Welcome to the documentation for SMCSMC!

This is the reference manual for SMCSMC (or smcsmc), a method and program for inferring ancestral population size and migration from whole genome sequences.

Contents:

• Introduction
  • Installation
  • Basic Usage
  • Other Methods
  • Citation
• Getting Started
  • Basic Concepts
  • Running smcsmc
  • Output
  • Visualising Output
• General Usage
  • Input Arguments
  • Overview of Inference Procedure
  • Clustering Computing
• Tutorials
  • Simons Global Diversity Panel
  • Simulated Data with SCRM
  • Simulated Data with msprime
• API Documentation
  • Format Conversions
  • Plotting
• Command Line Interface
• Glossary