diempy 0.9

Polarize genomes using diem

diemPy

A Python package for genome polarization and subsequent analyses using the diem (Diagnostic Index for the Expectation Maximization) method [1]

Overview

diemPy is a computational tool designed to polarize genomic data for hybrid zone analysis. The package implements an expectation-maximization (EM) algorithm to determine the optimal polarization of genetic markers, enabling researchers to identify and analyze patterns of introgression and hybridization in genomic datasets.

Key Features

• VCF processing and format conversion
• Automated genome polarization using EM algorithm
• Kernel smoothing and tract length analysis
• Parallel processing support
• Flexible I/O for various genomic formats

Documentation

The core concepts, installation, and API documentation can be found here:

📚 Introduction, Installation, and API Documentation

The primary documentation for using diemPy is provided as a self-guided tutorial with an example dataset:

**Tutorial This documentation The documentation provides:

• Installation Guide
• Quick Start Tutorial
• API Reference
• Example Workflows

License

This project is licensed under the GPL-3.0 License - see the LICENSE file for details.

Author

Derek Setter, Stuart J.E. Baird

Citation

[1] Baird, S. J. E., Petružela, J., Jaroň, I., Škrabánek, P., & Martínková, N. (2023). Genome polarisation for detecting barriers to geneflow. Methods in Ecology and Evolution, 14, 512–528. https://doi.org/10.1111/2041-210X.14010