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

Question

[anuragm]

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

[Ashutosh Pandey]

If it is a MSA, you can calculate Shannon's entropy for each position.

Answer 1

[Siva]

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.

[anuragm]

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