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Old 05-26-2016, 03:45 PM   #1
cfourps
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Location: West Lafayette, IN

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Default Comparing nucleotide diversity between two paralogs using a VCF file

I'm looking at two homeologs and trying to gain information about their potentially different evolutionary rates. There is a publicly available dataset in the form of a VCF file from whole genome sequencing of many different, diverse cultivars. Is there a way to get nucleotide diversity (and calculate for coding sequence, synonymous, nonsynonymous etc) or Ka/Ks values for the two paralogs?
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