ask questions like “how do I do X” or “what’s the best way to do Y”. Please make questions as clear as possible, and be respectful, helpful, and kind.
Important
If you use tsinfer in your work, please remember to cite it appropriately: see the citations page for details.
Contents#
Introduction
Installation
Usage
Inference
Interfaces
File Formats
Miscellaneous