I have sequenced the 18S from individual fungal spores using Sanger sequencing and then I sequenced a community of fungi from the same samples (plant roots) using Illumina MiSeq. I used the same primers for both types of sequencing and I would like to be able to compare directly the fungal communities from spores and from roots.
I followed the MiSeq SOP to classify the Illumina sequences into phylotypes (not OTUs as the dist.seq command produced too large a matrix).
Now I would like to know whether the sequences generated by Sanger belong to the same phylotypes found in the MiSeq dataset.
Is there a way to do that with mothur?
Thanks very much.