PyPop User Guide

📥 PDF version

User Guide for Python for Population Genomics

Alexander K. Lancaster, Mark P. Nelson, Diogo Meyer, Richard M. Single, Owen D. Solberg

Documenting release 1.3.1 of PyPop.

Document revision: 1.3.1.post22+gbc51f10d7

See Citing PyPop for how to cite PyPop in your publication.

Copyright © 2003-2009 Regents of the University of California
Copyright © 2025 PyPop contributors

License terms Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with no Invariant Sections no Front-Cover Texts and no Back-Cover Texts. A copy of the license is included in the License chapter. (GNU Free Documentation License).

How to use this guide

This guide to PyPop contains five main parts:

• Installing PyPop describes how to install PyPop, including pre-release binaries.

• Getting started with PyPop describes how to run PyPop.

• Interpreting PyPop output details the population genetic methods and statistics that PyPop computes.

• Contributing to PyPop details how to contribute to ongoing PyPop code and documentation.

• Authors and history acknowledges our contributors and project history.

• 1. Installing PyPop
  • 1.1. Quickstart Guide
  • 1.2. Examples
    • Checking version and installation
    • Run a minimal dataset:
  • 1.3. Detailed installation instructions
    • Install Python 3 and pip
    • Install package from PyPI
    • Post-install PATH adjustments
    • Uninstalling PyPop
  • 1.4. Support and development
• 2. Getting started with PyPop
  • 2.1. Introduction
  • 2.2. Running a population analysis
    • Interactive mode (pypop-interactive)
    • Command-line mode (pypop)
      • Output to different directory
      • Supplying multiple .pop files
    • Library (programmatic) mode
    • What happens when you run PyPop?
  • 2.3. Aggregating results from multiple runs (popmeta)
  • 2.4. The data file
    • Sample files
    • Missing data
  • 2.5. The configuration file
    • A simple configuration file
      • [General] settings
    • Specifying data formats
      • [ParseGenotypeFile]
      • [ParseAlleleCountFile]
    • Analysis options
      • [HardyWeinberg]
      • [HardyWeinbergGuoThompson]
      • [HomozygosityEWSlatkinExact]
      • [Emhaplofreq]
    • Advanced options
      • [General] advanced options
      • [ParseGenotypeFile] advanced options
      • [Emhaplofreq] advanced options
    • Advanced filtering sections
      • [Filters] extra section
      • [AnthonyNolan] filter section
      • [Sequence] filter section
      • [DigitBinning] filter section
      • [CustomBinning] filter section
  • 2.6. PyPop API examples
  • 2.7. Command-line interfaces
    • pypop usage
      • Options for pypop
      • TSV output options
      • Mutually exclusive input options
    • popmeta usage
      • Positional Arguments
      • Options for popmeta
      • Mutually exclusive popmeta options
• 3. Interpreting PyPop output
  • 3.1. Population summary
  • 3.2. Single locus analyses
    • Basic allele count information
    • Chi-square test for deviation from Hardy-Weinberg proportions (HWP).
    • Exact test for deviation from HWP
    • The Ewens-Watterson homozygosity test of neutrality
  • 3.3. Multi-locus analyses
    • All pairwise LD
    • Haplotype frequency estimation
• 4. Contributing to PyPop
  • 4.1. Reporting and requesting
    • Did you find a bug?
    • Documentation improvements
    • Feature requests and feedback
  • 4.2. Making a code contribution
    • Fork this repository
    • Clone the main repository
    • Make a new branch
    • Build locally and make your changes
    • Keep your branch in sync with upstream
    • Use nox for testing and code quality
      • Run unit tests
      • Run pre-commit checks
      • Build distribution packages
    • Update AUTHORS.rst
    • Make a Pull Request
  • 4.3. Installation for developers
    • Install the build environment
      • Install build environment via miniconda (recommended)
      • Install build environment via system packages (advanced)
    • Build PyPop
      • Build-and-install (not recommended for developers)
      • Build-and-install developer-mode (recommended for developers)
      • Cleaning up build
  • 4.4. Install package from GitHub Releases
  • 4.5. Making a documentation or website contribution
    • Overview
    • Structure
    • Modifying documentation
      • Minor modifications
      • Major modifications
  • 4.6. Crediting contributors
    • AUTHORS.rst, NEWS.md and GitHub Release Notes
    • Authorship on Zenodo archives of releases
    • Scientific publications (papers)
• 5. Authors and history
  • 5.1. PyPop contributors
    • Third-party modules
  • 5.2. PyPop Release History
    • 1.3.1 - 2025-10-07
      • Internal
      • Documentation
    • 1.3.0 - 2025-09-08
      • Features
      • Internal
    • 1.2.2 - 2025-07-28
      • Internal
      • Documentation
    • 1.2.1 - 2025-04-29
      • Features
      • Bug Fixes
      • Internal
    • 1.2.0 - 2025-02-04
      • Features
      • Bug Fixes
      • Internal
      • Documentation
    • 1.1.2 - 2024-11-18
      • Features
      • Internal
      • Documentation
    • 1.1.1 - 2024-09-10
      • Features
      • Bug Fixes
      • Internal
    • 1.1.0 - 2024-05-30
      • Internal
      • Documentation
    • 1.0.2 - 2024-02-24
      • Bug Fixes
      • Internal
      • Documentation
    • 1.0.1 - 2024-02-11
      • Features
      • Bug Fixes
      • Internal
      • Documentation
    • 1.0.0 - 2023-11-07
      • New features
      • Bug fixes
      • Internal
    • 0.7.0 - 2008-09-09
      • New features
      • Bug fixes
      • Other issues
    • 0.6.0 - 2005-04-13
      • New features
      • Bug fixes
    • 0.5.2 (public beta) - 2004-03-09
      • Bug fixes
    • 0.5.1 (public beta) - 2004-02-26
      • Changes
      • Bug fixes
    • 0.5 (public beta) - 2003-12-31
      • Changes
      • Bug fixes
    • 0.4.3beta
      • Bug fixes
• 6. Licenses
  • 6.1. License terms for PyPop
    • GNU General Public License
  • 6.2. License for PyPop documentation
    • GNU Free Documentation License

• References