How to determine Ka/Ks ratio for a gene or genome?

29 September 2018 1 2K Report

I determined the Ka/Ks ratio for the matK gene. The MAFFT alignment showed 6 SNPs which were non-synonyms and covert six amino acid. The whole size of the matK gene has 1509. I extract alignment of matK and open it in DNAsp. I have defined coding sequence and non-coding sequence (stop codon), and then run the command which given the following result (see fig).

I am a little bit confused if all the site is same in the sequence and their only difference of 6 SNPs then why the showed 1163 Non-synonyms site and 343 synonyms site. Moreover, I also want to know how to convert it to the Ka/Ks ratio when there is 0 synonyms site.

Abdul Rehman

I have used multiple times tbTools, it is very effective and user-friendly, so I recommend TbTools for ka/ks calculations.

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