I've recently completed a 16S project using a phylogenetic tree with aligned OTUs from QIIME. I got through the analysis without too many issues, but for the purpose of publication, we would like an "unaligned" tree with a topology that represents only the known taxonomy of a given tip (as opposed to a tree generated from the alignment of 16S data). I saw that in the FastTree workflow, there is the option to constrain the topology FastTree generates based on a matrix of the OTU (or tip/taxa) names and a series of ones and zeroes.

http://www.microbesonline.org/fasttree/constrained.html

My question is how can I generate a constraint matrix based on known taxonomy without resorting to manual assignment?

I'm pretty new to tree construction so any help would be greatly appreciated, thanks!