ASReml Cookbook

• Introduction
• Getting help
• Using a decent text editor
• Using ASReml with a mac
• Take me to the recipes!
• Other tips
• Citing or referencing the cookbook

Introduction

ASReml is a very powerful statistical software developed by Arthur Gilmour, with support from an international team of leading statisticians. It is specifically designed for fitting mixed models for large datasets, with unmatched model flexibility and high speed. I have a few reasons why I think that ASReml is the best software for genetic evaluation.

ASReml’s manual is the source of all knowledge, with over 300 pages. That is a bit of an overstatement, but it is certainly exhaustive and sometimes daunting. One of the problems when you start using ASReml is how do I start? How do I setup my models the way I used to in Genstat / DFREML, etc? I have trees, no animals, what do I do? I have spent a long time learning how to fit models with the software, and I have I decided to make some of the information available in this site, in case it can be of some use for you.

Getting help

Besides the manual, the cookbook and other web sites, you can contact VSNi support if you require assistance. Please do not contact me [Dr. Luis Apiolaza] for help with your analyses.

Using a decent text editor

To run an ASReml job you need to write an ASReml command file (the file with a .as extension). Hence, one of the first things you should get is a decent text editor. If you work in MS Windows you already know that Notepad is hopeless, and probably you do not want to spend any money. There are plenty of free or shareware editors around, but I recommend using ConTEXT, which is a free ‘ASReml aware’ programming text editor. There are a few instructions to setup ConTEXT for ASReml use.

Can I use ASReml with my Mac?

Yes. From December 2009, ASReml is natively supported in OS X (both 32 and 64 Bits). There is a version for ASReml-SA and another for ASReml-R

In addition, there are two other ways of running ASReml on Intel-based Apple computers (Macbook, Macbook Pro, Mac Pro and new Mac minis and imacs):

• Use Bootcamp to boot your mac in one of the operating systems supported by ASReml. For example, you could boot using Windows XP and the mac would essentially be a windows machine.
• Use a virtualization machine, for example Parallels, to have multiple operating systems running on your mac. In this case there is a windows containing a session of Windows (or Linux, or whatever) running inside OS-X. This is how I run ASReml in my Macbook Pro.

I have tried this only with the Windows version of ASReml, but I assume that it would work the same with the Unix versions. I now prefer dual booting, because the system is much more responsive (and a Mac is a very good windows machine). If you go for the second option be aware that you will require plenty of RAM; essentially you will be running two operating systems at once. With 1GB my system felt sluggish but it worked quite well with 2GB and higher.

The recipes

Here is what you are really looking for! Below are recipes to run the following types of analyses.

ASReml (standalone, not ASReml-R)

• Job anatomy
  • Basic structure
  • Equation model description

• Univariate analysis
  • Some basic models
  • Equivalent models
  • Diallels
  • Clonal data
  • Multiple site, single trait
• Covariance structures
• Multivariate analysis
• Estimating heritability
• Longitudinal analysis
  • Introduction
  • Longitudinal analysis in ASReml
  • Random regression models
• Spatial analysis
  • Introduction
  • Spatial analysis in ASReml
  • Spatial analysis for irregularly spaced trees
• Data tips
  • Truncating the dataset
  • Univariate to multivariate format
  • Starting values: the apocryphal Dutch method

ASReml-R

• Basic usage
• Model equations
• Univariate analysis
  • Some basic models
  • Diallels
  • Clonal data
  • Multiple site, single trait
• Covariance structures
• Multiple sites
  • Single site, multiple traits
  • Two sites, single trait treated as multivariate
• Extracting results

Other tips

The cookbook also includes some interesting replies to posts from a historical ASReml discussion group, two of which are presented below. Note: I have not necessarily used or checked the advice:

• How do I fit Generalized models?
  • Binomial and Poisson models
  • Problems with this type of analyses
• Problems Overlapping design matrices in genetic models

Citing or referencing the cookbook

If the ASReml Cookbook was useful for your analyses, you may cite it in the following way:

• Author. (Date of publication, use last modified date). Title. Retrieved date of access, from URL. For example:
• Apiolaza, L.A. (September 2021). ASReml cookbook. Retrieved 18 September 2021, from https://asreml.kb.vsni.co.uk/knowledge-base/apiolaza-asreml-cookbook/

Copyright (1997–2021) by Luis Apiolaza, some rights are reserved.