Question: How to find the diversity of nucleotides in each position of an alignment ?
2
gravatar for anuragm
4.3 years ago by
anuragm130
India
anuragm130 wrote:

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 • 2.6k views
ADD COMMENTlink modified 4.3 years ago by Siva1.6k • written 4.3 years ago by anuragm130

If it is a MSA, you can calculate Shannon's entropy for each position (http://en.wiktionary.org/wiki/Shannon_entropy)

ADD REPLYlink written 4.3 years ago by Ashutosh Pandey11k
4
gravatar for Siva
4.3 years ago by
Siva1.6k
United States
Siva1.6k wrote:

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.

ADD COMMENTlink written 4.3 years ago by Siva1.6k

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

ADD REPLYlink written 4.3 years ago by anuragm130
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