Quantgen software review

[jeromekelleher]

I've had a look around and not been able to find any guidance or overview on quantitative genetics software. What do people do, and how do they do it?

@timothymillar do you have any starting points here? A student-oriented beginners guide of some sort would be ideal.

[timothymillar]

@jeromekelleher Most of my work in this area has been around estimation of relationship matrices and I'm very much a novice when it comes to actually fitting quant-gen models. That being said, quant-gen problems are generally treated as (generalized) linear mixed models and commonly make use of 'generic' LMM solving packages like ASREML.

A good starting reference would be An ecologist’s guide to the animal model and the related online tutorial How to fit an animal model which demonstrates fitting an animal in several deferent packages including (ASREML-R, MCMCglmm and brms). My impression is that ASREML is one of the most commonly used packages.

There are quite a few R packages which are more specifically aimed at quantitative genetics. These include sommer, rrBLUP, StageWise, and AGHmatrix to name a few (but this list is biased towards the autopolyploid literature!).

When it comes to computing genetic relationship matrices there are a few options. AGHmatrix is one of the more common ones (particularly for autopolyploids). sommer has some options for computing GRMs and seems to be quite popular. Some command line tools like GCTA also have options for GRM estimations and quant-gen analyses, but I'm generally less familiar with them as they typically assume diploid genotypes.

I'll add more info here as I think of it.

[jeromekelleher]

Fantastic, thanks @timothymillar!