Should I remove mock before phylogeny-based analysis


I got confused and guess I might have misunderstood a certain steps, so I would like to ask :

What I understood is that in Schloss SOP, mock was not removed before phylogeny-based analysis. I am not sure if this does not matter to the result of phylogeny-based analysis, or the mock was removed before phylogeny-based analysis but I ignored it?

Thank you in advance!

It shouldn’t really matter.

Thank you for your prompt reply!