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More generally, I think it we should either a) keep the parallelism as is (one process per taxon/OTU) or b) split into threads and processes, p concurrent tasks run, each with the option of using t threads. Task-level parallelism (pplacer, cmalign) would use the t threads; total parallelism would be t * p.
Quoting from #8:
cc @nhoffman @crosenth
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