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  • #1

    A way to calculate mean divergence for lots of sequences?

    Hi,

    So I have some sequences of repetitive elements (~13k à 120bp) and am wondering if there is a good way to calculate the (mean) divergence between them, maybe find conserved regions or find sequences diverging more than others? My main problem is the number of sequences seems to be problematic for what I have tried.


    Has anyone here some experience with this task at this kind of scale? Maybe some leads to programs that can accomplish this in a reasonable runtime?


    Thanks for any input!
    Tags: divergence, msa, repeats
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