As I know that for 16S, we use mothur, and for shotgun, we use metaphalan2 and Humann2.
Am I right? Can we use mothur for shot gun sequencing analysis?
I think if you want people to answer your questions, you should consider upvoting those who answer you. In general, providing more closure to your posts - how they helped or didn't help with your problems - would make it more likely to get help in the future. As it is, you continue to show a stunning lack of interest in acknowledging those who help you, and at some point that will be reciprocated.
Just a sampling of your posts from the last week to remind you what you have (not) been doing:
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