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 1.1.2 of PyPop.

This guide is also available as a PDF
Document revision: 1.1.2.post1+g404f83e7

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 © 2024 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
    • popmeta usage
  • 2.4. The data file
    • Sample files
    • Missing data
  • 2.5. The configuration file
    • A minimal configuration file
    • Advanced 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
    • Update AUTHORS.rst
    • Run unit tests with pytest
    • Make a Pull Request
  • 4.3. Installation for developers
    • Install the build environment
    • Build PyPop
  • 4.4. Install package from GitHub Releases
  • 4.5. Making a documentation or website contribution
    • Overview
    • Structure
    • Modifying documentation
  • 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
    • 1.1.2 - 2024-11-18
    • 1.1.1 - 2024-09-10
    • 1.1.0 - 2024-05-30
    • 1.0.2 - 2024-02-24
    • 1.0.1 - 2024-02-11
    • 1.0.0 - 2023-11-07
    • 0.7.0 - 2008-09-09
    • 0.6.0 - 2005-04-13
    • 0.5.2 (public beta) - 2004-03-09
    • 0.5.1 (public beta) - 2004-02-26
    • 0.5 (public beta) - 2003-12-31
    • 0.4.3beta
• 6. Licenses
  • 6.1. License terms for PyPop
    • GNU General Public License
  • 6.2. License for PyPop documentation
    • GNU Free Documentation License

• References