Welcome to stdpopsim’s documentation!

Contents:

• Introduction
  • First steps
  • Getting involved
  • Citations
  • Licence and usage
• Installation
  • Requirements
  • Conda
  • Pip
  • Running the CLI
• Catalog
  • Aedes aegypti
  • Anas platyrhynchos
  • Anolis carolinensis
  • Anopheles gambiae
  • Apis mellifera
  • Arabidopsis thaliana
  • Bos taurus
  • Caenorhabditis elegans
  • Canis familiaris
  • Chlamydomonas reinhardtii
  • Drosophila melanogaster
  • Drosophila sechellia
  • Escherichia coli
  • Gasterosteus aculeatus
  • Gorilla gorilla
  • Helianthus annuus
  • Heliconius melpomene
  • Homo sapiens
  • Mus musculus
  • Oryza sativa
  • Pan troglodytes
  • Papio anubis
  • Phocoena sinus
  • Pongo abelii
  • Rattus norvegicus
  • Streptococcus agalactiae
  • Sus scrofa
  • Generic models
• Tutorials
  • Running stdpopsim with the command-line interface (CLI)
  • Running stdpopsim with the Python interface (API)
  • Example analyses with stdpopsim
• Command-line options
  • Positional Arguments
  • Named Arguments
  • msprime specific parameters
  • SLiM specific parameters
  • Sub-commands
• API
  • Quick reference
  • Species definitions
  • Demographic Models
  • Gene conversion and bacterial recombination
  • Selection and DFEs
  • Selection and sweeps
  • Generic models
  • Simulation Engines
• Development
  • Installation
  • GitHub workflow
  • Adding a new species
  • Adding a new demographic model
  • Adding a recombination/genetic map or annotation
  • Lifting over a recombination/genetic map
  • Adding a DFE model
  • Coding standards
  • Naming conventions
  • Unit tests
  • Code Coverage
  • Documentation
  • Making a new release
• Changelogs
  • Upcoming
  • [0.3.0] - 2025-03-18
  • [0.2.1a] - 2024-07-06
  • [0.2.0] - 2022-11-01
  • [0.1.2] - 2020-05-29
  • [0.1.1] - 2020-01-02
  • [0.1.0] - 2019-12-18

Indices and tables

• Index

• Module Index

• Search Page