I have seen other questions about retrieving representative sequences when cluster.split was used, and know I can just use the abundance method to get those. However, I have been requested to supply the “centroid” for each of my OTUs, is there any way to use the distance method to get those representative sequences even though I did use cluster.split or can you suggest an alternative option?
Not really. In our experience the most abundant sequence is generally pretty close to the centroid. Is this a request from a reviewer? That’s a pretty weird request since I’m not sure what you would do with a single sequence from an OTU. I’ve never run get.oturep for any of my projects