<p>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</p>

<p>You can use <a href="http://weblogo.threeplusone.com/create.cgi">WebLogo</a>. 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.</p>
