I have no personal experience of phylochips, but if they are what they sound like, this could be a useful tool for phylogeographers. Next gen sequencing is getting more affordable, but the cost for good quality phylogeography is still a bit steep. So much to do and some difficult choice to make!

Thanks for your opinion, yes indeed, the costs are about 5 times higher for phylochips than for e.g. V4 16 S sequencing via Illumina....hm..

Thanks Simon, I will do the assay in cooperation with experts in bioinformatics, I just need to know what could be more feasible. Very probably, I will use both method in combination, but I dunno the details now...just would like to have some opinion from you, guys, who have got already practical experiences with that...