I recently sequenced partial 18S sequences using Titanium for studying soil nematode and metazoan diversity.
SILVA SSU_Ref_111_NR_aligned DB (retrieving Eukaryote sequences only) was used as a reference. However, many sequences were wrongly aligned and I guess it’s partly because 18S sequences aligned are not that many (only 21,181 sequences in total and too small number of nematode sequences). As far as I know, SILVA is the only way I can get fully-aligned 18S sequences. In this case, would it be better to try alignment-free clustering to pick OTUs rather than using align.seqs()?


I guess I would try to invest the time in improving the alignment of the reference sequences you are interested in. The alignment is part of the issue but it’s also making sure they overlap the same alignment space which is not done by the other methods.