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.

Contents:

Contents:

• Introduction
• Installation
  • Binary packages
  • Installing from source
  • Potential issues
• Tutorial
  • Toy example
  • Simulation example
  • Data example
• Inference overview
  • Data requirements
  • Data model
  • Import samples data
  • Generate ancestors
  • Matching ancestors & samples
• API Documentation
  • File formats
  • Running inference
  • Exceptions
• Command line interface
  • Argument details
• File formats
  • Samples File
  • Ancestors File
  • Tree sequences
• Developer documentation

Indices and tables

• Index
• Module Index
• Search Page