How to do Tajima's D analysis?

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6.0 years ago

amitgourav.ghosh12 ▴ 70

Can anyone please suggest how to do Tajima's D analysis and the software required? Or can you please provide me with the links of similar answers. I want to detect signature of positive selection of certain alleles in my database.

snp genome • 3.1k views

ADD COMMENT • link updated 3.1 years ago by Biostar 20 • written 6.0 years ago by amitgourav.ghosh12 ▴ 70

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Did you try searching in the biostars search engine or Google with +site:biostars.org? I can see related questions in the sidebar. Please show us you've invested some effort.

ADD REPLY • link 6.0 years ago by Ram 43k

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Hello Sir, indeed there are plenty of questions in the site. What I learnt till now is that one can use the package "pegas" in R or use dnasp v.5 or vcf tools for this purpose. I have binary format files from plink and the individuals respective MAFs, but not sequences. I am planning to download vcf tools and try out there if possible.

Thank you!

ADD REPLY • link 6.0 years ago by amitgourav.ghosh12 ▴ 70

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