ssu-align is an HMM-based MSA tool for ribosome's small subunit (SSU) sequences. It's bundled with three SSU models: archaeal, bacterial and eukaryotic. Given a set of archaeal and bacterial sequences the tool will first identify the best model for each sequence and produce two separate alignments for archaea and bacteria, and the tool provides no merging functionality. While you can force it to use a single model for all sequences, aligning archaeal sequences to the bacterial model will produce poor results. Nevertheless, the authors of GreenGenes claim that they've used ssu-align to produce two MSAs (one for archaea and bacteria) and build a joint phylogenetic tree using FastTree, but they say nothing about the way they've managed to merge the alignments. Am I missing some functionality from SSU-align? Merging two giant MSAs using conventional tools, such as MAFFT, won't get me far.

P.S.

I've already tried contacting the authors of the GreenGenes paper, but the corresponding author hasn't responded.