Calculating K2P Distance in R using BLAST+ output
I've been trying to calculate the Kimura parameter distance between a query sequences and all BLAST hits to them from a genome in R. As outfmt 6 doesn't allow for the output of transitions and transversions I guessing I'll need to parse the XML output, extract the alignments and then count the transitions and transversions in the alignment. Does anyone know of an existing package/script which will do this?
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