mrpast Documentation

mrpast is a tool for inferring demographic parameters from phased genomic data. It uses Ancestral Recombination Graphs (for an overview of ARGs, see here). You can either infer ARGs from your data yourself, or use one of mrpast’s integrations with tsinfer (preferred), Relate, or SINGER.

In our experience, mrpast obtains the best results with tsinfer+tsdate (the latter using the variational_gamma method). For some models, the results can be substantially better than when using other ARG inference tools.

For an end-to-end example, see the tsinfer workflow.

Use the links below or on the menu-bar to learn more.

• Overview
  • Recommendations for use
  • Usage Modes
  • Simplest Usage Example
• Reference
  • Command Reference
  • Python API
• Workflows
  • tsinfer workflows
  • Externally-created ARGs
  • Examining results
  • Using real data
  • Very short examples
  • Relate workflows
  • SINGER workflows
• FAQ/HOWTO
  • Retaining coalescence counts
  • System temp dir problems
  • GIM vs. Bootstrapping