Querying QIIME’s plugins generally, and for making phylogenies specifically
Is there a way in QIIME to ask one’s current QIIME deployment how many different ways it has to produce a certain type of artifact? Specifically, I fell down the rabbit-hole of different inputs to
qiime diversity commands, and gave myself decision-paralysis over whether to use a Phylogeny[Rooted] qza that was output by
qiime phylogeny align-to-tree-mafft-fasttree or by
qiime fragment-insertion sepp—and what’s worse, that uncertainty bootstrapped itself on my scientist’s anxiety of “is there another, better way for me to do this?”
So I really have two specific questions. First, given that I installed a very boring standard QIIME 2021.2 into conda and haven’t added any plug-ins, does anyone know how many different ways there are to make a Phylogeny[Rooted] qza? Second, if there’s a quick rundown on the pros/cons balance on mafft-fasttree versus sepp—or any other options I have that I don’t know about—can someone tell me what it is?
Or if my questions are wrongly premised, I’d love more clarity. Thanks.