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..

I don't know anything about Phylochip, but with next generation sequencing it is a big project. If you sequence a sample of bacteria and fungus with the initial aim of knowing what the relative populations in the sample you will have to assemble them. Each contiguous assembly (contigs) will be a part of bacterial genome or a chromosome from a fungal genome. Then you can blast the contigs to find out if this species is known or unknown.

Based on the assemblies you can do all kinds of downstream analyses, but you probably need some bioinformatics experience for this project. I cannot compare this approach with phylochip, but it is a very general approach and you will obtain general results.

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...

Thanks Steve, I will look closely at the link you posted...