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Removing recombination from reference genome

Hi

I have aligned 100 bacterial isolates to a reference, to find the core genome. I have then used ClonalFrameML to detect recombination, which I have subsequently removed. However, for further analysis I need to search for these recombining regions just within my reference genome. How can I do this?

Thanks

recombination cfml core genome alignment vcf
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written by natasha • natasha

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