The best software for genetic evaluation
I am often contacted by breeders who are starting to work on quantitative genetic evaluation. A typical question they ask is ‘What software do you recommend for analysing progeny trials?’ I could start explaining all the elements that you should consider for choosing this type of software and then leave the decision to you; I won’t, because I am convinced that ASReml is your best bet given that:
- It makes the evaluation of simple trials easy and it also makes possible the evaluation of very complex models. Note: I say possible, not easy.
- It is highly optimised for working with genetics data, so it runs orders of magnitude faster than generic software (SAS, for example).
- There is a community of users that has tested the software under a large number of situations. This means that:
- You may ask for help and probably someone else already solved your problem, and
- There are resources for using the program in tree breeding. The ASReml cookbook demonstrates how to analyse common trials in tree breeding.
- The program scales very well and — with some care — it is possible to conduct a national breeding evaluation in a desktop PC.
- ASReml is inexpensive, or at least much cheaper than generic statistical software (again, SAS for example).
- The program is under constant development, meaning that:
- Bugs are quickly fixed.
- If you have particular needs that would benefit other users they may find their way into the program very soon.
Anyway, let’s say that I didn’t convince you with the previous explanation. What are your options?
- Use generic statistical software (for example, SAS, Genstat, Splus, R, etc). You may find that besides cost — which is not a problem with R — there are two big issues: they are very slow and there is plenty of coding involved for anything relatively complex (for example a diallel).
- Use ‘animal breeding’ software, which in general doesn’t lend itself to designed experiments, making life very miserable. An exception would be VCE by Eildert Groeneveld. I am not very familiar with this program, but you could give it a try, particularly if you are interested in Bayesian estimation using the Gibbs sampler.
- Develop your own software, which requires both plenty of experience and resources. Chances are that if you are reading this article you may not have such experience. An interesting example of this approach is Treeplan.
What to do next? Download the software, browse the cookbook and try a few examples. Have fun ASRemling!
Resources
- ASReml web site. Here you can download the software and request a quote.
- ASReml cookbook, home of all things ASReml for tree breeding. There are templates for typical analyses, documentation and links to other ASReml resources.
Disclosure: I have to make clear that I receive no commission if you buy ASReml. I am only a happy user. I do have a free copy though.