Over the past 35 years many statistical and bioinformatic tools have been developed to detect recombination, gene conversion, or horizontal gene transfer in sequence data. Five separate statistical signals have been commonly used to detect recombinant sequences, and two of these - mosaic signals and phylogenetic incongruence signals - have emerged as the preferred methods for generating evidence for recombination. I will review the derivation of a non-parametric mosaic statistic called Delta_mn2 that forms the basis of the 3SEQ recombination detection algorithm. The sensitivity, specificity, and exact p-values reported by 3SEQ give it some advantages as a screening tool for recombination in large data sets. I will show how to derive clonal subsegments, or breakpoint-free regions (BFRs), using this approach. And I will show how we have used this screening approach inidentifying recombinants in sarbecoviruses and SARS-CoV-2.
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