Querying QIIME's plugins generally, and for making phylogenies specifically

Good questions, @wburgess !
I'm not an expert on tree-building, but this topic should give you a good place to start exploring.

As for querying available methods by input or output, I don't think anything like that exists at this time. I can imagine tooling like that being a neat addition to the framework, or to specific interfaces, but I'm not sure whether anything like that is on the current roadmap. Searching the library for tools that take a certain input type or produce a certain type of output could be useful. @thermokarst or @ebolyen could probably give you a better sense of the likelihood of something like this being developed, potential technical barriers, etc.

Best,
Chris

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