Polarize genomes using diem
Project description
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
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
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