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How to align and compare thousands single-to-single ortholog's sequences?

There is a sheet with sequences of single-to-single orthologs (each row comprises: id of x organism, id of y organism, sequence of the X, sequence of the Y). How i can optimally align all of this pairs and keep a new sheet of the informations about gaps, identity and etc.?

single-to-single-orthologs alignment bigdata

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