Do the tree for calculating the kinship matrix should be rooted?

[Tonny-zhou]

Dear author,

Thank you very much for this GWAS tool! I have a small question, i.e., the core-genome phylogenetic tree used for calculating the kinship matrix (by the phylogeny_distance.py script) should be previously rooted (midpointed rooted or using outgroup etc.)? or we could use the unroot tree to calculate the kinship matrix?

Yours, Trump

[johnlees]

I usually midpoint root it (there's an option in the script for this), but it will depend on your dataset. Have a look at the QQ plot to confirm control is as expected