Hi Pat,

SCUEAL is a randomized algorithm, so some variation in output is expected. I presume that the differences that you see are not that a particular strain is reported as recombinant in one run and a pure subtype in another, but rather that the location and (possibly) the number of breakpoints may differ slightly between two runs. The latter is normal -- the online version of SCUEAL has been tuned to achieve a tradeoff between speed and accuracy on complex recombinants (these take a long time to run in order to map all the breakpoints). Can you provide an example of two different outputs (preferably links to result pages), so that I may be able to give you more specific advice?

Sergei