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[Container Request]: Gubbins
What tool are you looking for and why?
Gubbins detects recombinations through the locally elevated densities of polymorphisms that arise when sequence segments are acquired from a donor genetically divergent from the set of analyzed sequences.
Github: https://github.com/nickjcroucher/gubbins Paper: http://nar.oxfordjournals.org/content/43/3/e15