how gaps are treated?

I want to ask a basic question regarding OTU-based approaches.
There are three ways on treating gaps,calc=onegap,calc=nogaps and calc=eachgap.
I am new in this field,I had some Sanger 16s rRNA gene sequences of microorganism degrading petroleum hydrocarbon. I want to carry out OTU-based approaches.
but i don’t know which should i choose in the three ways treating gaps and why should i choose the way.
can anyone help me with this question?

Thank you so much!

Ernest Wang

Use the default - calc=onegap. You can see the Schloss PLoS Computational Biology paper for more details.