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What software do you use to design LAMP reaction primers for alignment? So far I have been using Primer Explorer v5 but I am looking for some alternatives.

Alignment includes some species from the same virus family. So I am looking for a set of primers that will capture species from the given alignment.

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  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Commented Mar 2, 2023 at 13:34
  • $\begingroup$ Welcome to the site. What is the depth of study and degeneracy, e.g. within a species, genera, or family ... or beyond? This is kinda important to identify which algorithm. $\endgroup$
    – M__ ♦
    Commented Mar 2, 2023 at 13:36
  • $\begingroup$ Thanks, woooaa thats difficult. I might have misunderstood this but if its an RNA virus diagnosis at the familial level that is not trivial. The mutation rate of RNA viruses is very high - at familial level, it's impossibly high excepting for the use of nested-PCR strategies. $\endgroup$
    – M__ ♦
    Commented Mar 3, 2023 at 3:34

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