After running sequence alignment; how do I look for evidence of evolution within the sequences?

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Javan Ochieng Okendo

you can do summary statistics like He,Ho Fst and many other tests based on what you want to look into. http://popgen.nescent.org/2016-01-26-SNP-selection.html will be of great help. you Can also use this R tutorial which will help you in understanding the evolutionary signatures http://popgen.nescent.org/PopDiffSequenceData.html

Kehinde Oyeniran

Thanks Javan.