phylogenetic tree with data from several regions of the 16S

Is it possible to use phylogenetic diversity measures on data that includes sequence from several regions of the 16S gene (eg. if they’ve been summarized/combined as a single taxonomy file)? The programs for building massive trees seem to require aligned sequences - but it seems like you ought to be able to map directly from a taxonomy file to branches on an already-built tree (eg. derived from an external database). Has anyone done this?

Yeah Rob Knight’s group has done this. I personally think this is fraught with all sorts of problems. Problem #1 is that all primer sets have different biases.

What if wanted to do anyway, how would I do that? Rob Knight has published that?

It sounds exactly like closed-reference OTU picking in QIIME. It’s here, just use one of the ‘_ref’ methods.

As Pat says though, this isn’t a great method to use without serious justification.

Their own paper seems to indicate that it’s pretty worthless:

“Together, these results show that cross-study comparisons of human microbiota are valuable when the studied parameter has a large effect size, but studies of more subtle effects on the human microbiota require carefully selected control populations and standardized protocols.”

In other words, why bother?