Taxonomy summary by experimental category?

Hi, how do I produce a taxonomy summary per experimental category (specified in a design file etc) instead of per sample?
I would like to make sequence-based summary, like the tax.summary file generated by classify.otu, but per category.

I think this is a bad idea. Here’s why: by pooling all of your samples from within a category you are removing all ability to measure the variation in your samples. I would strongly encourage you to keep the samples separate and then calculate a median and interquartile range for each category.