Parallelize over batches (say 10,000) LOO sets each sent to one instance of EPA-NG to benefit from the improvements we discussed Tuesday. I hope I'm clear there. 🙂 I'd aim for a self-contained Sativa first and do this when we see benefits. However, I also realized that the building of the phylogeny from the taxonomy (first two steps) could be factored out (as they are in my current implementation) since they clearly have different resource requirements than the later stages. Also for later discussion.