Unexpected similarity values

vanOosterhoutLab / HybridCheck

HybridCheck, an R package for quickly scripting scans of sequence data for recombination regions.

http://vanOosterhoutLab.github.io/HybridCheck/

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Unexpected similarity values #32

Open fhsantanna opened 2 years ago

fhsantanna commented 2 years ago

I utilized the tool for comparing SARS-COV-2 genomes under default parameters.

teste <- HC$new("~/Desktop/teste_XS_head.fas")
teste$showParameters("TripletGeneration")
teste$analyzeSS()
teste$plotTriplets()

However, I am not understanding the output, because the similarity values are lower than I expected. All three genome sequences are very similar, having more than 90% of identity. Am I missing something?