The order of right population impact the qpAdm result about admixtools HOT 1 OPEN

The qpadm_rotate function takes the first right population as the base, and there is no easy way to change that. But you could try using the qpadm_multi function instead. It allows you to specify the order of the right populations for each model, but you have to specify all the models you want to run.

I agree that it's a good idea to use the same right population as the base when comparing multiple models. However, I also think that when the results depend a lot on choices such as which right population is used as the basis (which should not matter in theory), it can be an indication that there isn't enough data to robustly test these models (meaning there aren't enough samples, not enough SNPs, or not enough drift differentiating the populations).

from admixtools.