Welcome to tskit’s documentation!

Contents:

• Introduction
• Installation
  • Requirements
  • conda
  • pip
  • Development versions
• Python API
  • Trees and tree sequences
  • Tables and Table Collections
  • Metadata API
  • Combinatorics API
  • Linkage disequilibrium
  • Provenance
• Statistics
  • Available statistics
  • Interface
  • General API
• C API
  • Overview
  • Basic Types
  • Common options
  • Tables API
  • Table indexes
  • Tree sequences
  • Trees
  • Low-level sorting
  • Miscellaneous functions
  • Constants
  • Examples
• Command line interface
  • Positional Arguments
  • Named Arguments
  • Sub-commands:
• Data model
  • Definitions
  • Table definitions
  • Tree structure
  • Missing data
  • Text file formats
  • Binary interchange
  • Tree sequence file format
• Metadata
  • Codecs
  • Examples
  • Python Metadata API Overview
  • Full metaschema
• Combinatorics
  • Interpreting Tree Ranks
  • Examples
  • Enumerating Topologies
• Provenance
  • Example
  • Software
  • Parameters
  • Environment
  • Full schema
• Development
  • Project structure
  • Getting started
  • Workflow
  • Documentation
  • Python library
  • C Library
  • Python C Interface
  • Continuous Integration tests
  • Best Practices for Development
  • Troubleshooting
  • Releasing a new version
• Tutorial
  • Trees
  • Moving along a tree sequence
  • Editing tree sequences
  • Working with Tables
  • Overview of the Tables Format
  • Working with Metadata
  • Calculating LD
  • Working with threads
  • Parsimony
  • Computing statistics
  • Allele frequency spectra
• Changelogs
  • Python
  • C API

Indices and tables

• Index

• Module Index

• Search Page