lineagekit: Python library with genealogy methods

Introduction

This is the manual for lineagekit, a population genetic library that contains various useful tools for working with genealogies. With lineagekit you can:

• Parse genealogies from files of different formats.

• Build custom genealogies from scratch.

• Modify the obtained genealogies.

• Obtain information by using utility function provided by the library.

• Calculate kinships in large genealogies.

Installation

1. Clone the repository and cd into the root of the project.

2. Run pip install .

Development policy

If you would like to contribute to the project, or if you have found a certain issue with the code, refer to our development policy for more information.

Contents

• Quickstart
  • Parsing files
  • Working with genealogies
• GenGraph
  • API
• Abstract Pedigree
  • API
• Pedigree
  • API
• Ploid Pedigree
  • API
• Coalescent Tree
  • API
• Use-cases
  • Calculating ascending genealogy
  • Calculating kinships