I have googled this and can not find any advice or answer. Hopefully, I have not overlooked it. I need phmmer to only write the top hit for each query I provide. Currently, it provides over a 100 hits for almost every query, which I have 12,000 of. It would take me way too much time to sort through all this information. Is it probably best to just use Blast instead where I can set this threshold? Not sure if it matters, but I set the evalue to 1e-3.