How to get all unique seqs from modified representative set?

Hi everybody,

I’ve just analyzed my entire dataset having OTU’s clustered at 97% similarity. However, now I’d like to repeat some beta diversity analyses but dealing with unique sequences reather than 97% OTUs.

After classifying the OTUs and building a shared file with make.shared I have picked representative sequences. I then had several steps of realigning those representative sequences and clustering the OTUs again because I found that some misaligned sequences were inflating the total number of OTUs I had. Now my question is, how can I take the final set of representative sequences that I have and from this data go back and make a fasta file with all the unique sequences that belong to these OTUs? Is there a way to do this?

Hope I could explain this properly…


have you used get.oturep? you can have it use method=abundance and you should generate a fasta and names file. probably the better way to do this would be to go back to the original align file (actually the reference file), fix the alignment and proceed.