Welcome to pyslim’s documentation!

Contents:

• Introduction
  • Overview
  • What does SLiM record in the tree sequence?
  • Who and what is in the tree sequence?
  • What else can I find out from the tree sequence?
• Installation
• Troubleshooting
• Tutorial
  • Recapitation
  • Simplification
  • Adding neutral mutations to a SLiM simulation
  • Extracting particular SLiM individuals
  • Reading SLiM metadata
  • Coalescent simulation for SLiM
  • Extracting information about selected mutations
  • Possibly important technical notes
• Vignette: A spatial simulation
  • Simulation
  • Recapitation and mutation
  • Take a sample of individuals
  • Plotting locations
  • Isolation by distance
  • VCF output
  • More information
  • What about simplification?
• Vignette: Following up with more coalescent simulation
  • Positive selection
  • Recapitation
  • Continuing the simulation
• Metadata
  • Converting from SLiM time to tskit time
  • Modifying SLiM metadata
  • Technical details
• Legacy metadata
• Python API
  • Additions to the tree sequence
  • Constants
  • Metadata
• Development
  • Quickstart

Indices and tables

• Index
• Module Index
• Search Page