PyPop User Guide

User Guide for Python for Population Genomics

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

Documenting release 1.2.1 of PyPop.

This guide is also available as a PDF
Document revision: 1.2.1.post5+g6e1bf380

How to use this guide

This guide to PyPop contains four 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.

License terms

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

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).

• 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
    • Interactive mode
    • Batch mode
    • What happens when you run PyPop?
  • 2.2. Using popmeta to aggregate results
  • 2.3. 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
  • 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
• 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
    • Pre-commit checks
    • Keep your branch in sync with upstream
    • Update AUTHORS.rst
    • Run unit tests with pytest
    • 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
    • 1.2.1 - 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