WOMBAT

A Program for Mixed Model Analyses by Restricted Maximum Likelihood

USER NOTES

Karin Meyer
Animal Genetics and Breeding Unit, University of New England
Armidale, NSW 2351, AUSTRALIA

© Karin Meyer 2006–2020

This copy of the manual has been produced on February 6, 2020. It is an ‘automatic’ translation from the LaTeX source (for the pdf version) using TeX4HT.

1 Introduction
2 Availability
3 Getting started
 3.1 Installation
 3.2 Using the manual
 3.3 Troubleshooting
 3.4 Additional documentation
4 Parameter file
 4.1 Overview
 4.2 General rules
 4.3 Run options
 4.4 Comment line
 4.5 Overriding default program limits
 4.6 Analysis type
 4.7 Pedigree file
 4.8 Marker counts file
 4.9 Data file
 4.10 Model of analysis
 4.11 Covariance components
 4.12 Additional functions of covariance components
 4.13 Pooling estimates of covariance components
 4.14 Dependencies among fixed effects
 4.15 Random effects to be treated as fixed
 4.16 Covariance components to be treated as fixed
 4.17 Special information
5 Run options
 5.1 Overview
 5.2 Basic run options
 5.3 Advanced run options
 5.4 Parameter file name
6 Input files
 6.1 Format
 6.2 Data File
 6.3 Pedigree File
 6.4 Marker models: Allele counts
 6.5 Parameter File
 6.6 Other Files
7 Output files
 7.1 Main results files
 7.2 Additional results
 7.3 ‘Utility’ files
 7.4 Miscellaneous
8 Work files
9 Examples
A Technical details
 A.1 Ordering strategies
 A.2 Convergence citeria
 A.3 Parameterisation
 A.4 Approximation of sampling errors
 A.5 Modification of the average information matrix
 A.6 Iterative summation