Splitting and merging data after chimera removal

Hi, is it possible to split and re-merge two datasets at the late stages of preprocessing, e.g. after chimera removal? I would like to first split my data to allow specific processing of some subsets but then combine them again to perform identical OTU clustering, but I don’t know how to perform this.

It’s really best to do everything in parallel since at some point you will filter your sequences to remove overlapping gaps from the alignment. If you do everything together, it is easier to use get.groups or remove.groups later.