When you start using mothur, assuming you have an input file (fasta or whatnot), there are a number of commands that you can use, and a number that you can’t. Some of the commands you can use will enable the use of previously unusable commands.
It would be nice to show the commands that can be used right now, based on which files exist in your directory or in memory. This might also be a good place to show common lists of tasks and the steps involved to perform them (pipelines? protocols?).