Parameter Estimation Codes for BLUPF90 and WOMBAT

This repository contains a variety of scripts and parameter estimation codes to be used with BLUPF90 and WOMBAT. These tools are widely used for mixed model analyses in animal breeding and genetics.

Overview

The scripts provided in this repository facilitate the estimation of genetic parameters using BLUPF90 and WOMBAT. They include:

• Data preparation scripts
• Model specification files
• Command-line execution scripts
• Post-processing utilities

These codes are designed to help users streamline parameter estimation workflows efficiently.

Requirements

To use these scripts, you must have:

• BLUPF90 suite installed (download here)
• WOMBAT installed (download here)
• Linux/Mac/Windows command-line interface

File Structure

├── blupf90/
│   ├── paramfile_STM.par        # Parameter file for a Single-Trait Model
|   ├── paramfile_rep_STM.par    # Parameter file for a Single-Trait Model with repeated records
│   ├── paramfile_MTM.par        # Parameter file for a Multi-Trait Model
│   ├── paramfile_GWAS.par       # Parameter file for GWAS 
│   └── se_AIREML.R              # Example of how AIREML calculate the standard errors
│
├── wombat/
│   ├── paramfile_GWAS.par      # Parameter file for WOMBAT
│   ├── script_iterGWAS.sh      # Script to run multiple analysis with WOMBAT
│
└── README.md         # This file

Citation

If you use these scripts in your research, please cite:

• BLUPF90: Misztal et al. (2002) "BLUPF90 – a flexible mixed model program."
• WOMBAT: Meyer (2007) "WOMBAT – A tool for mixed model analyses in quantitative genetics."

Contributions

Contributions are welcome! Please submit a pull request with any improvements or additional scripts.