Here is a Mothur Tutorial I wrote. It might be helpful if you are a beginner of Mothur like me.
Here is the link of the tutorial:
It contains flowchart of basic Mothur analysis indicating the function of each command, type of file resulted from each command as well as the usage of each file in the command. In my view It is great for beginner to understand how Mothur works.
I further write down the detail of my analysis in the following link
also you could refer to Analysis Example of 16s RNA gene for Beginners to find out what commands each step concludes