SimPlot (Similarity Plotting) (as well as bootscanning, quick tree generation, and informative-sites analysis) is a popular tool for recombination analysis.
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Reference to the paper in which author first described SimPlot
Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC.
Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.
J Virol. 1999 Jan;73(1):152-60.