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One potential way to further improve the speed of your new and interesting approach would be to use SWIPE as a replacement of SWPS3 for your pairwise sequence comparisons. I quote Torbjørn Rognes' paper: "SWIPE was about six times faster than SWPS3 and Farrar's own implementation for a typical length query, but the factor varied between 2 and 18 depending on...

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pairwise sequence comparisons
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