I haven't used TreeMix since qpGraph became freely available for Linux. Among other things, the latter offers greater control, reproducibility and transparency.
However, I'd say that in its current form qpGraph is not the most objective way to analyze data. That's because if you're really good with it, and you want a graph to work, then often you can make it work by tweaking whatever it is that needs to be tweaked.
It's not possible to do a lot of tweaking with TreeMix. Indeed, once the user picks the samples for the TreeMix run, the rest of the process can be totally unsupervised, and thus free from human interference. Obviously, that's not a guarantee of accuracy, but it can be useful.
I feel I need to run more unsupervised analyses, especially when exploring new data. So to that end, I've dusted off TreeMix and will be using it regularly again.
There's been some talk lately online about migrations from Central Asia giving rise to the Eneolithic populations of the North Caucasus Piedmont steppe. In my opinion, that sounds like nonsense. But let's see what TreeMix has to say on the matter. In the graphs below look for the samples labeled Progress_En and Vonyuchka_En, respectively.
As far as I can tell, both of these graphs essentially corroborate the results from my recent Principal Component Analyses (PCA) with many of the same ancients (see
here). In other words, Progress_En and Vonyuchka_En can be described as mixtures of populations closely related to the hunter-gatherers of the Caucasus on one hand, and those of Eastern Europe on the other. How does Central Asia fit into this, you might ask? It doesn't, unless you really want it to.
See also...
Did South Caspian hunter-fishers really migrate to Eastern Europe?