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How to find the diversity of nucleotides in each position of an alignment ?

I need to find the nucleotide diversity at each position of an alignment. Is there a way to do this with available software ? I would also be comfortable if there is a way to do this using R

dna alignment nucleotide
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updated by Ram Ram • written by anuragm anuragm

1 answer

You can use WebLogo. The output is either an image (in several formats) or a text file with relative frequency of each nucleotide/amino acid at every position in the alignment.

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written by Siva Siva

Thank you so much! Its one of the most useful things I came across in a long time. :)

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written by anuragm anuragm

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