Dear,
what is the basic difference between phytolype and OTUs if I still can classify the OTUs after obtaining phylotypes from its pipeline (basically, that is related to the comparison of sequences of my dataset against a database for phylotype and sequences compared to other sequences gathering similarity of them for the OTUs)?
another point is: the shared file show me 252 phylotypes on my experimental design, but in the summary.single command I have noticed ‘sobs’ varying between 90-110 depending on the sample. What would be responsible for that? bacteria_unclassified would not be assigned as ‘sobs’ ?? or what would be this?
Phylotypes are defined based on comparing sequences to a reference database where as OTUs are defined by comparing the sequences to each other with out a reference database. You can loosely think of OTUs as being like species and phylotypes at a higher taxonomic level. So, you should see more OTUs than phylotypes.
Your shared file may have 252 phylotypes across all of your samples. However, because many phylotypes might be absent from samples, an individual sample may have a lower richness.